Title of Invention

A COMPOSITION COMPRISING AN IMMUNOSTIMULATORY NUCLEIC ACID .

Abstract The invention provides immunostimulatory nucleic acids comprising the nucleotide sequence of SEQ ID NO:1, 19, 45, 118 or 141 and compositions thereof. The immunostimulatory nucleic acids may have a nucleotide backbone comprising at least one phosphorothioate modification, and/or the immunostimulatory nucleic acids may be less than or equal to 100 nucleotides. Immunostimulatory nucleic acids of the invention can be combined with antigens, adjuvants, cytokines and therapeutic agents.
Full Text NUCLEIC ACID COMPOSITIONS FOR STIMULATING IMMUNE RESPONSES
A COMPOSITION COMPRISING AN IMMUNOSTIMULATORY NUCLEIC ACID
Field of the Invention
The present invention relates generally to immnunostimulatory nucleic acids,
compositions thereof and methods of using the immunostimulatory nucleic acids.
Background of the Invention
Bacterial DNA has immune stimulatory effects to activate B cells and natural killer
cells, but vertebrate DNA does not (Tokunaga, T., et al., 1988. Jpn. J. Cancer Res. 79:682-
686; Tokunaga, T., et al., 1984, JNCJ 72:955-962; Messina, J.P., et al., 1991, J. Immunol.
147:1759-1764; and reviewed in Krieg, 1998, In: Applied Oligonucleotide Technology, C.A.
Stein and A.M. Krieg, (Eds.), John Wiley and Sons, Inc., New York, NY, pp. 431-448). It is
cow understood that these immune stimulatory effects of bacterial DNA are a result, of the
presence of unruethylated CpG dinucleotides in particular base contexts (CpG motifs), which
are common in bacterial DNA, but methylated and underrepresented in vertebrate DNA
( Krieget al, 1995 Nature 374:546-549; Krieg, 1999 Biochim. Biophys. Acta 93321:1-10).
The immune stimulatory effects of bacterial DNA can be mimicked wrth synthetic
oegdeoxynud.eotides (ODN) containing these CpG motifs. Such CpG- GDN have highly
stimulatory effects on human and murinc leukocytes, inducing B cell proliferation; eytokms
and irmnunoglobulin secretion; natural killer (NK) cell lytic activity and IFN-? secretion; and
activation of dendritic cells (DCs) and other antigen presenting cells to express costimulatory
mdcxules and sscreie cytokines, especially the Th1-like cytokines that are important in
pronioting the development of Thl-like T cell responses.
These immune stimulatory effects of native phosphodiester backbone CpG ODN are
ulghly CpG specific in that the effects are essentially abolished if the CpG motif is
methylated, changed to a GpC, or otherwise eliminated or altered (Krieg et al, 1995 Nature
374:546-549; Hartmann et al, 1999 Proc. Natl. Acad. Sci USA 96:9305-10). Phosphodiester
CpO ODN can be formulated in lipids, alum, or other types of vehicles with depot properties
or improved cell uptake in order to enhance the immune stimulatory effects (Yamamoto et al,
1994 Microbiol. Immunol. 38:831-836; Gramzinski et al, 1998 Mol. Med. 4:109-118).
In early studies, it was thought that the immune stimulatory CpG motif followed the
formula purine-purme-CpG-pyrmidine-pyrhnidhine (Krieg et al, 1995 Nature 374:546-549;
Pisetsky, 1996 J. Immunol. 156:421-423; Hacker et al., 1998 EMBO J. 17:6230-6240;
Lipford et al, 1998 Trends in Microbiol. 6:496-500). However, it is now clear that mouse
lymphocytes respond quite well to phosphodiester CpG motifs that do not follow this
"formula" (Yi et al., 1998 J. Immunol. 160:5898-5906) and the same is true of human B cells
and dendritic cells (Hartmann et al, 1999 Proc. Natl. Acad. Sci USA 96:9305-10; Liang, 1996
J. Clin. Invest. 98:1119-1129).
Several past investigators have looked at whether the nucleotide content of ODN may
have effects independently of the sequence of the ODN. Interestingly, antisense ODN have
been found to be generally enriched in the content of GG, CCC, CC, CAC, and CG
sequences, while having reduced frequency of TT or TCC nucleotide sequences compared to
what would be expected if base usage were random (Smetsers et al., 1996 Antisense Nucleic
Acid Drug Develop. 6:63-67). This raised the possibility that the over-represented sequences
may comprise preferred targeting elements for antisense oligonucleotides or visa versa. One
reason to avoid the use of thymidine-rich ODN for antisense experiments is that degradation
of the ODN by nucleases present in cells releases free thymidine which competes with 3H-
thynvidine which is frequently used in experiments to assess cell proliferation (Matson et al.,
1992 Antisense Research and Development 2:325-330).
Summary of the Invention
The invention is based in part on the surprising discovery of new families of nucleic
acids that induce higher levels of immune stimulation than previously known nucleic acids.
This finding was surprising in part because more than 100 nucleic acid sequences were
screened prior to discovering those disclosed herein.
The invention provides in one aspect, a composition comprising an
immunostimulatory nucleic acid molecule comprising the nucleotide sequence of SEQ ID
NO:1 (ODN 10102), SEQ ID NO:19 (ODN 10103), SEQ IDNO:45 (ODN 10104), SEQ ID
NO:118 (ODN 10105) or SEQ ID NO:141 (ODN 10106).
The invention further provides in another aspect, a method for stimulating an immune
response in a subject in need thereof comprising administering to a subject an
immunostimulatory nucleic acid molecule comprising the nucleotide sequence of SEQ ID
NO:1 (ODN 10102), SEQ IDNO:19 (ODN 10103), SEQ IDNO:45 (ODN 10104), SEQ ID
NO:118 (ODN 10105) or SEQ ID NO:141 (ODN 10106), in an amount effective to stimulate
an immune response.
Various embodiments of the invention apply equally to the aspects provided herein
and some of these are recited below.
In one embodiment, the immunostimulatory nucleic acid molecule consists of the
nucleotide sequence of SEQ IDNO:1 (ODN 10102), SEQ IDNO:19 (ODN 10103), SEQ ID
NO:45 (ODN 10104), SEQIDNO:118 (ODN 10105) or SEQIDNO.-141 (ODN 10106).
In another embodiment, the composition further comprises an antigen. Alternatively,
the subject to be treated is further administered an antigen. The antigen may be selected from
the group consisting of a microbial antigen, a self antigen, a cancer antigen, and an allergen,
but it is not so limited. In one embodiment, the microbial antigen is selected from the group
consisting of a bacterial antigen, a viral antigen, a fungal antigen and a parasitic antigen. In
another embodiment, the antigen is encoded by a nucleic acid vector. In a related
embodiment, the nucleic acid vector is separate from the immunostimulatory nucleic acid.
The antigen may be a peptide antigen.
In another embodiment, the composition further comprises an adjuvant, or the subject
is further administered an adjuvant. The adjuvant may be a mucosal adjuvant, but it is not so
limited.
In another embodiment, the composition farther comprises a cytokine, or the subject is
further administered a cytokine.
In still another embodiment, the composition further comprises a therapeutic agent
selected from the group consisting of an anti-microbial agent, an anti-cancer agent, and an
allergy/asthma medicament, or the subject is further administered a therapeutic agent selected
from the same group. In a related embodiment, the anti-microbial agent is selected from the
group consisting of an anti-bacterial agent, an anti-viral agent, an anti-fungal agent, and an
anti-parasite agent. In another related embodiment, the anti-cancer agent is selected from the
group consisting of a chemotherapeutic agent, a cancer vaccine, and an immunotherapeutic
agent. In still another related embodiment, the allergy/asthma medicament is selected from
the group consisting of PDE-4 inhibitor, bronchodilator/beta-2 agonist, K+ channel opener,
VLA-4 antagonist, neurokin antagonist, TXA2 synthesis inhibitor, xanthanine, arachidonic
acid antagonist, 5 lipoxygenase inhibitor, thromboxin A2 receptor antagonist, thromboxane
A2 antagonist, inhibitor of 5-lipox activation protein, and protease inhibitor.
The immunostimulatory nucleic acid may in some embodiments have a nucleotide
backbone which includes at least one backbone modification. In one embodiment, the
backbone modification is a phosphorothioate modification. In another embodiment, the
nucleotide backbone is chimeric. In one embodiment, the nucleotide backbone is entirely
modified.
In one embodiment, the composition further comprises a pharmaceutically acceptable
carrier.
In one embodiment, the immunostimulatory nucleic acid is free of methylated CpG
dinucleotides. In another embodiment, the immunostimulatory nucleic acid includes at least
four CpG motifs. In yet another embodiment, the immunostimulatory nucleic acid is T-rich.
In a related embodiment, the immunostimulatory nucleic acid includes a poly-T sequence. In
another embodiment, the immunostimulatory nucleic acid includes a poly-G sequence.
In certain embodiments, the immunostimulatory nucleic acid is formulated in a variety
of ways. In one embodiment, the immunostimulatory nucleic acid is formulated for oral
administration. The immunostimulatory nucleic acid may also be formulated as a nutritional
supplemenL In a related embodiment, the nutritional supplement is formulated as a capsule, a
pill, or a sublingual tablet. In another embodiment, the immunostimulatory nucleic acid is
formulated for local administration. The immunostimulatory nucleic acid may also be
formulated for parenteral administration or it may be formulated in a sustained release device.
The sustained release device may be a microparticle but it is not so limited. In another
embodiment, the immunostimulatory nucleic acid is formulated for delivery to a mucosal
surface. The mucosal surface may be selected from the group consisting of an oral, nasal,
rectal, vaginal, and ocular surface, but is not so limited.
In one embodiment, the immunostimulatory nucleic acid stimulates a mucosal immune
response. In another embodiment, the immunostimulatory nucleic acid stimulates a systemic
immune response. In important embodiments, the immunostimulatory nucleic acid stimulates
both a mucosal and systemic immune response. The immune response is an antigen-specific
immune response, in some embodiments. In related embodiments, the immunostimulatory
nucleic acid is provided in an amount effective to stimulate a mucosal immune response. In
other embodiments, the immunostimulatory nucleic acid is provided in an amount effective to
stimulate a systemic immune response. In still other embodiments, the immunostimulatory
nucleic acid is provided in an amount effective to stimulate an innate immune response.
In various embodiments, the immunostimulatory nucleic acid is intended for treatment
or prevention of a variety of diseases. Thus, in one embodiment, the immunostimulatory
nucleic acid is provided in an amount effective to treat or prevent an infectious disease. In
another embodiment, the immunostimulatory nucleic acid is provided in an amount effective
to treat or prevent an allergy. In still another embodiment, the immunostimulatory nucleic
acid is provided in an amount effective to treat or prevent asthma. In yet a further
embodiment, the immunostimulatory nucleic acid is provided in an amount effective to treat
or prevent a cancer.
In a related embodiment, the infectious disease is a herpes simplex virus infection.
In another embodiment, the immunostimulatory nucleic acid is intended for administration to
a subject that has or is at risk of developing an infection. The infection may be selected from
the group consisting of a bacterial infection, a viral infection, a fungal infection, and a parasite
infection. In one embodiment, the viral infection is selected from the group consisting of
Human immunodeficiency viruses (HTV-1 and HIV-2), Human T lymphotrophic virus type I
(HTLV-I), Human T lymphotrophic virus type II (HTLV-II), Herpes simplex virus type I
(HSV-1), Herpes simplex virus type 2 (HSV-2), Human papilloma virus (multiple types),
Hepatitis A virus, Hepatitis B virus, Hepatitis C and D viruses, Epstein-Barr virus (EBV),
Cytomegalovirus and Molluscum contagiosum virus. In an important embodiment, the viral
infection is a herpes simplex virus infection.
In other embodiments, the infection is an infection with a microbial species selected
from the group consisting of herpesviridae, retroviridae, orthomyroviridae, toxoplasma,
haemophilus, campylobacter, clostridium, E.coli, and staphylococcus. In related
embodiments, the antigen to be administered to the subject or to be included in the
composition is from one of the foregoing species.
In certain embodiments, the infection is a SARS infection or a monkey pox infection.
In other embodiments, the immunostimulatory nucleic acid is intended from
administration to a subject that has or is at risk of developing allergy, or a subject that has or
is at risk of developing asthma, or a subject that has or is at risk of developing a cancer.
In embodiments relating to the treatment of a subject, the method may further
comprise isolating an immune cell from the subject, contacting the immune cell with an
effective amount to activate the immune cell of the immunostimulatory nucleic acid and re-
administering the activated immune cell to the subject. In one embodiment, the immune cell
is a leukocyte. In another embodiment, the immune cell is a dendritic cell. In another
embodiment, the method further comprises contacting the immune cell with an antigen.
In important embodiments, the subject is a human. In other embodiments, the subject
is selected from the group consisting of a dog, cat, horse, cow, pig, sheep, goat, chicken,
monkey and fish.
Accordingly, the methods provided herein can be used on a subject that has or is at
risk of developing an infectious disease and therefore the method is a method for treating or
preventing the infectious disease. The methods can also be used on a subject that has or is at
risk of developing asthma and the method is a method of treating or preventing asthma in the
subject. The method can also be used on a subject that has or is at risk of developing allergy
and the method is a method of treating or preventing allergy. And it can further be used on a
subject that has or is at risk of developing a cancer and the method is a method of treating or
preventing the cancer. In one embodiment, the cancer is selected from the group consisting of
biliary tract cancer; bone cancer; brain and CNS cancer; breast cancer; cervical cancer;
choriocarcinoma; colon cancer; connective tissue cancer; endometrial cancer; esophageal
cancer; eye cancer; gastric cancer; Hodgkin's lymphoma; intraepithelial neoplasms; larynx
cancer; Iymphomas; liver cancer; lung cancer (e.g. small cell and non-small cell); melanoma;
neuroblastomas; oral cavity cancer; ovarian cancer; pancreas cancer; prostate cancer; rectal
cancer; sarcomas; skin cancer; testicular cancer; thyroid cancer; and renal cancer.
In yet another embodiment of the therapeutic or prophylactic methods provided
herein, the method may further comprise administering an antibody specific for a cell surface
antigen, and wherein the immune response results in antigen dependent cellular cytotoxicity
(ADCC).
The invention provides in another aspect, a method for preventing disease in a subject,
comprising administering to the subject an immunostirnulatory nucleic acid on a regular basis
to prevent disease in the subject, wherein the immunostimulatory nucleic acid has a
nucleotide sequence comprising SEQ ID NO:1 (ODN 10102), SEQ ID NO:19 (ODN 10103),
SEQ ID NO:45 (ODN 10104), SEQ ID NO:118 (ODN 10105) or SEQ ID NO:141 (ODN
10106).
In yet another aspect, the invention provides a method for inducing an innate immune
response, comprising administering to the subject an immunostimulatory nucleic acid in an
amount effective for activating an innate immune response, wherein the immunostimulatory
nucleic acid has a nucleotide sequence comprising SEQ ID NO:1 (ODN 10102), SEQ ID
NO:19 (ODN 10103), SEQ ID NO:45 (ODN 10104), SEQ IDNO:118 (ODN 10105) or SEQ
IDNO:141 (ODN 10106).
In still another aspect, the invention provides a method for identifying an
immunostimulatory nucleic acid comprising measuring a control level of activation of an
immune cell population contacted with an immunostimulatory nucleic acid comprising a
nucleotide sequence of SEQ ID NO:1 (ODN 10102), SEQ ID NO:19 (ODN 10103), SEQ ID
NO:45 (ODN 10104), SEQ IDNO:118 (ODN 10105) or SEQ ID NO:141 (ODN 10106),
measuring a test level of activation of an immune cell population contacted with a test nucleic
acid, and comparing the control level of activation to the test level of activation, wherein a
test level that is equal to or above the control level is indicative of an immunostimulatory
nucleic acid.
These and other aspects and embodiments of the invention will be described in greater
detail herein.
Accompanying
Brief Description of the/Figures
Fig. 1: TLR9 engagement by ODNs 7909 and 10102. A TLR9-expressing cell line was
incubated with the indicated concentrations of ODNs as described in Example 1. Shown is the
mean Stimulation Index above media control. IL-1 was used as a positive control for the
reporter gene.
Fig. 2: B cells up regulate the activation marker CD86 upon incubation of PBMC with
CpG ODNs. Human PBMC were incubated with ODNs 7909 and 10102 at the indicated
concentrations for 48h. Shown is the mean percentage of CD86 expressing CD19-positive B
cells (measured by flow cytometry) of three different donors.
Fig. 3: Proliferation of B cells induced by CpG ODNs 7909 and 10102. PBMC pre-
incubated with the dye CFSE were cultured for 5 days without or with the indicated ODN
concentrations. Cells were harvested and the decrease of the CFSE stain on proliferating
CD19-positive B cells was measured by flow cytometry on three different donors (see also
Example 1).
Fig. 4: IFN-alpha secretion induced by ODNs 7909 and 10102. Human PBMC of
three different donors were incubated with the indicated concentrations of ODNs for 48h. The
supernatant was harvested and IFN-a was measured by ELISA (see Example 1). Shown are
the mean, minimal and maximal amounts of IFN-alpha obtained for the three different donors
at each concentration.
Fig. 5: IP-10 secretion induced by ODNs 7909 and 10102. Human PBMC of three
different donors were incubated with the indicated concentrations of ODNs for 48h. The
supernatant was harvested and IP-10 was measured by ELISA (see Example 1). Shown are
the mean, minimal and maximal amounts of IP-10 obtained for the three different donors at
each concentration.
Fig. 6: IL-10 secretion induced by ODNs 7909 and 10102. PBMC of three different
blood donors were incubated with the indicated concentrations of ODNs 7909,10102 or a
control ODN. Supernatants were harvested and IL-10 measured by ELISA. Shown are the
mean, minimal and maximal IL-10 amounts obtained from the three donors at each
concentration.
Fig. 7: TNF-alpha secretion in response to ODNs 7909 and 10102. PBMC of three
different blood donors were incubated with the indicated concentrations of ODNs 7909,
10102 or a control ODN for 24h. Supernatants were harvested and TNF-alpha was measured
by ELISA. Shown are the mean, minimal and maximal amounts from the three donors at each
concentration.
Fig. 8: Naive BALB/c mouse splenocytes (5 x 106/ml or 2.5 x 106/ml) were incubated
with media (negative control) or different amounts of CpG ODN 10102. Cells were pulsed
with 3H-thymidine (20 mCi/ml) at 96 hr post incubation for 16 hours, harvested and measured
for radioactivity. Each bar represents the stimulation index (counts/min (CPM) of cells
incubated/CPM of cells incubated with media).
Fig. 9: Naive BALB/c mouse splenocytes (5 x 1O6/ml) were incubated with media
(negative control) or different amounts of CpG ODN 7909, 10102 or control ODN 2137.
Supernatants were harvested at 6 hr (for TNF-alpha, panel D), 24 hr (IL-12, panel B) or 48 hr
(for IL-6, panel C, and IL-10, panel A).
Fig. 10: Naive BALB/c mouse splenocytes (30 x 106/ml) were incubated with media
(negative control) or different amounts of CpG ODN 7909 and 10102. NK activity was
measured by using 51Cr release assay.
Fig. 11: Adult (6-8 wk) BALB/c mice were immunized with 1 mg of HBsAg alone or in
combination with CpG ODN (10 mg) 10102, 7909 or control ODN (10 mg) 2137. Animals were
bled at 4 weeks post immunization and plasma was assayed for total IgG levels against HBsAg
(Anti-HBs). Each bar represents the geometric mean (± SEM) of the ELISA end point dilution
titer for the entire group (n=10). Titers were defined as the highest dilution resulting in an
absorbance value two times that of non-immune plasma with a cut-off value of 0.05.
Fig. 12: Adult BALB/c mice (6-8 wks old) were immunized with 1 mg of HBsAg alone
or in combination with 10 mg CpG ODN 7909,10102 or 10 mg control ODN 2137. Animals
were bled at 4 weeks post immunization and plasma was assayed for IgGl and IgG2a levels
against HBsAg (Anti-HBs). Each bar represents the geometric mean (± SEM) of the ELISA end
point dilution titer for the entire group (n=10). Titers were defined as the highest dilution
resulting in an absorbance value two times that of non-immune plasma with a cut-off value of
0.05.
Fig. 13: TLR9 engagement by ODNs 7909 and 10103. A TLR9-expressing cell line
was incubated with the indicated concentrations of ODNs as described in Example 2. Shown
is the mean stimulation index above media control for 4 independent experiments. IL-1 was
used as a positive control for the reporter gene.
Fig. 14: B cells up regulate the activation marker CD86 upon incubation of PBMC
with CpG ODNs. Human PBMC were incubated with ODNs 7909 and 10103 as well as a
control ODN at the indicated concentrations for 48h. Shown is the mean percentage of CD86
expressing CD19-positive B cells (measured by flow cytometry) of three different donors.
Fig. 15: Proliferation of B cells induced by CpG ODNs 7909 and 10103. PBMC pre-
incubated with the dye CFSE were cultured for 5 days without or with the indicated ODN
concentrations. Cells were harvested and the decrease of the CFSE stain on proliferating
CD19-positive B cells was measured by flow cytometry (see also Example 2).
Fig. 16: IFN-a secretion induced by ODNs 7909 and 10103. Human PBMC of six
different donors were incubated with the indicated concentrations of ODNs for 48h. The
supernatant was harvested and IFN-a was measured by ELISA (see Example 2). Shown are
the amounts of IFN-a obtained for the six different donors at each concentration.
Fig. 17: IP-10 secretion induced by ODNs 7909 and 10103. Human PBMC of three
different donors were incubated with the indicated concentrations of ODNs for 48h. The
supernatant was harvested and IP-10 was measured by ELISA (see Example 2). Shown are
the mean amounts of IP-10 obtained for the three different donors at each concentration.
Fig. 18: showed the secretion of IL-10 upon incubation with different concentrations
of 7909,10103 and control ODN. Shown are the means from three different donors obtained
upon incubation for 48h as indicated.
Fig. 19: TNF-a secretion: PBMC of three different blood donors were incubated with
5 the indicated concentrations of ODNs 7909,10103 or a control for 48h. Supematants were
harvested and TNF-a was measured by ELISA. Shown are the mean amounts for three
donors.
Fig. 20: Naive BALB/c mouse splenocytes (5 x 106/ml or 2.5 x 106/rnl) were
incubated with media (negative control) or different amounts of CpG ODN 7909 (white bars),
10 10103 (black bars). Cells were pulsed with 3H-thymidine (20 mCi/ml) at 96 hr post incubation
for 16 hours, harvested and measured for radioactivity. Each bar represents the stimulation
index (counts/min (CPM) of cells incubated/CPM of cells incubated with media).
Fig. 21: Naive BALB/c mouse splenocytes (5 x 106/ml) were incubated with media
(negative control) or different amounts of CpG ODN 7909,10103 or control ODN 2137.
15 Supematants were harvested at 6 hr (for TNF-a, panel D), 24 hr (IL-12, panel B) or 48 hr (for
IL-6, panel C, and IL-10, panel A).
Fig. 22: Naive BALB/c mouse splenocytes (30 x 106/ml) were incubated with media
(negative control) or different amounts of CpG ODN 7909 and 10103. NK activity was
measured by using 51Cr release assay.
20 Fig. 23: Adult (6-8 wk) BALB/c mice were immunized with 1 mg of HBsAg alone or in
combination with CpG ODN (10 ug) 10103, 7909 or control ODN (10 ug) 2137. Animals were
bled at 4 weeks post irnmunization and plasma was assayed for total IgG levels against HBsAg
(Anti-HBs). Each bar represents the geometric mean (± SEM) of the ELISA end point dilution
titer for the entire group (n=5). Titers were defined as the highest dilution resulting in an
25 absorbance value two times that of non-immune plasma with a cut-off value of 0.05.
Fig. 24: Adult BALB/c mice (6-8 wks old) were immunized with 1 mg of HBsAg
alone or in combination with 10 mg CpG ODN 7909,10103 or 10 mg control ODN 2137.
Animals were bled at 4 weeks post immunization and plasma was assayed for IgGl and
IgG2a levels against HBsAg (Anti-HBs). Each bar represents the geometric mean (+ SEM) of
30 the ELISA end point dilution titer for the entire group (n=5). Titers were defined as the
highest dilution resulting in an absorbance value two times that of non-immune plasma with a
cut-off value of 0.05.
Fig. 25: Adult (6-8 wk) BALB/c mice were immunized with 1 mg of HBsAg in
combination with either CpG ODN (10 mg) 7909 or 10103. At 4 weeks post immunization,
spleens were removed and splenocytes were used for measuring CTL activity by 51Cr release
assay. CTL activity is indicated as mean % specific lysis (± SEM) for the group of animals
5 (n=5) at different effectorrtarget ratios.
Fig. 26 is a graph of mean pathological score as a function of days post infection in
mice challenged with HSV-2 and administered nucleic acid 10104.
Fig. 27 is a graph of percent survival as a function of days post infection in mice
challenged with HSV-2 and administered nucleic acid 10104.
10 Fig. 28 is a bar graph showing human IFN-alpha induction in human PBMC after 48
hours of culture with nucleic acid 10104 or control. IFN-alpha was measured by ELISA and
the results are the mean +/- SEM from three blood donors.
Fig. 29 is a bar graph showing human IL-10 induction in human PBMC after 48 hours
of culture with nucleic acid 10104 or control. IL-10 was measured by ELISA and the results
15 are the mean +/- SEM from three blood donors.
Fig. 30 is a bar graph showing human TLR9-mediated NFkB stimulation following 16
hour exposure to nucleic acid 10104 or control. Stimulation was measured using a reporter
gene upregulation assay.
Fig. 31: TLR9 engagement by ODNs 7909 and 10105. A TLR9-expressing cell line
20 was incubated with the indicated concentrations of ODNs as described in Example 4. Shown
is the mean Stimulation Index above media control for 4 independent experiments. IL-1 was
used as a positive control for the reporter gene.
Fig. 32: B cells up regulate the activation marker CD86 upon incubation of PBMC
with CpG ODNs. Human PBMC were incubated with ODNs 7909 and 10105 as well as a
25 control ODN at the indicated concentrations for 48h. Shown is the mean percentage of CD86
expressing CD19-positive B cells (measured by flow cytometry) of three different donors.
Fig. 33: Proliferation of B cells induced by CpG ODNs 7909 and 10105. PBMC pre-
incubated with the dye CFSE were cultured for 5 days without or with the indicated ODN
concentrations. Cells were harvested and the decrease of the CFSE stain on proliferating
30 CD 19-positive B cells was measured by flow cytometry (see also Example 4).
Fig. 34: IFN-a secretion induced by ODNs 7909 and 10105. Human PBMC of three
different donors were incubated with the indicated concentrations of ODNs for 48h. The
supernatant was harvested and IFN-a was measured by ELISA (see Example 4). Shown are
the mean amounts of IFN-a obtained for the three different donors at each concentration.
Fig. 35: IP-10 secretion induced by ODNs 7909 and 10105. Human PBMC of three
different donors were incubated with the indicated concentrations of ODNs for 48h. The
5 supernatant was harvested and IP-10 was measured by ELISA (see Example 4). Shown are
the mean amounts of IP-10 obtained for the three different donors at each concentration.
Fig. 36: Time kinetic for IFN-a secretion. PBMC of two different blood donors were
incubated with the indicated concentrations of ODNs 7909, 10105 or a control for 8h or 24h.
Supernatants were harvested and IFN-a measured by ELISA. Shown are the individual IFN-a
10 amounts obtained at the different time points for the two donors.
Fig. 37: Time kinetic for IFN-a secretion. PBMC of two different blood donors were
incubated with the indicated concentrations of ODNs 7909,10105 or a control for 36h or 48h.
Supernatants were harvested and IFN-a measured by ELISA. Shown are the individual IFN-a
amounts obtained at the different time points for the two donors.
15 Fig. 38: Time kinetic for IL-10 secretion. PBMC of three different blood donors were
incubated with the indicated concentrations of ODNs 7909, 10105 or a control for 8h, 24h or
48h. Supernatants were harvested and IL-10 measured by ELISA. Shown are the individual
IL-10 amounts obtained at the different time points for the three donors.
Fig. 39: Time kinetic for IL-10 secretion. Shown is the same experiment as in Fig. 8.
20 The mean amounts of IL-10 at each concentration and time point between the three donors
were calculated.
Fig. 40: Naive BALB/c mouse splenocytes (5 x 106/ml or 2.5 x 106/ml) were
incubated with media (negative control) or different amounts of CpG ODN 7909 and 10105.
Cells were pulsed with 3H-thymidine (20 mCi/ml) at 96 hr post incubation for 16 hours,
25 harvested and measured for radioactivity. Each bar represents the stimulation index
(counts/min (CPM) of cells incubated/CPM of cells incubated with media).
Fig. 41: Naive BALB/c mouse splenocytes (5 x 106/ml) were incubated with media
(negative control) or different amounts of CpG ODN 7909,10105 or control ODN 2137.
Supernatants were harvested at 6 hr (for TNF-alpha, panel D), 24 hr (IL-12, panel B) or 48 hr
30 (for IL-6, panel C, and IL-10, panel A).
Fig. 42: Naive BALB/c mouse splenocytes (30 x 106/ml) were incubated with media
(negative control) or different amounts of CpG ODN 7909 and 10105. NK activity was
measured by using 51Cr release assay.
Fig. 43: Adult (6-8 wk) BALB/c mice were immunized with 1 mg of HBsAg alone or in
5 combination with CpG ODN (10 mg) 10105, 7909 or control ODN (10 mg) 2137. Animals were
bled at 4 weeks post immunization and plasma was assayed for total IgG levels against HBsAg
(Anti-HBs). Each bar represents the geometric mean (± SEM) of the ELISA end point dilution
titer for the entire group (n=10). Titers were defined as the highest dilution resulting in an
absorbance value two times that of non-immune plasma with a cut-off value of 0.05.
10 Fig. 44: Adult BALB/c mice (6-8 wks old) were immunized with 1 ug of HBsAg alone
or in combination with 10 mg CpG ODN 7909, 10105 or 10 mg control ODN 2137. Animals
were bled at 4 weeks post immunization and plasma was assayed for IgGl and IgG2a levels
against HBsAg (Anti-HBs). Each bar represents the geometric mean (± SEM) of the ELISA end
point dilution titer for the entire group (n=10). Titers were defined as the highest dilution
15 resulting in an absorbance value two times that of non-immune plasma with a cut-off value of
0.05.
Fig. 45: Proliferation of B cells induced by CpG ODNs. PBMCs from normal, healthy
subjects (n=10) or subjects chronically infected with HCV (n=10) at a concentration of 0.5 x
106/ml were incubated with media (negative control) or increasing amounts of CpG ODN
20 7909 and 10106 or 4010 at 6 mg/mL. Cells were pulsed for 16 to 18 hours with 3H-thymidine
(1 mCi/well) 5 days post incubation, harvested and measured for radioactivity. Each bar
represents the mean stimulation index (counts/min (CPM) of cells incubated with ODN/CPM
of cells incubated with media).
Fig. 46: IFN-a secretion induced by CpG ODNs. Human PBMCs from normal,
healthy subjects and subjects chronically infected with HCV were incubated with the control
ODN 4010, 7909 or 10106 at concentrations ranging from 1 to 6 mg/mL. The supernatant was
harvested and IFN-a was measured by ELISA (see Example 5). The detection limit for the
assay was 31.2 pg/mL and the subjects with IFN-a results below the limit of detection are not
represented on the graph. The means, indicated by a straight line, were determined for those
subjects with detectable IFN-a.
Fig. 47: IP-10 secretion induced by CpG ODNs. Human PBMCs from 10 normal,
healthy subjects and 10 subjects chronically infected with HCV were incubated with the
control ODN 4010, 7909 or 10106 at concentrations ranging from 1 to 6 mg/mL. The
supernatant was harvested and IP-10 was measured by ELISA (see Example 5) with a
detection limit of 15.6 pg/mL.
Fig. 48: IL-10 secretion induced by CpG ODNs. Human PBMCs from 10 normal,
5 healthy subjects and 10 subjects chronically infected with HCV were incubated with the
control ODN 4010, 7909 or 10106 at concentrations ranging from 1 to 6 ug/mL. The
supernatant was harvested and IL-10 was measured by ELISA (see Example 5). The
detection limit for the ELISA assay was 23.4 pg/mL. When treatment groups have subjects
with undetectable IL-10 concentrations, the number of subjects with detectable IL-10 are
10 indicated on the graph as a ratio of the total number of subjects assessed. The mean and
standard deviation determined are for those subjects with detectable IL-10.
Fig. 49: TLR9 engagement by ODNs 7909 and 10106. A TLR9-expressing cell line
was incubated with the indicated concentrations of ODNs as described in Example 5. Shown
is the mean Stimulation Index above media control. IL-1 was used as a positive control for the
15 reporter gene.
Fig. 50: B cells up regulate the activation marker CD86 upon incubation of PBMC
with CpG ODNs. Human PBMC were incubated with ODNs 7909 and 10106 at the indicated
concentrations for 48h. Shown is the mean percentage of CD86 expressing CD19-positive B
cells (measured by flow cytometry) of three different donors.
20 Fig. 51: Proliferation of B cells induced by CpG ODNs 7909 and 10106. PBMC pre-
incubated with the dye CFSE were cultured for 5 days without or with the indicated ODN
concentrations. Cells were harvested and the decrease of the CFSE stain on proliferating
CD19-positive B cells was measured by flow cytometry on three different donors (see also
Example 5).
25 Fig. 52: IFN-a secretion induced by ODNs 7909 and 10106. Human PBMC of three
different donors were incubated with the indicated concentrations of ODNs for 48h. The
supernatant was harvested and IFN-a was measured by ELISA (see Example 5). Shown are
the mean, min. and max. amounts of IFN-a obtained for the three different donors at each
concentration.
Fig. 53: IP-10 secretion induced by ODNs 7909 and 10106. Human PBMC of three
different donors were incubated with the indicated concentrations of ODNs for 48h. The
supernatant was harvested and IP-10 was measured by ELISA (see Materials and Methods).
Shown are the mean, min. and max. amounts of IP-10 obtained for the three different donors
at each concentration.
Fig. 54: IL-10 secretion. PBMC of three different blood donors were incubated with
the indicated concentrations of ODNs 7909,10106 or a control. Supematants were harvested
5 and IL-10 measured by ELISA. Shown are the mean, min and max IL-10 amounts obtained
from the three donors.
Fig. 55: TNF-a secretion: PBMC of three different blood donors were incubated with
the indicated concentrations of ODNs 7909,10106 or a control for 16h. Supematants were
harvested and TNF-a was measured by ELISA. Shown are the mean, min. and max. amounts
10 for three donors.
Fig. 56: Naive BALB/c mouse splenocytes (5 x 106/ml or 2.5 x 106/ml) were
incubated with media (negative control) or different amounts of CpG ODN 7909 and 10106.
Cells were pulsed with 3H-thymidine (20 mCi/ml) at 96 hr post incubation for 16 hours,
harvested and measured for radioactivity. Each bar represents the stimulation index
15 (counts/min (CPM) of cells incubated/CPM of cells incubated with media).
Fig. 57: Naive BALB/c mouse splenocytes (5 x 106/ml) were incubated with media
(negative control) or different amounts of CpG ODN 7909, 10106 or control ODN 2137.
Supematants were harvested at 6 hr (for TNF-a, panel D), 24 hr (IL-12, panel B) or 48 hr (for
IL-6, panel C, and IL-10, panel A).
20 Fig. 58: Naive BALB/c mouse splenocytes (30x106/ml) were incubated with media
(negative control) or different amounts of CpG ODN 7909 and 10106. NK activity was
measured by using 51Cr release assay.
Fig. 59: Adult (6-8 wk) BALB/c mice were immunized with 1 ug of HBsAg alone or in
combination with CpG ODN (10 ug) 10106,7909 or control ODN (10 ug) 2137. Animals were
25 bled at 4 weeks post immunization and plasma was assayed for total IgG levels against HBsAg
(Anti-HBs). Each bar represents the geometric mean (± SEM) of the ELISA end point dilution
titer for the entire group (n=10). Titers were defined as the highest dilution resulting in an
absorbance value two times that of non-immune plasma with a cut-off value of 0.05.
Fig. 60: Adult BALB/c mice (6-8 wks old) were immunized with 1 ug of HBsAg alone
30 or in combination with 10 mg CpG ODN 7909,10106 or 10 mg control ODN 2137. Animals
were bled at 4 weeks post immunization and plasma was assayed for IgGl and IgG2a levels
against HBsAg (Anti-HBs). Each bar represents the geometric mean (± SEM) of the ELISA end
point dilution titer for the entire group (n=10). Titers were defined as the highest dilution
resulting in an absorbance value two times that of non-immune plasma with a cut-off value of
0.05.
Fig. 61A shows effects of topical CpG delivery using BEMA disks on local pathology
5 of mice following intravaginal challenge with HSV-2.
Fig. 6 IB shows effects of topical CpG delivery in saline on local pathology of mice
following intravaginal challenge with HSV-2.
Fig. 62 A shows the effects of topical CpG delivery using BEMA disks on survival of
mice following intravaginal challenge with HSV-2.
10 Fig. 62B shows the effects of topical CpG delivery in saline on survival of mice
following intravaginal challenge with HSV-2.
Fig. 63 shows the effects of parenteral CpG 10104 delivery on IP-10 levels in plasma
of mice.
Fig. 64 shows the effects of parenteral CpG 10104 delivery on IFN-g levels in plasma
15 of mice.
Fig. 65 shows the effects of intravaginal CpG 10104 delivery on IP-10 levels in
plasma of mice.
Fig. 66 shows the effects of topical CpG delivery on local pathology of mice following
intravaginal challenge with HSV-2.
20 Fig. 67 shows the effects of topical CpG delivery on survival of mice following
intravaginal challenge with HSV-2.
Fig. 68 shows the effects of intravaginal CpG 10104 delivery on IP-10 levels in
vaginal wash of mice.
Fig. 69A shows the effects of topical CpG delivery on local pathology of mice
25 following intravaginal challenge with HSV-2.
Fig. 69B shows the effects of topical CpG delivery on survival of mice following
intravaginal challenge with HSV-2.
Fig. 70A shows that CpG 10104 is as good as CpG 7909 in augmenting humoral
responses against HBsAg in BALB/c mice in the absence of alum.
30 Fig. 70A shows that CpG 10104 is as good as CpG 7909 in augmenting humoral
responses against HBsAg in BALB/c mice in the presence of alum.
Fig. 71A shows that CpG 10104 is as good as CpG 7909 in promoting Thl biased
immune responses (determined by high IgG2a titers compared to IgGl titers) against HbsAg
in BALB/c mice in the absence of alum.
Fig. 71B shows that CpG 10104 is as good as CpG 7909 in promoting Thl biased
5 immune responses (determined by high IgG2a titers compared to IgGl titers) against HbsAg
in BALB/c mice in the presence of alum.
Detailed Description of the Invention
It was known in the prior art that CpG containing nucleic acids stimulate the immune
10 system, and that can thereby be used to treat cancer, infectious diseases, allergy, asthma and
other disorders, and to help protect against opportunistic infections following cancer
chemotherapies. The strong yet balanced, cellular and humoral immune responses that result
from CpG stimulation reflect the body's own natural defense system against invading
pathogens and cancerous cells. CpG sequences, while relatively rare in human DNA, are
15 commonly found in the DNA of infectious organisms such as bacteria. The human immune
system has apparently evolved to recognize CpG sequences as an early warning sign of
infection, and to initiate an immediate and powerful immune response against invading
pathogens without causing adverse reactions frequently seen with other immune stimulatory
agents. Thus, CpG containing nucleic acids, relying on this innate immune defense
20 mechanism, can utilize a unique and natural pathway for immune therapy.
The effects of CpG nucleic acids on immune modulation were discovered by the
inventor of the instant patent application and have been described extensively in co-pending
patent applications, such as U.S. Patent Application Serial Nos: 08/386,063 filed on 02/07/95
(and related PCT US95/01570); 08/738,652 filed on 10/30/96, 08/960,774 filed on 10/30/97
25 (and related PCT/US97/19791, WO 98/18810); 09/191,170 filed on 11/13/98; 09/030,701
filed on 02/25/98 (and related PCT/US98/03678; 09/082,649 filed on 05/20/98 (and related
PCT/US98/10408); 09/325,193 filed on 06/03/99 (and related PCT/US98/04703); 09/286,098
filed on 04/02/99 (and related PCT/US99/07335); 09/306,281 filed on 05/06/99 (and related
PCT/US99/09863). The entire contents of each of these patents and patent applications is
?0 hereby incorporated by reference.
The invention is based, in part, on the unexpected discovery of several families of
nucleic acids that are more immunostimulatory than previously reported CpG nucleic acids.
Each family is represented by a particularly immunostimulatory nucleic acid. These nucleic
acid families and their representative members are described in more detail below.
ODN 10102 Family:
5 This family of nucleic acids comprises the nucleotide sequence having the formula of
5'X1X2X3X4X5X6X7 TTCGTCGTTTCGTCGTT 3' (SEQIDNO:3)
wherein X1, X2, X3, X4, X5, X6 and X7 are independently selected residues that may be
selected from the group of nucleotides consisting of adenosine, guanosine, thymidine, and
cytosine. In some embodiments, there may be no flanking residues. Such a nucleic acid
10 would comprise a nucleotide sequence of 5 'IT CGT CGT TTC GTC GTT 3' (SEQ ID
NO:4).
In other embodiments, the nucleic acid may lack X1; X1 and X2; X1, X2 and X3; X1,
X2, X3 and X4; or X1, X2, X3, X4 and X5, or may lack X1 through to X6 or may lack X1
through to X7.
15 In one embodiment, X1 is a thymidine, and /or X2 is cytosine, and/or X3 is a guanosine,
and/or X4 is a thymidine, and/or X5 is a cytosine, and/or X6 is a guanosine, and/or X1 is a
thymidine. Those of ordinary skill in the art will be able to determine the sequence of the
remaining nucleic acids belonging to this family.
The nucleic acids of this family are generally at least 17 nucleotides in length. In
20 some embodiments, the nucleic acids are at least 19, at least 20, at least 21, at least 22, at least
23, and at least 24 nucleotides in length. In a preferred embodiment, the nucleic acids are 24
nucleotides in length. In still further embodiments, the nucleic acids are more than 24
nucleotides in length. Examples include nucleic acids that are at least 50, at least 75, at least
100, at least 200, at least 500, at least 1000 nucleotides in length, or longer. Preferably, the
25 nucleic acids are 17-100, and more preferably 24-100 nucleotides in length.
All the nucleic acids of this first family contain at least three CpG motifs. These
nucleic acids may contain four or five or more CpG motifs. The CpG motifs may be
contiguous to each other, or alternatively, they may be spaced apart from each other at
constant or random distances.
30 The nucleic acids of this family also contain an overrepresentation of thymidine
nucleotides. These nucleic acids may contain greater than 60%, less than 60%, or less than
55% thymidines.
The invention is further premised, in part, on the unexpected discovery of another
family of nucleic acids that is more immunostimulatory than previously reported CpG nucleic
acids. This family of nucleic acids comprises the nucleotide sequence having the formula of
5' TCG TCGTTT CGT CGT TTC X1X2X3X4 X5 X6 3' (SEQ ID NO:5)
J wherein X1, X2, X3, X4, X5, and X6 are independently selected residues that may be selected
from the group of nucleotides consisting of adenosine, guanosine, thymidine, and cytosine. In
some embodiments, there may be no flanking residues. As an example, the nucleic acid may
comprise a nucleotide sequence of 5' TCG TCG TTT CGT CGT TTC 3' (SEQ ID NO:6).
In other embodiments, the nucleic acid may lack X6; X6 and X5; or X6, X5, and X4; X6
10 through to X3; X6 through to X2; or X6 through to X1.
In one embodiment, X1 is a cytosine. In another embodiment, X2 is guanosine. In
another embodiment, X3 is a thymidine. In another embodiment, X4 is a thymidine. Those of
ordinary skill in the art will be able to determine the sequence of the remaining nucleic acids
belonging to this family.
15 The nucleic acids of this latter family are generally at least 18 nucleotides in length.
In some embodiments, the nucleic acids are at least 20, at least 22, at least 23, and at least 24
nucleotides in length. In a preferred embodiment, the nucleic acids are 24 nucleotides in
length. In still further embodiments, the nucleic acids are more than 24 nucleotides in length.
Examples include nucleic acids that are at least 50, at least 75, at least 100, at least 200, at
20 least 500, at least 1000 nucleotides in length, or longer. Preferably, the nucleic acids are 18-
100, and more preferably 24-100 nucleotides in length.
All the nucleic acids of this second family contain at least four CpG motifs. These
nucleic acids may contain five or more CpG motifs, depending upon the embodiment. The
CpG motifs may be contiguous to each other, or alternatively, they may be spaced apart from
25 each other at constant or random distances.
The nucleic acids of this family also contain an overrepresentation of thymidine
nucleotides. These nucleic acids may contain greater than 60%, less than 60%, or less than
55% thymidines.
In another aspect, the invention provides a nucleic acid comprising the nucleotide
10 sequence of TCG TCG TTT CGT CGT TTC GTC GTT (SEQ ID NO: 1) (ODN 10102). As
described in greater detail in the Examples, this nucleic acid was identified only after
screening a multitude of nucleic acids for those having similar or greater immunostimulatory
activity than previously identified irnmunostirnulatory nucleic acids. More specifically, the
nucleic acids were compared to a nucleic acid having a nucleotide sequence of TCG TCG
TTT TGT CGT TTT GTC GTT (SEQ ID NO:2) that was previously shown to be
immunostimulatory. The nucleic acid comprising SEQ ID NO:1 was identified only after
5 screening approximately 165 nucleic acids for those having immunostimulatory capacity
greater than that of nucleic acids comprising SEQ ID NO:2. The difference in activity is
surprising because there is only a minimal difference between SEQ ID NO: I and SEQ ID
NO:2 (i.e., a difference in two nucleotides). It was unexpected that such a minimal change in
sequence would result in a statistically significant increase in immunostimulation.
10 In yet other aspects of the invention, nucleic acids having the following nucleotide
sequences are provided: 5' TCG TCG TTT CGT CGT TTC GTC GT 3' (SEQ ID NO:7); 5'
TCG TCG TTT CGT CGT TTC GTC G 3' (SEQ ID NO: 8); 5' TCG TCG TTT CGT CGT
TTC GTC 3' (SEQ ID NO:9); 5'TCG TCG TTT CGT CGT TTC GT 3' (SEQ IDNO:10);
5' TCG TCG TTT CGT CGT TTC G 3' (SEQ ID NO.l 1); 5' CG TCG TTT CGT CGT TTC
75 GTC GTT 3' (SEQ ID NO:12); 5' G TCG TTT CGT CGT TTC GTC GTT 3' (SEQ ID
NO-.13); 5' TCG TTT CGT CGT TTC GTC GTT 3' (SEQ ID NO:14); 5' CG TTT CGT
CGT TTC GTC GTT 3' (SEQ IDNO:15); 5' G TTT CGT CGT TTC GTC GTT 3' (SEQ ID
NO:16); 5' TTT CGT CGT TTC GTC GTT 3' (SEQ ID NO:17); 5' TT CGT CGT TTC GTC
GTT 3' (SEQIDNO-.18).
20 The nucleic acids of the invention can further contain other immunostimulatory motifs
such as poly T motifs, poly G motifs, TG motifs, poly A motifs, poly C motifs, and the like,
provided that the core sequences of SEQ ID NO:4 and SEQ ID NO:6 are present. These
immunostimulatory motifs are described in greater detail below or in U.S. Non-Provisional
Patent Application Serial No. 09/669,187, filed September 25,2000, and published PCT
25 Patent Application PCT/US00/263 83, having publication number WOO 1 /22972.
ODN 10103 Family:
This family of nucleic acids comprises the nucleotide sequence having the formula of
5' X1 X2X3 X4X5X6 X7X8 X1OX11X12 GGT CGT TTT 3' (SEQ ID NO:20)
'0 wherein X1 X2, X3, X4, X5, X6, X7, X8, X9, X10, X11, and X12 are independently selected
residues that may be selected from the group of nucleotides consisting of adenosine,
guanosine, thymidine, and cytosine. In some embodiments, there may be no flanking
residues. Such a nucleic acid would comprise a nucleotide sequence of 5' GGT CGT TTT
3' (SEQ ID NO:21).
In other embodiments, the nucleic acid may lack X1; X1, and X2; X1' X2 and X3; X1,
X2, X3 and X4; or X1, X2, X3, X4and X5, X1 through X6, X1 through X7, X1 through X8, X,
through X9, X1 through X10, X1 through X11, and X1 through X12.
In various embodiments, X1 is a thymidine, and/or X2 is cytosine, and/or X3 is a
guanosine, and/or X4 is a thymidine, and/or X5 is a cytosine, and/or X6 is a guanosine,
and/or X7 is a thymidine, and/or X6 is a thymidine, and/or X9 is a thymidine, and/or X10 is a
thymidine, and/or X11 is a thymidine, and/or X12 is a cytosine. Those of ordinary skill in
10 the art will be able to determine the sequence of the remaining nucleic acids belonging to
this family.
The nucleic acids of this family are generally at least 9 nucleotides in length. In
some embodiments, the nucleic acids are at least 10, at least 12, at least 15, at least 18, at
least 20, and at least 21 nucleotides in length. In a preferred embodiment, the nucleic acids
15 are 21 nucleotides in length. In still further embodiments, the nucleic acids are more than
21 nucleotides in length. Examples include nucleic acids that are at least 50, at least 75, at
least 100, at least 200, at least 500, at least 1000 nucleotides in length, or longer.
Preferably, the nucleic acids are 9-100, and more preferably 21-100 nucleotides in length.
All the nucleic acids of this first family contain at least one CpG motif. These
20 nucleic acids may contain two, three, four or more CpG motifs. The CpG motifs may be
contiguous to each other, or alternatively, they may be spaced apart from each other at
constant or random distances.
The nucleic acids of this family also contain an overrepresentation of thymidine
nucleotides. These nucleic acids may contain at least 60%, at least 55%, or at least 50%
25 thymidines.
The invention is further premised, in part, on the unexpected discovery of another
family of nucleic acids that is as immunostimulatory as previously reported CpG nucleic
acids. This family of nucleic acids comprises the nucleotide sequence having the formula of
5' TCG TCG TTT TTC X1X2X3, X4X5X6 X7XgX9 3' (SEQ ID NO:22)
30 wherein X1 through X9 are independently selected residues that may be selected from the
group of nucleotides consisting of adenosine, guanosine, thymidine, and cytosine. In some
embodiments, there may be no flanking residues. As an example, the nucleic acid may
comprise a nucleotide sequence of 5' TCG TCG TTT TTC 3' (SEQ ID NO:23).
In other embodiments, the nucleic acid may lack X9; X9 and X8; X9, X8 and X7; X9,
through X6; X9 through X5; X9 through X4; X9 through X3; X9 through X2; and X9 through
5 X1.
In various embodiments, X1 is a guanosine, and/or X2 is guanosine, and/or X3 is a
thymidine, and/or X4 is a cytosine, and/or X5 is a guanosine, and/or X6 is a thymidine,
and/or X7 is a thymidine, and/or X8 is a thymidine, and/or X9 is a thymidine. Those of
ordinary skill in the art will be able to determine the sequence of the remaining nucleic
JO acids belonging to this family.
The nucleic acids of this family are generally at least 12 nucleotides in length. In
some embodiments, the nucleic acids are at least 15, at least 18, and at least 21 nucleotides
in length. In a preferred embodiment, the nucleic acids are 21 nucleotides in length. In still
further embodiments, the nucleic acids are more than 21 nucleotides in length. Examples
15 include nucleic acids that are at least 50, at least 75, at least 100, at least 200, at least 500,
at least 1000 nucleotides in length, or longer. Preferably, the nucleic acids are 12-100, and
more preferably 21-100 nucleotides in length.
All the nucleic acids of this second family contain at least two CpG motifs. These
nucleic acids may contain three or four or more CpG motifs, depending upon the
20 embodiment. The CpG motifs may be contiguous to each other, or alternatively, they may
be spaced apart from each other at constant or random distances.
The nucleic acids of this family also contain an overrepresentation of thymidine
nucleotides. These nucleic acids may contain at least 60%, at least 55 %, or at least 50%
thymidines.
25 In another aspect, the invention provides a nucleic acid comprising the nucleotide
sequence of TCG TCG TTT TTC GGT CGT TTT (SEQ ID NO:19) (ODN 10103). As
described in greater detail in the Examples, this nucleic acid was identified only after
screening a multitude of nucleic acids for those having similar or greater
immunostimulatory activity than previously identified immunostimulatory nucleic acids.
More specifically, the nucleic acids were compared to a nucleic acid having a nucleotide
sequence of TCG TCG TTT TGT CGT TTT GTC GTT (SEQ ID NO:2) that was previously
shown to be immunostimulatory. The nucleic acid comprising SEQ ID NO: 19 was identified
only after screening approximately 165 nucleic acids for those having immunostimulatory
capacity similar to or greater than that of nucleic acids comprising SEQ ID NO:2. The
difference in activity is surprising because there is only a minimal difference between SEQ ID
5 NO:19 and SEQ ID NO:2 (i.e., SEQ ID NO:19 includes three additional internal nucleotides
(i.e., TCG), and lacks six 3' nucleotides as compared to SEQ ID NO:2). It was unexpected
that such a change in sequence would result in an increase in immunostimulation.
In yet other aspects of the invention, nucleic acids having the following nucleotide
sequences are provided: 5' TCG TCG TTT TTC GGT CGT TT 3' (SEQ ID NO:24); 5'
10 TCG TCG TTT TTC GGT CGT T 3' (SEQ ID NO:25); 5' TCG TCG TTT TTC GGT
CGT 3' (SEQ ID NO:26); 5' TCG TCG TTT TTC GGT CG 3' (SEQ ID NO:27); 5'
TCG TCG TTT TTC GGT C 3' (SEQ ID NO:28); 5' TCG TCG TTT TTC GGT 3' (SEQ
ID NO:29); 5' TCG TCG TTT TTC GG 3' (SEQ ID NO:30); 5' TCG TCG TTT TTC G
3' (SEQ ID NO:44); 5' TCG TCG TTT TTC 3' (SEQ ID NO:31); 5' TCG TCG TTT
75 TTC GGT CGT TTT 3' (SEQ ID NO:32), 5' CG TCG TTT TTC GGT CGT TTT 3'
(SEQ ID NO:33), 5' G TCG TTT TTC GGT CGT TTT 3' (SEQ ID NO:34), 5' TCG TTT
TTC GGT CGT TTT 3' (SEQ ID NO:35), 5' CG TTT TTC GGT CGT TTT 3' (SEQ ID
NO.-36), 5' G TTT TTC GGT CGT TTT 3' (SEQ ID NO:37), 5' TTT TTC GGT CGT
TTT 3' (SEQ ID NO:38), 5'TT TTC GGT CGT TTT 3' (SEQ ID NO:39), 5'T TTC
20 GGT CGT TTT 3' (SEQ ID NO: 40), 5'TTC GGT CGT TTT 3' (SEQ ID NO:41), 5'TC
GGT CGT TTT 3' (SEQ ID NO:42), 5' C GGT CGT TTT 3' (SEQ ID NO:43), 5' GGT
CGT TTT 3' (SEQ ID NO:21).
These immunostimulatory nucleic acids are capable of activating the innate immune
system, and augmenting both humoral and cellular antigen specific responses when co-
25 administered with an antigen, such as Hepatitis B surface antigen. The Examples provided
herein demonstrate that these nucleic acids can stimulate human immune cells in vitro, and
murine cells in vitro and in vivo. When compared to a sequence known to be a potent
adjuvant, the nucleic acid of SEQ ID NO:19 is at least 10-15% as a vaccine adjuvant.
The nucleic acids of the invention can further contain other immunostimulatory
30 motifs such as poly T motifs, poly G motifs, TG motifs, poly A motifs, poly C motifs, and
the like, provided that the core sequences of SEQ ID NO:21 and SEQ ID NO:23 are
present. These immunostimulatory motifs are described in greater detail below or in U.S.
Non-Provisional Patent Application Serial No. 09/669,187, filed September 25, 2000, and
published PCT Patent Application PCT/USQO/26383, having publication number
WO01/22972.
ODN 10104 Family:
This family of nucleic acids comprises the nucleotide sequence having the formula of
5'X1X2X3X4X5X6 TTTCGTCGTTTTGTCGTT 3' (SEQIDNO:46)
wherein X1, X2, X3, X4, X5, and X6 are independently selected residues that may be selected
from the group of nucleotides consisting of adenosine, guanosine, thymidine, and cytosine. In
some embodiments, there may be no flanking residues. Such a nucleic acid would comprise a
nucleotide sequence of 5' TTT CGT CGT TTT GTC GTT 3' (SEQ ID NO:47).
In other embodiments, the nucleic acid may lack X1; X1 and X2; X1, X2 and X3; X1,
X2, X3 and X4; or X1, X2, X3, X4 and X5. Accordingly, the invention intends to embrace
nucleic acids have the following nucleotide sequences: 5' X2X3X4X5X6 TTT CGT CGT TTT
GTC GTT 3' (SEQ ID NO:48); 5' X3X4X5X6 TTT CGT CGT TTT GTC GTT 3' (SEQ ID
NO:49); 5' X4X5X6 TTT CGT CGT TTT GTC GTT 3' (SEQ ID NO:50); 5' X5X6 TTT
CGT CGT TTT GTC GTT 3' (SEQ ID NO:51); 5' X6 TTT CGT CGT TTT GTC GTT 3'
(SEQ ID NO:52).
In one embodiment, X1 is a thymidine. In another embodiment, X2 is cytosine. In
another embodiment, X3 is a guanosine. In another embodiment, X4 is a thymidine. In yet
another embodiment, X5 is a cytosine. In still another embodiment, X6 is a guanosine. The
invention embraces further combinations of flanking residues as follows (where blank cells
are N residues, i.e., can be any of the naturally occurring or non-naturally occurring
nucleotides recited herein or known in the art):

Table 1 represents only some of the possible nucleic acids that are members of the first
family of nucleic acids. Those of ordinary skill in the art will be able to determine the
sequence of the remaining nucleic acids belonging to this family.
The nucleic acids of this family are generally at least 18 nucleotides in length. In
some embodiments, the nucleic acids are at least 19, at least 20, at least 21, at least 22, at least
23, and at least 24 nucleotides in length. In a preferred embodiment, the nucleic acids are 24
nucleotides in length. In still further embodiments, the nucleic acids are more than 24
nucleotides in length. Examples include nucleic acids that are at least 50, at least 75, at least
100, at least 200, at least 500, at least 1000 nucleotides in length, or longer. Preferably, the
nucleic acids are 18-100, and more preferably 24-100 nucleotides in length.
All the nucleic acids of this first family contain at least three CpG motifs. These
nucleic acids may contain four or five or more CpG motifs. The CpG motifs may be
contiguous to each other, or alternatively, they may be spaced apart from each other at
constant or random distances.
The nucleic acids of this family also contain an overrepresentation of thymidine
nucleotides. These nucleic acids may contain greater than 60%, less than 60%, or less than
55% thymidines.
The invention is further premised, in part, on the unexpected discovery of another
family of nucleic acids that is more immunostimulatory than previously reported CpG nucleic
acids. This family of nucleic acids comprises the nucleotide sequence having the formula of
5' TCG TCG TTT CGT CGT TTT GT X1X2X3X4 3' (SEQ ID NO:95)
wherein X1, X2, X3, and X4 are independently selected residues that may be selected from the
group of nucleotides consisting of adenosine, guanosine, thymidine, and cytosine. In some
embodiments, there may be no flanking residues. As an example, the nucleic acid may
comprise a nucleotide sequence of 5' TCG TCG TTT CGT CGT TTT GT 3' (SEQ ID
NO:96).
In other embodiments, the nucleic acid may lack X4; X4 and X3; X4 and X3; or X4, X3,
and X2. Accordingly, the invention intends to embrace nucleic acids have the following
nucleotide sequences: 5' TCG TCG TTT CGT CGT TTT GT X1X2X3 3' (SEQ ID NO:97); 5'
TCG TCG TTT CGT CGT TTT GT X1K2 3' (SEQ ID NO:98); and 5' TCG TCG TTT CGT
CGT TTT GT X1 3' (SEQ ID NO:99).
In one embodiment, X1 is a cytosine. In another embodiment, X2 is guanosine. In
another embodiment, X3 is a thymidine. In another embodiment, X4 is a thymidine. The
invention embraces further combinations of flanking residues as follows (where blank cells
are N residues, i.e., can be any of the naturally occurring or non-naturally occurring
nucleotides recited herein or known in the art):
Table 2 represents only some of the possible nucleic acids that are members of the
second family of nucleic acids. Those of ordinary skill in the art will be able to determine the
sequence of the remaining nucleic acids belonging to this family.
The nucleic acids of this latter family are generally at least 20 nucleotides in length.
In some embodiments, the nucleic acids are at least 21, at least 22, at least 23, and at least 24
nucleotides in length. In a preferred embodiment, the nucleic acids are 24 nucleotides in
length. In still further embodiments, the nucleic acids are more than 24 nucleotides in length.
Examples include nucleic acids that are at least 50, at least 75, at least 100, at least 200, at
least 500, at least 1000 nucleotides in length, or longer. Preferably, the nucleic acids are 20-
100, and more preferably 24-100 nucleotides in length.
All the nucleic acids of this second family contain at least four CpG motifs. These
nucleic acids may contain five or more CpG motifs, depending upon the embodiment. The
CpG motifs may be contiguous to each other, or alternatively, they may be spaced apart from
each other at constant or random distances.
The nucleic acids of this family also contain an overrepresentation of thymidine
nucleotides. These nucleic acids may contain greater than 60%, less than 60%, or less than
55% thymidines.
In another aspect, the invention provides a nucleic acid comprising the nucleotide
sequence of TCG TCG TTT CGT CGT TTT GTC GTT (SEQ ID NO:45) (ODN 10104). As
described in greater detail in the Examples, this nucleic acid was identified only after
screening a multitude of nucleic acids for those having similar or greater immunostimulatory
activity than previously identified immunostimulatory nucleic acids. More specifically, the
nucleic acids were compared to a nucleic acid having a nucleotide sequence of TCG TCG
TTT TGT CGT TTT GTC GTT (SEQ ID NO:2) that was previously shown to be
immunostimulatory. The nucleic acid comprising SEQ ID NO:45 was identified only after
screening approximately 165 nucleic acids for those having immunostimulatory capacity
greater than that of nucleic acids comprising SEQ ID NO:2. The difference in activity is
surprising because there is only a minimal difference between SEQ ID NO:45 and SEQ ID
NO:2 (i.e., substitution of a thymidine (SEQ ID NO:2) with a cytosine (SEQ ID NO:45). It
5 was unexpected that such a minimal change in sequence would result in a statistically
significant increase in immunostimulation.
In yet other aspects of the invention, nucleic acids having the following nucleotide
sequences are provided: 5' CG TCG TTT CGT CGT TTT GTC GTT 3' (SEQ ID NO:110);
5' G TCG TTT CGT CGT TTT GTC GTT 3' (SEQ ID NO: 111); 5' TCG ITT CGT CGT
10 TTTGTCGTT3' (SEQ ID NO: 112); 5'CG TTT CGT CGT TTT GTC GTT 3' (SEQ ID
NO:113); 5' G TTT CGT CGT TTT GTC GTT 3' (SEQ ID NO:114); 5' TTT CGT CGT
TTT GTC GTT 3' (SEQ ID NO:47); 5' TCG TCG TTT CGT CGT TTT GTC GT 3' (SEQ
ID NO:115); 5' TCG TCG TTT CGT CGT TTT GTC G 3' (SEQ ID NO:116); 5' TCG TCG
TTT CGT CGT TTT GTC 3' (SEQ ID NO:117); 5' TCG TCG TTT CGT CGT TTT GT 3'
15 (SEQIDNO:96).
The nucleic acids of the invention can further contain other immunostimulatory motifs
such as poly T motifs, poly G motifs, TG motifs, poly A motifs, poly C motifs, and the like,
provided that the core sequences of SEQ ID NO:47 and SEQ ID NO:96 are present. These
immunostimulatory motifs are described in greater detail below or in U.S. Non-Provisional
20 Patent Application Serial No. 09/669,187, filed September 25,2000, and published PCT
Patent Application PCT/US00/26383, having publication number WO01/22972.
ODN 10105 Family:
This family of nucleic acids comprises the nucleotide sequence having the formula of
25 5'X,X2X3 X4X5X6 X7X8X9 X10XnX12 X13X14X15 TTTTTTCGA 3' (SEQ ID NO:119)
wherein Xu X2, X3, X4) X5, X6, X7, X8, X9, X10, Xu, X121X13 X,4 and X15 are
independently selected residues that may be selected from the group of nucleotides
consisting of adenosine, guanosine, thymidine, and cytosine. In some embodiments, there
may be no flanking residues. Such a nucleic acid would comprise a nucleotide sequence of
30 5'TTTTTTCGA3'(SEQIDNO:120).
In other embodiments, the nucleic acid may lack X1; X1 and X2; X1, X2 and X3; X1,
X1, X3 and X4; or X1, X2, X3, X4and X5, X1 through X6, X1, through X7, X1, through X8, X1,
through X9, X1 through X10, X1 through X11, X1 through X12, X, through X13, X1 through
X14, and X1 through X15.
In various embodiments, X1 is a thymidine, and/or X2 is cytosine, and/or X3 is a
guanosine, and/or X4 is a thymidine, and/or X5 is a cytosine, and/or X5 is a guanosine,
5 and/or X7 is a thymidine, and/or X8 is a thymidine, and/or X9 is a thymidine, and/or X10 is a
thymidine, and/or X11 is a guanosine, and/or X12 is a thymidine, and/or X13 is a cytosine,
and/or XI4 is a guanosine, and/or X15 is a thymidine. Those of ordinary skill in the art will
be able to determine the sequence of the remaining nucleic acids belonging to this family.
The nucleic acids of this family are generally at least 9 nucleotides in length. In
10 some embodiments, the nucleic acids are at least 10, at least 12, at least 15, at least 18, at
least 20, at least 22, and at least 24 nucleotides in length. In a preferred embodiment, the
nucleic acids are 24 nucleotides in length. In still further embodiments, the nucleic acids
are more than 24 nucleotides in length. Examples include nucleic acids that are at least 50,
at least 75, at least 100, at least 200, at least 500, at least 1000 nucleotides in length, or
15 longer. Preferably, the nucleic acids are 9-100, and more preferably 24-100 nucleotides in
length.
All the nucleic acids of this first family contain at least one CpG motif. These
nucleic acids may contain two, three, four or more CpG motifs. The CpG motifs may be
contiguous to each other, or alternatively, they may be spaced apart from each other at
20 constant or random distances.
The nucleic acids of this family also contain an overrepresentation of thymidine
nucleotides. These nucleic acids may contain at least 60%, at least 55%, or at least 50%
thymidines.
The invention is further premised, in part, on the unexpected discovery of another
15 family of nucleic acids that is as unmunostimulatory as previously reported CpG nucleic
acids. This family of nucleic acids comprises the nucleotide sequence having the formula of
5'TCG TCG TTT TGT CGT TTT TX,X2 X3X4X5 3' (SEQ ED NO.121)
wherein X1 through X9 are independently selected residues that may be selected from the
group of nucleotides consisting of adenosine, guanosine, thymidine, and cytosine. In some
'0 embodiments, there may be no flanking residues. As an example, the nucleic acid may
comprise a nucleotide sequence of 5' TCG TCG TTT TGT CGT TTT T 3' (SEQ ID
NO: 122).
In other embodiments, the nucleic acid may lack X5; X5 and X4; X5, X4 aad X3; X3
through X2; and X5 through X1.
5 In various embodiments, X1 is a thymidine, and/or X2is thymidine, and/or X3 is a
cytosine, and/or X4 is a guanosine, and/or X5 is an adenine. Those of ordinary skill in the
art will be able to determine the sequence of the remaining nucleic acids belonging to this
family.
The nucleic acids of this family are generally at least 19 nucleotides in length. In
10 some embodiments, the nucleic acids are at least 20, at least 22, and at least 24 nucleotides
in length. In a preferred embodiment, the nucleic acids are 24 nucleotides in length. In still
further embodiments, the nucleic acids are more than 24 nucleotides in length. Examples
include nucleic acids that are at least 50, at least 75, at least 100, at least 200, at least 500,
at least 1000 nucleotides in length, or longer. Preferably, the nucleic acids are 19-100, and
15 more preferably 24-100 nucleotides in length.
All the nucleic acids of this second family contain at least three CpG motifs. These
nucleic acids may contain four or more CpG motifs, depending upon the embodiment. The
CpG motifs may be contiguous to each other, or alternatively, they may be spaced apart
from each other at constant or random distances.
20 The nucleic acids of this family also contain an overrepresentation of thymidine
nucleotides. These nucleic acids may contain at least 60%, at least 55%, or at least 50%
thymidines.
In another aspect, the invention provides a nucleic acid comprising the nucleotide
sequence of TCG TCG TTT TGT CGT TTT TTT CGA (SEQ ID NO: 118) (ODN 10105).
25 As described in greater detail in the Examples, this nucleic acid was identified only after
screening a multitude of nucleic acids for those having similar or greater
immunostimulatory activity than previously identified immunostimulatory nucleic acids.
More specifically, the nucleic acids were compared to a nucleic acid having a nucleotide
sequence of TCG TCG TTT TGT CGT TTT GTC GTT (SEQ ID NO:2) that was previously
30 shown to be immunostimulatory. The nucleic acid comprising SEQ ID NO: 118 was
identified only after screening approximately 165 nucleic acids for those having
immunostimulatory capacity similar to or greater than that of nucleic acids comprising SEQ
ID NO:2. The difference in activity is surprising because there is 79% identity between SEQ
ID NO:118 and SEQ ID NO:2 (i.e., five of the last 3' nucleotides differ between SEQ ID
NO: 118 and SEQ ID NO.2). It was unexpected that such a change in sequence would result
5 in an increase in immunostimulation.
In yet other aspects of the invention, nucleic acids having the following nucleotide
sequences are provided: 5' TCG TCG TTT TGT CGT TTT TTT CG 3' (SEQ ID
NO:123); 5' TCG TCG TTT TGT CGT TTT TTT C 3' (SEQ ID NO:124); 5' TCG TCG
TTT TGT CGT TTT TTT 3' (SEQ ID NO:125); 5' TCG TCG TTT TGT CGT TTT TT 3'
10 (SEQ ID NO:126); 5' CG TCG TTT TGT CGT TTT TTT CGA 3' (SEQ ID NO:127); 5'
G TCG TTT TGT CGT TTT TTT CGA 3' (SEQ ID NO:128); 5' TCG TTT TGT CGT
TTT TTT CGA 3' (SEQ ID NO: 129); 5'CG TTT TGT CGT TTT TTT CGA 3' (SEQ ID
NO: 130); 5' G TTT TGT CGT TTT TTT CGA 3' (SEQ ID NO: 131); 5' TTT TGT CGT
TTT TTT CGA 3' (SEQ ID NO: 132); 5" TT TGT CGT TTT TTT CGA 3' (SEQ ID
15 NO:133); 5' T TGT CGT TTT TTT CGA 3' (SEQ ID NO:134); 5' TGT CGT TTT TTT
CGA 3' (SEQ ID NO:135); 5' GT CGT TTT TTT CGA 3' (SEQ ID NO:136); 5' T CGT
TTT TTT CGA 3' (SEQ ID NO:137); 5' CGT TTT TTT CGA 3' (SEQ ID NO:138); 5'
GT TTT TTT CGA 3' (SEQ ID NO:139); and 5'T TTT TTT CGA 3' (SEQ ID NO: 140).
These immunostimulatory nucleic acids are capable of activating the innate immune
20 system, and augmenting both humoral and cellular antigen specific responses when co-
administered with an antigen, such as Hepatitis B surface antigen. The Examples provided
herein demonstrate that these nucleic acids can stimulate human immune cells in vitro, and
murine cells in vitro and in vivo. When compared to a sequence known to be a potent
adjuvant, the nucleic acid of SEQ ID NO:118 is found to work as well or better as a vaccine
25 adjuvant.
The nucleic acids of the invention can further contain other immunostimulatory
motifs such as poly T motifs, poly G motifs, TG motifs, poly A motifs, poly C motifs, and
the like, provided that the core sequences of SEQ ID NO: 120 and SEQ ID NO: 122 are
present. These immunostimulatory motifs are described in greater detail below or in U.S.
30 Non-Provisional Patent Application Serial No. 09/669,187, filed September 25, 2000, and
published PCT Patent Application PCT/US00/26383, having publication number
WO01/22972.
ODN 10106 Family:
5 This nucleic acid comprises the nucleotide sequence having the formula of
TCG TCG TTT TTC GTG CGT TTT T (SEQ ID NO: 141) (ODN 10106).
The sequence may be flanked by a number of nucleotide residues independently
selected residues that may be selected from the group of nucleotides consisting of adenosine,
guanosine, thymidine, and cytosine.
10 The nucleic acids of this family are at least 22 nucleotides in length. In a preferred
embodiment, the nucleic acids are 22 nucleotides in length. In still further embodiments,
the nucleic acids are more than 22 nucleotides in length. Examples include nucleic acids
that are at least 50, at least 75, at least 100, at least 200, at least 500, at least 1000
nucleotides in length, or longer. Preferably, the nucleic acids are 12-100.
15 All the nucleic acids of this first family contain at least four CpG motifs. These
nucleic acids may contain five or more CpG motifs. The CpG motifs may be contiguous to
each other, or alternatively, they may be spaced apart from each other at constant or
random distances.
The nucleic acids of this family also contain an overrepresentation of thymidine
20 nucleotides. These nucleic acids may contain greater than 60%, less than 60%, or less than
55% thymidines.
In another aspect, the invention provides a nucleic acid consisting of the nucleotide
sequence of TCG TCG TTT TTC GTG CGT TTT T (SEQ ID NO: 141). As described in
greater detail in the Examples, this nucleic acid was identified only after screening a
15 multitude of nucleic acids for those having similar or greater immunostimulatory activity
than previously identified immunostimulatory nucleic acids. More specifically, the nucleic
acids were compared to a nucleic acid having a nucleotide sequence of TCG TCG TTT TGT
CGT TTT GTC GTT (SEQ ID NO:2) that was previously shown to be immunostimulatory.
The nucleic acid comprising SEQ ID NO: 141 was identified only after screening
o approximately 165 nucleic acids for those having immunostimulatory capacity greater than
that of nucleic acids comprising SEQ ID NO:2. The difference in activity is surprising
because there is only a minimal difference between SEQ ID NO:141 and SEQ ID NO:2. It
was unexpected that such a minimal change in sequence would result in a statistically
significant increase in immunostimulation.
The nucleic acids of the invention can further contain other immunostrmulatory
5 motifs such as poly T motifs, poly G motifs, TG motifs, poly A motifs, poly C motifs, and
the like, provided that the core sequence of SEQ ID NO: 141 is present. These
immunostimulatory motifs are described in greater detail below or in U.S. Non-Provisional
Patent Application Serial No. 09/669,187, filed September 25, 2000, and published PCT
Patent Application PCT/US00/26383, having publication number WO01/22972.
10 It is to be understood that any embodiments recited herein apply equally to the nucleic
acids provided herein. Thus, if an embodiment refers to, for example, SEQ ID NO:1, it is to
be understood that it applies equally to SEQ ID NO:19, SEQ ID NO:45, SEQ ID NO:118 and
SEQE)NO:141.
The CpG motifs of the nucleic acids described herein are preferably unmethylated.
15 An unmetibylated CpG motif is an unmethylated cytosine-guanine dinucleotide sequence (i.e.
an unmethylated 5' cytosine followed by 3' guanosine and linked by a phosphate bond). All
the nucleic acid described herein are immunostimulatory. In some embodiments of the
invention, the CpG motifs are methylated. A methylated CpG motif is a methylated cytosine-
guanine dinucleotide sequence (i.e., a methylated 5' cytosine followed by a 3' guanosine and
20 linked by a phosphate bond).
A CpG nucleic acid is a nucleic acid that comprises the formula
5' X1 X2CGX3 X4 3'
wherein C is unmethylated, wherein X1X2 and X3X4 are nucleotides. In a related
embodiment, the 5' X1 X2CGX3 X4 3' sequence is a non-palindromic sequence. In certain
25 embodiments, X1X2 are nucleotides selected from the group consisting of GpT, GpG, GpA,
ApA, ApT, ApG, CpT, CpA, CpG, TpA, TpT, and TpG; andX3X4 are nucleotides selected
from the group consisting of TpT, CpT, ApT, TpG, ApG, CpG, TpC, ApC, CpC, TpA, ApA,
and CpA. In more particular embodiments, X1X2 are nucleotides selected from the group
consisting of GpA and GpT; and X3X4 are TpT. In yet other embodiments, X1X2 are both
30 purines and X3X4 are both pyrimidines. In another embodiment, X2 is a T and X3 is a
pyrimidine. Examples of CpG nucleic acids are described in U.S. Non-Provisional Patent
Application Serial No. 09/669,187, filed September 25,2000, and in published PCT Patent
Application PCT/USOO/26383, having publication number WO01/22972.
A T-rich nucleic acid is a nucleic acid which includes at least one poly T sequence
and/or which has a nucleotide composition of greater than 25% T nucleotide residues. A
5 nucleic acid having a poly-T sequence includes at least four Ts in a row, such as 5'TTTT3Preferably a T-rich nucleic acid includes more than one poly T sequence. In preferred
embodiments the T-rich nucleic acid may have 2, 3,4, etc poly T sequences. Other T-rich
nucleic acids according to the invention have a nucleotide composition of greater than 25% T
nucleotide residues, but do not necessarily include a poly T sequence. In these T-rich nucleic
10 acids the T nucleotide resides may be separated from one another by other types of nucleotide
residues, i.e., G, C, and A. In some embodiments the T-rich nucleic acids have a nucleotide
composition of greater than 35%, 40%, 50%, 60%, 70%, 80%, 90%, and 99%, T nucleotide
residues and every integer % in between. Preferably the T-rich nucleic acids have at least one
poly T sequence and a nucleotide composition of greater than 25% T nucleotide residues.
15 Poly G nucleic acids preferably are nucleic acids having the following formulas:
wherein X1, X2, X3, and X4 are nucleotides. In preferred embodiments at least one of X3 and X4
are a G. In other embodiments both of X3 and X4 area G. In yet other embodiments the
preferred formula is 5' GGGNGGG3', or 5' GGGNGGGNGGG3' wherein N represents
20 between 0 and 20 nucleotides.
A C-rich nucleic acid is a nucleic acid molecule having at least one or preferably at
least two poly-C regions or which is composed of at least 50% C nucleotides. A poly-C
region is at least four C residues in a row. Thus a poly-C region is encompassed by the
formula 5'CCCC 3'. In some embodiments it is preferred that the poly-C region have the
25 formula 5'CCCCCC 3'. Other C-rich nucleic acids according to the invention have a
nucleotide composition of greater than 50% C nucleotide residues, but do not necessarily
include a poly C sequence. In these C-rich nucleic acids the C nucleotide residues may be
separated from one another by other types of nucleotide residues, i.e., G, T, and A. In some
embodiments the C-rich nucleic acids have a nucleotide composition of greater than 60%,
30 70%, 80%, 90%, and 99%, C nucleotide residues and every integer % in between. Preferably
the C-rich nucleic acids have at least one poly C sequence and a nucleotide composition of
greater than 50% C nucleotide residues, and in some embodiments are also T-rich.
The immunostimulatory nucleic acids can be double-stranded or single-stranded.
Generally, double-stranded molecules are more stable in vivo, while single-stranded
molecules have increased immune activity. Thus in some aspects of the invention it is
preferred that the nucleic acid be single stranded and in other aspects it is preferred that the
5 nucleic acid be double stranded.
The terms "nucleic acid" and "oligonucleotide" are used interchangeably herein to
mean multiple nucleotides (i.e. molecules comprising a sugar (e.g. ribose or deoxyribose)
linked to a phosphate group and to an exchangeable organic base, which is either a
substituted pyrimidine (e.g. cytosine (C), thymidine (T) or uracil (U)) or a substituted
10 purine (e.g. adenine (A) or guanine (G)). As used herein, the terms refer to
oligoribonucleotides as well as oligodeoxyribonucleotides. The terms shall also include
polynucleosides (i.e. a polynucleotide minus the phosphate) and any other organic base
containing polymer. Nucleic acid molecules can be obtained from existing nucleic acid
sources (e.g., genomic or cDNA), but are preferably synthetic (e.g. produced by nucleic
15 acid synthesis).
The immunostimulatory oligonucleotides of the instant invention can encompass
various chemical modifications and substitutions, in comparison to natural RNA and DNA,
involving a phosphodiester internucleoside bridge, a p-D-ribose unit and/or a natural
nucleoside base (adenine, guanine, cytosine, thymine, uracil). Examples of chemical
20 modifications are known to the skilled person and are described, for example, in Uhlmann
E et al. (1990) Chem Rev 90:543; "Protocols for Oligonucleotides and Analogs" Synthesis
and Properties & Synthesis and Analytical Techniques, S. Agrawal, Ed, Humana Press,
Totowa, USA 1993; Crooke ST et al. (1996) Amu Rev Pharmacol Toxicol 36:107-129; and
Hunziker J et al. (1995) Mod Synth Methods 7:331-417. An oligonucleotide according to
25 the invention may have one or more modifications, wherein each modification is located at a
particular phosphodiester internucleoside bridge and/or at a particular B-D-ribose unit
and/or at a particular natural nucleoside base position in comparison to an oligonucleotide of
the same sequence which is composed of natural DNA or RNA.
For example, the oligonucleotides may comprise one or more modifications and
wherein each modification is independently selected from:
a) the replacement of a phosphodiester internucleoside bridge located at the 3' and/or
the 5' end of a nucleoside by a modified internucleoside bridge,
b) the replacement of phosphodiester bridge located at the 3' and/or the 5' end of a
nucleoside by a dephospho bridge,
5 c) the replacement of a sugar phosphate unit from the sugar phosphate backbone by
another unit,
d) the replacement of a p-D-ribose unit by a modified sugar unit, and
e) the replacement of a natural nucleoside base by a modified nucleoside base.
More detailed examples for the chemical modification of an oligonucleotide are as
io follows.
Nucleic acids also include substituted purines and pyrimidines such as C-5 propyne
pyrimidine and 7-deaza-7-subsutituted purine modified bases. Wagner RW et al. (1996) Nat
Biotechnol 14:840-4. Purines and pyrimidines include but are not limited to adenine,
cytosine, guanine, thymidine, 5-methylcytosine, 2-aminopurine, 2-amino-6-chloropurine,
15 2,6-diaminopurine, hypoxanthine, and other naturally and non-naturally occurring
nucleobases, substituted and unsubstituted aromatic moieties. Other such modifications are
well known to those of skill in the art. In all of the foregoing embodiments, an X residue
can also be a non-naturally occurring nucleotide, or a nucleotide analog, such as those
described herein.
20 A modified base is any base which is chemically distinct from the naturally
occurring bases typically found in DNA and RNA such as T, C, G, A, and U, but which
share basic chemical structures with these naturally occurring bases. The modified
nucleoside base may be, for example, selected from hypoxanthine, uracil, dihydrouracil,
pseudouracil, 2-thiouracil, 4-thiouracil, 5-aminouracil, 5-(C1-C6)-alkyluracil, 5-(C2-C6)-
25 alkenyluracil, 5-(C2-C6)-alkynyluracil, 5-(hydroxymethyl)uracil, 5-chlorouracil,
5-fiuorouracil, 5-bromouracil, 5-hydroxycytosine, 5-(C2-C6)-alkylcytosine, 5-(C2-C6)-
alkenylcytosine, 5-(C2-C6)-alkynylcytosine, 5-chlorocytosine, 5-fluorocytosine,
5-bromocytosine, N2-dimethylguanine, 2,4-diamino-purine, 8-azapurine, a substituted
7-deazapurine, preferably 7-deaza-7-substituted and/or 7-deaza-8-substituted purine, 5-
30 hydroxymethylcytosine, N4-alkylcytosme, e.g., N4-ethylcytosine, 5-hydroxydeoxycytidine,
5-hydroxymethyldeoxycytidine, N4-alkyldeoxycytidine, e.g., N4-ethyldeoxycytidine, 6-
thiodeoxyguanosine, and deoxyribonucleosides of nitropyrrole, C5-propynylpyrimidine, and
diaminopurine e.g., 2,6-diaminopurine, inosine, 5-methylcytosine, 2-aminopurine,
2-amino-6-chloropurine, hypoxanthine or other modifications of a natural nucleoside bases.
This list is meant to be exemplary and is not to be interpreted to be limiting.
5 In particular formulas described herein a set of modified bases is defined. For instance
the letter Y is used to refer to a nucleotide containing a cytosine or a modified cytosine. A
modified cytosine as used herein is a naturally occurring or non-naturally occurring
pyrimidine base analog of cytosine which can replace this base without impairing the
immunostimulatory activity of the oligonucleotide. Modified cytosines include but are not
10 limited to 5-substituted cytosines (e.g. 5-methyl-cytosine, 5-fluoro-cytosine, 5-chloro-
cytosine, 5-bromo-cytosine, 5-iodo-cytosine, 5-hydroxy-cytosine, 5-hydroxymethyl-
cytosine, 5-difiuoromethyl-cytosine, and unsubstituted or substituted 5-alkynyl-cytosine), 6-
substituted cytosines, N4-substituted cytosines (e.g. N4-ethyl-cytosine), 5-aza-cytosine, 2-
mercapto-cytosine, isocytosine, pseudo-isocytosine, cytosine analogs with condensed ring
15 systems (e.g. N,N'-propylene cytosine or phenoxazine), and uracil and its derivatives (e.g.
5-fluoro-uracil, 5-bromo-uracil, 5-bromovinyl-uracil, 4-thio-uracil, 5-hydroxy-uracil, 5-
propynyl-uracil). Some of the preferred cytosines include 5-methyl-cytosine, 5-fluoro-
cytosine, 5-hydroxy-cytosine, 5-hydroxymethyl-cytosine, and N4-ethyl-cytosine. In another
embodiment of the invention, the cytosine base is substituted by a universal base (e.g. 3-
20 nitropyrrole, P-base), an aromatic ring system (e.g. fluorobenzene or difiuorobenzene) or a
hydrogen atom (dSpacer). The letter Z is used to refer to guanine or a modified guanine base.
A modified guanine as used herein is a naturally occurring or non-naturally occurring purine
base analog of guanine which can replace this base without impairing the
immunostimulatory activity of the oligonucleotide. Modified guanines include but are not
25 limited to 7-deazaguanine, 7-deaza-7-substituted guanine (such as
7-deaza-7-(C2-C6)alkynylguanine), 7-deaza-8-substituted guanine, hypoxanthine, N2-
substituted guanines (e.g. N2-methyl-guanine), 5-amino-3-methyl-3H,6H-thiazolo[4,5-
d]pyrimidine-2,7-dione, 2,6-diaminopurine, 2-aminopurine, purine, indole, adenine,
substituted adenines (e.g. N6-methyl-adenine, 8-oxo-adenine) 8-substituted guanine (e.g.
30 8-hydroxyguanine and 8-bromoguanine), and 6-thioguanine. In another embodiment of the
invention, the guanine base is substituted by a universal base (e.g. 4-methyl-indole, 5-nitro-
indole, and K-base), an aromatic ring system (e.g. benzimidazole or dichloro-
benzimidazole, l-methyl-lH-[l,2,4]triazole-3-carboxylic acid amide) or a hydrogen atom
(dSpacer).
The oligonucleotides may include modified internucleotide linkages, such as those
5 described in a or b above. These modified linkages may be partially resistant to degradation
(e.g., are stabilized). A "stabilized nucleic acid molecule" shall mean a nucleic acid
molecule that is relatively resistant to in vivo degradation (e.g. via an exo- or endo-
nuclease). Stabilization can be a fimction of length or secondary structure. Nucleic acids
that are tens to hundreds of kilobases long are relatively resistant to in vivo degradation.
W For shorter nucleic acids, secondary structure can stabilize and increase their effect. For
example, if the 3' end of an nucleic acid has self-complementarity to an upstream region, so
that it can fold back and form a sort of stem loop structure, then the nucleic acid becomes
stabilized and therefore exhibits more activity.
Nucleic acid stabilization can also be accomplished via phosphate backbone
15 modifications. Oligonucleotides having phosphorothioate linkages, in some embodiments,
may provide maximal activity and protect the oligonucleotide from degradation by
intracellular exo- and endo-nucleases.
It has been demonstrated that modification of the nucleic acid backbone provides
enhanced activity of nucleic acids when administered in vivo. Constructs having
20 phosphorothioate linkages provide maximal activity and protect the nucleic acid from
degradation by intracellular exo- and endo-nucleases: Other modified nucleic acids include
phosphodiester modified nucleic acids, combinations of phosphodiester and
phosphorothioate nucleic acid, methylphosphonate, methylphosphorothioate,
phosphorodithioate, p-ethoxy, and combinations thereof. Each of these combinations and
25 their particular effects on immune cells is discussed in more detail with respect to CpG
nucleic acids in PCT Published Patent Applications PCT/US95/01570 (WO 96/02555) and
PCT/US97/19791 (WO 98/18810) and in U.S. Patents US 6,194,388 Bl issued February
27, 2001 and US 6,239,116 Bl issued May 29, 2001, the entire contents of which are
hereby incorporated by reference. It is believed that these modified nucleic acids may show
30 more stimulatory activity due to enhanced nuclease resistance, increased cellular uptake,
increased protein binding, and/or altered intracellular localization.
Other stabilized nucleic acids include: nonionic DNA analogs, such as alkyl- and
aryl-phosphates (in which the charged phosphonate oxygen is replaced by an alkyl or aryl
group), phosphodiester and alkylphosphotriesters, in which the charged oxygen moiety is
alkylated. Nucleic acids which contain diol, such as tetraethyleneglycol or
hexaethyleneglycol, at either or both termini have also been shown to be substantially
resistant to nuclease degradation.
The oligonucleotides may have one or two accessible 5' ends. It is possible to create
modified oligonucleotides having two such 5' ends, for instance, by attaching two
oligonucleotides through a 3'-3' linkage to generate an oligonucleotide having one or two
10 accessible 5' ends. The 3'3'-linkage may be a phosphodiester, phosphorothioate or any
other modified internucleoside bridge. Methods for accomplishing such linkages are known
in the art. For instance, such linkages have been described in Seliger, H. et al.,
Oligonucleotide analogs with terminal 3'-3'- and 5'-5'-internucleotidic linkages as antisense
inhibitors of viral gene expression, Nucleosides & Nucleotides (1991), 10(1-3), 469-77 and
15 Jiang, et al., Pseudo-cyclic oligonucleotides: in vitro and in vivo properties, Bioorganic &
Medicinal Chemistry (1999), 7(12), 2727-2735.
Additionally, 3'3'-linked ODNs where the linkage between the 3'-terminal
nucleosides is not a phosphodiester, phosphorothioate or other modified bridge, can be
prepared using an additional spacer, such as tri- or tetra-ethylenglycol phosphate moiety
20 (Durand, M. et al, Triple-helix formation by an oligonucleotide containing one (dA)12 and
two (dT)12 sequences bridged by two hexaethylene glycol chains, Biochemistry (1992),
31(38), 9197-204, US Patent No. 5658738, and US Patent No. 5668265). Alternatively,
the non-nucleotidic linker may be derived from ethanediol, propanediol, or from an abasic
deoxyribose (dSpacer) unit (Fontanel, Marie Laurence et al., Sterical recognition by T4
25 polynucleotide kinase of non-nucleosidic moieties 5'-attached to oligonucleotides; Nucleic
Acids Research (1994), 22(11), 2022-7) using standard phosphoramidite chemistry. The
non-nucleotidic linkers can be incorporated once or multiple times, or combined with, each
other allowing for any desirable distance between the 3'-ends of the two ODNs to be linked.
A phosphodiester internucleoside bridge located at the 3' and/or the 5' end of a
30 nucleoside can be replaced by a modified internucleoside bridge, wherein the modified
internucleoside bridge is for example selected from phosphorothioate, phosphorodithioate,
NR1R2phosphoramidate, boranophosphate, a-hydroxybenzyl phosphonate, phosphate-(C1-
C21)-O-alkyl ester, phosphate-[(C6-C12)aryl-(C1-C21)-O-alkyl]ester, (C1-C8)alkylphosphonate
and/or (C6-C12)arylphosphonate bridges, (C7-C12)-a-hydroxymethyl-aryl (e.g., disclosed in
WO 95/01363), wherein (C6-C12)aryl, (C6-C20)aryl and (C6-C14)aryl are optionally
substituted by halogen, alkyl, alkoxy, nitro, cyano, and where R1 and R2 are, independently
of each other, hydrogen, (C1-C18)-alkyl, (C6-C20-aryl, (C6-C14)-aryl-(C1-C8)-alkyl,
preferably hydrogen, (C1-C8)-alkyl, preferably (C1-C4)-alkyl and/or methoxyethyl, or Rl
and R2 form, together with the nitrogen atom carrying them, a 5-6-membered heterocyclic
ring which can additionally contain a further heteroatom from the group O, S and N.
10 The replacement of a phosphodiester bridge located at the 3' and/or the 5' end of a
nucleoside by a dephospho bridge (dephospho bridges are described, for example, in
Uhlmann E and Peyman A in "Methods in Molecular Biology", Vol. 20, "Protocols for
Oligonucleotides and Analogs", S. Agrawal, Ed., Humana Press, Totowa 1993, Chapter
16, pp. 355 ff), wherein a dephospho bridge is for example selected from the dephospho
15 bridges formacetal, 3'-thioformacetal, methylhydroxylamine, oxime, methylenedimethyl-
hydrazo, dimethylenesulfone and/or silyl groups.
The compositions of the invention may optionally be have chimeric backbones. As
used herein, a chimeric backbone is one that comprises more than one type of linkage. In
one embodiment, the chimeric backbone can be represented by the formula: 5' Y1N1ZN2Y2
20 3'. Y1 and Y2 are nucleic acid molecules having between 1 and 10 nucleotides. Y1 and Y2
each include at least one modified internucleotide linkage. Since at least 2 nucleotides of
the chimeric oligonucleotides include backbone modifications these nucleic acids are an
example of one type of "stabilized immunostimulatory nucleic acids."
With respect to the chimeric oligonucleotides, Y1 and Y2 are considered independent
25 of one another. This means that each of Y1 and Y2 may or may not have different
sequences and different backbone linkages from one anther in the same molecule. In some
embodiments Y1 and/or Y2 have between 3 and 8 nucleotides. N1 and N2 are nucleic acid
molecules having between 0 and 5 nucleotides as long as N1ZN2 has at least 6 nucleotides in
total. The nucleotides of N1ZN2 have a phosphodiester backbone and do not include nucleic
30 acids having a modified backbone. Z is an immunostimulatory nucleic acid motif,
preferably selected from those recited herein.
The center nucleotides (N1ZN2) of the formula Y1N1ZN2Y2 have phosphodiester
intemucleotide linkages and Y1 and Y2 have at least one, but may have more than one or
even may have all modified intemucleotide linkages. In preferred embodiments Y1, and/or
Y2 have at least two or between two and five modified intemucleotide linkages or Y1 has
5 two modified intemucleotide linkages and Y2 has five modified intemucleotide linkages or
Y1 has five modified intemucleotide linkages and Y2 has two modified mtemucleotide
linkages. The modified intemucleotide linkage, in some embodiments is a phosphorothioate
modified linkage, a phosphorodithioate modified linkage or a p-ethoxy modified linkage.
The nucleic acids also include nucleic acids having backbone sugars which are
10 covalently attached to low molecular weight organic groups other than a hydroxyl group at
the 2' position and other than a phosphate group at the 5' position. Thus, modified nucleic
acids may include a 2'-O-alkylated ribose group. In addition, modified nucleic acids may
include sugars such as arabinose or 2'-fluoroarabinose instead of ribose. Thus the nucleic
acids may be heterogeneous in backbone composition thereby containing any possible
75 combination of polymer units linked together such as peptide- nucleic acids (which have
amino acid backbone with nucleic acid bases). In some embodiments, the nucleic acids are
homogeneous in backbone composition. Other examples are described in more detail
below.
A sugar phosphate unit (i.e., a P-D-ribose and phosphodiester internucleoside bridge
20 together forming a sugar phosphate unit) from the sugar phosphate backbone (i.e., a sugar
phosphate backbone is composed of sugar phosphate units) can be replaced by another unit,
wherein the other unit is for example suitable to build up a "morpholino-derivative"
oligomer (as described, for example, in Stirchak EP et al. (1989) Nucleic Acids Res
17:6129-41), that is, e.g., the replacement by a morpholino-derivative unit; or to build up a
25 polyamide nucleic acid ("PNA"; as described for example, in Nielsen PE et al. (1994)
Bioconjug Chem 5:3-7), that is, e.g., the replacement by a PNA backbone unit, e.g., by 2-
aminoethylglycine. The oligonucleotide may have other carbohydrate backbone
modifications and replacements, such as peptide nucleic acids with phosphate groups
(PHONA), locked nucleic acids (LNA), and oligonucleotides having backbone sections with
30 aliyl linkers or amino linkers. The alkyl linker may be branched or unbranched, substituted
or unsubstituted, and chirally pure or a racemic mixture.
A p-ribose unit or a p-D-2'-deoxyribose unit can be replaced by a modified sugar
unit, wherein the modified sugar unit is for example selected from p-D-ribose, a-D-2'-
deoxyribose, L-2'-deoxyribose, 2'-F-2'-deoxyribose, 2'-F-arabinose, 2'-O-(C1-C6)alkyl-
ribose, preferably 2'-O-(C1-C6)alkyl-ribose is 2'-O-methylribose, 2'-O-(C2-C6)alkenyl-
J ribose, 2'-[O-(C1-C6)alkyl-O-(C1-C6)alkyl]-ribose, 2'-NH2-2'-deoxyribose, p-D-xylo-
furanose, a-arabinofuranose, 2,4-dideoxy-b-D-erythro-hexo-pyranose, and carbocyclic
(described, for example, in Froehler J (1992) Am Chew. Soc 114:8320) and/or open-chain
sugar analogs (described, for example, in Vandendriessche et al. (1993) Tetrahedron
49:7223) and/or bicyclosugar analogs (described, for example, in Tarkov M et al. (1993)
10 Helv Chim Acta 76:481).
In some embodiments the sugar is 2'-O-methylribose, particularly for one or both
nucleotides linked by a phosphodiester or phosphodiester-like internucleoside linkage.
For use in the instant invention, the oligonucleotides of the invention can be
synthesized de novo using any of a number of procedures well known in the art. For
15 example, the b-cyanoethyl phosphoramidite method (Beaucage, S.L., and Caruthers, M.H.,
Tet. Let. 22:1859, 1981); nucleoside H-phosphonate method (Garegg et al, Tet. Let.
27:4051-4054, 1986; Froehler et al, Nucl. Acid. Res. 14:5399-5407, 1986, ; Garegg etal,
Tet. Let. 27:4055-4058, 1986, Gaffney etal, Tet. Let. 29:2619-2622, 1988). These
chemistries can be performed by a variety of automated nucleic acid synthesizers available
20 in the market. These oligonucleotides are referred to as synthetic oligonucleotides.
Alternatively, T-rich and/or TG dinucleotides can be produced on a large scale in plasmids,
(see Sambrook, T., et al, "Molecular Cloning: A Laboratory Manual", Cold Spring
Harbor laboratory Press, New York, 1989) and separated into smaller pieces or
administered whole. Nucleic acids can be prepared from existing nucleic acid sequences
25 (e.g., genomic or cDNA) using known techniques, such as those employing restriction
enzymes, exonucleases or endonucleases.
Modified backbones such as phosphorothioates may be synthesized using automated
techniques employing either phosphoramidate or H-phosphonate chemistries. Aryl-and
alkyl-phosphonates can be made, e.g., as described in U.S. Patent No. 4,469,863; and
30 alkylphosphotriesters (in which the charged oxygen moiety is alkylated as described in U.S.
Patent No. 5,023,243 and European Patent No. 092,574) can be prepared by automated
solid phase synthesis using commercially available reagents. Methods for making other
DNA backbone modifications and substitutions have been described (e.g., Uhhnann, E. and
Peyman, A., Chem. Rev. 90:544, 1990; Goodchild, J., Bioconjugate Chem. 1:165, 1990).
Nucleic acids prepared in this manner are referred to as isolated nucleic acid. An
5 "isolated nucleic acid" generally refers to a nucleic acid which is separated from
components with which it is normally associated in nature. As an example, an isolated
nucleic acid may be one which is separated from a cell, from a nucleus, from mitochondria
or from chromatin.
In the case where the nucleic acid is administered in conjunction with an antigen that
10 is encoded in a nucleic acid vector (as described herein), it is preferred that the backbone of
the nucleic acid be a chimeric combination of phosphodiester and phosphorothioate (or other
phosphate modification). The cell may have a problem taking up a plasmid vector in the
presence of completely phosphorothioate nucleic acid. Thus when both a vector and a nucleic
acid are delivered to a subject, it is preferred that the nucleic acid have a chimeric backbone
15 or have a phosphorothioate backbone but that the plasmid be associated with a vehicle that
delivers it directly into the cell, thus avoiding the need for cellular uptake. Such vehicles are
known in the art and include, for example, liposomes and gene guns.
The invention further embraces the use of any of these foregoing nucleic acids in the
methods recited herein, as well as all previously described and previously known uses of
20 immunostimulatory nucleic acids.
It has been discovered according to the invention that the immunostimulatory nucleic
acids have surprisingly increased immune stimulatory effects. For example, it has been
demonstrated that the nucleic acids described herein are able to provide protection against
infection, probably by generally stimulating the immune system. The Examples illustrate the
25 ability of the nucleic acid having a nucleotide sequence of SEQ ID NO:1, SEQ ID NO:19,
SEQ ID NO:45, SEQ ID NO:118 or SEQ ID NO:141 to protect murine subjects challenged
with Herpes Simplex Virus 2 (HSV-2). The nucleic acid can administered prior to or at the
same time as viral challenge.
The demonstrated ability of these nucleic acids to induce immune stimulation is
30 evidence that the nucleic acids are effective therapeutic agents for vaccination, cancer
immunotherapy, asthma immunotherapy, general enhancement of immune function,
enhancement of hematopoietic recovery following radiation or chemotherapy, and other
immune modulatory applications in humans and other subjects.
The nucleic acids of the invention can be used as stand alone therapies. A stand alone
therapy is a therapy in which a prophylactically or therapeutically beneficial result can be
5 achieved from the administration of a single agent or composition. Accordingly, the nucleic
acids disclosed herein can be used alone in the prevention or treatment of infectious disease,
cancer, and asthma and allergy, because the nucleic acids are capable of inducing immune
responses that are beneficial to the therapeutic outcome of these diseases. Some of the
* methods described herein relate to the use of nucleic acids as a stand alone therapy, while
10 others related to the use of the nucleic acids in combination with other therapeutic agents.
When used in a vaccine, the nucleic acid is administered with an antigen. Preferably,
the antigen is specific for the disorder sought to be prevented or treated. For example, if the
disorder is an infectious disease, the antigen is preferably derived from the infectious
organism (e.g., bacterium, vims, parasite, fungus, etc.). If the disorder is a cancer, the antigen
75 is preferably a cancer antigen.
The immunostimulatory nucleic acids are useful in some aspects of the invention as a
prophylactic vaccine for the prevention of an infection (i.e., an infectious disease), a cancer,
an allergy, or asthma. Preferably, prophylactic vaccination is used in subjects that are not
diagnosed with one of these conditions, and more preferably the subjects are considered at
20 risk of developing one of these conditions. For example, the subject may be one that is at risk
of developing an infection with an infectious organism, or one that is at risk of developing a
cancer in which a specific cancer antigen has been identified, or one that is at risk of
developing an allergy for which an allergen is known, or one that is at risk of developing
asthma where the predisposition to asthma is known.
25 A subject at risk, as used herein, is a subject who has any risk of exposure to an
infection causing pathogen, a carcinogen, or an allergen. A subject at risk also includes
subjects that have a predisposition to developing such disorders. Some predispositions can be
genetic (and can thereby be identified either by genetic analysis or by family history). Some
predispositions are environmental (e.g., prior exposure to carcinogens, etc.) An example of a
30 subject at risk of developing an infection is a subject living in or expecting to travel to an area
where a particular type of infectious agent is or has been found, or it may be a subject who
through lifestyle or medical procedures is exposed to an organism either directly or indirectly
by contact with bodily fluids that may contain infectious organisms. Subjects at risk of
developing infection also include general populations to which a medical agency recommends
vaccination for a particular infectious organism.
If the antigen is an allergen and the subject develops allergic responses to that
5 particular antigen and the subject may be exposed to the antigen, i.e., during pollen season,
then that subject is at risk of exposure to the antigen. A subject at risk of developing an
allergy to asthma includes those subjects that have been identified as having an allergy or
asthma but that don't have the active disease during the immunostimulatory nucleic acid
treatment as well as subjects that are considered to be at risk of developing these diseases
10 because of genetic or environmental factors.
The immunostimulatory nucleic acids can also be given without the antigen or
allergen for shorter term protection against infection, allergy or cancer, and in this case
repeated doses will allow longer term protection.
A subject at risk of developing a cancer is one who is who has a high probability of
15 developing cancer (e.g., a probability that is greater than the probability within the general
public). These subjects include, for instance, subjects having a genetic abnormality, the
presence of which has been demonstrated to have a correlative relation to a likelihood of
developing a cancer that is greater than the likelihood of the general public, and subjects
exposed to cancer causing agents (i.e., carcinogens) such as tobacco, asbestos, or other
20 chemical toxins, or a subject who has previously been treated for cancer and is in apparent
remission. When a subject at risk of developing a cancer is treated with an antigen specific
for the type of cancer to which the subject is at risk of developing and a immunostimulatory
nucleic acid, the subject may be able to kill the cancer cells as they develop. If a tumor begins
to form in the subject, the subject will develop a specific immune response against the tumor
25 antigen.
In addition to the use of the immunostimulatory nucleic acids as a prophylactic, the
invention also encompasses the use of the immunostimulatory nucleic acids for the treatment
of a subject having an infection, an allergy, asthma, or a cancer.
A subject having an infection is a subject that has been exposed to an infectious
30 pathogen and has acute or chronic detectable levels of the pathogen in the body, or in bodily
waste. When used therapeutically, the immunostimulatory nucleic acids can be used as a
stand alone or in combination with another therapeutic agent. For example, the
immunostimulatory nucleic acids can be used therapeutically with an antigen to mount an
antigen specific systemic or mucosal immune response that is capable of reducing the level of,
or eradicating, the infectious pathogen.
An infectious disease, as used herein, is a disease arising from the presence of a
5 foreign microorganism in the body. It is particularly important to develop effective vaccine
strategies and treatments to protect the body's mucosal surfaces, which are the primary site of
pathogenic entry.
As used herein, the term treat, treated, or treating when used with respect to an
infectious disease refers to a prophylactic treatment which increases the resistance of a subject
10 (a subject at risk of infection) to infection with a pathogen or, in other words, decreases the
likelihood that the subject will become infected with the pathogen as well as a treatment after
the subject (a subject who has been infected) has become infected in order to fight the
infection, e.g., reduce or eliminate the infection or prevent it from becoming worse.
A subject having an allergy is a subject that has or is at risk of developing an allergic
15 reaction in response to an allergen. An allergy refers to acquired hypersensitivity to a
substance (allergen). Allergic conditions include but are not limited to eczema, allergic
rhinitis or coryza, hay fever, conjunctivitis, bronchial asthma, urticaria (hives) and food
allergies, and other atopic conditions.
Currently, allergic diseases are generally treated by the injection of small doses of
20 antigen followed by subsequent increasing dosage of antigen. It is believed that this
procedure induces tolerization to the allergen to prevent further allergic reactions. These
methods, however, can take several years to be effective and are associated with the risk of
side effects such as anaphylactic shock. The methods of the invention avoid these problems.
Allergies are generally caused by IgE antibody generation against harmless allergens.
25 The cytokines that are induced by systemic or mucosal administration of immunostimulatory
nucleic acids are predominantly of a class called Thl (examples are IL-12 and IFN-y) and
these induce both humoral and cellular immune responses. The types of antibodies associated
with a Thl response are generally more protective because they have high neutralization and
opsonization capabilities. The other major type of immune response, which is associated with
30 the production of IL-4, IL-5 and IL-10 cytokines, is termed a Th2 immune response. Th2
responses involve predominately antibodies and these have less protective effect against
infection and some Th2 isotypes (e.g., IgE) are associated with allergy. In general, it appeal's
that allergic diseases are mediated by Th2 type immune responses while Thl responses
provide the best protection against infection, although excessive Thl responses are associated
with autoimmune disease. Based on the ability of the immunostimulatory nucleic acids to
shift the immune response in a subject from a Th2 (which is associated with production of IgE
5 antibodies and allergy) to a Thl response (which is protective against allergic reactions), an
effective dose for inducing an immune response of a immunostimulatory nucleic acid can be
administered to a subject to treat or prevent an allergy.
Thus, the immunostimulatory nucleic acids have significant therapeutic utility in the
treatment of allergic and non-allergic conditions such as asthma. Th2 cytoldnes, especially
10 IL-4 and IL-5 are elevated in the airways of asthmatic subjects. These cytokines promote
important aspects of the asthmatic inflammatory response, including IgE isotope switching,
eosinophil chemotaxis and activation and mast cell growth. Thl cytokines, especially IFN-y
and IL-12, can suppress the formation of Th2 clones and production of Th2 cytokines.
Asthma refers to a disorder of the respiratory system characterized by inflammation,
15 narrowing of the airways and increased reactivity of the airways to inhaled agents. Asthma is
frequently, although not exclusively associated with atopic or allergic symptoms.
A subject having a cancer is a subject that has detectable cancerous cells. The cancer
may be a malignant or non-malignant cancer. Cancers or tumors include but are not limited to
biliary tract cancer; brain cancer; breast cancer; cervical cancer; choriocarcinoma; colon
20 cancer; endometrial cancer; esophageal cancer; gastric cancer; intraepithelial neoplasms;
lymphomas; liver cancer; lung cancer (e.g. small cell and non-small cell); melanoma;
neuroblastomas; oral cancer; ovarian cancer; pancreas cancer; prostate cancer; rectal cancer;
sarcomas; skin cancer; testicular cancer; thyroid cancer; and renal cancer, as well as other
carcinomas and sarcomas. In one embodiment the cancer is hairy cell leukemia, chronic
25 myelogenous leukemia, cutaneous T-cell leukemia, multiple myeloma, follicular lymphoma,
malignant melanoma, squamous cell carcinoma, renal cell carcinoma, prostate carcinoma,
bladder cell carcinoma, or colon carcinoma.
Some cancer cells are antigenic and thus can be targeted by the immune system. In
one aspect, the combined administration of immunostimulatory nucleic acids and cancer
30 medicaments, particularly those which are classified as cancer immunotherapies, is useful for
stimulating a specific immune response against a cancer antigen.
The theory of immune surveillance is that a prime function of the immune system is to
detect and eliminate neoplastic cells before a tumor forms. A basic principle of this theory is
that cancer cells are antigenically different from normal cells and thus elicit immune reactions
that are similar to those that cause rejection of immunologically incompatible allografts.
5 Studies have confirmed that tumor cells differ, either qualitatively or quantitatively, in their
expression of antigens. Such antigens are referred to interchangeably as tumor antigens or
cancer antigens. Some of these antigens may in turn be tumor-specific antigens or tumor-
associated antigens. "Tumor-specific antigens" are antigens that are specifically present in
tumor cells but not normal cells. Examples of tumor specific antigens are viral antigens in
10 tumors induced by DNA or RNA viruses. "Tumor-associated" antigens are present in both
tumor cells and normal cells but are present in a different quantity or a different form in tumor
cells. Examples of such antigens are oncofetal antigens (e.g., carcinoembryonic antigen),
differentiation antigens (e.g., T and Tn antigens), and oncogene products (e.g., HERAieu).
Different types of cells that can kill tumor targets in vitro and in vivo have been
15 identified: natural killer cells (NK cells), cytolytic T lymphocytes (CTLs), lymphokine-
activated killer cells (LAKs), and activated macrophages. NK cells can kill tumor cells
without having been previously sensitized to specific antigens, and the activity does not
require the presence of class I antigens encoded by the major histocompatibility complex
(MHC) on target cells. NK cells are thought to participate in the control of nascent tumors
20 and in the control of metastatic growth. In contrast to NK cells, CTLs can kill tumor cells
only after they have been sensitized to tumor antigens and when the target antigen is
expressed on the tumor cells that also express MHC class I. CTLs are thought to be effector
cells in the rejection of transplanted tumors and of tumors caused by DNA viruses. LAK cells
are a subset of null lymphocytes distinct from the NK and CTL populations. Activated
25 macrophages can kill tumor cells in a manner that is not antigen dependent nor MHC
restricted once activated. Activated macrophages are through to decrease the growth rate of
the tumors they infiltrate. In vitro assays have identified other immune mechanisms such as
antibody-dependent, cell-mediated cytotoxic reactions and lysis by antibody plus
complement. However, these immune effector mechanisms are thought to be less important
30 in vivo than the function of NK, CTLs, LAK, and macrophages in vivo (for review see
Piessens, W.F., and David, J., "Tumor Immunology", In: Scientific American Medicine, Vol.
2, Scientific American Books, N.Y., pp. 1-13,1996.
The goal of immunotherapy is to augment a patient's immune response to an
established tumor. One method of immunotherapy includes the use of adjuvants. Adjuvant
substances derived from microorganisms, such as bacillus Calmette-Guerin, heighten the
immune response and enhance resistance to tumors in animals.
5 An "antigen" as used herein is a molecule capable of provoking an immune response.
Antigens include but are not limited to cells, cell extracts, proteins, polypeptides, peptides,
polysaccharides, polysaccharide conjugates, peptide and non-peptide mimics of
polysaccharides and other molecules, small molecules, lipids, glycolipids, carbohydrates,
viruses and viral extracts and multicellular organisms such as parasites and allergens. The
10 term antigen broadly includes any type of molecule which is recognized by a host immune
system as being foreign. Antigens include but are not limited to cancer antigens, microbial
antigens, and allergens.
A "microbial antigen" as used herein is an antigen of a microorganism and includes
but is not limited to virus, bacteria, parasites, and fungi. Such antigens include the intact
15 microorganism as well as natural isolates and fragments or derivatives thereof and also
synthetic compounds which are identical to or similar to natural microorganism antigens and
induce an immune response specific for that microorganism. A compound is similar to a
natural microorganism antigen if it induces an immune response (humoral and/or cellular) to a
natural microorganism antigen. Such antigens are used routinely in the art and are well
20 known to those of ordinary skill in the art.
A "cancer antigen" as used herein is a compound, such as a peptide or protein, present
in a tumor or cancer cell and which is capable of provoking an immune response when
expressed on the surface of an antigen presenting cell in the context of an MHC molecule.
Cancer antigens can be prepared from cancer cells either by preparing crude extracts of cancer
25 cells, for example, as described in Cohen, et al., 1994, Cancer Research, 54:1055, by partially
purifying the antigens, by recombinant technology, or by de novo synthesis of known
antigens. Cancer antigens include but are not limited to antigens that are recombinantly
expressed, an immunogenic portion of, or a whole tumor or cancer. Such antigens can be
isolated or prepared recombinantly or by any other means known in the art.
30 Cancer or tumor antigens are differentially expressed by cancer cells and can thereby
be exploited in order to target cancer cells. Some of these antigens are encoded, although not
necessarily expressed, by normal cells. These antigens can be characterized as those which
are normally silent (i.e., not expressed) in normal cells, those that are expressed only at certain
stages of differentiation and those that are temporally expressed such as embryonic and fetal
antigens. Other cancer antigens are encoded by mutant cellular genes, such as oncogenes
(e.g., activated ras oncogene), suppressor genes (e.g., mutant p53), fusion proteins resulting
5 from internal deletions or chromosomal translocations. Still other cancer antigens can be
encoded by viral genes such as those carried on RNA and DNA tumor viruses.
In some aspects of the invention, the subject is "exposed to" the antigen. As used
herein, the term "exposed to" refers to either the active step of contacting the subject with an
antigen or the passive exposure of the subject to the antigen in vivo. Methods for the active
10 exposure of a subject to an antigen are well-known in the art. In general, an antigen is
administered directly to the subject by any means such as intravenous, intramuscular, oral,
transdermal, mucosal, intranasal, intratracheal, or subcutaneous administration. The antigen
can be administered systemically or locally. Methods for administering the antigen and the
immunostimulatory nucleic acid are described in more detail below. A subject is passively
/ J exposed to an antigen if an antigen becomes available for exposure to the immune cells in the
body. A subject may be passively exposed to an antigen, for instance, by entry of a foreign
pathogen into the body or by the development of a tumor cell expressing a foreign antigen on
its surface.
The methods in which a subject is passively exposed to an antigen can be particularly
20 dependent on timing of administration of the immunostimulatory nucleic acid. For instance,
in a subject at risk of developing a cancer or an infectious disease or an allergic or asthmatic
response, the subject may be administered the immunostimulatory nucleic acid on a regular
basis when that risk is greatest, i.e., during allergy season or after exposure to a cancer
causing agent. Additionally the immunostimulatory nucleic acid may be administered to
25 travelers before they travel to foreign lands where they are at risk of exposure to infectious
agents. Likewise the immunostimulatory nucleic acid may be administered to soldiers or
civilians at risk of exposure to biowarfare to induce a systemic or mucosal immune response
to the antigen when and if the subject is exposed to it.
The nucleic acids and other therapeutic agents may be administered systemically,
30 although in some preferred embodiments, the administration is local. Local administration
may include topical application to mucosal surfaces such as those of the mouth, vagina, anus
and penis. In embodiments, in which the administration is local, particularly to the mucosal
surfaces of the vagina, anus and mouth, it is preferred that the nucleic acid is one other than a
CpG nucleic acid.
In particular embodiments, the invention is intended to prevent or treat human
sexually transmitted diseases (STD)s caused by HIV-1, HIV-2, HIV-3, HTLV-I, -II, -HI,
J hepatitis A virus, hepatitis B virus, herpes simplex virus (HSV) 1 and 2, papilloma virus,
Neisseria gonorrhoeae, Treponemapattidum, Campylobacter sp., cytomegalovirus (CMV),
Chlamydia trachomatis and Candida albicans using local mucosal administration of
unmethylated CpG nucleic acids.
As used herein, an STD is an infection which is transmitted primarily, but not
10 exclusively, through sexual intercourse. In addition to being transmitted via sexual contact
with an infected subject, some STDs can also be transmitted through contact with bodily
fluids of an infected subject. As used herein, "a bodily fluid" includes blood, saliva, semen,
vaginal fluids, urine, feces and tears. STDs are most commonly transmitted through blood,
saliva, semen and vaginal fluids. As an example, blood and blood product transfusions are
15 common modes of transmission for many sexually transmitted pathogens, including HIV and
Hepatitis viruses.
Sexually transmitted pathogens are generally bacterial, viral, parasitic or fungal in
nature. Organisms that cause STDs include bacteria such as Neisseria gonorrhoeae,
Chlamydia trachomatis, Treponema pallidum, Haemophilus ducreyi, Condyloma acuminata,
20 Calymmatobacterium granulomatis and Ureaplasma urealyticum, viruses such as Human
immunodeficiency viruses (HTV-1 and HTV-2), Human T lymphotropic virus type I (HTLV-
I), Herpes simplex virus type 2 (HSV-2), Human papilloma virus (multiple types), Hepatitis B
virus, Cytomegalovirus and Molluscum contagiosum virus, parasites such as Trichomonas
vaginalis and Phthirus pubis, and fungi such as Candida albicans.
25 Other infections are known to be sexually transmitted, even if sexual transmission is
not their predominant mode of transmission. This latter category includes infections caused
by bacteria such as Mycoplasma hominis, Gardnerella vaginalis and Group B streptococcus,
viruses such as Human T lymphotrophic virus type II (HTLV-II), Hepatitis C and D viruses,
Herpes simplex virus type I (HSV-1) and Epstein-Barr virus (EBV), and parasites such as
30 Sarcoptes scabiei.
The invention also intends to embrace STDs which are transmitted by sexual contact
involving oral-fecal exposure. These STDs are caused by bacteria such as Shigella spp. and
Campylobacter spp., viruses such as Hepatitis A virus and parasites such as Giardia lamblia
and Entamoeba histolytica.
A "subject in need thereof may be a subject who is at risk of developing an STD or
one who has an STD (i.e., a subject having an STD).
5 The nucleic acids are useful in some aspects as a prophylactic for the prevention of an
STD in a subject at risk of developing an STD. A "subject at risk of developing an STD", as
used herein, is a subject who has any risk of developing an STD either by contact with an
infected subject or by contact with a bodily fluid from an infected subject. For instance, a
subject at risk is one who has or who will have a sexual partner who is infected with an STD-
10 causing pathogen. Subjects at risk also include those who engage in unprotected sexual
activity such as having sex, either oral, anal or vaginal, without a condom (i.e., male or female
condom), regardless of whether they or their partners are aware of the existing infection.
Subjects who have multiple sexual partners (e.g., prostitutes or those who frequent prostitutes)
or who have even one sexual partner who in turn has multiple sexual partners are also
15 considered to be at risk. Other subjects at risk of developing an STD are subjects who engage
in other forms of high risk transmission behavior such as sharing of hypodermic needles.
Subjects receiving blood products may also be considered to be at risk, particularly if the
surveillance of the blood supply system is lax. An example of this latter category of subject is
a subject in sub-Saharan African countries which have a blood supply system which is
20 partially or completely contaminated with STD-causing pathogens (e.g., HIV). A subject at
risk may also be one who is planning to travel to an area in which one or more STD-causing
pathogens are common, particularly if it is known that such pathogens are present in the blood
supply system of the area. Another subject at risk is one who has an occupation which
involves potential contact with a bodily fluid of another. Examples of this latter category
25 include, but are not limited to, nurses, doctors, dentists, and rescue personnel such as
ambulance attendants, paramedics, fire-fighters, and police officers. Subjects at risk also
include fetuses and newborns born to mothers who are infected with an STD-causing
pathogen.
All of the afore-mentioned activities that are associated with the transmission of an
30 STD causing pathogen are also referred to herein as "high risk activities". The nucleic acid
and potentially other prophylactic or therapeutic agents to be used in conjunction may be
administered before, or during, or following the time which the subject is engaged in the high
risk activity. A subject who is administered a nucleic acid before engaging in sexual activity,
for example, may receive the nucleic acid at least one month, at least one week, at least 48
hours, at least 24 hours, at least 12 hours, at least 6 hours, at least 4 hours, at least 2 hours (or
any time therebetween as if such time was explicitly recited herein) prior to having sex.
5 Preferably, the time of administration prior to engagement in the high risk activity is a time
sufficient to activate the immune system so that it is active while the infectious agent is
present in the body of the subject. A subject who is administered the nucleic acid following
engagement in the high risk activity may receive it within 2 hours, within 4 hours, within 6
hours, within 12 hours, within 24 hours, within 48 hours, or within 3,4, 5, 6, 7,14,28 days or
10 longer (or any time therebetween as if such time was explicitly recited herein) after engaging
in the high risk activity.
A subject preferably is a non-rodent subject. A non-rodent subject shall mean a
human or vertebrate animal including but not limited to a dog, cat, horse, cow, pig, sheep,
goat, chicken, primate, e.g., monkey, and fish (aquaculture species), e.g. salmon, but
15 specifically excluding rodents such as rats and mice.
Antigens can be derived from various sources including tumor, non-tumor cancers,
allergens, and infectious pathogens. Each of the lists recited herein is not intended to be
limiting.
Examples of viruses that have been found in humans include but are not limited to:
20 Retroviridae (e.g. human immunodeficiency viruses, such as HIV-l (also referred to as
HTLV-III, LAV or HTLV-III/LAV, or HIV-III; and other isolates, such as HIV-LP;
Picornaviridae (e.g. polio viruses, hepatitis A virus; enteroviruses, human Coxsackie viruses,
rhinoviruses, echoviruses); Calciviridae (e.g. strains that cause gastroenteritis); Togaviridae
(e.g. equine encephalitis viruses, rubella viruses); Flaviridae (e.g. dengue viruses, encephalitis
25 viruses, yellow fever viruses); Coronoviridae (e.g. coronaviruses); Rhabdoviradae (e.g.
vesicular stomatitis viruses, rabies viruses); Coronaviridae (e.g. coronaviruses);
Rhabdoviridae (e.g. vesicular stomatitis viruses, rabies viruses); Filoviridae (e.g. ebola
viruses); Paramyxoviridae (e.g. parainfluenza viruses, mumps virus, measles virus,
respiratory syncytial virus); Orthomyxoviridae (e.g. influenza viruses); Bungaviridae (e.g.
30 Hantaan viruses, bunga viruses, phleboviruses and Nairo viruses); Arena viridae (hemorrhagic
fever viruses); Reoviridae (e.g. reoviruses, orbiviurses and rotaviruses); Birnaviridae;
Hepadnaviridae (Hepatitis B virus); Parvovirida (parvoviruses); Papovaviridae (papilloma
viruses, polyoma viruses); Adenoviridae (most adenoviruses); Herpesviridae (herpes simplex
virus (HSV) 1 and 2, varicella zoster virus, cytomegalovirus (CMV), herpes virus; Poxviridae
(variola viruses, vaccinia viruses, pox viruses); and Iridoviridae (e.g. African swine fever
virus); and unclassified viruses (e.g. the etiological agents of Spongiform encephalopathies,
5 the agent of delta hepatitis (thought to be a defective satellite of hepatitis B virus), the agents
of non-A, non-B hepatitis (class 1 = internally transmitted; class 2 = parenterally transmitted
(i.e. Hepatitis C); Norwalk and related viruses, and astroviruses).
Although many of the microbial antigens described herein relate to human disorders,
the invention is also useful for treating other non-human vertebrates. Non-human vertebrates
10 are also capable of developing infections which can be prevented or treated with the
immunostimulatory nucleic acids disclosed herein. For instance, in addition to the treatment
of infectious human diseases, the methods of the invention are useful for treating infections of
animals.
Both gram negative and gram positive bacteria serve as antigens in vertebrate animals.
15 Such gram positive bacteria include, but are not limited to, Pasteurella species, Staphylococci
species, and Streptococcus species. Gram negative bacteria include, but are not limited to,
Escherichia coli, Pseudomonas species, and Salmonella species. Specific examples of
infectious bacteria include but are not limited to, Helicobacter pyloris, Borelia burgdorferi,
Legionella pneumophilia, Mycobacteria sps (e.g. M. tuberculosis, M. avium, M.
20 intracellulare, M. kansaii, M. gordonae), Staphylococcus aureus, Neisseria gonorrhoeae,
Neisseria meningitidis, Lister ia monocytogenes, Streptococcus pyogenes (Group A
Streptococcus), Streptococcus agalactiae (Group B Streptococcus), Streptococcus (viridans
group), Streptococcus faecalis, Streptococcus bovis, Streptococcus (anaerobic sps.),
Streptococcus pneumoniae, pathogenic Campylobacter sp., Enter ococcus sp.,Haemophilus
25 influenzae, Bacillus antracis, corynebacterium diphtheriae, corynebacterium sp.,
Erysipelothrix rhusiopathiae, Clostridiumperfringers, Clostridium tetani, Enterobacter
aerogenes, Klebsiella pneumoniae, Pasturella multocida, Bacteroides sp.,Fusobacterium
nucleatum, Streptobacillus moniliformis, Treponema pallidium, Treponema pertenue,
Leptospira, Rickettsia, and Actinomyces israelli.
30 Polypeptides of bacterial pathogens include but are not limited to an iron-regulated
outer membrane protein, (IROMP), an outer membrane protein (OMP), and an A-protein of
Aeromonis salmonicida which causes furunculosis, p57 protein of Renibacterium
salmoninarum which causes bacterial kidney disease (BKD), major surface associated antigen
(msa), a surface expressed cytotoxin (mpr), a surface expressed hemolysin (ish), and a
flagellar antigen of Yersiniosis; an extracellular protein (ECP), an iron-regulated outer
membrane protein (IROMP), and a structural protein of Pasteurellosis; an OMP and a
5 flagellar protein of Vibrosis anguiliarum and V. ordalii; a flagellar protein, an OMP protein,
aroA, and purA of Edwardsiellosis ictaluri and E. tarda; and surface antigen of
Ichthyophthirius; and a structural and regulatory protein of Cytophaga columnari; and a
structural and regulatory protein of Rickettsia.
Polypeptides of a parasitic pathogen include but are not limited to the surface antigens
10 of Ichthyophthirius.
Examples of fungi include Cryptococcus neoformans, Histoplasma capsulatum,
Coccidioides immitis, Blastomyces dermatitidis, Chlamydia trachomatis, Candida albicans.
Other infectious organisms (i.e., protists) include Plasmodhim spp. such as Plasmodium
falciparum, Plasmodium malariae, Plasmodium ovale, and Plasmodium vivax and
15 Toxoplasma gondii. Blood-borne and/or tissues parasites include Plasmodium spp., Babesia
microti, Babesia divergens, Leishmania tropica, Leishmania spp., Leishmania braziliensis,
Leishmania donovani, Trypanosoma gambiense and Trypanosoma rhodesiense (African
sleeping sickness), Trypanosoma cruzi (Chagas' disease), and Toxoplasma gondii.
Other medically relevant microorganisms have been described extensively in the literature,
20 e.g., see C.G.A Thomas, Medical Microbiology, Bailliere Tindall, Great Britain 1983, the
entire contents of which is hereby incorporated by reference.
Many vaccines for the treatment of non-human vertebrates are disclosed in Bennett, K.
Compendium of Veterinary Products, 3rd ed. North American Compendiums, Inc. ,1995. As
discussed above, antigens include infectious microbes such as virus, parasite, bacteria and
25 fungi and fragments thereof, derived from natural sources or synthetically. Infectious viruses
of both human and non-human vertebrates, include retroviruses, RNA viruses and DNA
viruses. This group of retroviruses includes both simple retroviruses and complex
retroviruses. The simple retroviruses include the subgroups of B-type retroviruses, C-type
retroviruses and D-type retroviruses. An example of a B-type retrovirus is mouse mammary
30 tumor virus (MMTV). The C-type retroviruses include subgroups C-type group A (including
Rous sarcoma virus (RSV), avian leukemia virus (ALV), and avian myeloblastosis virus
(AMV)) and C-type group B (including feline leukemia virus (FeLV), gibbon ape leukemia
virus (GALV), spleen necrosis virus (SNV), reticuloendotheliosis virus (RV) and simian
sarcoma virus (SSV)). The D-type retroviruses include Mason-Pfizer monkey virus (MPMV)
and simian retrovirus type 1 (SRV-1). The complex retroviruses include the subgroups of
lentiviruses, T-cell leukemia viruses and the foamy viruses. Lentiviruses include HIV-1, but
5 also include HTV-2, SIV, Visna virus, feline immunodeficiency virus (FIV), and equine
infectious anemia virus (EIAV). The T-cell leukemia viruses include HTLV-1,HTLV-II,
simian T-cell leukemia virus (STLV), and bovine leukemia virus (BLV). The foamy viruses
include human foamy virus (HFV), simian foamy virus (SFV) and bovine foamy virus
(BFV).
10 Examples of other RNA viruses that are antigens in vertebrate animals include, but are
not limited to, members of the family Reoviridae, including the genus Orthoreovirus (multiple
serotypes of both mammalian and avian retroviruses), the genus Orbivirus (Bluetongue virus,
Eugenangee virus, Kemerovo virus, African horse sickness virus, and Colorado Tick Fever
virus), the genus Rotavirus (human rotavirus, Nebraska calf diarrhea virus, simian rotavirus,
15 bovine or ovine rotavirus, avian rotavirus); the family Picornaviridae, including the genus
Enterovirus (poliovirus, Coxsackie virus A and B, enteric cytopathic human orphan (ECHO)
viruses, hepatitis A virus, Simian enteroviruses, Murine encephalomyelitis (ME) viruses,
Poliovirus muris, Bovine enteroviruses, Porcine enteroviruses , the genus Cardiovirus
(Encephalomyocarditis virus (EMC), Mengovirus), the genus Rhinovirus (Human
20 rhinoviruses including at least 113 subtypes; other rhinoviruses), the genus Apthovirus (Foot
and Mouth disease (FMDV); the family Calciviridae, including Vesicular exanthema of swine
virus, San Miguel sea lion virus, Feline picornavirus andNorwalk virus; the family
Togaviridae, including the genus Alphavirus (Eastern equine encephalitis virus, Semliki forest
virus, Sindbis virus, Cbikungunya virus, O'Nyong-Nyong virus, Ross river virus, Venezuelan
25 equine encephalitis virus, Western equine encephalitis virus), the genus Flavirius (Mosquito
borne yellow fever virus, Dengue virus, Japanese encephalitis virus, St. Louis encephalitis
virus, Murray Valley encephalitis virus, West Nile virus, Kunjin virus, Central European tick
borne virus, Far Eastern tick borne virus, Kyasanur forest virus, Louping III virus, Powassan
virus, Omsk hemorrhagic fever virus), the genus Rubivirus (Rubella virus), the genus
30 Pestivirus (Mucosal disease virus, Hog cholera virus, Border disease virus); the family
Bunyaviridae, including the genus Bunyvirus (Bunyamwera and related viruses, California
encephalitis group viruses), the genus Phlebovirus (Sandfly fever Sicilian virus, Rift Valley
fever virus), the genus Nairovirus (Crimean-Congo hemorrhagic fever virus, Nairobi sheep
disease virus), and the genus Uukuvirus (Uukuniemi and related viruses); the family
Orthomyxoviridae, including the genus Influenza virus (Influenza virus type A, many human
subtypes); Swine influenza virus, and Avian and Equine Influenza viruses; influenza type B
J (many human subtypes), and influenza type C (possible separate genus); the family
paramyxoviridae, including the genus Paramyxovirus (Parainfluenza virus type 1, Sendai
virus, Hemadsorption virus, Parainfluenza viruses types 2 to 5, Newcastle Disease Virus,
Mumps virus), the genus Morbillivirus (Measles virus, subacute sclerosing panencephalitis
virus, distemper virus, Rinderpest virus), the genus Pneumovirus (respiratory syncytial virus
10 (RSV), Bovine respiratory syncytial virus and Pneumonia virus); the family Rhabdoviridae,
including the genus Vesiculovirus (VSV), Chandipura virus, Flanders-Hart Park virus), the
genus Lyssavirus (Rabies virus), fish Rhabdoviruses, and two probable Rhabdovimses
(Marburg virus and Ebola virus); the family Arenaviridae, including Lymphocytic
choriomeningitis virus (LCM), Tacaribe virus complex, and Lassa virus; the family
75 Coronoaviridae, including Infectious Bronchitis Virus (IBV), Hepatitis virus, Human enteric
corona virus, and Feline infectious peritonitis (Feline coronavirus).
Illustrative DNA viruses that are antigens in vertebrate animals include, but are not limited to,
the family Poxviridae, including the genus Orthopoxvirus (Variola major, Variola minor,
Monkey pox Vaccinia, Cowpox, Buffalopox, Rabbitpox, Ectromelia), the genus
20 Leporipoxvirus (Myxoma, Fibroma), the genus Avipoxvirus (Fowlpox, other avian
poxvirus), the genus Capripoxvirus (sheeppox, goatpox), the genus Suipoxvirus (Swinepox),
the genus Parapoxvirus (contagious postular dermatitis virus, pseudocowpox, bovine papular
stomatitis virus); the family Iridoviridae (African swine fever virus, Frog viruses 2 and 3,
Lymphocystis virus offish); the family Herpesviridae, including the alpha-Herpesviruses
25 (Herpes Simplex Types 1 and 2, Varicella-Zoster, Equine abortion virus, Equine herpes virus
2 and 3, pseudorabies virus, infectious bovine keratoconjunctivitis virus, infectious bovine
rhinotracheitis virus, feline rhinotracheitis virus, infectious laryngotracheitis virus) the
Beta-herpesviruses (Human cytomegalovirus and cytomegaloviruses of swine and monkeys);
the gamma-herpesviruses (Epstein-Barr virus (EBV), Marek's disease virus, Herpes saimiri,
30 Herpesvirus ateles, Herpesvirus sylvilagus, guinea pig herpes virus, Lucke tumor virus); the
family Adenoviridae, including the genus Mastadenovirus (Human subgroups A,B,C,D,E and
ungrouped; simian adenoviruses (at least 23 serotypes), infectious canine hepatitis, and
adenoviruses of cattle, pigs, sheep, frogs and many other species, the genus Aviadenovirus
(Avian adenoviruses); and non-cultivatable adenoviruses; the family Papoviridae, including
the genus Papillomavirus (Human papilloma viruses, bovine papilloma viruses, Shope rabbit
papilloma virus, and various pathogenic papilloma viruses of other species), the genus
5 Polyomavirus (polyomavirus, Simian vacuolating agent (SV-40), Rabbit vacuolating agent
(RK.V), K virus, BK virus, JC virus, and other primate polyoma viruses such as
Lymphotrophic papilloma virus); the family Parvoviridae including the genus
Adeno-associated viruses, the genus Parvovirus (Feline panleukopenia virus, bovine
parvovirus, canine parvovirus, Aleutian mink disease virus, etc). Finally, DNA viruses may
10 include viruses which do not fit into the above families such as Kuru and Creutzfeldt-Jacob
disease viruses and chronic infectious neuropathic agents (CHINA virus).
The immunostimulatory nucleic acids can also be used to induce an immune response,
such as an antigen specific immune response, birds such as hens, chickens, turkeys, ducks,
geese, quail, and pheasant. Birds are prime targets for many types of infections.
15 Hatching birds are exposed to pathogenic microorganisms shortly after birth.
Although these birds are initially protected against pathogens by maternal derived antibodies,
this protection is only temporary, and the bird's own immature immune system must begin to
protect the bird against the pathogens. It is often desirable to prevent infection in young birds
when they are most susceptible. It is also desirable to prevent against infection in older birds,
20 especially when the birds are housed in closed quarters, leading to the rapid spread of disease.
Thus, it is desirable to administer the Immunostimulatory nucleic acid and the non-nucleic
acid adjuvant of the invention to birds to enhance an antigen-specific immune response when
antigen is present
An example of a common infection in chickens is chicken infectious anemia virus
25 (CIAV). CIAV was first isolated in Japan in 1979 during an investigation of a Marek's
disease vaccination break (Yuasa et al., 1979, Avian Dis. 23:366-385). Since that time, CIAV
has been detected in commercial poultry in all major poultry producing countries (van Bulow
et al., 1991, pp.690-699) in Diseases of Poultry, 9th edition, Iowa State University Press).
CIAV infection results in a clinical disease, characterized by anemia, hemorrhage and
30 immunosuppression, in young susceptible chickens. Atrophy of the thymus and of the bone
marrow and consistent lesions of CIAV-infected chickens are also characteristic of CIAV
infection. Lymphocyte depletion in the thymus, and occasionally in the bursa of Fabricius,
results in immunosuppression and increased susceptibility to secondary viral, bacterial, or
fungal infections which, then complicate the course of the disease. The immunosuppression
may cause aggravated disease after infection with one or more of Marek's disease virus
(MDV), infectious bursal disease virus, reticuloendotheliosis virus, adenovirus, or reovirus. It
5 has been reported that pathogenesis of MDV is enhanced by CIAV (DeBoer et al., 1989, p. 28
In Proceedings of the 38th Western Poultry Diseases Conference, Tempe, Ariz.). Further, it
has been reported that CIAV aggravates the signs of infectious bursal disease (Rosenberger et
al., 1989, Avian Dis. 33:707-713). Chickens develop an age resistance to experimentally
induced disease due to CAA. This is essentially complete by the age of 2 weeks, but older
10 birds are still susceptible to infection (Yuasa, N. et al., 1979 supra; Yuasa, N. et al., Arian
Diseases 24,202-209,1980). However, if chickens are dually infected with CAA and an
immunosuppressive agent (IBDV, MDV etc.), age resistance against the disease is delayed
(Yuasa, N. et al., 1979 and 1980 supra; Bulow von V. et al., J. Veterinary Medicine 33,
93-116,1986). Characteristics of CIAV that may potentiate disease transmission include high
15 resistance to environmental inactivation and some common disinfectants. The economic
impact of CIAV infection on the poultry industry is clear from the fact that 10% to 30% of
infected birds in disease outbreaks die.
Vaccination of birds, like other vertebrate animals can be performed at any age.
Normally, vaccinations are performed at up to 12 weeks of age for a live microorganism and
20 between 14-18 weeks for an inactivated microorganism or other type of vaccine. For in ovo
vaccination, vaccination can be performed in the last quarter of embryo development. The
vaccine may be administered subcutaneously, by spray, orally, intraocularly, intratracheally,
nasally, or by other mucosal delivery methods described herein. Thus, the
immunostimulatory nucleic acids of the invention can be administered to birds and other non-
25 human vertebrates using routine vaccination schedules and the antigen can be administered
after an appropriate time period as described herein.
Cattle and livestock are also susceptible to infection. Diseases which affect these
animals can produce severe economic losses, especially amongst cattle. The methods of the
invention can be used to protect against infection in livestock, such as cows, horses, pigs,
30 sheep, and goats.
Cows can be infected by bovine viruses. Bovine viral diarrhea virus (BVDV) is a
small enveloped positive-stranded RNA virus and is classified, along with hog cholera virus
(HOCV) and sheep border disease virus (BDV), in the pestivirus genus. Although,
Pestiviruses were previously classified in the Togaviridae family, some studies have
suggested their reclassification within the Flaviviridae family along with the flavivirus and
hepatitis C virus (HCV) groups (Francki, et al., 1991).
5 BVDV, which is an important pathogen of cattle can be distinguished, based on cell
culture analysis, into cytopathogenic (CP) and noncytopathogenic (NCP) biotypes. The NCP
biotype is more widespread although both biotypes can be found in cattle. If a pregnant cow
becomes infected with an NCP strain, the cow can give birth to a persistently infected and
specifically imrnunotolerant calf that will spread virus during its lifetime. The persistently
10 infected cattle can succumb to mucosal disease and both biotypes can then be isolated from
the animal. Clinical manifestations can include abortion, teratogenesis, and respiratory
problems, mucosal disease and mild diarrhea. In addition, severe thrombocytopenia,
associated with herd epidemics, that may result in the death of the animal has been described
and strains associated with this disease seem more virulent than the classical BVDVs.
15 Equine herpes viruses (EHV) comprise a group of antigenically distinct biological
agents which cause a variety of infections in horses ranging from subclinical to fatal disease.
These include Equine herpesvirus-1 (EHV-1), a ubiquitous pathogen in horses. EHV-1 is
associated with epidemics of abortion, respiratory tract disease, and central nervous system
disorders. Primary infection of upper respiratory tract of young horses results in a febrile
20 illness which lasts for 8 to 10 days. Immunologically experienced mares may be re-infected
via the respiratory tract without disease becoming apparent, so that abortion usually occurs
without warning. The neurological syndrome is associated with respiratory disease or abortion
and can affect animals of either sex at any age, leading to lack of co-ordination, weakness and
posterior paralysis (Telford, E. A. R. et al., Virology 189, 304-316,1992). Other EHV's
25 include EHV-2, or equine cytomegalovirus, EHV-3, equine coital exanthema virus, and
EHV-4, previously classified as EHV-1 subtype 2.
Sheep and goats can be infected by a variety of dangerous microorganisms including
visna-maedi.
Primates such as monkeys, apes and macaques can be infected by simian
30 immunodeficiency virus. Inactivated cell-virus and cell-free whole simian immunodeficiency
vaccines have been reported to afford protection in macaques (Stott et al. (1990) Lancet
36:1538-1541; Desrosiers et al. PNAS USA (1989) 86:6353-6357; Murphey-Corb et al.
(1989) Science 246:1293-1297; and Carlson et al. (1990) AIDS Res. Human Retroviruses
6:1239-1246). A recombinant HIV gpl20 vaccine has been reported to afford protection in
chimpanzees (Berman et al. (1990) Nature 345:622-625).
Cats, both domestic and wild, are susceptible to infection with a variety of
5 microorganisms. For instance, feline infectious peritonitis is a disease which occurs in both
domestic and wild cats, such as lions, leopards, cheetahs, and jaguars. When it is desirable to
prevent infection with this and other types of pathogenic organisms in cats, the methods of the
invention can be used to vaccinate cats to protect them against infection.
Domestic cats may become infected with several retroviruses, including but not
10 limited to feline leukemia virus (FeLV), feline sarcoma virus (FeSV), endogenous type
Concornavirus (RD-114), and feline syncytia-forming virus (FeSFV). Of these, FeLV is the
most significant patliogen, causing diverse symptoms, including lymphoreticular and myeloid
neoplasms, anemias, immune mediated disorders, and an immunodeficiency syndrome which
is similar to human acquired immune deficiency syndrome (AIDS). Recently, a particular
15 replication-defective FeLV mutant, designated FeLV-AIDS, has been more particularly
associated with immunosuppressive properties.
The discovery of feline T-lymphotropic lentivirus (also referred to as feline
immunodeficiency) was first reported in Pedersen et al. (1987) Science 235:790-793.
Characteristics of FIV have been reported in Yamamoto et al. (1988) Leukemia, December
20 Supplement 2:204S-215S; Yamamoto et al. (1988) Am. J. Vet. Res. 49:1246-1258; and
Ackley et al. (1990) J. Virol. 64:5652-5655. Cloning and sequence analysis of FIV have been
reported in Olmsted et al. (1989) Proc. Natl. Acad. Sci. USA 86:2448-2452 and
86:4355-4360.
Feline infectious peritonitis (FIP) is a sporadic disease occurring unpredictably in
25 domestic and wild Felidae. While FIP is primarily a disease of domestic cats, it has been
diagnosed in lions, mountain lions, leopards, cheetahs, and the jaguar. Smaller wild cats that
have been afflicted with FIP include the lynx and caracal, sand cat, and pallas cat. In
domestic cats, the disease occurs predominantly in young animals, although cats of all ages
are susceptible. A peak incidence occurs between 6 and 12 months of age. A decline in
30 incidence is noted from 5 to 13 years of age, followed by an increased incidence in cats 14 to
15 years old.
Viral, bacterial, and parasitic diseases in fin-fish, shellfish or other aquatic life forms
pose a serious problem for the aquaculture industry. Owing to the high density of animals in
the hatchery tanks or enclosed marine farming areas, infectious diseases may eradicate a large
proportion of the stock in, for example, a fin-fish, shellfish, or other aquatic life forms facility.
5 Prevention of disease is a more desired remedy to these threats to fish than intervention once
the disease is in progress. Vaccination offish is the only preventative method which may
offer long-term protection through immunity. Nucleic acid based vaccinations are described
in US Patent No. 5,780,448 issued to Davis.
The fish immune system has many features similar to the mammalian immune system,
10 such as the presence of B cells, T cells, lymphokines, complement, and immunoglobulins.
Fish have lymphocyte subclasses with roles that appear similar in many respects to those of
the B and T cells of mammals. Vaccines can be administered by immersion or orally.
Aquaculture species include but are not limited to fin-fish, shellfish, and other aquatic
animals. Fin-fish include all vertebrate fish, which may be bony or cartilaginous fish, such as,
15 for example, salmonids, carp, catfish, yellowtail, seabream, and seabass. Salmonids are a
family of fin-fish which include trout (including rainbow trout), salmon, and Arctic char.
Examples of shellfish include, but are not limited to, clams, lobster, shrimp, crab, and oysters.
Other cultured aquatic animals include, but are not limited to eels, squid, and octopi.
Polypeptides of viral aquaculture pathogens include but are not limited to glycoprotein
20 (G) or nucleoprotein (N) of viral hemorrhagic septicemia virus (VHSV); G or N proteins of
infectious hematopoietic necrosis virus (IHNV); VP1, VP2, VP3 or N structural proteins of
infectious pancreatic necrosis virus (IPNV); G protein of spring viremia of carp (SVC); and a
membrane-associated protein, tegumin or capsid protein or glycoprotein of channel catfish
virus (CCV).
25 Typical parasites infecting horses are Gasterophilus spp.; Eimeria leuckarti, Giardia
spp.; Tritrichomonas equi; Babesia spp. (RBC's), Theileria equi; Trypanosoma spp.;
Klossiella equi; Sarcocystis spp.
Typical parasites infecting swine include Eimeria bebliecki, Eimeria scabra, Isospora suis,
Giardia spp.; Balantidium coli, Entamoeba histotytica; Toxoplasma gondii and Sarcocystis
30 spp., and Trichinella spiralis.
The major parasites of dairy and beef cattle include Eimeria spp., Cryptosporidium
sp., Giardia spp.; Toxoplasma gondii; Babesia bovis (RBC), Babesia bigemina (RBC),
Trypcmosoma spp. (plasma), Theileria spp. (RBC); Theileria parva (lymphocytes);
Tritrichomonas foetus; and Sarcocystis spp.
The major parasites of raptors include Trichomonas gallinae; Coccidia (Eimeria spp.);
Plasmodium relictum, Leucocytozoon danilewskyi (owls), Haemoproteus spp., Trypanosoma
5 spp.; Histomonas; Cryptosporidium meleagridis, Cryptosporidium baileyi, Giardia, Eimeria;
Toxoplasma.
Typical parasites infecting sheep and goats include Eimeria spp., Cryptosporidium sp.,
Giardia sp.; Toxoplasma gondii; Babesia spp. (RBC), Trypanosoma spp. (plasma), Theileria
spp. (RBC); and Sarcocystis spp.
10 Typical parasitic infections in poultry include coccidiosis caused by Eimeria
acervulina, E. necatrix, E. tenella, Isospora spp. and Eimeria truncata; histomoniasis, caused
by Histomonas meleagridis and Histomonas gallinarum; trichomoniasis caused by
Trichomonas gallinae; and hexamitiasis caused by Hexamita meleagridis. Poultry can also be
infected Emeria maxima, Emeria meleagridis, Eimeria adenoeides, Eimeria meleagrimitis,
15 Cryptosporidium, Eimeria brunetti, Emeria adenoeides, Leucocytozoon spp., Plasmodium
spp., Hemoproteus meleagridis, Toxoplasma gondii and Sarcocystis.
The methods of the invention can also be applied to the treatment and/or prevention of
parasitic infection in dogs, cats, birds, fish and ferrets. Typical parasites of birds include
Trichomonas gallinae; Eimeria spp., Isospora spp., Giardia; Cryptosporidium; Sarcocystis
20 spp., Toxoplasma gondii, Haemoproteus/Parahaemoproteus, Plasmodium spp.,
Leucocytozoon/Akiba, Atoxoplasma, Trypanosoma spp. Typical parasites infecting dogs
include Trichinella spiralis; Isopora spp., Sarcocystis spp., Cryptosporidium spp.,
Hammondia spp., Giardia duodenalis (canis); Balantidium coli, Entamoeba histolytica;
Hepatozoon canis; Toxoplasma gondii, Trypanosoma cruzi; Babesia canis; Leishmania
25 amastigotes; Neospora caninum.
Typical parasites infecting feline species include Isospora spp., Toxoplasma gondii,
Sarcocystis spp., Hammondia hammondi, Besnoitia spp., Giardia spp.; Entamoeba
histolytica; Hepatozoon canis, Cytauxzoon sp., Cytauxzoon sp., Cytauxzoon sp. (red cells, RE
cells).
30 Typical parasites infecting fish include Hexamita spp., Eimeria spp.; Cryptobia spp.,
Nosema spp., Myxosoma spp., Chilodonella spp., Trichodina spp.; Plistophora spp.,
Myxosoma Henneguya; Costia spp., Ichthyophithirius spp., and Oodinium spp.
Typical parasites of wild mammals include Giardia spp. (carnivores, herbivores),
Isospora spp. (carnivores), Eimeria spp. (carnivores, herbivores); Theileria spp.
(herbivores), Babesia spp. (carnivores, herbivores), Trypanosoma spp. (carnivores,
herbivores); Schistosoma spp. (herbivores); Fasciola hepatica (herbivores), Fascioloides
5 magna (herbivores), Fasciola gigantica (herbivores), Trichinella spiralis (carnivores,
herbivores).
Parasitic infections in zoos can also pose serious problems. Typical parasites of the
bovidae family (blesbok, antelope, banteng, eland, gaur, impala, klipspringer, kudu, gazelle)
include Eimeria spp. Typical parasites in the pinnipedae family (seal, sea lion) include
10 Eimeria phocae. Typical parasites in the camelidae family (camels, llamas) include Eimeria
spp. Typical parasites of the giraffidae family (giraffes) include Eimeria spp. Typical
parasites in the elephantidae family (African and Asian) include Fasciola spp. Typical
parasites of lower primates (chimpanzees, orangutans, apes, baboons, macaques, monkeys)
include Giardia sp.; Balantidium coli, Entamoeba histolytica, Sarcocystis spp., Toxoplasma
15 gondii; Plasmodim spp. (RBC), Babesia spp. (RBC), Trypanosoma spp. (plasma),
Leishmania spp. (macrophages).
Cancer is one of the leading causes of death in companion animals (i.e., cats and
dogs). Cancer usually strikes older animals which, in the case of house pets, have become
integrated into the family. Forty-five % of dogs older than 10 years of age, are likely to
20 succumb to the disease. The most common treatment options include surgery, chemotherapy
and radiation therapy. Others treatment modalities which have been used with some success
are laser therapy, cryotherapy, hyperthermia and immunotherapy. The choice of treatment
depends on type of cancer and degree of dissemination. Unless the malignant growth is
confined to a discrete area in the body, it is difficult to remove only malignant tissue without
25 also affecting normal cells.
Malignant disorders commonly diagnosed in dogs and cats include but are not limited
to lymphosarcoma, osteosarcoma, mammary tumors, mastocytoma, brain tumor, melanoma,
adenosquamous carcinoma, carcinoid lung tumor, bronchial gland tumor, broncbiolar
adenocarcinoma, fibroma, myxochondroma, pulmonary sarcoma, neurosarcoma, osteoma,
30 papilloma, retinoblastoma, Ewing's sarcoma, Wilm's tumor, Burkitt's lymphoma,
microglioma, neuroblastoma, osteoclastoma, oral neoplasia, fibrosarcoma, osteosarcoma and
rhabdomyosarcoma. Other neoplasias in dogs include genital squamous cell carcinoma,
transmissable venereal tumor, testicular tumor, seminoma, Sertoli cell tumor,
hemangiopericytoma, histiocytoma, chloroma (granulocytic sarcoma), corneal papilloma,
corneal squamous cell carcinoma, hemangiosarcoma, pleural mesothelioma, basal cell tumor,
thymoma, stomach tumor, adrenal gland carcinoma, oral papillomatosis,
5 hemangioendothelioma and cystadenoma. Additional malignancies diagnosed in cats include
follicular lymphoma, intestinal lymphosarcoma, fibrosarcoma and pulmonary squamous cell
carcinoma. The ferret, an ever-more popular house pet is known to develop insulinoma,
lymphoma, sarcoma, neuroma, pancreatic islet cell tumor, gastric MALT lymphoma and
gastric adenocarcrnoma.
10 Neoplasias affecting agricultural livestock include leukemia, hemangiopericytoma and
bovine ocular neoplasia (in cattle); preputial fibrosarcoma, ulcerative squamous cell
carcinoma, preputial carcinoma, connective tissue neoplasia and mastocytoma (in horses);
hepatocellular carcinoma (in swine); lymphoma and pulmonary adenomatosis (in sheep);
pulmonary sarcoma, lymphoma, Rous sarcoma, reticulendotheliosis, fibrosarcoma,
15 nephroblastoma, B-cell lymphoma and lymphoid leukosis (in avian species); retinoblastoma,
hepatic neoplasia, lyrnphosarcoma (lymphoblastic lymphoma), plasmacytoid leukemia and
swimbladder sarcoma (in fish), caseous lumphadenitis (CLA): chronic, infectious, contagious
disease of sheep and goats caused by the bacterium Corynebacteriumpseudotuberculosis, and
contagious lung tumor of sheep caused by jaagsiekte.
20 An allergen refers to a substance (antigen) that can induce an allergic or asthmatic
response in a susceptible subject. The list of allergens is enormous and can include pollens,
insect venoms, animal dander dust, fungal spores and drugs (e.g. penicillin). Examples of
natural, animal and plant allergens include but are not limited to proteins specific to the
following genuses: Canine (Canisfamiliaris); Dermatophagoides (e.g. Dermatophagoides
25 farinae); Felis (Felis domesticus); Ambrosia (Ambrosia artemiisfolia; Lolium (e.g. Lolium
perenne or Lolium multijlorum); Cryptomeria (Cryptomeriajaponicd); Alternaria (Alternaria
alternatd); Alder; Alnus (Alnus gultinoasa); Betula (Betula vermcosa); Quercus (Quercus
alba); Olea (Olea europa); Artemisia (Artemisia vulgaris); Plantago (e.g. Plantago
lanceolata); Parietaria (e.g. Parietaria offlcinalis or Parietariajudaicd); Blattella (e.g.
30 Blattella germanica); Apis (e.g. Apis multiflorum); Cupressus (e.g. Cupressus sempervirens,
Cupressus arizonica and Cupressus macrocarpa); Junipems (e.g. Juniperus sabinoides,
Juniperus virginiana, Juniperus communis and Juniperus ashei); Thuya (e.g. Thuya
orientalis); Chamaecyparis (e.g. Chamaecyparis obtusa); Periplaneta (e.g. Periplaneta
americana); Agropyron (e.g. Agropyron repens); Secale (e.g. Secale cereale); Triticum (e.g.
Triticum aestivum); Dactylis (e.g. Dactylis glomerata); Festuca (e.g. Festuca elatior); Poa
(e.g. Poapratensis or Poa compressa); Avena (e.g. Avena sativa); Holcus (e.g. Holcus
5 lanatus); Anthoxanthum (e.g. Anthoxanthum odoratum); Arrhenatherum (e.g. Arrhenatherum
elatius); Agrostis (e.g. Agrostis alba); Phleum (e.g. Phleum pratense); Phalaris (e.g. Phalaris
arundinacea); Paspalum (e.g. Paspalum notatum); Sorghum (e.g. Sorghum halepensis); and
Bromus (e.g. Bromus inermis).
The antigen may be an antigen that is encoded by a nucleic acid vector or it may be
10 not encoded in a nucleic acid vector. In the former case the nucleic acid vector is
administered to the subject and the antigen is expressed in vivo. In the latter case the antigen
may be administered directly to the subject. An antigen not encoded in a nucleic acid vector
as used herein refers to any type of antigen that is not a nucleic acid. For instance, in some
aspects of the invention the antigen not encoded in a nucleic acid vector is a polypeptide.
75 Minor modifications of the primary amino acid sequences of polypeptide antigens may also
result in a polypeptide which has substantially equivalent antigenic activity as compared to
the unmodified counterpart polypeptide. Such modifications may be deliberate, as by
site-directed mutagenesis, or may be spontaneous. All of the polypeptides produced by these
modifications are included herein as long as antigenicity still exists. The polypeptide may be,
20 for example, a viral polypeptide.
The term "substantially purified" as used herein refers to a polypeptide which is
substantially free of other proteins, lipids, carbohydrates or other materials with which it is
naturally associated. One skilled in the art can purify viral or bacterial polypeptides using
standard techniques for protein purification. The substantially pure polypeptide will often
25 yield a single major band on a non-reducing polyacrylamide gel. In the case of partially
glycosylated polypeptides or those that have several start codons, there may be several bands
on a non-reducing polyacrylamide gel, but these will form a distinctive pattern for that
polypeptide. The purity of the viral or bacterial polypeptide can also be determined by
ammo-terminal amino acid sequence analysis. Other types of antigens not encoded by a
30 nucleic acid vector such as polysaccharides, small molecule, mimics etc are described above,
and included within the invention.
The invention also utilizes polynucleotides encoding the antigenic polypeptides. It is
envisioned that the antigen may be delivered to the subject in a nucleic acid molecule which
encodes for the antigen such that the antigen must be expressed in vivo. Such antigens
delivered to the subject in a nucleic acid vector are referred to as antigens encoded by a
5 nucleic acid vector. The nucleic acid encoding the antigen is operatively linked to a gene
expression sequence which directs the expression of the antigen nucleic acid within a
eukaryotic cell. The gene expression sequence is any regulatory nucleotide sequence, such as
a promoter sequence or promoter-enhancer combination, which facilitates the efficient
transcription and translation of the antigen nucleic acid to which it is operatively linked. The
10 gene expression sequence may, for example, be a mammalian or viral promoter, such as a
constitutive or inducible promoter. Constitutive mammalian promoters include, but are not
limited to, the promoters for the following genes: hypoxanthine phosphoribosyl transferase
(KPTR), adenosine deaminase, pyruvate kinase, b-actin promoter and other constitutive
promoters. Exemplary viral promoters which function constitutively in eukaryotic cells
15 include, for example, promoters from the cytomegalovirus (CMV), simian virus (e.g., SV40),
papilloma virus, adenovirus, human immunodeficiency virus (HIV), Rous sarcoma virus,
cytomegalovirus, the long terminal repeats (LTR) of Moloney leukemia virus and other
retro viruses, and the thymidine kinase promoter of herpes simplex virus. Other constitutive
promoters are known to those of ordinary skill in the art. The promoters useful as gene
20 expression sequences of the invention also include inducible promoters. Inducible promoters
are expressed in the presence of an inducing agent. For example, the metallothionein
promoter is induced to promote transcription and translation in the presence of certain metal
ions. Other inducible promoters are known to those of ordinary skill in the art.
In general, the gene expression sequence shall include, as necessary, 5'
25 non-transcribing and 5' non-translating sequences involved with the initiation of transcription
and translation, respectively, such as a TATA box, capping sequence, CAAT sequence, and
the like. Especially, such 5' non-transcribing sequences will include a promoter region which
includes a promoter sequence for transcriptional control of the operably joined antigen nucleic
acid. The gene expression sequences optionally include enhancer sequences or upstream
30 activator sequences as desired.
The antigen nucleic acid is operatively linked to the gene expression sequence. As
used herein, the antigen nucleic acid sequence and the gene expression sequence are said to be
operably linked when they are covalently linked in such a way as to place the expression or
transcription and/or translation of the antigen coding sequence under the influence or control
of the gene expression sequence. Two DNA sequences are said to be operably linked if
induction of a promoter in the 5' gene expression sequence results in the transcription of the
5 antigen sequence and if the nature of the linkage between the two DNA sequences does not
(1) result in the introduction of a frame-shift mutation, (2) interfere with the ability of the
promoter region to direct the transcription of the antigen sequence, or (3) interfere with the
ability of the corresponding RNA transcript to be translated into a protein. Thus, a gene
expression sequence would be operably linked to an antigen nucleic acid sequence if the gene
10 expression sequence were capable of effecting transcription of that antigen nucleic acid
sequence such that the resulting transcript is translated into the desired protein or polypeptide.
The antigen nucleic acid of the invention may be delivered to the immune system
alone or in association with a vector. In its broadest sense, a vector is any vehicle capable of
facilitating the transfer of the antigen nucleic acid to the cells of the immune system so that
15 the antigen can be expressed and presented on the surface of the immune cell. The vector
generally transports the nucleic acid to the immune cells with reduced degradation relative to
the extent of degradation that would result in the absence of the vector. The vector optionally
includes the above-described gene expression sequence to enhance expression of the antigen
nucleic acid in immune cells. In general, the vectors useful in the invention include, but are
20 not limited to, plasmids, phagemids, viruses, other vehicles derived from viral or bacterial
sources that have been manipulated by the insertion or incorporation of the antigen nucleic
acid sequences. Viral vectors are a preferred type of vector and include, but are not limited
to, nucleic acid sequences from the following viruses: retrovirus, such as Moloney murine
leukemia virus, Harvey murine sarcoma virus, murine mammary tumor virus, and Rous
25 sarcoma virus; adenovirus, adeno-associated virus; SV40-type viruses; polyoma viruses;
Epstein-Barr viruses; papilloma viruses; herpes virus; vaccinia virus; polio virus; and RNA
virus such as a retrovirus. One can readily employ other vectors not named but known in the
art.
Preferred viral vectors are based on non-cytopathic eukaryotic viruses in which
30 non-essential genes have been replaced with the gene of interest. Non-cytopathic viruses
include retroviruses, the life cycle of which involves reverse transcription of genomic viral
RNA into DNA with subsequent proviral integration into host cellular DNA. Retroviruses
have been approved for human gene therapy trials. Most useful are those retroviruses that are
replication-deficient (i.e., capable of directing synthesis of the desired proteins, but incapable
of manufacturing an infectious particle). Such genetically altered retroviral expression
vectors have general utility for the high-efficiency transduction of genes in vivo. Standard
5 protocols for producing replication-deficient retroviruses (including the steps of incorporation
of exogenous genetic material into a plasmid, transfection of a packaging cell lined with
plasmid, production of recombinant retroviruses by the packaging cell line, collection of viral
particles from tissue culture media, and infection of the target cells with viral particles) are
provided in Rriegler, M., Gene Transfer and Expression, A Laboratory Manual W.H.
10 Freeman CO., New York (1990) and Murry, E.J. Methods in Molecular Biology, vol. 7,
Humana Press, Inc., Cliffton, New Jersey (1991).
A preferred virus for certain applications is the adeno-associated virus, a
double-stranded DNA virus. The adeno-associated virus can be engineered to be replication
-deficient and is capable of infecting a wide range of cell types and species. It further has
15 advantages such as, heat and lipid solvent stability; high transduction frequencies in cells of
diverse lineages, including hemopoietic cells; and lack of superinfection inhibition thus
allowing multiple series of transductions. Reportedly, the adeno-associated virus can
integrate into human cellular DNA in a site-specific manner, thereby minimizing the
possibility of insertional mutagenesis and variability of inserted gene expression characteristic
20 of retroviral infection. In addition, wild-type adeno-associated virus infections have been
followed in tissue culture for greater than 100 passages hi the absence of selective pressure,
implying that the adeno-associated virus genomic integration is a relatively stable event. The
adeno-associated virus can also function in an extrachromosomal fashion.
Other vectors include plasmid vectors. Plasmid vectors have been extensively
25 described in the art and are well-known to those of skill in the art. See e.g., Sambrook et al.,
Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory
Press, 1989. In the last few years, plasmid vectors have been found to be particularly
advantageous for delivering genes to cells in vivo because of their inability to replicate within
and integrate into a host genome. These plasmids, however, having a promoter compatible
30 with the host cell, can express a peptide from a gene operatively encoded within the plasmid.
Some commonly used plasmids include pBR322, pUC18, pUC19, pRC/CMV, SV40, and
pBlueScript. Other plasmids are well-known to those of ordinary skill in the art.
Additionally, plasmids may be custom designed using restriction enzymes and ligation
reactions to remove and add specific fragments of DNA.
It has recently been discovered that gene carrying plasmids can be delivered to the
immune system using bacteria. Modified forms of bacteria such as Salmonella can be
J transfected with the plasmid and used as delivery vehicles. The bacterial delivery vehicles
can be administered to a host subject orally or by other administration means. The bacteria
deliver the plasmid to immune cells, e.g. B cells, dendritic cells, likely by passing through the
gut barrier. High levels of immune protection have been established using this methodology.
Such methods of delivery are useful for the aspects of the invention utilizing systemic
10 delivery of antigen, Immunostimulatory nucleic acid and/or other therapeutic agent.
Thus, in addition to being suitable as stand alone agents, the immunostimulatory
nucleic acids are useful, inter alia, as vaccine adjuvants. It was previously established that
CpG oligonucleotides are excellent vaccine adjuvants. In order to identify the best
immunostimulatory nucleic acids for use as a vaccine adjuvant in humans and other non-
75 rodent animals, in vivo screening of different nucleic acids for this purpose was conducted.
Several in vitro assays were evaluated in mice for their predictive value of adjuvant activity in
vivo. During the course of this study, an in vitro test that is predictive of in vivo efficacy was
identified. It was discovered, rather surprisingly, that both B cell and NK cell activation
correlated particularly well with the ability of an immunostimulatory nucleic acid to enhance
20 an in vivo immune response against an antigen.
The nucleic acids are also useful for improving survival, differentiation, activation and
maturation of dendritic cells. The immunostimulatory nucleic acids have the unique
capability to promote cell survival, differentiation, activation and maturation of dendritic
cells. Dendritic precursor cells isolated from blood by immunomagnetic cell sorting develop
25 morphologic and functional characteristics of dendritic cells during a two day incubation with
GM-CSF. Without GM-CSF these cells undergo apoptosis. The immunostimulatory nucleic
acids are superior to GM-CSF in promoting survival and differentiation of dendritic cells
(MHCII expression, cell size, granularity). The immunostimulatory nucleic acids also induce
maturation of dendritic cells. Since dendritic cells form the link between the innate and the
30 acquired immune system, by presenting antigens as well as through their expression of pattern
recognition receptors which detect microbial molecules like LPS in their local environment,
the ability to activate dendritic cells with immunostimulatory nucleic acids supports the use of
these immunostimulatory nucleic acid based strategies for in vivo and ex-vivo immunotherapy
against disorders such as cancer and allergic or infectious diseases. The immunostimulatory
nucleic acids are also useful for activating and inducing maturation of dendritic cells.
Immunostimulatory nucleic acids also increase natural killer cell lyric activity and
5 antibody dependent cellular cytotoxicity (ADCC). ADCC can be performed using a
immunostimulatory nucleic acid in combination with an antibody specific for a cellular target,
such as a cancer cell. When the immunostimulatory nucleic acid is administered to a subject
in conjunction with the antibody the subject's immune system is induced to kill the tumor
cell. The antibodies useful in the ADCC procedure include antibodies which interact with a
10 cell in the body. Many such antibodies specific for cellular targets have been described in the
art and many are commercially available. Examples of these antibodies are listed below
among the list of cancer immunotherapies.
The nucleic acids are also useful for redirecting an immune response from a Th2
immune response to a Thl immune response. Redirection of an immune response from a Th2
IS to a Thl immune response can be assessed by measuring the levels of cytokines produced in
response to the nucleic acid (e.g., by inducing monocytic cells and other cells to produce Thl
cytokines, including IL-12, IFN-y and GM-CSF). The redirection or rebalance of the immune
response from a Th2 to a Thl response is particularly useful for the treatment or prevention of
asthma. For instance, an effective amount for treating asthma can be that amount; useful for
20 redirecting a Th2 type of immune response that is associated with asthma to a Thl type of
response. Th2 cytokines, especially IL-4 and IL-5 are elevated in the airways of asthmatic
subjects. These cytokines promote important aspects of the asthmatic inflammatory response,
including IgE isotype switching, eosinophil chemotaxis and activation and mast cell growth.
Till cytokines, especially IFN-y and IL-12, can suppress the formation of Th2 clones and
25 production of Th2 cytokines. The immunostimulatory nucleic acids of the invention cause an
increase in Thl cytokines which helps to rebalance the immune system, preventing or
reducing the adverse effects associated with a predominately Th2 immune response.
The invention also includes a method for inducing antigen non-specific innate immune
activation and broad spectrum resistance to infectious challenge using the immunostimulatory
30 nucleic acids. The term antigen non-specific innate immune activation as used herein refers
to the activation of immune cells other than B cells and for instance can include the activation
of NK cells, T cells or other immune cells that can respond in an antigen independent fashion
or some combination of these cells. A broad spectrum resistance to infectious challenge is
induced because the immune cells are in active form and are primed to respond to any
invading compound or microorganism. The cells do not have to be specifically primed
against a particular antigen. This is particularly useful in biowarfare, and the other
5 circumstances described above such as travelers.
The nucleic acids of the invention can be used in combination with other therapeutic
agents including anti-microbial agents, adjuvants, cytokines, anti-cancer therapies, allergy
medicaments, asthma medicaments, and the like.
The nucleic acids of the invention may be administered to a subject with an anti-
10 microbial agent. An anti-microbial agent, as used herein, refers to a naturally-occurring or
synthetic compound which is capable of killing or inhibiting infectious microorganisms. The
type of anti-microbial agent useful according to the invention will depend upon the type of
microorganism with which the subject is infected or at risk of becoming infected. Anti-
microbial agents include but are not limited to anti-bacterial agents, anti-viral agents, anti-
15 fungal agents and anti-parasitic agents. Phrases such as "anti-infective agent", "anti-bacterial
agent", "anti-viral agent", "anti-fungal agent", "anti-parasitic agent" and "parasiticide" have
well-established meanings to those of ordinary skill in the art and are defined in standard
medical texts. Briefly, anti-bacterial agents kill or inhibit bacteria, and include antibiotics as
well as other synthetic or natural compounds having similar functions.
20 Antibiotics are low molecular weight molecules which are produced as secondary
metabolites by cells, such as microorganisms. In general, antibiotics interfere with one or
more bacterial functions or structures which are specific for the microorganism and which are
not present in host cells. Anti-viral agents can be isolated from natural sources or synthesized
and are useful for killing or inhibiting viruses. Anti-fungal agents are used to treat superficial
25 fungal infections as well as opportunistic and primary systemic fungal infections. Anti-
parasite agents kill or inhibit parasites.
Antibacterial agents kill or inhibit the growth or function of bacteria. A large class of
antibacterial agents is antibiotics. Antibiotics, which are effective for killing or inhibiting a
wide range of bacteria, are referred to as broad spectrum antibiotics. Other types of
30 antibiotics are predominantly effective against the bacteria of the class gram-positive or gram-
negative. These types of antibiotics are referred to as narrow spectrum antibiotics.
Other antibiotics which are effective against a single organism or disease and not
against other types of bacteria, are referred to as limited spectrum antibiotics. Antibacterial
agents are sometimes classified based on their primary mode of action. In general,
antibacterial agents are cell wall synthesis inhibitors, cell membrane inhibitors, protein
synthesis inhibitors, nucleic acid synthesis or functional inhibitors, and competitive inhibitors.
5 Anti-bacterial agents useful in the invention include but are not limited to natural
penicillins, semi-synthetic penicillins, clavulanic acid, cephalolsporins, bacitracin, ampicillin,
carbenicillin, oxacillin, azlocillin, mezlocillin, piperaciUin, methicillin, dicloxacillin, nafcillin,
cephalothin, cephapirin, cephalexin, cefamandole, cefaclor, cefazolin, cefuroxine, cefoxitin,
cefotaxime, cefsulodin, cefetamet, cefixime, ceftriaxone, cefoperazone, ceftazidine,
JO moxalactam, carbapenems, imipenems, monobactems, euztreonam, vancomycin, polymyxin,
amphotericin B, nystatin, imidazoles, clotrimazole, miconazole, ketoconazole, itraconazole,
fluconazole, rifampins, ethambutol, tetracyclines, chloramphenicol, macrolides,
aminoglycosides, streptomycin, kanamycin, tobramycin, amikacin, gentamicin, tetracycline,
minocycline, doxycycline, chlortetracycline, erythromycin, roxithromycin, clarithromycin,
15 oleandomycin, azithromycin, chloramphenicol, quinolones, co-trimoxazole, norfloxacin,
ciprofloxacin, enoxacin, nalidixic acid, temafloxacin, sulfonamides, gantrisin, and
trimethoprim; Acedapsone ; Acetosulfone Sodium; Alamecin; Alexidine; Amdinocillin;
Amdinocillin Pivoxil; Amicycline; Amifloxacin; Amifloxacin Mesylate; Amikacin; Amikacin
Sulfate; Aminosalicylic acid; Aminosalicylate sodium; Amoxicillin; Amphomycin;
20 Ampicillin; Ampicillin Sodium; Apalcillin Sodium; Apramycin; Aspartocin; Astromicin
Sulfate; Avilamycin; Avoparcin; Azithromycin; Azlocillin; Azlocillin Sodium; Bacampicillin
Hydrochloride; Bacitracin; Bacitracin Methylene Disalicylate; Bacitracin Zinc;
Bambermycins; Benzoylpas Calcium; Berythromycin; Betamicin Sulfate; Biapenem;
Biniramycin; Biphenamine Hydrochloride ; Bispyritlhione Magsulfex; Butikacin; Butirosin
25 Sulfate; Capreomycin Sulfate; Carbadox; Carbenicillin Disodium; Carbenicillin Indanyl
Sodium; Carbenicillin Phenyl Sodium; Carbenicillin Potassium; Carumonam Sodium;
Cefaclor; Cefadroxil; Cefamandole; Cefamandole Nafate; Cefamandole Sodium; Cefaparole;
Cefatrizine; Cefazaflur Sodium; Cefazolin; Cefazolin Sodium; Cefbuperazone; Cefdinir;
Cefepime; Cefepime Hydrochloride; Cefetecol; Cefixime; Cefmenoxime Hydrochloride;
30 Cefinetazole; Cefmetazole Sodium; Cefonicid Monosodium; Cefonicid Sodium;
Cefoperazone Sodium; Ceforanide; Cefotaxime Sodium; Cefotetan; Cefotetan Disodium;
Cefotiam Hydrochloride; Cefoxitin; Cefoxitin Sodium; Cefpitnizole; Cefpimizole Sodium;
Cefpiramide; Cefpiramide Sodium; Cefpirome Sulfate; Cefpodoxime Proxetil; Cefprozil;
Cefroxadine; Cefsulodin Sodium; Ceftazidime; Ceftibuten; Ceflizoxime Sodium; Ceftriaxone
Sodium; Cefuroxime; Cefuroxime Axetil; Cefuroxime Pivoxetil; Cefuroxime Sodium;
Cephacetrile Sodium; Cephalexin; Cephalexin Hydrochloride; Cephaloglycin; Cephaloridine;
5 Cephalothm Sodium; Cephapirin Sodium; Cephradine; Cetocycline Hydrochloride;
Cetophenicol; Chloramphenicol; Chloramphenicol Palmitate; Chloramphenicol Pantothenate
Complex ; Chloramphenicol Sodium Succinate; Chlorhexidine Phosphanilate; Chloroxylenol;
Chlortetracycline Bisulfate ; Chlortetracycline Hydrochloride ; Cinoxacin; Ciprofloxacin;
Ciprofloxacin Hydrochloride; Cirolemycin; Clarithromycin; Clinafloxacin Hydrochloride;
10 Clindamycin; Clindamycin Hydrochloride; Clindamycin Pahnitate Hydrochloride;
Clindamycin Phosphate; Clofazimine ; Cloxacillin Benzathine; Cloxacillin Sodium;
Cloxyquin; Colistimethate Sodium; Colistin Sulfate; Coumermycin; Coumermycin Sodium;
Cyclacillin; Cycloserine; Dalfopristin; Dapsone; Daptomycin; Demeclocycline;
Demeclocycline Hydrochloride; Demecycline; Denofungin; Diaveridine; Dicloxacillin;
75 Dicloxacillin Sodium; Dihydrostreptomycin Sulfate; Dipyrithione; Dirithromycin;
Doxycycline; Doxycycline Calcium; Doxycycline Fosfatex; Doxycycline Hyclate; Droxacin
Sodium; Enoxacin; Epicillin; Epitetracycline Hydrochloride; Erythromycin; Erythromycin
Acistrate; Erythromycin Estolate; Erythromycin Ethylsuccinate; Erythromycin Gluceptate;
Erythromycin Lactobionate; Erythromycin Propionate; Erythromycin Stearate; Ethambutol
20 Hydrochloride; Ethionamide; Fleroxacin; Floxacillin; Fludalanine; Flumequine; Fosfomycin;
Fosfomycin Trometliamine; Fumoxicillin; Furazolium Chloride; Furazolium Tartrate;
Fusidate Sodium; Fusidic Acid; Gentamicin Sulfate; Gloximonam; Gramicidin; Haloprogin;
Hetacillin; Hetacillin Potassium; Hexedine; Ibafloxacin; Imipenem; Isoconazole; Isepamicin;
Isoniazid; Josamycin; Kanamycin Sulfate; Kitasamycin; Levofuraltadone; Levopropylcillin
25 Potassium; Lexithromycin; Lincomycin; Lincomycin Hydrochloride; Lomefloxacin;
Lomefloxacin Hydrochloride; Lomefloxacin Mesylate; Loracarbef; Mafenide; Meclocycline;
Meclocycline Sulfosalicylate; Megalomicin Potassium Phosphate; Mequidox; Meropenem;
Methacycline; Methacycline Hydrochloride; Methenamine; Methenamine Hippurate;
Methenamine Mandelate; Methicillin Sodium; Metioprim; Metronidazole Hydrochloride;
30 Metronidazole Phosphate; Mezlocillin; Mezlocillin Sodium; Minocycline; Minocycline
Hydrochloride; Mirincamycin Hydrochloride ; Monensin; Monensin Sodium ; Nafcillin
Sodium; Nalidixate Sodium; Nalidixic Acid; Natamycin; Nebramycin; Neomycin Palmitate;
Neomycin Sulfate; Neomycin Undecylenate; Netilmicin Sulfate; Neutramycin; Nifuradene;
Nifuraldezone; Nifuratel; Nifuratrone; Nifurdazil; Nifurimide; Nifurpirinol; Nifurquinazol;
Nifurthiazole; Nitrocycline; Nitrofurantoin; Nitromide; Norfloxacin; Novobiocin Sodium;
Ofloxacin; Ormetoprim; Oxacillin Sodium; Oximonam; Oximonam Sodium; Oxolinic Acid;
5 Oxytetracycline; Oxytetracycline Calcium; Oxytetracycline Hydrochloride; Paldimycin;
Parachlorophenol; Paulomycin; Pefloxacin; Pefloxacin Mesylate; Penamecillin; Penicillin G
Benzathine; Penicillin G Potassium; Penicillin G Procaine; Penicillin G Sodium; Penicillin V;
Penicillin V Benzathine; Penicillin V Hydrabamine; Penicillin V Potassium; Pentizidone
Sodium; Phenyl Aminosalicylate; Piperacillin Sodium; Pirbenicillin Sodium; Piridicillin
10 Sodium; Pirlimycin Hydrochloride; Pivampicillin Hydrochloride; Pivampicillin Pamoate;
Pivampicillin Probenate; Polymyxin B Sulfate; Porfiromycin; Propilcacin; Pyrazinamide;
Pyrithione Zinc; Quindecamine Acetate; Quinupristin; Racephenicol; Ramoplanin;
Ranimycin; Relomycin; Repromicin; Rifabutin; Rifametane; Rifamexil; Rifamide; Rifampin;
Rifapentine; Rifaximin; Rolitetracycline; Rolitetracycline Nitrate; Rosaramicin; Rosaramicin
15 Butyrate; Rosaramicin Propionate; Rosaramicin Sodium Phosphate; Rosaramicin Stearate;
Rosoxacin; Roxarsone; Roxithromycin; Sancycline; Sanfetrinem Sodium; Sarmoxicillin;
Sarpicillin; Scopafungin ; Sisomicin; Sisomicin Sulfate; Sparfloxacin; Spectinomycin
Hydrochloride; Spiramycin; Stalh'mycin Hydrochloride; Steffimycin; Streptomycin Sulfate;
Streptonicozid; Sulfabenz ; Sulfabenzamide; Sulfacetamide; Sulfacetamide Sodium;
20 Sulfacytine; Sulfadiazine; Sulfadiazine Sodium; Sulfadoxine; Sulfalene; Sulfamerazine;
Sulfameter; Sulfamethazine; Sulfamethizole; Sulfamethoxazole; Sulfamonomethoxine;
Sulfamoxole; Sulfanilate Zinc; Sulfanitran; Sulfasalazine; Sulfasomizole; Sulfathiazole;
Sulfazamet; Sulfisoxazole; Sulfisoxazole Acetyl; Sulfisoxazole Diolamine; Sulfomyxin;
Sulopenem; Sultamicillin; Suncillin Sodium; Talampicillin Hydrochloride; Teicoplanin;
25 Temafloxacin Hydrochloride; Temocillin; Tetracycline; Tetracycline Hydrochloride;
Tetracycline Phosphate Complex; Tetroxoprim; Thiamphenicol; Thiphencillin Potassium;
Ticarcillm Cresyl Sodium; Ticarcillin Disodium; Ticarcillin Monosodium; Ticlatone;
Tiodonium Chloride; Tobramycin; Tobramycin Sulfate; Tosufioxacin; Trimethoprim;
Trinethoprim Sulfate; Trisulfapyrimidines; Troleandomycin; Trospectomycin Sulfate;
30 Tyrothricin; Vancomycin; Vancomycin Hydrochloride; Virginiamycin; and Zorbamycin.
Antiviral agents are compounds which prevent infection of cells by viruses or
replication of the virus within the cell. There are many fewer antiviral drugs than
antibacterial drugs because the process of viral replication is so closely related to DNA
replication within the host cell, that non-specific antiviral agents would often be toxic to the
host. There are several stages within the process of viral infection which can be blocked or
inhibited by antiviral agents. These stages include, attachment of the virus to the host cell
5 (immunoglobulin or binding peptides), uncoating of the virus (e.g. amantadine), synthesis or
translation of viral mRNA (e.g. interferon), replication of viral RNA or DNA (e.g. nucleoside
analogues), maturation of new virus proteins (e.g. protease inhibitors), and budding and
release of the virus.
Nucleotide analogues are synthetic compounds which are similar to nucleotides, but
10 which have an incomplete or abnormal deoxyribose or ribose group. Once the nucleotide
analogues are in the cell, they are phosphorylated, producing the triphosphate formed which
competes with normal nucleotides for incorporation into the viral DNA or RNA. Once the
triphosphate form of the nucleotide analogue is incorporated into the growing nucleic acid
chain, it causes irreversible association with the viral polymerase and thus chain termination.
75 Nucleotide analogues include, but are not limited to, acyclovir (used for the treatment of
herpes simplex virus and varicella-zoster virus), gancyclovir (useful for the treatment of
cytomegalovirus), idoxuridine, ribavirin (useful for the treatment of respiratory syncitial
virus), dideoxyinosine, dideoxycytidine, and zidovudine (azidothymidine).
The interferons are cytokines which are secreted by virus-infected cells as well as immune
20 cells. The interferons function by binding to specific receptors on cells adjacent to the
infected cells, causing the change in the cell which protects it from infection by the virus, a
and p-interferon also induce the expression of Class I and Class IIMHC molecules on the
surface of infected cells, resulting in increased antigen presentation for host immune cell
recognition, a and P-interferons are available as recombinant forms and have been used for
25 the treatment of chronic hepatitis B and C infection. At the dosages which are effective for
anti-viral therapy, interferons have severe side effects such as fever, malaise and weight loss.
Immunoglobulin therapy is used for the prevention of viral infection.
Immunoglobulin therapy for viral infections is different than bacterial infections, because
rather than being antigen-specific, the immunoglobulin therapy functions by binding to
30 extracellular virions and preventing them from attaching to and entering cells which are
susceptible to the viral infection. The therapy is useful for the prevention of viral infection for
the period of time that the antibodies are present in the host. In general there are two types of
immunoglobulin therapies, normal immunoglobulin therapy and hyper-imrnunoglobulin
therapy. Nonnal immune globulin therapy utilizes a antibody product which is prepared from
the serum of normal blood donors and pooled. This pooled product contains low titers of
antibody to a wide range of human viruses, such as hepatitis A, parvovirus, enterovirus
5 (especially in neonates). Hyper-immune globulin therapy utilizes antibodies which are
prepared from the serum of individuals who have high titers of an antibody to a particular
virus. Those antibodies are then used against a specific virus. Examples of hyper-immune
globulins include zoster immune globulin (useful for the prevention of varicella in immuno-
compromised children and neonates), human rabies immunoglobulin (useful in the post-
70 exposure prophylaxis of a subject bitten by a rabid animal), hepatitis B immune globulin
(useful in the prevention of hepatitis B virus, especially in a subject exposed to the virus), and
RSV immune globulin (useful in the treatment of respiratory syncitial virus infections).
Another type of immunoglobulin therapy is active immunization. This involves the
administration of antibodies or antibody fragments to viral surface proteins. Two types of
15 vaccines which are available for active immunization of hepatitis B include serum-derived
hepatitis B antibodies and recombinant hepatitis B antibodies. Both are prepared from
HBsAg. The antibodies are administered in three doses to subjects at high risk of infection
with hepatitis B virus, such as health care workers, sexual partners of chronic carriers, and
infants.
20 Thus, anti-viral agents useful in the invention include but are not limited to
immunoglobulins, amantadine, interferon, nucleoside analogues, and protease inhibitors.
Specific examples of anti-virals include but are not limited to Acemannan; Acyclovir;
Acyclovir Sodium; Adefovir; Alovudine; Alvircept Sudotox; Amantadine Hydrochloride;
Aranotin; Arildone; Atevirdine Mesylate; Avridine; Cidofovir; Cipamfylline; Cytarabine
25 Hydrochloride; Delavirdine Mesylate; Desciclovir; Didanosine; Disoxaril; Edoxudine;
Enviradene; Enviroxime; Famciclovir; Famotine Hydrochloride; Fiacitabine; Fialuridine;
Fosarilate; Foscarnet Sodium; Fosfonet Sodium; Ganciclovir; Ganciclovir Sodium;
Idoxuridine; Kethoxal; Lamivudine; Lobucavir; Memotine Hydrochloride; Methisazone;
Nevirapine; Penciclovir; Pirodavir; Ribavirin; Rimantadine Hydrochloride; Saquinavir
30 Mesylate; Somantadine Hydrochloride; Sorivudine; Statolon; Stavudine; Tilorone
Hydrochloride; Trifluridine; Valacyclovir Hydrochloride; Vidarabine; Vidarabine Phosphate;
Vidarabine Sodium Phosphate; Viroxime; Zalcitabine; Zidovudine; and Zinviroxime.
Anti-fungal agents are useful for the treatment and prevention of infective fungi.
Anti-fungal agents are sometimes classified by their mechanism of action. Some anti-fungal
agents function as cell wall inhibitors by inhibiting glucose synthase. These include, but are
not limited to, basiungin/ECB. Other anti-fungal agents function by destabilizing membrane
integrity. These include, but are not limited to, immidazoles, such as clotrimazole,
sertaconzole, fluconazole, itraconazole, ketoconazole, miconazole, and voriconacole, as well
as FK 463, amphotericin B, BAY 38-9502, MK 991, pradimicin, UK 292, butenafine, and
terbinafine. Other anti-fungal agents function by breaking down chitin (e.g. chitinase) or
immunosuppression (501 cream). Some examples of commercially-available agents are
shown in Table 3.

Thus, the anti-fungal agents useful in the invention include but are not limited to
imidazoles, FK 463, arnphotericin B, BAY 38-9502, MK 991, pradimicin, UK 292,
butenafine, chitinase, 501 cream, Acrisorcin; Ambruticin; Amorolfine, Amphotericin B;
Azaconazole; Azaserine; Basifungin; Bifonazole; Biphenamine Hydrochloride; Bispyrithione
Magsulfex; Butoconazole Nitrate; Calcium Undecylenate; Candicidin; Carbol-Fuchsin;
Clilordantoin; Ciclopirox; Ciclopirox Olamine; Cilofungin; Cisconazole; Clotrimazole;
Cuprimyxin; Denofungin; Dipyrithione; Doconazole; Econazole; Econazole Nitrate;
Enilconazole; Ethonam Nitrate; Fenticonazole Nitrate; Filipin; Fluconazole; Flucytosine;
Fungimycin; Griseofulvin; Hamycin; Isoconazole ; Itraconazole; Kalafungin; Ketoconazole;
Lomofungin; Lydimycin; Mepartricin; Miconazole; Miconazole Nitrate; Monensin ;
Monensin Sodium; Naftifine Hydrochloride; Neomycin Undecylenate ; Nifuratel;
Nifurmerone; Nitralamine Hydrochloride; Nystatin; Octanoic Acid; Orconazole Nitrate;
Oxiconazole Nitrate; Oxifungin Hydrochloride; Parconazole Hydrochloride; Partricin;
Potassium Iodide ; Proclonol; Pyrithione Zinc ; Pyrrolnitrin; Rutamycin; Sanguinarium
Chloride ; Saperconazole; Scopafungin; Selenium Sulfide ; Sinefungin; Sulconazole Nitrate;
Terbinafine; Terconazole; Thiram; Ticlatone ; Tioconazole; Tolciclate; Tolindate; Tolnaftate;
Triacetin; Triafungin; Undecylenic Acid; Viridofulvin; Zinc Undecylenate; and Zinoconazole
Hydrochloride.
Examples of anti-parasitic agents, also referred to as parasiticides useful for human
administration include but are not limited to albendazole, amphotericin B, benznidazole,
bithionol, chloroquine HC1, chloroquine phosphate, clindamycm, dehydroemetine,
diethylcarbamazine, diloxanide furoate, eflornithine, furazolidaone, glucocorticoids,
halofantrine, iodoquinol, ivermectin, mebendazole, mefloquine, meglumine antimoniate,
melarsoprol, metrifonate, metronidazole, niclosamide, nifurtimox, oxamniquine,
paromomycin, pentamidine isethionate, piperazine, praziquantel, primaquine phosphate,
proguanil, pyrantel pamoate, pyrimethanrnine-sulfonamides, pyrimethanmine-sulfadoxine,
quinacrine HC1, quinine sulfate, quinidine gluconate, spiramycin, stibogluconate sodium
(sodium antimony gluconate), suramin, tetracycHne, doxycycline, thiabendazole, tinidazole,
5 frirnethroprim-sulfamethoxazole, and tryparsamide some of which are used alone or in
combination with others.
Parasiticides used in non-human subjects include piperazine, diethylcarbamazine,
thiabendazole, fenbendazole, albendazole, oxfendazole, oxibendazole, febantel, levamisole,
pyrantel tartrate, pyrantel pamoate, dichlorvos, ivermectin, doramectic, milbemycin oxime,
10 iprinomectin, moxidectin, N-butyl chloride, toluene, hygromycin B thiacetarsemide sodium,
melarsomine, praziquantel, epsiprantel, benzimidazoles such as fenbendazole, albendazole,
oxfendazole, clorsulon, albendazole, amprolium; decoquinate, lasalocid, monensin
sulfadimethoxine; sulfamethazine, sulfaquinoxaline, metronidazole.
Parasiticides used in horses include mebendazole, oxfendazole, febantel, pyrantel,
15 dichlorvos, trichlorfon, ivermectin, piperazine; for & westeri: ivermectin, benzimiddazoles
such as thiabendazole, cambendazole, oxibendazole and fenbendazole. Useful parasiticides in
dogs include milbemycin oxine, ivermectin, pyrantel pamoate and the combination of
ivermectin and pyrantel. The treatment of parasites in swine can include the use of
levamisole, piperazine, pyrantel, thiabendazole, dichlorvos and fenbendazole. In sheep and
20 goats anthelmintic agents include levamisole or ivermectin. Caparsolate has shown some
efficacy in the treatment of D. immitis (heartworm) in cats.
The immunostimulatory nucleic acids may also be administered in conjunction with an
anti-cancer therapy. Anti-cancer therapies include cancer medicaments, radiation and
surgical procedures. As used herein, a "cancer medicament" refers to a agent which is
25 administered to a subject for the purpose of treating a cancer. As used herein, "treating
cancer" includes preventing the development of a cancer, reducing the symptoms of cancer,
and/or inhibiting the growth of an established cancer. In other aspects, the cancer
medicament is administered to a subject at risk of developing a cancer for the purpose of
reducing the risk of developing the cancer. Various types of medicaments for the treatment of
30 cancer are described herein. For the purpose of this specification, cancer medicaments are
classified as chemotherapeutic agents, immunotherapeutic agents, cancer vaccines, hormone
therapy, and biological response modifiers.
As used herein, a "cancer medicament" refers to an agent which is administered to a
subject for the purpose of treating a cancer. As used herein, "treating cancer" includes
preventing the development of a cancer, reducing the symptoms of cancer, and/or inhibiting
the growth of an established cancer. In other aspects, the cancer medicament is administered
5 to a subject at risk of developing a cancer for the purpose of reducing the risk of developing
the cancer. Various types of medicaments for the treatment of cancer are described herein.
For the purpose of this specification, cancer medicaments are classified as chemotherapeutic
agents, immunotherapeutic agents, cancer vaccines, hormone therapy, and biological response
modifiers. Additionally, the methods of the invention are intended to embrace the use of
10 more than one cancer medicament along with the imrnunostimulatory nucleic acids. As an
example, where appropriate, the immunostimulatory nucleic acids may be administered with a
both a chemotherapeutic agent and an immunotherapeutic agent. Alternatively, the cancer
medicament may embrace an immunotherapeutic agent and a cancer vaccine, or a
chemotherapeutic agent and a cancer vaccine, or a chemotherapeutic agent, an
15 immunotherapeutic agent and a cancer vaccine all administered to one subject for the purpose
of treating a subject having a cancer or at risk of developing a cancer.
Cancer medicaments function in a variety of ways. Some cancer medicaments work
by targeting physiological mechanisms that are specific to tumor cells. Examples include the
targeting of specific genes and their gene products (i.e., proteins primarily) which are mutated
20 in cancers. Such genes include but are not limited to oncogenes (e.g., Ras, Her2, bcl-2),
tumor suppressor genes (e.g., EGF, p53, Rb), and cell cycle targets (e.g., CDK4, p21,
telomerase). Cancer medicaments can alternately target signal transduction pathways and
molecular mechanisms which are altered in cancer cells. Targeting of cancer cells via the
epitopes expressed on their cell surface is accomplished through the use of monoclonal
25 antibodies. This latter type of cancer medicament is generally referred to herein as
immunotherapy.
Other cancer medicaments target cells other than cancer cells. For example, some
medicaments prime the immune system to attack tumor cells (i.e., cancer vaccines). Still other
medicaments, called angiogenesis inhibitors, function by attacking the blood supply of solid
30 tumors. Since the most malignant cancers are able to metastasize (i.e., exist the primary
tumor site and seed a distal tissue, thereby forming a secondary tumor), medicaments that
impede this metastasis are also useful in the treatment of cancer. Angiogenic mediators
include basic FGF, VEGF, angiopoietins, angiostatin, endostatin, TNFa, TNP-470,
thrombospondin-1, platelet factor 4, CAI, and certain members of the integrin family of
proteins. One category of this type of medicament is a metalloproteinase inhibitor, which
inhibits the enzymes used by the cancer cells to exist the primary tumor site and extravasate
5 into another tissue.
Immunotherapeutic agents are medicaments which derive from antibodies or antibody
fragments which specifically bind or recognize a cancer antigen. As used herein a cancer
antigen is broadly defined as an antigen expressed by a cancer cell. Preferably, the antigen is
expressed at the cell surface of the cancer cell. Even more preferably, the antigen is one
10 which is not expressed by nonnal cells, or at least not expressed to the same level as in cancer
cells. Antibody-based immunotherapies may function by binding to the cell surface of a
cancer cell and thereby stimulate the endogenous immune system to attack the cancer cell.
Another way in which antibody-based therapy functions is as a delivery system for the
specific targeting of toxic substances to cancer cells. Antibodies are usually conjugated to
15 toxins such as ricin (e.g., from castor beans), calicheamicin and maytansinoids, to radioactive
isotopes such as Iodine-131 and Yttrium-90, to chemotherapeutic agents (as described herein),
or to biological response modifiers. In this way, the toxic substances can be concentrated in
the region of the cancer and non-specific toxicity to normal cells can be minimized. In
addition to the use of antibodies which are specific for cancer antigens, antibodies which bind
20 to vasculature, such as those which bind to endothelial cells, are also useful in the invention.
This is because generally solid tumors are dependent upon newly formed blood vessels to
survive, and thus most tumors are capable of recruiting and stimulating the growth of new
blood vessels. As a result, one strategy of many cancer medicaments is to attack the blood
vessels feeding a tumor and/or the connective tissues (or stroma) supporting such blood
25 vessels.
The use of immunostimulatory nucleic acids in conjunction with immunotherapeutic
agents such as monoclonal antibodies is able to increase long-term survival through a number
of mechanisms including significant enhancement of ADCC (as discussed above), activation
of natural killer (NK) cells and an increase in IFNa levels. The nucleic acids when used in
30 combination with monoclonal antibodies serve to reduce the dose of the antibody required to
achieve a biological result.
Examples of cancer immunotherapies which are currently being used or which are in
development are listed in Table 4.

Yet other types of chemotherapeutic agents which can be used according to the
invention include Airdnoglutethimide, Asparaginase, Busulfan, Carboplatin, Chlorombucil,
Cytarabine HCI, Dactinomycin, Daunorubicin HCI, Estrarnustine phosphate sodium,
Etoposide (VP16-213), Floxuridine, Fluorouracil (5-FU), Flutamide, Hydroxyurea
(hydroxycarbamide), Ifosfamide, Interferon Alfa-2a, Alfa-2b, Leuprolide acetate (LHRH-
releasing factor analogue), Lomustine (CCNU), Mechlorethamine HCI (nitrogen mustard),
Mercaptopurine, Mesna, Mitotane (o.p'-DDD), Mitoxantrone HCI, Octreotide, Plicamycin,
Procarbazine HCI, Streptozocin, Tamoxifen citrate, Thioguanine, Thiotepa, Vinblastine
sulfate, Amsacrine (m-AMSA), Azacitidine, Erthropoietin, Hexamethyhnelamine (HMM),
Interleukin 2, Mitoguazone (methyl-GAG; methyl glyoxal bis-guanylhydrazone; MGBG),
Pentostatin (2'deoxycoformycin), Semustine (methyl-CCNU), Teniposide (VM-26) and
Vindesine sulfate.
Cancer vaccines are medicaments which are intended to stimulate an endogenous
immune response against cancer cells. Currently produced vaccines predominantly activate
the humoral immune system (i.e., the antibody dependent immune response). Other vaccines
currently in development are focused on activating the cell-mediated immune system
including cytotoxic T lymphocytes which are capable of killing tumor cells. Cancer vaccines
generally enhance the presentation of cancer antigens to both antigen presenting cells (e.g.,
macrophages and dendritic cells) and/or to other immune cells such as T cells, B cells, and
NK cells.
Although cancer vaccines may take one of several forms, as discussed infra, their
purpose is to deliver cancer antigens and/or cancer associated antigens to antigen presenting
cells (APC) in order to facilitate the endogenous processing of such antigens by APC and the
ultimate presentation of antigen presentation on the cell surface in the context of MHC class I
molecules. One form of cancer vaccine is a whole cell vaccine which is a preparation of
cancer cells which have been removed from a subject, treated ex vivo and then reintroduced
as whole cells in the subject. Lysates of tumor cells can also be used as cancer vaccines to
elicit an immune response. Another form cancer vaccine is a peptide vaccine which uses
cancer-specific or cancer-associated small proteins to activate T cells. Cancer-associated
proteins are proteins which are not exclusively expressed by cancer cells (i.e., other normal
cells may still express these antigens). However, the expression of cancer-associated antigens
is generally consistently upregulated with cancers of a particular type. Yet another form of
5 cancer vaccine is a dendritic cell vaccine which includes whole dendritic cells which have
been exposed to a cancer antigen or a cancer-associated antigen in vitro. Lysates or
membrane fractions of dendritic cells may also be used as cancer vaccines. Dendritic cell
vaccines are able to activate antigen-presenting cells directly. Other cancer vaccines include
ganglioside vaccines, heat-shock protein vaccines, viral and bacterial vaccines, and nucleic
10 acid vaccines.
The use of immunostimulatory nucleic acids in conjunction with cancer vaccines
provides an improved antigen-specific humoral and cell mediated immune response, in
addition to activating NK cells and endogenous dendritic cells, and increasing IFNa levels.
This enhancement allows a vaccine with a reduced antigen dose to be used to achieve the
15 same beneficial effect. In some instances, cancer vaccines may be used along with adjuvants,
such as those described above.
Other vaccines take the form of dendritic cells which have been exposed to cancer
antigens in vitro, have processed the antigens and are able to express the cancer antigens at
their cell surface in the context of MHC molecules for effective antigen presentation to other
20 immune system cells.
The immunostimulatory nucleic acids are used in one aspect of the invention in
conjunction with cancer vaccines which are dendritic cell based. A dendritic cell is a
professional antigen presenting cell. Dendritic cells form the link between the innate and the
acquired immune system by presenting antigens and through their expression of pattern
25 recognition receptors which detect microbial molecules like LPS in their local environment.
Dendritic cells efficiently internalize, process, and present soluble specific antigen to which it
is exposed. The process of internalizing and presenting antigen causes rapid upregulation of
the expression of major histocompatibility complex (MHC) and costimulatory molecules, the
production of cytokines, and migration toward lymphatic organs where they are believed to be
30 involved in the activation of T cells.
Table 5 lists a variety of cancer vaccines which are either currently being used or are
in development.
As used herein, chemotherapeutic agents embrace all other fonns of cancer
medicaments which do not fall into the categories of immunotherapeutic agents or cancer
vaccines. Chemotherapeutic agents as used herein encompass both chemical and biological
agents. These agents function to inhibit a cellular activity which the cancer cell is dependent
upon for continued survival. Categories of chemotherapeutic agents include
alkylating/alkaloid agents, antimetabolites, hormones or hormone analogs, and miscellaneous
antineoplastic drugs. Most if not all of these agents are directly toxic to cancer cells and do
not require immune stimulation. Combination chemotherapy and immunostimulatory nucleic
acid administration increases the maximum tolerable dose of chemotherapy.
Chemotherapeutic agents which are currently in development or in use in a clinical
setting are shown in Table 6.

In one embodiment, the methods of the invention use irrununostimulatory nucleic
acids as a replacement to the use of IFNa therapy in the treatment of cancer. Currently, some
treatment protocols call for the use of IFNa. Since IFNa is produced following the
administration of some immunostimulatory nucleic acids, these nucleic acids can be used to
generate IFNa endogenously.
In another embodiment, the asthma/allergy medicament is a medicament selected from
the group consisting of PDE-4 inhibitor, bronchodilator/beta-2 agonist, K+ channel opener,
VLA-4 antagonist, neurokm antagonist, TXA2 synthesis inhibitor, xanthanine, arachidonic
acid antagonist, 5 lipoxygenase inhibitor, thromboxin A2 receptor antagonist, thromboxane
A2 antagonist, inhibitor of 5-lipox activation protein, and protease inhibitor, but is not so
limited. In some important embodiments, the asthma/allergy medicament is a
bronchodilator/beta-2 agonist selected from the group consisting of salmeterol, salbutamol,
terbutaline, D2522/formoterol, fenoterol, and orciprenaline.
In another embodiment, the asthma/allergy medicament is a medicament selected from
the group consisting of anti-histamines and prostaglandin inducers. In one embodiment, the
anti-histamine is selected from the group consisting of loratidine, cetirizine, buclizhie,
ceterizine analogues, fexofenadine, terfenadine, desloratadine, norastemizole, epinastine,
5 ebastine, ebastine, astemizole, levocabastine, azelastine, tranilast, terfenadine, mizolastine,
betatastine, CS 560, and HSR 609. In another embodiment, the prostaglandin inducer is S-
5751.
In yet another embodiment, the asthma/allergy medicament is selected from the group
consisting of steroids and immunomodulators. The immunomodulators may be selected from
10 the group consisting of anti-inflammatory agents, leukotriene antagonists, IL-4 muteins,
soluble IL-4 receptors, immunosuppressants, anti-IL-4 antibodies, IL-4 antagonists, anti-IL-5
antibodies, soluble EL-13 receptor-Fc fusion proteins, anti-IL-9 antibodies, CCR3 antagonists,
CCR5 antagonists, VLA-4 inhibitors, and downregulators of IgE, but are not so limited. In
one embodiment, the downregulator of IgE is an anti-IgE.
15 In another embodiment, the steroid is selected from the group consisting of
beclomethasone, fluticasone, tramcinolone, budesonide, and budesonide. In still a further
embodiment, the immunosuppressant is a tolerizing peptide vaccine.
In one embodiment, the immunostimulatory nucleic acid is administered concurrently
with the asthma/allergy medicament. In another embodiment, the subject is an
20 immunocompromised subject.
Immunostimulatory nucleic acids can be combined with yet other therapeutic agents
such as adjuvants to enhance immune responses. The immunostimulatory nucleic acid and
other therapeutic agent may be administered simultaneously or sequentially. When the other
therapeutic agents are administered simultaneously they can be administered in the same or
25 separate formulations, but are administered at the same time. The other therapeutic agents are
administered sequentially with one another and with immunostimulatory nucleic acid, when
the administration of the other therapeutic agents and the immunostimulatory nucleic acid is
temporally separated. The separation in time between the administration of these compounds
may be a matter of minutes or it may be longer. Other therapeutic agents include but are not
30 limited to adjuvants, cytokines, antibodies, antigens, etc.
The compositions of the invention may also comprise a non-nucleic acid adjuvants. A
non-nucleic acid adjuvant is any molecule or compound except for the immunostimulatory
nucleic acids described herein which can stimulate the humoral and/or cellular immune
response. Non-nucleic acid adjuvants include, for instance, adjuvants that create a depot
effect, immune stimulating adjuvants, and adjuvants that create a depot effect and stimulate
the immune system.
5 An adjuvant that creates a depot effect as used herein is an adjuvant that causes the
antigen to be slowly released in the body, thus prolonging the exposure of immune cells to the
antigen. This class of adjuvants includes but is not limited to alum (e.g., aluminum
hydroxide, aluminum phosphate); or emulsion-based formulations including mineral oil, non-
mineral oil, water-in-oil or oil-in-water-in oil emulsion, oil-in-water emulsions such as Seppic
10 ISA series of Montanide adjuvants (e.g., Montanide ISA 720, AirLiquide, Paris, France); MF-
59 (a squalene-in-water emulsion stabilized with Span 85 and Tween 80; Chiron Corporation,
Emeryville, CA; and PROVAX (an oil-in-water emulsion containing a stabilizing detergent
and a micelle-forming agent; IDEC, Pharmaceuticals Corporation, San Diego, CA).
An immune stimulating adjuvant is an adjuvant that causes activation of a cell of the
15 immune system. It may, for instance, cause an immune cell to produce and secrete cytokines.
This class of adjuvants includes but is not limited to saponins purified from the bark of the Q.
saponaria tree, such as QS21 (a glycolipid that elutes in the 21st peak with HPLC
fractionation; Aquila Biopharmaceuticals, Inc., Worcester, MA);
poly[di(carboxylatophenoxy)phosphazene (PCPP polymer; Virus Research Institute, USA);
20 derivatives of lipopolysaccharides such as monophosphoryl lipid A (MPL; Ribi
ImmunoChem Research, Inc., Hamilton, MT), muramyl dipeptide (MDP; Ribi) and threonyl-
muramyl dipeptide (t-MDP; Ribi); OM-174 (a glucosamine disaccharide related to lipid A;
OM Pharma SA, Meyrin, Switzerland); and Leishmania elongation factor (a purified
Leishmania protein; Corixa Corporation, Seattle, WA).
25 Adjuvants that create a depot effect and stimulate the immune system are those
compounds which have both of the above- identified functions. This class of adjuvants
includes but is not limited to ISCOMS (immunostimulating complexes which contain mixed
saponins, lipids and form virus-sized particles with pores that can hold antigen; CSL,
Melbourne, Australia); SB-AS2 (SmithKline Beecham adjuvant system #2 which is an oil-in-
30 water emulsion containing MPL and QS21: SmithKline Beecham Biologicals [SBB],
Rixensart, Belgium); SB-AS4 (SmithKline Beecham adjuvant system #4 which contains alum
and MPL; SBB, Belgium); non-ionic block copolymers that form micelles such as CRL 1005
(these contain a linear chain of hydrophobic polyoxypropylene flanked by chains of
polyoxyethylene; Vaxcel, Inc., Norcross, GA); and Syntex Adjuvant Formulation (SAP, an
oil-in-water emulsion containing Tween 80 and a nonionic block copolymer; Syntex
Chemicals, Inc., Boulder, CO).
5 The immunostimulatory nucleic acids are themselves useful as adjuvants for inducing
a humoral immune response. Thus they can be delivered to a subject exposed to an antigen
to produce an enhanced immune response to the antigen.
The immunostimulatory nucleic acids are useful as mucosal adjuvants. It has
previously been discovered that both systemic and mucosal immunity are induced by mucosal
10 delivery of CpG nucleic acids. The systemic immunity induced in response to CpG nucleic
acids included both humoral and cell-mediated responses to specific antigens that were not
capable of inducing systemic immunity when administered alone to the mucosa.
Furthermore, both CpG nucleic acids and cholera toxin (CT, a mucosal adjuvant that induces
a Th2-like response) induced CTL. This was surprising since with systemic irnmunization,
15 the presence of Th2-like antibodies is normally associated with a lack of CTL (Schirmbeck et
al, 1995). Based on the results presented herein it is expected that the immunostimulatory
nucleic acids will function in a similar manner.
Additionally, the immunostimulatory nucleic acids induce a mucosal response at both
local (e.g., lung) and remote (e.g., lower digestive tract) mucosal sites. Significant levels of
20 IgA antibodies are induced at distant mucosal sites by the immunostimulatory nucleic acids.
CT is generally considered to be a highly effective mucosal adjuvant. As has been previously
reported (Snider 1995), CT induces predominantly IgGl isotype of antibodies, which are
indicative of Th2-type response. In contrast, the immunostimulatory nucleic acids are more
Thl with predominantly IgG2a antibodies, especially after boost or when the two adjuvants
25 are combined. Thl-type antibodies in general have better neutralizing capabilities, and
furthermore, a Th2 response in the lung is highly undesirable because it is associated with
asthma (Kay, 1996, Hogg, 1997). Thus the use of immunostimulatory nucleic acids as a
mucosal adjuvant has benefits that other mucosal adjuvants cannot achieve. The
immunostimulatory nucleic acids of the invention also are useful as mucosal adjuvants for
30 induction of both a systemic and a mucosal immune response.
Mucosal adjuvants referred to as non-nucleic acid mucosal adjuvants may also be
administered with the immunostimulatory nucleic acids. A non-nucleic acid mucosal
adjuvant as used herein is an adjuvant other than a immunostimulatory nucleic acid that is
capable of inducing a mucosal immune response in a subject when administered to a mucosal
surface in conjunction with an antigen. Mucosal adjuvants include but are not limited to
Bacterial toxins e.g., Cholera toxin (CT), CT derivatives including but not limited to CT B
5 subunit (CTB) (Wu et al.51998, Tochikubo et al., 1998); CTD53 (Val to Asp) (Fontana et al.,
1995); CTK97 (Val to Lys) (Fontana et al., 1995); CTK104 (Tyr to Lys) (Fontana et al.,
1995); CTD53/K63 (Val to Asp, Ser to Lys) (Fontana et al., 1995); CTH54 (Arg to His)
(Fontana et al., 1995); CTN107 (His to Asn) (Fontana et al., 1995); CTE114 (Ser to Glu)
(Fontana et al., 1995); CTE112K (Glu to Lys) (Yamamoto et al., 1997a); CTS61F (Ser to
10 Phe) (Yamamoto et al., 1997a, 1997b); CTS106 (Pro to Lys) (Douce et al., 1997, Fontana et
al., 1995); and CTK63 (Ser to Lys) (Douce et al., 1997, Fontana et al., 1995), Zonula
occludens toxin, zot, Escherichia coli heat-labile enterotoxin, Labile Toxin (LT), LT
derivatives including but not limited to LT B subunit (LTB) (Verweij et al., 1998); LT7K
(Arg to Lys) (Komase et al., 1998, Douce et al., 1995); LT61F (Ser to Phe) (Komase et al.,
15 1998); LT112K (Glu to Lys) (Komase et al., 1998); LT118E (Gly to Glu) (Komase et al.,
1998); LT146E (Arg to Glu) (Komase et al., 1998); LT192G (Arg to Gly) (Komase et al.,
1998); LTK63 (Ser to Lys) (Marchetti et al., 1998, Douce et al., 1997,1998, Di Tommaso et
al., 1996); and LTR72 (Ala to Arg) (Giuliani et al., 1998), Pertussis toxin, PT. (Lycke et al.,
1992, Spangler BD, 1992, Freytag and Clemments, 1999, Roberts et al., 1995, Wilson et al.,
29 1995) including PT-9K/129G (Roberts et al., 1995, Cropley et al., 1995); Toxin derivatives
(see below) (Holmgren et al., 1993, Verweij et al., 1998, Rappuoli et al., 1995, Freytag and
Clements, 1999); Lipid A derivatives (e.g., monophosphoryl lipid A, MPL) (Sasaki et al.,
1998, Vancott et al., 1998; Muramyl Dipeptide (MDP) derivatives (Fukushiraa et al., 1996,
Ogawa et al., 1989, Michalek et al., 1983, Morisaki et al., 1983); Bacterial outer membrane
25 proteins (e.g., outer surface protein A (OspA) lipoprotein of Borrelia burgdorferi, outer
membrane protine ofNeisseria meningitidis) (Marinaro et al., 1999, Van de Verg et al.,
1996); Oil-in-water emulsions (e.g., MF59) (Barchfield et al., 1999, Verschoor et al., 1999,
O'Hagan, 1998); Aluminum salts (Isaka et al., 1998,1999); and Saponins (e.g., QS21)
Antigenics, Inc., Woburn, MA) (Sasaki et al., 1998, MacNeal et al., 1998), ISCOMS, MF-59
30 (a squalene-in-water emulsion stabilized with Span 85 and Tween 80; Chiron Corporation,
Emeryville, CA); the Seppic ISA series of Montanide adjuvants (e.g., Montanide ISA 720;
AirLiquide, Paris, France); PROVAX (an oil-in-water emulsion containing a stabilizing
detergent and a micelle-forming agent; IDEC Pharmaceuticals Corporation, San Diego, CA);
Syntex Adjuvant Formulation (SAF; Syntex Chemicals, Inc., Boulder, CO);
poly[di(carboxylatophenoxy)phosphazene (PCPP polymer; Virus Research Institute, USA)
and Leishmania elongation factor (Corixa Corporation, Seattle, WA).
5 Immune responses can also be induced or augmented by the co-administration or co-
linear expression of cytokines (Bueler & Mulligan, 1996; Chow et al, 1997; Geissler et
al, 1997; Iwasaki et al, 1997; Kim et al, 1997) or B-7 co-stimulatory molecules (Iwasaki et
al, 1997; Tsuji et al, 1997) with the immunostimulatory nucleic acids. The cytokines can be
administered directly with immunostimulatory nucleic acids or may be administered in the
10 form of a nucleic acid vector that encodes the cytokine, such that the cytokine can be
expressed in vivo. In one embodiment, the cytokine is administered in the form of a plasmid
expression vector. The term cytokine is used as a generic name for a diverse group of soluble
proteins and peptides which act as humoral regulators at nano- to picomolar concentrations
and which, either under normal or pathological conditions, modulate the functional activities
15 of individual cells and tissues. These proteins also mediate interactions between cells directly
and regulate processes taking place in the extracellular environment.
Examples of cytokines include, but are not limited to EL-1, IL-2, IL-4, IL-5, IL-6, IL-
7, IL-10, IL-12, IL-15, IL-18, granulocyte-macrophage colony stimulating factor (GM-CSF),
granulocyte colony stimulating factor (G-CSF), interferon-y (y-IFN), IFN-cc, tumor necrosis
20 factor (TNF), TGF-ß, FLT-3 ligand, and CD40 ligand.
Cytokines play a role in directing the T cell response. Helper (CD4+) T cells
orchestrate the immune response of mammals through production of soluble factors that act
on other immune system cells, including other T cells. Most mature CD4+ T helper cells
express one of two cytokine profiles: Thl or Th2. The Thl subset promotes delayed-type
25 hypersensitivity, cell-mediated immunity, and immunoglobulin class switching to IgG2a- The
Th2 subset induces humoral immunity by activating B cells, promoting antibody production,
and inducing class switching to IgGi and IgE. In some embodiments, it is preferred that the
cytokine be a Thl cytokine.
The immunostimulatory nucleic acids may be directly administered to the subject or
30 may be administered in conjunction with a nucleic acid delivery complex. A nucleic acid
delivery complex shall mean a nucleic acid molecule associated with (e.g. ionically or
covalently bound to; or encapsulated within) a targeting means (e.g. a molecule that results in
higher affinity binding to target cell (e.g., B cell surfaces and/or increased cellular uptake by
target cells). Examples of nucleic acid delivery complexes include nucleic acids associated
with a sterol (e.g. cholesterol), a lipid (e.g. a cationic lipid, virosome or liposome), or a target
cell specific binding agent (e.g. a Iigand recognized by target cell specific receptor). Preferred
5 complexes may be sufficiently stable in vivo to prevent significant uncoupling prior to
internalization by the target cell. However, the complex can be cleavable under appropriate
conditions within the cell so that the nucleic acid is released in a functional form.
Delivery vehicles or delivery devices for delivering antigen and nucleic acids to
surfaces have been described. The Immunostimulatory nucleic acid and/or the antigen and/or
10 other therapeutics may be administered alone (e.g., in saline or buffer) or using any delivery
vehicles known in the art. For instance the following delivery vehicles have been described:
Cochleates (Gould-Fogerite et al., 1994, 1996); Emulsomes (Vancott et al., 1998, Lowell et
al., 1997); ISCOMs (Mowat et al., 1993, Carlsson et al., 1991, Hu et., 1998, Morein et al.,
1999); Liposomes (Childers et al., 1999, Michalek et al., 1989,1992, de Haan 1995a, 1995b);
15 Live bacterial vectors (e.g., Salmonella, Escherichia coli, Bacillus calmatte-guerin, Shigella,
Lactobacillus) (Hone et al., 1996, Pouwels et al., 1998, Chatfield et al., 1993, Stover et al.,
1991, Nugent et al., 1998); Live viral vectors (e.g., Vaccinia, adenovirus, Herpes Simplex)
(Gallichan et al., 1993, 1995, Moss et al., 1996, Nugent et al., 1998, Flexner et al., 1988,
Morrow et al., 1999); Microspheres (Gupta et al., 1998, Jones et al., 1996, Maloy et al., 1994,
20 Moore et al., 1995, O'Hagan et al., 1994, Eldridge et al., 1989); Nucleic acid vaccines (Fynan
et al., 1993, Kuklin et al., 1997, Sasaki et al., 1998, Okada et al., 1997, Ishii et al., 1997);
Polymers (e.g. carboxymethylcellulose, chitosan) (Hamajima et al., 1998, Jabbal-Gill et al.,
1998); Polymer rings (Wyatt et al., 1998); Proteosomes (Vancott et al., 1998, Lowell et al.,
1988,1996,1997); Sodium Fluoride (Hashi et al., 1998); Transgenic plants (Tacket et al.,
25 1998, Mason et al., 1998, Haq et al., 1995); Virosomes (Gluck et al., 1992, Mengiardi et al.,
1995, Cryz et al., 1998); Virus-like particles (Jiang et al., 1999, Leibl et al., 1998). Other
delivery vehicles are known in the art and some additional examples are provided below in
the discussion of vectors.
The stimulation index of a particular immunostimulatory nucleic acid can be tested in
30 various immune cell assays. Preferably, the stimulation index of the immunostimulatory
nucleic acid with regard to B cell proliferation is at least about 5, preferably at least about 10,
more preferably at least about 15 and most preferably at least about 20 as determined by
incorporation of 3H uridine in a murine B cell culture, which has been contacted with 20 uM
of nucleic acid for 20h at 37°C and has been pulsed with 1 uCi of 3H uridine; and harvested
and counted 4h later as described in detail in PCT Published Patent Applications
PCT/US95/01570 (WO 96/02555) and PCT/US97/19791 (WO 98/18810) claiming priority to
5 U.S. Serial Nos. 08/386,063 and 08/960,774, filed on February 7,1995 and October 30,1997
respectively. For use in vivo, for example, it is important that the immunostimulatory nucleic
acids be capable of effectively inducing an immune response, such as, for example, antibody
production.
Immunostimulatory nucleic acids are effective in non-rodent vertebrate. Different
10 immunostimulatory nucleic acid can cause optimal immune stimulation depending on the type
of subject and the sequence of the immunostimulatory nucleic acid. Many vertebrates have
been found according to the invention to be responsive to the same class of
immunostimulatory nucleic acids, sometimes referred to as human specific
immunostimulatory nucleic acids. Rodents, however, respond to different nucleic acids. As
15 shown herein an immunostimulatory nucleic acid causing optimal stimulation in humans may
not generally cause optimal stimulation in a mouse and vice versa. An immunostimulatory
nucleic acid causing optimal stimulation in humans often does, however, cause optimal
stimulation in other animals such as cow, horses, sheep, etc. One of skill in the art can identify
the optimal nucleic acid sequences useful for a particular species of interest using routine
20 assays described herein and/or known in the art, using the guidance supplied herein.
The term effective amount of a immunostimulatory nucleic acid refers to the amount
necessary or sufficient to realize a desired biologic effect. For example, an effective amount
of a immunostimulatory nucleic acid for inducing mucosal immunity is that amount necessary
to cause the development of IgA in response to an antigen upon exposure to the antigen,
25 whereas that amount required for inducing systemic immunity is that amount necessary to
cause the development of IgG in response to an antigen upon exposure to the antigen.
Combined with the teachings provided herein, by choosing among the various active
compounds and weighing factors such as potency, relative bioavailability, patient body
weight, severity of adverse side-effects and preferred mode of administration, an effective
30 prophylactic or therapeutic treatment regimen can be planned which does not cause
substantial toxicity and yet is entirely effective to treat the particular subject. The effective
amount for any particular application can vary depending on such factors as the disease or
condition being treated, the particular immunostimulatory nucleic acid being administered,
the antigen, the size of the subject, or the'severity of the disease or condition. One of ordinary
skill in the art can empirically determine the effective amount of a particular
immunostimulatory nucleic acid and/or antigen and/or other therapeutic agent without
5 necessitating undue experimentation.
Subject doses of the compounds described herein for mucosal or local delivery
typically range from about 0.1mg to 10 mg per administration, which depending on the
application could be given daily, weekly, or monthly and any other amount of time
therebetween. More typically mucosal or local doses range from about 10 ug to 5 mg per
10 administration, and most typically from about 100 ug to 1 mg, with 2-4 administrations
being spaced days or weeks apart. More typically, immune stimulant doses range from 1 ug
to 10 mg per administration, and most typically 10 ug to 1 mg, with daily or weekly
administrations. Subject doses of the compounds described herein for parenteral delivery for
the purpose of inducing an antigen-specific immune response, wherein the compounds are
15 delivered with an antigen but not another therapeutic agent are typically 5 to 10,000 times
higher than the effective mucosal dose for vaccine adjuvant or immune stimulant applications,
and more typically 10 to 1,000 times higher, and most typically 20 to 100 tunes higher.
Doses of the compounds described herein for parenteral delivery for the purpose of inducing
an innate immune response or for increasing ADCC or for inducing an antigen specific
20 immune response when the immunostimulatory nucleic acids are administered in combination
with other therapeutic agents or in specialized delivery vehicles typically range from about
0.1 |iig to 10 mg per administration, which depending on the application could be given daily,
weekly, or monthly and any other amount of time therebetween. More typically parenteral
doses for these purposes range from about 10 ug to 5 mg per administration, and most
25 typically from about 100 |j.g to 1 mg, with 2-4 administrations being spaced days or weeks
apart. In some embodiments, however, parenteral doses for these purposes may be used in a
range of 5 to 10,000 times higher than the typical doses described above.
For any compound described herein the therapeutically effective amount can be
initially determined from animal models. A therapeutically effective dose can also be
30 determined from human data for CpG oligonucleotides which have been tested in humans
(human clinical trials have been initiated) and for compounds which are known to exhibit
similar pharmacological activities, such as other mucosal adjuvants, e.g., LT and other
antigens for vaccination purposes, for the mucosal or local administration. Higher doses are
required for parenteral administration. The applied dose can be adjusted based on the relative
bioavailability and potency of the administered compound. Adjusting the dose to achieve
maximal efficacy based on the methods described above and other methods as are well-known
5 in the art is well within the capabilities of the ordinarily skilled artisan.
The formulations of the invention are administered in pharmaceutically acceptable
solutions, which may routinely contain pharmaceutically acceptable concentrations of salt,
buffering agents, preservatives, compatible carriers, adjuvants, and optionally other
therapeutic ingredients.
10 For use in therapy, an effective amount of the immunostimulatory nucleic acid can be
administered to a subject by any mode that delivers the nucleic acid to the desired surface,
e.g., mucosal, systemic. Administering the pharmaceutical composition of the present
invention may be accomplished by any means known to the skilled artisan. Preferred routes
of administration include but are not limited to oral, parenteral, intramuscular, intranasal,
15 intratracheal, inhalation, ocular, vaginal, and rectal.
For oral administration, the compounds (i.e., immunostimulatory nucleic acids,
antigens and other therapeutic agents) can be formulated readily by combining the active
compound(s) with pharmaceutically acceptable carriers well laiown in the art. Such carriers
enable the compounds of the invention to be formulated as tablets, pills, dragees, capsules,
20 liquids, gels, syrups, slurries, suspensions and the like, for oral ingestion by a subject to be
treated. Pharmaceutical preparations for oral use can be obtained as solid excipient,
optionally grinding a resulting mixture, and processing the mixture of granules, after adding
suitable auxiliaries, if desired, to obtain tablets or dragee cores. Suitable excipients are, in
particular, fillers such as sugars, including lactose, sucrose, mannitol, or sorbitol; cellulose
25 preparations such as, for example, maize starch, wheat starch, rice starch, potato starch,
gelatin, gum tragacanth, methyl cellulose, hydroxypropylmethyl-cellulose, sodium
carboxymethylcellulose, and/or polyvinylpyrrolidone (PVP). If desired, disintegrating agents
may be added, such as the cross-linked polyvinyl pyrrolidone, agar, or alginic acid or a salt
thereof such as sodium alginate. Optionally the oral formulations may also be formulated in
30 saline or buffers for neutralizing internal acid conditions or may be administered without any
carriers.
Dragee cores are provided with suitable coatings. For this purpose, concentrated sugar
solutions may be used, which may optionally contain gum arabic, talc, polyvinyl pyrrolidone,
carbopol gel, polyethylene glycol, and/or titanium dioxide, lacquer solutions, and suitable
organic solvents or solvent mixtures. Dyestuffs or pigments may be added to the tablets or
5 dragee coatings for identification or to characterize different combinations of active
compound doses.
Pharmaceutical preparations which can be used orally include push-fit capsules made
of gelatin, as well as soft, sealed capsules made of gelatin and a plasticizer, such as glycerol
or sorbitol. The push-fit capsules can contain the active ingredients in admixture with filler
10 such as lactose, binders such as starches, and/or lubricants such as talc or magnesium stearate
and, optionally, stabilizers. In soft capsules, the active compounds may be dissolved or
suspended in suitable liquids, such as fatty oils, liquid paraffin, or liquid polyethylene glycols.
In addition, stabilizers may be added. Microspheres formulated for oral administration may
also be used. Such microspheres have been well defined in the art. All formulations for oral
15 administration should be in dosages suitable for such administration.
For buccal administration, the compositions may take the form of tablets or lozenges
formulated in conventional manner.
For administration by inhalation, the compounds for use according to the present
invention may be conveniently delivered in the form of an aerosol spray presentation from
20 pressurized packs or a nebulizer, with the use of a suitable propellant, e.g.,
dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrailuoroethane, carbon dioxide
or other suitable gas. In the case of a pressurized aerosol the dosage unit may be determined
by providing a valve to deliver a metered amount. Capsules and cartridges of e.g. gelatin for
use in an inhaler or insufflator may be formulated containing a powder mix of the compound
25 and a suitable powder base such as lactose or starch.
The compounds, when it is desirable to deliver them systemically, may be formulated
for parenteral administration by injection, e.g., by bolus injection or continuous infusion.
Formulations for injection may be presented in unit dosage form, e.g., in ampoules or in
multi-dose containers, with an added preservative. The compositions may take such forms as
30 suspensions, solutions or emulsions in oily or aqueous vehicles, and may contain formulatory
agents such as suspending, stabilizing and/or dispersing agents.
Pharmaceutical formulations forparenteral administration include aqueous solutions
of the active compounds in water-soluble form. Additionally, suspensions of the active
compounds may be prepared as appropriate oily injection suspensions. Suitable lipophilic
solvents or vehicles include fatty oils such as sesame oil, or synthetic fatty acid esters, such as
5 ethyl oleate or triglycerides, or liposomes. Aqueous injection suspensions may contain
substances which increase the viscosity of the suspension, such as sodium carboxymethyl
cellulose, sorbitol, or dextran. Optionally, the suspension may also contain suitable stabilizers
or agents which increase the solubility of the compounds to allow for the preparation of
highly concentrated solutions.
10 Alternatively, the active compounds may be in powder form for constitution with a
suitable vehicle, e.g., sterile pyrogen-free water, before use.
The compounds may also be formulated in rectal or vaginal compositions such as
suppositories or retention enemas, e.g., containing conventional suppository bases such as
cocoa butter or other glycerides.
15 In addition to the formulations described previously, the compounds may also be
formulated as a depot preparation. Such long acting formulations may be formulated with
suitable polymeric or hydrophobic materials (for example as an emulsion in an acceptable oil)
or ion exchange resins, or as sparingly soluble derivatives, for example, as a sparingly soluble
salt.
20 The pharmaceutical compositions also may comprise suitable solid or gel phase
carriers or excipients. Examples of such carriers or excipients include but are not limited to
calcium carbonate, calcium phosphate, various sugars, starches, cellulose derivatives, gelatin,
and polymers such as polyethylene glycols.
Suitable liquid or solid pharmaceutical preparation forms are, for example, aqueous or
25 saline solutions for inhalation, microencapsulated, encochleated, coated onto microscopic
gold particles, contained in liposomes, nebulized, aerosols, pellets for implantation into the
skin, or dried onto a sharp object to be scratched into the skin. The pharmaceutical
compositions also include granules, powders, tablets, coated tablets, (micro)capsules,
suppositories, syrups, emulsions, suspensions, creams, drops or preparations with protracted
30 release of active compounds, in whose preparation excipients and additives and/or auxiliaries
such as disintegrants, binders, coating agents, swelling agents, lubricants, flavorings,
sweeteners or solubilizers are customarily used as described above. The pharmaceutical
compositions are suitable for use in a variety of drug delivery systems. For a brief review of
methods for drug delivery, see Langer, Science 249:1527-1533,1990, which is incorporated
herein by reference.
The immunostimulatory nucleic acids and optionally other therapeutics and/or
5 antigens may be administered per se (neat) or in the form of a pharmaceutically acceptable
salt. When used in medicine the salts should be pharmaceutically acceptable, but non-
pharmaceutically acceptable salts may conveniently be used to prepare pharmaceutically
acceptable salts thereof. Such salts include, but are not limited to, those prepared from the
following acids: hydrochloric, hydrobromic, sulphuric, nitric, phosphoric, maleic, acetic,
10 salicylic, p-toluene sulphonic, tartaric, citric, methane sulphonic, formic, malonic, succinic,
naphthalene-2-sulphonic, and benzene sulphonic. Also, such salts can be prepared as alkaline
metal or alkaline earth salts, such as sodium, potassium or calcium salts of the carboxylic acid
group.
Suitable buffering agents include: acetic acid and a salt (1-2% w/v); citric acid and a
15 salt (1-3% v/v); boric acid and a salt (0.5-2.5% w/v); and phosphoric acid and a salt (0.8-2%
w/v). Suitable preservatives include benzalkonium chloride (0.003-0.03% w/v);
chlorobutanol (0.3-0.9% w/v); parabens (0.01-0.25% w/v) and thimerosal (0.004-0.02% w/v).
As described in greater detail herein, the pharmaceutical compositions of the invention
contain an effective amount of a immunostimulatory nucleic acid and optionally antigens
20 and/or other therapeutic agents optionally included in a pharmaceutically-acceptable carrier.
The term pharmaceutically-acceptable carrier means one or more compatible solid or liquid
filler, diluents or encapsulating substances which are suitable for administration to a human or
other vertebrate animal. The term carrier denotes an organic or inorganic ingredient, natural
or synthetic, with which the active ingredient is combined to facilitate the application. The
25 components of the pharmaceutical compositions also are capable of being commingled with
the compounds of the present invention, and with each other, in a manner such that there is no
interaction which would substantially impair the desired pharmaceutical efficiency.
The immunostimulatory nucleic acids useful in the invention may be delivered in
mixtures with additional adjuvant(s), other therapeutics, or antigen(s). A mixture may consist
30 of several adjuvants in addition to the immunostimulatory nucleic acid or several antigens or
other therapeutics.
A variety of administration routes are available. The particular mode selected will
depend, of course, upon the particular adjuvants or antigen selected, the particular condition
being treated and the dosage required for therapeutic efficacy. The methods of this invention,
generally speaking, may be practiced using any mode of administration that is medically
5 acceptable, meaning any mode that produces effective levels of an immune response without
causing clinically unacceptable adverse effects. Preferred modes of administration are
discussed above.
The compositions may conveniently be presented in unit dosage form and may be
prepared by any of the methods well known in the art of pharmacy. All methods include the
10 step of bringing the compounds into association with a carrier which constitutes one or more
accessory ingredients. In general, the compositions are prepared by uniformly and intimately
bringing the compounds into association with a liquid carrier, a finely divided solid carrier, or
both, and then, if necessary, shaping the product. Liquid dose units are vials or ampoules.
Solid dose units are tablets, capsules and suppositories. For treatment of a patient, depending
75 on activity of the compound, manner of administration, purpose of the immunization (i.e.,
prophylactic or therapeutic), nature and severity of the disorder, age and body weight of the
patient, different doses may be necessary. The administration of a given dose can be carried
out both by single administration in the form of an individual dose unit or else several smaller
dose units. Multiple administration of doses at specific intervals of weeks or months apart is
20 usual for boosting the antigen-specific responses.
Other delivery systems can include time-release, delayed release or sustained release
delivery systems. Such systems can avoid repeated administrations of the compounds,
increasing convenience to the subject and the physician. Many types of release delivery
systems are available and known to those of ordinary skill in the art. They include polymer
25 base systems such as poly(lactide-glycolide), copolyoxalates, polycaprolactones,
polyesteramides, polyorthoesters, polyhydroxybutyric acid, and polyanhydrides.
Microcapsules of the foregoing polymers containing drugs are described in, for
example, U.S. Patent 5,075,109. Delivery systems also include non-polymer systems that are:
lipids including sterols such as cholesterol, cholesterol esters and fatty acids or neutral fats
30 such as mono-di-and tri-glycerides; hydrogel release systems; sylastic systems; peptide based
systems; wax coatings; compressed tablets using conventional binders and excipients;
partially fused implants; and the like. Specific examples include, but are not limited to: (a)
erosional systems in which an agent of the invention is contained in a form within a matrix
such as those described in U.S. Patent Nos. 4,452,775,4,675,189, and 5,736,152, and (b)
diffusional systems hi which an active component permeates at a controlled rate from a
polymer such as described in U.S. Patent Nos. 3,854,480, 5,133,974 and 5,407,686. In
5 addition, pump-based hardware delivery systems can be used, some of which are adapted for
implantation.
The present invention is further illustrated by the following Examples, which in no
way should be construed as further limiting. The entire contents of all of fee references
(including literature references, issued patents, published patent applications, and co-pending
10 patent applications) cited throughout this application are hereby expressly incorporated by
reference.
Examples
EXAMPLE 1 (ODN 10102);
IS Summary:
This resport summarizes in vitro data with human cells demonstrating that ODN
10102 (SEQ ID NO:1) behaves similarly and in some aspects in a superior manner to ODN
7909 (SEQ ID NO:2). In vitro and in vivo data in mice demonstrating that CpG ODN 10102
has similar and sometimes better properties as compared to CpG ODN 7909 for activation of
20 fee innate immune system, and for augmenting humoral and cellular HBsAg-specific
responses in mice when coadministered wife fee antigen.
The assays performed were receptor engagement (TLR9), B cell activation (expression
of cell surface activation marker and B cell proliferation) and cytokine secretion (IL-10, IP-
10, IFN-alpha and TNF-alpha). All assays demonstrated feat ODN 10102 has properties feat
25 are almost identical if not better to ODN 7909.
In vitro studies (i.e. B cell proliferation assays, NK lytic activity, cytokine secretion
profiles) were carried out using naive BALB/c mouse splenocytes. In vivo comparison studies
were carried out by examining fee potential of these two ODNs to enhance antigen specific
immune responses to hepatitis B antigen (HBsAg).

Materials and Methods:
Human Studies:
Oligodeoxynucleotides: All ODNs were provided by Coley Pharmaceutical GmbH
(Langenfeld, Germany). The control ODN contained no stimulatory CpG motif. ODNs
5 were diluted in phosphate-buffered saline, and stored at -20° C. All dilutions were carried
out using pyrogen-free reagents.
TLR9 assay: Cells used for this assay expressed the human TLR9 receptor and contained a
reporter gene construct. Cells were incubated with ODNs for 16h. Each data point was done
10 in triplicate. Cells were lysed and assayed for reporter gene activity. Stimulation indices
were calculated in reference to reporter gene activity of medium without addition of ODN.
Cell purification: Peripheral blood buffy coat preparations from healthy human donors
were obtained from the German Red Cross (Rathingen, Germany) and from these, PBMC
15 were purified by centrifugation over Ficoll-Hypaque (Sigma, Germany). The purified
PBMC were either used fresh or were suspended in freezing medium and stored at -70° C.
When required, aliquots of these cells were thawed, washed and resuspended in RPMI1640
culture medium supplemented with 10% (v/v) heat inactivated FCS, 1.5mM L-glutamine,
lOOU/ml penicillin and lOOug/ml streptomycin.
20
Cytokine detection: Thawed or fresh PBMC were resuspended at a concentration of
5xlO6/ml and added to 48 well flat-bottomed plates (lml/well), which had previously
received nothing or ODN in a variety of concentrations. The cells were cultured in a
humidified incubator at 37 °C. Culture superaatants were collected after the indicated time
25 points. If not used immediately, supernatants were frozen at -20°C until required. Amounts
of cytokines in the supernatants were assessed using commercially available ELISA Kits (IL-
10; Diaclone, USA) or in-house ELISAs (IP-10 and IFN-a) developed using commercially
available antibodies (from Pharmingen or PBL; Germany or USA, respectively).
30 Cultures for flow cytometric analysis of B cell activation: Monoclonal antibodies to
CD19 and CD86 were purchased from Becton Dickinson (Germany). PBMC were incubated
WO 2004/005476 PCT/US2003/021113
-108-
for 48 hours with or without the addition of different concentrations of ODNs. B cells were
identified by expression of CD19 by flow cytometry. Flow cytometric data were acquired
on a FACSCalibur (Becton Dickinson). Data were analyzed using the computer program
CellQuest (Becton Dickinson). Proliferating CD19 positive B cells were identified after
5 culturing CFSE-labelled PBMC (CFSE is a fluorescing dye binding to all cell surfaces) by
decreased CFSE content using flow cytometry methodology (see above).
Murine In Vitro/In Vivo Studies:
Oligodeoxynucleotides: CpG ODN (GMP quality) were supplied by Coley Pharmaceutical
Inc. (Wellesley, MA). All ODN were resuspended in sterile, endotoxin free TE at pH 8.0
10 (OmniPer®; EM S cience, Gibbstown, NJ) and stored and handle under aseptic conditions
to prevent both microbial and endotoxin contamination. Dilution of ODNs for assays was
carried out in sterile, endotoxin free PBS a pH 7.2 (Sigma Chemical Company, St. Louis,
MO).
15 Animals: Female BALB/c mice (6-8 weeks of age) were used for all experiments. Animals
were purchased from Charles River Canada (Quebec, Canada) and housed in micro isolators
at the animal care facility of the Ottawa Hospital Research Institute, Civic Site.
Splenocyte harvest and culture: Naive BAL B/c mouse splenocytes were used for all in
vitro assays. Animals were anesthetized with isofluorane and euthanized by cervical
20 dislocation. Spleens were removed under aseptic conditions and placed in PBS + 0.2%
bovine serum albumin (Sigma Chemical Company). Spleens were then homogenized and
splenocytes were re-suspended in RPMI1640 (Life Technologies, Grand Island, NY) tissue
culture medium supplemented with 2% normal mouse serum (Cedarlane Laboratories,
Ontario, Canada), penicillin-streptomycin solution (final concentration of 1000 U/ml and 1
25 mg/ml respectively; Sigma Chemical Company), and 5 X 10'5 M p-mercaptoethanol (Sigma
Chemical Company).
B cell proliferation assays: Spleen cell suspensions were prepared and adjusted to a final
concentration of 5 X 106 cells per ml in complete RPMI 1640. Splenocyte suspension was
plated onto 96-well U-bottom tissue culture plates (100 pl/well) along with 100 \A of each
stimulant diluted to appropriate concentrations in complete RPMI 1640. The stimulants used
were CpG ODN (at 1, 3, 10 mg/ml) 7909 and 10102, 10103, 10104, 10105 or 10106.
Concanavalin A (10 jig/ml, Sigma Chemical Company) and LPS (10 jig/ml, Sigma
Chemical Company) were used as positive controls and cells cultured with media alone were
5 used as negative controls. Each splenocyte sample was plated in triplicate and cells were
incubated in a humidified 5% COZ incubator at 37°C for 96 hr. At the end of the incubation
period, cells were pulsed with 3H-thymidine (20 u-Ci/ml) at 96 hr post incubation for 16
hours, harvested and measured for radioactivity.
'0 Cytokine secretion profiles: Spleen cell suspensions were prepared and plated in 96-well
U-bottom tissue culture plates as described for B cell proliferation assays. Each splenocyte
sample was plated in triplicate and the cells were incubated in a humidified 5 % CO2
incubator at 37°C for 6, 12 or 48 hr. At the end of the incubation period, 96-well plates were
centrifuged for 5 min at 1200 rpm and culture supernatants harvested and stored at -80°C
15 until assayed. Commercially available assay kits (mouse OptEIA kits; PharMingen,
Mississauga, ON) were used according to manufacturers instructions to assay cytokine levels
in culture supernatants taken at 6 hr (TNF-alpha), 24 hr (IL-12) and 48 hr QL-6 and IL-10).
NK assays: Splenocyte suspensions were prepared as described previously and adjusted to
20 a final concentration of 3 X 105 cells per ml in complete RPMI 1640. Splenocyte suspension
(10 ml; 30 x 106 cells) was plated in T-25 tissue culture flasks (Fisher Scientific, Ottawa,
ON) along with either CpG ODN (at 1, 3, 10 ug/ml) 7909 and 10102, 10103, 10104, 10105
or 10106. Splenocytes cultured with media alone were used as negative controls. Each
splenocyte culture was incubated in a humidified 5% CO2 incubator at 37°C for 24 hr. At the
25 end of the incubation period, cells were plated at different effectontarget ratios onto 96-well
U-bottom tissue culture plates (100 ul/well) along with 100 ul of 51Cr labeled target cells at
5 x 104 cells/ml. NK sensitive mouse lymphoma cell line YAC-1 (ATCC # TIB-160, ATCC,
Manassas, VA) was used as the target cell line. Each sample was plated in triplicate and the
cells were incubated in a humidified 5% CO2 incubator at 37°C for 4 hr. Target cells were
30 incubated with media alone or with 2N HC1 to determine spontaneous release and maximum
release respectively. At the end of the incubation period, supernatants were harvested and
radioactivity levels were determined using a gamma counter. The % lysis was determined
using the following formula;
% specific release = experimental release - spontaneous release x 100
maximum release - spontaneous release
5
Immunization of mice: BALB/c mice (n=10/group) were immunized with 1 ug HBsAg
sub type ad (International Enzymes, CA) alone or in combination with either 10 u.g CpG
ODN 7909 or CpG ODN 10102, 10103, 10104, 10105 or 10106. Animals were bled and
boosted at 4 weeks post-primary immunization. At 1 week post boost 5 animals from each
10 group was euthanized and spleens removed for CTL assays.
Determination of antibody responses: Antibodies (total IgG, IgGl and IgG2a) specific to
HBsAg (anti-HBs) were detected and quantified by endpoint dilution ELISA assay, which
was performed in triplicate on samples from individual animals. End-point titers were
15 defined as the highest plasma dilution that resulted in an absorbance value (OD 450) two
times greater than that of non-immune plasma with a cut-off value of 0.05. These were
reported as group mean titers ± SEM.
Statistical analysis: Statistical analysis was performed using InStat program (Graph PAD
20 Software, San Diego). The statistical difference between groups were determined by
Student's t test (for two groups) or by 1-factor ANOVA followed by Tukey's test (for three
or more groups) on raw data or transformed data (logio. for heteroscedastic populations).
Results:
25 TLR9 engagement: Recently the receptor for the recognition of CpG sequences was
identified and shown to be a member of the Toll-Like Receptor (TLR) family (Hemmi et
al., 2000). This receptor, TLR9, is readily activated by ODNs containing optimal
immunostimulatory CpG sequences. We incubated a cell line stably expressing the human
TLR9 with different concentrations of ODNs 7909 and 10102 as well as a control ODN
30 (Fig. 1).
The results demonstrate that there ODN 10102 activated TLR9 as well as or better
than ODN 7909. Both ODNs showed the same dose-response curve and reached maximum
activation at the same concentrations. The control ODN used did not induce TLR9 activation
even at the highest concentration of 12 mg/ml.
Human B cells: One characteristic of type B ODNs is their ability to very efficiently
5 activate B cells (Krieg et al., 1995). B cells and plasmacytoid DC are at the moment the
only immune cell types known to express TLR9 (Krug et al., 2001; Bauer et al., 2001).
We, therefore, measured the direct activation of B cells induced by ODNs 7909 and 10102
by: a. up regulation of the cell surface marker CD86 (Fig. 2), and b. measuring the
proliferation of B cells (Fig. 3). For CD86 expression on human B cells PBMC of healthy
10 blood donors were incubated with different ODNs and B cell activation measured as
described in Materials and Methods.
Both results demonstrate that 10102 as well as 7909 are very potent stimulators of
human B cells. Fig. 2 shows that these CpG ODNs were capable to stimulate B cells at an in
vitro concentration of only 0.4mg/ml. The plateau was reached at about 1.6mg/ml. A similar
15 result was obtained for the induction of B cell proliferation (Fig. 3), here the stimulation index
reached a maximum at about 1.6 mg/ml.
Cytokine secretion: ODNs of the B class lead to a Thl dominated immune response in
vivo as well as in vitro. It was found that they are capable to induce typical Thl cytokines
20 such as IFN- and IFN- as well as Thl-related chemokines such as MCP-1 and IP-10. In
addition, low secretion of the pro-inflammatory cytokines IL-6 as well as TNF- and
secretion of the negative regulator IL-10 can be observed. We, therefore, measured the
secretion of the Thl cytokine IFN-, the chemokine IP-10 as well as the regulatory cytokine
IL-10 and the pro-inflammatory cytokine TNF- . Fig. 4 shows the result for an experiment
25 performed with 3 different donors at 0.2, 0.4, 1.6 and 5mg/ml to measure in vitro IFN-
secretion.
Both CpG ODNs, 7909 as well as 10102, induced high levels of IFN-a with a
maximum reached at 0.4 (7909) or 1.6mg/ml (10102). However, maximal elevation of IFN-a
secretion was more pronounced after stimulation with 10102 in comparison to 7909. hi
30 contrast, the control ODN induced low amounts of IFN-a starting only at 5.0(j.g/ml.
In addition, ODNs 7909 and 10102, in contrast to the control ODN, induced high amounts of
the chemokine EP-10 as shown in Fig. 5.
A very similar experiment was performed for IL-10 secretion (Fig. 6). Again, as
demonstrated above for IFN-a, both CpG ODNs 7909 and 10102 demonstrated almost
identical properties, with 10102 working better in some instance in these assays. In
comparison, the control ODN induces IL-10 secretion only at the highest concentration.
5 As shown in Fig. 7, both ODNs 7909 and 10102 as well as the control ODN showed a
weak secretion profile of the pro-inflammatory cytokine TNF-a in comparison to LPS. Again,
the two ODNs were found to have very similar characteristics also in this assay.
In a first set of experiments, the induction of the proliferation of murine spleen cells
was investigated. According to the data shown in Fig. 8, CpG ODN 10102 is equally potent as
10 CpG ODN 7909 in inducing murine B cell proliferation at all concentrations tested.
In a next set of experiments, the secretion of a variety of cytokines upon incubation of
spleen cells with 10102, 7909 and the control 2137 was tested. According to the data shown
in Fig. 9, both CpG ODN 7909 and 10102 have essentially equal potency in enhancing
cytokine secretion by murine splenocytes.
15 According to the data in Fig. 10, both CpG ODN 7909 and 10102 have essentially
equal potency in enhancing lytic activity of NK cells in mouse splenocyte cultures.
According to the results of this study (Fig. 11), use of either CpG ODN 7909 or 10102
significantly enhanced antibody titers against HBsAg compared to antigen alone (p whereas there was no significant increase in anti-HBs responses when control ODN was used in
20 combination with HBsAg (p=0.86).
The increase in total IgG levels is slightly but significantly (p=0.04) greater when CpG
ODN 7909 used compared to when CpG ODN 10102 is used.
In mice IgG isotype distribution is widely used as an indication of the nature of the
immune response where a high IgG2a/IgGl ratios are indicative of a Thl biased immune
25 response (Constant and Bottomly, 1997). In the present study, the use of CpG ODN
significantly enhanced IgG2a titers compared to when antigen was used alone or in
combination with control ODN 2137 (pO.OOl for Ag vs. 7909 or 10102 or Ag vs. Ag +
2137). However, the level of IgG2a response was similar when either CpG ODN 7909 or
10102 was used in combination with HBsAg (p>0.05). Therefore, both CpG ODN 7909 and
30 10102 are equally potent in their ability to induce Thl biased immune responses as measured
by the increased levels of IgG2a over IgGl.
Conclusion:
In vitro data with human cells demonstrated that the ODN 10102 behaves similarly or
better than previously identified ODN 7909 in a variety of assays performed.
According to the results of the murine in vivo and in vitro studies, CpG ODN 10102
5 has similar or better immune potentiating properties than ODN 7909, both for in vitro effects
on innate immune responses as well as the ability to augment antigen specific responses in
vivo when administered together with an antigen.
EXAMPLE 2 (ODN 10103);
10 Summary:
The in vitro ability of ODN 10103 (SEQ ID NO:19) to stimulate human PBMC was
compared to that of ODN 7909 (SEQ ID NO:2). Immune stimulation was analyzed in terms
of receptor (i.e., TLR9) engagement, B cell activation (e.g., expression of cell surface
activation markers and B cell proliferation), and cytokine secretion (e.g., secretion of IL-10,
15 IP-10, IFN-a and TNF-ot). All assays demonstrated that ODN 10103 has properties similar
to or superior to those of ODN 7909.
The ability of ODN 10103 to stimulate murine immune cells in vitro and in vivo was
compared to that of ODN 7909. In vitro studies (e.g., B cell proliferation assays, NK lytic
activity, and cytokine secretion profiles) were carried out using naive BALB/c mouse
20 splenocytes. In vivo studies were carried out by examining the potential of these two ODNs
to enhance antigen specific immune responses to hepatitis B surface antigen (HBsAg), with
both humoral (antibody) and cell mediated immune responses (CTL activity) analyzed. In
addition, the Th-bias of the induced immune response was examined by deterraining the
strength of the CTL response as well as the IgG2a/IgGl ratio.
25
Materials and Methods:
With respect to human studies, refer to Example 1 for descriptions of
oligodeoxynucleotides, TLR9 assays, human cell purification, cytokine detection, and cultures
for flow cytometric analysis of B cell activation.
30 With respect to murine in vitro and in vivo studies, refer to Example 1 for
descriptions of oligodeoxynucleotides, animals, splenocyte harvest and culture, B cell
proliferation assays, cytokine secretion profiles, NK assays, immunization of mice,
determination of antibody responses, and statistical analysis.
Murine In Vitro/In Vivo Studies:
5 Evaluation of CTL responses: CTL assays were conducted as previously described by
Davis et al. The results are presented as % specific lysis at different effector: target (E:T)
ratios.
Results:
10 TLR9 engagement: We incubated a cell line stably expressing the human TLR9 with
different concentrations of ODNs 7909 and 10103 as well as a control ODN (Fig. 13).
Both ODNs showed a concentration dependent dose-response curve reaching their maximum
activation at the same concentration. A control ODN did not induce TLR9 activation even at
the highest concentration of 24mg/ml. ODN 10103 showed higher stimulation capacity at
75 lower doses than did ODN 7909 (e.g., at 6 and 12 g/ml), suggesting that ODN 10103 can
be used at lower doses to achieve similar immunostimulation indices, and thereby reducing
potential toxicity.
Human B cells: One characteristic of type B ODNs is their ability to very efficiently
20 activate B cells (Krieg et al., 1995). B cells and plasmacytoid DC are at the moment the
only immune cell types known to express TLR9 (Krug et al., 2001; Bauer et al., 2001).
We, therefore, measured the direct activation of B cells induced by ODNs 7909 and 10103
by up regulation of the cell surface marker CD86 (Fig. 14), and measuring the proliferation
of B cells (Fig. 15). For CD86 expression on human B cells PBMC of healthy blood donors
25 were incubated with different ODNs and B cell activation measured as described in
Materials and Methods.
Both results demonstrate that 10103 at least as well as 7909 as a stimulator of human
B cells. Fig. 14 shows that these CpG ODNs were able to stimulate B cells starting at an in
vitro concentration of only 0.4mg/ml. The plateau was reached at about 1.6mg/ml and more
30 than 60% of B cells were found to have up regulated CD86 in contrast to the control that was
much less potent at the same concentration. The results indicate that ODN 10103 stimulates
CD86 expression to a higher level at a lower dose than dose ODN 7909 (e.g., at 0.4 mg/ml) in
all three donors tested, again suggesting that smaller doses of ODN 10103 could be used to
achieve desired levels of immunostimulation. A similar result was obtained for the induction
of B cell proliferation (Fig. 15).
5 Cytokine secretion: ODNs of the B class lead to a Thl dominated immune response in
vivo as well as in vitro. It was found that they are able to induce typical Thl cytokines such
as IFN-? and IFN-a as well as chemokines such as MCP-1 and HMO. In addition, low
secretion of the pro-inflammatory cytokines IL-6 as well as TNF-a and secretion of the
negative regulator IL-10 can be observed. We, therefore, measured the secretion of the Thl
10 cytokine IFN-a, the chemokine IP-10 as well as the regulatory cytokine IL-10 and pro-
inflammatory cytokine TNF-a.
Fig. 16 shows the result for an experiment performed with 6 different donors at 0.2,
0.4 and 1.6 /ng/ml to measure in vitro IFN-a secretion. Both CpG ODNs, 7909 as well as
10103, induced significant amounts of IFN-a in different donors. In contrast, the control
15 ODN induced no or low amounts of IFN-a in one donor. The data suggests that a patient
variability may exist with some patients responding better to ODNs such as 10103, as
compared to ODN 7909. This finding indicates that ODN may be classified in terms of the
subjects that are likely to be high responders.
In addition to IFN-a, ODNs 7909 and 10103 induced chemokine IP-10 as shown in
20 Fig. 17. ODN 10103 induced equal or higher levels of IP-10 than did ODN 7909, at all doses
tested. In particular, at the 0.4 mg/ml concentration, ODN 7909 produced higher amounts of
IP-10 than did ODN 7909. At a 1.6 mg/ml concentration, ODN 10103 induced roughly 25%
more IP-10 than did ODN 7909.
As demonstrated in Fig. 18, CpG ODNs 7909 and 10103 demonstrated almost
25 identical IL-10 induction capacity.
As shown in Fig. 19, both ODNs 7909 and 10103 as well as the control ODN showed
a low secretion profile of the pro-inflammatory cytokine TNF-a in all tested concentrations in
comparison to LPS. At the highest dose tested (i.e., 6 mg/ml), ODN 7909 stimulated the
secretion of higher levels of IL-10 than did ODN 7909. The dose responses are shown in Fig.
30 21.
In vitro mouse studies: According to the data, both CpG ODN 7909 and 10103 are equally
potent in inducing mouse B cell proliferation, have essentially equal potency in enhancing
cytokine secretion by mouse splenocytes, and have essentially equal potency in enhancing
5 lytic activity of NK cells in mouse splenocyte cultures (Fig. 22). ODN 10103 appears to
have a higher capacity for stimulating secretion of IL-6 and TNF- , particularly at the lower
doses tested. Similary, the lytic activity profiles of these ODNs differ according to the
concentration.
10 In vivo mouse studies: According to the results of this study use of either CpG ODN 7909
or 10103 significantly enhanced antibody titers against HBsAg compared to antigen alone
(p responses when control ODN was used in combination with HBsAg (p=0.85). (See Figs
23 and 24.)
15 Furthermore, both CpG ODN 7909 and 10103 were equally potent in enhancing
antibody responses against HBsAg hi that there was no significant difference in anti-HBs
responses in mice immunized with HBsAg + CpG ODN 7909 and HBsAg + CpG ODN
10103 (p=0.13).
In mice IgG isotype distribution is widely used as an indication of the nature of the
20 immune response where a high IgG2a/IgGl ratios are indicative of a Thl biased immune
response (1). In the present study, the use of CpG ODN significantly enhanced IgG2a titers
compared to when antigen was used alone or in combination with control ODN 2137
(p Ag + 10103 vs. Ag + 2137). However, the level of IgG2a response was similar when either
25 CpG ODN 7909 or 10103 was used in combination with HBsAg (p>0.05). Therefore, both
CpG ODN 7909 and 10103 are equally potent in their ability to induce Thl biased immune
responses as measured by the increased levels of IgG2a over IgGl.
The CTL responses hi animals immunized with HBsAg using ODN 10103 appear to
be greater than those induced CpG ODN 7909, as shown in Fig. 25.
30
Conclusions:
The in vitro data on human PBMC demonstrates that the molecules of the B class
(7909 and 10103) behave similarly but not identically in all of the assays performed. Of
particular importance is the observation that for several of the tested assays and
functionalities, the ODN 10103 induced greater irnmunostimulation than did previously
5 identified ODN 7909. This difference suggests that CpG nucleotides can be tailored for use
in subjects, and also that lower levels of CpG ODNs can achieve desired therapeutic
endpoints, with potentially lower toxicity events.
EXAMPLE 3 (ODN 10104):
10 In vivo effects;
Summary:
Synthetic oligodeoxynucleotides (ODN) containing unmethylated CpG dinucleotides
have been shown to induce potent innate immune responses against infectious agents and
trigger Thl-like immune activation. The ability of transmucosal delivery of CpG ODN
15 applied to the genital mucosa to protect against or treat intravaginal (IVAG) infection with
herpes simplex virus type 2 (HSV-2) was tested.
Materials and Methods:
All ODN were provided by Coley Pharmaceutical Group (Langenfeld, Germany) and
20 had undetectable endotoxin levels ( (BioWhittaker, Venders, Belgium). ODN were suspended in sterile, endotoxin-free Tris-
EDTA (Sigma, Deisenhofen, Germany), and stored and handled under aseptic conditions to
prevent both microbial and endotoxin contamination. All dilutions were carried out using
pyrogen-free phosphate-buffered saline (Life Technologies, Eggenstein, Germany).
25 CpG ODN and non-CpG ODN were applied into the vagina of female C57B1/6 mice
at various time points prior to or after IVAG HSV-2 infection. Mice were monitored daily
following challenge for genital pathology, survival, and genital viral titer.
Results:
30 Female mice treated with CpG ODN in the genital tract 24 hours prior to IVAG HSV-
2 challenge survived infection, showed minimal vaginal pathology, and had virtually no virus
in vaginal washes for the first 6 days following infection. Importantly, transmucosal delivery
of CpG ODN to the genital tract prior to infection conferred superior protection against local
IVAG challenge compared to intramuscular delivery of CpG ODN. In contrast, mice
pretreated with control ODN alone were not protected, showed severe pathology, and had
high titers of HSV-2 in vaginal washes. Mice treated with CpG ODN shortly after IVAG
5 HSV-2 infection were protected and had low vaginal virus titers, whereas mice treated with
CpG ODN 24 and 72 hours after IVAG HSV-2 infection were not protected. (See Figs. 26
and 27.)
Conclusions:
10 These results indicate that local transmucosal delivery of CpG ODN to the genital tract
prior to or shortly after genital HSV-2 challenge was very effective at preventing infection by
a sexually transmitted virus and suggest that local CpG-induced innate immunity is
involved.
15 In vitro effects:
Materials and Methods:
Peripheral blood buffy coat preparations from healthy human donors were obtained
from the German Red Cross (Rathingen, Germany) and from these, PBMC were purified by
centrifugation over Ficoll-Hypaque (Sigma, Germany). The purified PBMC were either used
20 fresh or were suspended in freezing medium and stored at -70°C. When required, aliquots of
these cells were thawed, washed and resuspended in RPMI 1640 culture medium
supplemented with 10% (v/v) heat inactivated FCS, 1.5mM L-glutamine, lOOU/ml penicillin
and 100u,g/ml streptomycin.
Thawed or fresh PBMC were resuspended at a concentration of 5xl06/ml and added to
25 48 well fiat-bottomed plates (1 ml/well), which had previously received nothing or ODN in a
variety of concentrations. The cells were cultured in a humidified incubator at 37°C. Culture
supernatants were collected after 48 hours. If not used immediately, supernatants were frozen
at -20°C until required. Amounts of cytokines in the supernatants were assessed using
commercially available ELISA Kits (IL-10; Diaclone, USA) or in-house ELISAs (IFN-alpha)
30 developed using commercially available antibodies (from Pharmingen or PBL; Germany or
USA, respectively).
Results:
ODNs of the B class lead to a Thl dominated immune response in vivo as well as in
vitro. It was found that they are capable to induce typical Thl cytokines such as IFN-alpha
and IFN-gamma as well as Thl-related chemokines such as MCP-1 and IP-10. In addition,
5 low secretion of the pro-inflammatory cytokines IL-6 as well as TNF-alpha and secretion of
the negative regulator IL-10 can be observed. We, therefore, measured the secretion of the
Thl cytokine IFN-alpha and the regulatory cytokine IL-10. Fig. 28 shows the result for an
experiment performed with 3 different donors at 0.02, 0.05, 0.1, 0.2, 0.5 and 1.0 ug/ml of
10104 or control nucleic acid to measure in vitro IFN-alpha secretion.
; 0 Nucleic acid 10104 induced high levels of IFN-alpha in a dose dependent manner,
with a peak induction at 0.1 mg/ml 10104 nucleic acid. In contrast, control nucleic acid
induced low amounts of IFN-alpha that were comparable to those induced in the presence of
medium alone (Fig. 28).
A similar experiment was performed for IL-10 secretion (Fig. 4). Again, as
15 demonstrated above for IFN-alpha, nucleic acid 10104 induced IL-10 in a dose dependent
manner with a peak induction at 0.2 ug/ml 10104 nucleic acid. Control nucleic acid
demonstrated a similar but lower induction profile, although the peak was shifted to 0.5 ug/ml
control nucleic acid. In this case, control levels were greater than medium levels (Fig. 29).
20 TLR 9 engagement:
Materials and Methods:
Stably transfected HEK293 cells expressing the human TLR9 were described before
[Bauer et al.; PNAS; 2001]. Briefly, HEK293 cells were transfected by electroporation with
vectors expressing the human TLR9 and a 6xNFkB-luciferase reporter plasmid. Stable
25 transfectants (3x104 cells/well) were incubated with ODN for 16h at 37°C in a humidified
incubator. Each data point was done in triplicate. Cells were lysed and assayed for luciferase
gene activity (using the Brightlite kit from Perkin-Elmer, Ueberlingen, Germany). Stimulation
indices were calculated in reference to reporter gene activity of medium without addition of
ODN.
Results:
Recently the receptor for the recognition of CpG sequences was identified and shown
to be a member of the Toll-Like Receptor (TLR) family (Hemmi et al., 2000). This receptor,
5 TLR9, is readily activated by ODNs containing optimal immunostimulatory CpG sequences.
We incubated a cell line stably expressing the human TLR9 with different concentrations of
10104 and control ODNs (Fig. 30).
The results demonstrate that 10104 ODN activated TLR9 in a dose dependent manner
with maximal stimulation at 0.625 ug/ml. The control ODN on the other hand stimulated at
10 only lOjxg/ml and at that was much lower than the stimulation observed with 10104 nucleic
acid.
CpG 10104 effect regardless of delivery vehicle:
Figs. 61A and 61B show the effects of topical CpG delivery using BEMA disks or in
15 saline on local pathology of mice following intravaginal challenge with HSV-2. Female
C57/B16 mice were injected SC with 2 mg of progesterone per mouse (4 days prior to viral
challenge). CpG 10104 (1,10 or 100 mg) in saline or impregnated onto bio-erodible
mucoadhesive disks (BEMA) was instilled into the vaginal cavity (IVAG) 24 hrs before viral
challenge. For viral challenge, mice were swabbed IVAG with a cotton applicator, turned on
20 their backs and infected by IVAG instillation of 10 ml containing 104 PFU HSV-2 (strain
333) during 1 hr while being maintained under halothane anesthesia. Genital pathology was
monitored daily following HSV-2 challenge and scoring performed blinded. Pathology was
scored on a 5-point scale: 0, no apparent infection; 1, slight redness of external vagina; 2,
redness and swelling of external vagina; 3, severe redness and swelling of external vaginal
25 and surrounding tissue; 4, genital ulceration with severe redness, swelling and hair loss of
genital and surrounding tissue; 5, severe genital ulceration extending to surrounding tissue.
Mice were sacrificed upon reaching stage 5. Graph shows mean pathology score relative to
time post infection (days) for CpG on BEMA disks (Figure 61A) or CpG in saline (Figure
61B).
30 The results demonstrate that IVAG delivery to mice of CpG 10104 in saline or on
BEMA disks can reduce vaginal pathology associated with subsequent IVAG HSV-2
infection.
Figs. 62 A and 62B show the effects of topical CpG delivery using BEMA disks on in
saline on survival of mice following intravaginal challenge with HSV-2. Mice were treated
essentially as described above. Mice were monitored daily and were sacrificed when severe
genital ulceration extending to surrounding tissue was noted. Graph shows % survival relative
5 to time post infection (days) for CpG on BEMA disks (Figure 62A) or CpG in saline (Figure
62B).
The results demonstrate that IVAG delivery to mice of CpG 10104 in saline or on
BEMA disks can enhance survival following subsequent IVAG HSV-2 infection.
10 Parental administration of CpG 10104:
Figs. 63 and 64 show the effects of parenteral CpG 10104 delivery on IP-10 and IFN-
gamma levels in plasma of mice. Female BALB/c mice were injected SC with 100 nmoles of
CpG 10104 in saline, CpG 7909 in saline or resiquimod (R-848). At various time-points after
injection (1,2, 3, 4, 5, 6, 7, 8, 9,10,11,12 hrs) mice were bled, plasma collected and IP-10
15 levels determined by ELISA.
The results indicate that CpG 10104 can induce significant amounts of IP-10 and IFN-
gamma in plasma after SC injection, and that levels attained are greater than those with R-
848.
20 Mucosal administration of CpG 10104:
Fig. 65 shows the effects of intravaginal CpG 10104 delivery on IP-10 levels in
plasma of mice. Female BALB/c mice had 100 nmoles of CpG 10104 in saline, CpG 7909 in
saline or resiquimod (R-848) instilled into the vaginal cavity. At various time-points after
injection (1,2, 3, 4, 5, 6, 7, 8, 9,10, 11,12 hrs) mice were bled, plasma collected and IP-10
25 levels determined by ELISA. The results indicate that CpG 10104 can induce significant
amounts of IP-10 in plasma after IVAG instillation.
Fig. 69 shows the effects of intravaginal CpG 10104 delivery on IP-10 levels in
vaginal wash of mice. Female BALB/c mice had 100 nmoles of CpG 10104 in saline, CpG
7909 in saline or resiquimod (R-848) instilled into the vaginal cavity. At various time-points
30 after injection (15 min, 30 min, 1,2, 3,4, 5, 6,7, 8, 9,10,11,12 hrs), vaginal cavity of mice
was washed three tunes with 75 ml of PBS. IP-10 levels in vaginal wash were determined by
ELISA. The results indicate that CpG 10104 can induce significant local production of IP-10
in vaginal cavity after IVAG instillation.
Topical administration of CpG 10104:
5 Fig. 67 shows the effects of topical CpG delivery on local pathology of mice following
intravaginal challenge with HSV-2. Female C57/B16 mice were injected SC with 2 ing of
progesterone per mouse (4 days prior to viral challenge). CpG 10104 (1,10 or 100 mg) in
saline, or Resiquimod (1,10 or 100 mg) was instilled into the vaginal cavity (IVAG) 24 hrs
before viral challenge. For viral challenge, mice were swabbed IVAG with a cotton
10 applicator, turned on their backs and infected by IVAG instillation of 10 ml containing 104
PFU HSV-2 (strain 333) during 1 hr while being maintained under halothane anesthesia.
Genital pathology was monitored daily following HSV-2 challenge and scoring performed
blinded. Pathology was scored on a 5-point scale: 0, no apparent infection; 1, slight redness of
external vagina; 2, redness and swelling of external vagina; 3, severe redness and swelling of
15 external vaginal and surrounding tissue; 4, genital ulceration with severe redness, swelling
and hair loss of genital and surrounding tissue; 5, severe genital ulceration extending to
surrounding tissue. Mice were sacrificed upon reaching stage 5.
The graph shows mean pathology score relative to time post infection (days) for CpG
ODN 10104 in saline or Resiquimod. The results demonstrate that IVAG delivery of CpG
20 10104 to mice can reduce vaginal pathology associated with subsequent IVAG HSV-2
infection, and that CpG 10104 can be more efficacious than a ten-fold higher dose of R-848.
Fig. 68 shows the effects of topical CpG delivery on survival of mice following
intravaginal challenge with HSV-2. Mice were treated essentially as described above. Mice
were monitored daily and were sacrificed when severe genital ulceration extending to
25 surrounding tissue was noted. Graph shows % survival relative to time post infection (days)
for CpG ODN 10104 in saline or Resiquimod.
The results demonstrate that IVAG delivery of CpG 10104 to mice can enhance
survival following subsequent IVAG HSV-2 infection, and that CpG 10104 can be more
efficacious than a ten-fold higher dose of R-848.
30 Figs. 70A and 70B show the effects of topical CpG delivery on survival and local
pathology of mice following intravaginal challenge with HSV-2. Mice were treated
essentially as described above. CpG 10104 (100 mg) in saline, or in an oil-in-water cream
was instilled into the vaginal cavity (IVAG) either as a single application 4 hrs after viral
infection, or as a multiple application, once daily for 5 days. Genital pathology was monitored
daily following HSV-2 challenge and scoring performed blinded. Pathology was scored on a
5-point scale: 0, no apparent infection; 1, slight redness of external vagina; 2, redness and
5 swelling of external vagina; 3, severe redness and swelling of external vaginal and
surrounding tissue; 4, genital ulceration with severe redness, swelling and hair loss of genital
and surrounding tissue; 5, severe genital ulceration extending to surrounding tissue. Mice
were sacrificed upon reaching stage 5. The graphs show % survival (Figure 70 A) and local
pathology score (Figure 70B) relative to time post infection (days) for CpG ODN 10104 in
10 saline.
The results demonstrate that IVAG delivery of CpG 10104 in saline or in an oil-in-
water cream can reduce pathology and enhance survival of mice previously infected with a
letha] dose of HSV-2.
15 Immunization of mice:
Figs. 71A and 71B show that CpG 10104 is as good as CpG 7909 in augmenting
humoral responses against HBsAg in BALB/c mice. BALB/c mice were immunized with 1
mg HBsAg alone or with 10 mg ODN and/or alum (25 mg AL3+) by infra muscular injection
into the left tibialis anterior muscle. Animals were boosted at 4 week post primary
20 immunization. Antibody titers were determined at 2 weeks post boost by end point ELISA.
Fig. 71A shows experiments conducted without alum, and Fig. 71B shows experiments
conducted with alum.
Figs. 72A and 72B show that CpG 10104 is as good as CpG 7909 in promoting Thl
biased immune responses (determined by high IgG2a titers compared to IgGl titers) against
25 HbsAg in BALB/c mice. BALB/c mice were immunized with 1 mg HBsAg alone or with 10
mg ODN and/or alum (25 mg AL3+) by intra muscular injection into the left tibialis anterior
muscle. Animals were boosted at 4 week post primary immunization. IgG isotype levels were
determined at 2 wks post boost using end point ELISA.
30 EXAMPLE 4 (ODN 10105):
Summary:
This report summarizes in vitro data with, human cells demonstrating that ODN 10105
behaves as well or better than ODN 7909 in human cell assays. In addition, ODN 10105
behaves as well or better than ODN 7909 in in vitro and in vivo data in mice demonstrating
that CpG ODN 10105 is useful in the activation of the innate immune system, and in
5 augmenting humoral and cellular HBsAg-specific responses in mice when coadministered
with the antigen.
The assays performed were receptor engagement (TLR9), B cell activation (expression
of cell surface activation marker and B cell proliferation) and cytokine secretion (EL-10, IP-10
and IFN-a). All assays demonstrated that ODN 10105 has properties that were similar or
10 superior to ODN 7909. In vitro studies (i.e. B cell proliferation assays, NK lytic activity,
cytokine secretion profiles) were carried out using naive BALB/c mouse splenocytes. In vivo
comparison studies were carried out by comparing the potential of these two ODNs to
enhance antigen specific immune responses to hepatitis B antigen (HBsAg).
15 Materials and Methods:
With respect to human studies, refer to Example 1 for descriptions of
oligodeoxynucleotides, TLR9 assays, human cell purification, cytokine detection, and cultures
for flow cytometric analysis of B cell activation.
With respect to murine in vitro and in vivo studies, refer to Example 1 for
20 descriptions of oligodeoxynucleotides, animals, splenocyte harvest and culture, B cell
proliferation assays, cytokine secretion profiles, NK assays, immunization of mice,
determination of antibody responses, and statistical analysis.
Results:
25 TLR9 engagement: We incubated a cell line stably expressing the human TLR9 with
different concentrations of ODNs 7909 and 10105 as well as a control ODN (Fig. 31). The
results demonstrate that there was no statistically significant difference between the two B
class ODNs in activating TLR9. Both ODNs showed the same dose-response curve and
reached maximum activation at the same concentrations. The control ODN used did not
30 induce TLR9 activation even at the highest concentration of 24mg/ml.
Human B cells: One characteristic of type B ODNs is their ability to very efficiently
activate B cells (Krieg et al., 1995). B cells and plasmacytoid DC are at the moment the
only immune cell types known to express TLR9 (Krug et al., 2001; Bauer et al., 2001).
The direct activation of B cells induced by ODNs 7909 and 10105 was measured by up
5 regulation of the cell surface marker CD86 (Fig. 32), and proliferation of B cells (Fig. 33).
For CD86 expression on human B cells PBMC of healthy blood donors were incubated with
different ODNs and B cell activation measured as described in Materials and Methods.
The results demonstrate that 10105 as well as 7909 are very potent stimulators of
human B cells. Fig. 32 shows that these CpG ODNs were capable to stimulate B cells at an in
J0 vitro concentration of only 0.4mg/ml. The plateau was reached at about 1.6mg/ml and more
than 70% of B cells were found to have up regulated CD86 in contrast to the control that was
much less potent. A similar result was obtained for the induction of B cell proliferation, with
exception that 10105 was able to induce B cell proliferation even at the highest dose test of 6
ug/ml, while 7909 plateaued at the dose of 1.6 to 3.0 ug/ml (Fig. 33).
15
Cytokine secretion: ODNs of the B class induce a Thl dominated immune response in vivo
as well as in vitro. It was found that they are able to induce typical Thl cytokines such as
IFN-y and IFN-a as well as chemokines such as MCP-1 and IP-10. In addition, low
secretion of the pro-inflammatory cytokines IL-6 as well as TNF-a and secretion of the
20 negative regulator IL-10 can be observed. The secretion of the Thl cytokine IFN-a, the
chemokine IP-10 as well as the regulatory cytokine IL-10 and the pro-inflammatory
cytokine TNF-a were measured following administration of 10105 and 7909. Fig. 34
shows the result for an experiment performed with 6 different donors at 0.2, 0.4 and 1.6
mg/ml to measure in vitro IFN-a secretion.
25 Both CpG ODNs induced high levels of IFN-a with a maximum reached at 0.4 to
1.6mg/ml. In contrast, the control ODN induced low amounts of IFN-a starting only at
5.0mg/ml. ODN 10105 induced higher levels of IFN-a at both the 1.6 andr5.0 mg/ml doses, as
compared to ODN 7909. The ODNs 7909 and 10105, in contrast to the control ODN, induced
the chemokine IP-10 as shown in Fig. 35, again with ODN 10105 inducing higher levels at
30 the 0.4 mg/ml dose.
The time-dependent effects on different cytokines were also analyzed. Therefore,
PBMC from different donors were incubated for 8h, 24h, 36h and/or 48h and the secretion of
IL-10 or IFN-a was measured. Figs. 36 and 37 demonstrate the results obtained for IFN-a
with two different donors upon incubation for 8h and 24h (Fig. 36) or 36h and 48h (Fig. 37).
5 IFN-a was initially secreted as early as 8h upon incubation with CpG ODN, maximum
amounts were reached at 24h and the amounts stayed at that level or even increased between
24h and 48h. LPS did not induce any IFN-a. For both donors, the ODN 10105 stimulated
higher levels of FN-a at the 8 hour time point at a concentration of 1.6 mg/ml.
A very similar experiment was performed for IL-10 secretion (Figs. 38 and 39). This
10 cytoldne showed similar characteristics to IFN-a although maximum amounts were obtained
at a 48h. Again, as demonstrated above for IFN-a, both CpG ODNs 7909 and 10105
demonstrated almost identical properties in these as in all other assays performed.
In vitro mouse studies: As shown in Fig. 40, ODN 10105 is able to stimulate higher levels
15 of B cell proliferation than ODN 7909 at all concentrations tested. According to the data
shown in Fig. 41, both CpG ODN 7909 and 10105 are able to stimulate IL-10, IL-12, EL-6
and TNF- secretion. For IL-12 and TNF- secretion, ODN 10105 elicits more factor
secretion at all concentrations tested than does 7909.
The CpG ODN have essentially equal potency in enhancing lytic activity of NK cells
20 in mouse splenocyte cultures (Fig. 42).
As shown in Fig. 43, either CpG ODN 7909 or 10105 significantly enhanced antibody
titers against HBsAg compared to antigen alone (pO.OOOl) whereas there was no significant
increase in anti-HBs responses when control ODN was used in combination with HBsAg
(p=0.85).
25 As shown in Fig. 44, the increase in total IgG levels is similar both the CpG ODN. In
mice IgG isotype distribution is widely used as an indication of the nature of the immune
response where high IgG2a/IgGl ratios are indicative of a Thl biased immune response
(Constant and Bottomly, 1997). In the present study, the use of CpG ODN significantly
enhanced IgG2a titers compared to when antigen was used alone or in combination with
30 control ODN 2137 (p 2137 and p similar when either CpG ODN 7909 or 10105 was used in combination with HBsAg (p>0.05).
Therefore, both CpG ODN 7909 and 10105 are equally potent in their ability to induce Thl
biased immune responses as measured by the increased levels of IgG2a over IgGl.
Conclusions:
5 In vitro data with human cells demonstrating that ODN 10105 behaves similarly and
in some instances, in a manner superior to that of ODN 7909 is demonstrated. According to
the results of the murine studies, CpG ODN 7909 and 10105 have similar immune
potentiating properties, both for their in vitro effects on innate immune responses as well as
their ability to augment antigen specific responses in vivo when administered together with an
10 antigen.
EXAMPLE 5 (ODN 10106):
HCVstudies:
Summary:
15 This study was undertaken to compare CpG ODN 10106 to CpG ODN 7909 for it's
immune activating properties on PBMCs isolated from both normal, healthy, adult subjects
and adult subjects chronically infected with HCV. The ability of the ODNs to stimulate B
cell proliferation, cytokine secretion (IL-10 and IFN-a) and chemolcine secretion (IP-10) was
evaluated. All assays demonstrated that ODN 10106 has properties that are almost identical to
20 or better than ODN 7909 and similar results were observed with PBMCs isolated from
normal, healthy, adult subjects and adult subjects chronically infected with HCV.
Materials and Methods:
Human (HCV) Studies:
25 Oligodeoxynudeotides: CpG ODN 7909,10106 and control ODN 4010 were manufactured
under contract for Coley Pharmaceutical Group. All ODN were resuspended in sterile,
endotoxin free TE at pH 8.0 (OmniPer®; EM Science, Gibbstown, NJ) and stored and
handled under aseptic conditions to prevent both microbial and endotoxin contamination. The
control ODN, 4010, does not contain stimulatory CpG motifs. Dilutions of the ODNs were
30 made in RPMI 1640 complete media (Gibco BRL, Grand Island, NY) containing 10% normal
human AB serum (Wisent Inc, St. Bruno, QC) (heat inactivated) and 1%
penicillin/streptomycin (Gibco BRL, Grand Island, NY) just prior to their use.
PBMC isolation: 200 mL of whole blood was collected by venous puncture into heparinised
green top vacutainers from ten (10) normal, healthy, adult subjects and ten (10) adult subjects
chronically infected with HCV who had failed a previous 6-month course of an IFN-a-based
therapy. Peripheral blood mononuclear cells (PBMCs) were purified by centrifugation over
Ficoll-Pacque at 400 x g for 35 min. Cells were resuspended at a concentration of 10x106/Vml
in RPMI complete media containing 10% normal human AB serum (heat inactivated) and 1%
penicillin/streptomycin.
B cell proliferation assays: ODNs were diluted in RPMI media containing 10% normal
human AB serum (heat inactivated) and 1% penicillin/streptomycin to the following
concentrations 2, 6, and 12 mg/ml. 100 mL of the diluted ODNs were added to the wells of a
96 well round bottom plate. Freshly isolated PBMCs were resuspended to 1x106/Vml in
complete RPMI media containing 10% normal human AB serum (heat inactivated) and 1%
penicillin/streptomycin, the cell suspension was then added to each well (100 mL/well)
resulting in final ODN concentrations of 1, 3 and 6 mg/mL. Cells were cultured for 5 days and
then pulsed with 3H-Thymidine (1 mCi/well) for 16 to 18 hours. Following the incubation,
cells were harvested onto filter paper and the amount of radioactivity measured. Results are
reported as stimulation index (SI) with respect to untreated media control.
Cytokine detection: ODNs were diluted in RPMI media containing 10% normal human AB
serum (heat inactivated) and 1% penicillin/streptomycin to the following concentrations 2, 6,
and 12 mg/ml. 100 mL of the diluted ODNs were added to the wells of a 96 well flat bottom
plate. Freshly isolated PBMCs resuspended at a concentration of 10xl06/ml were added to
each well (100 mL per well) resulting in final ODN concentrations of 1,3 and 6 mg/mL. Cells
were incubated at 37°C with 5% CO2 for 48 hours. Following the incubation, cell
supernatants were collected from each well and frozen at -80°C until assayed.
IFNa and .IL-10and IP-10 levels in supernatants were measured using commercial
J ELISA Kits from R&D Systems, Minneapolis, MN (Catalogued 41105, D1000 and DIP100
respectively) according to the manufacturer's instructions.
Statistical analysis: Statistical analysis was performed using InStat (Graph PAD Software,
San Diego). The statistical difference between groups was determined by one-way ANOVA
10 followed by Tukey-Kramer multiple comparisons test on raw data or transformed data (logio).
If following transformation of the data, the Bartlett test indicated that the difference among
standard deviations was significant a nonparametric ANOVA (Kurskal-Wallis Test) was used.
Results:
15 B cell proliferation: One characteristic of type B ODNs is their ability to very efficiently
activate B cells (Krieg et al., 1995). The ability of the two B class ODNs, 7909 and 10106, to
stimulate B cell proliferation is shown below in Fig. 45.
When compared to CpG ODN 7909,10106 was equally effective at stimulating B cell
proliferation. Additionally, there was no significant difference in their ability to stimulate
20 PBMCs from either population, normal, healthy subjects or subjects chronically infected with
HCV.
Cytokine/chemokine secretion: ODNs of the B class lead to a Thl dominated immune
response in vivo as well as in vitro. It was found that they are capable of inducing typical Thl
25 cytokines such as IFNa and IFN-a as well as chemokines such as MCP-1 and IP-10. In
addition, low secretion of the pro-inflammatory cytokines IL-6 as well as TNF-a and
secretion of the negative regulator IL-10 can be observed. Figs. 46, 47 and 48, illustrate the
ability of the B class ODNs to stimulate secretion of the Thl cytokine IFN-a, the chemokine
IP-10 as well as the regulatory cytokine IL-10.
30 The B class ODNs, 7909 and 10106, induced the secretion of similar concentrations of
IFN-a.
Equivalent concentrations of IP-10 were secreted following stimulation of PBMCs
with either B class ODN, 7909 or 10106. There was no difference observed in the ability of
the ODNs to stimulate IP-10 secretion from PBMCs isolated fiom normal, healthy subjects or
subjects chronically infected with HCV. The maximum concentration of IP-10 was achieved
5 at an ODN concentration of 3 mg/ml for both 7909 and 10106. The same analysis was
performed for IL-10 secretion (Fig. 48).
CpG ODNs 7909 and 10106 were able to induce the secretion of similar
concentrations of IL-10 from PBMCs isolated from both adult populations. Maximum IL-10
induction for both ODNs was observed at 6 mg/mL.
10
Conclusions:
In vitro data with human peripheral blood mononuclear cells isolated from two
distinct adult populations, (1) normal healthy subjects and (2) subjects chronically infected
with HCV who failed previous IFN-a therapy, demonstrate that the B class CpG ODNs 7909
75 and 10106 are equally capable of stimulating B cell proliferation and secretion of IFN-a, IL-
10 and IP-10 within the same population, and furthermore that effects were the same for the
two populations
Non-HCV Studies:
20 Summary:
CpG ODN 10106 is a class B nucleic acid. These experiments compare the immune
activating properties of CpG ODN 10106 to CpG ODN 7909. Both in vitro and in vivo
immunological parameters were used for this assessment.
The in vitro data were obtained by comparing ODNs 10106 and 7909 on human
25 PBMC. The assays performed included receptor engagement (TLR9), B cell activation
(expression of cell surface activation marker and B cell proliferation) and cytokine secretion
(IL-10, IP-10, EFN-alpha and TNF-alpha). All assays demonstrated that ODN 10106 has
properties that are almost identical to ODN 7909.
In vitro studies (i.e., B cell proliferation assays, NK lytic activity, cytokine secretion
30 profiles) were also carried out using naive BALB/c mouse splenocytes.
In vivo comparison studies were carried out by examining the potential of these 2 ODNs to
enhance antigen specific immune responses to hepatitis B antigen (HBsAg). For in vivo
comparison studies, both the enhancement of humoral responses (antibody) as well as cell
mediated immune responses (CTL activity) were examined, In addition, nature of the
immune response induced (i.e., Thl vs. Th2) was examined by determining the IgG2a/IgGl
ratio as well as the strength of the CTL response.
5
Materials and Methods:
With respect to human studies, refer to Example 1 for descriptions of
oligodeoxynucleotides, TLR9 assays, human cell purification, cytokine detection, and cultures
for flow cytometric analysis of B cell activation.
With respect to murine in vitro and in vivo studies, refer to Example 1 for
descriptions of oligodeoxynucleotides, animals, splenocyte harvest and culture, B cell
proliferation assays, cytokine secretion profiles, NK assays, immunization of mice,
determination of antibody responses, and statistical analysis.
15 Results:
TLR9 engagement: We incubated a cell line stably expressing the human TLR9 with
different concentrations of ODNs 7909 and 10106 as well as a control ODN (Fig. 49). The
results demonstrate that there was no significant difference between the two B class ODNs in
activating TLR9. Both ODNs showed the same dose-response curve. The control ODN used
20 did not induce TLR9 activation even at the highest concentration of 12 mg/ml.
Activation of human B cells: One characteristic of type B ODNs is their ability to very
efficiently activate B cells (Krieg et al., 1995). B cells and plasmacytoid DC are at the
moment the only immune cell types known to express TLR9 (Krug et al., 2001; Bauer et al.,
25 2001). We, therefore, measured the direct activation of B cells induced by ODNs 7909 and
10106 by up regulation of the cell surface marker CD86 (Fig. 50), and proliferation of B cells
(Fig. 51). For CD86 expression on human B cells PBMC of healthy blood donors were
incubated with different ODNs and B cell activation measured as described in Materials and
Methods.
30
Proliferation of B cells: Both results demonstrate that 10106 as well as 7909 are very potent
stimulators of human B cells. Fig. 50 shows that these CpG ODNs were capable to stimulate
B cells very strongly at an in vitro concentration of only 0.4mg/ml. The plateau was reached at
about 1.6mg/ml. A similar result was obtained for the induction of B cell proliferation (Fig.
51) where the stimulation index reached maximum at about 0.8 mg/ml.
5 Cytokine secretion: ODNs of the B class lead to a Thl dominated immune response in vivo
as well as in vitro. It was found that they are capable to induce typical Thl cytokines such as
IFN-y and IFN-a as well as chemokines such as MCP-1 and IP-10. In addition, low secretion
of the pro-inflammatory cytokines IL-6 as well as TNF-a and secretion of the negative
regulator IL-10 can be observed. We, therefore, measured the secretion of the Thl cytokine
10 IFN-a, the chemokine IP-10 as well as the regulatory cytokine IL-10 and the pro-
inflammatory cytokine TNF-a.
Fig. 52 shows the result for an experiment performed with 3 different donors at 0.2,
0.4,1.6 and 5mg/ml to measure in vitro IFN-a secretion. Both CpG ODNs, 7909 as well as
10106, induced high levels of IFN-a with a maximum reached at 0.4 (7909) or 1.6|ig/ml
15 (10106). However, maximal elevation of IFN-a secretion was of about a factor of three more
pronounced after 10106 stimulation compared to 7909. In contrast, the control ODN induced
low amounts of IFN-a starting only at 5.0mg/ml.
In addition, ODNs 7909 and 10106, in contrast to the control ODN, induced higher
amounts of the chemokine IP-10 as shown in Fig. 53, the plateau was already reached at about
20 0.2mg/ml in this experiment.
A very similar experiment was performed for IL-10 secretion (Fig. 54). Again, as
demonstrated above for IFN-a, both CpG ODNs 7909 and 10106 demonstrated almost
identical properties in this as in all other assays performed. In comparison, the control ODN
induces IL-10 secretion only at the highest concentration.
25 As shown in Fig. 55, both ODNs 7909 and 10106 as well as the control ODN showed
a low secretion profile of the pro-inflammatory cytoldne TNF-a in all tested concentrations in
comparison to LPS. Again, one can observe comparable characteristics after stimulation with
these two ODNs.
According to the data both CpG ODN 7909 and 10106 have essentially equal potency
30 in enhancing cytokine secretion by mouse splenocytes (Fig. 57).
B cell proliferation: According to the data, CpG ODN 10106 is equally potent if not
superior to CpG ODN 7909 in inducing mouse B cell proliferation at all concentrations
tested (Fig. 56).
5 NK assays: According to the data both CpG ODN 7909 and 10106 have essentially equal
potency in enhancing lytic activity of NK cells in mouse splenocyte cultures (Fig. 58).
Total IgG responses: According to the results of this study use of either CpG ODN 7909 or
10106 significantly enhanced antibody titers against HBsAg compared to antigen alone
10 (p with Ag + CpG ODN 7909 or Ag + CpG ODN 10106 (p= 0.86). Furthermore, the control ODN
did not significantly increase the anti-HBs responses when used in combination with HBsAg
(p=0.86) (Fig. 59). The increase in total IgG levels is slightly but significantly (p=0.04) greater
when CpG ODN 7909 used compared to when CpG ODN 10106 is used.
15
Nature of the humoral response (IgGl vs. IgG2a ratio): In mice IgG isotype distribution is
widely used as an indication of the nature of the immune response where a high IgG2a/IgGl
ratios are indicative of a Thl biased immune response (Constant and Bottomry, 1997). In the
present study, the use of CpG ODN significantly enhanced IgG2a titers compared to when
20 antigen was used alone or in combination with control ODN 2137 (p p 10106 vs. Ag + 2137). However, the level of IgG2a response was similar when either CpG
ODN 7909 or 10106 was used in combination with HBsAg (p>0.05). Therefore, both CpG
ODN 7909 and 10106 are equally potent in their ability to induce Thl biased immune
25 responses as measured by the increased levels of IgG2a over IgGl (Fig. 60).
Conclusion:
In vitro data with human peripheral mononuclear cells demonstrate that two molecules
of the B class (7909 and 10106) behave very similarly if not identical hi a variety of assays
30 performed, in some assays, ODN 10106 performed better than ODN 7909.
According to the results of the murine studies, CpG ODN 7909 and 10106 have
similar immune potentiating properties, both for their in vitro effects on innate immune
responses as well as their ability to augment antigen specific responses in vivo when
administered together with an antigen.
References:
5 1. Bauer, S. et al.; Human TLR9 confers responsiveness to bacterial DNA via species-
specific CpG motif recognition; PNAS 98, 2001.
2. Constant, S. L., and K. Bottomly 1997. Induction of Thl and Th2 CD4+ T cell
responses: the alternative approaches Annu Rev Immunol. 15:297-322.
3. Hemmi, H. et al.; A Toll-like receptor recognizes bacterial DNA; Nature 408, 2000.
10 4. Rrieg, A. M. et al.; CpG motifs in bacterial DNA trigger direct B-cell activation;
Nature 374, 1995.
5. Rrug, A. et al.; Toll-like receptor expression reveals CpG DNA as a unique microbial
stimulus for pDC which synergizes with CD40 ligand to induce high amounts of IL-12; Eur.
J.Immunol. 31; 2001.
15 6. Davis, H. L., R. Weeratna, T. J. Waldschmidt, L. Tygrett, J. Schorr, and A. M. Krieg
1998. CpG DNA is a potent enhancer of specific immunity in mice immunized with
recombinant hepatitis B surface antigen J Immunol. 160:870-6.
7. McCluskie, M. J., and H. L. Davis 1998. CpG DNA is a potent enhancer of systemic
and mucosal immune responses against hepatitis B surface antigen with intranasal
20 administration to mice J Immunol. 161:4463 -6
Equivalents
The foregoing written specification is considered to be sufficient to enable one skilled
in the art to practice the invention. The present invention is not to be limited in scope by
25 examples provided, since the examples are intended as a single illustration of one aspect of
the invention and other functionally equivalent embodiments are within the scope of the
invention. Various modifications of the invention in addition to those shown and described
herein will become apparent to those skilled in the art from the foregoing description and fall
within the scope of the appended claims. The advantages and objects of the invention are not
30 necessarily encompassed by each embodiment of the invention.

WE CLAIM:
1. A composition comprising
(a) an immunostimulatory nucleic acid molecule comprising the nucleotide sequence of
SEQ ID NO:1 or SEQ ID NO: 19, wherein the immunostimulatory nucleic acid has a nucleotide
backbone comprising at least one phosphorothioate modification,
(b) an immunostimulatory nucleic acid molecule comprising the nucleotide sequence of
SEQ ID NO:1 or SEQ ID NO: 19, wherein the immunostimulatory nucleic acid is less than or
equal to 100 nucleotides,
(c) an immunostimulatory nucleic acid molecule comprising the nucleotide sequence of
SEQ ID NO:1 or SEQ ID NO: 19, wherein the composition further comprises an antigen,
(d) an immunostimulatory nucleic acid molecule consisting of SEQ ID NO: 1 or SEQ ID
NO:19,
(e) an immunostimulatory nucleic acid molecule comprising the nucleotide sequence of
SEQ ID NO:45,
(f) an immunostimulatory nucleic acid molecule comprising the nucleotide sequence of
SEQ ID NO: 118, or
(g) an immunostimulatory nucleic acid molecule comprising the nucleotide sequence of
SEQ ID NO: 141.
2. The composition as claimed in claim 1, wherein the immunostimulatory nucleic
acid molecule consists of the nucleotide sequence of SEQ ID NO:45, SEQ ID NO: 118 or SEQ
ID NO: 141.
3. The composition as claimed in claim 1, wherein the immunostimulatory nucleic
acid molecule comprises the nucleotide sequence of SEQ ID NOs:45, 118 or 141, further
comprising an antigen.
4. The composition as claimed in claim 3, wherein the antigen is selected from the
group consisting of a microbial antigen, a cancer antigen, and an allergen.
5. The composition as claimed in claim 4, wherein the microbial antigen is selected
from the group consisting of a bacterial antigen, a viral antigen, a fungal antigen and a parasitic
antigen.
6. The composition as claimed in claim 3, wherein the antigen is encoded by a
nucleic acid vector.
7. The composition as claimed in claim 6, wherein the nucleic acid vector is
separate from the immunostimulatory nucleic acid.
8. The composition as claimed in claim 3, wherein the antigen is a peptide antigen.
9. The composition as claimed in claim 1, further comprising an adjuvant.
10. The composition as claimed in claim 9, wherein the adjuvant is a mucosal
adjuvant.
11. The composition as claimed in claim 1, further comprising a cytokine.
12. The composition as claimed in claim 1, further comprising a therapeutic agent
selected from the group consisting of an anti-microbial agent, an anti-cancer agent, and an
allergy/asthma medicament.
13. The composition as claimed in claim 12, wherein the anti-microbial agent is
selected from the group consisting of an anti-bacterial agent, an anti-viral agent, an anti-fungal
agent, and an anti-parasite agent.
14. The composition as claimed in claim 12, wherein the anti-cancer agent is selected
from the group consisting of a chemotherapeutic agent, a cancer vaccine, and an
immunotherapeutic agent.
15. The composition as claimed in claim 12, wherein the allergy/asthma medicament
is selected from the group consisting of PDE-4 inhibitor, bronchodilator/beta-2 agonist, K+
channel opener, VLA-4 antagonist, neurokin antagonist, TXA2 synthesis inhibitor, xanthanine,
arachidonic acid antagonist, 5 lipoxygenase inhibitor, thromboxin A2 receptor antagonist,
thromboxane A2 antagonist, inhibitor of 5-lipox activation protein, and protease inhibitor.
16. The composition as claimed in claim 1, wherein the immunostimulatory nucleic
acid comprises the nucleotide sequence of SEQ ID NOs: 45, 118 or 141, and wherein the
immunostimulatory nucleic acid has a nucleotide backbone which includes at least one backbone
modification.
17. The composition as claimed in claim 16, wherein the backbone modification is a
phosphorothioate modification.
18. The composition as claimed in claim 1, wherein the nucleotide backbone is
chimeric.
19. The composition as claimed in claim 1, wherein the nucleotide backbone is
entirely modified.
20. The composition as claimed in claim 1, further comprising a pharmaceutically
acceptable carrier.
21. The composition as claimed in claim 1, wherein the immunostimulatory nucleic
acid is free of methylated CpG dinucleotides.
22. The composition as claimed in claim 1, wherein the immunostimulatory nucleic
acid includes at least four CpG motifs.
23. The composition as claimed in claim 1, wherein the immunostimulatory nucleic
acid is T-rich.
24. The composition as claimed in claim 1, wherein the immunostimulatory nucleic
acid includes a poly-T sequence.
25. The composition as claimed in claim 1, wherein the immunostimulatory nucleic
acid includes a poly-G sequence.
26. The composition as claimed in claim 1, wherein the immunostimulatory nucleic
acid is formulated for oral administration.
27. The composition as claimed in claim 1, wherein the immunostimulatory nucleic
acid is formulated as a nutritional supplement.
28. The composition as claimed in claim 27, wherein the nutritional supplement is
formulated as a capsule, a pill, or a sublingual tablet.
29. The composition as claimed in claim 1, wherein the immunostimulatory nucleic
acid is formulated for local administration.
30. The composition as claimed in claim 1, wherein the immunostimulatory nucleic
acid is formulated for parenteral administration.
31. The composition as claimed in claim 1, wherein the immunostimulatory nucleic
acid is formulated in a sustained release device.
32. The composition as claimed in claim 1, wherein the immunostimulatory nucleic
acid is formulated for delivery to a mucosal surface.
33. The composition as claimed in claim 1, wherein the mucosal surface is selected
from the group consisting of an oral, nasal, rectal, vaginal, and ocular surface.
34. The composition as claimed in claim 1, wherein the immunostimulatory nucleic
acid stimulates a mucosal immune response.
35. The composition as claimed in claim 1, wherein the immunostimulatory nucleic
acid stimulates a systemic immune response.
36. The composition as claimed in claim 1, wherein the immunostimulatory nucleic
acid is provided in an amount effective to stimulate a mucosal immune response.
37. The composition as claimed in claim 1, wherein the immunostimulatory nucleic
acid is provided in an amount effective to stimulate a systemic immune response.
38. The composition as claimed in claim 1, wherein the immunostimulatory nucleic
acid is provided in an amount effective to stimulate an innate immune response.
39. The composition as claimed in claim 1, wherein the immunostimulatory nucleic
acid is provided in an amount effective to treat or prevent an infectious disease.
40. The composition as claimed in claim 1, wherein the immunostimulatory nucleic
acid is provided in an amount effective to treat or prevent an allergy.
41. The composition as claimed in claim 1, wherein the immunostimulatory nucleic
acid is provided in an amount effective to treat or prevent asthma.
42. The composition as claimed in claim 1, wherein the immunostimulatory nucleic
acid is provided in an amount effective to treat or prevent a cancer.
43. The composition as claimed in claim 31, wherein the sustained release device is a
microparticle.
44. The composition as claimed in claim 39, wherein the infectious disease is a herpes
simplex virus infection.
45. A composition as claimed in claim 1, for stimulating an immune response in a
subject in need thereof,
wherein the composition is administered to a subject in an amount effective to stimulate
an immune response.
46. The composition as claimed in claim 45, wherein the subject has or is at risk of
developing an infection.
47. The composition as claimed in claim 46, wherein the infection is selected from
the group consisting of a bacterial infection, a viral infection, a fungal infection, and a parasite
infection.
48. The composition as claimed in claim 47, wherein the viral infection is selected
from the group consisting of Human immunodeficiency viruses (HIV-1 and HIV-2), Human T
lymphotropic virus type I (HTLV-I), Human T lymphotrophic virus type II (HTLV-II), Herpes
simplex virus type I (HSV-1) Herpes simplex virus type 2 (HSV-2), Human papilloma virus
(multiple types), Hepatitis A virus, Hepatitis B virus, Hepatitis C and D viruses, Epstein-Barr
virus (EBV), Cytomegalovirus and Molluscum contagiosum virus.
49. The composition as claimed in claim 48, wherein the viral infection is a herpes
simplex virus infection.
50. The composition as claimed in claim 45, wherein the subject has or is at risk of
developing allergy.
51. The composition as claimed in claim 45, wherein the subject has or is at risk of
developing asthma.
52. The composition as claimed in claim 45, wherein the subject has or is at risk of
developing a cancer.
53. The composition as claimed in claim 45, further comprising an antigen.
54. The composition as claimed in claim 53, wherein the antigen is selected from the
group consisting of a microbial antigen, a cancer antigen, a self antigen, and an allergen.
55. The composition as claimed in claim 54, wherein the microbial antigen is selected
from the group consisting of a bacterial antigen, a viral antigen, a fungal antigen, and a parasitic
antigen.
56. The composition as claimed in claim 55, wherein the antigen is derived from a
microorganism selected from the group consisting of herpesviridae, retroviridae,
orthomyroviridae, toxoplasma, haemophilus, campylobacter, clostridium, E.coli, and
staphylococcus.
57. The composition as claimed in claim 45, wherein the immune response is an
antigen-specific immune response.
58. The composition as claimed in claim 53, wherein the antigen is encoded by a
nucleic acid vector.
59. The composition as claimed in claim 58, wherein the nucleic acid vector is
separate from the immunostimulatory nucleic acid.
60. The composition as claimed in claim 53, wherein the antigen is a peptide antigen.
61. The composition as claimed in claim 45, further comprising an adjuvant.
62. The composition as claimed in claim 61, wherein the adjuvant is a mucosal
adjuvant.
63. The composition as claimed in claim 45, further comprising a second therapeutic
agent.
64. The composition as claimed in claim 63, wherein the second therapeutic agent is
an anti-microbial agent.
65. The composition as claimed in claim 64, wherein the anti-microbial agent is
selected from the group consisting of an anti-bacterial agent, an anti-viral agent, an anti-fungal
agent, and an anti-parasite agent.
66. The composition as claimed in claim 63, wherein the second therapeutic agent is
an anti-cancer agent.
67. The composition as claimed in claim 66, wherein the anti-cancer agent is selected
from the group consisting of a chemotherapeutic agent, a cancer vaccine, and an
immunomodulatory agent.
68. The composition as claimed in claim 63, wherein the second therapeutic agent is
an allergy/asthma medicament.
69. The composition as claimed in claim 68, wherein the allergy/asthma medicament
is selected from the group consisting of PDE-4 inhibitor, bronchodilator/beta-2 agonist, K+
channel opener, VLA-4 antagonist, neurokin antagonist, TXA2 synthesis inhibitor, xanthanine,
arachidonic acid antagonist, 5 lipoxygenase inhibitor, thromboxin A2 receptor antagonist,
thromboxane A2 antagonist, inhibitor of 5-lipox activation protein, and protease inhibitor.
70. The composition of claim 45, wherein the immunostimulatory nucleic acid
comprises the nucleotide sequence of SEQ ID NOs:45, 118 or 141, and wherein the
immunostimulatory nucleic acid has a nucleotide backbone which includes at least one backbone
modification.
71. The composition of claim 70, wherein the backbone modification is a
phosphorothioate modification.
72. The composition as claimed in claim 45, wherein the nucleotide backbone is
chimeric.
73. The composition as claimed in claim 45, wherein the nucleotide backbone is
entirely modified.
74. The composition as claimed in claim 45, wherein the immunostimulatory nucleic
acid is free of methylated CpG dinucleotides.
75. The composition as claimed in claim 45, wherein the immunostimulatory nucleic
acid includes a poly-G sequence.
76. The composition as claimed in claim 45, wherein the immunostimulatory nucleic
acid is administered orally.
77. The composition as claimed in claim 45, wherein the immunostimulatory nucleic
acid is administered locally.
78. The composition as claimed in claim 45, wherein the immunostimulatory nucleic
acid is administered parenterally.
79. The composition as claimed in claim 45, wherein the immunostimulatory nucleic
acid is administered in a sustained release device.
80. The composition as claimed in claim 45, wherein the immunostimulatory nucleic
acid is administered to a mucosal surface.
81. The composition as claimed in claim 45, wherein the immune response is a
mucosal immune response.
82. The composition as claimed in claim 45, wherein the immune response is a
systemic immune response.
83. The composition as claimed in claim 80, wherein the mucosal surface is selected
from the group consisting of an oral, nasal, rectal, vaginal, and ocular surface.
84. The composition as claimed in claim 46, further comprising an activated immune
cell.
85. The composition as claimed in claim 84, wherein the immune cell is a leukocyte.
86. The composition as claimed in claim 84, wherein the immune cell is a dendritic
cell.
87. The composition as claimed in claim 84, further comprising contacting the
immune cell with an antigen.
88. The composition as claimed in claim 45, wherein the subject is a human.
89. The composition as claimed in claim 45, wherein the subject is selected from the
group consisting of a dog, cat, horse, cow, pig, sheep, goat, chicken, monkey and fish.
90. The composition as claimed in claim 45, wherein the subject has or is at risk of
developing an infectious disease.
91. The composition as claimed in claim 52, wherein the cancer is selected from the
group consisting of biliary tract cancer; bone cancer; brain and CNS cancer; breast cancer;
cervical cancer; choriocarcinoma; colon cancer; connective tissue cancer; endometrial cancer;
esophageal cancer; eye cancer; gastric cancer; Hodgkin's lymphoma; intraepithelial neoplasms;
larynx cancer; lymphomas; liver cancer; lung cancer (e.g. small cell and non-small cell);
melanoma; neuroblastomas; oral cavity cancer; ovarian cancer; pancreas cancer; prostate cancer;
rectal cancer; sarcomas; skin cancer; testicular cancer; thyroid cancer; and renal cancer.
92. The composition as claimed in claim 45, further comprising an antibody specific
for a cell surface antigen.
93. An in vitro assay for identifying an immunostimulatory nucleic acid comprising
measuring a control level of activation of an immune cell population contacted with an
immunostimulatory nucleic acid comprising a nucleotide sequence of SEQ ID NO:1, SEQ ID
NO:19, SEQ ID NO:45, SEQ ID NO:118 or SEQ ID NO:141,
measuring a test level of activation of an immune cell population contacted with a test
nucleic acid, and
comparing the control level of activation to the test level of activation,
wherein a test level that is equal to or above the control level is indicative of an
immunostimulatory nucleic acid.
The invention provides immunostimulatory nucleic acids comprising the
nucleotide sequence of SEQ ID NO:1, 19, 45, 118 or 141 and compositions thereof.
The immunostimulatory nucleic acids may have a nucleotide backbone comprising at
least one phosphorothioate modification, and/or the immunostimulatory nucleic
acids may be less than or equal to 100 nucleotides. Immunostimulatory nucleic
acids of the invention can be combined with antigens, adjuvants, cytokines and
therapeutic agents.

Documents:

122-KOLNP-2005-CORRESPONDENCE 1.1.pdf

122-KOLNP-2005-CORRESPONDENCE.pdf

122-KOLNP-2005-FORM 27.pdf

122-KOLNP-2005-FORM-27.pdf

122-kolnp-2005-granted-abstract.pdf

122-kolnp-2005-granted-assignment.pdf

122-kolnp-2005-granted-claims.pdf

122-kolnp-2005-granted-correspondence.pdf

122-kolnp-2005-granted-description (complete).pdf

122-kolnp-2005-granted-drawings.pdf

122-kolnp-2005-granted-examination report.pdf

122-kolnp-2005-granted-form 1.pdf

122-kolnp-2005-granted-form 13.pdf

122-kolnp-2005-granted-form 18.pdf

122-kolnp-2005-granted-form 3.pdf

122-kolnp-2005-granted-gpa.pdf

122-kolnp-2005-granted-reply to examination report.pdf

122-kolnp-2005-granted-specification.pdf

122-KOLNP-2005-PA.pdf

122-KOLNP-2005-PETITION UNDER RULE 137.pdf


Patent Number 234013
Indian Patent Application Number 122/KOLNP/2005
PG Journal Number 18/2009
Publication Date 01-May-2009
Grant Date 29-Apr-2009
Date of Filing 02-Feb-2005
Name of Patentee COLEY PHARMACEUTICAL GROUP, INC.
Applicant Address 93, WORCESTER STREET, SUITE 101, WELLESLEY MA
Inventors:
# Inventor's Name Inventor's Address
1 KRIEG, ARTHUR, M 173 WINDING RIVER ROAD, WELLESLEY MA 02481
PCT International Classification Number A01K 43/04
PCT International Application Number PCT/US2003/021113
PCT International Filing date 2003-07-03
PCT Conventions:
# PCT Application Number Date of Convention Priority Country
1 60/394,090 2002-07-03 U.S.A.
2 60/393,880 2002-07-03 U.S.A.
3 60/394,091 2002-07-03 U.S.A.
4 60/394,164 2002-07-03 U.S.A.
5 60/394,193 2002-07-03 U.S.A.