Title of Invention

AN IMMUNOGENIC COMPOSITION

Abstract There is disclosed an immunogenic composition comprising a polypeptide which has at least 70% identity to the amino acid sequence of SEQ ID NO:2 or SEQ ID NO:10 over the entire length of SEQ ID NO:2 or SEQ ID NO: 10; a pharmaceutically acceptable carrier; and a TH-1 inducing adjuvant for use in medicine.
Full Text AN IMMUNOGENIC COMPOSITION
The present invention relates to pharmaceutical compositions and methods for inducing
an immune response against tumours-related antigens. More specifically, the invention
relates to polynucleotides, herein referred to as CASB7439 polynucleotides, polypeptides
encoded thereby (referred to herein as CASB7439 polypeptides), recombinant materials
and methods for their production.. In another aspect, the invention relates to methods for
using such polypeptides and polynucleotides, including the treatment of cancer, more
particularly colorectal cancer, and autoimmune diseases and other related conditions. In
another aspect, the invention relates to pharmaceutical compositions containing
CASB7439 polypeptides and polynucleotides, to methods of manufacture of such
compositions and to their use in medicine. In a further aspect, the invention relates to
methods for identifying agonists and antagonists/inhibitors using the materials provided
by the invention, and treating conditions associated with CASB7439 polypeptide
imbalance with the identified compounds. In a still further aspect, the invention relates to
diagnostic assays for detecting diseases associated with inappropriate CASB7439
polypeptide activity or levels.
Polypeptides and polynucleotides of the present invention are believed to be important
immunogens for specific prophylactic or therapeutic immunization against tumours, because
they are specifically expressed or highly over-expressed in tumours compared to normal
cells and can thus be targeted by antigen-specific immune mechanisms leading to the
destruction of the tumour cell. They can also be used to diagnose the occurrence of tumour
cells. Furthermore, their inappropriate expression in certain circumstances can cause an
induction of autoimmune, inappropriate immune responses, which could be corrected
through appropriate vaccination using the same polypeptides or polynucleotides. In this
respect the most important biological activities to our purpose are the antigenic and
immunogenic activities of the polypeptide of the present invention. A polypeptide of the
present invention may also exhibit at least one other biological activity of a CASB7439
polypeptide, which could qualify it as a target for therapeutic or prophylactic intervention
different from that linked to the immune response.
In a first aspect, the present invention relates to CASB7439 polypeptides. Such peptides
include isolated polypeptides, comprising an amino acid sequence which has at least 70%
identity, preferably at least 80% identity, more preferably at least 90% identity, yet more
preferably at least 95% identity, most preferably at least 97-99% identity, to that of SEQ
ID NO:2, SEQ ID NO:3, SEQ ID NO:7, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID
NO: 12 or SEQ ID NO: 14 over the entire length of SEQ ID NO:2, SEQ ID NO:3, SEQ
ID NO:7, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12 or SEQ ID NO: 14
respectively, with the proviso that said isolated polypeptide is not SEQ ID NO:2, SEQ
ID NO: 12 or SEQ ID NO: 14- Such polypeptides include those comprising the amino
acid of SEQ ID NO:3, SEQ ID NO:7, SEQ ID NO: 10 and SEQ ID NO: 11-
Further peptides of the present invention include isolated polypeptides, in which the
amino acid sequence has at least 70% identity, preferably at least 80% identity, more
preferably at least 90% identity, yet more preferably at least 95% identity, most
preferably at least 97-99% identity, to the amino acid sequence of SEQ ID NO "2 SEQ
ID NO:3, SEQ ID NO:7, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12 or SEQ ID
NO: 14 over the entire length of SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:7, SEQ ID
NO: 10, SEQ ID NO: 11, SEQ ID NO: 12 or SEQ ID NO: 14 respectively, with the
proviso that said isolated polypeptide is not SEQ ID NO:2, SEQ ID NO: 12 or SEQ ID
NO: 14- Such polypeptides include the polypeptides of SEQ ID NO:3, SEQ ID NO:7,
SEQ ID NO: 10 and SEQ ID NO: 11.
Preferably the aforementioned polypeptides are recombinantly produced. Most preferably
the polypeptides according to the invention are purified, and are substantially free of any
other proteins or contaminating host-originating material.
Further peptides of the present invention include isolated polypeptides encoded by a
polynucleotide comprising the sequence contained in SEQ ID NO:1.
The invention also provides an immunogenic fragment of a CASB7439 polypeptide, that is a
contiguous portion of the CASB7439 polypeptide which has the same or similar
immunogenic properties to the polypeptide comprising the amino acid sequence of SEQ ID
NO:2, SEQ ID NO:3, SEQ ID NO:7, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12
or SEQ ID NO: 14- That is to say, the fragment (if necessary when coupled to a carrier or
as part of a larger fusion protein) is capable of raising an immune response which recognises
the CASB7439 polypeptide. Such an immunogenic fragment may include, for example, the
CASB7439 polypeptide lacking an N-terminal leader sequence, a transmembrane domain or
a C-terminal anchor domain. In a preferred aspect the immunogenic fragment of
CASB7439 according to the invention comprises substantially all of the extracellular
domain of a polypeptide which has at least 70% identity, preferably at least 80% identity,
more preferably at least 90% identity, yet more preferably at least 95% identity, most
preferably at least 97-99% identity, to that of SEQ ID NO:2, SEQ ID NO:3, SEQ ID
NO:7, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12 or SEQ ID NO: 14 over the
entire length of SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:7, SEQ ID NO: 10, SEQ ID
NO: 11, SEQ ID NO: 12 or SEQ ID NO: 14, respectively- Preferably an immunogenic
fragment according to the invention comprises at least one epitope.
Peptide fragments incorporating an epitope of CASB7439 typically will comprise at least
7, preferably 9 or 10 contiguous amino acids from SEQ ID NO:2. Preferred epitopes are
shown in SEQ ID NO: 16 to SEQ ID NO:33.
Peptides that incorporate these epitopes form a preferred aspect of the present invention.
Mimotopes which have the same characteristics as these epitopes, and immunogens
comprising such mimotopes which generate an immune response which cross-react with
an epitope in the context of the CASB7439 molecule, also form part of the present
invention.
The present invention, therefore, includes isolated peptides encompassing these epitopes
themselves, and any mimotope thereof. The meaning of mimotope is defined as an entity
which is sufficiently similar to the native CASB7439 epitope so as to be capable of being
recognised by antibodies which recognise the native molecule; (Gheysen, H.M., et al.,
1986, Synthetic peptides as antigens. Wiley, Chichester, Ciba foundation symposium
119, pl30-149; Gheysen, H.M., 1986, Molecular Immunology, 23,7, 709-715); or are
capable of raising antibodies, when coupled to a suitable carrier, which antibodies cross-
react with the native molecule.
Peptide mimotopes of the above-identified epitopes may be designed for a particular
purpose by addition, deletion or substitution of elected amino acids. Thus, the peptides of
the present invention may be modified for the purposes of ease of conjugation to a protein
carrier. For example, it may be desirable for some chemical conjugation methods to
include a terminal cysteine to the epitope. In addition it may be desirable for peptides
conjugated to a protein carrier to include a hydrophobic terminus distal from the
conjugated terminus of the peptide, such that the free unconjugated end of the peptide
remains associated with the surface of the carrier protein. This reduces the
conformational degrees of freedom of the peptide, and thus increases the probability that
the peptide is presented in a conformation which most closely resembles that of the
peptide as found in the context of the whole molecule. For example, the peptides may be
altered to have an N-terminal cysteine and a C-terminal hydrophobic amidated tail.
Alternatively, the addition or substitution of a D-stereoisomer form of one or more of the
amino acids may be performed to create a beneficial derivative, for example to enhance
stability of the peptide. Those skilled in the art will realise that such modified peptides, or
mimotopes, could be a wholly or partly non-peptide mimotope wherein the constituent
residues are not necessarily confined to the 20 naturally occurring amino acids. In
addition, these may be cyclised by techniques known in the art to constrain the peptide
into a conformation that closely resembles its shape when the peptide sequence is in the
context of the whole molecule. A preferred method of cyclising a peptide comprises the
addition of a pair of cysteine residues to allow the formation of a disulphide bridge.
Further, those skilled in the art will realise that mimotopes or immunogens of the present
invention may be larger than the above-identified epitopes, and as such may comprise the
sequences disclosed herein. Accordingly, the mimotopes of the present invention may
consist of addition of N and/or C terminal extensions of a number of other natural
residues at one or both ends. The peptide mimotopes may also be retro sequences of the
natural sequences, in that the sequence orientation is reversed; or alternatively the
sequences may be entirely or at least in part comprised of D-stereo isomer amino acids
(inverso sequences). Also, the peptide sequences may be retro-inverso in character, in
that the sequence orientation is reversed and the amino acids are of the D-stereoisomer
form. Such retro or retro-inverso peptides have the advantage of being non-self, and as
such may overcome problems of self-tolerance in the immune system.
Alternatively, peptide mimotopes may be identified using antibodies which are capable
themselves of binding to the epitopes of the present invention using techniques such as
phage display technology (EP 0 552 267 B1). This technique, generates a large number of
peptide sequences which mimic the structure of the native peptides and are, therefore,
capable of binding to anti-native peptide antibodies, but may not necessarily themselves
share significant sequence homology to the native peptide. This approach may have
significant advantages by allowing the possibility of identifying a peptide with enhanced
immunogenic properties, or may overcome any potential self-antigen tolerance problems
which may be associated with the use of the native peptide sequence. Additionally this
technique allows the identification of a recognition pattern for each native-peptide in
terms of its shared chemical properties amongst recognised mimotope sequences.
The covalent coupling of the peptide to the immunogenic carrier can be carried out in a
manner well known in the art. Thus, for example, for direct covalent coupling it is
possible to utilise a carbodiimide, glutaraldehyde or (N-[?-maleimidobutyryloxy]
succinimide ester, utilising common commercially available heterobifunctional linkers
such as CDAP and SPDP (using manufacturers instructions). After the coupling reaction,
the immunogen can easily be isolated and purified by means of a dialysis method, a gel
filtration method, a fractionation method etc.
The types of carriers used in the immunogens of the present invention will be readily
known to the man skilled in the art. The function of the carrier is to provide cytokine help
in order to help induce an immune response against the peptide. A non-exhaustive list of
carriers which may be used in the present invention include: Keyhole limpet
Haemocyanin (KLH), serum albumins such as bovine serum albumin (BSA), inactivated
bacterial toxins such as tetanus or diptheria toxins (TT and DT), or recombinant
fragments thereof (for example, Domain 1 of Fragment C of TT, or the translocation
domain of DT), or the purified protein derivative of tuberculin (PPD). Alternatively the
mimotopes or epitopes may be directly conjugated to liposome carriers, which may
additionally comprise immunogens capable of providing T-cell help. Preferably the ratio
of mimotopes to carrier is in the order of 1:1 to 20:1, and preferably each carrier should
carry between 3-15 peptides.
In an embodiment of the invention a preferred carrier is Protein D from Haemophilus
influenzae (EP 0 594 610 Bl). Protein D is an IgD-binding protein from Haemophilus
influenzae and has been patented by Forsgren (WO 91/18926, granted EP 0 594 610 Bl).
In some circumstances, for example in recombinant immunogen expression systems it
may be desirable to use fragments of protein D, for example Protein D l/3rd (comprising
the N-terminal 100-110 amino acids of protein D (GB 9717953.5)).
Another preferred method of presenting the peptides of the present invention is in the
context of a recombinant fusion molecule. For example, EP 0 421 635 B describes the use
of chimaeric hepadnavirus core antigen particles to present foreign peptide sequences in a
virus-like particle. As such, immunogens of the present invention may comprise peptides
presented in chimaeric particles consisting of hepatitis B core antigen. Additionally, the
recombinant fusion proteins may comprise the mimotopes of the present invention and a
carrier protein, such as NS1 of the influenza virus. For any recombinantly expressed
protein which forms part of the present invention, the nucleic acid which encodes said
immunogen also forms an aspect of the present invention.
Peptides used in the present invention can be readily synthesised by solid phase
procedures well known in the art. Suitable syntheses may be performed by utilising "T-
boc" or "F-moc" procedures. Cyclic peptides can be synthesised by the solid phase
procedure employing the well-known "F-moc" procedure and polyamide resin in the fully
automated apparatus. Alternatively, those skilled in the art will know the necessary
laboratory procedures to perform the process manually. Techniques and procedures for
solid phase synthesis are described in 'Solid Phase Peptide Synthesis: A Practical
Approach' by E. Atherton and R.C. Sheppard, published by IRL at Oxford University
Press (1989). Alternatively, the peptides may be produced by recombinant methods,
including expressing nucleic acid molecules encoding the mimotopes in a bacterial or
mammalian cell line, followed by purification of the expressed mimotope. Techniques for
recombinant expression of peptides and proteins are known in the art, and are described
in Maniatis, T., Fritsch, E.F. and Sambrook et al, Molecular cloning, a laboratory
manuab 2nd Ed.; Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York
(1989).
In a further embodiment of the invention is provided a method of producing a
polypeptide as described herein. The process of the invention may be performed by
conventional recombinant techniques such as described in Maniatis et al., Molecular
Cloning - A Laboratory Manual; Cold Spring Harbor, 1982-1989. Accordingly there is
provided a process for producing a polypeptide according to the invention, comprising
culturing a host cell under conditions sufficient for the production of said polypeptide
and recovering the polypeptide from the culture medium. In particular, the process of
the invention may preferably comprise the steps of:
i) preparing a replicable or integrating expression vector capable, in a host
cell, of expressing a DNA polymer comprising a nucleotide sequence that
encodes the protein or an immunogenic derivative thereof;
ii) transforming a host cell with said vector;
ii) culturing said transformed host cell under conditions permitting expression
of said DNA polymer to produce said protein; and
iv) recovering said protein.
The polypeptides or immunogenic fragment of the invention may be in the form of the
"mature" protein or may be a part of a larger protein such as a precursor or a fusion
protein. It is often advantageous to include an additional amino acid sequence which
contains secretory or leader sequences, pro-sequences, sequences which aid in
purification such as multiple histidine residues, or an additional sequence for stability
during recombinant production. Furthermore, addition of exogenous polypeptide or lipid
tail or polynucleotide sequences to increase the immunogenic potential of the final
molecule is also considered.
In one aspect, the invention relates to genetically engineered soluble fusion proteins
comprising a polypeptide of the present invention, or a fragment thereof, and various
portions of the constant regions of heavy or light chains of immunoglobulins of various
subclasses (IgGs IgM, IgA, IgE). Preferred as an immunoglobulin is the constant part of
the heavy chain of human IgG, particularly IgGl, where fusion takes place at the hinge
region. In a particular embodiment, the Fc part can be removed simply by incorporation
of a cleavage sequence which can be cleaved with blood clotting factor Xa. Furthermore,
this invention relates to processes for the preparation of these fusion proteins by genetic
engineering, and to the use thereof for drug screening, diagnosis and therapy. A
particularly preferred aspect of the invention relates to the use of a polypeptide or a
polynucleotide in the manufacture of a vaccine for immunotherapeutically treating a
patient suffering from or susceptible to carcinoma, especially colon cancer or other colon-
associated tumours or diseases. A further aspect of the invention also relates to
polynucleotides encoding such fusion proteins. Examples of fusion protein technology
can be found in International Patent Application Nos. WO94/29458 and WO94/22914.
The proteins may be chemically conjugated, or expressed as recombinant fusion proteins
allowing increased levels to be produced in an expression system as compared to non-
fused protein. The fusion partner may assist in providing T helper epitopes
(immunological fusion partner), preferably T helper epitopes recognised by humans, or
assist in expressing the protein (expression enhancer) at higher yields than the native
recombinant protein. Preferably the fusion partner will be both an immunological fusion
partner and expression enhancing partner.
Fusion partners include protein D from Haemophilus influenza B and the non-structural
protein from influenzae virus, NS1 (hemagglutinin). Another immunological fusion
partner is the protein known as LYTA. Preferably the C terminal portion of the molecule
is used. Lyta is derived from Streptococcus pneumoniae which synthesize an N-acetyl-L-
alanine amidase, amidase LYTA, (coded by the lytA gene {Gene, 43 (1986) page 265-
272} an autolysin that specifically degrades certain bonds in the peptidoglycan backbone.
The C-terminal domain of the LYTA protein is responsible for the affinity to the choline
or to some choline analogues such as DEAE. This property has been exploited for the
development of E.coli C-LYTA expressing plasmids useful for expression of fusion
proteins. Purification of hybrid proteins containing the C-LYTA fragment at its amino
terminus has been described {Biotechnology: 10, (1992) page 795-798}. It is possible to
use the repeat portion of the Lyta molecule found in the C terminal end starting at residue
178, for example residues 188 - 305.
The present invention also includes xenogeneic forms (also termed ortholog
forms) of the aforementioned polypeptides, said xenogeneic forms referring to an
antigen having substantial sequence identity to the human antigen (also termed
autologous antigen) which serves as a reference antigen but which is derived from a
different non-human species. In this context the substantial identity refers to
concordance of an amino acid sequence with another amino acid sequence or of a
polynucleotide sequence with another polynucleotide sequence when such sequence are
arranged in a best fit alignment in any of a number of sequence alignment proteins
known in the art. By substantial identity is meant at least 70-95 %, and preferably at
least 85-95%, most preferably at least 90%-95%, sequence identity between the
compared sequences. Therefore according to the invention the xenogeneic CASB7439
polypeptide will be a CASB7439 polypeptide which is xenogeneic with respect to
human CASB7439, in other words which is isolated from a species other than human.
In a preferred embodiment, the polypeptide is isolated from mouse, rat, pig, or rhesus
monkey, most preferably from mouse or rat. Accordingly the present invention also
provides a method of inducing an immune response against human CASB7439 having
an amino acid sequence as set forth in any of the sequences SEQ ID NO:2, SEQ ID
NO:3, SEQ ID NO:7, SEQ ID NO: 10 or SEQ ID NO: 11 in a human, comprising
administering to the subject an effective dosage of a composition comprising a
xenogeneic form of said human CASB7439 as described herein. A preferred
embodiment is a method of inducing an immune response against human CASB7439
using the xenogeneic CASB7439isolated from mouse, rat, pig or rhesus monkey.
Another preferred method of inducing an immune response according to the present
invention is using an antigen composition including a live viral expression system which
expresses said xenogeneic antigen. The preferred xenogeneic CASB7439 polypeptide
has the sequence set forth in SEQ ID N°12 (mouse) or in SEQ ID N°14 (rat).
The isolated xenogeneic CASB7439 polypeptide will generally share substantial
sequence similarity, and include isolated polypeptides comprising an amino acid sequence
which has at least 70% identity, preferably at least 80% identity, more preferably at least
90% identity, yet more preferably at least 95% identity, most preferably at least 97-99%
identity, to that of SEQ ID NO:12 or SEQ ID NO:14 over the entire length of SEQ ID
NO: 12 or SEQ ID NO: 14. Accordingly the xenogeneic polypeptide will comprise an
immunogenic fragment of the polypeptide °f SEQ ID NO: 12 or SEQ ID NO: 14 in which
the immunogenic activity of the immunogenic fragment is substantially the same as the
polypeptide of SEQ ID NO: 12 or SEQ ID NO: 14. In addition the xenogeneic
CASB7439 polypeptide can be a fragment of at least about 20 consecutive amino acids,
preferably about 30, more preferably about 50, yet more preferably about 100, most
preferably about 150 contiguous amino acids selected from the amino acid sequences as
shown in SEQ ID NO:12 or in SEQ ID NO: 14. More particularly xenogeneic CASB7439
fragments will retain some functional property, preferably an immunological activity, of
the larger molecule set forth in SEQ ID NO:12 or in SEQ ID NO: 14,and are useful in the
methods described herein (e.g. in pharmaceutical and vaccine compositions, in
diagnostics, etc.). In particular the fragments will be able to generate an immune response
against the human counterpart, such as the generation of cross-reactive antibodies which
react with the autologous human form of CASB7439 as set forth in any of the SEQ ID
NO: 2. In a specific embodiment the xenogeneic polypeptide of the invention may be
part of a larger fusion, comprising the xenogeneic CASB7439 polypeptide or fragment
thereof and a heterologous protein cr part of a protein acting as a fusion partner as
described hereabove-
The present invention also includes variants of the aforementioned polypeptides, that is
polypeptides that vary from the referents by conservative amino acid substitutions, whereby
a residue is substituted by another with like characteristics. Typical such substitutions are
among Ala, Val, Leu and He; among Ser and Thr, among the acidic residues Asp and Glu;
among Asn and Gln; and among the basic residues Lys and Arg; or aromatic residues Phe
and Tyr. Particularly preferred are variants in which several, 5-10,1-5,1-3,1-2 or 1 arnino
acids are substituted, deleted, or added in any combination.
Polypeptides of the present invention can be prepared in any suitable manner. Such
polypeptides include isolated naturally occurring polypeptides, recombinantly produced
polypeptides, synthetically produced polypeptides,. or polypeptides produced by a
combination of these methods. Means for preparing such polypeptides are well understood
in the art.
In a further aspect, the present invention relates to CASB7439 polynucleotides. Such
polynucleotides include isolated polynucleotides comprising a nucleotide sequence encoding
a polypeptide which has at least 70% identity, preferably at least 80% identity, more
preferably at least 90% identity, yet more preferably at least 95% identity, to the amino
acid sequence of SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:7, SEQ ID NO: 10 or SEQ
ID NO: 11. over the entire length of SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:7, SEQ
ID NO: 10 or SEQ ID NO: 11 respectively. In this regard, encoded polypeptides which
have at least 97% identity are highly preferred, whilst those with at least 98-99% identity are
more highly preferred, and those with at least 99% identity are most highly preferred.
Further polynucleotides of the present invention include isolated polynucleotides comprising
a nucleotide sequence that has at least 70% identity, preferably at least 80% identity, more
preferably at least 90% identity, yet more preferably at least 95% identity, to a nucleotide
sequence encoding a polypeptide of SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:7, SEQ
ID NO: 10, or SEQ ID NO: 11. over the entire coding region. In this regard,
polynucleotides which have at least 97% identity are highly preferred, whilst those with at
least 98-99% identity are more highly preferred, and those with at least 99% identity are
most highly preferred.
Further polynucleotides of the present invention include isolated polynucleotides
comprising a nucleotide sequence which has at least 70% identity, preferably at least 80%
identity, more preferably at least 90% identity, yet more preferably at least 95% identity,
to SEQ ID NO:1, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:8 or SEQ
ID NO:9, over the entire length of said sequences, or to the coding sequence of SEQ ID
NO:1, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:8 or SEQ ID NO:9
over the entire length of said coding sequence of SEQ ID NO: 1, SEQ ID NO:4, SEQ ID
NO:5, SEQ ID NO:6, SEQ ID NO:8 or SEQ ID NO:9. In this regard, polynucleotides
which have at least 97% identity are highly preferred, whilst those with at least 98-99%
identiy are more highly preferred, and those with at least 99% identity are most highly
preferred. Such polynucleotides include a polymicleotide comprising the polynucleotide of
SEQ ID NO:1, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:8 or SEQ ID
NO:9 as wel1 as the polynucleotide of SEQ ID NO:1, SEQ ID NO:4, SEQ ID NO:5, SEQ
ID NO:6, SEQ ID NO:8, SEQ ID NO:9 or the coding region of SEQ ID NO l, SEQ ID
NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:8 or SEQ ID NO:9-
The present invention also provides a nucleic acid encoding the aforementioned
xenogeneic proteins of the present invention and their use in medicine. In a preferred
embodiment, the xenogeneic CASB7439 polynucleotide for use in pharmaceutical
compositions has the sequence set forth in SEQ ID NO: 13 (mouse) or in SEQ ID NO: 15
(rat). The isolated xenogeneic CASB7439 polynucleotides according to the invention
may be single-stranded (coding or antisense) or double-stranded, and may be DNA
(genomic, cDNA or synthetic) or RNA molecules. Additional coding or non-coding
sequences may, but need not, be present within a polynucleotide of the present
invention. In other related embodiments, the present invention provides polynucleotide
variants having substantial identity to the sequences disclosed herein in SEQ ID NO: 13 or
in SEQ ID NO: 15, for example those comprising at least 70% sequence identity,
preferably at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% or higher,
sequence identity compared to a polynucleotide sequence of this invention using the
methods described herein, (e.g., BLAST analysis using standard parameters). In a
related embodiment, the isolated xenogeneic polynucleotide of the invention will
comprise a nucleotide sequence encoding a polypeptide mat has at least 90%, preferably
95% and above, identity to the ammo acid sequence of SEQ ID NO: 12 or of SEQ ID
NO:14, over the entire length of SEQ ID NO:12 or of SEQ ID NO:14; or a nucleotide
sequence complementary to said isolated polynucleotide.
The invention also provides polynucleotides which are complementary to all the above
described polynucleotides.
Said polynucleotides can be inserted in a suitable plasmid, recombinant microorganism
vector or a recombinant live microorganism and used for immunization ( see for example
Wolff et al., Science 247:1465-1468 (1990); Corr et. al., J. Exp. Med. 184:1555-1560
(1996); Doe et al., Proc. Nail. Acad. Sci. 93:8578-8583 (1996)). Accordingly there is
provided in the present invention an expression vector or recombinant live microorganism
comprising said polynucleotides as hereabove defined.
The invention also provides a fragment of a CASB7439 polynucleotide which when
administered to a subject has the same immunogenic properties as the polynucleotide of
SEQ ID NO:1, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:8, SEQ ID
NO:9, SEQ ID NO: 13 or SEQ ID NO: 15-
The invention also provides a polynucleotide encoding an immunological fragment of a
CASB7439 polypeptide as hereinbefore defined.
The fragments have a level of immunogenic activity of at least about 50%, preferably at
least about 70% and more preferably at least about 90% of the level of immunogenic
activity of a polypeptide sequence set forth in SEQ ID NO:2, SEQ ID NO:3, SEQ ID
NO:7, SEQ ID NO: 10 or SEQ ID NO: 11, SEQ ID NO: 12 or SEQ ID NO: 14 or a
polypeptide sequence encoded by a polynucleotide sequence set forth in SEQ ID NO: 1,
SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:9, SEQ ID
NO:13 or SEQ ID NO:15.
The polypeptide fragments according to the invention preferably comprise at least about
5, 10,15, 20,25, 50, or 100 contiguous amino acids, or more, including all intermediate
lengths, of a polypeptide composition set forth herein, such as those set forth in SEQ ID
NO:2, SEQ ID NO:3, SEQ ID NO:7, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO:12
or SEQ ID NO: 14, or those encoded by a polynucleotide sequence set forth in a sequence
of SEQ ID NO:1, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:8, SEQ
ID NO:9, SEQ ID NO: 13 or SEQ ID NO: 15-
The nucleotide sequence of SEQ ID NO:1 is a cDNA sequence which comprises a
polypeptide encoding sequence (nucleotide 545 to 1126) encoding a polypeptide of 193
amino acids, the polypeptide of SEQ ID NO:2. The nucleotide sequence encoding the
polypeptide of SEQ ID NO:2 may be identical to the polypeptide encoding sequence
contained in SEQ ED NO:1 or it may be a sequence other than the one contained in SEQ
ID NO:1, which, as a result of the redundancy (degeneracy) of the genetic code, also
encodes the polypeptide of SEQ ID NO:2. The polypeptide of the SEQ ID NO:2 is
structurally related to other proteins of the achaete scute family, and is also named "human
Achaete Scute homologue 2" (HASH2) (accession number NP_005161 and AAB86993).
Human Achaete Scute homologue 2 (HASH2) gene, officially designated human ASCL2
(Achaete Scute complex like 2) is a homologue of the Drosophila Achaete and Scute genes.
Human ASCL2 is expressed in the extravillus trophoblasts of the developing placenta only,
and maps on chromosome 11pl5 close to IGF2 and H19. The mouse achaete-scute
homolog-2 gene (MASH2) encodes a transcription factor playing a role in the development
of the trophoblast. The Mash2 gene is paternally imprinted in the mouse, and the lack of
human ASCL2 expression in non-malignant hydatidiform (androgenetic) moles indicates
that human Ascl2 is also imprinted in man.
Ascl2 genes are members of the basic helix-loop-helix (BHLH) family of transcription
factors. They activate transcription by binding to the E box (5'-CANNTG-3'). Dimerization
with other BHLH proteins is required for efficient DNA binding. They are involved in the
determination of the neuronal precursors in the peripheral nervous system and the central
nervous system in drosophila melanogaster, and probably in mammals as well.
The complementary strand of the nucleotide sequence of SEQ ID NO: 1 is the
polynucleotide sequence of SEQ ID NO:6. This strand also comprises two other polypeptide
encoding sequences. The first polypeptide encoding sequence (nucleotide 1184 to 399 of
SEQ ID: 1, nucleotide 608 to 1393 of SEQ ID NO:6) encodes a polypeptide of 262 amino
acids, the polypeptide of SEQ ID NO:3. The second polypeptide encoding sequence
(nucleotide 840 to 262 of SEQ ID NO:1, nucleotide 952 to 1530 of SEQ ID NO:6) encodes
a polypeptide of 193 amino acids, the polypeptide of SEQ ID NO: 11. The nucleotide
sequence encoding the polypeptides of SEQ ID NO:3 and SEQ ED NO:11 may be identical
to the polypeptides encoding sequence contained in SEQ ID NO: 6 or it may be a sequence
other than the one contained in SEQ ID NO: 6, which, as a result of the redundancy
(degeneracy) of the genetic code, also encodes the polypeptides of SEQ ID NO:3 and 11.
The polypeptide of the SEQ ID NO:3 is structurally related to other proteins of the splicing
coactivator protein family, having homology and/or structural similarity with homo sapiens
splicing coactivator subunit srm300 (genbank accession AAF21439). The polypeptide of
SEQ ID NO:11 is not related to any known protein. Polypeptide sequences as set forth in
SEQ ID NO:3 and SEQ ID NO:11, and polynucleotide sequences as set forth in SEQ ID
NO:6 are novel and also form part of the invention.
Preferred polypeptides and polynucleotides of the present invention are expected to have,
inter alia, similar biological functions/properties to their homologous polypeptides and
polynucleotides. Furthermore, preferred polypeptides, immunological fragments and
polynucleotides of the present invention have at least one activity of either SEQ ED NO: 1,
SEQ ID NO:2, SEQ ID NO:3 or SEQ ID NO:11 as appropriate.
The present invention also relates to partial or other incomplete polynucleotide and
polypeptide sequences which were first identified prior to the determination of the
corresponding full length sequences of seQ ID NO:1, SEQ ED NO:2, SEQ ID NO:3, and SEQ
ID NO: 11.
Accordingly, in a further aspect, the present invention provides for an isolated
polynucleotide which:
(a) comprises a nucleotide sequence which has at least 70% identity, preferably at least
80% identity, more preferably at least 90% identity, yet more preferably at least 95%
identity, even more preferably at least 97-99% identity to SEQ ID NO:4 and 5 over the
entire length of SEQ ID NO 4 and 5;
(b) has a nucleotide sequence which has at least 70% identity, preferably at least 80%
identity, more preferably at least 90% identity, yet more preferably at least 95% identity,
even more preferably at least 97-99% identity, to SEQ ID NO:1 or SEQ ID NO:6 over the
entire length of SEQ ID NO:4 and SEQ ED NO:5 respectively;
(c) the polynucleotide of SEQ ID NO:4 and SEQ ID NO:5; or
(d) a nucleotide sequence encoding a polypeptide which has at least 70% identity,
preferably at least 80% identity, more preferably at least 90% identity, yet more
preferably at least 95% identity, even more preferably at least 97-99% identity, to the
amino acid sequence of SEQ ID NO:2 and SEQ ID NO:7 respectively, over the entire
length of SEQ ID NO:2 and 7, as well as the polynucleotides of SEQ ID NO:4 and 5.
The present invention further provides for a polypeptide which:
(a) comprises an amino acid sequence which has at least 70% identity, preferably at least
80% identity, more preferably at least 90% identity, yet more preferably at least 95%
identity, most preferably at least 97-99% identity, to that of SEQ ID NO:2 and 7 over the
entire length of SEQ ID NO:2 or 7;
(b) has an amino acid sequence which is at least 70% identity, preferably at least 80%
identity, more preferably at least 90% identity, yet more preferably at least 95% identity,
most preferably at least 97-99% identity, to the amino acid sequence of SEQ ID NO:2 or
7 over the entire length of SEQ ID NO:2 or 7;
(c) comprises the amino acid of SEQ ID NO:2 or 7; and
(d) is the polypeptide of SEQ ID NO: 7;
as well as polypeptides encoded by a polynucleotide comprising the sequence contained ..
in SEQ ID NO:4 and 5.
Polynucleotides of the present invention may be obtained, using standard cloning and
screening tecnniques, from a cDNA library derived from mRNA in cells of human colon
cancer, (for example Sambrook et al., Molecular Cloning: A Laboratory Manual, 2nd Ed.,
Cold Spring harbor Laboratory Press, Cold Spring harbor, N.Y. (1989)). Polynucleotides of
the invention can also be obtained from natural sources such as genomic DNA libraries or
can be synthesized using well known and commercially available techniques.
When polynucleotides of the present invention are used for the recombinant production of
polypeptides of the present invention, the polynucleotide may include the coding sequence
for the mature polypeptide, by itself; or the coding sequence for the mature polypeptide in
reading frame with other coding sequences, such as those encoding a leader or secretory
sequence, a pre-, or pro- or prepro- protein sequence, or other fusion peptide portions. For
example, a marker sequence which facilitates purification of the fused polypeptide can be
encoded. In certain preferred embodiments of this aspect of the invention, the marker
sequence is a hexa-histidine peptide, as provided in the pQE vector (Qiagen, Inc.) and
described in Gentz et al, Proc Natl Acad Sci USA (1989) 86:821-824, or is an HA tag. The
polynucleotide may also contain non-coding 5' and 3' sequences, such as transcribed, non-
. translated sequences, splicing and polyadenylation signals, ribosome binding sites and
sequences that stabilize mRNA.
Further embodiments of the present invention include polynucleotides encoding polypeptide
variants which comprise the amino acid sequence of SEQ ID NO:2, SEQ ID NO:3, SEQ ID
NO:7, SEQ ID NO:11, SEQ ID NO: 13 or SEQ ID NO: 15 and in which several, for instance
from 5 to 10, 1 to 5, 1 to 3, 1 to 2 or 1, amino acid residues are substituted, deleted or added,
in any combination.
Polynucleotides which are identical or sufficiently identical to a nucleotide sequence
contained in SEQ ID NO:1 or in SEQ ID NO:6, may be used as hybridization probes for
cDNA and genomic DNA or as primers for a nucleic acid amplification (PCR) reaction, to
isolate full-length cDNAs and genomic clones encoding polypeptides of the present
invention and to isolate cDNA and genomic clones of other genes (including genes encoding
paralogs from human sources and orthologs and paralogs from species other than human)
that have a high sequence similarity to SEQ ID NO:1 or to SEQ ID NO:6. Typically these
nucleotide sequences are 70% identical, preferably 80% identical, more preferably 90%
identical, most preferably 95% identical to that of the referent. The probes or primers will
generally comprise at least 15 nucleotides, preferably, at least 30 nucleotides and may have
at least 50 nucleotides. Particularly preferred probes will have between 30 and 50
nucleotides. Particularly preferred primers will have between 20 and 25 nucleotides. In
particular, polypeptides or polynucleotides derived from sequences from homologous
animal origin could be used as immunogens to obtain a cross-reactive immune response to
the human gene.
A polynucleotide encoding a polypeptide of the present invention, including homologs from
species other than human, may be obtained by a process which comprises the steps of
screening an appropriate library under stringent hybridization conditions with a labeled
probe having the sequence of SEQ ID NO: 1 or SEQ ID NO:6 or a fragment thereof; and
isolating full-length cDNA and genomic clones containing said polynucleotide sequence.
Such hybridization techniques are well known to the skilled artisan. Preferred stringent
hybridization conditions include overnight incubation at 42°C in a solution comprising: 50%
formamide, 5xSSC (150mM NaCl, 15mM trisodium citrate), 50 mM sodium phosphate
(pH7.6), 5x Denhardt's solution, 10 % dextran sulfate, and 20 micTogram/ml denatured,
sheared salmon sperm DNA; followed by washing the filters in 0.1 x SSC at about 65°C.
Thus the present invention also includes polynucleotides obtainable by screening an
appropriate library under stingent hybridization conditions with a labeled probe having the
sequence of SEQ ID NO: 1 or SEQ ID NO:6 or a fragment thereof.
The skilled artisan will appreciate that, in many cases, an isolated cDNA sequence will be
incomplete, in that the region coding for the polypeptide is short at the 5' end of the
cDNA.
There are several methods available and well known to those skilled in the art to obtain
full-length cDNAs, or extend short cDNAs, for example those based on the method of
Rapid Amplification of cDNA ends (RACE) (see, for example, Frohman et al., PNAS
USA 85, 8998-9002, 1988). Recent modifications of the technique, exemplified by the
MarathonTM technology (Clontech Laboratories Inc.) for example, have significantly
simplified the search for longer cDNAs. In the MarathonTM technology, cDNAs have
been prepared from mRNA extracted from a chosen tissue and an 'adaptor' sequence
ligated onto each end. Nucleic acid amplification (PCR) is then carried out to amplify the
'missing' 5' end of the cDNA using a combination of gene specific and adaptor specific
oligonucleotide primers. The PCR reaction is then repeated using 'nested' primers, that is,
primers designed to anneal within the amplified product (typically an adaptor specific
primer that anneals further 3' in the adaptor sequence and a gene specific primer that
anneals further 5' in the known gene sequence). The products of this reaction can then be
analysed by DNA sequencing and a full-length cDNA constructed either by joining the
product directly to the existing cDNA to give a complete sequence, or carrying out a
separate full-length PCR using the new sequence information for the design of the 5'
primer.
Recombinant polypeptides of the present invention may be prepared by processes well
known in the art from genetically engineered host cells comprising expression systems.
Accordingly, in a further aspect, the present invention relates to an expression system which
comprises a polynucleotide of the present invention, to host cells which are genetically
engineered with such expression sytems and to the production of polypeptides of the
invention by recombinant techniques. Cell-free translation systems can also be employed to
produce such proteins using RNAs derived from the DNA constructs of the present
invention.
For recombinant production, host cells can be genetically engineered to incorporate
expression systems or portions thereof for polynucleotides of the present invention.
Introduction of polynucleotides into host cells can be effected by methods described in many
standard laboratory manuals, such as Davis et al, Basic Methods in Molecular Biology
(1986) and Sambrook et al., Molecular Cloning: A Laboratory Manual, 2nd Ed., Cold
Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989). Preferred such methods
include, for instance, calcium phosphate transfection, DEAE-dextran mediated transfection,
transvection, microinjection, cationic lipid-mediated transfection, electroporation,
transduction, scrape loading, ballistic introduction or infection.
Preferably the proteins of the invention are coexpressed with thioredoxin in trans (TIT).
Coexpression of thioredoxin in trans versus in cis is preferred to keep antigen free of
thioredoxin without the need for protease. Thioredoxin coexpression eases the
solubilisation of the proteins of the invention. Thioredoxin coexpression has also a
significant impact on protein purification yield, on purified-protein solubility and quality.
Representative examples of appropriate hosts include bacterial cells, such as Streptococci'
Staphylococci E. coli Streptomyces and Bacillus subtilis cells; fungal cells, such as yeast
cells and Aspergillus ceIls; insect cells such as Drosophila S2 and Spodoptera Sf9 cells;
animal cells such as CHO, COS, HeLa, C127, 3T3, BHK, HEK 293 and Bowes melanoma
cells; and plant cells.
A great variety of expression systems can be used, for instance, chromosomal, episomal
and virus-derived systems, e.g., vectors derived from bacterial plasmids, from
bacteriophage, from transposons, from yeast episomes, from insertion elements, from
yeast chromosomal elements, from viruses such as baculoviruses, papova viruses, such as
SV40, vaccinia viruses, adenoviruses, fowl pox viruses, pseudorabies viruses and
retroviruses, and vectors derived from combinations thereof, such as those derived from
plasmid and bactsriophage genetic elements, such as cosmids and phageraids. The
expression systems may contain control regions that regulate as well as engender
expression. Generally, any system or vector which is able to maintain, propagate or
express a polynucleotide to produce a polypeptide in a host may be used. The appropriate
nucleotide sequence may be inserted into an expression system by any of a variety of
well-known and routine techniques, such as, for example, those set forth in Sambrook et
al., Molecular Cloning, A Laboratory Manual (supra). Appropriate secretion signals may
be incorporated into the desired polypeptide to allow secretion of the translated protein
into the lumen of the endoplasmic reticulum, the periplasmic space or the extracellular
environment. These signals may be endogenous to the polypeptide or they may be
heterologous signals.
The expression system may also be a recombinant live microorganism, such as a virus or
bacterium. The gene of interest can be inserted into the genome of a live recombinant
virus or bacterium. Inoculation and in vivo infection with this live vector will lead to in
vivo expression of the antigen and induction of immune responses.
Therefore, in certain embodiments, polynucleotides encoding immunogenic polypeptides
of the present invention are introduced into suitable mammalian host cells for expression
using any of a number of known viral-based systems. In one illustrative embodiment,
retroviruses provide a convenient and effective platform for gene delivery systems. A
selected nucleotide sequence encoding a polypeptide of the present invention can be
inserted into a vector and packaged in retroviral particles using techniques known in the
art. The recombinant virus can then be isolated and delivered to a subject. A number of
illustrative retroviral systems have been described (e.g., U.S. Pat. No. 5,219,740; Miller
and Rosman (1989) BioTechniques 7:980-990; Miller, A. D. (1990) Human Gene
Therapy 1:5-14; Scarpa et al. (1991) Virology 180:849-852; Bums et al. (1993) Proc.
Natl. Acad. Sci. USA 90:8033-8037; and Boris-Lawrie and Temin (1993) Cur. Opin.
Genet. Develop. 3:102-109.
In addition, a number of illustrative adenovirus-based systems have also been described.
Unlike retroviruses which integrate into the host genome, adenoviruses persist
extrachromosomally thus minimizing the risks associated with insertional mutagenesis
(Haj-Ahmad and Graham (1986) J. Virol. 57:267-274; Bett et al. (1993) J. Virol.
67:5911-5921; Mittereder et al. (1994) Human Gene Therapy 5:717-729; Seth et al.
(1994) J. Virol. 68:933-940; Barr et al. (1994) Gene Therapy 1:51-58; Berkner, K. L.
(1988) BioTechniques 6:616-629; and Rich et al. (1993) Human Gene Therapy 4:461-
476).
Various adeno-associated virus (AAV) vector systems have also been developed for
polynucleotide delivery. AAV vectors can be readily constructed using techniques well
known in the art. See, e.g., U.S. Pat. Nos. 5,173,414 and 5,139,941; International
Publication Nos. WO 92/01070 and WO 93/03769; Lebkowski et al. (1988) Molec. Cell.
Biol. 8:3988-3996; Vincent et al. (1990) Vaccines 90 (Cold Spring Harbor Laboratory
Press); Carter, B. J. (1992) Current Opinion in Biotechnology 3:533-539; Muzyczka, N.
(1992) Current Topics in Microbiol. and Immunol. 158:97-129; Kotin, R. M. (1994)
Human Gene Therapy 5:793-801; Shelling and Smith (1994) Gene Therapy 1:165-169;
and Zhou et al. (1994) J. Exp. Med. 179:1867-1875.
Additional viral vectors useful for delivering the nucleic acid molecules encoding
polypeptides of the present invention by gene transfer include those derived from the pox
family of viruses, such as vaccinia virus and avian poxvirus. By way of example, vaccinia
virus recombinants expressing the novel molecules can be constructed as follows. The
DNA encoding a polypeptide is first inserted into an appropriate vector so that it is
adjacent to a vaccinia promoter and flanking vaccinia DNA sequences, such as the
sequence encoding thymidine kinase (TK). This vector is then used to transfect cells
which are simultaneously infected with vaccinia. Homologous recombination serves to
insert the vaccinia promoter plus the gene encoding the polypeptide of interest into the
viral genome. The resulting TK.sup.(-) recombinant can be selected by culturing the cells
in the presence of 5-bromodeoxyuridine and picking viral plaques resistant thereto.
A vaccinia-based infection/transfection system can be conveniently used to provide for
inducible, transient expression or coexpression of one or more polypeptides described
herein in host cells of an organism. In this particular system, cells are first infected in
vitro with a vaccinia virus recombinant that encodes the bacteriophage T7 RNA
polymerase. This polymerase displays exquisite specificity in that it only transcribes
templates bearing T7 promoters. Following infection, cells are transfected with the
polynucleotide or polynucleotides of interest, driven by a T7 promoter. The polymerase
expressed in the cytoplasm from the vaccinia virus recombinant transcribes the
transfected DNA into RNA which is then translated into polypeptide by the host
translational machinery. The method provides for high level, transient, cytoplasmic
production of large quantities of RNA and its translation products. See, e.g., ELroy-Stein
and Moss, Proc. Natl. Acad. Sci. USA (1990) 87:6743-6747; Fuerst et al. Proc. Natl.
Acad. Sci. USA (1986) 83:8122-8126.
Alternatively, avipoxviruses, such as the fowlpox and canarypox viruses, can also be used
to deliver the coding sequences of interest. Recombinant avipox viruses, expressing
immunogens from mammalian pathogens, are known to confer protective immunity when
administered to non-avian species. The use of an Avipox vector is particularly desirable
in human and other mammalian species since members of the Avipox genus can only
productively replicate in susceptible avian species and therefore are not infective in
mammalian cells. Methods for producing recombinant Avipoxviruses are known in the
art and employ genetic recombination, as described above with respect to the production
of vaccinia viruses. See, e.g., WO 91/12882; WO 89/03429; and WO 92/03545.
Any of a number of alphavirus vectors can also be used for delivery of polynucleotide
compositions of the present invention, such as those vectors described in U.S. Patent Nos.
5,843,723; 6,015,686; 6,008,035 and 6,015,694. Certain vectors based on Venezuelan
Equine Encephalitis (VEE) can also be used, illustrative examples of which can be found
in U.S. Patent Nos. 5,505,947 and 5,643,576.
Moreover, molecular conjugate vectors, such as the adenovirus chimeric vectors
described in Michael et al. J. Biol. Chem. (1993) 268:6866-6869 and Wagner et al. Proc.
Natl. Acad. Sci. USA (1992) 89:6099-6103, can also be used for gene delivery under the
invention.
Additional illustrative information on these and other known viral-based delivery systems
can be found, for example, in Fisher-Hoch et al., proc. Natl. Acad. Sci. USA 86: :317-321,
1989; Flexner et al., Ann. N.Y.. Acad. Sci. 569:86-103, 1989; Flexner et al., Vaccine
5:17-21, 1990; U.S. Patent Nos. 4,603,112, 4,769,330, and 5,017,487; WO 89/01973;
U.S. Patent No. 4,777,127; GB 2,200,651; EP 0,345,242; WO 91/02805; Berkner,
Biotechniques 5:616-627, 1988; Rosenfeld et al., Science 252:431-434, 1991; Kolls et al.,
Proc. Natl. Acad. Sci. USA 91:215-219, 1994; Kass-Eisler et al., Proc. Natl. Acad. sci.
USA 90:11498-11502, 1993; Guzman et al., Circulation 88:2838-2848, 1993; and
Guzman et al., Cir. Res. 73:1202-1207, 1993.
The recombinant live microorganisms described above can be virulent, or attenuated in
various ways in order to obtain live vaccines. Such live vaccines also form part of the
invention.
In certain embodiments, a polynucleotide may be integrated into the genome of a target
cell. This integration may be in the specific location and orientation via homologous
recombination (gene replacement) or it may be integrated in a random, non-specific
location (gene augmentation). In yet further embodiments, the polynucleotide may be
stably maintained in the cell as a separate, episomal segment of DNA. Such
polynucleotide segments or "episomes" encode sequences sufficient to permit
maintenance and replication independent of or in synchronization with the host cell cycle.
The manner in which the expression construct is delivered to a cell and where in the cell
the polynucleotide remains is dependent on the type of expression construct employed.
In another embodiment of the invention, a polynucleotide is administered/delivered as
"naked" DNA, for example as described in Ulmer et al., Science 259-1745-1749,1993
and reviewed by Cohen, Science 259:1691-1692, 1993. The uptake of naked DNA may
be increased by coating the DNA onto biodegradable beads, which are efficiently
transported into the cells.
In still another embodiment, a composition of the present invention can be delivered via a
particle bombardment approach, many of which have been described. In one illustrative
example, gas-driven particle acceleration can be achieved with devices such as those
manufactured by Powderject Pharmaceuticals PLC (Oxford, UK) and Powderject
Vaccines Inc. (Madison, WI), some examples of which are described in U.S. Patent Nos.
5,846,796; 6,010,478; 5,865,796; 5,584,807; and EP Patent No. 0500 799. This approach
offers a needle-free delivery approach wherein a dry powder formulation of microscopic
particles, such as polynucleotide or polypeptide particles, are accelerated to high speed
within a helium gas jet generated by a hand held device, propelling the particles into a
target tissue of interest.
In a related embodiment, other devices and methods that may be useful for gas-driven
needle-less injection of compositions of the present invention include those provided by
Bioject, Inc. (Portland, OR), some examples of which are described in U.S. Patent Nos.
4,790,824; 5,064,413; 5,312,335; 5,383,851; 5,399,163; 5,520,639 and 5,993,412.
Polypeptides of the present invention can be recovered and purified from recombinant cell
cultures by well-known methods including ammonium sulfate or ethanol precipitation, acid
extraction, anion or cation exchange chromatography, phosphocellulose chromatography,
hydrophobic interaction chromatography, affinity chromatography, hydroxylapatite
chromatography and lectin chromatography. Most preferably, ion metal affinity
chromatography (IMAC) is employed for purification. Well known techniques for
refolding proteins may be employed to regenerate active conformation when the polypeptide
is denatured during intracellular synthesis, isolation and or purification.
Another important aspect of the invention relates to a method for inducing, re-inforcing
or modulating an immunological response in a mammal which comprises inoculating the
mammal with a fragment or the entire polypeptide or polynucleotide of the invention,
adequate to produce antibody and/or T cell immune response for immunoprophylaxis or
for therapeutic treatment of cancer, more particularly colorectal cancer, and autoimmune
disease and related conditions. Yet another aspect of the invention relates to a method of
inducing, re-inforcing or modulating immunological response in a mammal which
comprises, delivering a polypeptide of the present invention via a vector or cell directing
expression of the polynucleotide and coding for the polypeptide in vivo in order to induce
such an immunological response to produce immune responses for prophylaxis or
treatment of said mammal from diseases.
A further aspect of the invention relates to an immunological/vaccine formulation
(composition) and to their use in medicine. These compositions, when introduced into a
mammalian host, induce, re-inforce or modulate an immunological response in that
mammal to a polypeptide of the present invention wherein the composition comprises a
polypeptide or polynucleotide of the invention or an immunological fragment thereof as
herein before defined. More particularly the immunogenic composition according to the
present invention comprises a safe and effective amount of a CASB7439 polypeptide, or
immunogenic fragment thereof wherein the CASB7439 polypeptide is selected from the
group comprising SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:7, SEQ ID NO: 10, SEQ
ID NO: 11, SEQ ID NO: 12 or SEQ ID NO: 14. In another embodiment, the imunogenic
composition comprises a safe and effective amount of a CASB7439 -encoding
polynucleotide, or fragment thereof wherein the CASB7439-encoding polynucleotide is
selected from the group comprising SEQ ID NO:1, SEQ ID NO:4, SEQ ID NO:5, SEQ
ID NO:6, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO: 13 or SEQ ID NO: 15.
The vaccine formulation according to the invention may further comprise a suitable, i.e.
pharmaceutically acceptable carrier. Since a polypeptide may be broken down in the
stomach, it is preferably administered parenterally (for instance, subcutaneous,
intramuscular, intravenous, or intradermal injection). Formulations suitable for parenteral
administration include aqueous and non-aqueous sterile injection solutions which may
contain anti-oxidants, buffers, bacteriostats and solutes which render the formulation
isotonic with the blood of the recipient; and aqueous and non-aqueous sterile suspensions
which may include suspending agents or thickening agents. The formulations may be
presented in unit-dose or multi-dose containers, for example, sealed ampoules and vials
and may be stored in a freeze-dried condition requiring only the addition of the sterile
liquid carrier immediately prior to use.
A further aspect of the invention relates to the in vitro induction of immune responses to a
fragment or the entire polypeptide or polynucleotide of the present invention or a
molecule comprising the polypeptide or polynucleotide of the present invention, using
cells from the immune system of a mammal, and reinfusing these activated immune cells
of the mammal for the treatment of disease. Activation of the cells from the immune
system is achieved by in vitro incubation with the entire polypeptide or polynucleotide of
the present invention or a molecule comprising the polypeptide or polynucleotide of the
present invention in the presence or absence of various immunomodulator molecules.
A further aspect of the invention relates to the immunization of a mammal by
administration of antigen presenting cells modified by in vitro loading with part or the
entire polypeptide of the present invention or a molecule comprising the polypeptide of
the present invention and administered in vivo in an immunogenic way. Alternatively,
antigen presenting cells can be transfected in vitro with a vector containing a fragment or
the entire polynucleotide of the present invention or a molecule comprising the
polynucleotide of the present invention, such as to express the corresponding polypeptide,
and administered in vivo m an immunogenic way. Accordingly, the pharmaceutical
compositions of the invention will comprise an effective amount of antigen presenting
cells, modified by in vitro loading with a CASB7439 polypeptide, or genetically
modified in vitro to. express a CASB7439 polypeptide and a pharmaceutically effective
carrier.
According to another embodiment, the pharmaceutical/immunogenic compositions
described herein will comprise one or more immunostimulants in addition to the
immunogenic polynucleotide, polypeptide, antibody, T-cell and/or antigen presenting cell
(APC) compositions of this invention. Accordingly there is herein provided a process for
the production of said immunogenic composition, comprising admixing a CASB7439
polypeptide or a CASB7439 -encoding polynucleotide with a suitable
adjuvant/immunostimulant, diluent or other pharmaceutically acceptable carrier. An
immunostimulant refers to essentially any substance that enhances or potentiates an
immune response (antibody and/or cell-mediated) to an exogenous antigen. One
preferred type of immunostimulant comprises an adjuvant. Many adjuvants contain a
substance designed to protect the antigen from rapid catabolism, such as aluminum
hydroxide or mineral oil, and a stimulator of immune responses, such as lipid A,
Bortadella pertussis or Mycohactenum tuberculosis derived proteins. Certain adjuvants
are commercially available as, for example, Freund's Incomplete Adjuvant and Complete
Adjuvant (Difco Laboratories, Detroit, MI); Merck Adjuvant 65 (Merck and Company,
Inc., Rahway, NJ); AS-2 (SmithKline Beecham, Philadelphia, PA); aluminum salts such
as aluminum hydroxide gel (alum) or aluminum phosphate; salts of calcium, iron or zinc;
an insoluble suspension of acylated tyrosine; acylated sugars; cationically or anionically
derivatized polysaccharides; polyphosphazenes; biodegradable microspheres;
monophosphoryl lipid A and quil A. Cytokines, such as GM-CSF, interleukin-2, -7, -12,
and other like growth factors, may also be used as adjuvants.
Within certain embodiments of the invention, the adjuvant composition is preferably one
that induces an immune response predominantly of the Thl type. High levels of Thl -
type cytokines (e.g., IFN-?. TNFa, IL-2 and IL-12) tend to favor the induction of cell
mediated immune responses to an administered antigen. In contrast, high levels of Th2-
type cytokines (e.g., IL-4, IL-5, IL-6 and IL-10) tend to favor the induction of humoral
immune responses. Following application of a vaccine as provided herein, a patient will
support an immune response that includes Thl- and Th2-type responses. Within a
preferred embodiment, in which a response is predominantly Thl-type, the level of Thl-
type cytokines will increase to a greater extent than the level of Th2-type cytokines. The
levels of these cytokines may be readily assessed using standard assays. For a review of
the families of cytokines, see Mosmann and Coffman, Ann. Rev. Immunol. 7-145-173,
1989.
Certain preferred adjuvants for eliciting a predominantly Thl-type response include, for
example, a combination of monophosphoryl lipid A, preferably 3-de-O-acylated
monophosphoryl lipid A, together with an aluminum salt. MPL® adjuvants are available
from Corixa Corporation (Seattle, WA; see, for example, US Patent Nos. 4,436,727;
4,877,611; 4,866,034 and 4,912,094). CpG-containing oligonucleotides (in which the
CpG dinucleotide is unmethylated) also induce a predominantly Thl response. Such
oligonucleotides are well known and are described, for example, in WO 96/02555, WO
99/33488 and U.S. Patent Nos. 6,008,200 and 5,856,462. Immunostimulatory DNA
sequences are also described, for example, by Sato et al., Science 273:352, 1996.
Another preferred adjuvant comprises a saponin, such as Quil A, or derivatives thereof,
including QS21 and QS7 (Aquila Biopharmaceuticals Inc., Framingham, MA); Escin;
Digitonin; or Qypsophila Or Chenopodium quinoa saporans . Other preferred
formulations include more than one saponin in the adjuvant combinations of the present
invention, for example combinations of at least two of the following group comprising
QS21, QS7, Quil A, b-escin, or digitonin.
Alternatively the saponin formulations may be combined with vaccine vehicles composed
of chitosan or other polycationic polymers, polylactide and polylactide-co-glycolide
particles, poly-N-acetyl glucosamine-based polymer matrix, particles composed of
polysaccharides or chemically modified polysaccharides, liposomes and lipid-based
particles, particles composed of glycerol monoesters, etc. The saponins may also be
formulated in the presence of cholesterol to form particulate structures such as liposomes
or ISCOMs. Furthermore, the saponins may be formulated together with a
polyoxyethylene ether or ester, in either a non-particulate solution or suspension, or in a
particulate structure such as a paucilamelar liposome or ISCOM. The saponins may also
be formulated with excipients such as CarbopolR to increase viscosity, or may be
formulated in a dry powder form with a powder excipient such as lactose.
In one preferred embodiment, the adjuvant system includes the combination of a
monophosphoryl lipid A and a saponin derivative, such as the combination of QS21 and
3D-MPL® adjuvant, as described in WO 94/00153, or a less reactogenic composition
where the QS21 is quenched with cholesterol, as described in WO 96/33739. Other
preferred formulations comprise an oil-in-water emulsion and tocopherol. Another
particularly preferred adjuvant formulation employing QS21, 3D-MPL® adjuvant and
tocopherol in an oil-in-water emulsion is described in WO 95/17210.
Another enhanced adjuvant system involves the combination of a CpG-containing
oligonucleotide and a saponin derivative particularly the combination of CpG and QS21
as disclosed in WO 00/09159. Preferably the formulation additionally comprises an oil in
water emulsion and tocopherol.
Additional illustrative adjuvants for use in the pharmaceutical compositions of the
invention include Montanide ISA 720 (Seppic, France), SAP (Chiron, California, United
States), ISCOMS (CSL), MF-59 (Chiron), the SBAS series of adjuvants (e g., SBAS-2 or
SBAS-4, available from SmithKline Beecham, Rixensart, Belgium), Detox (Enhanzyn®)
(Corixa, Hamilton, MT), RC-529 (Corixa, Hamilton, MT) and other aminoalkyl
glucosaminide 4-phosphates (AGPs), such as those described in pending U.S. Patent
Application Serial Nos. 08/853,826 and 09/074,720, the disclosures of which are
incorporated herein by reference in their entireties, and polyoxyethylene ether adjuvants
such as those described in WO 99/52549A1.
Other preferred adjuvants include adjuvant molecules of the general formula (I):
HO(CH2CH2O)n-A-R
Wherein, n is 1-50, A is a bond or -C(O)-, R is C1-50 alkyl or Phenyl C1-50 alkyl.
One embodiment of the present invention consists of a vaccine formulation comprising a
polyoxyethylene ether of general formula (I), wherein n is between 1 and 50, preferably
4-24, most preferably 9; the R component is C1-50, preferably C4-C20 alkyl and most
preferably C12 alkyl, and A is a bond. The concentration of the polyoxyethylene ethers
should be in the range 0.1-20%, preferably from 0.1-10%, and most preferably in the
range 0.1-1%. Preferred polyoxyethylene ethers are selected from the following group:
polyoxyethylene-9-lauryl ether, polyoxyethylene-9-steoryl ether, polyoxyethylene-8-
steoryl ether, polyoxyethylene-4-lauryl ether, polyoxyethylene-35-lauryl ether, and
polyoxyethylene-23-lauryl ether. Polyoxyethylene ethers such as polyoxyethylene lauryl
ether are described in the Merck index (12th edition: entry 7717). These adjuvant
molecules are described in WO 99/52549.
The polyoxyethylene ether according to the general formula (I) above may, if desired, be
combined with another adjuvant. For example, a preferred adjuvant combination is
preferably with CpG as described in the pending UK patent application GB 9820956.2.
Preferably a carrier is also present in the vaccine composition according to the invention.
The carrier may be an oil in water emulsion, or an aluminium salt, such as aluminium
phosphate or aluminium hydroxide.
A preferred oil-in-water emulsion comprises a metabolisible oil, such as squalene, alpha
tocopherol and Tween 80. In a particularly preferred aspect the antigens in the vaccine
composition according to the invention are combined with QS21 and 3D-MPL in such an
emulsion. Additionally the oil in water emulsion may contain span 85 and/or lecithin
and/or tricaprylin.
Typically for human administration QS21 and 3D-MPL will be present in a vaccine in the
range of µg - 200µg, such as 10-100µg, preferably 10µg - 50µg per dose. Typically the
oil in water will comprise from 2 to 10% squalene, from 2 to 10% alpha tocopherol and
from 0.3 to 3% tween 80. Preferably the ratio of squalene: alpha tocopherol is equal to
or less than 1 as this provides a more stable emulsion. Span 85 may also be present at a
level of 1 %. In some cases it may be advantageous that the vaccines of the present
invention will further contain a stabiliser.
Non-toxic oil in water emulsions preferably contain a non-toxic oil, e.g. squalane or
squalene, an emulsifier, e.g. Tween 80, in an aqueous carrier. The aqueous carrier may
be, for example, phosphate buffered saline.
A particularly potent adjuvant formulation involving QS21, 3D-MPL and tocopherol in
an oil in water emulsion is described in WO 95/17210.
The present invention also provides a polyvalent vaccine composition comprising a vaccine
formulation of the invention in combination with other antigens, in particular antigens useful
for treating cancers, more particularly colorectal cancer, autoimmune diseases and related
conditions. Such a polyvalent vaccine composition may include a TH-1 inducing adjuvant
as hereinbefore described.
According to another embodiment of this invention, an immunogenic composition
described herein is delivered to a host via antigen presenting cells (APCs), such as
dendritic cells, macrophages, B cells, monocytes and other cells that may be engineered
to be efficient APCs. Such cells may, but need not, be genetically modified to increase
the capacity for presenting the antigen, to improve activation and/or maintenance of the T
cell response, to have anti-tumor effects per se and/or to be immunologically compatible
with the receiver (i.e., matched HLA haplotype). APCs may generally be isolated from
any of a variety of biological fluids and organs, including tumor and peritumoral tissues,
and may be autologous, allogeneic, syngeneic or xenogeneic cells.
Certain preferred embodiments of the present invention use dendritic cells or progenitors
thereof as antigen-presenting cells. Dendritic cells are highly potent APCs (Banchereau
and Steinman, Mature 392:245-251, 1998) and have been shown to be effective as a
physiological adjuvant for eliciting prophylactic or therapeutic antitumor immunity (see
Timmerman and Levy, Ann. rev. Med.50:507-529, 1999). In general, dendritic cells
may be identified based on their typical shape (stellate in situ, with marked cytoplasmic
processes (dendrites) visible in vitro), their ability to take up, process and present
antigens with high efficiency and their ability to activate naive T cell responses.
Dendritic cells may, of course, be engineered to express specific cell-surface receptors or
ligands that are not commonly found on dendritic cells in vivo or ex vivo and such
modified dendritic cells are contemplated by the present invention. As an alternative to
dendritic cells, secreted vesicles antigen-loaded dendritic cells (called exosomes) may be
used within a vaccine (see Zitvogel et al., Nature Med. 4:594-600, 1998).
Dendritic cells and progenitors may be obtained from peripheral blood, bone marrow,
tumor-infiltrating cells, peritumoral tissues-infiltrating cells, lymph nodes, spleen, skin,
umbilical cord blood or any other suitable tissue or fluid. For example, dendritic cells
may be differentiated ex vivo by adding a combination of cytokines such as GM-CSF, IL.-
4, IL-13 and/or TNFa to cultures of monocytes harvested from peripheral blood.
Alternatively, CD34 positive cells harvested from peripheral blood, umbilical cord blood
or bone marrow may be differentiated into dendritic cells by adding to the culture
medium combinations of GM-CSF, IL-3, TNFa, CD40 ligand, LPS, flt3 ligand and/or
other compound(s) that induce differentiation, maturation and proliferation of dendritic
cells.
Dendritic cells are conveniently categorized as "immature" and "mature" cells, which
allows a simple way to discriminate between two well characterized phenotypes.
However, this nomenclature should not be construed to exclude all possible intermediate
stages of differentiation. Immature dendritic cells are characterized as APC with a high
capacity for antigen uptake and processing, which correlates with the high expression of
Fc? receptor and mannose receptor. The mature phenotype is typically characterized by a
lower expression of these markers, but a high expression of cell surface molecules
responsible for T cell activation such as class I and class II MHC, adhesion molecules
(e.g., CD54 and CD11) and costimulatory molecules (e.g., CD40, CD80, CD86 and 4-
1BB).
APCs may generally be transfected with a polynucleotide of the invention (or portion or
other variant thereof) such that the encoded polypeptide, or an immunogenic portion
thereof, is expressed on the cell surface. Such transfection may take place ex vivo, and a
pharmaceutical composition comprising such transfected cells may then be used for
therapeutic purposes, as described herein. Alternatively, a gene delivery vehicle that
targets a dendritic or other antigen presenting cell may be administered to a patient,
resulting in transfection that occurs in vivo. In vovo and ex vivo transfection of dendritic
cells, for example, may generally be performed using any methods known in the art, such
as those described in WO 97/24447, or the gene gun approach described by Mahvi et al.,
Immunology and cell Biology 75::456-460, 1997. Antigen loading of dendritic cells may
be achieved by incubating dendritic cells or progenitor cells with the rumor polypeptide,
DNA (naked or within a plasmid vector) or RNA; or with antigen-expressing
recombinant bacterium or viruses (e.g., vaccinia, fowlpox, adenovirus or lentivirus
vectors). Prior to loading, the polypeptide may be covalently conjugated to an
immunological partner that provides T cell help (e.g., a carrier molecule). Alternatively,
a dendritic cell may be pulsed with a non-conjugated immunological partner, separately
or in the presence of the polypeptide.
While any suitable carrier known to those of ordinary skill in the art may be employed in
the pharmaceutical compositions of this invention, the type of carrier will typically vary
depending on the mode of administration. Compositions of the present invention may be
formulated for any appropriate manner of administration, including for example, topical,
oral, nasal, mucosal, intravenous, intracranial, intraperitoneal, subcutaneous and
intramuscular administration.
Carriers for use within such pharmaceutical compositions are biocompatible, and may
also be biodegradable. In certain embodiments, the formulation preferably provides a
relatively constant level of active component release. In other embodiments, however, a
more rapid rate of release immediately upon administration may be desired. The
formulation of such compositions is well within the level of ordinary skill in the art using
known techniques. Illustrative carriers useful in this regard include microparticles of
poly(lactide-co-glycolide), polyacrylate, latex, starch, cellulose, dextran and the like.
Other illustrative delayed-release carriers include supramolecular biovectors, which
comprise a non-liquid hydrophilic core (e.g., a cross-linked polysaccharide or
oligosaccharide) and, optionally, an external layer comprising an amphiphilic compound,
such as a phospholipid (see e.g., U.S. Patent No. 5,151,254 and PCT applications WO
94/20078, WO/94/23701 and WO 96/06638). The amount of active compound contained
within a sustained release formulation depends upon the site of implantation, the rate and
expected duration of release and the nature of the condition to be treated or prevented.
In another illustrative embodiment, biodegradable microspheres (e.g., polylactate
polyglycolate) are employed as carriers for the compositions of this invention. Suitable
biodegradable microspheres are disclosed, for example, in U.S. Patent Nos. 4,897,268;
5,075,109; 5,928,647; 5,811,128; 5,820,883; 5,853,763; 5,814,344, 5,407,609 and
5,942,252. Modified hepatitis B core protein carrier systems, such as described in
WO/99 40934, and references cited therein, will also be useful for many applications.
Another illustrative carrier/delivery system employs a carrier comprising particulate-
protein complexes, such as those described in U.S. Patent No. 5,928,647, which are
capable of inducing a class I-restricted cytotoxic T lymphocyte responses in a host
The pharmaceutical compositions of the invention will often further comprise one or
more buffers (e.g., neutral buffered saline or phosphate buffered saline), carbohydrates
(e.g., glucose, mannose, sucrose or dextrans), mannitol, proteins, polypeptides or amino
acids such as glycine, antioxidants, bacteriostats, chelating agents such as EDTA or
glutathione, adjuvants (e.g., aluminum hydroxide), solutes that render the formulation
isotonic, hypotonic or weakly hypertonic with the blood of a recipient, suspending agents,
thickening agents and/or preservatives. Alternatively, compositions of the present
invention may be formulated as a lyophilizate.
The pharmaceutical compositions described herein may be presented in unit-dose or
multi-dose containers, such as sealed ampoules or vials. Such containers are typically
sealed in such a way to preserve the sterility and stability of the formulation until use. In
general, formulations may be stored as suspensions, solutions or emulsions in oily or
aqueous vehicles. Alternatively, a pharmaceutical composition may be stored in a freeze-
dried condition requiring only the addition of a sterile liquid carrier immediately prior to
use.
The development of suitable dosing and treatment regimens for using the particular
compositions described herein in a variety of treatment regimens, including e.g., oral,
parenteral, intravenous, intranasal, and intramuscular administration and formulation, is
well known in the art, some of which are briefly discussed below for general purposes of
illustration.
In certain applications, the pharmaceutical compositions disclosed herein may be
delivered via oral administration to an animal. As such, these compositions may be
formulated with an inert diluent or with an assimilable edible carrier, or they may be
enclosed in hard- or soft-shell gelatin capsule, or they may be compressed into tablets, or
they may be incorporated directly with the food of the diet.
The active compounds may even be incorporated with excipients and used in the form of
ingestible tablets, buccal tables, troches, capsules, elixirs, suspensions, syrups, wafers,
and the like (see, for example, Mathiowitz et al., Nature 1997 Mar 27;386(6623):410-4;
Hwang et al. Crit Rev Ther Drug Carrier Syst 1998;15(3):243-84; U. S. Patent
5,641,515; U. S. Patent 5,580,579 and U. S. Patent 5,792,451). Tablets, troches, pills,
capsules and the like may also contain any of a variety of additional components, for
example, a binder, such as gum tragacanth, acacia, comstarch, or gelatin; excipients, such
as dicalcium phosphate; a disintegrating agent, such as corn starch, potato starch, alginic
acid and the like; a lubricant, such as magnesium stearate; and a sweetening agent, such
as sucrose, lactose or saccharin may be added or a flavoring agent, such as peppermint,
oil of wintergreen, or cherry flavoring. When the dosage unit form is a capsule, it may
contain, in addition to materials of the above type, a liquid carrier. Various other
materials may be present as coatings or to otherwise modify the physical form of the
dosage unit. For instance, tablets, pills, or capsules may be coated with shellac, sugar, or
both. Of course, any material used in preparing any dosage unit form should be
pharmaceutically pure and substantially non-toxic in the amounts employed. In addition,
the active compounds may be incorporated into sustained-release preparation and
formulations.
Typically, these formulations will contain at least about 0.1% of the active compound or
more, although the percentage of the active ingredient(s) may, of course, be varied and
may conveniently be between about 1 or 2% and about 60% or 70% or more of the
weight or volume of the total formulation. Naturally, the amount of active compound(s)
in each therapeutically useful composition may be prepared is such a way that a suitable
dosage will be obtained in any given unit dose of the compound. Factors such as
solubility, bioavailability, biological half-life, route of administration, product shelf life,
as well as other pharmacological considerations will be contemplated by one skilled in
the art of preparing such pharmaceutical formulations, and as such, a variety of dosages
and treatment regimens may be desirable.
For oral administration the compositions of the present invention may alternatively be
incorporated with one or more excipients in the form of a mouthwash, dentifrice, buccal
tablet, oral spray, or sublingual orally-administered formulation. Alternatively, the active
ingredient may be incorporated into an oral solution such as one containing sodium
borate, glycerin and potassium bicarbonate, or dispersed in a dentifrice, or added in a
therapeutically-effective amount to a composition that may include water, binders,
abrasives, flavoring agents, foaming agents, and humectants. Alternatively the
compositions may be fashioned into a tablet or solution form that may be placed under
the tongue or otherwise dissolved in the mouth.
In certain circumstances it will be desirable to deliver the pharmaceutical compositions
disclosed herein parenterally, intravenously, intramuscularly, or even intraperitoneally.
Such approaches are well known to the skilled artisan, some of which are further
described, for example, in U. S. Patent 5,543,158; U. S. Patent 5,641,515 and U. S. Patent
5,399,363. In certain embodiments, solutions of the active compounds as free base or
pharmacologically acceptable salts may be prepared in water suitably mixed with a
surfactant, such as hydroxypropylcellulose. Dispersions may also be prepared in
glycerol, liquid polyethylene glycols, and mixtures thereof and in oils. Under ordinary
conditions of storage and use, these preparations generally will contain a preservative to
prevent the growth of microorganisms.
Illustrative pharmaceutical forms suitable for injectable use include sterile aqueous
solutions or dispersions and sterile powders for the extemporaneous preparation of sterile
injectable solutions or dispersions (for example, see U. S. Patent 5,466,468). In all cases
the form must be sterile and must be fluid to the extent that easy syringability exists. It
must be stable under the conditions of manufacture and storage and must be preserved
against the contaminating action of microorganisms, such as bacteria and fungi. The
carrier can be a solvent or dispersion medium containing, for example, water, ethanol,
polyol (e.g., glycerol, propylene glycol, and liquid polyethylene glycol, and the like),
suitable mixtures thereof, and/or vegetable oils. Proper fluidity may be maintained, for
example, by the use of a coating, such as lecithin, by the maintenance of the required
particle size in the case of dispersion and/or by the use of surfactants. The prevention of
the action of microorganisms can be facilitated by various antibacterial and antifungal
agents, for example, parabens, chlorobutanol, phenol, sorbic acid, thimerosal, and the
like. In many cases, it will be preferable to include isotonic agents, for example, sugars
or sodium chloride. Prolonged absorption of the injectable compositions can be brought
about by the use in the compositions of agents delaying absorption, for example,
aluminum monostearate and gelatin.
In one embodiment, for parenteral administration in an aqueous solution, the solution
should be suitably buffered if necessary and the liquid diluent first rendered isotonic with
sufficient saline or glucose. These particular aqueous solutions are especially suitable for
intravenous, intramuscular, subcutaneous and intraperitoneal administration. In this
connection, a sterile aqueous medium that can be employed will be known to those of
skill in the art in light of the present disclosure. For example, one dosage may be
dissolved in 1 ml of isotonic NaCl solution and either added to 1000 ml of
hypodermoclysis fluid or injected at the proposed site of infusion, (see for example,
"Remington's Pharmaceutical Sciences" 15th Edition, pages 1035-1038 and 1570-1580).
Some variation in dosage will necessarily occur depending on the condition of the subject
being treated. Moreover, for human administration, preparations will of course
preferably meet sterility, pyrogenicity, and the general safety and purity standards as
required by FDA Office of Biologies standards.
In another embodiment of the invention, the compositions disclosed herein may be
formulated in a neutral or salt form. Illustrative pharmaceutically-acceptable salts include
the acid addition salts (formed with the free amino groups of the protein) and which are
formed with inorganic acids such as, for example, hydrochloric or phosphoric acids, or
such organic acids as acetic, oxalic, tartaric, mandelic, and the like. Salts formed with the
free carboxyl groups can also be derived from inorganic bases such as, for example,
sodium, potassium, ammonium, calcium, or ferric hydroxides, and such organic bases as
isopropylamine, trimethylamine, histidine, procaine and the like. Upon formulation,
solutions will be administered in a manner compatible with the dosage formulation and in
such amount as is therapeutically effective.
The carriers can further comprise any and all solvents, dispersion media, vehicles,
coatings, diluents, antibacterial and antifungal agents, isotonic and absorption delaying
agents, buffers, carrier solutions, suspensions, colloids, and the like. The use of such
media and agents for pharmaceutical active substances is well known in the art. Except
insofar as any conventional media or agent is incompatible with the active ingredient, its
use in the therapeutic compositions is contemplated. Supplementary active ingredients
can also be incorporated into the compositions. The phrase
"pharmaceutically-acceptable" refers to molecular entities and compositions that do not
produce an allergic or similar untoward reaction when administered to a human.
In certain embodiments, the pharmaceutical compositions may be delivered by intranasal
sprays, inhalation, and/or other aerosol delivery vehicles. Methods for delivering genes,
nucleic acids, and peptide compositions directly to the lungs via nasal aerosol sprays has
been described, e.g., in U. S. Patent 5,756,353 and U. S. Patent 5,804,212. Likewise, the
delivery of drugs using intranasal microparticle resins (Takenaga et. al., J Controlled
Release 1998 Mar 2;52(l-2):81-7) and lysophosphatidyl-glycerol compounds (U. S.
Patent 5,725,871) are also well-known in the pharmaceutical arts. Likewise, illustrative
transmucosal drug delivery in the form of a polytetrafluoroetheylene support matrix is
described in U. S. Patent 5,780,045.
In certain embodiments, liposomes, nanocapsules, microparticles, lipid particles, vesicles,
and the like, are used for the introduction of the compositions of the present invention
into suitable host cells/organisms. In particular, the compositions of the present invention
may be formulated for delivery either encapsulated in a lipid particle, a liposome, a
vesicle, a nanosphere, or a nanoparticle or the like. Alternatively, compositions of the
present invention can be bound, either covalently or non-covalently, to the surface of
such carrier vehicles.
The formation and use of liposome and liposome-like preparations as potential drug
carriers is generally known to those of skill in the art (see for example, Lasic, Trends
Biotechnol 1998 Jul; 16(7):307-21; Takakura, Nippon Rinsho 1998 Mar;56(3):691-5;
Chandran et al.,., Indian J Exp Biol. 1997 Aug;35(8):801-9; Margalit, Crit Rev Ther Drug
Carrier Syst. 1995;12(2-3):233-61; U.S. Patent 5,567,434; U.S. Patent 5,552,157; U.S.
Patent 5,565,213; U.S. Patent 5,738,868 and U.S. Patent 5,795,587, each specifically
incorporated herein by reference in its entirety).
Liposomes have been used successfully with a number of cell types that are normally
difficult to transfect by other procedures, including T cell suspensions, primary
hepatocyte cultures and PC 12 cells (Renneisen et al., J Biol Chem. 1990 Sep
25;265(27): 16337-42; Muller et al. DNA Cell Biol. 1990 Apr;9(3):221-9). In addition,
liposomes are free of the DNA length constraints that are typical of viral-based delivery
systems. Liposomes have been used effectively to introduce genes, various drugs,
radiotherapeutic agents, enzymes, viruses, transcription factors, allosteric effectors and
the like, into a variety of cultured cell lines and animals. Furthermore, he use of
liposomes does not appear to be associated with autoimmune responses or unacceptable
toxicity after systemic delivery.
In certain embodiments, liposomes are formed from phospholipids that are dispersed in
an aqueous medium and spontaneously form multilamellar concentric bilayer vesicles
(also termed multilamellar vesicles (MLVs).
Alternatively, in other embodiments, the invention provides for pharmaceutically-
acceptable nanocapsule formulations of the compositions of the present invention.
Nanocapsules can generally entrap compounds in a stable and reproducible way (see, for
example, Quintanar-Guerrero et al. Drug Dev Ind Pharm. 1998 Dec;24(12):l 113-28).
To avoid side effects due to intracellular polymeric overloading, such ultrafine particles
(sized around 0.1 µm) may be designed using polymers able to be degraded in vivo. Such
particles can be made as described, for example, by Couvreur et al. Crit Rev Ther Drug
Carrier Syst. 1988;5(l):l-20; zur Muhlen et al. Eur J Pharm Biopharm. 1998
Mar;45(2): 149-55; Zambaux et al. J Controlled Release. 1998 Jan 2;50(l-3):31-40; and
U.S. Patent 5,145,684.
This invention also relates to the use of polynucleotides, in the form of primers derived from
the polynucleotides of the present invention, and of polypeptides, in the form of antibodies
or reagents specific for the polypeptide of the present invention, as diagnostic reagents.
The identification of genetic or biochemical markers in blood or tissues that will enable the
detection of very early changes along the carcinogenesis pathway will help in determining
the best treatment for the patient. Surrogate tumour markers, such as polynucleotide
expression, can be used to diagnose different forms and states of cancer. The identification
of expression levels of the polynucleotides of the invention will be useful in both the
staging of the cancerous disorder and grading the nature of the cancerous tissue. The staging
process monitors the advancement of the cancer and is determined on the presence or
absence of malignant tissue in the areas biopsied. The polynucleotides of the invention can
help to perfect the staging process by identifying markers for the aggresivity of a cancer, for
example the presence in different areas of the body. The grading of the cancer describes
how closely a tumour resembles normal tissue of its same type and is assessed by its cell
morphology and other markers of differentiation. The polynucleotides of the invention can
be useful in determining the tumour grade as they can help in the determination of the
differentiation status of the cells of a tumour.
The diagnostic assays offer a process for diagnosing or determining a susceptibility to
cancers, autoimmune disease and related conditions through diagnosis by methods
comprising determining from a sample derived from a subject an abnormally decreased or
increased level of polypeptide or mRNA. This method of diagnosis is known as
differential expression. The expression of a particular gene is compared between a
diseased tissue and a normal tissue. A difference between the polynucleotide-related
gene, mRNA, or protein in the two tissues is compared, for example in molecular weight,
amino acid or nucleotide sequence, or relative abundance, indicates a change in the gene,
or a gene which regulates it, in the tissue of the human that was suspected of being
diseased.
Decreased or increased expression can be measured at the RNA level. PolyA RNA is
first isolated from the two tissues and the detection of mRNA encoded by a gene
corresponding to a differentially expressed polynucleotide of the invention can be
detected by, for example, in situ hybridization in tissue sections, reverse trascriptase-
PCR, using Northern blots containing poly A+ mRNA, or any other direct or inderect
RNA detection method. An increased or decreased expression of a given RNA in a
diseased tissue compared to a normal tissue suggests that the transcript and/or the expressed
protein has a role in the disease. Thus detection of a higher or lower level of mRNA
corresponding to SEQ ID NO: 1 relative to normal level is indicative of the presence of
cancer in the patient.
mRNA expression levels in a sample can be determined by generation of a library of
expressed sequence tags (ESTs) from the sample. The relative representation of ESTs in
the library can be used to assess the relative representation of the gene transcript in the
starting sample. The EST analysis of the test can then be compared to the EST analysis
of a reference sample to determine the relative expression levels of the polynucleotide of
interest.
Other mRNA analyses can be carried out using serial analysis of gene expression (SAGE)
methodology (Velculescu et. Al. Science (1995) 270:484) , differential display
methodology (For example, US 5,776,683) or hybridization analysis which relies on the
specificity of nucleotide interactions.
Alternatively, the comparison could be made at the protein level. The protein sizes in the
two tissues may be compared using antibodies to detect polypeptides in Western blots of
protein extracts from the two tissues. Expression levels and subcellular localization may
also be detected immunologically using antibodies to the corresponding protein. Further
assay techniques that can be used to determine levels of a protein, such as a polypeptide of
the present invention, in a sample derived from a host are well-known to those of skill in the
art. A raised or decreased level of polypeptide expression in the diseased tissue compared
with the same protein expression level in the normal tissue indicates that the expressed
protein may be involved in the disease.
In the assays of the present invention, the diagnosis can be determined by detection of gene
product expression levels encoded by at least one sequence set forth in SEQ ID NO: 1. A
comparison of the mRNA or protein levels in a diseased versus normal tissue may also be
used to follow the progression or remission of a disease.
A large number of polynucleotide sequences in a sample can be assayed using
polynucleotide arrays. These can be used to examine differential expression of genes and to
determine gene function. For example, arrays of the polynucleotide sequences SEQ ID
NO:1 can be used to determine if any of the polynucleotides are differentially expressed
between a normal and cancer cell. In one embodiment of the invention, an array of
oligonucleotides probes comprising the SEQ ID NO:1 nucleotide sequence or fragments
thereof can be constructed to conduct efficient screening of e.g., genetic mutations. Array
technology methods are well known and have general applicability and can be used to
address a variety of questions in molecular genetics including gene expression, genetic
linkage, and genetic variability (see for example: M.Chee et al., Science, Vol 274, pp 610-
613 (1996)).
"Diagnosis" as used herein includes determination of a subject's susceptibility to a
disease, determination as to whether a subject presently has the disease, and also the
prognosis of a subject affected by the disease.
The present invention, further relates to a diagnostic kit for performing a diagnostic assay
which comprises:
(a) a polynucleotide of the present invention, preferably the nucleotide sequence of SEQ
ID NO: 1, or a fragment thereof;
(b) a nucleotide sequence complementary to that of (a), preferably the nucleotide
sequence of SEQ ED NO: 6;
(c) a polypeptide of the present invention, preferably the polypeptide of SEQ ID NO: 2 or
3, or a fragment thereof; or
(d) an antibody to a polypeptide of the present invention, preferably to the polypeptide of
SEQ ID NO:2 or 3.
The nucleotide sequences of the present invention are also valuable for chromosomal
localisation. The sequence is specifically targeted to, and can hybridize with, a particular
location on an individual human chromosome. The mapping of relevant sequences to
chromosomes according to the present invention is an important first step in correlating
those sequences with gene associated disease. Once a sequence has been mapped to a
precise chromosomal location, the physical position of the sequence on the chromosome can
be correlated with genetic map data. Such data are found in, for example, V. McKusick,
Mendelian Inheritance in Man (available on-line through Johns Hopkins University Welch
Medical Library). The relationship between genes and diseases that have been mapped to
the same chromosomal region are then identified through linkage analysis (coinheritance of
physically adjacent genes).The differences in the cDNA or genomic sequence between
affected and unaffected individuals can also be determined.
The polypeptides of the invention or their fragments or analogs thereof, or cells expressing
them, can also be used as imrnunogens to produce antibodies immunospecific for
polypeptides of the present invention. The term "immunospecific" means that the antibodies
have substantially greater affinity for the polypeptides of the invention than their affinity for
other related polypeptides in the prior art
In a further aspect the invention provides an antibody immunospecific for a polypeptide
according to the invention or an immunological fragment thereof as hereinbefore defined.
Preferably the antibody is a monoclonal antibody.
Antibodies generated against polypeptides of the present invention may be obtained by
administering the polypeptides or epitope-bearing fragments, analogs or cells to an animal,
preferably a non-human animal, using routine protocols. For preparation of monoclonal
antibodies, any technique which provides antibodies produced by continuous cell line
cultures can be used. Examples include the hybridoma technique (Kohler, G. and Milstein,
C., Nature (1975) 256:495-497), the trioma technique, the human B-cell hybridoma
technique (Kozbor et al. Immunology Today (1983) 4:72) and the EBV-hybridoma
technique (Cole et al., Monoclonal Antibodies and Cancer Therapy, 77-96, Alan R. Liss,
Inc., 1985).
Techniques for the production of single chain antibodies, such as those described in U.S.
Patent No. 4,946,778, can also be adapted to produce single chain antibodies to polypeptides
of this invention. Also, transgenic mice, or other organisms, including other mammals, may
be used to express humanized antibodies.
The above-described antibodies may be employed to isolate or to identify clones expressing
the polypeptide or to purify the polypeptides by affinity chromatography.
The antibody of the invention may also be employed to prevent or treat cancer, particularly
colorectal cancer, autoimmune disease and related conditions.
Another aspect of the invention relates to a method for inducing or modulating an
immunological response in a mammal which comprises inoculating the mammal with a
polypeptide of the present invention, adequate to produce antibody and/or T cell immune
response to protect or ameliorate the symptoms or progression of the disease. Yet
another aspect of the invention relates to a method of inducing or modulating
immunological response in a mammal which comprises, delivering a polypeptide of the
present invention via a vector directing expression of the polynucleotide and coding for
the polypeptide in vivo in order to induce such an immunological response to produce
antibody to protect said animal from diseases.
It will be appreciated that the present invention therefore provides a method of treating
abnormal conditions such as, for instance, cancer and autoimmune diseases, in particular,
colorectal cancer, related to either a presence of, an excess of, or an under-expression of,
CASB7439 polypeptide activity. Other abnormal conditions related to CASB7439
expression that the invention seeks to treat are chronic lymphocytic leukemiae and germ cell
tumours.
The present invention further provides for a method of screening compounds to identify
those which stimulate or which inhibit the function of the CASB7439 polypeptide. In
general, agonists or antagonists may be employed for therapeutic and prophylactic purposes
for such diseases as hereinbefore mentioned. Compounds may be identified from a variety
of sources, for example, cells, cell-free preparations, chemical libraries, and natural product
mixtures. Such agonists, antagonists or inhibitors so-identified may be natural or modified
substrates, ligands, receptors, enzymes, etc., as the case may be, of the polypeptide; or may
be structural or functional mimetics thereof (see Coligan et al., Current Protocols in
Immunology l(2):Chapter 5 (1991)). Screening methods will be known to those skilled in
the art. Further screening methods may be found in for example D. Bennett et al., J Mol
Recognition, 8:52-58 (1995); and K. Johanson et al., J Biol Chem, 270(16):9459-9471
(1995) and references therein.
Thus the invention provides a method for screening to identify compounds which stimulate
or which inhibit the function of the polypeptide of the invention which comprises a method
selected from the group consisting of:
(a) measuring the binding of a candidate compound to the polypeptide (or to the cells or
membranes bearing the polypeptide) or a fusion protein thereof by means of a label
directly or indirectly associated with the candidate compound;
(b) measuring the binding of a candidate compound to the polypeptide (or to the cells or
membranes bearing the polypeptide) or a fusion protein thereof in the presense of a
labeled competitior,
(c) testing whether the candidate compound results in a signal generated by activation or
inhibition of the polypeptide, using detection systems appropriate to the cells or cell
membranes bearing the polypeptide;
(d) mixing a candidate compound with a solution containing a polypeptide of claim 1, to
form a mixture, measuring activity of the polypeptide in the mixture, and comparing the
activity of the mixture to a standard; or
(e) detecting the effect of a candidate compound on the production of mRNA encoding
said polypeptide and said polypeptide in cells, using for instance, an ELISA assay.
The polypeptide of the invention may be used to identify membrane bound or soluble
receptors, if any, through standard receptor binding techniques known in the art. Well
known screening methods may also be used to identify agonists and antagonists of the
polypeptide of the invention which compete with the binding of the polypeptide of the
invention to its receptors, if any.
Thus, in another aspect, the present invention relates to a screening kit for identifying
agonists, antagonists, ligands, receptors, substrates, enzymes, etc. for polypeptides of the
present invention; or compounds which decrease or enhance the production of such
polypeptides, which comprises:
(a) a polypeptide of the present invention;
(b) a recombinant cell expressing a polypeptide of the present invention;
(c) a cell membrane expressing a polypeptide of the present invention; or
(d) antibody to a polypeptide of the present invention;
which polypeptide is preferably that of SEQ ID NO:2 or 3.
It will be readily appreciated by the skilled artisan that a polypeptide of the present
invention may also be used in a method for the structure-based design of an agonist,
antagonist or inhibitor of the polypeptide, by:
(a) determining in the first instance the three-dimensional structure of the polypeptide;
(b) deducing the three-dimensional structure for the likely reactive or binding site(s) of
an agonist, antagonist or inhibitor;
(c) synthesing candidate compounds that are predicted to bind to or react with the
deduced binding or reactive site; and
(d) testing whether the candidate compounds are indeed agonists, antagonists or
inhibitors.
Gene therapy may also be employed to effect the endogenous production of CASB7439
polypeptide by the relevant cells in the subject. For an overview of gene therapy, see
Chapter 20, Gene Therapy and other Molecular Genetic-based Therapeutic Approaches,
(and references cited therein) in Human Molecular Genetics, T Strachan and A P Read,
BIOS Scientific Publishers Ltd (1996).
Vaccine preparation is generally described in Pharmaceutical Biotechnology, Vol.61
Vaccine Design - the subunit and adjuvant approach, edited by Powell and Newman,
Plenum Press, 1995. New Trends and Developments in Vaccines, edited by Voller et al.,
University Park Press, Baltimore, Maryland, U.S.A. 1978. Encapsulation within
liposomes is described, for example, by Fullerton, U.S. Patent 4,235,877. Conjugation of
proteins to macromolecules is disclosed, for example, by Likhite, U.S. Patent 4,372,945
and by Armor et al., U.S. Patent 4,474,757.
The amount of protein in each vaccine dose is selected as an amount which induces an
immunoprotective response without significant, adverse side effects in typical vaccinees.
Such amount will vary depending upon which specific immunogen is employed.
Generally, it is expected that each dose will comprise l-lOOO^g of protein, preferably
2-100µg, most preferably 4-40µg. An optimal amount for a particular vaccine can be
ascertained by standard studies involving observation of antibody titres and other
responses in subjects. Following an initial vaccination, subjects may receive a boost in
about 4 weeks.
"Isolated" means altered "by the hand of man" from the natural state. If an "isolated"
composition or substance occurs in nature, it has been changed or removed from its
original environment, or both. For example, a polynucleotide or a polypeptide naturally
present in a living animal is not "isolated," but the same polynucleotide or polypeptide
separated from the coexisting materials of its natural state is "isolated", as the term is
employed herein.
"Polynucleotide" generally refers to any polyribonucleotide or polydeoxribonucleotide,
which may be unmodified RNA or DNA or modified RNA or DNA including single and
double stranded regions.
"Variant" refers to a polynucleotide or polypeptide that differs from a reference
polynucleotide or polypeptide, but retains essential properties. A typical variant of a
polynucleotide differs in nucleotide sequence from another, reference polynucleotide.
Changes in the nucleotide sequence of the variant may or may not alter the amino acid
sequence of a polypeptide encoded by the reference polynucleotide. Nucleotide changes
may result in amino acid substitutions, additions, deletions, fusions and truncations in the
polypeptide encoded by the reference sequence, as discussed below. A typical variant of
a polypeptide differs in amino acid sequence from another, reference polypeptide.
Generally, differences are limited so that the sequences of the reference polypeptide and
the variant are closely similar overall and, in many regions, identical. A variant and
reference polypeptide may differ in amino acid sequence by one or more substitutions,
additions, deletions in any combination. A substituted or inserted amino acid residue
may or may not be one encoded by the genetic code. A variant of a polynucleotide or
polypeptide may be a naturally occurring such as an allelic variant, or it may be a variant
that is not known to occur naturally. Non-naturally occurring variants of polynucleotides
and polypeptides may be made by mutagenesis techniques or by direct synthesis.
"Identity," as known in the art, is a relationship between two or more polypeptide sequences
or two or more polynucleotide sequences, as determined by comparing the sequences. In the
art, "identity" also means the degree of sequence relatedness between polypeptide or
polynucleotide sequences, as the case may be, as determined by the match between
strings of such sequences. "Identity" and "similarity" can be readily calculated by known
methods, including but not limited to those described in (Computational Molecular
Biology, Lesk, A.M., ed., Oxford University Press, New York, 1988; Biocomputing:
Informatics and Genome Projects, Smith, D.W., ed., Academic Press, New York, 1993;
Computer Analysis of Sequence Data, Part I, Griffin, A.M., and Griffin, H.G., eds.,
Humana Press, New Jersey, 1994; Sequence Analysis in Molecular Biology, von Heinje,
G., Academic Press, 1987; and Sequence Analysis Primer, Gribskov, M. and Devereux,
J., eds., M Stockton Press, New York, 1991; and Carillo, H., and Lipman, D., SIAM j
Applied Math., 48: 1073 (1988). Preferred methods to determine identity are designed to
give the largest match between the sequences tested. Methods to determine identity and
similarity are codified in publicly available computer programs. Preferred computer
program methods to determine identity and similarity between two sequences include, but
are not limited to, the GCG program package (Devereux, J., et al., Nucleic Acids
Research 12(1):387 (1984)), BLASTP, BLASTN, and FASTA (Atschul, S.F. et al., J.
Molec. Biol 215: 403-410 (1990). The BLAST X program is publicly available from
NCBI and other sources (BLAST Manual, Altschul, S., et al., NCBI NLM NIH Bethesda,
MD 20894; Altschul, S., et al., J. Mol. Biol. 215: 403-410 (1990). The well known Smith
Waterman algorithm may also be used to determine identity.
The preferred algorithm used is FASTA. The preferred parameters for polypeptide or
polynuleotide sequence comparison using this algorithm include the following:
Gap Penalty: 12
Gap extension penalty: 4
Word size: 2, max 6
Preferred parameters for polypeptide sequence comparison with other methods include
the following:
1) Algorithm: Needleman and Wunsch, J. Mol Biol. 48: 443-453 (1970)
Comparison matrix: BLOSSUM62 from Hentikoff and Hentikoff, Proc. Natl. Acad. Sci.
USA. 89:10915-10919 (1992)
Gap Penalty: 12
Gap Length Penalty: 4
A program useful with these parameters is publicly available as the "gap" program from
Genetics Computer Group, Madison WI. The aforementioned parameters are the default
parameters for polypeptide comparisons (along with no penalty for end gaps).
Preferred parameters for polynucleotide comparison include the following:
1) Algorithm: Needleman and Wunsch, J. Mol Biol. 48: 443-453 (1970)
Comparison matrix: matches = +10, mismatch = 0
Gap Penalty: 50

Gap Length Penalty: 3
A program useful with these parameters is publicly available as the "gap" program from
Genetics Computer Group, Madison WI. The aforementioned parameters are the default
parameters for polynucleotide comparisons.
By way of example, a polynucleotide sequence of the present invention may be identical
to the reference sequence of SEQ ID NO:1, that is be 100% identical, or it may include
up to a certain integer number of nucleotide alterations as compared to the reference
sequence. Such alterations are selected from the group consisting of at least one
nucleotide deletion, substitution, including transition and transversion, or insertion, and
wherein said alterations may occur at the 51 or 3' terminal positions of the reference
nucleotide sequence or anywhere between those terminal positions, interspersed either
individually among the nucleotides in the reference sequence or in one or more
contiguous groups within the reference sequence. The number of nucleotide alterations is
determined by multiplying the total number of nucleotides in SEQ ID NO:1 by the
numerical percent of the respective percent identity(divided by 100) and subtracting that
product from said total number of nucleotides in SEQ ID NO:1, or:
nn wherein nn is the number of nucleotide alterations, xn is the total number of nucleotides
in SEQ ID NO:1, and y is, for instance, 0.70 for 70%, 0.80 for 80%, 0.85 for 85%, 0.90
for 90%, 0.95 for 95%,etc, and wherein any non-integer product of xn and y is rounded
down to the nearest integer prior to subtracting it from xn. Alterations of a
polynucleotide sequence encoding the polypeptide of SEQ ID NO:2 may create nonsense,
missense or frameshift mutations in this coding sequence and thereby alter the
polypeptide encoded by the polynucleotide following such alterations.
Similarly, a polypeptide sequence of the present invention may be identical to the
reference sequence of SEQ ED NO:2, that is be 100% identical, or it may include up to a
certain integer number of amino acid alterations as compared to the reference sequence
such that the % identity is less than 100%. Such alterations are selected from the group
consisting of at least one amino acid deletion, substitution, including conservative and
non-conservative substitution, or insertion, and wherein said alterations may occur at the
amino- or carboxy-terminal positions of the reference polypeptide sequence or anywhere
between those terminal positions, interspersed either individually among the amino acids
in the reference sequence or in one or more contiguous groups within the reference
sequence. The number of amino acid alterations for a given % identity is determined by
multiplying the total number of amino acids in SEQ ED NO:2 by the numerical percent of
the respective percent identity(divided by 100) and then subtracting that product from
said total number of amino acids in SEQ ID NO:2, or:

wherein na is the number of amino acid alterations, xa is the total number of amino acids
in SEQ ID NO:2, and y is, for instance 0.70 for 70%, 0.80 for 80%, 0.85 for 85% etc.,
and wherein any non-integer product of xa and y is rounded down to the nearest integer
prior to subtracting it from xa.
"Homolog" is a generic term used in the art to indicate a polynucleotide or polypeptide
sequence possessing a high degree of sequence relatedness to a subject sequence. Such
relatedness may be qunnfied by determining the degree of identity and/or similarity between
the sequences being compared as hereinbefore described. Falling within this generic term
are the terms "ortholog", meaning a polynucleotide or polypeptide that is the functional
equivalent of a polynucleotide or polypeptide in another species and "paralog" meaning a
functionally similar sequence when considered within the same species.
FIGURE LEGENDS
Figure 1: shows Real-time PCR data using the Taqman probe. The legend is as follows:
Adrenal gland: Ad_Gl; Bladder: Bl; Bone marrow: Bo_Ma; Cervix: Ce; Colon: Co;
Fallopian tube: Fa_Tu; Ileon: II; Liver: Li; Lung: Lu; Lymph node: Ly_No; Oesophagus:
Oe; Parathyroid gland: Pa_Thy; Placenta: PI; Prostate: Pr; Rectum: Re; Skin: Sk; Skeletal
muscle: Sk_Mu; Small intestine: Sm_In; Spleen: Sp; Testis: Te; Thyroid gland: Thy;
Trachea: Tr.
Figure 2 shows Real-time PCR expression using Sybr protocol. The legend is as follows:
Adrenal gland: Ad_Gl; Bladder: Bl; Bone marrow: BoMa; Cervix: Ce; Colon: Co;
Lymph node: Ly_No; Oesophagus: Oe; Parathyroid gland: Pa_Thy; Placenta: PI;
Prostate: Pr; Rectum: Re; Skin: Sk; Skeletal muscle: Sk_Mu; Small intestine: Sm In;
Spleen: Sp; Testis: Te; Thyroid gland: Thy; Trachea: Tr; Heart: He.
Figure 3 shows Coomassie blue stained SDS PAGE of the cell extract from the strain
expressing CASB7439. Lane 1 shows the molecular markers, lane 2 the cellular extract
induced 5h at 39°C; lane 3 shows the supernatant of cellular extract induced; and lane 4
shows the pellet of cellular extract induced.
Figure 4 shows a Western blot analysis of NS1-CASB7439 expressed protein. The gel is
loaded with the cell extract from the strain expressing CASB7439 and revealed with anti-
NS1 monoclonal antibody.
Figure 5 shows a Coomassie-blue stained SDS-PAGE of CASB7439 after purification.
Lanes 1 and 5 represent the molecular weight markers; lanes 2, 3, 4 are respectively
loaded with 2 µ1, 4 µl and 6 µl of purified protein.
Figure 6 shows a Western blot CASB7439 after purification as revealed by an anti-
polyhistidine monoclonal antibody.
Examples
Example 1
Real-time RT-PCR analysis
Real-time RT-PCR (U. Gibson. 1996. Genome Research: 6,996) is used to compare
mRNA transcript abundance of the candidate antigen in matched tumour and normal
colon tissues from multiple patients. In addition, mRNA levels of the candidate gene in a
panel of normal tissues are also evaluated by this approach.
Total RNA from normal and tumour colon is extracted from snap frozen biopsies using
TriPure reagent (Boehringer). Total RNA from normal tissues is purchased from
InVitrogen or is extracted from snap frozen biopsies using TriPure reagent. Poly-A+
mRNA is purified from total RNA after DNAase treatment using oligo-dT magnetic
beads (Dynal). Quantification of the mRNA is performed by spectrofluorimetry
(VersaFluor, BioRad) using Sybrll dye (Molecular Probes). Primers for real-time PCR
amplification are designed with the Perkin-Elmer Primer Express software using default
options for TaqMan amplification conditions.
Real-time reactions are assembled according to standard PCR protocols using 2 ng of
purified mRNA for each reaction. SybrI dye (Molecular Probes) is added at a final
dilution of 1/75000 for real-time detection. Amplification (40 cycles) and real-time
detection is performed in a Perkin-Elmer Biosystems PE7700 system using conventional
instrument settings. Ct values are calculated using the PE7700 Sequence Detector
software. Several Ct values are obtained for each samples : for the patient samples, the
tumour Ct (CtT) and the matched normal colon Ct (CtN) values on the candidate TAA,
and for the panel of normal tissue samples, a CtXY for each normal tissue XY. An
another Ct (CtA) is also calculated on Actin gene, as an internal reference, for all of the
samples. Alternatively, real-time PCR amplification can be monitored using a Taqman
probe. Amplification (40 cycles) and real-time detection is performed in a Perkin-Elmer
Biosystems PE7700 system using conventional instrument settings. Ct values are
calculated using the PE7700 Sequence Detector Software. Ct values are obtained from
each tissue sample for the target mRNA (CtX) and for the actin mRNA (CtA).
As the efficiency of PCR amplification under the prevailing experimental
conditions is close to the theoretical amplification efficiency, 2(CtN/T/xy-ctA) value is an
estimate of the relative TAA transcript level of the sample, standardised with respect to
Actin transcript level. A value of 1 thus suggests the candidate antigen and Actin have the
same expression level.
Real-time PCR reactions were first performed on tumour colon and matching normal
colon from biopsies of 12 patients. Reactions were then performed on a more complete data
set totalling 18 patients (are included in this data set the first 12 patients). Duplicates for 6
out of these 18 patients were made in this data set. Six further patients were tested, and the
results were pooled with the previous 18. The statistics on the final pool are shown in table
3, and illustrated in figure 1.
A series of 48 normal tissue samples, representing 29 different tissues, were also
tested by the same procedure (analysed normal tissues are given in table 3). TAA transcript
levels are calculated as described above. The proportion of patients over-expressing the
candidate antigen, as well as the average transcript over-expression versus normal tissues is
also calculated from this data set. The results are illustrated in figure 1.
Normal tissues where CASB7439 transcript expression is equivalent none
to tumour transcript level in tumours
Real-time PCR reactions were also performed using the Taqman protocol ( as
described above) on tumour colon and adjacent normal colon from biopsies of 6 patients.
Three replicate measures were taken for each, and the average was used for further
calculations. Results are shown in figure 1. Moreover, 36 normal tissue samples,
representing 28 different tissues (see table 5), were also tested by the same procedure.
Results are shown in figure 2.
The results clearly suggest CASB7439 transcript is over-expressed in colorectal tumours
compared to adjacent normal colon and to all of the above mentioned normal tissues.
More than 90% of the patients strongly over-express CASB7439 transcript in tumour, as
compared to adjacent normal colon. Average over-expression fold in the tumors is at least
of 100. Moreover, more than 90% of the patients over-express the CASB7439 transcript
in colorectal tumors as compared to other normal tissues, more than 60 % of them over-
expressing it at least 10 fold.
Table 5 : listing of normal tissues used for CASB7439 transcript expression analysis.
Example 2
Differential Screening of cDNA arrays.
Identification of tumour-associated genes in the subtracted cDNA library is accomplished by
differential screening.
Total bacterial DNA is extracted from 100 µl over-night cultures. Bacteria are lysed with
guanidium isothiocyantate and the bacterial DNA is affinity purified using magnetic glass
(Boehringer). Plasmid inserts are recovered from the bacterial DNA by Advantage PCR
amplification (Clontech). The PCR products are dotted onto two nylon membranes to
produce high density cDNA arrays using the Biomek 96 HDRT tool (Beekman). The
spotted cDNA is covalently linked to the membrane by UV irradiation. The first membrane
is hybridised with a mixed cDNA probe prepared from the tumour of a single patient. The
second membrane is hybridised with an equivalent amount of mixed cDNA probe prepared
from normal colon of the same patient. The probe cDNA is prepared by PCR amplification
as described above and is labelled using the AlkPhos Direct System (Amersham).
Hybridisation conditions and stringency washes are as described in the AlkPhos Direct kit.
Hybridized probe is detected by chemiluminescence. Hybridisation intensities for each
cDNA fragment on both blots are measured by film densitometry or direct measurement
(BioRad Fluor-S Max). The ratio of the tumour to normal hybridisation intensities (T/N) is
calculated for each gene to evaluate the degree of over-expression in the tumour. Genes
which are significantly over-expressed in colon tumours are followed-up. Significance is
arbitrarily defined as one standard deviation of the T/N frequency distribution. Differential
screening experiments are repeated using RNA from multiple patient donors (>18) to
estimate the frequency of over-expressing tumours in the patient population.
In addition, the DNA arrays are hybridised with mixed cDNA probes from normal tissues
other than colon (see list above) to determine the level of expression of the candidate gene in
these tissues.
Example 3
DNA microarrays
DNA micro-arrays are used to examine mRNA expression profiles of large collections of
genes in multiple samples. This information is used to complement the data obtained by
real-time PCR and provides an independent measure of gene expression levels in tumors
and normal tissues.
Examples of current technologies for production of DNA micro-arrays include 1) The
Affymetrix "GeneChip" arrays in which oligonucleotides are synthetized on the surface
of the chip by solid phase chemical synthesis using a photolithographic process 2) DNA
spotting technology in which small volumes of a DNA solution are robotically deposited
and then immobilized onto the surface of a solid phase (e.g. glass). In both instances, the
chips are hybridized with cDNA or cRNA which has been extracted from the tissue of
interest (e.g. normal tissue, tumour etc...) and labeled with radioactivity or with a
fluorescent reporter molecule. The labeled material is hybridized to the chip and the
amount of probe bound to each sequence on the chip is determined using a specialized
scanner. The experiment can be set-up with a single fluorescent reporter (or radioactivity)
or, alternatively, can be performed using two fluorescent reporters. In this latter case,
each of the two samples is labeled with one of the reporter molecules. The two labeled
samples are then hybridized competitively to the sequences on the DNA chip. The ratio
of the two fluorescent signals is determined for each sequence on the chip. This ratio is
used to calculate the relative abundance of the transcript in the two samples. Detailed
protocols are available from a number of sources including "DNA Microarrays: A
practical approach. Schena M. Oxford University Press 1999" and the World Wide Web
(http://cmgm.stanford.edu/pbrown/protocols/index.html), http://arrayit.com/DNA-
Microarray-Protocols/) and specialized distributors (e.g. Affymetrix).
Example 5
Northern-Southern blot analysis
Limited amounts of mixed tumour and matched normal colon cDNA are amplified by
Advantage PCR (see above). Messenger RNA from multiple normal tissues is also
amplified using the same procedure. The amplified cDNA (1 ug) is electrophoresed on a
1.2% agarose gel and transferred onto a nylon membrane. The membrane is hybridised
(AlkPhos Direct System) with a probe prepared using a fragment of the candidate TAA
cDNA. Northem-Southem analysis provides information on transcript size, presence of
splice variants and transcript abundance in tumour and normal tissues.
Example 6
Northern blot analysis
Northern blots are produced according to standard protocols using 1 ug of poly A+
mRNA. Radioactive probes are prepared using the Ready-to-Go system (Pharmacia).
Example 7
Experimental identification of the full length cDNA sequence
Colon tumour cDNA libraries are constructed using the Lambda Zap II system
(Stratagene) from 5 ug of polyA+ mRNA. The supplied protocol is followed except that
Superscriptn (Life Technologies) is used for the reverse transcription step. Oligo dT-
primed and random-primed libraries are constructed. About 1.5 xlO6 independent phages
are plated for each screening of the library. Phage plaques are transferred onto nylon
filters and hybridised using a cDNA probe labelled with AlkPhos Direct/Positive phages
are detected by chemiluminescence. Positive phage are excised from the agar plat, eluted
in 500ul SM buffer and confirmed by gene-specific PCR. Eluted phages are converted to
single strand Ml 3 bacteriophage by in vivo excision. The bacteriophage is then converted
to double strand plasmid DNA by infection of E. coli. Infected bacteria are plated and
submitted to a second round of screening with the cDNA probe. Plasmid DNA is purified
from positive bacterial clones and sequenced on both strands.
When the full length gene cannot be obtained directly from the cDNA library, missing
sequence is isolated using RACE technology (Marathon Kit, ClonTech.). This approach
relies on reverse transcribing mRNA into double strand cDNA, ligating linkers onto the
ends of the cDNA and amplifying the desired extremity of the cDNA using a gene-
specific primer and one of the linker oligonucleotides. Marathon PCR products are cloned
into a plasmid (pCRII-TOPO, InVitrogen) and sequenced.
The polynucleotide of SEQ ID NO:1 was obtained using this procedure.
Example 8.
EST profiles
A complementary approach to experimental antigen tissue expression characterization is
to explore the human EST database. ESTs ('Expressed Sequence Tags ) are small
fragments of cDNA made from a collection of mRNA extracted from a particular tissue
or cell line. Such database currently provides a massive amount of human ESTs (2 106)
from several thousands of cDNA tissue libraries, including tumoral tissues from various
types and states of disease. By means of informatics tools (Blast), a comparison search of
the CASB7439 sequence is performed in order to have further insight into tissue
expression.
These ESTs match perfectly with CASB7439. The list contains 9 ESTs from 4 different
tumor colon libraries, one EST from one normal colon library, 3 ESTs from one tumor
germ cell library, one EST from one chronic lymphocyte leukemia cells library, 2 ESTs
from 2 mixed tumors libraries, 2 ESTs from libraries of unknown type.This clearly
suggests, as expected, that CASB7439 is over-expressed in tumor tissues, with an
emphasis in colorectal tumor tissues, as compared to normal tissues.
Example 9 :
9.1 Expression and purification of tumour-specific antigens
Expression in microbial hosts, or alternatively in vitro transcription/translation, is used to
produce the antigen of the invention for vaccine purposes and to produce protein
fragments or whole protein for rapid purification and generation of antibodies needed for
characterization of the naturally expressed protein by immunohistochemistry or for
follow-up of purification.
Recombinant proteins may be expressed in two microbial hosts, E. coli. and in yeast
(such as Saccharomyces cerevisiae or Pichia pastoris). This allows the selection of the
expression system with the best features for this particular antigen production. In
general, the recombinant antigen will be expressed in E. coli. and the reagent protein
expressed in yeast.
The expression strategy first involves the design of the primary structure of the
recombinant antigen. In general an expression fusion partner (EFP) is placed at the N
terminal extremity to improve levels of expression that could also include a region useful
for modulating the immunogenic properties of the antigen, an immune fusion partner
(IFP). In addition, an affinity fusion partner (AFP) useful for facilitating further
purification is included at the C-terminal end.
As mentioned above, several constructs might undergo comparative evaluation :
For rapid expression and purification as well as generation of antibodies against
CASB7439, it is proposed to generate in E. Coli. a fulllength CASB7439 protein with
NS1 as EFP and a histidine tail as AFP.
Therefore, two constructs are proposed :
Construct 1: Full length wild type CASB7439 cDNA in fusion with NS1 cDNA as EFP
and with a histidine tail coding cDNA as an AFP (SEQ ID NO: 8). The encoded fusion
protein sequence is SEQ ID NO: 10.
Construct 2: Full length mutated CASB7439 cDNA in fusion with NS1 cDNA as EFP
and with a histidine tail coding cDNA as an AFP (SEQ ID NO:9). It is proposed in this
construct to have the first 50 codons of native CASB7439 cDNA replaced by codons
specific of the E. Coli. codon usage, to enhance expression potential of CASB7439 in its
E coli, host. The encoded fusion protein sequence is SEQ ID NO: 10.
The CASB7439 protein design is as shown below:
"NS1" is the N-terminal fragment (80 mino acids) of the Influenza protein NS1. "HIS" is
a polyhistidine tail.
When the recombinant strains are available, the recombinant product is characterized by
the evaluation of the level of expression and the prediction of further solubility of the
protein by analysis of the behavior in the crude extract.
After growth on appropriate culture medium and induction of the recombinant protein
expression, total extracts are analyzed by SDS-PAGE. The recombinant proteins are
visualized in stained gels and identified by Western blot analysis using specific
antibodies.
Plasmid :
name: TCM 281 pRIT.. 15143
replicon: pMB 1
selection: Kan
promotor: PL long
insert: NSl-C74-39-His
Expression of the recombinant protein from construct 1:
Bacteria was grown in LB medium + 50 µg/ml Kan at 30°C
When the culture reached OD = 0.5 (620nm), the culture was heated
up to 39°C, after 5hours of induction, cells were harvested
Extract preparation:
Cell concentration: .50X.. in buffer PBS + complete...
Disruption: press french 3X
Centrifugation: 30 min at 14000t
Comment: > 90% in the supernatant of cellular extract
The cell extract was run on a 12.5% SDS PAGE, and subsequently stained with
Coomassie blue. A Western blot was also performed using an commercial monoclonal
antibody against the poly-histidine tail (Quiagen). The resulting gels (figures 3 and 4),
show that the protein is expressed, and visible in the cell extract supernatant.
The purification scheme follows a classical approach based on the presence of an His
affinity tail in the recombinant protein. In a typical experiment the disrupted cells are
filtered and the acellular extracts loaded onto an Ion Metal Affinity Chromatography
(IMAC; Ni++NTA from Qiagen) that will specifically retain the recombinant protein.
The retained proteins are eluted by 0-500 mM imidazole gradient (possibly in presence of
a detergent) in a phosphate buffer.
The supernatant from the harvested culture was denatured in 6M urea, 100mM NaH2PO4,
10mM Tris, PH 8, and loaded on a chromatographic column IMAC Qiagen NTA Ni++
under the following conditions:
The eluted protein in 500mM imidazole + 6M urea is dialysed under the following
conditions:
- PBS PH 7,2 + sarkosyl 0.5% + 4M urea
idem at 2M urea 2hrs
- idem at 0M urea 2hrs
The final material is freezed and stored. The protein content was quantified using a
Lowry protein assay (0,9 mg / 1.2 ml). The purity was assessed by a 12.5% PAGE SDS
stained with Coomassie blue (figure 5), and the presence of the recombinant protein was
checked by Western blot, using a anti-polyhistidine monoclonal antibody (figure 6)
A comparative evaluation of the different versions of the expressed antigen will allow the
selection of the most promising candidate that is to be used for further purification and
immunological evaluation.
9.2 Antibody production and immunohistochemistry
Small amounts of relatively purified protein can be used to generate immunological
tools in order to
a) detect the expression by immunohistochemistry in normal or cancer tissue sections;
b) detect the expression, and to follow the protein during the purification process
(ELISA/ Western Blot); or
c) characterise/ quantify the purified protein (ELISA).
9.2.1 Polyclonal antibodies:
Immunization
Rabbits are immunised , intramuscularly (I.M.), 3 times at 3 weeks intervals with
l00µg of protein, formulated in the adjuvant 3D-MPL/QS21. Three weeks after each
immunisation a blood sample is taken and the antibody titer estimated in the serum by
ELISA using the protein as coating antigen following a standard protocol.
ELISA
96 well microplates (maxisorb Nunc) are coated with 5µg of protein overnight at 4°C.
After 1hour saturation at 37°C with PBS NCS 1%, serial dilution of the rabbit sera is
added for 1H 30 at 37°C (starting at 1/10). After 3 washings in PBS Tween, anti rabbit
biotinylated anti serum (Amersham ) is added (1/5000). Plates are washed and
peroxydase coupled streptavidin (1/5000) is added for 30 min at 37°C. After washing,
50ul TMB (BioRad) is added for 7 min and the reaction then stopped with H2SO4 0.2M.
The OD can be measured at 450 ran and midpoint dilutions calculated by SoftmaxPro.
9.2.2 Monoclonal antibodies:
Immunization
5 BALB/c mice are immunized 3 times at 3 week intervals with 5 µg of purified protein.
Bleedings are performed 14 days post II and 1 week post 3. The sera are tested by Elisa
on purified protein used as coated antigen. Based on these results (midpoint dilution >
10000 ) one mouse is selected for fusion.
Fusion/ HATselection
Spleen cells are fused with the SP2/0 myeloma according to a standard protocol using
PEG 40% and DMSO 5%. Cells are then seeded in 96 well plates 2.5 xl04 - 105
cells/well and resistant clones will be selected in HAT medium. The supernatant of these
hybridomas will be tested for their content in specific antibodies and when positive,
will be submitted to 2 cycles of limited dilution . After 2 rounds of screening, 3
hybridomas will be chosen for ascitis production.
9.2.3 Immunohistochemistry
When antibodies are available, immuno staining is performed on normal or cancer tissue
sections, in order to determine :
0 the level of expression of the antigen of the invention in cancer relative to normal
tissue or
0 the proportion of cancer of a certain type expressing the antigen
0 if other cancer types also express the antigen
0 the proportion of cells expressing the antigen in a cancer tissue
Tissue sample preparation
After dissection, the tissue sample is mounted on a cork disk in OCT compound and
rapidly frozen in isopentane previously super cooled in liquid nitrogen (-160°C). The
block will then be conserved at -70°C until use. 7-10µm sections will be realised in a
cryostat chamber (-20, -30°C).
Staining
Tissue sections are dried for 5 min at room Temperature (RT), fixed in acetone for
l0min at RT, dried again, and saturated with PBS 0.5% BSA 5% serum. After 30 min at
RT either a direct or indirect staining is performed using antigen specific antibodies. A
direct staining leads to a better specificity but a less intense staining whilst an indirect
staining leads to a more intense but less specific staining.
9.3 Analysis of human cellular immune responses to the antigen of the invention
The immunological relevance of the antigen of the invention can be assessed by in vitro
priming of human T cells. All T cell lymphocyte lines and dendritic cells are derived
from PBMCs (peripheral blood mononuclear cells) of healthy donors (preferred HLA-A2
subtype). An HLA-A2.1/Kb trans genie mouse model is also used for screening of HLA-
A2.1 peptides.
Newly discovered antigen-specific CD8+ T cell lines are raised and maintained by
weekly in vitro stimulation. The lytic activity and the y-IFN production of the CD8+ lines
in response to the antigen or antigen derived-peptides is tested using standard procedures.
Two strategies to raise the CD8+ T cell lines are used: a peptide-based approach and a
whole gene-based approach. Both approaches require the full-length cDNA of the newly
discovered antigen in the correct reading frame to be either cloned in an appropriate
delivery system or to be used to predict the sequence of HLA binding peptides.
Peptide-based approach
Briefly, transgenic mice are immunized with adjuvanted HLA-A2 peptides, those unable
to induce a CD8+ response (as defined by an efficient lysis of peptide-pulsed autologous
spleen cells) will be further analyzed in the human system.
Human dendritic cells (cultured according to Romani et al.) will be pulsed with peptides
and used to stimulate CD8+ -sorted T cells (by Facs). After several weekly stimulations,
the CD8+ lines will be first tested on peptide-pulsed autologous BLCL (EBV-B
transformed cell lines). To verify the proper in vivo processing of the peptide, the CD8+
lines will be tested on cDNA-transfected tumour cells (HLA-A2 transfected LnCaP,
Skov3 or CAMA tumour cells).
Whole gene-based approach
CD8+ T cell lines will be primed and stimulated with either gene-gun transfected
dendritic cells, retrovirally transduced B7.1-transfected fibroblasts, recombinant pox
virus or adenovirus infected dendritic cells. Virus infected cells are very efficient to
present antigenic peptides since the antigen is expressed at high level but can only be
used once to avoid the over-growth of viral T cells lines.
After alternated stimulations, the CD8+ lines are tested on cDNA-transfected tumour
cells as indicated above. Peptide specificity and identity is determined to confirm the
immunological validation.
CD4+ T-cell response
Similarly, the CD4+ T-cell immune response can also be assessed. Generation of specific
CD4+ T-cells is made using dendritic cells loaded with recombinant purified protein or
peptides to stimulate the T-cells.
Predicted epitopes (nonamers and decamers) binding HLA alleles :
The HLA Class I binding peptide sequences are predicted either by the Parker's
algorithm (Parker, K. C, M. A. Bednarek, and J. E. Coligan. 1994. Scheme for ranking
potential HLA-A2 binding peptides based on independent binding of individual peptide
side-chains. J. Immunol. 152:163 and http://bimas.dcrt.nih.gov/molbio/hla_bind/) or the
Rammensee method (Rammensee, Friede, Stevanovic, MHC ligands and peptide motifs:
1st listing, Immunogenetics 41, 178-228, 1995 ; Rammensee, Bachmann, Stevanovic:
MHC ligands and peptide motifs. Landes Bioscience 1997, and
http://l34.2.96.221/scripts/hlaserver.dll/home.htm). Peptides are then screened in the
HLA-A2.1/Kb transgenic mice model (Vitiello et al.).
The HLA Class II binding peptide sequences are predicted using the Tepitope algorithm,
with a score cut-offset to 6 (Stumiolo, Hammer at al., Nature Biotechnology. 1999.
17;555-561).
The following tables gather the Class I and II predicted epitope sequences :
There is disclosed an immunogenic composition comprising a polypeptide which
has at least 70% identity to the amino acid sequence of SEQ ID NO:2 or SEQ ID NO:10
over the entire length of SEQ ID NO:2 or SEQ ID NO: 10;
a pharmaceutically acceptable carrier; and
a TH-1 inducing adjuvant for use in medicine.

Documents:

IN-PCT-2002-01026-KOL-FORM-27.pdf

IN-PCT-2002-1026-KOL-CORRESPONDENCE.pdf

IN-PCT-2002-1026-KOL-FORM 27.pdf

IN-PCT-2002-1026-KOL-FORM-27.pdf

in-pct-2002-1026-kol-granted-abstract.pdf

in-pct-2002-1026-kol-granted-assignment.pdf

in-pct-2002-1026-kol-granted-claims.pdf

in-pct-2002-1026-kol-granted-correspondence.pdf

in-pct-2002-1026-kol-granted-description (complete).pdf

in-pct-2002-1026-kol-granted-drawings.pdf

in-pct-2002-1026-kol-granted-examination report.pdf

in-pct-2002-1026-kol-granted-form 1.pdf

in-pct-2002-1026-kol-granted-form 18.pdf

in-pct-2002-1026-kol-granted-form 3.pdf

in-pct-2002-1026-kol-granted-form 5.pdf

in-pct-2002-1026-kol-granted-gpa.pdf

in-pct-2002-1026-kol-granted-reply to examination report.pdf

in-pct-2002-1026-kol-granted-sequence listing.pdf

in-pct-2002-1026-kol-granted-specification.pdf


Patent Number 225012
Indian Patent Application Number IN/PCT/2002/1026/KOL
PG Journal Number 44/2008
Publication Date 31-Oct-2008
Grant Date 29-Oct-2008
Date of Filing 08-Aug-2002
Name of Patentee SMITHKLINE BEECHAM BIOLOGICALS S.A.
Applicant Address RUE DE L'INSTITUT 89, B-1330 RIXENSART
Inventors:
# Inventor's Name Inventor's Address
1 CABEZON-SIL VA TERESA ELISA VIRGINIA SMITHKLINE BEECHAM BIOLOGICALS S.A., RUE DE L'INSTITUT 89, B-1330 RIXENSART
2 CASSART JEAN-POL SMITHKLINE BEECHAM BIOLOGICALS S.A., RUE DE L'INSTITUT 89, B-1330 RIXENSART
3 COCHE THIERRY SMITHKLINE BEECHAM BIOLOGICALS S.A., RUE DE L'INSTITUT 89, B-1330 RIXENSART
4 GAULIS SWANN ROMAN JEAN-THOMAS SMITHKLINE BEECHAM BIOLOGICALS S.A., RUE DE L'INSTITUT 89, B-1330 RIXENSART
5 VINALS DE BASSOLS CARLOTA SMITHKLINE BEECHAM BIOLOGICALS S.A., RUE DE L'INSTITUT 89, B-1330 RIXENSART
PCT International Classification Number C07K 14/47
PCT International Application Number PCT/EP/01/01779
PCT International Filing date 2001-02-16
PCT Conventions:
# PCT Application Number Date of Convention Priority Country
1 0021080.7 2000-08-25 U.K.
2 0004269.7 2000-02-23 U.K.
3 0009905.1 2000-04-20 U.K.