Title of Invention

A METHOD FOR GENERATING A COLLECTION OF CELLS SUITABLE AS A RECOMBINANT POLYCLONAL MANUFACTURING CELL LINE.

Abstract The present invention provides a method for preparing a polyclonal cell line where each cell produces a protein that binds one single target. The method utilises site specific integration of different expression vectors into one single batch of host cells so that the batch of cells expresses the different expression vectors to produce the polyclonal protein. The expression vectors each encodes a member of the polyclonal binding protein and one or more recombinases. Also provided is a method for producing a polyclonal protein, a polyclonal cell line, and a library of expression vectors.
Full Text A METHOD FOR GENERATING A COLLECTION OF CELLS SUITABLE AS A RECOMBINANT
POLYCLONAL MANUFACTURING CELL LINE
FIELD OF-THE INVENTION
The present invention forms the basis of a technology platform for producing recombinant
polyclonal proteins, such as proteins from the immunoglobulin superfamlly, e.g. soluble or
membrane-bound forms of B or T eel! receptors, to be used as a new class of therapeutic in
the treatment, amelioration or prevention of various infections, inflammatory diseases,
transplantation rejection, cancer, and allergies.
BACKGROUND OF THE INVENTION
A number of infectious diseases and cancers lacks efficient therapies. Monoclonal antibodies
have generally not been successful against these targets, partly due to variability of the complex
targets and adaptive mutations of target proteins causing Immune escape from monoclonal
antibody recognition. Polyclonal antibodies on the other hand are able to target a plurality
of dynamic targets, e.g., on viruses or cancer cells. Also, polyclonal antibodies have the
highest probability of retaining activity in the event of antlgenic-mutation.
Different commercially available polyclonal anybody therapeutics exist including: 1) normal
human immunoglobulin isolated from the blood of normal human donors; 2) human hyper-
immune immunoglobulln derived from the blood of individual human donors carrying antibodies
against a particular disease target, e.g., a virus, which they previously have encountered
either through infection or vaccination; and 3) animal hyperimmune immunoglobulin
derived from the blood of Immunized animals.
Immunoglobulin purified from human biood has proved effective against infections with
hepatitis B virus, respiratory syncytial virus, cytomegalovirus and other herpes viruses, rabies
virus, botulinum toxin, etc, as well as in the neonatal rhesus D prophylaxis. Immunoglobulin
purified from the blood of rabbits immunized with human T cells is used to afford T
cell immunosuppression in the treatment or prevention of transplant rejection (e.g., Thymo-
globulin). Normal human immunoglobulin has been utilized to boost the immune system of
immunodeficient patients, as well as in the therapy of various autoimmune disorders.
Nevertheless, widespread immunoglobulin use has been limited due to the constrained supply
of donor blood raw material, problems with batch-to-batch variations, and variable safety.
Animal-derived immunoglobulins in particular are faced with the same problems of immuno-
genicity as was observed for animal-derived monoclonal antibodies in the 1980s and 1990s.
Finally, as with other blood products, the risk of transmission of infectious agents such as
HIV, herpes or hepatitis viruses or prions remains. Accordingly, while clinicians acknowledge
that poiyclonal antibodies are a preferred therapeutic in some situations, their use has been
very limited.
New approaches to generate human immunoglobullns arose with the transgenic animal techniques.
Transgenic mice carrying human immunoglobulin loci have been created (U.S. Patent
No. 6,111,166). These mice produce fully human Immunoglobullns, and antibodies against a
specific target can be raised by usual immunization techniques. However, larger antibody
yields are limited because of the relatively small size of mice. Larger animals have also been
made transgenic for the human immunoglobulin genes, e.g., cows, sheep, rabbits, and chickens
(Kuroiwa, Y. etal. Nature Biotechnology, 2002; 20: 889-893). However, producing poly
clonal antibodies for therapy from the blood of such animals is not without complications.
First, the immunophyslology of the animal and humans may display considerable differences,
causing a difference in the resulting immune repertoire, functional rearrangement, and diversity
of the antibody response. Second, mitotic instability of the introduced immunoglobulin
loci might influence the long-term production of antibodies. Third, it is technically challenging
to delete the animal's own immunoglobulin loci so that e.g., the animal antibody pro-
duction will not exceed the production of human antibody. Fourth, the risk of transmission of
infectious agents such as viruses, prions or other pathogens accompanies the administration
of human antibodies produced in animals.
Accordingly, there is a need for manufacturing technologies for producing recombinant polyclonal
proteins, such as antibodies, in sufficiently large amounts and with minimal batch-to-
batch variations for safe clinical uses. Efficient methods for manufacturing homogenous recombinant
proteins using eukaryotlc (in particular mammalian) expression cell lines have
been developed for the production of a variety of proteins including monoclonal antibodies,
interleukins, interferons, tumor necrosis factor, coagulation factors VII, VIII and IX. Many of
these techniques are based on transfectlon and random integration of the gene of interest
into the genome of the expression cell line followed by selection, amplification, and characterization
of a high-producer expression clone and propagation of this clone as a master ex-
pression cell line.
The expression of an inserted foreign gene may be influenced by "position effects" from surrounding
genomic DNA. in many cases, the gene Is inserted into sites where the position
effects are strong enough to inhibit the synthesis of the product of the introduced gene. Furthermore,
the expression is often unstable due to silencing mechanisms (i.e. methylation)
imposed by the surrounding chromosomal host DNA.
Systems allowing integration and expression of a gene of interest in mammalian cells at a
specific genomic location have been developed for the expression of a homogenous recombi-
nant protein composition (U.S. Patent Nos. 4,959,317 and 5,654,182; WO 98/41645; WO
01/07572). WO 98/41645 describes the site-spectfic integration for production of a mammalian
cell line that secretes, for example, antibody. However, this expression is monoclonal
and there is no indication that transfectlons could be done with a library of vectors. Nor are
there any suggestions how to maintain the original diversity generated by specific VH-VL combinations
in a library.
DISCLOSURE OF CONTRIBUTION
The present invention provides solutions for generating a manufacturing cell line for expression
and production of a recombinant polyclonal protein, avoiding significant bias among the
individual members constituting the polyclonal protein.
Further, the present invention does not utilize animals in the polyclonal protein production,
thereby obviating the ethical and clinical difficulties associated with such approaches.
SUMMARY OF THE INVENTION
The present invention provides methods for producing a recombinant polyclonal manufacturing
cell line for the production of a recombinant polyclonal protein, often selected from the
immunoglobulln superfamily. Especially the production of polyclonal antibodies, polyclonal T
cell receptors or polyclonal fragments thereof are of interest. The present invention allows for
the commercial production of a recombinant polyclonal protein for use in pharmaceutical
compositions. One important feature of the invention is that during the manufacturing process
biased expression of the individual molecules constituting the polyclonal protein is kept
to a non-significant level, minimizing unwanted batch-to-batch variation.
One aspect of the present invention relates to a method for manufacturing a recombinant
polyclonal protein of interest, wherein said polyclonal protein comprises (or consists of) distinct
members that bind a particular antigen, said method comprising: a) providing a collection
of cells comprising a library of variant nucleic acid sequences, where each of said nucleic
acid sequences encodes a distinct member of said polyclonal protein and where each of said
nucleic acid sequences are integrated at the same, single site of the genome of each individual
cell in said collection of cells; b) culturing said collection of cells under conditions facilitating
expression of said polyclonal protein; and c) recovering said expressed polyclonal
protein from the cell culture, cell fraction or cell culture medium.
A further aspect of the present invention relates to a method for generating a collection of
cells suitable as ajrecombinant polyclonal manufacturing cell line, said method comprising: a)
providing a library of vectors comprising a population of variant nucleic acid sequences,
wherein each of said vectors comprises 1) one single copy of a distinct nucleic acid sequence
encoding a distinct member of a polyclonal protein comprising (or consisting of) distinct
members that bind a particular antigen and 2) one or more recomblnase recognition sequences;
b) introducing said library of vectors into a host cell line, wherein the genome of each
individual cell of said host cell line comprises recombinase recognition sequences, matching
those of the vector, at a single specific site in Its genome; c) ensuring the presence in said
cells of one or more recombinases so that the variant nucleic add sequences of step (a) are
integrated site-specifically in the cells of the host cell line, where said one or more recombinases
is/are either I) expressed by said cells into which said nucleic acid sequence is introduced;
ii) operatively encoded by the vectors of step a; ill) provided through expression from
a second vector; or Iv) provided to the cell as a protein; and d) selecting cells comprising an
integrated copy from said library of variant nucleic acid sequences.
in both methods of the invention, it will be understood that the polyclonal protein normally is
one that is not naturally associated with the cells wherein expression is effected.
The present invention describes several methods by which a library of variant nucleic add
sequences can be introduced into a host cell line in order to generate a collection of cells
suitable as polyclonal manufacturing cell line. These methods include bulk transfection of a
collection of cells with the library, semi-bulk transfection of aliquots of cells with fractions of
the library or individual transfection where host cells are transfected with individual members
of the library followed by pooling of the clones generated upon selection. Preferably the present
invention utilizes mammalian cells (cell lines or cell types) as host cell line.
in one aspect of the invention, the individual members of a polyclonal protein are encoded
from pairs of independent gene segments. Polyclonal proteins, where the individual members
are comprised of two polypeptide chains, include soluble or membrane-bound forms of antibodies
and T cell receptors. in further embodiments of the present invention a pair of gene
segments encode an antibody heavy chain and light chain variable region, or a T cell receptor
alpha chain and beta chain variable region or a T cell receptor gamma chain and delta chain
variable region.
The present invention further provides a recombinant polyclonal manufacturing cell line
comprising a collection of cells transfected with a library of variant nucleic acid sequences,
wherein each cell in the collection is transfected with and capable of expressing one member
of the library, which encodes a distinct member of a polyclonal protein that binds a particular
antigen and which is located at the same single site in the genome of individual cells in said
collection, wherein said nucleic acid sequence is not naturally associated with said cell in the
collection. The cell line preferably originates from a mammalian cell line such as Chinese
hamster ovary (CHO) cells, COS cells, BHK cells, myeloma cells (e.g., Sp2/0 cells, NSO),
YB2/0, NIH 3T3, fibroblast or Immortalized human cells such as Heia cells, HEK 293 cells, or
PER.C6. However, non-mammalian eukaryotic or prokaryotic cells, such as plant cells, insect
cells, yeast cells, bacteria, fungi etc., can also be used.
Also embraced by the present invention Is a library of vectors for stte-spedfic integration
comprising a population of naturally occurring variant nucleic acid sequences, wherein each
of said vectors comprises 1) one copy of a distinct nucleic acid sequence encoding a distinct
member of a poly dona I protein that binds a particular antigen and 2) one or more recombinase
recognition sequences.
in another aspect, the invention provides a pharmaceutical composition comprising, as an
active ingredient, a recombinant polyclonal antibody (or fragment thereof) or poiyclonal T cell
receptor (or fragment thereof), preferably obtained by the methods of the invention. The
recombinant polyclonal protein of the composition Is specific for or reactive against a predetermined
disease target. Such pharmaceutical compositions can be used for the treatment,
amelioration or prevention of diseases such as cancer, infections, inflammatory diseases,
allergy, asthma and other respiratory diseases, autoimmune diseases, immunological malfunctions,
cardiovascular diseases, diseases in the central nervous system, metabolic and
endocrine diseases, transplant rejection, or undesired pregnancy, in a mammal such as a
human, a domestic animal, or a pet.
Definitions
By "protein" or "polypeptide" is meant any chain of amino acids, regardless of length or post-
translational modification. Proteins can exist as monomers or multimers, comprising two or
more assembled polypeptide chains, fragments of proteins, polypeptides, oligopeptldes, or
peptides.
As used herein, the term "polyclonal protein" or "polyclonality" refers to a protein composition
comprising different, but homologous protein molecules, preferably selected from the
i immunoglobulin superfamily. Thus, each protein molecule is homologous to the other molecules
of the composition, but also contains one or more stretches of variable polypeptide
sequence, which is/are characterized by differences in the amino acid sequence between the
individual members of the polyclonal protein. Known examples of such polyclonal proteins
include antibody or immunoglobulin molecules, T cell receptors and B cell receptors. A poly-
donal protein may consist of a defined subset of protein molecules, which has been defined
by a common feature such as the shared binding activity towards a desired target, e.g., in
the case~bf a polyclonal antibody against the desired target antigen.
The term ""polyclonal protein of interest" covers a defined polyclonal protein subset, which
shares a common feature, such as binding activity towards a desired target, e.g., in the case
of polyclonal antibodies described by the binding activity or specificity against the target antigen,
said antigen being one or more of e.g., separate proteins, microorganisms, parasites,
cell types, allergens, or carbohydrate molecules, or any other structures, molecules, or substances,
which may be the target of specific antibody binding, or mixtures of said antigens.
The terms "one member of a recombinant polyclonal protein composition" or "one member of
a recombinant polyclonal protein" denote one protein molecule of a protein composition comprising
different, but homologous protein molecules, where each protein molecule Is homologous
to the other molecules of the composition, but also contains one or more stretches of
variable polypeptide sequence, which is/are characterized by differences in the amino acid
sequence between the individual members of the polyclonal protein.
The terms "variable polypeptide sequence" and 'variable region" are used interchangeably.
The terms "a distinct member of a recombinant polyclonal protein" denotes one protein molecule
of a protein composition comprising different, but homologous protein molecules, where
each protein molecule is homologous to the other molecules of the composition, but also
contains one or more stretches of variable polypeptide sequence, which is/are characterized
by differences in the amino acid sequence between the individual members of the polyclonal
protein.
The term "antibody" describes a functional component of serum and is often referred to either
as a collection of molecules (antibodies or immunoglobulin) or as one molecule (the an-
tibody molecule or immunoglobulin molecule). An antibody molecule is capable of binding to
or reacting with a specific antigenic determinant (the antigen or the antigenic epitope), which
in turn may lead to induction of immunological effector mechanisms. An individual antibody
molecule is usually regarded as monospecific, and a composition of antibody molecules may
be monoclonal (I.e., consisting of identical antibody molecules) or polyclonal (i.e., consisting
of different antibody molecules reacting with the same or different epitopes on the same antigen
or even on distinct, different antigens). Each antibody molecule has a unique structure
that enables it to bind specifically to its corresponding antigen, and all natural antibody molecules
have the same overall basic structure of two identical light chains and two Identical
heavy chains. Antibodies are also known collectively as immunoglobulins. The terms antibody
or antibodies as used herein are also intended to indude chimeric and single chain antibodles,
as well as binding fragments of antibodies, such as Fab, Fv fragments or scFv fragments,
as well as multimeric forms such as dimeric IgA molecules or pentavalent IgM.
The term "polyclonal antibody" describes a composition of different antibody molecules which
is capable of binding to or reacting with several different specific antigenlc determinants on
the same or on different antigens. Usually, the variability of a polyclonal antibody is thought
to be located in the so-called variable regions of the polyclonal antibody. However, in the
context of the present invention, polyclonallty can also be understood to describe differences
between the individual antibody molecules residing in so-called constant regions, e.g., as in
the case of mixtures of antibodies containing two or more antibody Isotypes such as the human
isotypes IgGl, IgG2, IgG3, IgG4, IgAl, and IgA2, or the murine isotypes IgGl, IgG2a,
IgG2b, IgG3, and IgA.
A "recombinant polyclonal antibody of interest" describes a defined recombinant polyclonal
antibody subset, which is characterized by the ability to bind to a desired target or desired
set of targets, said targets being e.g., a separate protein, a microorganism, a parasite, a cell,
an allergen, or a carbohydrate molecule, or another structure, molecule, or substance which
may be the target of specific antibody binding, or mixtures thereof.
The term "immunoglobulin" commonly is used as a collective designation of the mixture of
antibodies found in blood or serum, but may also be used to designate a mixture of antibodies
derived from other sources.
The term "immunoglobulin molecule" denotes an individual antibody molecule, e.g., as being
a part of immunoglobulin, or part of any polyclonal or monoclonal antibody composition.
When stating that a member of a polyclonal protein binds to an antigen, it is herein meant a
binding having binding constant that is below 1 mM, preferably below 100 nM, even more
i preferred below 10 nM.
The term "a library of variant nucleic acid molecules of interest" is used to describe the collection
of nucleic acid molecules, which collectively encode a "recombinant polyclonal protein
of interest". When used for transfection, the library of variant nucleic acid molecules of interest
is contained in a library of expression vectors. Such a library typically have at least 3, 5,
10, 20, 50, 1000,10", 105 or 106 distinct members.
As used herein the terms "one copy of a distinct nucleic acid sequence of interest" are not to
be taken literally as a single stretch of nucleic acids corresponding to a single gene segment,
but rather as one copy of all the gene segments required to produce all the subunlts of one
molecule of the protein of interest, and assembled into one nucleic add molecule such as e.g.
a vector. Some examples, where more than one gene segment usually is required to give rise
to a complete molecule of a protein of interest include B cell receptors, antibodies and fragments
of antibodies such as Fab's and variable domains, or T cell receptors. When introduced
into the cell, the gene segments, which together encode the fully assembled protein of interest,
reside in the same vector, thus being linked together in one nucleic add sequence, possibly
as separate transcriptlonal elements under control of different promoters.
The term "a gene of interest" as used herein, refer to a nucleic acid sequence composed of
one or more gene segments (genomic or cDNA) that encode one member of a protein of interest.
The plural form "genes of interest" refers to a library of nucleic acid sequences encoding
a polyclonal protein of interest. The term "601" is used as an abbreviation of (a)
gene(s) of interest.
As used herein, the term "vector" refers to a nucleic acid molecule into which a nucleic acid
sequence can be inserted for transport between different genetic environments and/or for
expression in a host cell. A vector capable of integrating into the genome of a host cell at a
pre-determined, specific locus in the genome is herein named "a vector for site-specific integration".
If the vector carries regulatory elements for transcription of the nucleic add sequence
inserted in the vector (at least a suitable promoter), the vector is herein called "an
expression vector". If the expression vector is capable of integrating at a pre-determined,
specific locus in the genome of the host cell, the expression vector may be called "an expression
vector for site-specific integration". If the nucleic acid sequence inserted into the above
identified vectors encodes a protein of interest as herein defined, the following terms are
used "vector of interest", "vector of interest for site-specific integration", "expression vector
of interest" and "expression vector of interest for site-specific integration". The term "an iso-
type-encoding vector" refers to a vector carrying nucleic acid sequences encoding an antibody
isotype. in the present specification, "phagemid vector" and "phage vector" are used
interchangeably. The terms "plasmid" and "vector" are used interchangeably. The invention is
intended to include such other forms of vectors, which serve equivalent functions for example
plasmids, phagemids and virus genomes or any nucleic acid molecules capable of directing
the production of a desired protein in a proper host.
The term "each member of the library of vectors of interest" is used to describe individual
vector molecules with a distinct nucleic acid sequence derived from a library of vectors of
interest, where the nucleic acid sequence encodes for one member of the recombinant poly-
clonal protein of interest.
The term "mass transfer" is used to describe the transfer of nucleic add sequences of interest
from one population of vectors to another population of vectors and doing so for each DNA
simultaneously without resorting to isolation of the individual DNA's of interest. Such populations
of vectors can be libraries containing for example variable regions, promoters, leaders
or enhancing elements of interest. These sequences can then be moved without prior isolation
from for example a phage vector to a mammalian expression vector. Especially for antibody
sequences this technique ensures that the linkage between VH and VL diversity is not
lost while moving libraries from, for example, a selection vector (e.g., a phage display vector)
to a mammalian expression vector. Hereby the original pairing of VH and VL is retained.
The term "transfectlon" is herein used as a broad term for introducing foreign DNA into a cell.
The term is also meant to cover other functional equivalent methods for introducing foreign
DNA into a cell, such as e.g., transformation, infection, transductlon or fusion of a donor cell
and an acceptor cell.
The term "selection" is used to describe a method where cells have acquired a certain characteristic
that enable the isolation from cells that have not acquired that characteristic. Such
characteristics can be resistance to a cytotoxic agent or production of an essential nutrient,
enzyme, or color.
The terms "selectable marker gene", "selection marker gene", "selection gene" and "marker
gene" are used to describe a gene encoding a selectable marker (e.g., a gene conferring resistance
against some cytotoxic drug such as certain antibiotics, a gene capable of producing
an essential nutrient which can be depleted from the growth medium, a gene encoding an
enzyme producing analyzable metabolites or a gene encoding a colored protein which for
example can be sorted by FACS ) which is co-introduced into the cells together with the
gene(s) of interest.
The term "recomblnant protein" is used to describe a protein that is expressed from a cell line
transfected with an expression vector comprising the coding sequence of the protein.
As used herein, the term "operably linked" refers to a segment being linked to another segment
when placed into a functional relationship with the other segment. For example, DNA
encoding a signal sequence is operably linked to DNA encoding a polypeptide if it is ex-
pressed as a leader that participates in the transfer of the polypeptide to the endoplasmic
reticulum. Also, a promoter or enhancer is operably linked to a coding sequence if it stimulates
the transcription of the sequence.
The term "a majority of the individual cells" refers to a percentage of the cells such as more
than 80%, preferably more than 85%, more preferably 90%, 95%, or even 99% or higher.
As used herein, the term "genome" is not to be taken literally as the normal complement of
chromosomes present in a cell, but also extra-chromosomal elements that can be introduced
into and maintained in a cell. Such extra-chromosomal elements can include, but are not
limited to, mini-chromosomes, YACs (yeast artificial chromosomes), MACs (mouse artificial
chromosomes), or HACs (human artificial chromosomes).
The term "promoter" refers to a region of DNA involved in binding the RNA polymerase to
initiate transcription.
The term "head-to-head promoters" refers to a promoter pair being placed in close proximity
so that transcription of two gene fragments driven by the promoters occurs in opposite directions.
A head-to-head promoter can also be constructed with a stuffer composed of irrelevant
nucleic acids between the two promoters. Such a stuffer fragment can easily contain more
than 500 nucleotides.
An "antibiotic resistance gene" Is a gene encoding a protein that can overcome the inhibitory
or toxic effect that an antibiotic has on a cell ensuring the survival and continued proliferation
of cells in the presence of the antibiotic.
The term "internal ribosome entry site" or "IRES" describes a structure different from the
normal 5' cap-structure on an mRNA. Both structures can be recognized by a ribosome to
initiate scanning for an AUG codon to initiate translation. By using one promoter sequence
and two initiating AUG's, a first and a second polypeptide sequence can be translated from a
single mRNA. Thus, to enable co-translation of a first and a second polynucleotide sequence
from a single bl-cistronic mRNA, the first and second polynucleotide sequence can be tran-
scriptionally fused via a linker sequence including an IRES sequence that enables translation
of the polynucleotide sequence downstream of the IRES sequence. in this case, a transcribed
bi-cistronic RNA molecule will be translated from both the capped 5' end and from the internal
IRES sequence of the bi-cistronlc RNA molecule to thereby produce both the first and the
second polypeptide.
The term "indudble expression" is used to describe expression that requires interaction of an
inducer molecule or the release of a co-repressor molecule and a regulatory protein for expression
to take place.
The term "constitutive expression" refers to expression which is not usually inducible.
The term "recombinase" refers to an enzyme that catalyses recombination between two or
more recombination sites. Recombinases useful in the present invention catalyze recombination
at specific recombination sites that are specific nucleic acid sequences recognized by a
particular recombtnase.
The term "scrambling" describes situations where two or more distinct members of a poly-
clonal protein comprised of two different polypeptlde chains, e.g. from the immunoglobulln
superfamily, is expressed from an individual cell. This situation may arise when the individual
cell has integrated, into the genome, more than one pair of gene segments, where each pair
of gene segments encode a distinct member of the polyclona I protein. in such situations unintended
combinations of the polypeptide chains expressed from the gene segments can be
made. These unintended combinations of polypeptide chains might not have any therapeutic
effect.
The term "VH-VL chain scrambling" Is an example of the scrambling defined above. in this
example the VH and VL encoding gene segments constitute a pair of gene segments. The
scrambling occurs when unintended combinations of VH and VL polypeptides are produced
from a cell where two different VH and VL encoding gene segment pairs are integrated into
the same cell. Such a scrambled antibody molecule is not likely to retain the original specificity,
and thus might not have any therapeutic effect.
The term "recombinant polycional manufacturing cell line" refers to a population of protein
expressing cells that are transfected with a library of variant nucleic acid sequences of interest
such that the individual cells, which together constitute the recombinant polycional
manufacturing cell line, carry only one copy of a distinct nucleic acid sequence of interest,
which encodes one member of the recombinant polycional protein of interest, and that each
copy is integrated into the same site of the genome of each cell. The cells constituting the
recombinant polycional manufacturing cell line are selected for their ability to retain the integrated
copy of the distinct nucleic acid sequence of interest, for example by antibiotic selection.
Cells which can constitute such a manufacturing cell line can be for example bacteria,
fungi, eukaryotic cells, such as yeast, insect cells or mammalian cells, especially immortal
mammalian cell lines such as CHO cells, COS ceils, BHK cells, myeloma cells (e.g., Sp2/0
cells, NSO), NIH 3T3, YB2/0 and immortalized human cells, such as HeLa cells, HEK 293 cells,
or PER.C6.
The term "hot spot" as in "hot spot cell line" refers to a pre-established locus of the genome
of the cell that has been selected or generated and characterized for highly efficient transcription
of an integrated nucleic acid sequence of interest upon integration of the expression
vector into that site.
The term "bias" is used to denote the phenomenon during recombinant polyclonal protein
production, wherein the composition of a polyclonal vector, polyclonal cell line, or polyclonal
protein alters over time due to random genetic mutations, differences in proliferation kinetics
between individual cells, differences in expression levels between different expression construct
sequences, or differences in the cloning efficiency of DNA.
The term "RFLP" refers to "restriction fragment length polymorphism", a method whereby the
migratory gel pattern of nucleic acid molecule fragments are analyzed after cleavage with
restriction enzymes.
The term "HDS" refers to a high density screening method where many discrete molecules
are tested in parallel on membranes so that large numbers of test compounds are screened
for a given activity simultaneously.
As used herein, "TaqMan PCR" refers to a PCR assay based on the TaqMan system described
by Holland, P. M. et al., Proc. Natl. Acad. Scl. U.S.A. 88: 7276-7280 (1991).
The term "5' UTR" refers to a 5' untranslated region of the mRNA.
The term "Pfu PCR" refers to a PCR reaction carried out using a Pfu DNA polymerase (isolated
from Pyrococcus furiosus), which is utilized because it has the highest fidelity among known
thermostable polymerases.
Abbreviations: "CMV" = (human) Cytomegalo Virus. "MSPSV" = Myeioproliferative Sarcoma
Virus. "AdMLP" = Adenovirus Major Late Promoter. SV40 poly A = Simian Virus 40 poly A
signal sequence. GFP = Green Flourescent Proteins. PVDF = polyvinylidene difluorid. TcR = T
cell receptor. ELISA = Enzyme-Linked Immunosorbent Assay. LTR= Long Terminal Repeat.
ACCOMPANYING
DESCRIPTION OF THE DRAWINGS
Fig. 1: Schematic representation of a "head-to-head promoter" expression vector comprising
the following elements: Amp pro= A promoter allowing expression of the ampicillin resistance
gene. Amp= An ampicillin resistance gene. pUC origin= A pUC origin of replication. Restriction
enzyme sites: NotI and EcoRI. Promoter A/Promoter B= head-to-head promoter cassette
including leader sequences (e.g., CMV/ MPSV). V Heavy= Sequence coding for the variable
heavy chain of a GOI. C Heavy Chain= Sequences coding for the constant heavy chain (e.g.,
the sequences for mouse IgGl or IgG2B constant heavy chain). R-B-globin pA= Rabbit B-
i globin poly A sequence. bGH polyA= Bovine Growth Hormone poly A sequence. V Kappa=
Sequence coding for the variable kappa of a GOI. C Kappa chain= Sequence coding for the
constant kappa chain. FRT slte= A FRT recombination site. Hygromycln= gene for hygromy-
cin resistance. SV40 poly A= poly A signal sequence.
Fig. 2: Schematic representation of an expression vector for uni-directional expression
comprising the following elements: Amp pro= A promoter allowing expression of the ampicll-
lin resistance gene. Amp= An ampidllin resistance gene. pUC orl=A pUC origin of replication.
Promoter A- mammalian promoter including leader sequences (e.g., AdMLP). V Heavy= Sequence
coding for the variable heavy chain of a GOI. C Heavy chain- Sequences coding for
the constant heavy chain (e.g., the sequences for mouse IgGl constant heavy chain). hGH
poly A= Human growth hormone poly A sequence. bGH polyA= Bovine Growth Hormone poly
A sequence. V Kappa = Sequence coding for the variable kappa light chain of a GOI. C
Kappa= Sequence coding for the constant kappa chain. FRT= A FRT recombination site. Hy-
gromycin= gene for hygromycin resistance. SV40 poly A= poly A signal sequence. The sequences
of hGH poly A and promoter A could be replaced by an IRES structure.
Fig. 3: Flow chart outlining the generation of a recomblnant polyclonal manufacturing cell line
and the production of a recombinant polyclonal protein. 1) Illustrates a bulk transfection strategy;
2) Illustrates a semi-bulk transfection strategy and 3) illustrates an individual transfection
strategy. A) Illustrates the library of vectors (horizontal lines), the arrowheads illustrate
the grouping of the vectors. in strategy 1 the vectors are grouped in bulk, in strategy 2 they
are grouped in smaller fractions (semi-bulk), whereas in strategy 3 they are kept separate
from each other (individual). B) Illustrates the transfection, where the number of tubes depend
on the grouping of the vectors constituting the library. C) Illustrates selection of cells
that site-specifically have integrated a GOI into the host cell genome, D) Illustrates the generation
of a polyclonal GOI library stock, where the selected cells constituting the integrated
library are stored in a freezer. It is optional to bank individual clones or pool the clones. E)
Illustrates the beginning of the manufacturing phase, where clones from the stock are
thawed (either individually, from smaller fractions or from a pool) and adapted to growth in
suspension. Adaptation to serum free media can be performed after the selection stage or at
this stage. F) Illustrates the stage in the production where the polyclonal cell line is propagated
for seeding of a larger bioreactor (intermediate seeding steps are an option although
not illustrated). in strategy 2 and 3, this is the stage where the polyclonal cell clone stock no
longer is kept as individual clones or semi-bulk fractions, but pooled into a collection of cells,
forming a recombinant polyclonal manufacturing cell line. G) Illustrates the final production
obtained from the bioreactor manufacturing. Following the production phase, the polyclonal
protein composition is harvested for purification and characterization of the product.
Fig. 4: Flow chart illustrating the generation of a mammalian expression vector.
(A). A schematic representation of a phagemld vector, pSymvc10, which carries a sequence
encoding a member of the GOI. P tac and P lacZ = bacterial head-to-head promoter cassette.
V kappa = sequence encoding a variable kappa light chain of a GOI. C Kappa chain = Sequence
coding for the mouse constant kappa light chain. V heavy = a sequence encoding a
variable heavy chain of a GOI. C heavy chain = Sequence coding for the constant heavy
chain CHI domain. Restriction enzyme sites: EcoKL, Notl, Sad and Xhol. cpIII = phage protein
III. Amp pro= A promoter allowing expression of the ampidllin resistance gene. Amp=
An amplcillin resistance gene. pUC Ori=A pUC origin of replication.
Step 1: By restriction digestion with Sad and Xhol, the bacterial promoter cassette can be
exdsed from pSymvclO and by llgatlon, replaced with a mammalian promoter cassette (B)
that has also been prepared by restriction digestion with Sad and Xhol.
(C) Schematic representation of a phagemid vector, pSymvd2, carrying sequences from the
GOI, after promoter exchange with a mammalian head-to-head promoter cassette. Promoter
A/Promoter B = head-to-head promoter cassette of choice (e.g., CMV/MPSV). V kappa = sequence
encoding for a variable kappa light chain of a GOI. C Kappa chain= Sequence coding
for the mouse constant kappa chain. V heavy = sequence encoding for a variable heavy chain
of a GOI. C heavy chain = Sequence coding for the constant heavy chain CHI domain. Restriction
enzyme sites: Notl, SacI, Xhol and EcoRI. cpIII = phage protein III. Amp pro= A
promoter allowing expression of the ampicillin resistance gene. Amp= An ampicillin resistance
gene. pUC Ori=A pUC origin of replication.
Step 2: By restriction digestion of pSymvcl2 with EcoRI and Notl, a nucleic acid fragment
containing the whole of the kappa, promoter cassette and V heavy can be excised from
pSymvcl2 and ligated into an isotype-encoding vector, for example pSymvc20, that has also
been prepared by restriction digestion with EcoRI and Notl, thereby generating the mammalian
expression vector pSymvc21 (E).
(E) Schematic representation of a mammalian expression vector, pSymvc21, with the variable
heavy and kappa regions from the GOI, for antibody expression. This mammalian expression
vector comprises the following elements: Amp pro= A promoter allowing expression
of the ampicillin resistance gene. Amp= An ampicillin resistance gene.. pUC Ori=A pUC origin
of replication. Restriction enzyme sites: Notl and EcoRI. Promoter A/Promoter B = head-to-
head promoter cassette of choice (e.g., CMV/MPSV). V kappa = V kappa sequence encoding
for a variable kappa light chain of a GOI. C Kappa chain= Sequence coding for a mammalian
constant kappa light chain (e.g., a mouse constant kappa chain). V heavy = V heavy sequence
coding for a variable heavy chain of a GOI. C heavy chain= Sequences coding for a
mammalian constant heavy chain (e.g., the sequences for mouse IgGl or IgG2B constant
heavy chain). R-B-globin pA= A Rabbit p-globin poly A sequence. bGH poly A= Bovine
Growth Hormone poly A sequence. FRT site = A FRT recombination site. Hygromydn= gene
for hygromycin resistance. SV40 poly A= SV40 poly A sequence sequence.
Naturally, the order of steps 1 and 2 can be reversed such that a fragment from pSymvclO
containing the whole of the kappa, bacterial promoter cassette and V heavy can be excised
from pSymvclO using EcoKL and NotI restriction digestion, which can then be ligated into an
Isotype-encodlng vector, for example pSymvc20. The promoter exchange can then be performed
on pSymvc20 by restriction digest using Sad and Xhol and llgatlon with a SacI +
Xhol digested mammalian promoter cassette fragment, for example such as Figure 4B.
Fig. 5: Histogram showing the genotype distribution in TGI cells transformed with Plasmid
Preparation 1. Em 223-228 refer to vectors with bacterial promoters encoding antl-b2-mlcro-
globulln (anti-B2M), anti-alkaline phosphate (anti-AP), antl-ovalbumln (antl-OVA), anti-Factor
VIII (antl-FVIII), anty-lysozyme (anti-LYS), anti-haptoglobin (anti-HAP), respectively. Em223-
228 are vectors of the pSymvc10-type. The number of individual genotypes resembled by the
fragment pattern determined by RFLP corresponds to the number of individual colonies
among the total number of picked colonies.
Fig. 6: Histogram showing the genotype distribution in TGI cells transformed with Plasmid
Preparation 2. Em 229-234 refer to vectors with mammalian promoters (CMV/MPSV) encoding
antl-b2-mlcroglobulin (antl-B2M), anti-alkaline phosphate (anti-AP), antl-ovalbumln
(anti-OVA), anti-Factor VIII (antl-FVIII), antHysozyme (antl-LYS), anti-haptoglobln (anti-
HAP), respectively. Em 229-234 are vectors of the pSymvcl2-type. The number of clones
represents the number of clones observed that resemble the sequence pattern determined by
RFLP of that Em-type (a complete sequence analysis has not been carried out).
Fig. 7: Histogram showing the genotype distribution in TGI cells transformed with Plasmid
Preparation 3. Em 235-240 refer to a mouse IgGl mammalian expression vector (including a
rabbit b-globin poly A signal) and encoding anti-b2-microglobulin (anti-B2M), anti-alkaline
phosphate (anti-AP), antl-ovalbumln (anti-OVA), anti-Factor VIII (anti-FVIll), antHysozyme
(anti-LYS), anti-haptoglobin (anti-HAP), respectively. Em235-240 are vectors of the
pSymvc21-type. The number of clones represents the number of clones observed that resemble
the sequence pattern determined by RFLP of that Em-type (a complete sequence
analysis has not been carried out).
Fig. 8: Histogram showing the genotype distribution in TGI cells transformed with double
digestion/ligation Plasmid Preparation (mass transfer into the mammalian expression vector
without DNA amplification in E. coli after Plasmid Preparation 1 step).
Fig. 9: Histograms showing the genotype distribution in CHO-Flp-in cells transfected with a
mixture of mammaNan expression vectors encoding the six genes of interest at A) day 16 and
B) day 34 post-transfection.
Fig. 10: Antigen-specific EUSA of supernatants derived from CHO-Flp-ln cells 34 days after
bulk transfection with a mixture of expression vectors encoding the six genes of interest.
Fig. 11: Anti-kappa coat EUSA of supernatants derived from pools of CHO-Rp-in cells 34
days after transfection either with a single expression vector encoding one gene of interest or
a mixture of expression vectors encoding the six genes of interest.
Fig. 12: Quantitative antigen-specific EUSA of supernatants derived from CHO Flp-in clone
019 at day 17, 31, 45, 59 and 73 after bulk transfection with a mixture of expression vectors
encoding the six genes of interest. A, B, and C represent three different transfection experi-
ments.
Fig. 13: Antigen-specific EUSA of supernatants derived from CHO Flp-in cell cultures at day
8, 17, 30, 45, 57, 72 and 85 after mixing CHO Flp-in cell lines expressing individual members
of the mini six library. Results shown as mean ± SD of three independent experiments.
DETAILED DESCRIPTION OF THE INVENTION
The recomblnant polyclonal protein expression system
The present invention provides methods for the consistent manufacturing of recombinant
polyclonal proteins that are preferably selected from the Immunoglobulln superfamily, a family
of proteins with immunoglobulin-iike domains. Most of the members are involved in cell
surface recognition events. Sequence homology suggests that antibodies, T cell receptors,
MHC molecules, some cell adhesion molecules and cytokines receptors share close homology.
Especially members of this family that contain variable regions are suitable for the generation
of recombinant polyclonal proteins according to the present invention. Such members include
antibodies, membrane bound antibodies (B cell receptors), Fab fragments, Fv fragments,
single chain Fv (scFv) fragments, T cell Receptors (TcRs), soluble TcRs, TcR variable domain
fragments, TcR variable domain fragments linked by a polypeptide linker or other antibody
or TcR derived fragments. in particular, it is contemplated that the present invention will
open up the possibility for large-scale manufacturing and production of a new class of therapeutics
comprising recombinant therapeutic polyclonal antibodies or TcRs.
One of the major advantages of the manufacturing method of the present invention is that all
the members constituting the recombinant polyclonal protein can be produced in between
one and approximately 10 bloreactors or equivalents thereof. Further, the recombinant polyclonal
protein composition can be purified from the reactor as a single preparation without
having to separate the individual members constituting the recombinant polyclonal protein
during the process. in contrast, if one wanted to mimic a recombinant polyclonal antibody
composition by mixing purified monoclonal antibodies (as for example proposed in WO
91/16074) it would require the separate manufacturing in a bloreactor, of each antibody to
be included in the composition and most likely the antibodies would be purified individually as
well. Such a production of a monoclonal mixture would be very costly, and time and space
consuming compared to the method of producing recombinant polyclonal antibody or other
polyclonal proteins as described herein. Thus, the method as described in WO 91/16074
would naturally result in a practical limit to the number of monoclonal antibodies that could
be included in such a mixture, most likely below 10, whereas the technology as described
herein generally can produce a polyclonal antibody with as many individual members as desired.
in order to obtain predictable expression of a recombinant polyclonal protein from a recombinant
polyclonal manufacturing cell line, the regulatory properties of the genomic integration
site should be reasonably well understood.
Conventional transfection and recombinant protein expression techniques using random integration
are undesirable for the production of a recombinant polyclonal protein, since the random
nature of the process will cause the number and positions of the integrated nucleic add
sequences to vary from cell to cell. Thus, if recombinant polyclonal protein is produced by
such traditional protocols, it is likely to result in a heterogeneous cell culture with variable
expression rates of individual members of the polyclonal protein, and genetic instability due
to positional effects of the integrated DNA. This will most likely result in a biased expression
of the members constituting the polyclonal protein.
introduction into a predefined genomic site is therefore desirable, this can in principle be
achieved by homologous recombination. However, owing to the dominance of illegitimate
recombination events, homologous recombination is very inefficient.
Moreover, where the polyclonal protein is an antibody or T cell receptor (TcR), another problem
arises with the use of conventional transfection protocols resulting in random integration.
Antibodies and TcRs are encoded from pairs of independent gene segments, the light
and heavy chain encoding sequences for antibodies and the alpha and beta chain or delta and
gamma encoding sequences for TcRs. The polypeptide products from these gene segments
become covalently linked during intracellular processing of the antibody molecule or TcR.
Conventional transfection technology resulting in random integration leads to the introduction
of several copies of different heavy and light chains or alpha and beta chains in the same cell,
which results in random combinations of heavy and light chains, so-called VH-VL chain scram-
bllng or alpha-beta chain scrambling. Consequently, this deteriorates the performance of the
expressed antibodies or TcRs causing loss of affinity and/or specificity, the possible occurrence
of new specificities and/or reduced specific activity.
To circumvent these problems the expression system of the present invention uses site-specific
integration into the genome of the individual host cells The system of the present invention
ensures that a library of vectors of interest comprising the variant nucleic acid sequences
of interest can be inserted into a pre-characterized chromosomal location by a re-
comblnase-mediated cassette exchange procedure, thereby generating a cell line, wherein
the individual cells expresses a single distinct member of the recombinant polyclonal protein
of interest. As described below, multiple integrations might occur in some of the cells constituting
the recombinant polyclonal manufacturing cell line. This, however, is not considered to
pose a problem as long as a majority of the individual cells express a single distinct member
of the recombinant polyclonal protein.
Recomblnases such as Cre, Flp, beta-recombinase, Gin, Pin, PlnB, PlnD, ft/RS, lambda inte-
grase, or phage C31 integrase can be used. Suitable recomblnases for integration into the
chromosomal location can be provided either (i) by expression from the cell's own genome
into which said nucleic acid sequence is introduced, (ii) by being operatively encoded by the
nucleic acid sequence inserted into the cell, (iii) through expression from a second nucleic
acid molecule, or (iv) as a protein. in a preferred embodiment, the variant nucleic acid sequence
contained in the vector of interest is integrated into a locus that mediates high-level
transcription and expression of the nucleic acid sequence of interest, a so-called "hot spot".
The host cell line used is preferably a mammalian cell line comprising those typically used for
biopharmaceutical protein expression, e.g., CHO cells, COS cells, BHK cells, myeloma cells
(e.g., Sp2/0 cells, NSO), YB2/0, NIH 3T3, and immortalized human cells, such as HeLa cells,
HEK 293 cells, or PER.C6. in the present invention CHO cells were used. However, a person
of ordinary skill in the art would easily be able to substitute CHO cells with other mammalian
cells as described, or even utilize other types of cells, including plant cells, yeast cells, insect
cells, fungi and bacteria. Thus the choice of cell type is not intended to be limiting to the invention.
in a preferred embodiment, mammalian cells containing a pre-characterized hot
spot, mediating high expression levels of the recombinant polyclonal protein of interest are
used for the manufacture.
in a further embodiment of the present invention, variant nucleic acid sequences of interest
are integrated in a site-specific manner utilizing the same chromosomal integration site in the
host cells. Such incorporation into a single specific site minimizes positional effects otherwise
seen with random integration or integration into multiple sites in a genome. Especially, when
expressing polyclonal proteins composed of more than one polypeptide chain it is further
relevant to have a single site, into which the site-specific integration occurs into the genome.
This is due to the fact that if a single cell expresses more than one integrant, scrambling
among subunits Is likely to occur.
in a site-specific integration system, the individual host cells are expressing the same overall
protein structure apart from the differences observed in the variable region of the recombl-
nant polyclonal protein of interest, e.g., the antigen-binding region of antibodies or TcRs.
Therefore, a majority of cells within such a pool of cells should display similar characteristics
with respect to productivity and genetic stability and hence this technology offers the possibility
of a controlled production of a recomblnant polyclonal protein, e.g,, a recomblnant polyclonal
antibody or TcRs.
The recombinant polyclonal protein of the present invention is intended to cover a protein
composition comprising different, but homologous protein molecules, which are naturally
variable, meaning that, in preferred embodiments, the library of variant nucleic acids comprises
a naturally occurring diversity. Thus, each protein molecule is homologous to the other
molecules of the composition, but also contains one or more stretches of variable polypeptide
sequence, which is/are characterized by differences in the amino add sequence between the
individual members of the polyclonal protein. The differences in the amino acid sequence(s)
that constitute the variable polypeptide sequence might be as little as one amino acid. Preferably
the differences in the amino acid sequence constitute more than one amino acid.
Usually, the natural variability of a polyclonal antibody or TcR is considered to be located in
the so-called variable regions or V-regions of the polypeptide chains.
in one aspect of the present invention individual members in a polyclonal protein comprise
variable regions that are approximately between 80 and 120 amino acids long. The variable
regions might contain hyper-variable domains, e.g. complementarity determining regions
(CDR).
in naturally occurring TcRs there are four CDRs in each variable region. in natural occuring
antibodies there are three CDRs in the heavy chain and three CDRs in the light chain.
in an additional aspect of the present invention the variable regions of the individual mem-
bers of a polyclonal protein contain at least one hyper-variable domain that is between 1 and
26 amino acids long, preferably between 4 and 16 amino acids long. This hyper-variable domain
can correspond to a CDR3 region. For antibodies each variable region preferably constitute
three hyper-variable domains. These can correspond to CDRl, CDR2 and CDR3. For
TcRs each variable region preferably constitutes four hyper-variable domains. These can
correspond to CDR1, CDR2, CDR3 and CDR4. The hyper-variable domains might alone constitute
the variable sequences within a variable region of a recombinant polyclonal protein of
the present invention.
in the context of the present invention, variability in the polypeptlde sequence (the polyclonality)
can also be understood to describe differences between the individual antibody molecules
residing in so-called constant regions or C regions of the antibody polypeptlde chains,
e.g., as in the case of mixtures of antibodies containing two or more different antibody isotopes,
such as the human isotypes IgGl, IgG2, lgG3, Ig.G4, IgAl, and IgA2, or the murine
isotypes IgGl, IgG2a, IgG2b, IgG3, and IgA. Thus, a recombinant polyclonal antibody may
comprise antibody molecules that are characterized by sequence differences between the
individual antibody molecules in the variable region (V region) or in the constant region (C
region) or both.
in order to provide variant nucleic acid sequences that encode proteins that bind a particular
antigen, a number of methods known in the art may be utilized. Typically, the invention will
benefit from the use of a screening procedure that enables identification and/or isolation of
nucleic acids that encode protein that bind a particular antigen. Several of these methods
include a so-called biopanning step, known from technologies such as phage display (Rang,
A.S. et al. 1991. Proc Natl Acad Sci U S A 88, 4363-4366), ribosome display (Schaffitzel, C.
et al. 1999. 3. Immunol. Methods 231, 119-135), DNA display (Cull, M.G. et al. 1992. Proc
Natl Acad Sci U S A 89, 1865-1869), RNA-peptide display (Roberts,R.W., Szostak,J.W., 1997.
Proc Natl Acad SdUSA 94, 12297-12302), covalent display (WO 98/37186), bacterial surface
display (Fuchs, P. et al. 1991. Biotechnology 9, 1369-1372), yeast surface display
(Boder, E.T., Wittrup, K.D., 1997. Nat Biotechnol 15, 553-557) and eukaryotic virus display
(Grabherr,R., Emst,W., 2001. Comb. Chem. High Throughput. Screen. 4, 185-192), methods
that are all known in the art and all are interesting aids in the practice of the present invention.
FACS and magnetic bead sorting are also applicable for enrichment (panning) purposes
using labeled antigen. Immunodetection assays such as ELISA (Dreher, M.L et al. 1991. J.
Immunol. Methods 139, 197-205) and ELJSPOT (Czerkinsky, CC. et.al.1983. J Immunol
Methods. 65, 109-21) can also be used either following a biopanning step or alone.
A composition of a recombinant polyclonal protein of interest comprises a defined subset of
proteins, which have been defined by a common feature such as the shared binding activity
towards a desired target, e.g., in the case of polyclonal antibodies against the desired target
antigen. Typically a polyclonal protein composition have at least 3, 4, 5, 10, 20, 50, 100,
1000,104, 105 or 106 distinct variant members. The number of distinct members needed in
the polyclonal protein composition will depend on the complexity of the target. in the case of
antibodies the complexity of the antigen(s) targeted will influence the number of distinct
variant members necessary in the polyclonal antibody composition. With small or not very
complex targets, for example a small protein, a polyclonal antibody composition that comprises
between 3 to 100 distinct variant members will be sufficient, and It is preferred that
the number of variants does not exceed 90, or even 80 or 70. in many instances, the number
of distinct variants will not exceed 60 or 50, and it is preferred that the number of variants
are in the range between 5 and 40, such as between 5 and 30. Whereas for more complex
targets, for example viruses with complex or interchangeable surface proteins, or encompassing
several virus subtypes, a polyclonal antibody composition that comprises between 20
to 500 distinct variant members will be sufficient. Very complex targets, where the antigen
comprises many different molecules, a polyclonal antibody composition comprising between
50 to 10,000 distinct variant members may be required.
in mammals, there are several known examples of naturally occurring polyclonal proteins
either circulating freely in the blood such as antibodies or immunoglobulln molecules or present
on cell surfaces such as T cell receptors and B cell receptors. The diversity of these
naturally occurring polyclonal proteins are, in some mammals, achieved by genetic recombination
of genes encoding variable regions of these proteins. Antibodies are further known to
increase their diversity by somatic mutation. The present invention can utilize these natural
diversities by isolating the sequences responsible for the diversity (e.g., the variable domains
or CDR regions of immunoglobulin molecules orTcRs) and generating a library from them.
For proteins encoded from two independent gene segments, e.g. antibody variable heavy
chain and variable light chain, TcRa chain and b chain or TcR5 chain and g chain, each vector
in the library will constitute a pair of these variable region encoding sequences. The generation
of libraries of pairs of variable region encoding sequences is well known in the art.
Libraries comprising naturally occurring diversities are for example, combinatorial libraries
(random pairing of the variable region encoding sequences) as well as cognate pair libraries
(pairs of variable region encoding sequences derived from the same cell). Further libraries
generated from isolated CDR gene fragments, which are incorporated into an appropriate
framework (e.g. Soderlind, E. et al., 2000. Nat. Biotechnol. 18, 852-856), such as an antibody
or TcR variable region are applicable with the present invention. The libraries are preferably
screened to obtain sub-libraries (libraries of interest) with a desired specificity.
Diversities of proteins can also be made in an artificial way, for example synthetic or by mutation.
Mutations can either be random or point mutations of a nucleic acid sequence encoding
a single protein, thereby generating a polyclonal population of the single protein. An-
other example of generating artificial antibody libraries are described in EP 0 859 841, a
method which is based on generating a library of variable region frameworks which can be
combined with another library of CDRs.
in a preferred embodiment of the invention, the recombinant polyclonal protein is a recombl-
nant polyclonal antibody or antibody fragment.
in another preferred embodiment of the invention, the recombinant polyclonal protein is a
recombinant polyclonal TcR or TcR fragment.
in addition to the diversity achieved by the genetic and somatic recombination in the so-
called variable regions, there are different isotypes of the immunoglobulins, which are defined
by the heavy chain. The main Isotypes are IgM, IgG, IgA, IgD, and IgE.
A recombinant polyclonal protein of the present invention can therefore also be constituted of
the different Isotypes or more preferred of different subclasses. polyclonality of the immunoglobulins
can occur in the constant part or in the variable domain of the immunoglobulin
molecule or in both the constant part and the variable domain.
polyclonality in the so-called constant region, particularly the heavy chain of the antibodies,
is of interest with regard to therapeutic application of antibodies. The various immunoglobulin
Isotypes have different biological functions (summarized in Table 1), which might be desirable
to combine when utilizing antibodies for treatment because different Isotypes of Immunoglobulin
may be implicated in different aspects of natural Immune responses (Canfield and
Morrison 1991. 3.Exp.Med. 173,1483-91; Kumpel etal. 2002. Transfus.Clin.Blol. 9, 45.-53;
Stirnadel et al. 2000. Epidemiol. infect. 124, 153-162).
Table 1: Biological functions of the human immunoglobulin isotypes
A further embodiment of the present invention is a recombinant polyclonal manufacturing cell
line, comprising a collection of cells transfected with a library of variant nucleic acid se-
quences, wherein each cell in the collection is transfected with and capable of expressing one
member of the library, which encodes a distinct member of a polyclonal protein that binds a
particular antigen and which Is located at the same single site in the genome of individual
cells in said collection, wherein said nucleic acid sequence Is not naturally associated with
said cell in the collection.
in an additional embodiment of the above embodiment the variant nucleic acid sequences
encoding the polyclonal protein (preferably from the Immunoglobulln superfamily) are all
derived from naturally occurring sequences, for example isolated from a donor.
Compositions of cells that contain variant nucleic acids located at a single specific site in the
genome within each cell has been described in WO 02/44361. This document discloses the
use of the cells to identify molecules having desirable properties, but the reference does not
deal with the provision of a production system or with the provision of polyclonal protein
characterized by a specific binding to an antigen
C\ona\ Diversity
One of the characteristics of a polyclonal protein is that it is constituted by a number of indi-
vidual protein molecules where each protein molecule is homologous to the other molecules
of the polyclonal protein but also has a variability that is characterized by differences in the
amino acid sequence between the individual members of the polyclonal protein. Preferably,
the differences are confined to distinct areas of the overall structure of the polyclonal protein.
Such areas are for example the variable region of an antibody or TcR and possibly further
confined to the CDR regions in these areas. This variability can also be described as a diver-
; sity, which can be Identified both on the nucleic acid level as well as on the protein functional
level, e.g., specificity and affinity differences towards a target.
Clonal diversity of the cell line may be analyzed by RFLP (or sequencing of (RT)-PCR pro-
ducts) on isolated clones from a pool of cells expressing a recombinant polyclonal protein.
The diversity can also be analyzed by functional tests (e.g., EUSA) on the recomblnant poly-
donal protein produced by the cell line.
Clonal bias (i.e., a gradual change in the content of the individual antibodies constituting the
polyclonal antibody), if it exists, can be estimated by comparing the clonal diversity of the
initial library, used for transfectlon, with the diversity found in the pool of cells (cell line) ex-
pressing the recombinant polyclonal protein.
Clonal diversity of a polyclonal protein expressed from a cell line can be assessed as the tar-
get coverage by the polyclonal protein. in this case sufficient diversity is considered to be
acquired when approximately 25-100% of the desired target molecules are bound by the
polyclonal protein. For example in the case of a polyclonal antibody, the binding of antibody
to at least 25% of the non-identical epitopes on the surface of a target antigen provides a
sufficient diversity in the composition. Preferably, clonal diversity by target coverage Is at
least 50%, and even more preferable at least 75%. For antibodies such a target coverage
could for example be assessed by epitope mapping.
Alternatively clonal diversity can be assessed as the distribution of individual members of the
polyclonal composition. This distribution can be assessed as the total number of different
individual members in the final polyclonal protein composition compared to the number of
different encoding sequences originally introduced into the cell line during transfection. in
this case sufficient diversity is considered to be acquired when at least 50% of the encoding
sequences originally used in the transfection can be identified as different individual members
of the final polyclonal proteins and preferably at least 75%.
The distribution of individual members of the polyclonal composition can also be assessed
with respect to the mutual distribution among the individual members. in this case sufficient
clonal diversity is considered to be acquired if no single member of the composition constitutes
more than 75 % of the total number of individual members in the final polyclonal protein
composition. Preferably, no individual member exceeds more that 50%, even more preferred
25 % and most preferred 10% of the total number of individual members in the final
polyclonal composition. The assessment of clonal diversity based on the distribution of the
individual members in the polyclonal composition can be performed by RFLP analysis, se-
quence analysis and protein analysis such as the approaches described later on for characterization
of a poiyclonal composition.
Clonal diversity may be reduced as a result of clonal bias which can arise a) during the cloning
process, b) as a result of variations in cellular proliferation, or c) through scrambling of
multiple integrants. If such biases arise, each of these sources of a loss of clonal diversity is
easily remedied by minor modifications to the methods as described herein.
in order to limit bias introduced by cloning of the variable domains into the appropriate vectors,
the transfer of the genes of interest from one vector to another may be designed in
such a way that cloning bias is limited. Mass transfer techniques and a careful selection of the
E. coll strain used for amplification can reduce the cloning bias. Another possibility is to perform
an individual transfer of each polynucleotide encoding an individual member of the poly-
clonal protein, between vectors of the invention.
It is possible that variations in cellular proliferation rates of the individual cells in the cell line
could, over a prolonged period of time, introduce a bias into the recombinant polyclonal protein
expression, increasing or reducing the presence of some members of the recombinant
polyclonal protein expressed by the cell line. One reason for such variations in proliferation
rates could be that the population of cells constituting the starting cell line used for the initial
transfection is heterogeneous. It is known that individual cells in a cell line develop differently
over a prolonged period of time. To ensure a more homogeneous starting material, sub-
cloning of the cell line prior to transfection with the library of interest may be performed u-
sing a limiting dilution of the cell line down to the single cell level and growing each single
cell to a new population of cells (so-called cellular sub-cloning by limiting dilution). One or
more of these populations of cells are then selected as starting material based on their proliferation
and expression properties.
Further, the selection pressure used to ensure that only cells that have received site-specific
integrants will survive, might affect proliferation rates of individual cells within a polyclonal
cell line. This might be due to the favoring of cells that undergo certain genetic changes in
order to adapt to the selection pressure. Thus, the choice of selection marker might also influence
proliferation rate-induced bias. If this occurs, different selection markers should be
tested. in cases where selection is based on a substance that is toxic to the cells, the optimal
concentration should be tested carefully, as well as whether selection is needed throughout
the entire production period or only in the initial phase.
An additional approach to ensure a well defined cell population is to use fluorescence acti-
vated cell sorting (FACS) after the transfection and selection procedures. Fluorescence labeled
antibodies can be used to enrich for highly productive cells derived from a pool of cells
transfected with IgG constructs (Brezinsky et al. J. 2003. Immunol Methods 277, 141-155).
This method can also be used to sort cells expressing similar levels of immunoglobulin,
thereby creating a homogenous cell population with respect to productivity. Likewise, by u-
sing labeling with the fluorescent dye 5,6-carboxylfluorescein dlacetate succinlmldyl ester
(CFSE) cells showing similar proliferation rates can be selected by FACS methods.
Even if a proliferation rate-induced bias does develop, the loss or over-representation of individual
members might not necessarily be critical, depending on the diversity requirements of
the final recomblnant polyclonal protein product and the stability of the diversity over time.
in site-specific single integrants, the cells will only differ in the sequence of the variable regions
of the antibodies to be expressed. Therefore, the different cellular effects imposed by
variation in integration site and gene regulatory elements are eliminated and have minimal
effects on the cellular proliferation rate. Neither scrambling nor multiple integrations is likely
to cause problems in the proliferation rate of the manufacturing cell line, since these are rare
events. Random integrations generally occur with an efficiency of approximately 10-5,
whereas site-specific integration occurs with an efficiency of approximately 10"3. If multiple
integrations should unexpectedly pose a problem, an alternative is to repeat the transfection
with the library of vectors of interest, because the likelihood that the event will reoccur is
very small, as described above. Additional alternatives are described in Example 3 below.
Another method of controlling unwanted clonal bias is to perform the transfection with the
entire library of vectors of interest in several sub-pools or to split the cell pool at an early
time point after transfection into sub-pools. At this point, the bias should not have become
significant and it should be statistically possible to acquire sub-pools that lack clones with an
unwanted proliferation advantage. The resulting exclusion of unwanted clones has to be in
agreement with the requirements of diversity in the final recombinant poiyclonal protein
product. Considering statistics, bulk transfection of a large number of cells also constitutes a
way to circumvent an undesired clonal bias. in this approach, a host cell line is transfected in
bulk with the library of variant nucleic acid sequences. Such a library constitutes many copies
of each distinct member of the library. These copies should preferably be integrated into a
large number of host cells. Preferably at least 100, 1000, 10000 or 100000 individual cells
are transfected with copies of distinct members of the library of variant nucleic acid sequen-
ces. Thus, if a library of distinct variant nucleic acid sequences is composed of 1000 distinct
members which are each integrated into 1000 individual cells, 106 clones containing a site-
specifically integrated GOI should arise from the transfection. in this manner the gausian
curve of individual cell doubling rates should influence the general population only in very
small degrees. This will increase the probability of keeping the clonal composition constant
over time even if a low percentage of the manufacturing cells should exhibit aberrant growth
and/or expression properties.
Alternatively, the library of vectors of interest can be split into fractions containing approximately
5 to 50 individual vectors of the library. Preferably, a fraction of the library constitutes
10 to 15 individual vectors. Each fraction is then transfected into an aliquot of cells. The individual
aliquots of cells can then be followed for a period of time to see if clonal bias develops
in any of them. If this happens such aliquots of cells can be omitted before the collection of
cells is reconstituted by pooling the remaining aliquots of cells. Optionally, the aliquots of
cells are kept separate throughout production, and the polyclonal antibody composition is
assembled by combining the products of each aliquot rather than the aliquots of cells before
production. The number of pools that can be handled are expected to be between five to ten
(see the previous description of monoclonal antibodies).
Alternatively, a high throughput method may be implemented in which cells are transfected
separately using vectors and cells based on single clones from the initial library of vectors of
interest. This may eliminate any possible sequence bias during transfection and integration.
Optionally, the single transfectants may be genotyped and a fully diverse pool of cells as-
sembled just prior to production or earlier if appropriate. Alternatively, the individual trans-
fection of a large number of cells, generating many clones with the same distinct member of
the library of variant nucleic add sequences may produce the same statistical advantages
described for bulk transfection, when the individually transfected cells are pooled prior to the
manufacture of the polyclonal protein.
The host cell
A suitable host cell comprises, in a region of its genome, one or more suitable recombination
sites, i.e., nucleic acid sequences recognizable by one or more recombinase enzymes. To be
able to select for integrants, (i.e., cells having an integrated copy of the nucleic add sequence
of interest in an integration site) the recombination site is operably linked to a first selection
gene (e.g., an antibiotic resistance gene) situated 3' to the recombination site. Furthermore,
a weak promoter (e.g., a truncated SV40 early promoter) and a transcription start
codon may be situated 5' to the recombination site that constitutes an integral part of the
resistance marker-coding region. Thus, the transcription start codon initiates the start of
transcription of the selection gene in the host cell before transfection with the library of ex-
pression vectors encoding the polyclonal protein.
Host cells for site-specific integration as described above can be generated from any cell
which can integrate DNA into their chromosomes or retain extra-chromosomal elements such
as mini-chromosomes, YACs (Yeast artificial chromosomes), MACs (Mouse artificial chromosomes),
or HACs (Human artificial chromosomes). MACs and HACs are described in detail in
WO 97/40183, hereby incorporated by reference. Preferably mammalian cells such as CHO
cells, COS cells, BHK cells, myeloma cells (e.g., Sp2/0 or NSO cells), fibroblasts such as NIH
3T3, and Immortalized human cells, such as HeLa cells, HEK 293 cells, or PER.C6, are used.
However, non-mammalian eukaryotic or prokaryotic cells, such as plant cells, insect cells,
yeast cells, fungi, E. coli etc., can also be employed.
in one embodiment of the present invention, the cell line which Is to be used as starting material
is sub-cloned by performing a so-called limiting dilution of the cell line down to a single
cell level, followed by growing each single cell to a new population of cells prior to transfec-
tion with the library of vectors of interest. Such sub-cloning can also be performed later in
the process of selecting the right cell line, If desired.
The host cells for site-specific integration may be obtained by transfection with a randomly
integrating plasmid comprising a weak promoter (e.g., a truncated SV40 early promoter), a
transcription start codon, a recombination site situated 3' to the start codon. Preferably, the
integrating plasmid also comprises a marker gene coupled to a first selection gene. One example
of such an integrating plasmid is the pFRT/LacZeo2 from invitrogen (Carlsbad, CA).
The marker gene can be used to evaluate the relative strength of expression at the genomic
location used for inserting a nucleic acid sequence of interest. A marker gene, (e.g., beta-
galactosidase (LacZ), green fluorescent protein (GFP) or a cell surface marker) can be linked
to the first selection gene in a gene fusion or transcriptionally linked by an IRES (internal
ribosomal entry site) such that co-expression of the first selection gene and marker gene
occurs. The use of a selection gene that establishes a survival pressure on the cells (e.g. drug
resistance or nutritional depletion) combined with a marker allowing for evaluation of the
relative expression levels from cell line to cell line is an efficient method to ensure high producing
cells which maintain the integrated plasmid within the genome. Cells with the recombination
sequence inserted at a spot with particularly active transcription will lead to high
expression of the marker gene e.g. GFP or LacZ. High expressers can be selected by fluorescence
activated cell sorting (FACS) and cloned. At this point it should also be analyzed
whether the integrant is a single integrant. This can be performed by real-time PCR and
Southern blotting.
Another method for evaluating relative expression levels from cells transfected with an integrating
plasmid is to perform an additional integration-excision step on the cells generated as
described above. This pool of selected cells are transfected again, with a plasmid encoding a
recombinase corresponding to the recombination site of the integrating plasmid and a second
plasmid containing a second selection marker without a start codon, the coding region of
which is preceded by a recombination sequence likewise corresponding to the first integrating
plasmid. This second plasmid also contains the coding sequence for a fluorescent marker
protein (e.g., GFP (or equivalent fluorescent proteins) driven by a mammalian promoter. The
recombinase mediates integration of this plasmid into the host cell genome where a similar
recombination sequence previously has been inserted by the integrating plasmid. Cells with
the recombination sequence insetted at a spot with particularly active transcription will lead
to high expression of the fluorescent protein. High expressers are selected by fluorescence
activated cell sorting (FACS) and cloned. Clones with consistently high expression and containing
one copy of the inserted plasmid are transfected with the recombinase and selected
by the first selection marker, identifying cells where the second plasmid sequence has been
removed by the recombinase, making the first selection marker work again. These cells still
contain the first recombination sequence inserted at a transcriptional hot-spot and can now
be used for the expression of genes of interest.
Cell lines, which achieve high expression of the marker gene upon integration of a single copy
of the plasmid, are used for transfection with the gene of interest. The recombination site in
the host cell Is preferably located in a gene or region of particularly active expression, I.e., in
a so-called hot spot.
The vector for site-specific integration
A suitable vector comprises a suitable recombination site linked to a suitable selection gene
different from the selection gene used for construction of the host cell. Suitable selection
genes for use in mammalian cell expression include, but are not limited to, genes enabling
for nutritional selection, such as the thymidine kinase gene (TK), glutamine synthetase gene
(GS), tryptophan synthase gene (trpB) or histidinol dehydrogenese gene (hisD). Further,
selection markers are antimetabolite resistance genes conferring drug resistance, such as the
dihydrofolate reductase gene (dhfr) which can be selected for with hypoxanthine and
thymidine deficient medium and further selected for with methotrexate, the xanthine-guanine
phosphoribosyltransferase gene(gpt), which can be selected for with mycophenolic acid, the
neomycln phosphotransferase gene (neo) which can be selected for with G418 in eukaryotic
cell and neomycin or kanamycln in prokaryotic celts, the hygromydn B phosphotransferase
(hyg, hph, hpt) gene which can be selected for with hygromycin, the puromycin N-acetyl-
transferase gene (pac) which can be selected with puromycin or the Blasticidin S deaminase
gene(Bsd) which can be selected with blasticidin. Finally, genes encoding proteins that enables
sorting e.g. by flow cytometry can also be used as selection markers, such as green
fluorescent protein (GFP), the nerve growth factor receptor (NGFR) or other membrane proteins,
or beta-galactosidase (LacZ).
in one aspect of the present invention, the selectable gene Is neither preceded by a promoter
nor equipped with a translation initiating codon. The promoter and ATG codon is provided at
the selected site-specific recombination site. If this vector is integrated at a location other
than the selected recombination site in the genome of the host cell, no expression of this
second selection gene can occur due to lack of promoter and initiation codon. If integration
occurs at the selected recombination site in the genome of the host cell, the second selection
gene is expressed and expression of the first selection gene is lost.
integration may e.g., be carried out using a so-called FRT site
(5'-gaagttcctattccgaagttcctattctctagaaagtataggaacttc-3' (SEQ ID NO 1) and variants
thereof) in the genome and on the vector for site-specific integration together with the Flp
recomblnase or mutants thereof from Saccharomyces cerevisiae. However, other recomblna-
se systems may equally well be used, including those of Cre recombinase and a variety of lox
sites such as loxP from bacterlophage PI or variants or mutants thereof, e.g., Iox66, Iox71,
10x76, Iox75, Iox43, Iox44 and Iox511 (C. Gorman and C. Bullock, Curr. Opinion in Biotechnology
2000,11: 455-460) or by using phage integrase carries out recombination between the attP site and the attB site (A.C. Groth et al. PNAS
2000, 97: 5995-6000). Further recombinase systems that could be utilized in the present
invention are, but are not limited to, the p-recombinase-slx system from bacterial plasmid
pSM 19035, the Gln-gix system from bacteriophage Mu or the R-RS system from Zygosac-
charomyces rouxii.
A further variant to the site-specific recombination system is to use non-homologous recombination
sites. in such a system, two non-identical recombination sites are introduced into
the host genome for the generation of specific target sites. Recombination sites corresponding
to those flanking the target site also flank the construct containing the gene of interest.
Such a system has been described in WO 99/25854, which is hereby incorporated by reference
in its entirety. The use of non-homologous recombination sites was shown to suppress
excision of the GOI from the chromosome. The non-identical recombination sites can be
composed of any of the recombination sites described above as long as the corresponding
recombinases are provided. For example, non-identical recombination sites could consist of a
FRT site and a mutant FRT site utilizing a Flp recombinase for integration or a FRT site and a
loxP site utilizing Flp and Cre recombinases for the integration.
Further, a system using two different FRT sites has been described in Verhoeyen et al., Hum.
Gene Ther. 2001 12, 933-44. in this approach the integrating plasmid is transferred to the
host cells by retro viral infection. The plasmid consists of a combination of a reporter gene
and a first selection marker gene as well as the retroviral elements required for infection. The
retrovlral 3'LTR contains two different FRT sites. A non functional second selection marker
gene, which lacks a promoter and the translation initiating codon is located 3' to theses sites.
During the process of retroviral infection the 3'LTR sequence is copied to the 5'LTR. This results
in the flanking of the reporter gene and the first selection marker gene by two different
FRT sites on each side. The sequence between the outer FRT sites can be exchanged against
a GOI under the control of a strong promoter. The cassette containing the GOI Is flanked by
the same set of FRT sites. The reaction is catalyzed by the Flp recombinase. in the transfected
exchange plasmid an IRES element and a translation initiating codon are located further
downstream of the GOI. After replacement of the integrated cassette the non functional
selection marker gene located in the 3' LTR sequence outside the FRT sites is activated by the
translation initiating codon provided by the GOI constituting cassette. The exchange status
can further be enriched if a negative selection marker (e.g. thymidine kinase) Is present in
the integrating vector.
The integrating vector can also be transferred to the host cells by standard transfection. in
this case the integrating cassette is flanked by an FRT at the 5' end and a different FRT'site at
the 3' end. The ATG-deficient second resistance marker gene is positioned further downstream
of the 3' FRT' site. The exchange for a GOI proceeds as described for the retroviral
system.
Another system that prevents excision of the GOI after its site-specific integration into the
chromosome is the FC31 integrase, also mentioned above. This system has been described
thoroughly in patent applications WO 01/07572 and WO 02/08409, hereby incorporated by
reference in their entirety.
in a further aspect of the invention, the vector for site-specific integration of the gene of in-
terest further comprises DNA encoding one member of the recomblnant polyclonal protein of
interest, optionally preceded by its own mammalian promoter directing expression of the
protein. If a member of the recombinant polyclonal protein of interest comprises more than
one protein chain, e.g., if the member is an antibody or T cell receptor, the DNA encoding the
chains of the protein can be preceded by their own mammalian promoter directing high levels
5 of expression (bi-directional or uni-directional, see figure 1 and 2, respectively) of each of the
chains. in a bi-directional expression a head-to-head promoter configuration in the expression
vector can be used and for a uni-directional expression two promoters or one promoter
combined with e.g., an IRES sequence can be used for expression. Suitable head-to-head
promoter configurations are for example, but not limited to, the AdMLP promoter together
with the mouse metailothionein-1 promoter in both orientations, the AdMLP promoter together
with the elongation factor-1 promoter in both orientations or the CMV promoter together
with the MPSV promoter in both orientations.
A nucleic acid sequence encoding a functional leader sequence can be included in the expression
vector to direct the gene product to the endoplasmic reticulum or a specific location
within the cell such as an organelle. A strong polyadenylation signal can be situated 3' of the
protein-encoding DNA sequence. The polyadenylation signal ensures termination and
polyadenylatlon of the nascent RNA transcript and is correlated with message stability. The
DNA encoding a member of the recomblnant polyclonal protein of interest can, for example,
encode both the heavy and light chains of an antibody or antibody fragments, each gene sequence
optionally being preceded by their own mammalian promoter elements and/or followed
by strong poly A signals directing high level expression of each of the two chains.
The expression vector for site-specific integration can carry additional transcriptional regulatory
elements, such as enhancers or UCOE (ubiquitous chromatln opening elements) for increased
expression at the site of integration. Enhancers are nucleic acid sequences that interact
specifically with cellular proteins involved in transcription. The UCOE opens chromatin
or maintains chromatin in an open state and facilitates reproducible expression of an operably-linked
gene (described in more detail in WO 00/05393, hereby incorporated by reference
in its entirety). When one or more of the regulatory elements described in the above are integrated
into the chromosome of a host cell they are termed heterologous regulatory elements.
Establishing an expression system for high-level expression of proteins
Methods for introducing a nucleic acid sequence into a cell are known in the art. These methods
typically include the use of a DNA vector to introduce the sequence of interest into the
cell, the genome or an extra-chromosomal element. Transfection of cells may be accomplished
by a number of methods known to those skilled in the art, including calcium phosphate
precipitation, electroporation, microinjection, liposome fusion, RBC ghost fusion, protoplast
fusion, and the like.
For the transfection of a host cell line, a library of vectors of interest, wherein each vector
comprises only one copy of a nucleic acid sequence encoding one member of a recombinant
polyclonal protein of interest, is used. This library of expression vectors of interest collectively
encodes the. recombinant polyclonal protein of interest. Suitable vectors for site-specific integration
was described in the previous section. The individual vectors constituting the library
of variant nucleic acid sequences of interest can either be mixed together into a single composition,
or the individual vectors encoding each library member can be kept in separate
compositions or in mixtures of approximately 5 to 50 individual vectors of the library in a
composition.
The generation of a recombinant polyclonal manufacturing cell line and the production of a
recombinant polyclonal protein from such a cell line can be obtained by several different
transfection and manufacturing strategies. These strategies are outlined in figure 3.
One way, is to use a library of vectors mixed together into a single composition for the
transfectlon of a host cell line. This method is termed bulk transfectlon or transfection in
bulk. Generally the vector and host cell design previously described will ensure that a poly-
clonal cell line will be obtained upon appropriate selection. in such a cell line a majority of the
individual cells have integrated one copy of a nucleic acid molecule, encoding a distinct
member of a recombinant polyclonal protein, from a library of nucleic acid sequences of interest
into the genome. The single copy of the nucleic add sequence is integrated into a single
specific site of the genome of each cell in the collection of cells, thereby generating a
polycional cell line comprised of individual cells expressing individual members of the polyclonal
protein of interest. A frozen stock of the polyclonal cell line will be generated before
initiation of the recombinant polyclonal protein manufacturing.
Another way is to use a library of vectors split into fractions, containing approximately 5 to
50 individual vectors of the library in a composition, for transfectlon. Preferably, a fraction of
the library constitutes 10 to 20 individual vectors. Each composition is then transfected into
an aliquot of host cells. This method is termed semi-bulk transfection. The number of aliquots
transfected will depend on the size of the library and the number of individual vectors in each
fraction. If the library for example constitutes 100 distinct variant members, which are split
into fractions containing 20 distinct variant members in a composition, 5 aliquots of host cells
would need to be transfected with a library composition constituting a distict fraction of the
original library. The aliquots of host cells are selected for site-specific: integration. Preferably,
the distinct aliquots are selected separately. However, they can also be pooled before selection.
The aliquots can be analyzed for their clonal diversity and only those with sufficient diversity
will be used to generate a polyclonal GOI library stock. To obtain the desired polyclonal
cell line for manufacturing, the aliquots can be mixed before generating the freezing
stock, immediately after they have been retrieved from the stock or after a short proliferation
and adaptation time. Optionally, the aliquots of cells are kept separate throughout production,
and the polyclonal protein composition is assembled by combining the products of each
aliquot rather than the aliquots of cells before production.
A third way, is a high throughput method in which host cells are transfected separately using
the individual vectors constituting the library of interest. This method is termed individual
transfection. The individually transfected host cells are preferably selected for site-specific
integration separately. However, they can also be pooled before selection. The individual cell
clones generated upon selection may be analyzed with respect to proliferation time and integration
pattern and preferably, those with similar growth rates and a single site-specific inte-
gration are used to generate a polyclonal GOI library stock. The individual cell clones can be
mixed to obtain the desired polyclonal cell line before generating the stock, immediately after
they have been retrieved from the stock, or after a short proliferation and adaptation time.
This approach may eliminate any possible residual sequence bias during transfection, integration
and selection. Alternatively the individually transfected host cells are mixed before
selection is performed, this will enable control of sequence bias due to transfection.
A shared feature in the manufacturing strategies outlined in the above is that all the individual
members constituting the recomblnant polyclonal protein can be produced in one, or a
limited number of bioreactors, with approximately 10 as the maximum. The only difference Is
the stage at which one chooses to generate the collection of cells that constitutes the recomblnant
polyclonal manufacturing cell line.
The host cell line to be used for expression and production of a recomblnant polyclonal protein
of interest has one or more nucleic acid molecule(s) recognizable by a recombinase en-
zyme(s) (e.g., cells prepared beforehand having an FRT site at a pre-determined location in
the genome as described in e.g., US 5,677,177).
The vector for site-specific integration is preferably integrated in a predefined genomic locus
that mediates high-level expression, a so-called hot spot.
If expression levels need to be increased, gene amplification can be performed using selection
for a DHFR gene or a glutamine synthetase (GS) gene. This requires the use of vectors
comprising such a selection marker.
For the manufacturing of a polyclonal protein, where each protein member is comprised of
more than two polypeptide chains, the combination of the chains might be of importance for
the affinity, specificity and activity of the protein they form. This is for example seen for antibodies
and TcRs. For example, is the combination of antibody variable heavy chain and variable
light chain known to affect affinity and specificity of an antibody formed from the chains.
Thus, when a library of antibody encoding sequences has been selected for their ability to
produce antibodies with affinity to a certain target it is desirable to ensure that the combination
of the variable heavy chain and variable light chain in the final product correspond to
this. For this reason the polypeptide chains constituting an individual member of the polyclonal
protein are placed in the same vector used for integration, thereby ensuring that they
will be kept together throughout the process.
The following description is one example of how to obtain a recombinant polyclonal antibody
expressing cell line, where scrambling of the chains is minimal if existing at all.
A universal promoter cassette for constitutive expression having two promoters placed in
opposite transcriptional direction, such as a head-to-head construction surrounded by the
variable heavy chain and the whole of the kappa light chain was constructed, allowing transfer
of the whole construct into a vector for site-specific integration said vector comprising a
FRTsite and a hygromydn resistance gene and the heavy chain consta.it region. It is contemplated
that a promoter cassette for indudble expression can also be used. Furthermore,
the promoters can be placed tail-to-tail which will result in transcription in opposite direction
or tall-to-head for unidirectional transcription. CHO-Flp-in cells (invitrogen, Carlsbad, CA)
which stably express the lacZ-Zeocin fusion gene, were used for the experiment, rendering
the cells resistant to the antibiotic Zeocin. The cells were maintained in a medium containing
Zeocln. The cells were transfected in bulk with the library of vectors for site-specific integration
encoding the polyclonal antibody and a different selection marker (hygromydn phospho-
transferase) together with a plasmld expressing the Flp recomblnase. An indudble promoter
can also be used for control of the expression. After transfectlon, the cells were cultivated in
the presence of hygromycin. Cells that were resistant to hygromydn were subsequently
grown in different culture systems, such as conventional small culture flasks, Nunc multilayer
cell factories, small high yield bloreactors (MlniPerm, INTEGRA-CELLine) and spinner flasks to
hollow fiber-and bloreactors. The cells were tested for antibody production using ELJSA. Polyclonal
cell lines were selected for viability in suspension growth in serum free medium with-
out selection pressure for extended periods. Stocks of cell lines were grown in the presence
of hygromycin.
Evaluation of the preservation of polyclonalfty in the expression system
According to the present invention, it is often important to ensure that the polyclonality in the
expression system Is not seriously altered during production so that it is possible to stop the
production when polyclonality is indeed altered. This is according to the invention done by
monitoring the relative expression levels of the variant nucleic acid sequences. The expression
levels can for example be monitored at mRNA level using for example RFLP analysis,
arrays or real-time PCR, or at the protein level using for example two-dimensional polyacryl-
amide gel electrophoresis, mass spectrometry or various chromatographlc techniques. With
these techniques it will be possible to establish a baseline value for a number of all of the
individual expression levels and then take out samples from the culture during production in
order to gauge whether expression levels have changed (both in total and relatively). in
normal practice of the invention, a range of values surrounding the baseline values can be
established, and if the relative expression levels are found to be outside the ranges, then
production is terminated.
To be able to evaluate the stability and reprodudbllity of the expression system, vectors encoding
six distinct Fab fragments (the mini six library) with reactivity against chicken oval-
bumin (OVA), bovine alkaline phosphatase (AP), human b2-microglobulln ((b2m), human hap-
toglobln (HAP), human Factor VIII (FVIII) and hen egg white lysozyme (LYS) were prepared.
The different Fab fragment encoding sequences are not identical and therefore exhibit different
RFLP patterns, whereby RFLP can be used for analyzing the genotype composition.
The mini six library was introduced into CHO-Flp-in cells by transfectlon using an expression
vector with a head-to-head promoter cassette. The CHO-Flp-in cells were either transfected
in bulk with a mixture of expression vectors of interest encoding the six distinct antibodies
resulting in a polyclonal cell line expressing the six antibodies in known combination or the
cells were transfected individually with one member of the expression library of interest followed
by mixing of the transfected cells, generating a recombinant polyclonal antibody expressing
cell line expressing the six antibodies in known combination. in this manner, it was
possible to test whether the transfectlon of the mammalian cells occurs without generating a
bias to one or several individual clones of the recombinant polyclonal antibody expressing cell
line. Furthermore, It was possible to check for proliferation bias and bias caused by the purification
of the polyclonal composition of antibodies.
Establishment of an anti-ovalbumin recombinant polyclonal antibody manufacturing cell line
Ovalbumin-binding phage clones were selected using phage display and ELISA to identify the
relevant clones. Two setups were used for identifying antibodies from the ovalbumin-binding
clones, i.e., ELISA plates coated with ovalbumin or a high density screening method (HDS),
based on immobilization of ovalbumin on PVDF membranes. in this manner a panel of antibodies
were obtained, of which some recognize ovalbumin immobilized on the ELISA plate
and others recognize ovalbumin immobilized on the PVDF membrane.
The selected ovalbumin-binding phage clones may have their variable heavy and kappa chain
DNA sequences linked to mammalian promoters and transferred into a vector of the
pSymvc20 type (figure 4D) for antibody expression generating a collection of clones of the
pSymvc21 type (figure 4E). The CHO-Flp-in cells are either transfected in bulk with a mixture
of the pSymvc21 clones or the cells are transfected individually with one pSymvc21 antibody
expressing plasmid followed by mixing of the transfected cells expressing the other ovalbumin
binding antibodies. The procedure of creating an anti-ovalbumin polyclonal antibody producing
cell line can be monitored by DNA sequencing, TaqMan PCR and RFLP analysis of indi-
vidual antibody expressing cells, as well as ELISA, 2-dlmensional (2D) liquid chromatography
(LC) and mass spectrometry (MS) of the produced antibody mixture.
Cultivation of cells and production of a recombinant polyclonal antibody
The polyclonal cell line produced as described above is grown in suitable media under suitable
conditions for expressing the polyclonal protein of interest encoded by the variant nucleic
acid.sequences inserted into the genome of the cells. The cell cultivation may be performed
in several steps. A first step is where the polyclonal cell line is selected for site-specific inte-
grants. When using mammalian cells, the selected cells are then preferably adapted to
growth in suspension as well as serum free conditions. This can be performed in one or two
steps and with or without selection pressure. When the polyclonal cell line Is adapted to the
appropriate conditions scaling up can be initiated. At this point a working cell stock can be
frozen down. Preferably bioreactors of between 30 and 100 liters are used, but smaller or
larger bloreactors may be employed. The suitable production time and choice of bioreactor
size are dependent on the desired yield of protein from the batch and expression levels from
the cell line. Times might vary from a couple of days up to three month The expressed re-
combinant polyclonal protein is isolated from the cells or the supernatant. The recombinant
protein is purified and characterized according to procedures known by a person skilled in the
art. Examples of purification and characterization procedures are listed below.
Purification of a recombinant polyclonal protein from culture supernatant
Isolation of specific proteins from culture supernatants is possible using various chroma-
tographic techniques that utilize differences in the physico-chemical properties of proteins,
e.g. differences in molecular weight, net charge, hydrophobiclty, or affinity towards a specific
ligand or protein. Proteins may thus be separated according to molecular weight using gel
filtration chromatography or according to net charge using ion-exchange (cation/anion)
chromatography or alternatively using chromatofocusing, Similarly, proteins may be sepa-
rated after hydrophobicity using hydrophobic interaction chromatography or affinity chroma-
tography utilizing differences in affinity towards a specific immobilized ligand or protein.
Separation of complex mixtures of proteins may thus be achieved by sequential combination
of various chromatographic principles. A mixture of proteins may thus initially be separated
according to e.g. net charge using ion-exchange chromatography and proteins of similar net
charge may subsequently be separated according to molecular weight using gelfiltration
chromatography or after hydrophobicity using hydrophobic interactions chromatography in
the presence of a high concentration of a selected salt.
Affinity chromatography combined with subsequent purification steps such as ion- exchange
chromatography, hydrophobic interactions and gel filtration has frequently been used for the
purification of IgG (polyclonal as well as monoclonal) and TcR from different sources e.g.,
ascites fluid, cell culture supernatants and serum. Affinity purification, where the separation
is based on a reversible interaction between the protein(s) and a specific ligand coupled to a
chromatographic matrix, is an easy and rapid method, which offers high selectivity, usually
high capacity and concentration into a smaller volume. Protein A and protein G, two bacterial
cell surface proteins, have high affinity for the Fc region, and haye, in an Immobilized form,
been used for many routine applications, including purification of. polyclonal IgG and its subclasses
from various species and absorption and purification of immune complexes.
Following affinity chromatography, downstream chromatography steps, e.g. ion-exchange
and/or hydrophobic interaction chromatography, can be performed to remove host ceil proteins,
leaked Protein A, and DNA.
Gel filtration, as a final purification step, can be used to remove contaminant molecules such
as dimers and other aggregates, and transfer the sample into storage buffer. Depending on
the source and expression conditions it may be necessary to include an additional purification
step to achieve the required level of antibody purity. Hydrophobic interaction chromatography
or ion-exchange chromatography are thus frequently used, in combination with Protein A
and gelfiltratlon chromatography, to purify antibodies for therapeutic use.
in order to purify other classes of antibodies, alternative affinity chromatography media have
to be used since proteins A and G do not bind IgA and IgM. An immunoaffinity purification
can be used (anti-IgA or anti-IgM monoclonal antibodies coupled to solid phase) or, alternatively,
multistep purification strategies including ion-exchange and hydrophobic interaction
can be employed.
Structural Characterization
Structural characterization of polyclonal proteins such as antibodies and TcRs requires high
resolution due to the complexity of the mixture (clonal diversity and glycosylation). Traditional
approaches such as gel filtration, ion-exchange chromatography or electrophoresis may
not have sufficient resolution to differentiate among the individual antibodies. Two-dimensional
polyacrylamide gel electrophoresis (2D-PAGE) has been used for profiling of complex
protein mixtures followed by mass spectrometry (MS) or liquid chromatography (LC)-MS
(e.g., proteomics). 2D-PAGE, which combines separation on the basis of a protein's charge
and mass, has proven useful for differentiating among polyclonal, ollgoclonal and monoclonal
immunoglobulin in serum samples. However, this method has some limitations. Chromatographic
techniques, in particular capillary and LC coupled to electrospray ionizatlon MS are
increasingly being applied for the analysis of complex peptide mixtures. LC-MS has been used
for the characterization of monoclonal antibodies and recently also for profiling of polyclonal
antibody light chains. The analysis of very complex samples requires more resolving power of
the chromatographlc system, which can be obtained by separation in two dimensions (or
more). Such an approach could be based on ion-exchange in the first dimension and rever-
sed-phase chromatography (or hydrophoblc interaction) in the second dimension optionally
coupled to MS.
Functional Characterization
A polyclonal protein can for example be characterized functionally through comparability
studies with polyclonal proteins with specificity towards the same target or a similar activity.
Such studies can be performed in vitro as well as in vivo.
An in vitro functional characterization of a polyclonal antibody could for example be immuno-
preclpltatlon which is a highly specific technique for the analytical separation of target antigens
from crude cell lysates. By combining immunoprecipitation with other techniques, such
as SDS-PAGE followed by protein staining (Coomassle Blue, silver staining or biotin labeling)
and/or immunoblottlng, It is possible to detect and quantify antigens e.g., and thus evaluate
some of the functional properties of the antibodies. Although this method does not give an
estimate of the number of antibody molecules nor their binding affinities, it provides a visualization
of the target proteins and thus the specificity. This method can likewise be used to
monitor potential differences of the antibodies toward antigens (the integrity of the clonal
diversity) during the expression process.
An in vivo functional characterization of a polyclonal antibody could for example be infection
studies. An experimental animal such as a mouse can for example be infected with a specific
virus, towards which a polyclonal antibody has been developed. The degree to which the infection
can be inhibited will indicate functionality of the polyclonal antibody.
Therapeutic compositions
in an embodiment of the invention, a pharmaceutical composition comprising a recombinant
polyclonal protein selected from the immunoglobulin super family as it active ingredient is
intended for the treatment or prevention of a disease in a mammal such as a disease selected
from cancer, infections, inflammatory diseases, allergy, asthma and other respiratory
diseases, autoimmune diseases, immunological malfunctions, cardiovascular diseases, diseases
in the central nervous system, metabolic and endocrine diseases, transplantation re-
jections and undesired pregnancy. The mammal is preferably a human, a domestic animal or
a pet.
in a preferred embodiment of the present invention, the pharmaceutical composition comprises
a recombinant polyclonal antibody or antibody fragment as the active ingredient and a
pharmaceutically acceptable exciplent.
in another preferred embodiment of the present invention, the pharmaceutical composition
comprises a recombinant polyclonal T cell receptor or T cell receptor fragment as the active
ingredient and a pharmaceutically acceptable exclpient.
For the treatment or prevention of infections, the pharmaceutical composition according to
the invention comprises a recombinant polyclonal protein of interest capable of reacting with
or binding to an infectious microorganism such as a microorganism selected from bacteria,
myoobacteria, virus, mycoplasma, rickettsia, spirochetes, protozoa, fungi, helminthes and
ectoparasites.
Recombinant human polyclonal proteins may be administered within a pharmaceutlcaliy-ac-
ceptable diluent, carrier, or excipient, in unit dosage form. Conventional pharmaceutical
practice may be employed to provide suitable formulations or compositions to administer the
compounds to patients suffering from a disease, for example, caused by excessive cell proliferation.
Administration may begin before the patient is symptomatic. Any appropriate route
of administration may be employed, for example, administration may be parenteral, intravenous,
intra-arterial, subcutaneous, intramuscular, intracranial, intraorbital, ophthalmic, intra-
ventricular, intracapsular, intraspinal, intradsternal, intraperitoneal, intranasal, aerosol, suppository,
or oral administration. For example, therapeutic formulations may be in the form of,
liquid solutions or suspensions; for oral administration, formulations may be in the form of
tablets or capsules chewing gum, pasta, compositions suitable for the application onto the
skin may be in the form of creams, ointments, lotions, gels, pads or other, compositions suitable
for application onto the vaginal or urogenital mucosa may be in the form of vagitories,
gels or other and for intranasal formulations, in the form of powders, nasal drops, or aerosols.
The pharmaceutical compositions of the present invention are prepared in a manner known
perse, for example, by means of conventional dissolving, lyophilising, mixing, granulating or
confectioning processes. The pharmaceutical compositions may be formulated according to
conventional pharmaceutical practice (see for example, in Remington: The Science and Practice
of Pharmacy (20th ed.), ed. A.R. Gennaro, 2000, Llppincott Williams & Wilkins, Philadelphia,
PA and Encyclopedia of Pharmaceutical Technology, eds. J. Swarbrick and J. C. Boylan,
1988-1999, Marcel Dekker, New York, NY).
Solutions of the active ingredient, and also suspensions, and especially isotonic aqueous solutions
or suspensions, are preferably used, it being possible, for example in the case of lyo-
philized compositions that comprise the active ingredient alone or together with a carrier, for
example mannitol, for such solutions or suspensions to be produced prior to use. The pharmaceutical
compositions may be sterilized and/or may comprise exclpients, for example preservatives,
stabilisers, wetting and/or emulsifying agents, solubillsers, salts for regulating the
osmotic pressure and/or buffers, and are prepared in a manner known per se, for example by
means of conventional dissolving or lyophilising processes. The said solutions or suspensions
may comprise viscosity-increasing substances, such as sodium carboxyrnethylcellulose, car-
boxy methylcellulose, dextran, poly vlnylpyrrolidone or gelatin.
The injection compositions are prepared in customary manner under sterile conditions; the
same applies also to introducing the compositions into ampoules or vials and sealing the
containers.
Pharmaceutical compositions for oral administration can be obtained by combining the active
ingredient with solid carriers, if desired granulating a resulting mixture, and processing the
mixture, if desired or necessary, after the addition of appropriate exclpients, into tablets,
drage cores or capsules. It is also possible for them to be incorporated into plastics carriers
that allow the active ingredients to diffuse or be released in measured amounts.
The pharmaceutical compositions comprise from approximately 1% to approximately 95%,
preferably from approximately 20% to approximately 90%, active ingredient. Pharmaceutical
compositions according to the invention may be, for example, in unit dose form, such as in
the form of ampoules, vials, suppositories, drages, tablets or capsules.
The formulations can be administered to human patients in therapeutically effective amounts
(e.g., amounts which prevent, eliminate, or reduce a pathological condition) to provide the-
rapy for a disease or condition. The preferred dosage of therapeutic agent to be administered
is likely to depend on such variables as the type and extent of the disorder, the overall health
status of the particular patient, the formulation of the compound excipients, and its route of
administration.
If desired, treatment with recomblnant human polyclonal antibodies may be combined with
more traditional therapies. For example in the treatment of cancer such combinatorial therapies
could take the form of surgery or administration of chemotherapeutics or other anti-cancer
agents.
in another embodiment of the invention, the pharmaceutical composition according to the
invention comprises a recomblnant polyclonal protein of interest capable of reacting with or
binding to an infectious microorganism such as a microorganism selected from bacteria, my-
cobacteria, virus, mycoplasma, rlckettsia, splrochetes, protozoa, fungi, helmlnthes and ectoparasites.
Therapeutic uses of the compositions according to the invention
The pharmaceutical compositions according to the present invention may be used for the
treatment, amelioration or prevention of a disease in a mammal. Diseases that can be
treated with the present pharmaceutical compositions include cancer, infectious diseases,
inflammatory diseases, allergy, asthma and other respiratory diseases, autoimmune diseases,
cardiovascular diseases, diseases in the central nervous system, metabolic and endocrine
diseases, transplantation rejections and undesired pregnancy.
One aspect of the present invention is a method for disease treatment, amelioration or prophylaxis
in an animal, wherein an effective amount of the recombinant polyclonal antibody or
antibody fragment is administered. in further aspect an effective amount of the recombinant
polyclonal T cell receptor or T cell receptor fragment is administered.
An additional aspect of the present invention is the use of a recombinant polyclonal antibody
or recombinant polyclonal T cell receptor or fragments of antibodies or T cell receptors for the
preparation of a composition for the treatment of diseases selected from a group consisting
of a cancer, an infection, an inflammatory disease, an allergy, asthma or other respiratory
disease, immunological malfunctions, an autoimmune disease, a cardiovascular disease, a
disease in the central nervous system, a metabolic disease, an endocrine diseases, transplant
rejection, and undesired pregnancy.
Diagnostic use and environmental detection use
Another embodiment of the invention is directed to diagnostic kits and kits for environmental
detection use as well as methods for using these kits. Kits according to the present invention
comprise a recombinant polyclonal protein prepared according to the invention which protein
may be labeled with a detectable label or non-labeled for non-label detection. If labeled, the
present recombinant polyclonal protein may be added to a sample suspected of containing
the target molecule and the presence or absence of the label indicate the presence or absence
of the target molecule. The sample to be tested may be a sample of bodily fluid such
as blood, serum, plasma, spinal fluid, lymph or urine or a non-mammalian sample such as a
sample from an environmental source suspected of harboring a contaminant. Non-mammal-
ian samples may be water, air or contaminated earth. Non-label detection encompasses the
measurement of refractive change in BlAcore upon binding, wherein the recomblnant poly-
clonal protein is used to capture the target molecule.
EXAMPLES
The following examples describe how recombinant polyclonal antibodies are expressed and
produced in a high-producer cell line, where gene(s)/vector(s) of interest have been inserted
by site-specific integration into a pre-characterized chromosomal "hot spot" site.
in the examples, CHO cells were utilized as host cell. The advantages thereof include the
availability of suitable growth medium, their ability to grow efficiently to a high density in
culture, and their ability to express mammalian proteins such as antibodies in a biologically
active form.
in general, transformation of E. coll and transfection of mammalian cells according to the
subject invention will be performed according to conventional methods. To improve the understanding
of the invention, construction of exemplary vectors and their usage in producing
a recombinant polyclonal manufacturing cell line for recomblnant polyclonal protein expression
are described in the examples below.
The following examples illustrate the invention, but should not be viewed as limiting the
scope of the invention.
EXAMPLE 1
Site-specific integration versus random integration
For the following transfection experiment, the CHO Flp-in cells (invitrogen, Carlsbad, CA)
were used. The efficiency of the system was tested using human secreted alkaline phos-
phatase (SEAP) as a reporter gene. Two plasmid constructs were prepared:
1. SEAP inserted into pcDNA3.1hygro+ (invitrogen, Carlsbad, CA) (for random integration)
2. SEAP inserted into pcDNA5/FRT (invitrogen, Carlsbad, CA) (for site-specific integration)
The two plasmid constructs were very similar with respect to regulatory elements, i.e. promoter,
polyadenylation etc. which made It possible to use the plasmlds for comparing random
integration with site-specific integration.
CHO Flp-in cells were transfected with plasmid construct 1 alone or plasmid construct 2 together
with the recomblnase-encodlng plasmid pOG44 according to the procedure described
by invitrogen. Transfectants were selected using hygromycin and the production of 5EAP
from pools of transfectants was measured.
Cells transfected by site-specific integration produced approximately 6 times more SEAP than
cells transfected by random integration proving the efficiency of the system and the cell line.
EXAMPLE 2
Design and preparation of an expression vector for site-specific integration in a host cell
An expression vector suitable for site-specific integration into a hot spot chromosomal region
of a host cell may be assembled comprising the following DNA elements:
a) an FRT recombination site linked to the hygromycin resistance gene,
b) a pUC origin of replication,
c) an ampicillin resistance gene (bla),
d) a bla-promoter allowing expression of the ampicillin (bla) resistance gene,
e) gene(s), encoding a protein of interest (GOls),
f) promoters) allowing expression of the GOI, and
g) optionally, additional transcriptional or translational regulatory elements, such as enhancers
or UCOE's, for increased expression at the site of integration or an IRES.
To provide a better understanding of the construction of the expression vector, each of the
elements are described in more details:
a) An FRT recombination site linked to the hygromycin resistance gene for Flp recombinase-
mediated integration and selection of a cell line with a majority of single integrants was used.
The hygromycin gene was neither preceded by a promoter nor equipped with a transcription
initiating codon, but a polyadenylation signal was added 3' of the gene. The FRT site used
was 5'-gaagttcctattccgaagttcctattctctagaaagtataggaacttc-3' (SEQ ID NO 1).
b) A pUC origin of replication was included to permit high copy number replication in an E.
coll host cell.
c) An Ampiclltin (bla) resistance gene (p-lactamase) allowing selection of E. coll transfor-
mants was included.
d) A bla-promoter allowed expression of the amplclllln (bla) resistance gene in E. coll.
e) GOI encoding a protein of interest, e.g., a recomblnant polyclonal protein, antibody, the
heavy and light chains of an antibody, as well as nucleotide sequences that encode all or a
portion of either the constant region or variable region of an antibody molecule, and optionally
all or a portion of a regulatory nucleotide sequence that controls expression of an antibody
molecule were included.
Immunoglobulln loci for heavy chains may include but is not limited to all or a portion of the
V, D, J and switch region (including intervening sequences, also known as introns) and
flanking sequences associated with or adjacent to the particular heavy chain constant region
gene and it may include regions located within or downstream of the constant region (including
introns).
Immunoglobulin loci for the light chains may include but are not limited to the V and J regions,
their upstream flanking sequences, and intervening sequences (introns) associated
with or adjacent to the light chain constant region gene, and it may include regions located
within or downstream of the constant region (including introns).
For the modification of all or a portion of a constant region of an antibody, modifying sequences
of the invention may include, but are not limited to an antibody constant region having a
particular effector function, class and/or origin (e.g., igG, IgA, IgM, IgD, or IgE constant regions
of a human immunogiobulins or any other species) or a portion of a constant region
which modifies the activity or properties of the constant region of the ;antibody; as well as
genes which encode other molecules that confer some new function to a modified antibody
molecule, e.g., an enzyme, toxin and the like.
The gene(s) encoding a protein of interest may be operatively linked to nucleotide sequences
encoding functional leader sequences directing the gene product to the secretory pathway.
Further, 3' to the GOI encoding the protein of interest, e.g., such as a polyclonal antibody
comprising heavy and light chains, there may be strong polyadenylation signals. The use of
the mouse isotype IgGl in the following examples is for illustrative purposes and is not intended
to limit the scope of the invention.
f) Promoters allowing expression of the GOI are provided. Therefore, a cassette comprising
promoter and enhancer elements for expression is described. in the expression vector, each
of the antibody genes may be preceded by their own mammalian promoter elements directing
high level expression of each of the two chains, whether uni-dlrectlonally, bi-directionally
or a tail-to-tail orientation of transcription cassettes is used.
in a bl-dlrectlonal orientation of expression, a head-to-head promoter configuration can be
used (construction of such a system is described in details in US Patent No. 5,789,208, which
is incorporated by reference in its entirety). in a uni-directional expression system, two promoters
or one promoter combined with e.g., an IRES sequence can also be used for expression.
For construction of head-to-head promoters, a Pfu PCR amplification of the promoters is performed
individually. The 5'-primer will initiate on the 5'-most base of the promoter, the 3'-
end primer will include a unique restriction site, such as, a Xbal site. Following PCR amplification,
the fragments may be separated on an agarose gel, and isolated from the gel using
QiaQuick columns (Qiagen). This is followed by an Xbal restriction digestion, heat inactivation
at 65°C for 20 minutes, and column purification of the fragments using QiaQuick. The fragments
are then mixed and ligated together using E. colt ligase {New England Bioiabs (NEB)),
an enzyme that preferentially llgates sticky ends. The ligation mix is PCR amplified with the
5'-prlmers of each promoter to yield the complete head-to-head promoter (promoter A /
promoter B) fragment. This fragment is kinased with T4 polynucleotide kinase (PNK) (NEB),
the enzyme is heat inactivated at 65°C for 20 minutes, and the fragment is ligated (blunt
end) into the vector of interest (PCR amplified pSymvclO (see Figure 4) fragment, where the
primers used for amplification anneal on each side of the promoter region amplifying everything
except the promoter) using T4 ligase (NEB).
Figs 1 and 2 show expression vectors comprising promoters for bi-directional and uni-dl-
rectional, respectively. These promoters intend to illustrate, but not limit, the promoter
choice in the invention.
g) The expression vector can carry additional transcriptional and/or translational regulatory
elements, such as enhancers and/or UCOE's, for increased expression at the site of integra-
tion and/or IRES.
Evaluation of polyclonallty preservation in the manufacturing system developed
in order to be able to evaluate the stability and reproducibility of the manufacturing system,
a ceil line expressing a polyclonal composition of distinct antibodies in known combination
was prepared. The polyclonal antibody composition was termed the mini six composition. The
library of nucleic acid sequences encoding the mini six composition was termed the mini six
library.
(a) Clone origin
The following sequences encoding Fab fragments (the genes of interest) with reactivity
against antigens 1-6 were used in this example:
1. Ovalbumin (OVA). The Fab encoding fragments were selected from a murine anti-OVA
phage display library.
2. Alkaline phosphatase (AP). The Fab encoding fragments were selected from a murine anti-
AP phage display library.
3. p2-mlcroglobulin (pzm). The Fab encoding fragments were cloned from the hybridoma
BBM.l (a gift from Dr. L. 0. Pedersen, Denmark), which was generated against p2m.
4. Human haptoglobin (HAP). The Fab encoding fragments were selected from a murine anti-
human haptoglobin phage display library.
5. Factor VIII (FVIII). The parental monoclonal antibody of this Fab fragment was a FVIII F25
monoclonal antibody (gift from Novo Nordisk, Denmark). The DNA encoding the VH and complete
Kappa chains of this Fab fragment was sub-cloned into a phagemid, followed by insertion
of the prokaryotic promoter cassette into the construct.
6. Hen egg lysozyme (LYS). This construct was generated from the D1.3 scFv clone (Boulot,
G. ef a/., J. Mol. Biol., 213(4) (1990) 617-619), by PCR amplification of VH and VK fragments
and cloning into a phagemid.
The phagemid clones exist either in transformed Escherlchla coll strain TGI glycerol stocks
(kept at -80°C) or as phagemid DNA preparations.
;b) RFLP analysis and DNA sequencing of the mini six library.
The nucleotide sequences encoding the heavy chains of the Fab fragments were analyzed by
HFLP as follows: The band patterns obtained after digest of the PCR generated fragments
with the Nlalll and Hint I enzyme were examined. The different Fab fragment encoding sequences
exhibited very different and easily distinguishable patterns. The nucleotide sequences
encoding the VH and VL fragments were sequenced and sequences corresponding to
the RFLP pattern were found. Furthermore, the nucleotide sequences encoded open reading
frames and translated into well-defined polypeptides.
(c) ELISA analysis of the mini six composition
The Fab fragments expressed from the clones were analyzed using ELISA, in which all Fab
fragments were analyzed for reactivity with all antigens. Fab expression was monitored using
an anti-kappa EUSA. All Fab fragments were tested in duplicate in ELISA. Ail clones expressed
Fab fragments, and the Fab fragments reacted specifically with their relevant antigen.
No background problems were found in the ELISA analyses.
The six phagemid clones exist in individually transformed Escherichia coll strain TGI glycerol
stocks, which were used in the model system for inoculation as described below.
(d) Design of a polyclonal model system with six distinct antibodies in known combination.
The six selected Fab-expressing clones (clones expressing Fab fragments of anti-OVA, antl-
AP, anti-p2m, anti-HAP, antl-FVIII, and anti-LYS) were characterized by testing the reactivity
of the expressed Fab fragments against the relevant antigens. These clones formed part of a
polyclonal model system for testing the expression and production of six distinct antibodies in
a known combination (the mini six composition). All Fab fragments encoding nucleotide sequences
(the mini six library) were transferred into a phagemid vector (illustrated by
pSymvclO, Figure 4A).
(d.l) individual transfer of the GOI's from the phagemid vector into a vector for mammalian
expression
The transfer of the genes of interest (the mini six library) from a phagemid vector to a vector
for mammalian expression was, in this example, performed by a two-step procedure. The
first step was to replace the prokaryotic promoters with a mammalian promoter cassette in a
head-to-head orientation. This step was followed by transferring the variable region of the
GOI's, the promoter cassette and the constant kappa to the expression vector as described in
detail below, and illustrated in figure 4.
The head-to-head promoter cassette (promoter A / promoter B) was inserted into the
phagemid vector for each clone by using a Sad/Xhol digestion followed by a ligatlon resulting
in exchange of promoters from bacterial to mammalian. An EcoRI and Notl digest was
then used to move the variable heavy chain, the head-to-head promoter cassette (promoter
A / promoter B) and the complete kappa chain (fcoRI /Not I fragment) from the phagemid
vector into the expression vector.
An example of the individual transfer of each clone is given with the flow chart in figure 4.
This figure shows plasmld pSymvclO where the heavy and kappa coding sequences of interest
(e.g., gcO32 OVA) are present in the phagemid vector into which the head-to-head
mammalian promoter cassette construct was ligated to replace the bacterial promoters using
a SaclfXhol fragment transfer generating pSymvcl2.
From this construct, the variable heavy chain-coding sequence including the promoter cassette
and the whole of the kappa chain coding sequence was transferred into the mammalian
isotype-encoding vector (pSymvc20) by a Nott/EcoKL transfer. The resulting vector
(pSymvc2l) expressed the mouse antibody of interest (e.g., anti-OVA IgGl antibody).
The variable heavy chain coding sequence, the mammalian promoter cassette and the entire
kappa chain coding sequence from each of the six clones were transferred individually by a
Notl/EcoRI transfer resulting in the mammalian expression vector pSymvc21, which expresses
each of the GOI encoded antibody sequences as mouse IgGl antibodies.
The six individual pSymvc21 clones containing the six GOIs were kept as TGI glycerol stocks.
For transfectlori into CHO Flp-in cells, the TGI stocks were propagated individually, and after
OD600 normalization for the number of E coli cells, the six cultures were mixed and used for
plasmid preparation. This plasmid preparation comprising the six GOIs (the mini six library)
was used for bulk transfection of mammalian cells for recombinant polyclonal protein expression.
(d.2) Mass transfer of the GOI's from phagemid vectors into vectors for mammalian expression
The GOIs (the mini six library)(here the EcoKl/Nott fragments), which were located in
phagemid vectors and coding for six distinct Fab fragments (anti-OVA, anti-AP, anti-fom,
antl-HAP, anti-FVTJI, and antl-LYS)r were transferred in-mass as a mixture of the six vector
constructs into vectors for mammalian expression resulting in a mixture of six distinct expression
vectors.
The experimental procedure concerning the mass transfer follows the procedure described in
(d.1) with the exception that it was performed in-mass, I.e. all six GOIs (encoding the variable
heavy chains, including the head-to-head promoter cassette and complete kappa chains)
were transferred simultaneously as a mixture of the six phagemid vectors.
Plasmld preparations of the mini six library
Plasmid Preparation 1 refers to a plasmid preparation of a mix of the six phagemid vectors
(with the antibody coding sequences contained in the vector pSymvclQ).
Plasmid Preparation 2 refers to a plasmid preparation of six phagemid vectors with the coding
sequences contained in the vector pSymvcl2 after mass transfer step 1 (see figure 4C),
which results in the exchange of the prokaryotic promoters with the mammalian promoter
cassette constructs.
Plasmid Preparation 3 refers to a plasmid preparation after mass transfer step 2 (see figure
4D), which affords exchange of the variable heavy chain, the head-to-head promoter cassette,
and the complete kappa chain from the pSymvcl2 to the mammalian expression vector
(pSymvc21), thus allowing expression of the six selected antibodies as full length mouse
IgGl antibodies.
Genotyping of TGI cells transformed with plasmid preparations used in mass transfer
TGI cells were transformed with the mini six library in bulk by electroporation and after an
overnight incubation on 2xYT (Sigma Y 2627) plates, individual colonies were picked. in each
experiment 180 colonies were picked and incubated in 96 well formats in 2xYT liquid medium
for 4 hours. Aliquots of the cultures were diluted with water, denatured and used as template
in PCR. in all experiments, the variable heavy chain was amplified. Primer sequences for the
phagemid vectors (pSymvclO-type) were:
5'-GCATTGACAGGAGGTTGAGGC-3' (SEQ ID NO 2) and
5'-GCTGCCGACCGCTGCTGCTGGTC-3' (SEQ ID NO 3)
Primers for vectors with mammalian promoter cassette were (pSymvcl2-type):
5'-GCATTGACAGGAGGTTGAGGC-3' (SEQ ID NO 4) and
5'-GTGTCCACTCTGAGGTTCAG-3' (SEQ ID NO 5)
Primers for pSymvc21 constructs were:
5'-CAAATAGCCCTTGACCAGGC-3' (SEQ ID NO 6) and
5'-GTGTCCACTCTGAGGTTCAG-3' (SEQ ID NO 7)
All PCR products were digested with both Nlalll and Hinfl to ensure unambiguous genoty-
ping. The digestion fragments were analyzed by agarose gel electrophoresis and bands were
visualized by EtBr staining. The number of individual genotypes resembled by the fragment
pattern determined by RFLP corresponds to the number of individual colonies representing
each of the six antibodies among the total number of picked colonies.
(d.2a) Mass transfer from the phagemid vector to a mammalian vector after DNA amplification
in E. coli cells (two-step amplification method)
The Plasmid Preparation 1 was prepared from each of the six E. coli TGI glycerol stocks,
containing one of the six phagemid vectors constituting the mini six library. The stocks were
propagated individually, and after OD600 normalization for the number of E. coli, the six cultures
were mixed in equal amounts and used for plasmid preparation resulting in Plasmid
Preparation 1. The genotype distribution of the six phagemid vectors in Plasmid Preparation 1
was tested by transformation into electrocompetent TGI cells and subsequent RFLP analysis.
The distribution of the different genotypes in TGI cells is shown in Figure 5.
The Plasmid Preparation 1 comprising the polyclonal phagemid vector expressing an equal
mixture of the six selected Fab fragment genotypes was digested with Sacl/Xhol. Then the
head-to-head promoter cassette (CMV promoter/MPSV promoter) was inserted by ligation.
The genotype distribution of the vectors after the promoter exchange in the vector was
tested in TGI cells after transformation with DNA from the ligation step (Figure 6).
The cells were plated and grown on large (245mm x 245mm) 2x YT agar plates and the
Plasmid Preparation 2 was prepared to generate the phagemid vector now containing the
head-to-head promoter cassette (pSymvcl2).
From the Plasmid Preparation 2, the variable heavy chain coding sequence, including the
promoter cassette and the complete kappa chain sequence was cut out from the phagemid
vector by a Notl/EcoRl digest and transferred into a vector (pSymvc20) already containing
the constant region domains of mouse IgGl. This resulted in a collection of pSymvc21 vectors,
which expresses the variable region of the six selected antibody clones as full-length
mouse IgGl antibodies.
The promoter transfer can alternatively be performed in the mammalian vector encoding an
isotype, reversing the order of restriction digest starting with Notl/EcoRl for transfer of the
DNA of interest to the mammalian vector and then Sacl/Xhol restriction digest fragment for
insertion of the promoter region.
The distribution of genotypes after transferring the variable heavy chain coding sequence, the
promoter cassette and the whole kappa chain encoding sequence into the expression vector
was tested by transforming TGI cells with DNA from the second ligation step (Figure 7). Cells
were plated on large (245 mm x 245 mm) 2x YT agar plates and Plasmid Preparation 3 was
prepared (pSymvc21), in which the variable region of the six clones are expressed in the
context of a mouse IgGl antibody framework.
The Plasmid Preparation 3 can be used for the bulk transfection of mammalian cells to generate
a recombinant polyclonal manufacturing cell line for recombinant polyclonal antibody
expression.
The results of the mass transfer from the phagemid vector to an isotype-encoding mammalian
vector after DNA amplification in E. coli cells showed that it was possible to obtain a balanced
distribution of the six vector constructs after they had been propagated individually
and mixed (Plasmid Preparation 1, Figure 5). The six constructs, after exchange of promoter
cassette (Plasmid Preparation 2, Figure 6) as well as after insertion into a mouse IgGl isotype-encoding
vector (Plasmid Preparation 3, Figure 7), were all detectable at comparable
levels.
(d.2b) Mass transfer from a phagemid vector to a vector for mammalian expression without
DNA amplification in E. coli after the Plasmid Preparation 1 step (one-step amplification
method)
DNA from the Plasmid Preparation 1 (here was used 25 ug) comprising the polyclonal
phagemid vector (pSymvclO) expressing an equal mixture of the six selected Fab fragment
genotypes was digested with Sacl/Xhol for exchange of promoters. The Sacl/Xhol vector
fragment was purified and ligated with the head-to-head promoter cassette (CMV pro-
moter/MPSV promoter). After the exchange of promoters without performing any amplification,
the vector with CMV/MPSV promoter cassette was digested with Notl/EcoRl for cutting
out the whole region with the variable heavy chain encoding sequence, including the promoter
cassette and the entire kappa chain encoding sequence from the phagemid vector for
mass transfer into a vector for mammalian expression. After ligating the Notl/EcoRl fragment
encoding the variable heavy chain, the promoter cassette and the kappa chain into a mouse
IgGl-encodlng vector (pSymvc20), an expression vector, which expresses the variable region
of the six selected clones in the context of mouse IgGl full length antibodies was obtained.
The composition of this expression vector is illustrated in Figure 1.
After the mass transfer resulting in the promoter exchange in the vector and transfer of the
nucleotide sequences encoding the variable heavy chain, the promoter cassette and the complete
kappa chain into a vector for mammalian expression, the distribution of genotypes was
tested by transformation of TGI cells with plasmid from the second ligation step. Cells were
plated on large (245 mm x 245 mm) 2xYT agar plates and a plasmid preparation of this
double digestlon/ligation Plasmid Preparation was prepared (vector pSymvc21, in which the
variable region of the six clones are expressed in the context of mouse IgGl antibodies, corresponding
to Plasmid Preparation 3 from d.2a). The genotype distribution in TGI cells after
transformation with the plasmid preparation from the one-step amplification method is shown
in Figure 8.
The one-step amplification method might introduce some scrambling among the heavy and
light chains from the six Fab encoding sequences resulting from the generation of undesired
ligation products, which are normally omitted during amplification in E.cali. However, if such
scrambling occurs, a screening step can be introduced to ensure that sufficient clonal diversity
is maintained.
(d.2c) Direct transaction of mammalian cells following promoter exchange
The product from the plasmid preparations of the mini six library from either the two-step
amplification method or one-step amplification method can be used directly to transfect
mammalian cells in bulk for recombinant polyclonal antibody expression.
(d.3) Testing of the Transfected Mammalian Cells
The known antibody combination of the mini six polyclonal model system can be used to test
and ensure that the mass transfer and transfection into mammalian cells occur in a way that
maintains the clonal diversity and without introducing bias in the composition of the antibody
variable sequence genotypes during transfection and subsequent culturing. The methods by
which the genotypic composition will be monitored throughout the process of mass transfer,
bulk transfection and mammalian expression, can comprise the following:
- DNA sequencing of isolated clones
- RFLP analysis of individual clones
- ELISA of the produced antibody mixture
- Mass spectrometry of the produced antibody mixture
- Taqman PCR of the relative composition of the genomlc sequences and mRNA expressing
the different heavy and light chains
Deviations in the genotypic composition introduced during the transfection process, should
they occur, could be caused by random integration or multiple integrants. As described in the
detailed description it is not likely to cause problems when using a host cell line pre-designed
for site-specific integration. However, it can be controlled in a variety of ways. Selection
against integration in a random genomic location (a location other than the site-specific location)
may be done using very low quantities of DNA, e.g., ltig/107 celis when performing
transfection with Lipofectamine or Q.2ng/107 cells when performing transfection by electro-
poration. Also, the DNA to be integrated may be supplied in supercoiled form; a form known
to be unfavorable for random integration.
Single or multiple integrations outside of the pre-designed target site will be eliminated by
negative selection, because the selectable marker will be present in the genome without a
promoter or a start codon. Thus, recipients of these random integration events do not survive
the selection process.
Transformants having multiple integrations where one of the recombination events occurs at
the target site will survive the selection process; however, the probability of this type of multiple
integrations is extremely low. This event would, therefore, lead to minimal scrambling of
the polyclonal protein. Further, because there would be 100 to 1000 other clones encoding
the same recombinant polyclonal protein, even if ectopic expression is high, the scrambling
effect would be less than about 1% if multiple integrations occurred. As mentioned previously,
the probability of ectopic integration can be reduced by reducing the quantity of DNA
used in the method.
The least likely event Is a multiple tandem integration at the target site. Using the Flp recombinase
system described here, this type of event will be rare because the excision activity
from the chromosome is significantly higher than the integration activity. However, should
tandem integration occur at an unacceptably high frequency, the Flp system can be ex-
changed for one in which only a single copy insert Is possible (see, for example, WO
99/25854; incorporated by reference).
(e) Expression of the six distinct antibodies in known combination in mammalian cells
Generally in order to minimize variable proliferation rates, it is preferable to integrate each
specific GOI (in this case each individual member of the mini six library) into at least 100,
preferably 1000 and most preferred into 10000 cells. A polyclonal cell line containing a large
number of individual cells expressing the same GOI (for all the GOI's) is statistically expected
to be less influenced by differences in proliferation rates of individual cells and have reduced
possibility of bias in the final polyclonal protein composition.
Further, it might be an advantage to ensure a homogeneous host cell line for the expression.
This can be achieved by sub-cloning the host cell line prior to trasfection. This process is described
in the paragraph regarding clonal diversity.
For poiyclonal libraries in which further bias control is desirable, the final composition of the
polyclonal protein product can be controlled by introducing an inducibie transcriptional control
element into the expression vector platform. Suitable inducibie control elements include, for
example, BD Tet on/off (BD Biosdence, Franklin Lakes, NJ) and GeneSwitch (invltrogen,
Carlsbad, CA). These transcriptional switches can be induced at an appropriate time point
(e.g., when the pool of cells is fully expanded) to minimize any proliferation bias due to
variation in gene expression or the protein product. The present experiment was not performed
with such control elements.
After transferring the six selected GOI from the phagemid vector to the mammalian expression
vectors, either individually as described in (d.l) or by mass transfer as described in
(d.2), the mammalian expression vectors were used for transfection into a hot spot in a CHO-
Flp-in cell line by using site-specific integration for expressing the six distinct antibodies as
described below.
For the individually transferred GOI (d.l), plasmid DNA's were propagated individually and
used for individual transfection into CHO Flp-in cells or the TGI stocks were propagated individually,
and after OD600 normalization for numbers of E. coli cells, the six cultures were
mixed and used for plasmid preparation. This plasmid preparation containing the six genes of
interest was used for bulk transfection of mammalian cells for recombinant polyclonal antibody
expression.
For the mass transferred GOI (d.2a or d.2b) plasmld DNA's are either transfected into CHO-
Flp-in cells or ampllfled and purified (Plasmid Preparation 3) according to the procedure described
in (d.2a or d2.b) and then used for bulk transfection.
(e.l) Cell culture
The CHO Flp-in host cell line (invitrogen, Carlsbad, CA) was maintained in Ham's F-12 medium,
with the addition of glutamine (2 mM) and FCS (10%) and 100 ng/mJ Zeodn (invitrogen,
Carlsbad, CA). For sub-culturing, the cells were detached by trypsln and split according
to manufacturer's instructions. Cells were grown at 5% CO2, 37"C. Medium and medium additives
were from Gibco.
This cell line stably expresses the lacZ-Zeodn fusion gene, rendering the cells resistant to the
antibiotic Zeodn, a resistance that upon site-specific integration of a foreign gene will be lost.
The cells contain a single copy of the Flp Recombination Target (FRT) site, and are thus ready
to be used as host cell line for site-directed integration by use of the Flp-in system (invitrogen,
Carlsbad, CA).
(e.2) Transfection of CHO cells
Tissue culture plates with 6 wells were inoculated with 4.0 x 10s CHO-Flp-in cells/ well, and
incubated O/N at 37°C / 5 % CO2. Transfection of these cells was performed testing different
transfection methods using FuGENE™6 (Roche), Lipofectine™, LipofectAmine™, or Lipofec-
tAMINE 2000™ (Gibco) according to the manufacturer's instructions. in this example, Lipo-
fecAMlNE 2000™ was used as transfection reagent. Briefly, on the day before the transfection,
exponentially growing CHO-Flp-in cells were seeded as described above and incubated
O/N at 37°C / 5 % CO2. Wells with an 85-95 % cell confluence were used for the co-transfection.
Two tubes with the following contents were prepared:
Tube 1: 0.5 ug of an individual expression vector with GOI described in (d.l) (e.g.,
pSymvc21 with OVA) + 4.5 ug mpO4O (a maxi preparation of pOG44) (a plasmid expressing
recombinase Flp) were added to 250 ul Optimem (1.5 ml Eppendorf tubes).
Tube 2: 7.5 ul LipofectAMlNE 2000™ was added to 250 ul Optimem (1.5 ml Eppendorf tubes)
and incubated at room temperature (RT) for 5 min.
The content of tube 2 was transferred to tube 1 followed by incubation at RT for 20 min.
The DNA-Lipofectamine complexes were transferred to the wells with cells according to the
manufacturer's instructions.
After 24 h, the cells were detached by trypsin, split (1:3) and distributed to a T-25 flask and
to 100 mm petri dishes and cultivated in fresh Nutrient Mixture F-12 Ham + 10% FCS + 2
mM L-Glutamine medium with 900 pg Hygromydn B/mt as selection pressure.
(e.3) Selection of site-speciftc integrants and sub-cultivation of transacted cells
Cells were cultivated under Hygromycin B selection pressure for two to three weeks, in this
period cells were refreshed every 2 to 4 days with new medium containing the same concentration
of selecting agent. The surviving pool of cells in the T-25 flask and in Petri dishes
were detached by trypsin, split (1:6) and distributed to T-fiasks for further propagation under
the above mentioned selection pressure. Some single clones were picked (using so-called
doning cylinders) from the Petri dishes containing the transfectants generated according to
the method described in (d.l), and transferred to new wells for propagation and use in expression
level studies.
Each pool of cells or single clones, that was resistant to the threshold Hygromydn B concentration,
was subsequently grown to confluence in 6-well plates, replated in Petri dishes, T-25,
T-80 and T-175 flasks in their respective medium plus Hygromycin B. When exponentially
growing cells reached 80% confluence in T80 tissue culture flasks, vials of each cell line were
frozen and stored in liquid nitrogen N2(L)- freezer.
For transfection with a mixture of plasmids containing the six genes of interest (the mini six
library), the six individual cultures were normalized at OD600for numbers of E. coli, mixed and
used for a polyclonal plasmid preparation containing the six genes of interest. A transfection
procedure using 7.5 times as much of the reagents and cells described above was carried
out, producing a recombinant polyclonal cell line expressing a mixture of the six distinct antibodies.
The six cell lines expressing individual members of the selected antibodies and the ceil line
expressing the mixture of the six distinct antibodies were during cultivation and propagation
tested for antibody production by antigen-specific ELISA.
(f) Monitoring the composition of a polyclonal cell line expressing six distinct antibodies of
known combination
By generating a mixture of the six selected genes of interest situated in expression vectors
followed by bulk transfection and site-specific integration into CHO-Flp-in cells, a polyclonal
cell line expressing six distinct antibodies was generated.
The cell line was followed for 34 days in which genotype distribution, antibody expression and
proliferation rates were followed. Results are described below.
(f.1) Genotype distribution of the six selected genes of interest in CHQ-Flp-in cells trans-
fected with the plasmid preparation from the ODeoo normalized mixture of cells.
The polyclonal CHO-Flp-in cell line was trypsinized and the cell suspension diluted to 10
cells/ml. Hereafter, 200 nl were transferred to each well of a total of ten 96-well plates. Approximately
10 days later, wells with single colonies were identified by microscopy. Wells with
single colonies were washed lx in PBS and 50 yl water was added. Plates were incubated at
80 °C for 10 mln and lysates were transferred to another 96-weii plate. Ten ml of the lysates
were used in 25 ml OneStep RT-PCR (Qiagen) with the following primers:
5'-CAAATAGCCCTTGACCAGGC-3' (SEQ ID NO 6) and
5'-GTGTCCACTCTGAGGTTCAG-3' (SEQ ID NO 7)
RFLP was performed using Hinfl and W/alll on 10 ul of RT-PCR mixtures in 15 ml reactions
that were incubated at 37 °C for 2 hours. The digestion fragments were visualized using
agarose gel electrophoresis followed by EtBr staining of the gel. The genotype distribution of
cells producing anti- OVA, anti-AP, anti-p2m, anti-HAP, anti-FVIII, and anti-LYS was followed
over time (days 16 and 34 after transfection), see Figure 9.
(f.2) ELISA of samples derived from CHO-Flp-in cells transfected with the plasmid prepara-
tion from the OD600 normalized mixture of E. coti (d.l)
The polyclonal CHO-Flp-in cell line (e.3) was trypsinized and 3 x 106 cells were plated in T-75
flasks in F-12 HAM + 10% FCS + 2 mM L-glutamine and 900 mg hygromycin. Medium was
changed every day and at day 3 supernatants were selected for ELISA. Antigens, (b2-micro-
globulin (a gift from University of Copenhagen), alkaline phosphatase (Sigma), ovalbumin
(Sigma), factor VIII (a gift from Novo Nordisk, Denmark), hen egg white lysozyme (Sigma),
and haptoglobin (Sigma)) were diluted in 50 mM carbonate buffer to .10 mg/ml. ELISA plates
were coated with antigen (50 ml to each well) and incubated O/N at 4 °C. Wells were washed
4 times with washing buffer (lx PBS/0.05% Tween 20) and blocked for 1 hour with 2% skim
milk powder in washing buffer (100 ml to each well). 50 ml samples were added to the wells
and plates incubated for 1 hour at RT. Plates were washed 4x and secondary antibodies (Goat
anti-mouse IgG/HRP conjugate (Sigma)) were added for 1 hour followed by 4x wash. The
ELISA was developed with TMB substrate (50 ixl in each well, DAKO S1600) for 5 min and
reactions stopped by adding 50 nl 1 M H2SO4. Plates were read immediately at 450 nm. Data
demonstrating expression of all six antibodies of interest in lysates derived on day 34 post-
transfection with the mixture of expression vectors encoding the six genes of interest is
shown in Figure 10. It should be noted that since the data presented in Figure 10 is derived
from six different antigen-specific ELISA assays, the OD450 readings are not directly comparable
in terms of antibody quantity.
Antibody expression levels were further analyzed by anti-kappa coat EUSA in pools of CHO-
Flp-in cells transfected with each individual GOI or the mixture of the six GOI. The result is
shown in Figures 11. This shows that the antibody expression levels are comparable among
the individually transfected cell lines (e.g. a cell line transfected with an anti-p2m encoding
vector expresses a comparable amount of antibody compared to a cell line transfected with a
vector encoding anti-AP antibody). The term pools of CHO-Flp-in cells transfected with individual
GOI, is used here because the individual cell lines are not derived from single clones,
but pools of clones as described in e.3.
(g) Conclusions from the experiment
Firstly, these evaluations (tests) of preservation of the polyclonality in the manufacturing
system showed that mass transfer of the six selected genes of interest from the mini six library
(encoding anti-OVA, antl-AP, anti-p2m, anti-HAP, anti-FVIII, and anti-LYS) from
phagemid vectors into mammalian expression vectors was possible without introduction of
selection or proliferation bias (Figure 7), thereby ending up with comparable frequencies of
the six selected genes of interest.
Secondly, bulk transfection of CHO-Flp-in cells with a mixture of the constructs containing the
six selected genes of interest also resulted in comparable distribution of the constructs in
isolated mammalian cells. The genotype distributions of the six selected genes of interest
over time (day 16 and 34 after transfection) were also similar (Figure 9), indicating that the
expression system up to day 34 maintained the original, equal distribution of the six genotypes,
without introducing proliferation bias.
Thirdly, the cells transfected in bulk with the mixture of the six genes of interest showed expression
of all six antibodies, as examined by antigen-specific ELISA on supernatants from
cells 34 days after transfection (Figure 10). The ELISA results for the different antigens are
not directly comparable in terms of antibody amounts, due to different binding affinities.
However, a capture ELISA based on coating with goat anti-mouse kappa chain antibody performed
on supernatants from a) the six individually transfected CHO-Flp-in cell lines generated
using the vector preparation as described in (d.l) and b) on supernatants of the polyclonal
cell line expressing a mixture of the six selected genes of interest showed comparable
antibody expression levels from the six genotypes.
in summary, it has been demonstrated that it is feasible to transfer a polyclonal GOI in mass
from a phagemid vector to a mammalian expression vector. This has previously been described
by Sharon (US 5,789,208). Furthermore, a mixture of mammalian expression constructs
could be transfected into mammalian cells in bulk and maintained at a comparable
frequency at least up to day 34 post-transfection.
EXAMPLE 3A
Evaluation of potyclonality preservation in cell cultures generated by bulk transfection of a
sub-clone from the CHO-Flp-in cell fine with the mini six library.
(a) Sub-cloning of "original" CHO Flp-in cell line
The original CHO Flp-in cell line (invitrogen) was cultured as described (Example 3 section
e.l). After trypsination cells were counted and plated with \ cell per well in a 96-well culture
plate. Approximately 14 days later 20 wells with single colonies were identified and cells were
trypsinated and transferred to 24-well plates. One of the sub-clones, CHO-Flp-in clone 019,
was selected for future studies after characterization of growth behavior as well as expression
levels.
(b) Bulk transfection and selection of CHO-Flp-in clone 019 cells
Transfection was performed in triplicate, and selection of the CHO-Flp-in clone 019 cells were
essential carried out as described (Example 3, section e.2 and e.3), with the exception that a
Neomycin selection marker replaced the Hygromycin marker in pSymvc21 (figure 4.e). Consequently,
Geniticin (450 ug/ml) was used instead of Hygromycin B during selection and cultivation
of the cells.
(c) ELISA of samples obtained from CHO Flp-in clone 019 cells transfected in bulk with the
mini six library
The cells were cultured for 73 days post transfection and samples for ELISA were taken at
day 17, 31, 45, 59 and 73. A quantitative EUSA (using individually purified mini six antibodies
as standards) was performed as described (Example 3, section, f.2). The results from
three independent transfections are shown in figure 12. Different expression profiles between
different transfections were observed. However, all six antibodies were detectable in all experiments
up to day 59.
(d) Conclusion from the experiment
Experiments with the Neomycin selection system on CHO Flp-in clone 019 ceils showed relatively
preserved expression profiles of individual batches, for two months after bulk transfection
(figure 12). Such a period of stability is sufficient for manufacturing purposes. The batch
to batch variation observed can be dealt with by generating and banking a large freezing
stock of the individual batch prior to production.
EXAMPLE 3B
Evaluation of polyclonality preservation in cell cultures generated by mixing individually
transfected CHO Flp-in cells after selection.
(a) individual transfection and selection of CHO-Flp-in cells
The experimental procedures for generation of the six cell lines expressing the individual
members of the mini six library has been described previously (Example 3, section e.3). The
six cell lines expressing individual members of the mini six library were mixed immediately
after selection in equal numbers (5x105 of each cell line) and the mixed cell population was
cultivated for 85 days. Three separate mixtures were made from the individual cell lines.
(b) ELISA of samples obtained from polyclonal cell cultures generated in (a)
Samples were taken every fortnight and the composition of the antibodies expressed from
the mini six library was determined by EUSA as described (Example 3, section f.2). ELISA
was performed at day 8, 17, 30, 45, 57, 72 and 85 after the mixing. The results (mean ± SD
of triplicate experiment) are shown in figure 13. All six antibodies were detectable 85 day
post mixing. As previously mentioned (Example 3, section f.2), the readings for different antibodies
were not directly comparable but data presented in figure 13 shows relatively stable
expression profiles at least up to day 45 after mixing, after which a general drop in productivity
is observed. Furthermore, comparison of results obtained from three independent mixes
showed similar expression profiles over time of the mini six antibodies indicating that the
results were reproducible.
(c) Conclusion from the experiments
Polyclonal cell cultures composed of mixtures of cells transfected individually with distinct
members of the mini six library showed compositional preservation at least up to day 45 after
mixing. A compositional preservation for 45 days will in most cases be sufficient time for
manufacturing purposes. Furthermore, triplicate experiments gave similar results, thereby
indicating that mixing of cells transfected individually with different constructs results in
mixed cell cultures with low batch to batch variation.
EXAMPLE 4
Establishment of an anti-ovalbumin recomblnant polyclonal antibody manufacturing cell line
(a) Expression of an anti-ovalbumin polyclonal antibody composition
A collection of fully characterized ovalbumin-binding phage clones has been identified as follows.
Four eight-week old female BALB/c mice were immunized i.p. and s.c. with 50 mg OVA
in complete Freunds Adjuvant and boosted with OVA in incomplete Freunds adjuvant at days
21 and 42 after immunization day 0, and it was confirmed that all animals had sera converted
against OVA, as measured by an antigen-specific EUSA. Spleens were harvested from
the best responding mice at days 31 and 52. Fab-displaying phagemid libraries were generated
from splenic RNA, using the phagemid vector (SymvclO) as previously described. The
resulting libraries contained approximately 106 independent clones. Selection of these libraries
was performed by reacting 5 x 1011 Fab-displaying phagemids with OVA coated on NUNC
immunotubes, followed by washing and acid elution of binding phages, As eluates from the
first round of panning contained a significant proportion of OVA binders, eluates from first
and second rounds of panning were screened for OVA-binding phage clones.
initially, OVA-reactive phage clones were identified by EUSA. in brief, ELISA plates were
coated with OVA and reacted with the phage-displayed Fabs, followed by an HRP-conjugated
secondary antibody. For negative controls, irrelevant antigens (BSA) or irrelevant phage-dls-
played Fabs (anti-AP) were used.
in addition, a HDS method, based on OVA immobilization on PVDF membranes, was established.
These two methods resulted in the identification of separate subsets of clones, i.e.
some clones that recognized OVA in one set-up and not in the other and vice versa. For Fab-
dlsplaylng phage clones that reacted with OVA by either ELJSA or HDS, the nudeotide sequence
encoding the variable domain of the VH was determined by DNA sequencing, and the
genetic diversity was estimated by phylogenetic analysis, using the Vector NTI software
package. The resulting panel includes 127 OVA-binding clones, for all of which the nudeotide
sequences of the variable part of the VH have been established.
Fab fragments expressed by the 127 OVA-binding clones all have the ability to bind to oval-
bumin either in native or denatured form. From this set we have identified approximately 30
different clones contained in a phagemid vector, e.g., pSymvclO, to be used for mass transfer
and mammalian expression. These antibodies are expressed either in the form of mouse
IgA, IgG2A or lgG2B antibodies. Because we have fully characterized the DNA sequences of
these antibody producing clones, we are able to monitor the distribution of the genotypes
throughout the mass transfer and mammalian expression procedure using the same methods
as used for the model system with the six distinct antibodies described in example 3.
(b) Mass transfer of the OVA-specific antibody sequences to a vector for mammalian expression
The transfer of genes of interest from a phagemid vector to an expression vector is a two
step procedure (illustrated in Figure 4), where the first step, is exchange of promoters with
the promoter cassette with head-to-head orientation of the selected mammalian promoters,
this is followed by transferring the variable region of the genes of interest and the promoter
cassette to an expression vector. The head-to-head promoter cassette (promoter A/ promoter
B) can be inserted into the phagemid vector of each clone by using a Sacl/Xhol digest
followed by a ligation resulting in exchange of promoters from bacterial to mammalian promoter
(pSymvcl2).
An EcoRl and Notl digest will then move the sequences encoding the variable heavy chain,
the head-to-head promoter cassette (promoter A/ promoter B) and the complete kappa chain
from the phagemid vector (pSymvcl2) into an isotype-encoding vector, pSymvc20. The
pSymvc20 vector can accept any Notl/EcoRl fragment from the phagemid vector. This fragment
would transfer the sequence encoding the variable heavy chain to connect with the
constant heavy chain sequences in pSymvc20 as well as the entire sequence encoding the
kappa chain to be connected with bGH PolyA sequence. This mass transfer will result in expression
vectors as shown in Figure 1, which express the variable heavy regions and the entire
kappa chains as mouse IgG2B antibodies after the mass transfer.
The vector, pSymvc20, can contain the mouse constant regions of the heavy chain of the
IgA, IgG2A, IgG2B, IgE or IgGl genes, and is thus capable of expressing any of the relevant
mouse immunoglobulln Isotypes of choice.
(c) Expression of an anti-ovalbumin recombinant polyclonal antibody
By mass transfer, the sequences encoding the variable region of the heavy chain, the promoters
and the entire kappa chain are moved from a phage vector library to isotype-enco-
ding vectors resulting in a polyclonal mammalian expression vector composition. This is followed
by transfection and site-specific integration into a CHO-Flp-in cell line, generating a
recombinant polyclonal antibody manufacturing cell line. This latter cell line is generated by
targeting the gene of interest encoding each member of the recombinant polyclonal protein
into the same specific location in the genome of each transfected cell, and at the same time
integrating only one copy of the expression construct containing said nucleic acid sequence in
each transfected cell.
The cell cultures and the transfection and selection procedure is the same as described in
example 3 (e.l-e.3).
(d) monitoring composition stability
To ensure that the mass transfer and transfection into mammalian cells occur without introduction
of considerable bias with regard to cloning, expression and diversity among the individual
clones the process of mass transfer and mammalian expression can be monitored with
the following methods:
1) Analysis of generation time of the pools of cells from each transfected construct,
2) Analysis of expression level of the pools of celts from each transfected construct,
3) Analysis by RFLP on single cells,
4) ELISA of the produced antibody mixture,
5) Mass spectrometry of the produced antibody mixture,
6) Analysis by Taqman PCR (real-time PCR) on a defined batch size using V region-specific
primers to identify ratio's of each different clone, or
7) Analysis of the batch over time cultivated with and without selection pressure (hygromy-
cin) can be performed for the following parameters:
a) clonal distribution
b) protein expression levels (quantity and distribution)
c) genomic stability
d) effects of adaptation to serum-free media.
(e ) Production of an anti-ovalbumin recombinant polyclonal antibody composition
The recombinant polyclonal antibody producing CHO-Flp-in cell line is grown in different culture
systems, including conventional small culture flasks, Nunc multilayer cell factories, and
small high yield bloreactors (MiniPerm, INTEGRA-CELLJne). Further, the cell lines are adapted
to serum free suspension for subsequent cultivation in spinner flasks, hollow fibers, and bio-
reactors.
The media used to grow the selected cell lines are serum free, protein free or chemically defined
media as recommended by the manufacturer (invitrogen, B&D, Hyclone).
Supernatants from attached or suspension cells that are cultured without selection (hygromy-
cin) are collected. The collected supernatants are analyzed and characterized as described
(3f). Production yields, functionality, and quality of the produced antibodies are checked
during and after growth of the cells under fed batch or perfusion conditions. Cells in suspension
are used for inoculation of larger spinner flasks or bioreactors.
The polyclonal antibody from the collected supernatants is purified for later use in animal
studies.
Other embodiments and uses of the invention will be apparent to those skilled in the art from
consideration of the specification and practice of the invention disclosed herein. It is intended
that the specification and examples be considered exemplary only, with the true scope and
spirit of the invention being indicated by the following claims.
WE CLAIM:
1. A method for generating a collection of cells suitable as a recombinant polyclonal
manufacturing cell line, said method comprising:
a) providing a library of vectors comprising a population of variant nucleic acid sequences,
wherein each of said vectors comprises 1) one single copy of a distinct nucleic acid sequence
encoding a distinct member of a polyclonal protein comprising distinct members that
bind a particular antigen and 2) one or more recombinase recognition sequences;
b) introducing said library of vectors into a host cell line, wherein the genome of each
individual cell of said host cell line comprises recombinase recognition sequences, matching
those of the vector, at a single specific site in its genome;
c) ensuring the presence in said cells of one or more recombinases so that the variant
nucleic acid sequences of step (a) are integrated site-specifically in the cells of the host cell
line, where said one or more recombinases is/are either i) expressed by said cells into which
said nucleic acid sequence is introduced; ii) operatively encoded by the vectors of step a; iii)
provided through expression from a second vector; or iv) provided to the cell as a protein;
and
d) selecting cells comprising an integrated copy from said library of variant nucleic
acid sequences.
2. The method as claimed in claim 1, wherein the polyclonal protein is not naturally
associated with said collection of cells.
3. The method as claimed in claim 1 or 2, wherein said polyclonal protein is a polyclonal
antibody or antibody fragment.
4. The method as claimed in claim 1 or 2, wherein said polyclonal protein is a polyclonal
T cell receptor or T cell receptor fragment.
5. The method as claimed in any one of the preceding claims, wherein said library of
vectors is introduced into said host cell line by bulk transfection of a collection of said host
cells with said library of vectors.
6. The method as claimed in any one of claims 1-4, wherein said library of vectors is
introduced into said host cell line by semi-bulk transfection of aliquots of said host cells with
fractions comprising 5 to 50 individual vectors of said library of vectors, and said cells are
pooled to form a collection of cells suitable as a recombinant polyclonal manufacturing cell
line prior or subsequent to the selection of step (d).
7. The method as claimed in any one of claims 1-4, wherein said library of vectors for
site-specific integration is introduced into said host cell line by transfecting said host cells
separately with individual members of said library of vectors, and said cells are pooled to
form a collection of cells suitable as a recombinant polyclonal manufacturing cell line prior or
subsequent to the selection of step (d).
8. The method as claimed in any one of the preceding claims, wherein the population of
variant nucleic acids in step (a) are isolated or identified by the aid of a screening procedure
that enables identification and/or isolation of nucleic acids that encode protein which bind
said particular antigen.
9. The method as claimed in claim 8, wherein the screening procedure aomprises a
biopanning step and/or an immunodetection assay.
10 The method as claimed in claim 8 or 9, wherein said screening procedure is selected
from the group consisting of phage display, ribosome display, DNA display, RNA-peptide
display, covalent display, bacterial surface display, yeast surface display, cukaryotic virus
display, ELISA and ELISPOT.
11. The method as claimed ii\any one of the preceding claims, wherein said library of
variant nucleic acid sequences comprises at least 3 variant nucleic acid sequences.
12. The method as claimed in any one of the preceding claims., wherein individual
members of said library of variant nucleic acid sequences are integrated in a single predefined
genomic locus of individual cells in said collection of cells, said locus being capable of
mediating high-level expression of each member of said recombinant polyclonal protein.
13. The method as claimed in any one of the preceding claims, wherein each distinct
nucleic acid sequence comprises a pair of gene segments that encode a member of a
polyclonal protein comprised of two different polypeptide chains.
14. The method as claimed in claim 13, wherein said pair of gene segments comprise an
antibody heavy chain variable region encoding sequence and an antibody light chain variable
region encoding sequence.
15. The method as claimed in claim 13, wherein said pair of gene segments comprise a T
cell receptor alpha chain variable region encoding sequence and a T cell receptor beta chain
variable region encoding sequence.
16. The method as claimed in claim 13, wherein said pair of gene segments comprise a T
cell receptor gamma chain variable region encoding sequence and a T cell receptor delta
chain variable region encoding sequence.
17. The method as claimed in any one of the preceding claims, wherein said library of
variant nucleic acid sequences comprises a naturally occurring diversity located within the
variant nucleic acid sequences.
18. The method as claimed in claim 17, wherein the naturally occurring diversity is
located in CDR regions present in said variant nucleic acid sequences.
19. The method as claimed in any one of the preceding claims, wherein said collection of
cells is derived from a mammalian cell line or cell type.
20. The method as claimed in claim 19, wherein said mammalian cell line is selected
from the group consisting of Chinese hamster ovary (CHO) cells, COS cells, BHK cells,
YB2/0, NIH 3T3, myeloma cells, fibroblasts, HeLa, HEK 293, PER.C6, and cell lines derived
thereof.
21. A method for the manufacture of a polyclonal protein, wherein said polyclonal protein
comprises distinct members that bind a particular antigen, said method comprising:
a) providing a collection of cells comprising a library of variant nucleic acid
sequences, where each of said nucleic acid sequences encode a distinct member of said
polyclonal protein and where each of said nucleic acid sequences are integrated at the same,
single site of the genome of each individual cell in said collection of cells;
b) culturing said collection of cells under conditions facilitating expression of said
polyclonal protein: and
c) recovering said expressed polyclonal protein from the cell culture cells or cell
culture supernatant.
22. The method as claimed in claims 21, wherein the collection of cells in step (a) is
generated as claimed in the method of any one of claims 1 -20.
23. The method as claimed in claim 21 or 22, wherein the polyclonal protein is not
naturally associated with said collection of cells.
24. The method as claimed in any one of claims 21-23, wherein the library of variant
nucleic acids in step (a) are isolated or identified in an earlier step by the aid of a screening
procedure that enables identification and/or isolation of nucleic acids that encode protein
which bind said particular antigen.
25. The method as claimed in claim 24, wherein the screening procedure comprises a
biopanning step and/or an immunodetection assay.
26. The method as claimed in claim 24 or 25, wherein said screening procedure is
selected from the group consisting of phage display, ribosome display, DNA display, RNA-
peptide display, covalent display, bacterial surface display, yeast surface display, eukaryotic
virus display, ELISA, and ELISPOT.
27. The method as claimed! in any one of claims 21-26, wherein said polyclonal protein is a
polyclonal antibody or antibody fragment.
28. The method as claimed in any one of claims 21-26, wherein said polyclonal protein is
a polyclonal T cell receptor or T cell receptor fragment.
29. The method as claimed in any of claims 21-28, wherein the relative expression levels
of the variant nucleic acid sequences are monitored.
30. The method as claimed in claim 29, wherein said expression levels are monitored at
mRNA level and/or protein level.
31. The method as claimed in claim 29 or 30, wherein the culturing in step (b) is
terminated at the latest when the relative expression levels are outside a predetermined range.
32. A library of vectors for site-specific integration comprising a population of naturally
occurring variant nucleic acid sequences, wherein each of said vectors comprises 1) one copy
of a distinct nucleic acid sequence encoding a distinct member of a polyclonal protein that
binds a particular antigen and 2) one or more recombinase recognition sequences.
33. The library as claimed in claim 32, wherein said population of naturally occurring
variant nucleic acid sequences encode a polyclonal antibody or antibody fragment.
34. The library as claimed in claim 32, wherein said population of naturally occurring
variant nucleic acid sequences encode a polyclonal T cell receptor T cell receptor fragment.
35. The library as claimed in any one of claims 32-34, wherein each member of said
library of vectors further comprises a recombinase encoding nucleic acid sequence.
The present invention provides a method for preparing a polyclonal cell line
where each cell produces a protein that binds one single target. The method utilises site
specific integration of different expression vectors into one single batch of host cells so that
the batch of cells expresses the different expression vectors to produce the polyclonal protein.
The expression vectors each encodes a member of the polyclonal binding protein and one or
more recombinases. Also provided is a method for producing a polyclonal protein, a
polyclonal cell line, and a library of expression vectors.

Documents:


Patent Number 224714
Indian Patent Application Number 01233/KOLNP/2005
PG Journal Number 43/2008
Publication Date 24-Oct-2008
Grant Date 22-Oct-2008
Date of Filing 24-Jun-2005
Name of Patentee SYMPHOGEN A/S
Applicant Address ELEKTROVEJ, BYGNING 375, DK-2800, KONGENS LYNGBY
Inventors:
# Inventor's Name Inventor's Address
1 HAURUM JOHN S GUSTAV ADOLFSGADE 6, 3.TH., DK-2100, KOBENHAVN O
2 WIBERG FINN C VINKEL VEJ 16, DK-3520 FARUM
3 COLJEE VINCENT W HESLEGAARDSVEJ 8, LEJLIGHED 0-4 DK-2900 HELLERUP
4 SHARON JACQUELINE 478 CLINTON ROAD, CHESTNUT HILL, MA 02467
5 YANG CHIOU-YING 336 HO TSO ST. 5F, 402 TAICHUNG
PCT International Classification Number C12N 15/10
PCT International Application Number PCT/DK2004/000001
PCT International Filing date 2004-01-07
PCT Conventions:
# PCT Application Number Date of Convention Priority Country
1 60/476,018 2003-06-05 Denmark
2 60/438,403 2003-01-07 Denmark
3 PA 2003 00008 2003-01-07 Denmark