# Patent

## Title
Rapid way to obtain high expression clones of mammalian cells using a methylcellulose and immunoprecipitation screening method

## Abstract

The invention provides a genetic screening method for identifying a transfected cell expressing the polypeptide of interest. The methods allows for high throughput screening of recombinant cells for elevated levels of expression of the polypeptide of interest. The invention also provides capture media, formulations and methods of making and using thereof.

## Background
This application claims priority to U.S. provisional application Ser. No. 60/498,828, filed on Aug. 29, 2003. The contents of provisional application Ser. No. 60/498,828 are incorporated by reference herein.


BACKGROUND OF THE INVENTION
1. Field of the Invention
The present invention pertains to genetic screening methods, related cells and culturing media thereof, useful in identifying clones of mammalian cells expressing the polypeptide of interest. The methods allows for high throughput screening of recombinant cells for elevated levels of expression of polypeptide of interest. The present invention also provides a screening method useful in screening and isolating clones of mammalian cells expressing high levels of immunoglobulin.
2. Related Background
Recombinant proteins (r-proteins) are an emerging class of therapeutic agents. To obtain a stable clone for recombinant protein production usually requires the transfection of cells with an expression vector containing gene of interest and a dominant genetic marker. Typically, for the selection of stable transfectants, a selectable marker such as an antibiotic resistance gene is transfected along with the target gene of interest. Selection is then carried out in the presence of the specific antibiotic. Cells that have taken up the expression vector DNA survive in appropriate selection media.
Currently, cloning of stably transfected cells relies on performing a series of limiting dilution procedures, a time consuming and labor-intensive process. For example, many commonly used mammalian expression systems are based on stably transfected Chinese Hamster Ovary (CHO) cells and transfection efficiencies in this system range from 10-60% of cells taking up the vector DNA. However, a wide variation in recombinant gene expression exists among clones that stably incorporate the foreign DNA into the genome due to the position effect by which different regions of the chromosome modulate the expression of the transfected gene. Many hundreds, even thousands of transfected clones are typically screened for random high producers because of the random variation in recombinant protein production. Therefore in many cases, screening for high producers has been one of the rate limiting procedures in developing of cell lines expressing r-proteins due to the huge amount of cells to screen and the complicated assays to perform.
Soluble proteins interact with their corresponding antibody to form a precipitate in solid or semisolid substrates such as agarose. One such application is the immunoplate assay used to detect mouse myeloma mutants. Briefly, cells are cloned in soft agarose over feeder layers that undergo contact inhibition. Antibody or antigen reactive with the immunoglobulin that is secreted by the cloned cells is added to the plate and diffuses through the agarose forming an antigen-antibody precipitate surrounding the clone. This precipitate appears as a collection of dark granules and specks under low or medium power with an inverted microscope. This assay was used not only to look for mutants of hybridoma and myeloma cells, but also to clone hybridomas and identify subclones producing the desired antibody. It can also be used to identify high producers.
However, several difficulties were reported previously when using this semi-solid agarose technique for screening clones producing the desired antibody. For example, poor growth of mammalian cells is caused by inability to utilize the correct temperature to seed cells while agarose is cooling. Another common problem is the difficulty in viewing the precipitate in the agarose media even under a microscope. It is also difficult to correlate the precipitate size to the level of protein secretion.
Accordingly, there is a need to provide improved and/or modified screening methods, which overcome and/or substantially ameliorate one or more of these and other problems known in the art.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 is a representative showing of a halo-producing NSO cell.



SUMMARY OF THE INVENTION
The present invention relates to genetic screening methods, related cells and culturing media thereof, useful in identifying and/or characterizing clones of mammalian cells expressing the polypeptide of interest. The methods allow for high throughput screening of recombinant cells for elevated levels of expression of polypeptide of interest.
In one embodiment, the present invention provides a method for selecting high expression cell clones expressing a polypeptide of interest, comprising: (a) selecting high expression cell clones among cells cultured in a semi-solid culture medium and expressing said polypeptide of interest, wherein said cells are contacted with a capture molecule that interacts with the polypeptide of interest such that said interaction indicates relative expression of said polypeptide for each cell or group of cells. In addition, the present invention further relates to a cell clone identified by such a method.
The cells may be any cell type including prokaryotic and eukaryotic cells. Prokaryotic cells may include but are not limited to bacterial cells or blue-green algae cells. Eukaryotic cells may include but are not limited to mammalian cells, yeast cells or insect cells. Preferably, the cells are eukaryotic cells. In a preferred embodiment, suitable cell lines that can be used according to the present invention include any transformed or immortalized mammalian cell line. Such cell lines include myeloma cell lines, such as Sp2/0, NSO, NS1, CHO, BHK, Ag653, P3X63Ag8.653 cells (ATCC Accession Number CRL-1580) and SP2/0-Ag14 cells (ATCC Accession Number CRL-1851), COS-1 (e.g., ATCC CRL 1650), COS-7 (e.g., ATCC CRL-1651), HEK293, BHK21 (e.g., ATCC CAL-10), CHO (e.g., ATCC CRL 1610, CHO DXB-11, CHO DG44), BSC-1 (e.g., ATCC CAL-26) cell lines, HepG2 cells, P3X63Ag8.653, 293 cells, HeLa cells, NIH 3T3, CDS-1, CDS-7, NIH 273, and the like, or any cells derived therefrom, including cell fusions of the above, such as to protein producing cells, such as B-cells, antibody producing cells, isolated or cloned spleen or lymph node cells, and the like.
The present invention further provides a method of isolating a polypeptide of interest comprising, in addition to above mentioned step (a), harvesting and culturing the cell clones; and isolating the polypeptide of interest therefrom. Moreover, the present invention further relates to at least one polypeptide of interest isolated by such a method.
The polypeptide of interest may be any suitable soluble or membrane-bound polypeptide including, for example but not limited to, an antibody, a growth factor, a hormone, a biopharmaceutical, a receptor or a synthetic polypeptide of interest or portions thereof.
In a preferred embodiment, the polypeptide of interest is a diagnostic or a therapeutic protein. The diagnostic or therapeutic protein may be an immunoglobulin, a cytokine, an integrin, an antigen, a growth factor, a receptor or fusion protein thereof, any fragment thereof, or any structural or functional analog thereof. The diagnostic or therapeutic protein may also be a cell cycle protein, a hormone, a neurotransmitter, a blood protein, an antimicrobial, any fragment thereof, or any structural or functional analog thereof.
In a preferred embodiment, the cell clones selected using the method of the present invention may produce an immunoglobulin or fragment thereof derived from a rodent or a primate. Alternatively, the immunoglobulin or fragment thereof may be chimeric or engineered. Indeed, the present invention further contemplates methods of identifying cell clones that express an immunoglobulin or fragment thereof which is humanized, CDR grafted, phage displayed, transgenic mouse-produced, optimized, mutagenized, randomized or recombined.
The immunoglobulin or fragment thereof may include, but not limited to, IgG1, IgG2, IgG3, IgG4, IgA1, IgA2, IgD, IgE, IgM, and any structural or functional analog thereof. In a specific embodiment, the immunoglobulin expressed in the cells, cell lines, and cell cultures of the present invention is infliximab. Furthermore, the immunoglobulin fragment isolated using the method of the present invention may include, but is not limited to, F(ab′)2, Fab′, Fab, Fc, Facb, Fc′, Fd, Fv and any structural or functional analog thereof. In a specific embodiment, the immunoglobulin fragment is abciximab.
The polypeptide of interest may further include, but not limited to an antigen, a cytokine, an integrin, an antigen, a growth factor, a hormone, a neurotransmitter, a receptor or fusion protein thereof, a blood protein, an antimicrobial, any fragment thereof, and any structural or functional analog of any of the foregoing.
In one embodiment of the present invention, the polypeptide of interest is an integrin. Examples of integrins contemplated by the present invention include, but are not limited to, α1, α2, α3, α4, α5, α6, α7, α8, α9, αD, αL, αM, αV, αX, αIIb, αIELb, β1, β2, β3, β4, β5, β6, β7, β8, α1β1, α2β1, α3β1, α4β1, α5β1, α6β1, α7β1, α8β1, α9β1, α4β7, α6β4, αDβ2, αLβ2, αMβ2, αVβ3, αVβ5, αVβ6, αVβ8, αXβ2, αIIbβ3, αIELbβ7, and any structural or functional analog thereof.
In an embodiment of the present invention, the polypeptide of interest is an antigen. The antigen may be derived from a number of sources including, but not limited to, a bacterium, a virus, a blood protein, a cancer cell marker, a prion, a fungus, and any structural or functional analog thereof.
In yet another embodiment, the polypeptide of interest is a growth factor. Examples of the growth factors contemplated by the present invention include, but are not limited to, a human growth factor, a platelet derived growth factor, an epidermal growth factor, a fibroblast growth factor, a nerve growth factor, a chorionic gonadotropin, an erythrpoeitin, an activin, an inhibin, a bone morphogenic protein, a transforming growth factor, an insulin-like growth factor, and any structural or functional analog thereof.
In yet another embodiment, the polypeptide of interest is a cytokine. Examples of cytokines contemplated by the present invention include, but are not limited to, an interleukin, an interferon, a colony stimulating factor, a tumor necrosis factor, an adhesion molecule, an angiogenin, an annexin, a chemokine, and any structural or functional analog thereof.
In another embodiment, the polypeptide of interest is a growth hormone. The growth hormone may include, but is not limited to, a human growth hormone, a prolactin, a follicle stimulating hormone, a chorionic gonadotrophin, a leuteinizing hormone, a thyroid stimulating hormone, a parathyroid hormone, an estrogen, a progesterone, a testosterone, an insulin, a proinsulin, and any structural or functional analog thereof.
The present invention further relates to the expression of neurotransmitters using the method taught herein. Examples of neurotransmitters include, but are not limited to, an endorphin, a coricotropin releasing hormone, an adrenocorticotropic hormone, a vasopressin, a giractide, an N-acytlaspartylglutamate, a peptide neurotransmitter derived from pre-opiomelanocortin, any antagonists thereof, and any agonists thereof.
In another embodiment, the polypeptide of interest is a receptor or fusion protein. The receptor or fusion protein may be, but is not limited to, an interleukin-1, an interleukin-12, a tumor necrosis factor, an erythropoeitin, a tissue plasminogen activator, a thrombopoetin, and any structural or functional analog thereof.
Alternatively, recombinant blood proteins may be isolated by the method of the present invention. Such recombinant proteins include, but are not limited to, an erythropoeitin, a thrombopoeitin, a tissue plasminogen activator, a fibrinogen, a hemoglobin, a transferrin, an albumin, a protein c, and any structural or functional analog thereof.
In another embodiment, the polypeptide of interest is a recombinant antimicrobial agent. Examples of antimicrobial agents contemplated by the present invention include, for example, a beta-lactam, an aminoglycoside, a polypeptide antibiotic, and any structural or functional analog thereof.
The present invention further provides semi-solid capture medium comprising cell growth medium, a gelatinization agent and a capture molecule selected from a receptor or a ligand of or an antibody against the polypeptide of interest. The gelatinization agent may be any polymer that when dissolved in an aqueous cell growth medium, forms semi-solid gel under the temperature suitable for culturing cells. The gelatinization agent may be selected from, but not limited to, agar, agarose, methylcellulose, matrigel, collagen, gelatin, or other similar materials. Preferably, the gelatinization agent is methylcellulose. Such media composition and formulation of the present invention allow the identification of cells expressing the polypeptide of interest by monitoring the precipitate halo formed between the polypeptide of interest and the capture molecule. Accordingly the present invention provides specific media, formulations and methods of making and using thereof.
DESCRIPTION OF THE INVENTION
For many commonly used mammalian expression systems, cloning of stably transfected cells is a time consuming and labor-intensive process. Many hundreds, even thousands of transfected clones are typically screened for high producers because of the random variation in recombinant protein production. The present invention relates to a rapid way to screen for clones producing high levels of polypeptide of interest. The method is based on the precipitates formed between the polypeptide of interest and its corresponding antibody, receptor and/or ligand in a semi-solid capture medium. A halo-like antigen-antibody or receptor-ligand precipitate surrounding the colonies can be observed, the size of which correlates to the level of polypeptide of interest production.
It is well known in the art that if the transfected cells have been in continuous culture for a long time, or the cells in culture are not derived from a single cell clone, they may need to be recloned. The present invention also provides a method to rapidly achieve this goal.
In one embodiment of the present invention, methods are provided for selecting high expression cell clones expressing a polypeptide of interest, comprising: (a) selecting high expression cell clones among cells cultured in a semi-solid culture medium and expressing said polypeptide of interest, wherein said cells are contacted with a capture molecule that interacts with the polypeptide of interest such that said interaction indicates relative expression of said polypeptide for each cell or group of cells. In a preferred embodiment, the semi-solid capture medium is methylcellulose or agar based.
In another embodiment, the present invention provides a method of isolating a polypeptide of interest comprising the steps in addition to above mentioned (a), harvesting and culturing the cell clone; and isolating the polypeptide of interest therefrom.
Polypeptides of Interest
The polypeptides of interest include, but are not limited to, immunoglobulins, integrins, antigens, growth factors, cell cycle proteins, cytokines, hormones, neurotransmitters, receptor or fusion proteins thereof, blood proteins, antimicrobials, or fragments, or structural or functional analogs thereof. These following descriptions do not serve to limit the scope of the invention, but rather illustrate the breadth of the invention.
For example, in one embodiment of the invention, the immunoglobulin may be derived from human or non-human polyclonal or monoclonal antibodies. Specifically, these immunoglobulins (antibodies) may be recombinant and/or synthetic human, primate, rodent, mammalian, chimeric, humanized or CDR-grafted, antibodies and anti-idiotype antibodies thereto. These antibodies can also be produced in a variety of truncated forms in which various portions of antibodies are joined together using genetic engineering techniques. As used presently, an “antibody,” “antibody fragment,” “antibody variant,” “Fab,” and the like, include any protein- or peptide-containing molecule that comprises at least a portion of an immunoglobulin molecule, such as but not limited to at least one CDR of a heavy or light chain or a ligand binding portion thereof, a heavy chain or light chain variable region, a heavy chain or light chain constant region, a framework region, or any portion thereof, which may be expressed in the cell culture of the present invention. Such antibodies optionally further affect a specific ligand, such as but not limited to, where such antibody modulates, decreases, increases, antagonizes, agonizes, mitigates, alleviates, blocks, inhibits, abrogates and/or interferes with at least one target activity or binding, or with receptor activity or binding, in vitro, in situ and/or in vivo.
In one embodiment of the invention, such antibodies, or functional equivalents thereof, may be “human,” such that they are substantially non-immunogenic in humans. These antibodies may be prepared through any of the methodologies described herein or well know in the art.
The term “antibody” is further intended to encompass antibodies, digestion fragments, specified portions and variants thereof, including antibody mimetics or comprising portions of antibodies that mimic the structure and/or function of an antibody or specified fragment or portion thereof, including single chain antibodies and fragments thereof, that are expressed in the cell culture of the present invention. The present invention thus encompasses antibody fragments capable of binding to a biological molecule (such as an antigen or receptor) or portions thereof, including but not limited to Fab (e.g., by papain digestion), Fab′ (e.g., by pepsin digestion and partial reduction) and F(ab′)2 (e.g., by pepsin digestion), facb (e.g., by plasmin digestion), pFc′ (e.g., by pepsin or plasmin digestion), Fd (e.g., by pepsin digestion, partial reduction and reaggregation), Fv or scFv (e.g., by molecular biology techniques) fragments. See, e.g., Current Protocols in Immunology, (Coligan et al., John Wiley & Sons, Inc., NY, N.Y. 1992-2003).
The nature and source of the polypeptide of interest expressed in the cell clones of the present invention are not limited. The following is a general discussion of the variety of proteins, peptides and biological molecules that may be used in the in accordance with the teachings herein. These descriptions do not serve to limit the scope of the invention, but rather illustrate the breadth of the invention.
Thus, an embodiment of the present invention may include the production of one or more growth factors. Briefly, growth factors are hormones or cytokine proteins that bind to receptors on the cell surface, with the primary result of activating cellular proliferation and/or differentiation. Many growth factors are quite versatile, stimulating cellular division in numerous different cell types; while others are specific to a particular cell-type. The following Table 1 presents several factors, but is not intended to be comprehensive or complete, yet introduces some of the more commonly known factors and their principal activities.







TABLE 1







Growth Factors










Factor
Principal Source
Primary Activity
Comments





Platelet Derived
Platelets, endothelial
Promotes proliferation of
Dimer required for


Growth Factor
cells, placenta.
connective tissue, glial and
receptor binding.


(PDGF)

smooth muscle cells. PDGF
Two different




receptor has intrinsic
protein chains, A




tyrosine kinase activity.
and B, form 3





distinct dimer





forms.


Epidermal
Submaxillary gland,
promotes proliferation of
EGF receptor has


Growth Factor
Brunners gland.
mesenchymal, glial and
tyrosine kinase


(EGF)

epithelial cells.
activity, activated





in response to EGF





binding.


Fibroblast
Wide range of cells;
Promotes proliferation of
Four distinct


Growth Factor
protein is associated
many cells including
receptors, all with


(FGF)
with the ECM; nineteen
skeletal and nervous system;
tyrosine kinase



family members.
inhibits some stem cells;
activity. FGF



Receptors widely
induces mesodermal
implicated in



distributed in bone,
differentiation. Non-
mouse mammary



implicated in several
proliferative effects include
tumors and



bone-related diseases.
regulation of pituitary and
Kaposi's sarcoma.




ovarian cell function.



NGF

Promotes neurite outgrowth
Several related




and neural cell survival.
proteins first





identified as proto-





oncogenes; trkA





(trackA), trkB,





trkC.


Erythropoietin
Kidney.
Promotes proliferation and
Also considered a


(Epo)

differentiation of
‘blood protein,’ and




erythrocytes.
a colony





stimulating factor.


Transforming
Common in
Potent keratinocyte growth
Related to EGF.


Growth Factor a
transformed cells,
factor.



(TGF-a)
found in macrophages





and keratinocytes.




Transforming
Tumor cells, activated
Anti-inflammatory
Large family of


Growth Factor v
TH1 cells (T-helper)
(suppresses cytokine
proteins including


(TGF-b)
and natural killer (NK)
production and class II
activin, inhibin and



cells.
MHC expression),
bone morpho-




proliferative effects on
genetic protein.




many mesenchymal and
Several classes and




epithelial cell types, may
subclasses of cell-




inhibit macrophage and
surface receptors.




lymphocyte proliferation.



Insulin-Like
Primarily liver,
Promotes proliferation of
Related to IGF-II


Growth Factor-I
produced in response to
many cell types, autocrine
and proinsulin, also


(IGF-I)
GH and then induces
and paracrine activities in
called



subsequent cellular
addition to the initially
Somatomedin C.



activities, particularly
observed endocrine
IGF-I receptor, like



on bone growth.
activities on bone.
the insulin receptor,





has intrinsic





tyrosine kinase





activity. IGF-I can





bind to the insulin





receptor.


Insulin-Like
Expressed almost
Promotes proliferation of
IGF-II receptor is


Growth
exclusively in
many cell types primarily of
identical to the


Factor-II
embryonic and
fetal origin. Related to
mannose-6-


(IGF-II)
neonatal tissues.
IGF-I and proinsulin.
phosphate receptor





that is responsible





for the integration





of lysosomal





enzymes.









Additional growth factors that may be produced in accordance with the present invention include Activin (Vale et al., 321 Nature 776 (1986); Ling et al., 321 Nature 779 (1986)), Inhibin (U.S. Pat. Nos. 4,737,578; 4,740,587), and Bone Morphongenic Proteins (BMPs) (U.S. Pat. No. 5,846,931; Wozney, Cellular & Molecular Biology of Bone 131-167 (1993)).
In addition to the growth factors discussed above, the present invention may target or use other cytokines. Secreted primarily from leukocytes, cytokines stimulate both the humoral and cellular immune responses, as well as the activation of phagocytic cells. Cytokines that are secreted from lymphocytes are termed lymphokines, whereas those secreted by monocytes or macrophages are termed monokines. A large family of cytokines are produced by various cells of the body. Many of the lymphokines are also known as interleukins (ILs), because they are not only secreted by leukocytes, growth factors targeted to cells of hematopoietic origin. The list of identified interleukins grows continuously. See, e.g., U.S. Pat. No. 6,174,995; U.S. Pat. No. 6,143,289; Sallusto et al., 18 Annu. Rev. Immunol. 593 (2000); Kunkel et al., 59 J. Leukocyto Biol. 81 (1996).
Additional growth factor/cytokines encompassed in the present invention include pituitary hormones such as human growth hormone (HGH), follicle stimulating hormones (FSH, FSHα, and FSHβ), Human Chorionic Gonadotrophins (HCG, HCGα, HCGβ), uFSH (urofollitropin), Gonatropin releasing hormone (GRH), Growth Hormone (GH), leuteinizing hormones (LH, LHα, LHβ), somatostatin, prolactin, thyrotropin (TSH, TSHα, TSHβ), thyrotropin releasing hormone (TRH), parathyroid hormones, estrogens, progesterones, testosterones, or structural or functional analog thereof. All of these proteins and peptides are known in the art.
The cytokine family also includes tumor necrosis factors, colony stimulating factors, and interferons. See, e.g., Cosman, 7 Blood Cell (1996); Gruss et al., 85 Blood 3378 (1995); Beutler et al., 7 Annu. Rev. Immunol. 625 (1989); Aggarwal et al., 260 J. Biol. Chem. 2345 (1985); Pennica et al., 312 Nature 724 (1984); R & D Systems, Cytokine Mini-Reviews, at http://www.rndsystems.com.
Several cytokines are introduced, briefly, in Table 2 below.







TABLE 2







Cytokines









Cytokine
Principal Source
Primary Activity





Interleukins
Primarily macrophages but also
Costimulation of APCs and T cells;


IL1-a and -b
neutrophils, endothelial cells,
stimulates IL-2 receptor production



smooth muscle cells, glial cells,
and expression of interferon-γ; may



astrocytes, B- and T-cells,
induce proliferation in non-lymphoid



fibroblasts, and keratinocytes
cells.


IL-2
CD4+ T-helper cells, activated TH1
Major interleukin responsible for



cells, NK cells
clonal T-cell proliferation. IL-2 also




exerts effects on B-cells,




macrophages, and natural killer (NK)




cells. IL-2 receptor is not expressed




on the surface of resting T-cells, but




expressed constitutively on NK cells,




that will secrete TNF-α, IFN-γ and




GM-CSF in response to IL-2, which in




turn activate macrophages.


IL-3
Primarily T-cells
Also known as multi-CSF, as it




stimulates stem cells to produce all




forms of hematopoietic cells.


IL-4
TH2 and mast cells
B cell proliferation, eosinophil and




mast cell growth and function, IgE and




class II MHC expression on B cells,




inhibition of monokine production


IL-5
TH2 and mast cells
eosinophil growth and function


IL-6
Macrophages, fibroblasts,
IL-6 acts in synergy with IL-1 and



endothelial cells and activated T-
TNF-α in many immune responses,



helper cells. Does not induce
including T-cell activation; primary



cytokine expression.
inducer of the acute-phase response in




liver; enhances the differentiation of




B-cells and their consequent




production of immunoglobulin;




enhances Glucocorticoid synthesis.


IL-7
thymic and marrow stromal cells
T and B lymphopoiesis


IL-8
Monocytes, neutrophils,
Chemoattractant (chemokine) for



macrophages, and NK cells
neutrophils, basophils and T-cells;




activates neutrophils to degranulate.


IL-9
T cells
hematopoietic and thymopoietic




effects


IL-10
activated TH2 cells, CD8+ T and B
inhibits cytokine production, promotes



cells, macrophages
B cell proliferation and antibody




production, suppresses cellular




immunity, mast cell growth


IL-11
stromal cells
synergisitc hematopoietic and




thrombopoietic effects


IL-12
B cells, macrophages
proliferation of NK cells, INF-g




production, promotes cell-mediated




immune functions


IL-13
TH2 cells
IL-4-like activities


IL-18
macrophages/Kupffer cells,
Interferon-gamma-inducing factor



keratinocytes, glucocorticoid-
with potent pro-inflammatory activity



secreting adrenal cortex cells, and




osteoblasts



IL-21
Activated T cells
IL21 has a role in proliferation and




maturation of natural killer (NK) cell




populations from bone marrow, in the




proliferation of mature B-cell




populations co-stimulated with anti-




CD40, and in the proliferation of T




cells co-stimulated with anti-CD3.


IL-23
Activated dendritic cells
A complex of p19 and the p40 subunit




of IL-12. IL-23 binds to IL-12R beta 1




but not IL-12R beta 2; activates Stat4




in PHA blast T cells; induces strong




proliferation of mouse memory T




cells; stimulates IFN-gamma




production and proliferation in PHA




blast T cells, as well as in CD45RO




(memory) T cells.


TumorNecrosis
Primarily activated macrophages.
Once called cachectin; induces the


Factor

expression of other autocrine growth


TNF-α

factors, increases cellular




responsiveness to growth factors;




induces signaling pathways that lead




to proliferation; induces expression of




a number of nuclear proto-oncogenes




as well as of several interleukins.


(TNF-β)
T-lymphocytes, particularly
Also called lymphotoxin; kills a



cytotoxic T-lymphocytes (CTL
number of different cell types, induces



cells); induced by IL-2 and antigen-
terminal differentiation in others;



T-Cell receptor interactions.
inhibits lipoprotein lipase present on




the surface of vascular endothelial




cells.


Interferons
macrophages, neutrophils and some
Known as type I interferons; antiviral


INF-a and -b
somatic cells
effect; induction of class I MHC on all




somatic cells; activation of NK cells




and macrophages.


Interferon
Primarily CD8+ T-cells, activated
Type II interferon; induces of class I


INF-γ
TH1 and NK cells
MHC on all somatic cells, induces




class II MHC on APCs and somatic




cells, activates macrophages,




neutrophils, NK cells, promotes cell-




mediated immunity, enhances ability




of cells to present antigens to T-cells;




antiviral effects.


Monocyte
Peripheral blood
Attracts monocytes to sites of vascular


Chemoattractant
monocytes/macrophages
endothelial cell injury, implicated in


Protein-1

atherosclerosis.


(MCP1)




Colony

Stimulate the proliferation of specific


Stimulating

pluripotent stem cells of the bone


Factors (CSFs)

marrow in adults.


Granulocyte-

Specific for proliferative effects on


CSF (G-CSF)

cells of the granulocyte lineage;




proliferative effects on both classes of




lymphoid cells.


Macrophage-

Specific for cells of the macrophage


CSF (M-CSF)

lineage.


Granulocyte-

Proliferative effects on cells of both


MacrophageCSF

the macrophage and granulocyte


(GM-CSF)

lineages.









Other cytokines of interest that may be produced by the invention described herein include adhesion molecules (R & D Systems, Adhesion Molecule (1996), at http://www.rndsystems.com); angiogenin (U.S. Pat. No. 4,721,672; Moener et al., 226 Eur. J. Biochem. 483 (1994)); annexin V (Cookson et al., 20 Genomics 463 (1994); Grundmann et al., 85 Proc. Natl. Acad. Sci. USA 3708 (1988); U.S. Pat. No. 5,767,247); caspases (U.S. Pat. No. 6,214,858; Thornberry et al., 281 Science 1312 (1998)); chemokines (U.S. Pat. Nos. 6,174,995; 6,143,289; Sallusto et al., 18 Annu. Rev. Immunol. 593 (2000) Kunkel et al., 59 J. Leukocyte Biol. 81 (1996)); endothelin (U.S. Pat. Nos. 6,242,485; 5,294,569; 5,231,166); eotaxin (U.S. Pat. No. 6,271,347; Ponath et al., 97(3) J. Clin. Invest. 604-612 (1996)); Flt-3 (U.S. Pat. No. 6,190,655); heregulins (U.S. Pat. Nos. 6,284,535; 6,143,740; 6,136,558; 5,859,206; 5,840,525); Leptin (Leroy et al., 271(5) J. Biol. Chem. 2365 (1996); Maffei et al., 92 Proc. Natl. Acad. Sci. USA 6957 (1995); Zhang Y. et al. (1994) Nature 372: 425-432); Macrophage Stimulating Protein (MSP) (U.S. Pat. Nos. 6,248,560; 6,030,949; 5,315,000); Neurotrophic Factors (U.S. Pat. Nos. 6,005,081; 5,288,622); Pleiotrophin/Midkine (PTN/MK) (Pedraza et al., 117 J. Biochem. 845 (1995); Tamura et al., 3 Endocrine 21 (1995); U.S. Pat. No. 5,210,026; Kadomatsu et al., 151 Biochem. Biophys. Res. Commun. 1312 (1988)); STAT proteins (U.S. Pat. Nos. 6,030,808; 6,030,780; Darnell et al., 277 Science 1630-1635 (1997)); Tumor Necrosis Factor Family (Cosman, 7 Blood Cell (1996); Gruss et al., 85 Blood 3378 (1995); Beutler et al., 7 Annu. Rev. Immunol. 625 (1989); Aggarwal et al., 260 J. Biol. Chem. 2345 (1985); Pennica et al., 312 Nature 724 (1984)).
The present invention may also be used to affect blood proteins, a generic name for a vast group of proteins generally circulating in blood plasma, and important for regulating coagulation and clot dissolution. See, e.g., Haematologic Technologies, Inc., HTI CATALOG, at www.haemtech.com. Table 3 introduces, in a non-limiting fashion, some of the blood proteins contemplated by the present invention.







TABLE 3







Blood Proteins









Protein
Principle Activity
Reference





Factor V
In coagulation, this glycoprotein pro-
Mann et al., 57 ANN. REV. BIOCHEM.



cofactor, is converted to active
915 (1988); see also Nesheim et al.,



cofactor, factor Va, via the serine
254 J. BIOL. CHEM. 508 (1979);



protease α-thrombin, and less
Tracy et al., 60 BLOOD 59 (1982);



efficiently by its serine protease
Nesheim et al., 80 METHODS



cofactor Xa. The prothrombinase
ENZYMOL. 249 (1981); Jenny et al.,



complex rapidly converts zymogen
84 PROC. NATL. ACAD. SCI. USA



prothrombin to the active serine
4846 (1987).



protease, α-thrombin. Down




regulation of prothrombinase




complex occurs via inactivation of




Va by activated protein C.



Factor VII
Single chain glycoprotein zymogen
See generally, Broze et al., 80



in its native form. Proteolytic
METHODS ENZYMOL. 228 (1981);



activation yields enzyme factor VIIa,
Bajaj et al., 256 J. BIOL. CHEM. 253



which binds to integral membrane
(1981); Williams et al., 264 J. BIOL.



protein tissue factor, forming an
CHEM. 7536 (1989); Kisiel et al., 22



enzyme complex that proteolytically
THROMBOSIS RES. 375 (1981);



converts factor X to Xa. Also known
Seligsohn et al., 64 J. CLIN. INVEST.



as extrinsic factor Xase complex.
1056 (1979); Lawson et al., 268 J.



Conversion of VII to VIIa catalyzed
BIOL. CHEM. 767 (1993).



by a number of proteases including




thrombin, factors IXa, Xa, XIa, and




XIIa. Rapid activation also occurs




when VII combines with tissue factor




in the presence of Ca, likely initiated




by a small amount of pre-existing




VIIa. Not readily inhibited by




antithrombin III/heparin alone, but is




inhibited when tissue factor added.



Factor IX
Zymogen factor IX, a single chain
Thompson, 67 BLOOD, 565 (1986);



vitamin K-dependent glycoprotein,
Hedner et al., HEMOSTASIS AND



made in liver. Binds to negatively
THROMBOSIS 39-47 (R. W. Colman, J.



charged phospholipid surfaces.
Hirsh, V. J. Marder, E. W. Salzman



Activated by factor XIα or the factor
ed., 2nd ed. J. P. Lippincott Co.,



VIIa/tissue factor/phospholipid
Philadelphia) 1987; Fujikawa et al.,



complex. Cleavage at one site yields
45 METHODS IN ENZYMOLOGY 74



the intermediate IXα, subsequently
(1974).



converted to fully active form IXaβ




by cleavage at another site. Factor




IXaβ is the catalytic component of




the “intrinsic factor Xase complex”




(factor VIIIa/IXa/Ca2+/phospholipid)




that proteolytically activates factor X




to factor Xa.



Factor X
Vitamin K-dependent protein
See Davie et al., 48 ADV. ENZYMOL



zymogen, made in liver, circulates in
277 (1979); Jackson, 49 ANN. REV.



plasma as a two chain molecule
BIOCHEM. 765 (1980); see also



linked by a disulfide bond. Factor Xa
Fujikawa et al., 11 BIOCHEM. 4882



(activated X) serves as the enzyme
(1972); Discipio et al., 16 BIOCHEM.



component of prothrombinase
698 (1977); Discipio et al., 18



complex, responsible for rapid
BIOCHEM. 899 (1979); Jackson et al.,



conversion of prothrombin to
7 BIOCHEM. 4506 (1968); McMullen



thrombin.
et al., 22 BIOCHEM. 2875 (1983).


Factor XI
Liver-made glycoprotein homodimer
Thompson et al., 60 J. CLIN. INVEST.



circulates, in a non-covalent complex
1376 (1977); Kurachi et al., 16



with high molecular weight
BIOCHEM. 5831 (1977); Bouma et



kininogen, as a zymogen, requiring
al., 252 J. BIOL. CHEM. 6432 (1977);



proteolytic activation to acquire
Wuepper, 31 FED. PROC. 624 (1972);



serine protease activity. Conversion
Saito et al., 50 BLOOD 377 (1977);



of factor XI to factor XIa is catalyzed
Fujikawa et al., 25 BIOCHEM. 2417



by factor XIIa. XIa unique among
(1986); Kurachi et al., 19 BIOCHEM.



the serine proteases, since it contains
1330 (1980); Scott et al., 69 J. CLIN.



two active sites per molecule. Works
INVEST. 844 (1982).



in the intrinsic coagulation pathway




by catalyzing conversion of factor IX




to factor IXa. Complex form, factor




XIa/HMWK, activates factor XII to




factor XIIa and prekallikrein to




kallikrein. Major inhibitor of XIa is




a1-antitrypsin and to lesser extent,




antithrombin-III. Lack of factor XI




procoagulant activity causes bleeding




disorder: plasma thromboplastin




antecedent deficiency.



Factor XII
Glycoprotein zymogen. Reciprocal
Schmaier et al., 18-38, and Davie,


(Hageman
activation of XII to active serine
242-267 HEMOSTASIS &


Factor)
protease factor XIIa by kallikrein is
THROMBOSIS (Colman et al., eds.,



central to start of intrinsic
J. B. Lippincott Co., Philadelphia,



coagulation pathway. Surface bound
1987).



α-XIIa activates factor XI to XIa.




Secondary cleavage of α-XIIa by




kallikrein yields β-XIIa, and




catalyzes solution phase activation of




kallikrein, factor VII and the




classical complement cascade.



Factor XIII
Zymogenic form of glutaminyl-
See McDonaugh, 340-357



peptide γ-glutamyl transferase factor
HEMOSTASIS & THROMBOSIS



XIIIa (fibrinoligase, plasma
(Colman et al., eds., J. B. Lippincott



transglutaminase, fibrin stabilizing
Co., Philadelphia, 1987); Folk et al.,



factor). Made in the liver, found
113 METHODS ENZYMOL. 364



extracellularly in plasma and
(1985); Greenberg et al., 69 BLOOD



intracellularly in platelets,
867 (1987). Other proteins known to



megakaryocytes, monocytes,
be substrates for Factor XIIIa, that



placenta, uterus, liver and prostrate
may be hemostatically important,



tissues. Circulates as a tetramer of 2
include fibronectin (Iwanaga et al.,



pairs of nonidentical subunits (A2B2).
312 ANN. NY ACAD. SCI. 56



Full expression of activity is
(1978)), a2-antiplasmin (Sakata et al.,



achieved only after the Ca2+ - and
65 J. CLIN. INVEST. 290 (1980)),



fibrin(ogen)- dependent dissociation
collagen (Mosher et al., 64 J. CLIN.



of B subunit dimer from A2′ dimer.
INVEST. 781 (1979)), factor V



Last of the zymogens to become
(Francis et al., 261 J. BIOL. CHEM.



activated in the coagulation cascade,
9787 (1986)), von Willebrand Factor



the only enzyme in this system that is
(Mosher et al., 64 J. CLIN. INVEST.



not a serine protease. XIIIa stabilizes
781 (1979)) and thrombospondin



the fibrin clot by crosslinking the α
(Bale et al., 260 J. BIOL. CHEM. 7502



and γ-chains of fibrin. Serves in cell
(1985); Bohn, 20 MOL. CELL



proliferation in wound healing, tissue
BIOCHEM. 67 (1978)).



remodeling, atherosclerosis, and




tumor growth.



Fibrinogen
Plasma fibrinogen, a large
FURLAN, Fibrinogen, IN HUMAN



glycoprotein, disulfide linked dimer
PROTEIN DATA, (Haeberli, ed., VCH



made of 3 pairs of non-identical
Publishers, N.Y.,1995); Doolittle, in



chains (Aa, Bb and g), made in liver.
HAEMOSTASIS & THROMBOSIS, 491-513



Aa has N-terminal peptide
(3rd ed., Bloom et al., eds.,



(fibrinopeptide A (FPA), factor XIIIa
Churchill Livingstone, 1994);



crosslinking sites, and 2
HANTGAN, et al., in HAEMOSTASIS &



phosphorylation sites. Bb has
THROMBOSIS 269-89 (2d ed., Forbes



fibrinopeptide B (FPB), 1 of 3 N-
et al., eds., Churchill Livingstone,



linked carbohydrate moieties, and an
1991).



N-terminal pyroglutamic acid. The g




chain contains the other N-linked




glycos. site, and factor XIIIa cross-




linking sites. Two elongated subunits




((AaBbg)2) align in an antiparallel




way forming a trinodular




arrangement of the 6 chains. Nodes




formed by disulfide rings between




the 3 parallel chains. Central node




(n-disulfide knot, E domain) formed




by N-termini of all 6 chains held




together by 11 disulfide bonds,




contains the 2 IIa-sensitive sites.




Release of FPA by cleavage




generates Fbn I, exposing a




polymerization site on Aa chain.




These sites bind to regions on the D




domain of Fbn to form proto-fibrils.




Subsequent IIa cleavage of FPB from




the Bb chain exposes additional




polymerization sites, promoting




lateral growth of Fbn network. Each




of the 2 domains between the central




node and the C-terminal nodes




(domains D and E) has parallel ahelical




regions of the Aa, Bb and g




chains having protease- (plasmin-)




sensitive sites. Another major




plasmin sensitive site is in




hydrophilic preturbance of a-chain




from C-terminal node. Controlled




plasmin degradation converts Fbg




into fragments D and E.



Fibronectin
High molecular weight, adhesive,
Skorstengaard et al., 161 Eur. J.



glycoprotein found in plasma and
BIOCHEM. 441 (1986); Kornblihtt et



extracellular matrix in slightly
al., 4 EMBO J. 1755 (1985);



different forms. Two peptide chains
Odermatt et al., 82 PNAS 6571



interconnected by 2 disulfide bonds,
(1985); Hynes, R.O., ANN. REV.



has 3 different types of repeating
CELL BIOL., 1, 67 (1985); Mosher 35



homologous sequence units.
ANN. REV. MED. 561 (1984);



Mediates cell attachment by
Rouslahti et al., 44 Cell 517 (1986);



interacting with cell surface
Hynes 48 CELL 549 (1987); Mosher



receptors and extracellular matrix
250 BIOL. CHEM. 6614 (1975).



components. Contains an Arg-Gly-




Asp-Ser (RGDS) cell attachment-




promoting sequence, recognized by




specific cell receptors, such as those




on platelets. Fibrin-fibronectin




complexes stabilized by factor XIIIa-




catalyzed covalent cross-linking of




fibronectin to the fibrin a chain.



b2-
Also called b2I and Apolipoprotein
See, e.g., Lozier et al., 81 PNAS


Glycoprotein I
H. Highly glycosylated single chain
2640-44 (1984); Kato & Enjyoi 30



protein made in liver. Five repeating
BIOCHEM. 11687-94 (1997); Wurm,



mutually homologous domains
16 INT'L J. BIOCHEM. 511-15 (1984);



consisting of approximately 60
Bendixen et al., 31 BIOCHEM. 3611-17



amino acids disulfide bonded to form
(1992); Steinkasserer et al., 277



Short Consensus Repeats (SCR) or
BIOCHEM. J. 387-91 (1991); Nimpf



Sushi domains. Associated with
et al., 884 BIOCHEM. BIOPHYS. ACTA



lipoproteins, binds anionic surfaces
142-49 (1986); Kroll et.al. 434



like anionic vesicles, platelets, DNA,
BIOCHEM. BIOPHYS. Acta 490-501



mitochondria, and heparin. Binding
(1986); Polz et al., 11 INT'L J.



can inhibit contact activation
BIOCHEM. 265-73 (1976); McNeil et



pathway in blood coagulation.
al., 87 PNAS 4120-24 (1990); Galli



Binding to activated platelets inhibits
et al;. I LANCET 1544-47 (1990);



platelet associated prothrombinase
Matsuuna et al., II LANCET 177-78



and adenylate cyclase activities.
(1990); Pengo et al., 73 THROMBOSIS



Complexes between b2I and
& HAEMOSTASIS 29-34 (1995).



cardiolipin have been implicated in




the anti-phospholipid related immune




disorders LAC and SLE.



Osteonectin
Acidic, noncollagenous glycoprotein
Villarreal et al., 28 BIOCHEM. 6483



(Mr = 29,000) originally isolated from
(1989); Tracy et al., 29 INT'L J.



fetal and adult bovine bone matrix.
BIOCHEM. 653 (1988); Romberg et



May regulate bone metabolism by
al., 25 BIOCHEM. 1176 (1986); Sage



binding hydroxyapatite to collagen.
& Bornstein 266 J. BIOL. CHEM.



Identical to human placental SPARC.
14831 (1991); Kelm & Mann 4 J.



An alpha granule component of
BONE MIN. RES. 5245 (1989); Kelm



human platelets secreted during
et al., 80 BLOOD 3112 (1992).



activation. A small portion of




secreted osteonectin expressed on the




platelet cell surface in an activation-




dependent manner



Plasminogen
Single chain glycoprotein zymogen
See Robbins, 45 METHODS IN



with 24 disulfide bridges, no free
ENZYMOLOGY 257 (1976); COLLEN,



sulfhydryls, and 5 regions of internal
243-258 BLOOD COAG. (Zwaal et al.,



sequence homology, “kringles”, each
eds., New York, Elsevier, 1986); see



five triple-looped, three disulfide
also Castellino et al., 80 METHODS IN



bridged, and homologous to kringle
ENZYMOLOGY 365 (1981); Wohl et



domains in t-PA, u-PA and
al., 27 THROMB. RES. 523 (1982);



prothrombin. Interaction of
Barlow et al., 23 BIOCHEM. 2384



plasminogen with fibrin and α2-
(1984); SOTTRUP-JENSEN ET AL., 3



antiplasmin is mediated by lysine
PROGRESS IN CHEM. FIBRINOLYSIS &



binding sites. Conversion of
THROMBOLYSIS 197-228 (Davidson



plasminogen to plasmin occurs by
et al., eds., Raven Press, New York



variety of mechanisms, including
1975).



urinary type and tissue type




plasminogen activators,




streptokinase, staphylokinase,




kallikrein, factors IXa and XIIa, but




all result in hydrolysis at Arg560-Val561,




yielding two chains that




remain covalently associated by a




disulfide bond.



tissue
t-PA, a serine endopeptidase
See Plasminogen.


Plasminogen
synthesized by endothelial cells, is



Activator
the major physiologic activator of




plasminogen in clots, catalyzing




conversion of plasminogen to




plasmin by hydrolising a specific




arginine-alanine bond. Requires




fibrin for this activity, unlike the




kidney-produced version, urokinase-




PA.



Plasmin
See Plasminogen. Plasmin, a serine
See Plasminogen.



protease, cleaves fibrin, and activates




and/or degrades compounds of




coagulation, kinin generation, and




complement systems. Inhibited by a




number of plasma protease inhibitors




in vitro. Regulation of plasmin in




vivo occurs mainly through




interaction with a2-antiplasmin, and




to a lesser extent, a2-macroglobulin.



Platelet Factor-4
Low molecular weight, heparin-
Rucinski et al., 53 BLOOD 47 (1979);



binding protein secreted from
Kaplan et al., 53 BLOOD 604 (1979);



agonist-activated platelets as a
George 76 BLOOD 859 (1990); Busch



homotetramer in complex with a
et al., 19 THROMB. RES. 129 (1980);



high molecular weight, proteoglycan,
Rao et al., 61 BLOOD 1208 (1983);



carrier protein. Lysine-rich, COOH-
Brindley, et al., 72 J. CLIN. INVEST.



terminal region interacts with cell
1218 (1983); Deuel et al., 74 PNAS



surface expressed heparin-like
2256 (1981); Osterman et al., 107



glycosaminoglycans on endothelial
BIOCHEM. BIOPHYS. RES. COMMUN.



cells, PF-4 neutralizes anticoagulant
130 (1982); Capitanio et al., 839



activity of heparin exerts
BIOCHEM. BIOPHYS. ACTA 161



procoagulant effect, and stimulates
(1985).



release of histamine from basophils.




Chemotactic activity toward




neutrophils and monocytes. Binding




sites on the platelet surface have




been identified and may be important




for platelet aggregation.



Protein C
Vitamin K-dependent zymogen,
See Esmon, 10 PROGRESS IN



protein C, made in liver as a single
THROMB. & HEMOSTS. 25 (1984);



chain polypeptide then converted to a
Stenflo, 10 SEMIN. IN THROMB. &



disulfide linked heterodimer.
HEMOSTAS. 109 (1984); Griffen et



Cleaving the heavy chain of human
al., 60 BLOOD 261 (1982); Kisiel et



protein C converts the zymogen into
al., 80 METHODS ENZYMOL. 320



the serine protease, activated protein
(1981); Discipio et al., 18 BIOCHEM.



C. Cleavage catalyzed by a complex
899 (1979).



of α-thrombin and thrombomodulin.




Unlike other vitamin K dependent




coagulation factors, activated protein




C is an anticoagulant that catalyzes




the proteolytic inactivation of factors




Va and VIIIa, and contributes to the




fibrinolytic response by complex




formation with plasminogen




activator inhibitors.



Protein S
Single chain vitamin K-dependent
Walker 10 SEMIN. THROMB.



protein functions in coagulation and
HEMOSTAS. 131 (1984); Dahlback et



complement cascades. Does not
al., 10 SEMIN. THROMB. HEMOSTAS.,



possess the catalytic triad.
139 (1984); Walker 261 J. BIOL.



Complexes to C4b binding protein
CHEM. 10941 (1986).



(C4BP) and to negatively charged




phospholipids, concentrating C4BP




at cell surfaces following injury.




Unbound S serves as anticoagulant




cofactor protein with activated




Protein C. A single cleavage by




thrombin abolishes protein S




cofactor activity by removing gla




domain.



Protein Z
Vitamin K-dependent, single-chain
Sejima et al., 171 BIOCHEM.



protein made in the liver. Direct
BIOPHYSICS RES. COMM. 661 (1990);



requirement for the binding of
Hogg et al., 266 J. BIOL. CHEM.



thrombin to endothelial
10953 (1991); Hogg et al., 17



phospholipids. Domain structure
BIOCHEM. BIOPHYSICS RES. COMM.



similar to that of other vitamin K-
801 (1991); Han et al., 38 BIOCHEM.



dependant zymogens like factors VII,
11073 (1999); Kemkes-Matthes et



IX, X, and protein C. N-terminal
al., 79 THROMB. RES. 49 (1995).



region contains carboxyglutamic acid




domain enabling phospholipid




membrane binding. C-terminal




region lacks “typical” serine protease




activation site. Cofactor for




inhibition of coagulation factor Xa




by serpin called protein Z-dependant




protease inhibitor. Patients diagnosed




with protein Z deficiency have




abnormal bleeding diathesis during




and after surgical events.



Prothrombin
Vitamin K-dependent, single-chain
Mann et al., 45 METHODS IN



protein made in the liver. Binds to
ENZYMOLOGY 156 (1976);



negatively charged phospholipid
Magnusson et al., PROTEASES IN



membranes. Contains two “kringle”
BIOLOGICAL CONTROL 123-149



structures. Mature protein circulates
(Reich et al., eds. Cold Spring



in plasma as a zymogen and, during
Harbor Labs., New York 1975);



coagulation, is proteolytically
Discipio et al., 18 BIOCHEM. 899



activated to the potent serine
(1979).



protease α-thrombin.



α-Thrombin
See Prothrombin. During
45 METHODS ENZYMOL. 156 (1976).



coagulation, thrombin cleaves




fibrinogen to form fibrin, the




terminal proteolytic step in




coagulation, forming the fibrin clot.




Thrombin also responsible for




feedback activation of procofactors




V and VIII. Activates factor XIII and




platelets, functions as vasoconstrictor




protein. Procoagulant activity




arrested by heparin cofactor II or the




antithrombin III/heparin complex, or




complex formation with




thrombomodulin. Formation of




thrombin/thrombomodulin complex




results in inability of thrombin to




cleave fibrinogen and activate factors




V and VIII, but increases the




efficiency of thrombin for activation




of the anticoagulant, protein C.



b-Thromboglobulin
Low molecular weight, heparin-
See, e.g., George 76 BLOOD 859



binding, platelet-derived tetramer
(1990); Holt & Niewiarowski 632



protein, consisting of four identical
BIOCHIM. BIOPHYS. ACTA 284



peptide chains. Lower affinity for
(1980); Niewiarowski et al., 55



heparin than PF-4. Chemotactic
BLOOD 453 (1980); Varma et al., 701



activity for human fibroblasts, other
BIOCHIM. BIOPHYS. ACTA 7 (1982);



functions unknown.
Senior et al., 96 J. CELL. BIOL. 382




(1983).


Thrombopoietin
Human TPO (Thrombopoietin, Mpl-
Horikawa et al., 90(10) BLOOD 4031-38



ligand, MGDF) stimulates the
(1997); de Sauvage et al., 369



proliferation and maturation of
NATURE 533-58 (1995).



megakaryocytes and promotes




increased circulating levels of




platelets in vivo. Binds to c-Mpl




receptor.



Thrombospondin
High-molecular weight, heparin-
Dawes et al., 29 THROMB. RES. 569



binding glycoprotein constituent of
(1983); Switalska et al., 106 J. LAB.



platelets, consisting of three,
CLIN. MED. 690 (1985); Lawler et al.



identical, disulfide-linked
260 J. BIOL. CHEM. 3762 (1985);



polypeptide chains. Binds to surface
Wolff et al., 261 J. BIOL. CHEM.



of resting and activated platelets,
6840 (1986); Asch et al., 79 J. CLIN.



may effect platelet adherence and
CHEM. 1054 (1987); Jaffe et al., 295



aggregation. An integral component
NATURE 246 (1982); Wright et al.,



of basement membrane in different
33 J. HISTOCHEM. CYTOCHEM. 295



tissues. Interacts with a variety of
(1985); Dixit et al., 259 J. BIOL.



extracellular macromolecules
CHEM. 10100 (1984); Mumby et al.,



including heparin, collagen,
98 J. CELL. BIOL. 646 (1984); Lahav



fibrinogen and fibronectin,
et al, 145 EUR. J. BIOCHEM. 151



plasminogen, plasminogen activator,
(1984); Silverstein et al, 260 J. BIOL.



and osteonectin. May modulate cell-
CHEM. 10346 (1985); Clezardin et al.



matrix interactions.
175 EUR. J. BIOCHEM. 275 (1988);




Sage & Bornstein (1991).


Von Willebrand
Multimeric plasma glycoprotein
Hoyer 58 BLOOD 1 (1981); Ruggeri


Factor
made of identical subunits held
& Zimmerman 65 J. CLIN. INVEST.



together by disulfide bonds. During
1318 (1980); Hoyer & Shainoff 55



normal hemostasis, larger multimers
BLOOD 1056 (1980); Meyer et al., 95



of vWF cause platelet plug formation
J. LAB. CLIN. INVEST. 590 (1980);



by forming a bridge between platelet
Santoro 21 THROMB. RES. 689



glycoprotein IB and exposed
(1981); Santoro, & Cowan 2



collagen in the subendothelium. Also
COLLAGEN RELAT. RES. 31 (1982);



binds and transports factor VIII
Morton et al., 32 THROMB. RES. 545



(antihemophilic factor) in plasma.
(1983); Tuddenham et al., 52 BRIT. J. HAEMATOL.




259 (1982).









Additional blood proteins contemplated herein include the following human serum proteins, which may also be placed in another category of protein (such as hormone or antigen): Actin, Actinin, Amyloid Serum P, Apolipoprotein E, B2-Microglobulin, C-Reactive Protein (CRP), Cholesterylester transfer protein (CETP), Complement C3B, Ceruplasmin, Creatine Kinase, Cystatin, Cytokeratin 8, Cytokeratin 14, Cytokeratin 18, Cytokeratin 19, Cytokeratin 20, Desmin, Desmocollin 3, FAS (CD95), Fatty Acid Binding Protein, Ferritin, Filamin, Glial Filament Acidic Protein, Glycogen Phosphorylase Isoenzyme BB (GPBB), Haptoglobulin, Human Myoglobin, Myelin Basic Protein, Neurofilament, Placental Lactogen, Human SHBG, Human Thyroid Peroxidase, Receptor Associated Protein, Human Cardiac Troponin C, Human Cardiac Troponin 1, Human Cardiac Troponin T, Human Skeletal Troponin I, Human Skeletal Troponin T, Vimentin, Vinculin, Transferrin Receptor, Prealbumin, Albumin, Alpha-1-Acid Glycoprotein, Alpha-1-Antichymotrypsin, Alpha-1-Antitrypsin, Alpha-Fetoprotein, Alpha-1-Microglobulin, Beta-2-microglobulin, C-Reactive Protein, Haptoglobulin, Myoglobulin, Prealbumin, PSA, Prostatic Acid Phosphatase, Retinol Binding Protein, Thyroglobulin, Thyroid Microsomal Antigen, Thyroxine Binding Globulin, Transferrin, Troponin I, Troponin T, Prostatic Acid Phosphatase, Retinol Binding Globulin (RBP). All of these proteins, and sources thereof, are known in the art. Many of these proteins are available commercially from, for example, Research Diagnostics, Inc. (Flanders, N.J.).
The cell clone of the present invention may also express neurotransmitters, or functional portions thereof. Neurotransmitters are chemicals made by neurons and used by them to transmit signals to the other neurons or non-neuronal cells (e.g., skeletal muscle; myocardium, pineal glandular cells) that they innervate. Neurotransmitters produce their effects by being released into synapses when their neuron of origin fires (i.e., becomes depolarized) and then attaching to receptors in the membrane of the post-synaptic cells. This causes changes in the fluxes of particular ions across that membrane, making cells more likely to become depolarized, if the neurotransmitter happens to be excitatory, or less likely if it is inhibitory. Neurotransmitters can also produce their effects by modulating the production of other signal-transducing molecules (“second messengers”) in the post-synaptic cells. See, e.g., COOPER, BLOOM & ROTH, THE BIOCHEMICAL BASIS OF NEUROPHARMACOLOGY (7th Ed. Oxford Univ. Press, NYC, 1996); http://web.indstate.edu/theme/mwking/nerves. Neurotransmitters contemplated in the present invention include, but are not limited to, Acetylcholine, Serotonin, γ-aminobutyrate (GABA), Glutamate, Aspartate, Glycine, Histamine, Epinephrine, Norepinephrine, Dopamine, Adenosine, ATP, Nitric oxide, and any of the peptide neurotransmitters such as those derived from pre-opiomelanocortin (POMC), as well as antagonists and agonists of any of the foregoing.
Numerous other proteins or peptides may serve as either targets, or as a source of target-binding moieties as described herein. Table 4 presents a non-limiting list and description of some pharmacologically active peptides that may serve as, or serve as a source of a functional derivative of, the target of the present invention.







TABLE 4







Pharmacologically active peptides









Binding partner/




Protein of interest




(form of peptide)
Pharmacological activity
Reference





EPO receptor
EPO mimetic
Wrighton et al., 273 SCIENCE 458-63


(intrapeptide

(1996); U.S. Pat. No. 5,773,569,


disulfide-bonded)

issued Jun. 30, 1998.


EPO receptor
EPO mimetic
Livnah et al., 273 SCIENCE 464-71


(C-terminally cross-

(1996); Wrighton et al., 15 NATURE


linked dimer)

BIOTECHNOLOGY 1261-5 (1997); Int'l




Patent Application WO 96/40772,




published Dec. 19, 1996.


EPO receptor
EPO mimetic
Naranda et al., 96 PNAS 7569-74


(linear)

(1999).


c-Mpl
TPO-mimetic
Cwirla et al., 276 SCIENCE 1696-9


(linear)

(1997); U.S. Pat. No. 5,869,451,




issued Feb. 9, 1999; U.S. Pat. No.




5,932,946, issued Aug. 3, 1999.


c-Mpl
TPO-mimetic
Cwirla et al., 276 SCIENCE 1696-9


(C-terminally cross-

(1997).


linked dimer)




(disulfide-linked
stimulation of
Paukovits et al., 364 HOPPE-SEYLERS


dimer)
hematopoesis
Z. PHYSIOL. CHEM. 30311 (1984);



(“G-CSF-
Laerurngal., 16 EXP. HEMAT. 274-80



mimetic”)
(1988).


(alkylene-linked dimer)
G-CSF-mimetic
Batnagar et al., 39 J. MED. CHEM.




38149 (1996); Cuthbertson et al., 40 J.




MED. CHEM. 2876-82 (1997); King et




al., 19 EXP. HEMATOL. 481 (1991);




King et al., 86(Suppl. 1) BLOOD 309




(1995).


IL-1 receptor
inflammatory and
U.S. Pat. No. 5,608,035; U.S. Pat. No.


(linear)
autoimmune diseases
5,786,331; U.S Pat. No. 5,880,096;



(“IL-1 antagonist” or “IL-1
Yanofsky et al., 93 PNAS 7381-6



ra-mimetic”)
(1996); Akeson et al., 271 J. BIOL.




CHEM. 30517-23 (1996); Wiekzorek et




al., 49 POL. J. PHARMACOL. 107-17




(1997); Yanofsky, 93 PNAS 7381-7386




(1996).


Facteur thyrnique
stimulation of
Inagaki-Ohara et al., 171 CELLULAR


(linear)
lymphocytes (FTS-
IMMUNOL. 30-40 (1996); Yoshida, 6



mimetic)
J. IMMUNOPHARMACOL 141-6 (1984).


CTLA4 MAb
CTLA4-mimetic
Fukumoto et al., 16 NATURE BIOTECH.


(intrapeptide di-sulfide

267-70 (1998).


bonded)




TNF-a receptor
TNF-a antagonist
Takasaki et al., 15 NATURE BIOTECH.


(exo-cyclic)

1266-70 (1997); WO 98/53842,




published Dec. 3, 1998.


TNF-a receptor
TNF-a antagonist
Chirinos-Rojas, J. IMM., 5621-26.


(linear)




C3b
inhibition of complement
Sahu et al., 157 IMMUNOL. 884-91


(intrapeptide di-sulfide
activation; autoimmune
(1996); Morikis et al., 7 PROTEIN SCI.


bonded)
diseases (C3b antagonist)
619-27 (1998).


vinculin
cell adhesion processes,
Adey et al., 324 BIOCHEM. J. 523-8


(linear)
cell growth, differentiation
(1997).



wound healing, tumor




metastasis (“vinculin




binding”)



C4 binding protein (C413P)
anti-thrombotic
Linse et al. 272 BIOL. CHEM. 14658-65


(linear)

(1997).


urokinase receptor
processes associated with
Goodson et al., 91 PNAS 7129-33


(linear)
urokinase interaction with
(1994); International patent



its receptor (e.g.
application WO 97/35969, published



angiogenesis, tumor cell
Oct. 2, 1997.



invasion and metastasis;




(URK antagonist)



Mdm2, Hdm2
Inhibition of inactivation
Picksley et al., 9 ONCOGENE 2523-9


(linear)
of p53 mediated by Mdm2
(1994); Bottger et al. 269 J. MOL.



or hdm2; anti-tumor
BIOL. 744-56 (1997); Bottger et al., 13



(“Mdm/hdm antagonist”)
ONCOGENE 13: 2141-7 (1996).


p21WAF1
anti-tumor by mimicking
Ball et al., 7 CURR. BIOL. 71-80


(linear)
the activity of p21WAF1
(1997).


farnesyl transferase
anti-cancer by preventing
Gibbs et al., 77 CELL 175-178 (1994).


(linear)
activation of ras oncogene



Ras effector domain
anti-cancer by inhibiting
Moodie et at., 10 TRENDS GENEL 44-48


(linear)
biological function of the
(1994); Rodriguez et al., 370



ras oncogene
NATURE 527-532 (1994).


SH2/SH3 domains
anti-cancer by inhibiting
Pawson et al, 3 CURR. BIOL. 434-432


(linear)
tumor growth with
(1993); Yu et al., 76 CELL 933-945



activated tyrosine kinases
(1994).


p16INK4
anti-cancer by mimicking
Fahraeus et al., 6 CURR. BIOL. 84-91


(linear)
activity of p16; e.g.,
(1996).



inhibiting cyclin D-Cdk




complex (“p, 16-mimetic”)



Src, Lyn
inhibition of Mast cell
Stauffer et al., 36 BIOCHEM. 9388-94


(linear)
activation, IgE-related
(1997).



conditions, type I




hypersensitivity (“Mast




cell antagonist”).



Mast cell protease
treatment of inflammatory
International patent application WO


(linear)
disorders mediated by
98/33812, published Aug. 6, 1998.



release of tryptase-6




(“Mast cell protease




inhibitors”)



SH3 domains
treatment of SH3-
Rickles et al., 13 EMBO J.


(linear)
mediated disease states
5598-5604 (1994); Sparks et



(“SH3 antagonist”)
al., 269 J. BIOL. CHEM.




238536 (1994); Sparks et al.,




93 PNAS 1540-44 (1996).


HBV core antigen (HBcAg)
treatment of HBV viral
Dyson & Muray, PNAS 2194-98


(linear)
antigen (HBcAg)
(1995).



infections (“anti-HBV”)



selectins
neutrophil adhesion
Martens et al., 270 J. BIOL.


(linear)
inflammatory diseases
CHEM. 21129-36 (1995);



(“selectin antagonist”)
European Pat. App. EP 0 714 912,




published Jun. 5, 1996.


calmodulin
calmodulin
Pierce et al., 1 MOLEC.


(linear, cyclized)
antagonist
DIVEMILY 25965 (1995);




Dedman et al., 267 J. BIOL.




CHEM. 23025-30 (1993);




Adey & Kay, 169 GENE 133-34




(1996).


integrins
tumor-homing; treatment
International patent applications WO


(linear, cyclized)
for conditions related to
95/14714, published Jun. 1, 1995;



integrin-mediated cellular
WO 97/08203, published Mar.



events, including platelet
6, 1997; WO 98/10795, published



aggregation, thrombosis,
Mar. 19, 1998; WO 99/24462,



wound healing,
published May 20, 1999; Kraft et al.,



osteoporosis, tissue repair,
274 J. BIOL. CHEM. 1979-85 (1999).



angiogenesis (e.g., for




treatment of cancer) and




tumor invasion (“integrin-




binding”)



fibronectin and
treatment of inflammatory
International patent application WO


extracellular matrix
and autoimmune
98/09985, published Mar. 12, 1998.


components of T-cells and
conditions



macrophages




(cyclic, linear)




somatostatin and cortistatin
treatment or prevention of
European patent application EP 0 911 393,


(linear)
hormone-producing
published Apr. 28, 1999.



tumors, acromegaly,




giantism, dementia, gastric




ulcer, tumor growth,




inhibition of hormone




secretion, modulation of




sleep or neural activity



bacterial lipopoly-saccharide
antibiotic; septic shock;
U.S. Pat. No. 5,877,151, issued Mar.


(linear)
disorders modulatable by
2, 1999.



CAP37



parclaxin, mellitin
antipathogenic
International patent application WO


(linear or cyclic)

97/31019, published Aug. 28 1997.


VIP
impotence, neuro-
International patent application WO


(linear, cyclic)
degenerative disorders
97/40070, published Oct. 30,




1997.


CTLs
cancer
European patent application EP 0 770 624,


(linear)

published May 2, 1997.


THF-gamma2

Burnstein, 27 BIOCHEM. 4066-71


(linear)

(1988).


Amylin

Cooper, 84 PNAS 8628-32 (1987).


(linear)




Adreno-medullin

Kitamura, 192 BBRC 553-60 (1993).


(linear)




VEGF
anti-angiogenic; cancer,
Fairbrother, 37 BIOCHEM. 17754-64


(cyclic, linear)
rheumatoid arthritis,
(1998).



diabetic retinopathy,




psoriasis (“VEGF




antagonist′”)



MMP
inflammation and
Koivunen, 17 NATURE BIOTECH. 768-74 (1999).


(cyclic)
autoimmune disorders;




tumor growth (“MMP




inhibitor”)



HGH fragment

U.S. Pat. No. 5,869,452,


(linear)

issued Feb. 9, 1999.


Echistatin
inhibition of platelet
Gan, 263 J. BIOL. 19827-32 (1988).



aggregation



SLE autoantibody
SLE
International patent application WO


(linear)

96/30057, published Oct. 3, 1996.


GD1 alpha
suppression of tumor
Ishikawa et al., 1 FEBS LETT. 20-4 (1998).



metastasis



anti-phospholipid β-2
endothelial cell activation,
Blank Mal., 96 PNAS 5164-8 (1999).


glycoprotein-1 (β2GPI)
anti-phospholipid



antibodies
syndrome (APS),




thromboembolic




phenomena,




thrombocytopenia, and




recurrent fetal loss



T-Cell Receptor β chain
diabetes
International patent application WO


(linear)

96/101214, published Apr. 18, 1996.


Binding partner/
Pharmacological activity
Reference


Protein of interest




(form of peptide)




EPO receptor
EPO mimetic
Wrighton et al. (1996), Science 273:


(intrapeptide

458-63; U.S. Pat. No. 5,773,569,


disulfide-bonded)

issued Jun. 30, 1998 to Wrighton et




al.


EPO receptor
EPO mimetic
Livnah et al. (1996), Science 273:


(C-terminally cross-

464-71; Wrighton et al. (1997),


linked dimer)

Nature Biotechnology 15: 1261-5;




int'l patent application WO




96/40772, published Dec. 19, 1996


EPO receptor
EPO mimetic
Naranda et al., 96 PNAS 7569-74


(linear)

(1999)


c-Mpl
TPO-mimetic
Cwirla et al.(1997) Science 276: 1696-9;


(linear)

U.S. Pat. No. 5,869,451, issued Feb.




9, 1999; U.S. Pat. No. 5,932,946,




issued Aug. 3, 1999


c-Mpl
TPO-mimetic
Cwirla et al. (1997) Science 276: 1696-9


(C-terminally cross-




linked dimer)




(disulfide-linked
stimulation of
Paukovits et al. (1984), Hoppe-


dimer)
hematopoesis
Seylers Z. Physiol. Chem. 365:



(“G-CSF-
30311; Laerurn gal. (1988), Exp.



mimetic”)
Hemat. 16: 274-80


(alkylene-linked dimer)
G-CSF-mimetic
Batnagar 91-al. (1996), linked dimer J.




Med. Chem. 39: 38149; Cuthbertson et




al. (1997), J. Med. Chem. 40: 2876-82;




King et al. (1991), Exp. Hematol.




19: 481; King et al. (1995), Blood 86




(Suppl. 1): 309


IL-1 receptor
inflammatory and
U.S. Pat. No. 5,608,035; U.S. Pat. No.


(linear)
autoimmune diseases
5,786,331; U.S-Pat. No. 5,880,096;



(“IL-1 antagonist” or “IL-
Yanofsky 91-al. (1996) PNAS



1 ra-mimetic”)
93: 7381-6; Akeson et al. (1996), J.




Biol. Chem. 271: 30517-23;




Wiekzorek et al. (1997), Pol. J.




Pharmacol. 49: 107-17; Yanofsky




(1996), PNAs, 93: 7381-7386.


Facteur thyrnique
stimulation of
Inagaki-Ohara et al. (1996), Cellular


(linear)
lymphocytes (FTS-
Immunol. 171: 30-40; Yoshida (1984),



mimetic)
J. Immunopharmacol, 6: 141-6.


CTLA4 MAb
CTLA4-mimetic
Fukumoto et al. (1998), Nature


(intrapeptide di-sulfide

Biotech. 16: 267-70


bonded)




TNF-a receptor
TNF-a antagonist
Takasaki et al. (1997), Nature Biotech.


(exo-cyclic)

15: 1266-70; WO 98/53842, published




Dec. 3, 1998.


TNF-a receptor
TNF-a antagonist
Chirinos-Rojas J. Imm., 5621-26.


(linear)




C3b
inhibition of complement
Sahu et al. (1996), Immunol. 157: 884-91;


(intrapeptide di-sulfide
activation; autoimmune
Morikis et al. (1998), Protein Sci.


bonded)
diseases (C3b antagonist)
7: 619-27.


vinculin
cell adhesion processes,
Adey et al. (1997), Biochem. J.


(linear)
cell growth, differentiation
324: 523-8



wound healing, tumor




metastasis (“vinculin




binding”)



C4 binding protein (C413P)
anti-thrombotic
Linse et al. 272 Biol. Chem. 14658-65


(linear)

(1997)


urokinase receptor
processes associated with
Goodson et al. (1994), 91 PNAS 7129-33;


(linear)
urokinase interaction with
International application WO



its receptor (e.g.
97/35969, published Oct. 2, 1997



angiogenesis, tumor cell




invasion and metastasis;




(URK antagonist)



Mdm2, Hdm2
Inhibition of inactivation
Picksley et al. (1994), Oncogene 9:


(linear)
of p53 mediated by Mdm2
2523-9; Bottger et al. (1997) J. Mol.



or hdm2; anti-tumor
Biol. 269: 744-56; Bottger et al.



(“Mdm/hdm antagonist”)
(1996), Oncogene 13: 2141-7


p21WAF1
anti-tumor by mimicking
Ball et al.(1997), Curr. Biol. 7: 71-80.


(linear)
the activity of p21WAF1



farnesyl transferase
anti-cancer by preventing
Gibbs et al. (1994), Cell 77: 175-178


(linear)
activation of ras oncogene



Ras effector domain
anti-cancer by inhibiting
Moodie et at. (1994), Trends Genel


(linear)
biological function of the
10: 44-48 Rodriguez et al. (1994),



ras oncogene
Nature 370: 527-532.


SH2/SH3 domains
anti-cancer by inhibiting
Pawson et al (1993), Curr. Biol.


(linear)
tumor growth with
3: 434-432, Yu et al. (1994), Cell



activated tyrosine kinases
76: 933-945.


p16INK4
anti-cancer by mimicking
Fahraeus et al. (1996), Curr. Biol.


(linear)
activity of p16; e.g.,
6: 84-91



inhibiting cyclin D-Cdk




complex (“p,16-mimetic”)



Src, Lyn
inhibition of Mast cell
Stauffer et al. (1997), Biochem. 36:


(linear)
activation, IgE-related
9388-94.



conditions, type I




hypersensitivity (“Mast




cell antagonist”).



Mast cell protease
treatment of inflammatory
International application WO


(linear)
disorders mediated by
98/33812, published Aug. 6, 1998



release of tryptase-6




(“Mast cell protease




inhibitors”)



SH3 domains
treatment of SH3-
Rickles et al. (1994), EMBO


(linear)
mediated disease states
J. 13: 5598-5604; Sparks aLal.



(“SH3 antagonist”)
(1994), J. Biol. Chem. 269:




238536; Sparks et al. (1996),




PNAS 93: 1540-44.


HBV core antigen (HBcAg)
treatment of HBV viral
Dyson & Muray (1995), Proc.


(linear)
antigen (HBcAg)
NatI. Acad. Sci. 92: 2194-98.



infections (“anti-HBV”)



selectins
neutrophil adhesion
Martens et al. (1995), J. Biol.


(linear)
inflammatory diseases
Chem. 270: 21129-36;



(“selectin antagonist”)
European pat. app. EP 0 714 912,




published Jun. 5, 1996


calmodulin
calmodulin
Pierce et al. (1995), Molec.


(linear, cyclized)
antagonist
Divemily 1: 25965; Dedman




et al. (1993), J. Biol. Chem.




268: 23025-30; Adey & Kay




(1996), Gene 169: 133-34.


integrins
tumor-homing; treatment
International applications WO


(linear, cyclized)
for conditions related to
95/14714, published Jun. 1, 1995;



integrin-mediated cellular
WO 97/08203, published Mar.



events, including platelet
6, 1997; WO 98/10795, published



aggregation, thrombosis,
Mar. 19, 1998; WO 99/24462,



wound healing,
published May 20, 1999; Kraft et al.



osteoporosis, tissue repair,
(1999), J. Biol. Chem. 274: 1979-85.



angiogenesis (e.g., for




treatment of cancer) and




tumor invasion (“integrin-




binding”)



fibronectin and
treatment of inflammatory
WO 98/09985, published Mar. 12,


extracellular matrix
and autoimmune
1998.


components of T-cells and
conditions



macrophages




(cyclic, linear)




somatostatin and cortistatin
treatment or prevention of
European patent application 0 911 393,


(linear)
hormone-producing
published Apr. 28, 1999.



tumors, acromegaly,




giantism, dementia, gastric




ulcer, tumor growth,




inhibition of hormone




secretion, modulation of




sleep or neural activity



bacterial lipopoly-saccharide
antibiotic; septic shock;
U.S. Pat. No. 5,877,151, issued Mar.


(linear)
disorders modulatable by
2, 1999.



CAP37



parclaxin, mellitin
antipathogenic
WO 97/31019, published 28 Aug.


(linear or cyclic)

1997.


VIP
impotence, neuro-
WO 97/40070, published Oct. 30,


(linear, cyclic)
degenerative disorders
1997.


CTLs
cancer
EP 0 770 624, published May


(linear)

2, 1997.


THF-gamma2

Burnstein (1988), Biochem., 27: 4066-71


(linear)




Amylin

Cooper (1987), PNAS 84: 8628-32.


(linear)




Adreno-medullin

Kitamura (1993), BBRC, 192: 553-60


(linear)




VEGF
anti-angiogenic; cancer,
Fairbrother (1998), Biochem.,


(cyclic, linear)
rheumatoid arthritis,
37: 17754-64.



diabetic retinopathy,




psoriasis (“VEGF




antagonist'”)



MMP
inflammation and
Koivunen 17 Nature Biotech., 768-74


(cyclic)
autoimmune disorders;
(1999).



tumor growth (“MMP




inhibitor”)



HGH fragment

U.S. Pat. No. 5,869,452.


(linear)




Echistatin
inhibition of platelet
Gan (1988), J. Biol. 263: 19827-32.



aggregation



SLE autoantibody
SLE
WO 96/30057, published Oct. 3, 1996.


(linear)




GD1 alpha
suppression of tumor
Ishikawa et al., 1 FEBS Lett. 20-4



metastasis
(1998).


anti-phospholipid β-2
endothelial cell activation,
Blank Mal. (1999), PNAS 96: 5164-8.


glycoprotein-1 (β2GPI)
anti-phospholipid



antibodies
syndrome (APS),




thromboembolic




phenomena,




thrombocytopenia, and




recurrent fetal loss



T-Cell Receptor β chain
diabetes
WO 96/101214, published Apr. 18,


(linear)

1996.









There are two pivotal cytokines in the pathogenesis of rheumatoid arthritis, IL-1 and TNF-α. They act synergistically to induce each other, other cytokines, and COX-2. Research suggests that IL-1 is a primary mediator of bone and cartilage destruction in rheumatoid arthritis patients, whereas TNF-α appears to be the primary mediator of inflammation.
In a preferred embodiment of the invention, the polypeptide of interest binds to tumor necrosis factor alpha (TNFα), a pro-inflamatory cytokine. U.S. Pat. No. 6,277,969, issued Aug. 21, 2001; U.S. Pat. No. 6,090,382, issued Jul. 10, 2000. Anti-TNFα antibodies have shown great promise as therapeutics. For example, Infliximab, provided commercially as REMICADE® by Centocor, Inc. (Malvern, Pa.) has been used for the treatment of several chronic autoimmune diseases such as Crohn's disease and rheumatoid arthritis. Treacy, 19(4) HUM. Exp. TOXICOL. 226-28 (2000); see also Chantry, 2(1) CURR. OPIN. ANTI-INFLAMMATORY IMMUNOMODULATORY INVEST. DRUGS 31-34 (2000); Rankin et al., 34(4) BRIT. J. RHEUMATOLOGY 334-42 (1995). Preferably, any exposed amino acids of the TNFα-binding moiety of the polypeptide of interest are those with minimal antigenicity in humans, such as human or humanized amino acid sequences. These peptide identities may be generated by screening libraries, as described above, by grafting human amino acid sequences onto murine-derived paratopes (Siegel et al., 7(1) CYTOKINE 15-25 (1995); WO 92/11383, published Jul. 9, 1992) or monkey-derived paratopes (WO 93/02108, published Feb. 4, 1993), or by utilizing xenomice (WO 96/34096, published Oct. 31, 1996). Alternatively, murine-derived anti-TNFα antibodies have exhibited efficacy. Saravolatz et al., 169(1) J. INFECT. DIS. 214-17 (1994).
Alternatively, instead of being derived from an antibody, the TNFα binding moiety of the polypeptide of interest may be derived from the TNFα receptor. For example, Etanercept is a recombinant, soluble TNFα receptor molecule that is administered subcutaneously and binds to TNFα in the patient's serum, rendering it biologically inactive. Etanercept is a dimeric fusion protein consisting of the extracellular ligand-binding portion of the human 75 kilodalton (p75) tumor necrosis factor receptor (TNFR) linked to the Fc portion of human IgG1. The Fc component of etanercept contains the CH2 domain, the CH3 domain and hinge region, but not the CH1 domain of IgG1. Etanercept is produced by recombinant DNA technology in a Chinese hamster ovary (CHO) mammalian cell expression system. It consists of 934 amino acids and has an apparent molecular weight of approximately 150 kilodaltons. Etanercept may be obtained as ENBRELTM, manufactured by Immunex Corp. (Seattle, Wash.). Etanercept may be efficacious in rheumatoid arthritis. Hughes et al., 15(6) BIODRUGS 379-93 (2001).
Another form of human TNF receptor exists as well, identified as p55. Kalinkovich et al., J. INFERON & CYTOKINE RES. 15749-57 (1995). This receptor has also been explored for use in therapy. See, e.g., Qian et al., 118 ARCH. OPHTHALMOL. 1666-71 (2000). A previous formulation of the soluble p55 TNF receptor had been coupled to polyethylene glycol [r-metHuTNFbp PEGylated dimer (TNFbp)], and demonstrated clinical efficacy but was not suitable for a chronic indication due to the development antibodies upon multiple dosing, which resulted in increased clearance of the drug. A second generation molecule was designed to remove the antigenic epitopes of TNFbp, and may be useful in treating patients with rheumatoid arthritis. Davis et al., Presented at the Ann. European Cong. Rheumatology, Nice, France (Jun. 21-24, 2000).
IL-1 receptor antagonist (IL-1Ra) is a naturally occurring cytokine antagonist that demonstrates anti-inflammatory properties by balancing the destructive effects of IL-1α and IL-1β in rheumatoid arthritis but does not induce any intracellular response. Hence, in a preferred embodiment of the invention, the polypeptide of interest comprises IL-1Ra, or any structural or functional analog thereof. Two structural variants of IL-1Ra exist: a 17-kDa form that is secreted from monocytes, macrophages, neutrophils, and other cells (sIL-1Ra) and an 18-kDa form that remains in the cytoplasm of keratinocytes and other epithelial cells, monocytes, and fibroblasts (icIL-1Ra). An additional 16-kDa intracellular isoform of IL-1Ra exists in neutrophils, monocytes, and hepatic cells. Both of the major isoforms of IL-1Ra are transcribed from the same gene through the use of alternative first exons. The production of IL-1Ra is stimulated by many substances including adherent IgG, other cytokines, and bacterial or viral components. The tissue distribution of IL-1Ra in mice indicates that sIL-1Ra is found predominantly in peripheral blood cells, lungs, spleen, and liver, while icIL-1Ra is found in large amounts in skin. Studies in transgenic and knockout mice indicate that IL-1Ra is important in host defense against endotoxin-induced injury. IL-1Ra is produced by hepatic cells with the characteristics of an acute phase protein. Endogenous IL-1Ra is produced in human autoimmune and chronic inflammatory diseases. The use of neutralizing anti-IL-1Ra antibodies has demonstrated that endogenous IL-1Ra is an important natural anti-inflammatory protein in arthritis, colitis, and granulomatous pulmonary disease. Patients with rheumatoid arthritis treated with IL-1Ra for six months exhibited improvements in clinical parameters and in radiographic evidence of joint damage. Arend et al., 16 ANN. REV. IMMUNOL. 27-55 (1998).
Yet another example of an IL-1Ra that may be expressed by the cell clone of the present invention is a recombinant human version called interleukin-117.3 Kd met-IL1ra, or Anakinra, produced by Amgen, (San Francisco, Calif.) under the name KINERETTM. Anakinra has also shown promise in clinical studies involving patients with rheumatoid arthritis (Presented at the 65th Ann. Sci. Meeting of Am. College Rheumatology. Nov. 12, 2001).
In another embodiment of the invention, the polypeptide of interest expressed by the cell clone of the present invention is interleukin 12 (IL-12) or an antagonist thereof. IL-12 is a heterodimeric cytokine consisting of glycosylated polypeptide chains of 35 and 40 kD which are disulfide bonded. The cytokine is synthesized and secreted by antigen presenting cells, including dendritic cells, monocytes, macrophages, B cells, Langerhans cells and keratinocytes, as well as natural killer (NK) cells. IL-12 mediates a variety of biological processes and has been referred to as NK cell stimulatory factor (NKSF), T-cell stimulating factor, cytotoxic T-lymphocyte maturation factor and EBV-transformed B-cell line factor. Curfs et al., 10 CLIN. MICRO. REV. 742-80 (1997). Interleukin-12 can bind to the IL-12 receptor expressed on the plasma membrane of cells (e.g., T cells, NK cell), thereby altering (e.g., initiating, preventing) biological processes. For example, the binding of IL-12 to the IL-12 receptor can stimulate the proliferation of pre-activated T cells and NK cells, enhance the cytolytic activity of cytotoxic T cells (CTL), NK cells and LAK (lymphokine activated killer) cells, induce production of gamma interferon (IFN GAMMA) by T cells and NK cells and induce differentiation of naive Th0 cells into Th1 cells that produce IFN GAMMA and IL-2. Trinchieri, 13 ANN. REV. IMMUNOLOGY 251-76 (1995). In particular, IL-12 is vital for the generation of cytolytic cells (e.g., NK, CTL) and for mounting a cellular immune response (e.g., a Th1 cell mediated immune response). Thus, IL-12 is critically important in the generation and regulation of both protective immunity (e.g., eradication of infections) and pathological immune responses (e.g., autoimmunity). Hendrzak et al., 72 LAB. INVESTIGATION 619-37 (1995). Accordingly, an immune response (e.g., protective or pathogenic) can be enhanced, suppressed or prevented by manipulation of the biological activity of IL-12 in vivo, for example, by means of an antibody.
In another embodiment of the present invention, the polypeptide of interest comprises or targets an integrin. Integrins have been implicated in the angiogenic process, by which tumor cells form new blood vessels that provide tumors with nutrients and oxygen, carry away waste products, and to act as conduits for the metastasis of tumor cells to distant sites, Gastl et al., 54 ONCOL. 177-84 (1997). Integrins are heterodimeric transmembrane proteins that play critical roles in cell adhesion to the extracellular matrix (ECM) which, in turn, mediates cell survival, proliferation and migration through intracellular signaling. During angiogenesis, a number of integrins that are expressed on the surface of activated endothelial cells regulate critical adhesive interactions with a variety of ECM proteins to regulate distinct biological events such as cell migration, proliferation and differentiation. Specifically, the closely related but distinct integrins aVb3 and aVb5 have been shown to mediate independent pathways in the angiogenic process. An antibody generated against αVβ3 blocked basic fibroblast growth factor (bFGF) induced angiogenesis, whereas an antibody specific to αVβ5 inhibited vascular endothelial growth factor-induced (VEGF-induced) angiogenesis. Eliceiri et al., 103 J. CLIN. INVEST. 1227-30 (1999); Friedlander et al., 270 SCIENCE 1500-02 (1995).
In another preferred embodiment of the invention, the polypeptide of interest comprises at least one glycoprotein IIb/IIIa receptor antagonist. More specifically, the final obligatory step in platelet aggregation is the binding of fibrinogen to an activated membrane-bound glycoprotein complex, GP IIb/IIIa. Platelet activators such as thrombin, collagen, epinephrine or ADP, are generated as an outgrowth of tissue damage. During activation, GP IIb/IIIa undergoes changes in conformation that results in exposure of occult binding sites for fibrinogen. There are six putative recognition sites within fibrinogen for GP IIb/IIIa and thus fibrinogen can potentially act as a hexavalent ligand to crossing GP IIb/IIIa molecules on adjacent platelets. A deficiency in either fibrinogen or GP IIb/IIIa a prevents normal platelet aggregation regardless of the agonist used to activate the platelets. Since the binding of fibrinogen to its platelet receptor is an obligatory component of normal aggregation, GP IIb/IIIa is an attractive target for an antithrombotic agent.
Results from clinical trials of GP IIb/IIIa inhibitors support this hypothesis. A Fab fragment of the monoclonal antibody 7E3, which blocks the GP IIb/IIIa receptor, has been shown to be an effective therapy for the high risk angioplasty population. It is used as an adjunct to percutaneous transluminal coronary angioplasty or atherectomy for the prevention of acute cardiac ischemic complications in patients at high risk for abrupt closure of the treated coronary vessel. Although 7E3 blocks both the IIb/IIIa receptor and the αvβ3 receptor, its ability to inhibit platelet aggregation has been attributed to its function as a IIb/IIIa receptor binding inhibitor. The IIb/IIIa receptor antagonist may be, but is not limited to, an antibody, a fragment of an antibody, a peptide, or an organic molecule. For example, the target-binding moiety may be derived from 7E3, an antibody with glycoprotein IIb/IIIa receptor antagonist activity. 7E3 is the parent antibody of c7E3, a Fab fragment known as abciximab, known commercially as REOPRO® produced by Centocor, Inc. (Malvern, Pa.). Abciximab binds and inhibits the adhesive receptors GPIIb/IIIa and αvβ3, leading to inhibition of platelet aggregation and thrombin generation, and the subsequent prevention of thrombus formation. U.S. Pat. Nos. 5,976,532, 5,877,006, 5,770,198; Coller, 78 THROM HAEMOST. 730-35 (1997); JORDAN ET AL., in ADHESION RECEPTORS AS THERAPEUTIC TARGETS 281-305 (Horton, ed. CRC Press, New York, 1996); Jordan et al., in NEW THERAPEUTIC AGENTS IN THROMBOSIS & THROMBOLYSIS (Sasahara & Loscalzo, eds. Marcel Kekker, Inc. New York, 1997).
Additionally, the glycoprotein IIb/IIIa receptor antagonist expressed by the cell clone of the present invention may comprise a thrombolytic. For example, the thrombolytic may be tPA, or a functional variation thereof. RETAVASE®, produced by Centocor, Inc. (Malvern, Pa.), is a variant tPA with a prolonged half-life. In mice, the combination of Retavase and the IIb/IIIa receptor antagonist c7E3 Fab markedly augmented the dissolution of pulmonary embolism. See Provisional Patent Application Ser. No. 60/304,409.
Alternatively, the method of the present invention can be used to identify cell clones secreting non-peptide molecules. For example, natural signaling molecules are endogenous compounds which chemically effect receptors. Many pharmacologically active drugs act on the cellular receptor level by either mimicking the action of a natural signal molecule (agonist) or by blocking the action of the natural signal molecule (antagonist). As a non-limiting example, tirofiban hydrochloride is a non-peptide antagonist of the platelet glycoprotein IIb/IIIa receptor that inhibits platelet aggregation. See U.S. Pat. No. 6,117,842, issued Sep. 12, 2000. Tirofiban is commercially available as AGGRASTAT® from Merck & Co., Inc., (Whitehouse Station, N.J.), manufactured by Baxter Healthcare Corp. (Deerfield, Ill.) and Ben Venue Labs. (Bedford, Ohio). The structure of Tirofiban is illustrated below where X is or contains a functional group capable of forming the ΨAb structure. The position of X is selected at any of those aromatic sites on the molecule for which substitution will retain some activity of the parent structure, and is not limited to that position depicted in the drawing.




The polypeptide of interest expressed by the cell clone of the present invention also include receptors or fragments thereof, and activated receptors, i.e., recombinant peptides that mimic ligands associated with their corresponding receptors, or fragments thereof. These complexes may mimic activated receptors and thus affect a particular biological activity. An example of activated-receptor moieties concerns the peptido mimetics of the erythropoietin (Epo) receptor. By way of background, the binding of Epo to the Epo receptor (EpoR) is crucial for production of mature red blood cells. The Epo-bound, activated EpoR is a dimer. See, e.g., Constantinescu et al., 98 PNAS 4379-84 (2001). In its natural state, the first EpoR in the dimer binds Epo with a high affinity whereas the second EpoR molecule binds to the complex with a low affinity. Bivalent anti-EpoR antibodies have been reported to activate EopR, probably by dimerization of the EpoR. Additionally, small synthetic peptides, that do not have any sequence homology with the Epo molecule, are also able to mimic the biologic effects of Epo but with a lower affinity. Their mechanism of action is probably also based on the capacity to produce dimerization of the EpoR. Hence, an embodiment of the present invention provides for a method of identifying and characterizing cell clones expressing an activated EpoR mimetic.
In another preferred embodiment, the method of the present invention may be used to identify cell clone that secrets antimicrobial agents or portions thereof, which include antibacterial agents, antivirals agents, antifungal agents, antimycobacterial agents, and antiparasitic agents. Antibacterials include, but are not limited to, Beta-lactams (such as Penicillins and Cephalosporins), Aminoglycosides (such as Gentamicin), Macrolides (such as Erythromycin), Fluoroquinolones, Metronidazole, Sulfonamides, Tetracyclines, Trimethroprim, and Vancomycin. Antifungal agents include, but are not limited to Amphotericin, Fluconazole, Flucytosine, Itraconazole, and Ketoconazole. Antiparasitic agents include, but are not limited to, Ivermectin, Mebendazole, Mefloquine, Pentamidine, Praziquantel, Pyrimethamine, and Quinine. Antiviral agents include, but are not limited to, Acyclovir, Amantadine, Didanosine, Famciclovir, Foscarnet, Ganciclovir, Rimatandine, Stavudine, Zalcitabine, and Zidovudine. Antimycobacterial agents include, but are not limited to, Isoniazid, Rifampin, Streptomycin, Dapsone. SANFORD ET AL., GUIDE TO ANTIMICROBIAL THERAPY (25th ed., Antimicrobial Therapy, Inc., Dallas, Tex. 1995).
The method of the present invention may also be used to identify and/or characterize cell clones expressing a particular antigen. Antigens, in a broad sense, may include any molecule to which an antibody, or functional fragment thereof, binds. Such antigens may be pathogen derived, and be associated with either MHC class I or MHC class II reactions. These antigens may be proteinaceous or include carbohydrates, such as polysaccharides, glycoproteins, or lipids. Carbohydrate and lipid antigens are present on cell surfaces of all types of cells, including normal human blood cells and foreign, bacterial cell walls or viral membranes. Nucleic acids may also be antigenic when associated with proteins, and are hence included within the scope of antigens encompassed in the present invention. See SEARS, IMMUNOLOGY (W. H. Freeman & Co. and Sumanas, Inc., 1997), available on-line at http://www.whfreeman.com/immunology. For example, antigens may be derived from a pathogen, such as a virus, bacterium, mycoplasm, fungus, parasite, or from another foreign substance, such as a toxin. Such bacterial antigens may include or be derived from Bacillus anthracis, Bacillus tetani, Bordetella pertusis; Brucella spp., Corynebacterium diphtheriae, Clostridium botulinum, Clostridium perfringens, Coxiella burnetii, Francisella tularensis, Mycobacterium leprae, Mycobacterium tuberculosis, Salmonella typhimurium, Streptocccus pneumoniae, Escherichia coli, Haemophilus influenzae, Shigella spp., Staphylococcus aureus, Neisseria gonorrhoeae, Neisseria meningiditis, Treponema pallidum, Yersinia pestis, Vibrio cholerae. Often, the oligosaccharide structures of the outer cell walls of these microbes afford superior protective immunity, but must be conjugated to an appropriate carrier for that effect.
Viruses and viral antigens that are within the scope of the current invention include, but are not limited to, HBeAg, Hepatitis B Core, Hepatitis B Surface Antigen, Cytomegalovirus B, HIV-1 gag, HIV-1 nef, HIV-1 env, HIV-1 gp41-1, HIV-1 p24, HIV-1 MN gp120, HIV-2 env, HIV-2 gp 36, HCV Core, HCV NS4, HCV NS3, HCV p22 nucleocapsid, HPV LI capsid, HSV-1 gD, HSV-1 gG, HSV-2 gG, HSV-II, Influenza A (H1N1), Influenza A (H3N2), Influenza B, Parainfluenza Virus Type 1, Epstein Barr virus capsid antigen, Epstein Barr virus, Poxyiridae Variola major, Poxyiridae Variola minor, Rotavirus, Rubella virus, Respiratory Syncytial Virus, Surface Antigens of the Syphilis spirochete, Mumps Virus Antigen, Varicella zoster Virus Antigen and Filoviridae. 
Other parasitic pathogens such as Chlamydia trachomatis, Plasmodium falciparum, and Toxoplasma gondii may also be included in the scope of the present invention. Numerous bacterial and viral, and other microbe-generated antigens are available from commercial suppliers such as Research Diagnostics, Inc. (Flanders, N.J.).
Toxins, toxoids, or antigenic portions of either, within the scope of the present invention include those produced by bacteria, such as diphteria toxin, tetanus toxin, botulin toxin and enterotoxin B; those produced by plants, such as Ricin toxin from the castor bean Ricinus cummunis. Mycotoxins, produced by fungi, that may serve in the present invention include diacetoxyscirpenol (DAS), Nivalenol, 4-Deoxynivalenol (DON), and T-2 Toxin. Other toxins and toxoids produced by or derived from other organisms may also be included in the scope of the present invention.
Vectors
In a preferred embodiment, the cell clone of the present invention expresses at least one polypeptide of interest in detectable amount. A variety of mammalian expression vectors may be used to express the polypeptide of interest in the cell clone of the present invention. Expression vectors will preferably but optionally include at least one selectable marker. Such markers include, e.g., but not limited to, methotrexate (MTX), dihydrofolate reductase (DHFR, U.S. Pat. Nos. 4,399,216; 4,634,665; 4,656,134; 4,956,288; 5,149,636; 5,179,017, ampicillin, neomycin (G418), mycophenylic acid, orglutamine synthetase (GS, U.S. Pat. Nos. 5,122,464; 5,770,359; 5,827,739) resistance for eukaryotic cell culture, and tetracycline or ampicillin resistance genes for culturing in E. coli and other bacteria or prokaryotics (the above patents are entirely incorporated hereby by reference).
Suitable vectors are readily apparent to the skilled artisan. For example, commercially available mammalian expression vectors that may be suitable for the present invention include, but are not limited to, pMAMneo (Clontech, Palo Alto, Calif.), pcDNA3 (Invitrogen, Carlsbad, Calif.), pMClneo (Stratagene, La Jolla, Calif.), pXT1 (Stratagene, La Jolla, Calif.), pSG5 (Stratagene, La Jolla, Calif.), EBO-pSV2-neo (ATCC, Manassas, Va., ATCC No. 37593), pBPV-[(8-2) (ATCC No. 37110), pdBPV-MMTneo(342-12) (ATCC No. 37224), pRSVgpt (ATCC No.] 37199), pRSVneo (ATCC No. 37198), pSV2-dhfr (ATCC No. 37146), pUCTag (ATCC No. 37460), and 17D35 (ATCC No. 37565).
The nucleic acid encoding at least one polypeptide of interest may be introduced by one of several methods well known in the art, including but not limited to, transfection, including but not limited to, calcium phosphate transfection, DEAE-dextran mediated transfection and cationic lipid-mediated transfection, electroporation, sonication, transduction, transformation, and viral infection. Such methods are described in the art, see, e.g., Samsrook et al., Molecular Cloning: a Lab Manual, 3rd edition, Cold Spring Harbor, N.Y. (2001); Ausubel et al., Current Protocols in Molecular Biology, John Wiley & Sons, Inc., NY, N.Y. (1987-2003).
Host Cell Lines
The host cells in the present invention can be at least one selected from prokaryotic or eukaryotic cells, or fusion cells thereof, e.g., but not limited to, bacterial cells, blue-green algae cells, yeast cells, silk worm cells, plant cells, insect cells, amphibian cells, fish cells, avian cells, mammalian cells, or any derivative, immortalized or transformed cell thereof. Preferably, the cells are eukaryotic cells. More preferably, the cells are mammalian cells.
In a preferred embodiment, suitable cell lines that can be used according to the present invention include any transformed or immortalized mammalian cell line. The host cell can optionally be at least one selected from myeloma cells, such as but not limited to Sp2/0, NSO, NS1, CHO, BHK, Ag653, P3X63Ag8.653 (ATCC Accession Number CRL-1580) and SP2/0-Ag14 (ATCC Accession Number CRL-1851), COS-1(e.g., ATCC CRL-1650), COS-7 (e.g., ATCC CRL-1651), HEK293, BHK21 (e.g., ATCC CAL-10), CHO (e.g., ATCC CRL-1610, CHO DXB-11, CHO DG44), BSC-1 (e.g., ATCC CAL-26), HepG2, 293, HeLa, NIH 3T3, CDS-1, CDS-7, NIH 273, or lymphoma cells, or any derivative, immortalized or transformed cell thereof. A preferred cell line is C463A, which is derived from Sp2/0 and can be used as a transfection host. See U.S. application 60/339,428, WO2003051720 and WO993052964, herein entirely incorporated by reference.
As used herein, the term “colony” or “colonies” may be defined by the number of cells or total diameter, which is determined by the researcher. Typically, a colony has at least 40 or 50 cells, although sometimes as few as 30 cells or less. The incubation period required for a given cell type to reach the critical size or number of cells to be called a colony varies between cell types, but typically requires an incubation period of between 7-14 days, with longer periods needed if the cell growth is slow. If diameter is used as the defining criterion, a colony is typically defined as being 10-50 microns, such as 10-20, 20-30, 30-40, 40-50 microns or any range or value therein.
Media
Appropriate culture media and conditions for the above-described host cells are well known in the art. Numerous types of growth media are commercially available, such as but not limited to Iscove's Modified Medium, Dulbecco's Modified Eagel Medium, RPMI, Ham's F10, Ham's F12, Minimum Essential Medium and alpha medium etc. In addition to growth media, cells cultured in vitro require many growth factors to either promote growth or maintain viability. The growth factors may be supplied by for example, 5-10% fetal bovine serum (FBS) to promote cell growth and protein production. However, cell growth media include serum-free (containing 0-0.5% serum) or serum-reduced (containing 0.5-5.0% serum) media.
To support the growth of mammalian cells, a variety of components, e.g. but not limited to, glutamine, glucose, vitamins, amino acids and growth factors, may be included in the culture media. Trace elements such as zinc, iron, selenium, copper, molybdenum, and manganese etc. are important for cloning and continuous passage of mammalian cells in stringent conditions of serum-free media. Alternatively, cell growth media include deficient media, where one or more nutrients are deleted. Growth media also include specialty media which are designed to promote growth of specific cell types.
Growth media may include additional antibiotics, attachment and matrix factors which are usually added to facilitate attachment and spreading of many types of anchorage dependent cells. Buffers may also be added to growth media in order to maintain pH levels. Such buffers may include but are not limited to MOPS, HEPES, sodium phosphate, potassium phosphate, Tris or other known buffers.
In addition, chemically defined media (CDM) can be used in the present invention. CDM provide certain compounds, amino acids, lipids, carbohydrates, trace elements and/or vitamins and exclude the use of non-defined animal derived raw materials, e.g. but not limited to, primatone, albumin and ExcyteTM, as well as other similar materials derived from serum or other animal derived proteins or products. Such media allow the growth of cells to provide commercially useful amounts of the desired proteins expressed in such cell cultures. Some of the advantages of CDM include but not limited to better protein producing, commercially suitable, cost-effective, and/or pose reduced regulatory concerns for proteins produced in cell lines grown therein. For detailed compositions and formulations of CDM, see e.g. but not limited to WO2002066603, herein entirely incorporated by reference.
As used herein the term “semi-solid medium” refers to a cell growth medium that does not provide a solid substrate to which cells can attach, and that is sufficiently viscous such that cells added to the semi-solid medium are suspended therein, and are thereby prevented from sinking through the semi-solid medium and contacting, and attaching to, the inner surface of the container within which the semi-solid medium is dispensed. Because a semi-solid medium holds the cells in situ, it permits continuous observation of a single cell or individual colony.
Semi-solid media useful in the practice of the present invention typically include a gelatinization agent dissolved in an aqueous medium in an amount of from 0.1% to 5.0% (w/v), such as 0.1-0.5%, 0.5-1.0%, 1.0-1.5%, 1.5-2.0%, 2.0-2.5%, 2.5-3.0%, 3.0-3.5%, 3.5-4.0%, 4.0-4.5%, 4.5-5.0% or any range or value therein. Preferred semi-solid media are those capable of sustaining growth of cells. Non-limiting examples of gelatinization agents include agar, agarose, methylcellulose, or any other polymer suitable for the purpose of the present invention.
One category of the semi-solid media forms a liquid at temperatures above room temperature or above the temperature required to incubate the cells, and forms a semi-solid or gel when at room temperature or the temperature at which the cells are incubated. For example, agar is a class of polysaccharide complex generally defined as a dried mucilaginous substance extracted from the agarocytes of algae of the Rhodophyceae. Agar-producing genera include but not limited to, Gelidium, Gracilaria, Acanthopeltis, Ceramim, Pterocladia etc. Agar melts at about 100° C. and solidifies into a gel at about 40° C. It is not digested by most bacteria. Agarose is a modified agar, whereby sugars, methyl groups, and other chemical groups are chemically bonded to agar in order to enhance desired physical properties, such as low gelling temperature.
Additional gelatinization agents include, but are not limited to a wide variety of polymers, including proteins and their derivatives, may be used as semi-solid matrices in the present invention. Matrigel®, collagen or gelatin, or other similar materials may also be used as the semi-solid matrix.
Methylcellulose (cellulose methyl ether) belongs to a group of compounds known as cellulose ethers. The cellulose ethers are manufactured by a reaction of purified cellulose with alkylating reagents (methyl chloride) in presence of a base, typically sodium hydroxide and an inert diluent. The addition of the base in combination with water activates the cellulose matrix by disrupting the crystalline structure and increasing the access for the alkylating agent and promotes the etherification reaction. This activated matrix is called alkali cellulose. Methylcellulose is prepared from wood pulp or chemical cotton by treatment with alkali and methylation of the alkali cellulose with methyl chloride that adds methyl ether groups. The reaction can be characterized as:

RcellOH:NaOH+CH3Cl→RcellOCH3+NaCl

One significant property of methylcellulose is its reversible thermal gelation: it is soluble in cold water but insoluble in hot water. An aqueous solution is best prepared by dispersing the granules in hot (but not boiling) water with stirring and chilling to +5° C. Presence of inorganic salts increases the viscosity. At room temperature, methylcellulose solution is stable and stays in semi-solid gel form. It supports mammalian cell growth when mixed with the proper growth medium. The viscosity of methylcellulose prevents aggregation of the cells. In one embodiment, the final concentration of methylcellulose in the semi-solid capture medium is 1%. In another embodiment, the final concentration is around 0.7%. Less methylcellulose in the medium allows better diffusion of the capture molecule and accordingly increases the detection sensitivity.
Alternatively, premixed methylcellulose based semi-solid media are commercially available, such as but not limited to, ClonaCellTM-TCS and MethCultTM media (StemCell Technologies), StemlineTM methylcellulose media (Sigma-Aldrich, St. Louis, Mo.).
Addition of methylcellulose is traditionally used when culturing erythroid progenitor cells. The application of methylcellulose for screening and selection of antibiotic resistant clones has been described and commercially available, e.g. see Technical Manual ClonalCellTM-TCS, Transfected Cell Selection Kit, Stemcell Technologies.
Capture Molecule
As used herein the term “the capture molecule” refers to a molecule that can bind or react with the polypeptide of interest and form a halo-like precipitate visible under a microscope. Potential capture molecule can be but are not limited to, receptor or ligand of the polypeptide of interest, antibody or antigen against the polypeptide of interest etc. Accordingly, as used herein the term “the capture medium” refers to the semi-solid cell growth medium with at least one capture molecule incorporated.
The capture molecule can be directly added to the semi-solid medium, either by mixing it with the medium before pouring the plates, or by overlaying the pored plates with a layer of medium containing the capture molecule. The capture molecule can be radio-labeled, fluorescent-labeled or labeled by any other methods known in the art to facilitate the detection of precipitate. For example, a capture antibody is fluorescent-labeled and added to the semi-solid medium. Upon binding to the polypeptide of interest (i.e., the antigen), the antigen-antibody complex can be easily observed under fluorescent microscope and the cell clone expressing the polypeptide of interest can be identified.
In one embodiment, the capture molecule is an antibody against the polypeptide of interest. The final concentration of the capture antibody used can be 0.0225-0.225 mg/ml, such as 0.0225-0.045, 0.045-0.0675, 0.0675-0.09, 0.09-0.1125, 0.1125-0.135, 0.135-0.1575, 0.1575-0.18, 0.18-0.2025, 0.2025-0.225 mg/ml, or any range or value therein. In a preferred embodiment, the final concentration of the capture antibody is 0.1125 mg/ml. In general, lower concentration of the capture molecule increases the detection sensitivity by selecting cell clones expressing the polypeptide of interest at higher levels.
In one variation of the aforedescribed methods, this strategy is used to screen a nucleic acid library, such as a cDNA library, that encodes a population of candidate protein molecules that are being screened for their ability to bind or to react with the capture molecule and form precipitate. The cDNA library is introduced into cells by means well known in the art, such as by transfection or transduction. The cells are cultured in a semi-solid medium, preferably a methylcellulose based medium, in which a capture molecule is added. The colonies around which a precipitated halo is observed can be isolated and further studied. The foreign DNA can be retrieved from such colonies to identify and isolate the capture binding/interacting molecule that was responsible for the formation of the precipitate halo.
Isolating Polypeptide of Interest
In one embodiment, after the cell clone being identified, it is harvested and expanded in culture and the polypeptide of interest is isolated therefrom using techniques well established in the art. The polypeptide of interest preferably is recovered from the culture medium as a secreted polypeptide. As a first step, the culture medium is centrifuged to remove particulate cell debris. The polypeptide thereafter is purified from contaminant soluble proteins and polypeptides, with the following procedures being exemplary of suitable purification procedures: by fractionation on immunoaffinity or ion-exchange columns; ethanol precipitation; reverse phase HPLC; chromatography on silica or on a cation-exchange resin such as DEAE; chromatofocusing; SDS-PAGE; ammonium sulfate precipitation; gel filtration etc. A protease inhibitor such as phenyl methyl sulfonyl fluoride (PMSF) also may be useful to inhibit proteolytic degradation during purification. Additionally, the polypeptide of interest can be fused in frame to a marker sequence, such as but not limited to a hexahistidine (HA) tag, which allows for purification of the polypeptide of interest.
The methods of the present invention are also useful in identifying cell clones expressing G-protein coupled receptors (GPCRs) and other transmembrane proteins. These proteins may be purified as part of a membrane fraction or purified from the membranes by methods known in the art.
Advantage
In the present invention, cells producing the polypeptide of interest can be identified by reference to the formation of halo. It will be clear to the skilled artisan that one of the benefits of the present invention is that it eliminates intermediate steps normally required in conventional screening methods, such as ELISA. In addition, high level producers can be identified by reference to the timing of the halo formation and the size of the formed halo. Therefore, the present invention provides a simple yet powerful qualitative screening method in contrast to conventional methods, such as ELISA, which are largely quantitative. Accordingly, the method of the present invention can be used as the primary screening method to examine large number of cells and is less labor-intensive and less time-consuming.
It will also be clear to the skilled artisan that this method can be used in robotic screening and in protocols for high throughput selection of cells producing high levels of a product of interest.
A preferred embodiment of the present invention is described by reference to the following examples, which are provided by way of illustration and are not intended as limiting. In this embodiment exemplified below, selection can be visually monitored by the immunoprecipitate (halo) formed between the chimeric anti-TNF antibody cA2 and the capture antibody rabbit anti-human IgG (H&L), while the production level of cA2 correlates with the size of the halo.
Example 1
Preparation of Methylcellulose Based Semi-Solid Capture Medium with Capture Antibody
Pre-made semi-solid matrix (4000 cps) containing methylcellulose in growth medium such as IMDM, EMDM, CD CHO, CD Hybridoma are commercially available. For example, Methocult from StemCell Technologies was used in the following experiments.
The semi-solid capture medium was prepared by adding 1 ml capture antibody (2 mg/ml) to 13 ml methylcellulose medium. Antibiotic reagent and cell suspension were added to the mixture along with FBS, L-glutamine and additional growth medium to make 20 ml of final volume. In this example, the final concentration of the components are 1% methylcellulose, 30% FBS and 2 mM L-glutamine. It is readily understood that other concentrations suitable for the specific cell line are within the scope of this invention.
This working mixture was placed in a proper container (such as a 50 ml conical centrifuge tube) and mixed or vortexed vigorously for 30 seconds. After mixing, the tubes sat at room temperature for 5-10 minutes to allow air bubbles to disappear. The 20 ml of cells in the capture medium was evenly dispensed into a 6-well plate. The plate was incubated in a 37° C. CO2 incubator without disturbance for 7 to 10 days. The plates were then removed for examination.
The sensitivity of this assay can be optimized by changing the concentration of capture antibody and the amount of methylcellulose used to make the semi-solid capture meidum. Combination of lower capture antibody concentration and less methylcellulose routinely result in better detection sensitivity.
Example 2
Transfection and Initial Selection of Myeloma Cells Using Antibiotics
Murine myeloma Sp2/0 derived cell line C463A was transfected with chimeric anti-TNF antibody cA2 expression plasmids by electroporation as described by Knight et al.
In brief, the expression plasmid for cA2 heavy chain was linearized by digestion with XhoI and the expression plasmid for cA2 light chain was linearized using KpnI restriction enzyme. 10×106 C463A cells were transfected with about 10 μg of linearized plasmid by electroporation (200V and 1180 uF). Following the electroporation, the cells were plated in T-75 flasks for 72 hours. After recovery, cells were selected with 0.5 μg/ml mycophenylic acid for 2-5 passages.
Example 3
Colony Formation and Halo Detection in Methylcellulose Based Semi-Solid Capture Medium
Transfected cells from the antibiotic selected culture were plated in methylcellulose based semi-solid capture medium in 6-well plates at 1-3×103 cells per well. The rabbit anti-human IgG (H&L) antibody was purchased from Jackson ImmunoResearch Laboratories, Inc. This capture antibody recognizes the chimeric anti-TNF cA2 mAb used in the experiment and has been used in Nephelometry for IgG quantitation.
In this assay, the capture antibody was incorporated to the methylcellulose based semi-solid capture medium at the final concentration of 1 mg/ml. The cultures in semi-solid methylcellulose capture medium were incubated at 37° C., 5% CO2 and >95% humidity without disturbance for 7-10 days before examination for colony and precipitate halo formation. The multiplication of cells was observed within 20 to 24 hours after plating and colonies were formed within 10 days.
Precipitates were found around cells in about two days. The precipitate became halo-like under a phase microscope in about 7 to 8 days. Selection of colonies with distinct halo was done no later than day 12. Single colonies were picked up carefully under a microscope and expanded in CD hybridoma growth medium (Invitrogen) for studying cell growth and IgG production.
Two negative control experiments were performed in this experiment. One is host cell line C463A in methylcellulose medium with capture antibody. The other one is cA2 producing C463A cells in methylcellulose medium without capture antibody. No halo-like structure was found in either of the negative controls.
Example 4
Selection of Clones Through Correlation Between the Halo Size and the Level of IgG Production
Previously, some of the major obstacles to use agarose based semi-solid growth medium for screening high production cell lines include the difficulty to observe the halo formation even under the microscope as well as the poor correlation between the size of halos and the actual protein production. The new method improves the halo formation, which makes the correlation of halo size to protein production more accurate and reliable.
To correlate halo size to protein production, 20 colonies from each of the following categories were picked and grown in 24-well plates with 1 ml of IMDM+5% FBS growth medium:

    
    
        large halo: the width of the halo is equal to or greater than the radius of the colony that the halo surrounds;
        small halo: the width of halo is equal or less than half of the radius of the colony that the halo surrounds; and
        haloless: no surrounding halo was observed.
    
    


Colonies from each category were grown for 12 days. The supernatant of these cultures was then collected for IgG quantitation by a nephlometer. IgG titers from different sizes of halo were then analyzed statistically (T test and F test). The results (Table 1) clearly showed a positive correlation between the halo size and the IgG production. The confidence level of obtaining high expressing clones using halo size was above 95%.







TABLE 5







Correlation between halo size and OG titer (mg/ml) in 5% FBS











Halo






Size

Large
Small
Zero














OG Titer
1
48.7
20.72
30.16


(mg/L)
2
47.25
5.33
30.56



3
26.93
26.33
18.13



4
33.41
19.41
17.37



5
34.55
37.4
7.02



6
34.26
29.1
23.14



7
33.41
19.59
4.12



8
35.4
42.29
18.72



9
13.81
27.36
22.94



10
22.37
22.37
22.71



11
44.04
23.38
3.43



12
52.02
16.2
4.68



13
54.44
26.64
4.43



14
26.93
26.64
2.99



15
30.84
23.35
5.76



16
34.83
23.23
3.23



17
22.37
22.17
7.39



18
33.69
31.98
19.56



19
47.84
49.62
4.56



20
40.27
10.7




Average
35.9
25.2
13.2









Example 5
Primary Screening for High IgG Producing Clones
Murine myeloma cells Sp2/0 or NSO were transfected with plasmids encoding an antibody against human IL-13 by electroporation as previously described in Example 2. Transfected cells from the antibiotic selected culture were plated in methylcellulose based semi-solid capture medium. After 8-14 days, colonies with halos were observed and picked into suitable growth medium. The titers of spent culture from representative transfectants in shake flasks are consistently higher than those of transfectants identified by ELISA. For example, the titer in shaker flask is in the range of 33-100 μg/ml for transfected Sp2/0 cells, and 55-108 μg/ml for transfected NSO cells.
Example 6
Subcloning of High IgG Producer
It is well known in the art that if the transfected cells have been in continuous culture for a long time, or the cells in culture are not derived from a single cell clone, they may need to be recloned. The present invention also provides a method to rapidly achieve this goal.
For cells expressing chimeric anti-TNF cA2 mAb, several clones screened by halo assay produced IgG greater than 180 ug/ml in IMDM derived medium while parental cells (before subcloning) routinely produced 120 ug/ml in the same condition. When cultured in CD hybridoma medium, greater than 80 ug/ml IgG titers were observed.
It will be clear that the invention can be practiced otherwise than as particularly described in the foregoing description and examples. Numerous modifications and variations of the present invention are possible in light of the above teachings and, therefore are within the scope of the appended claims.

## Claims

1. The method for selecting eukaryotic clones highly expressing a polypeptide of interest from a population of eukaryotic cells expressing said polypeptide of interest comprising:
(a) culturing said population of eukaryotic cells on a semi-solid culture medium;
(b) contacting said population of cultured eukaryotic cells with a capture molecule that interacts with said polypeptide of interest, wherein the concentration of said capture molecule is between about 0.2 and 2.0 mg/ml, and said capture molecule comprises a detectable label;
(c) incubating said population of cultured eukaryotic cells expressing said polypeptide of interest with said capture molecule for a period of time;
(d) measuring the relative size of haloes produced by said detectable label following interaction of said polypeptide of interest with said capture molecule and wherein high expressing eukaryotic clones have a halo with a width that is equal to, or greater than, the radius of a eukaryotic cell clone lacking a halo; and
(e) selecting at least one of said high expressing eukaryotic cell clones from said population of said eukaryotic cells.

2. The method according to claim 1, wherein said capture molecule is an antibody or a polypeptide binding fragment thereof.

3. The method according to claim 1, wherein said detectable label is selected from the group consisting of: a chemical label, a biological label, a fluorescent label and a radioactive label.

4. The method according to claim 1, wherein the semi-solid culture medium comprises a gelatinization agent comprising cellulose or agar.

5. The method according to claim 1, wherein said eukaryotic cells are selected from the group consisting of: mammalian cells, yeast cells and insect cells.

6. The method according to claim 5, wherein said mammalian cells are selected from the group consisting of: COS-1, COS-7, HEK293, HK21, CHO, BSC-1, HepG2, 653, SP2/0, 293, NSO, DG44 CHO, CHO K1, HeLa, myeloma, and lymphoma cells, or any derivative, immortalized or transformed cells thereof.

7. The method according to claim 1, wherein said polypeptide of interest is a soluble polypeptide.

8. The method according to claim 1, wherein said polypeptide of interest is an immunoglobulin or at least a portion thereof.

9. The method according to claim 1, wherein the capture molecule is selected from the group consisting of a portion of a ligand wherein the portion binds to the polypeptide of interest, a portion of a receptor wherein the portion of said receptor binds to the polypeptide of interest, and an antibody that binds to the polypeptide of interest.

10. The method according to claim 9, wherein said capture molecule is an antibody that binds said polypeptide of interest.

11. The method according to claim 1, wherein the cells are myeloma cells, said polypeptide of interest is an immunoglobulin, the capture molecule is an antibody against the immunoglobulin, and the semi-solid culture medium is methylcellulose based.

12. The method according to claim 1, wherein the concentration of said capture molecule is 1.0 mg/ml.

13. The method according to claim 1, wherein said polypeptide of interest is at least one member selected from the group consisting of: a growth factor, a cytokine, a blood protein, a neurotransmitter, and a pharmacologically active peptide, or any portion or derivative thereof.

14. The method according to claim 1, wherein said polypeptide of interest is an antagonist of at least one member selected from the group consisting of: growth factors, cytokines, blood proteins, neurotransmitters, and pharmacologically active peptides, or portions or derivatives thereof.

15. The method according to claim 14, wherein said antagonist is at least one member selected from the group consisting of: an antibody, an antibody fusion, and an antibody fragment, or any portion or derivative thereof.