# Patent

## Title
Antibodies and methods for generating genetically altered antibodies with enhanced effector function

## Abstract

Dominant negative alleles of human mismatch repair genes can be used to generate hypermutable cells and organisms. By introducing these genes into cells and transgenic animals, new cell lines and animal varieties with novel and useful properties can be prepared more efficiently than by relying on the natural rate of mutation. These methods are useful for generating genetic diversity within immunoglobulin genes directed against an antigen of interest to produce altered antibodies with enhanced biochemical activity. Moreover, these methods are useful for generating antibody-producing cells with increased level of antibody production. The invention also provides methods for increasing the effector function of monoclonal antibodies and monoclonal antibodies with increased effector function.

## Background
CROSS REFERENCE TO RELATED APPLICATIONS
This is a continuation of U.S. Application Ser. No. 10/901,650, filed Jul. 29, 2004, now abandoned, which claims the benefit of U.S. Provisional Application 60/491,310, filed Jul. 29, 2003. Both applications are hereby incorporated by reference.


FIELD OF THE INVENTION
The invention is related to the area of antibody effector function and cellular production. In particular, it is related to the field of mutagenesis.
BACKGROUND OF THE INVENTION
The use of antibodies to block the activity of foreign and/or endogenous polypeptides provides an effective and selective strategy for treating the underlying cause of disease. For example, monoclonal antibodies (MAb), such as the FDA-approved ReoPro (Glaser, V. (1996) “Can ReoPro repolish tarnished monoclonal therapeutics?” Nat. Biotechnol. 14:1216-1217), an anti-platelet MAb from Centocor; Herceptin (Weiner, L. M. (1999) “Monoclonal antibody therapy of cancer” Semin. Oncol. 26:43-51), an anti-Her2/neu MAb from Genentech; and Synagis (Saez-Llorens, X. E., et al. (1998) “Safety and pharmacokinetics of an intramuscular humanized monoclonal antibody to respiratory syncytial virus in premature infants and infants with bronchopulmonary dysplasia” Pediat. Infect. Dis. J. 17:787-791), an anti-respiratory syncytial virus MAb produced by Medimmune, have been used as effective therapeutics.
Standard methods for generating MAbs against candidate protein targets are known by those skilled in the art. Briefly, rodents such as mice or rats are injected with a purified antigen in the presence of adjuvant to generate an immune response (Shield, C. F., et al. (1996) A cost-effective analysis of OKT3 induction therapy in cadaveric kidney transplantation. Am. J. Kidney Dis. 27:855-864). Rodents with positive immune sera are sacrificed and splenocytes are isolated. Isolated splenocytes are fused to melanomas to produce immortalized cell lines that are then screened for antibody production. Positive lines are isolated and characterized for antibody production. The direct use of rodent MAbs as human therapeutic agents were confounded by the fact that human anti-rodent antibody (HARA) responses occurred in a significant number of patients treated with the rodent-derived antibody (Khazaeli, M. B., et al, (1994) Human immune response to monoclonal antibodies. J. Immunother. 15:42-52). In order to circumvent the problem of HARA, the grafting of the complementarity determining regions (CDRs), which are the critical motifs found within the heavy and light chain variable regions of the immunoglobulin (Ig) subunits making up the antigen binding domain, onto a human antibody backbone found these chimeric molecules are able to retain their binding activity to antigen while lacking the HARA response (Emery, S. C., and Harris, W. J. “Strategies for humanizing antibodies” In: ANTIBODY ENGINEERING C. A. K. Borrebaeck (Ed.) Oxford University Press, N.Y. 1995. pp. 159-183). A common problem that exists during the “humanization” of rodent-derived MAbs (referred to hereon as HAb) is the loss of binding affinity due to conformational changes in the 3-dimensional structure of the CDR domain upon grafting onto the human Ig backbone (U.S. Pat. No. 5,530,101 to Queen et al.). To overcome this problem, additional HAb vectors usually need to be engineered by inserting or deleting additional amino acid residues within the framework region and/or within the CDR coding region itself in order to recreate high affinity HAbs (U.S. Pat. No. 5,530,101 to Queen et al.). This process is a very time consuming procedure that involves the use of expensive computer modeling programs to predict changes that may lead to a high affinity HAb. In some instances, the affinity of the HAb is never restored to that of the MAb, rendering them of little therapeutic use.
Another problem that exists in antibody engineering is the generation of stable, high yielding producer cell lines that are required for manufacturing of the molecule for clinical materials. Several strategies have been adopted in standard practice by those skilled in the art to circumvent this problem. One method is the use of Chinese Hamster Ovary (CHO) cells transfected with exogenous Ig fusion genes containing the grafted human light and heavy chains to produce whole antibodies or single chain antibodies, which are a chimeric molecule containing both light and heavy chains that form an antigen-binding polypeptide (Reff, M. E. (1993) High-level production of recombinant immunoglobulins in mammalian cells. Curr. Opin. Biotechnol. 4:573-576). Another method employs the use of human lymphocytes derived from transgenic mice containing a human grafted immune system or transgenic mice containing a human Ig gene repertoire. Yet another method employs the use of monkeys to produce primate MAbs, which have been reported to lack a human anti-monkey response (Neuberger, M., and Gruggermann, M. (1997) Monoclonal antibodies. Mice perform a human repertoire. Nature 386:25-26). In all cases, the generation of a cell line that is capable of generating sufficient amounts of high affinity antibody poses a major limitation for producing sufficient materials for clinical studies. Because of these limitations, the utility of other recombinant systems such as plants are currently being explored as systems that will lead to the stable, high-level production of humanized antibodies (Fiedler, U., and Conrad, U. (1995) High-level production and long-term storage of engineered antibodies in transgenic tobacco seeds. Bio/Technology 13:1090-1093).
Still another aspect of antibody function is the effector mechanisms of the Mab. One of many possible ways to increase effector function of antibodies is via changes in glycosylation. This topic has been recently reviewed by Ruju who summarized the proposed importance of the oligosaccharides found on human IgGs with their degree of effector function (Raju, T S. BioProcess International April 2003. 44-53). According to Wright and Morrison, the microheterogeneity of human IgG oligosaccharides can affect biological functions such as complement dependent cytotoxicty (CDC) and antibody-dependent cytotoxicity (ADCC), binding to various Fc receptors, and binding to C1q protein (Wright A. Morrison S L. TIBTECH 1997, 15 26-32). It is well documented that glycosylation patterns of antibodies can differ depending on the producing cell and the cell culture conditions (Raju, T S. BioProcess International April 2003. 44-53). Such differences can lead to changes in both effector function and pharmacokinetics (Israel E J, Wilsker D F, Hayes K C, Schoenfeld D, Simister N E. Immunology. 1996 December; 89(4):573-578; Newkirk M M, Novick J, Stevenson M M, Fournier Mi, Apostolakos P. Clin. Exp. 1996 November; 106(2):259-64). Differences in effector function may be related to the IgGs ability to bind to the Fcγ receptors (FcγRs) on the effector cells. Shields, et al., have shown that IgG1 with variants in amino acid sequence that have improved binding to FcγR can exhibit up to 100% enhanced ADCC using human effector cells (Shields R L, Namenuk A K, Hong K, Meng Y G, Rae J, Briggs J, Xie D, Lai J, Stadlen A, Li B, Fox J A, Presta L G. J Biol. Chem. 2001 Mar. 2; 276(9):6591-604). While these variants include changes in amino acids not found at the binding interface, both the nature of the sugar component as well as its structural pattern may also contribute to the differences seen. In addition, the presence or absence of fucose in the oligosaccharide component of an IgG1 can improve binding and ADCC (Shields R L, Lai J, Keck R, O'Connell L Y, Hong K, Meng Y G, Weikert S H, Presta L G. J Biol. Chem. 2002 Jul. 26; 277(30):26733-40). An IgG1 that lacked a fucosylated carbohydrate linked to Asn297 exhibited normal receptor binding to the Fcγ receptor. In contrast, binding to the FcγRIIA receptor was improved 50% and accompanied by enhanced ADCC, especially at lower antibody concentrations.
Work by Shinkawa, et al., demonstrated that an antibody to the human IL-5 receptor produced in a rat hybridoma showed more than 50% higher ADCC when compared to the antibody produced in Chinese hamster ovary cells (CHO)(Shinkawa T, Nakamura K, Yaman N, Shoji-Hosaka E, Kanda Y, Sakurada M, Uchida K, Anazawa H, Satoh M, Yamasaki M, Hanai N, Shitara K. J Biol Chem. 2003 Jan. 31; 278(5):3466-73). Monosaccharide composition and oligosaccharide profiling showed that the rat hybridoma-produced IgG1 had a lower content of fucose than the CHO-produced protein. The authors concluded that the lack of fucosylation of an IgG1 has a critical role in enhancement of ADCC activity.
A different approach was taken by Umana, et al., who changed the glycosylation pattern of chCE7, a chimeric IgG1 anti-neuroblastoma antibody (Umana P. Jean-Mairet J, Moudry R, Amstutz H, Bailey J E. Nat Biotechnol. 1999 February; 17(2): 176-80). Using tetracycline, they regulated the activity of a glycosyltransferase enzyme (GnTIII) which bisects oligosaccharides that have been implicated in ADCC activity. The ADCC activity of the parent antibody was barely above background level. Measurement of ADCC activity of the chCE7 produced at different tetracycline levels showed an optimal range of GnTIII expression for maximal chCE7 in vitro ADCC activity. This activity correlated with the level of constant region-associated, bisected complex oligosaccharide. Newly optimized variants exhibited substantial ADCC activity.
A method for generating diverse antibody sequences within the variable domain that results in HAbs and MAbs with high binding affinities to antigens would be useful for the creation of more potent therapeutic and diagnostic reagents respectively. Moreover, the generation of randomly altered nucleotide and polypeptide residues throughout an entire antibody molecule will result in new reagents that are less antigenic and/or have beneficial pharmacokinetic properties. The invention described herein is directed to the use of random genetic mutation throughout an antibody structure in vivo by blocking the endogenous mismatch repair (MMR) activity of a host cell producing immunoglobulins that encode biochemically active antibodies. The invention also relates to methods for repeated in vivo genetic alterations and selection for antibodies with enhanced binding and pharmacokinetic profiles. The methods of the invention may be used to enhance the effector function of the antibodies.
In addition, the ability to develop genetically altered host cells that are capable of secreting increased amounts of antibody will also provide a valuable method for creating cell hosts for product development. The invention described herein is directed to the creation of genetically altered cell hosts with increased antibody production via the blockade of MMR.
The invention facilitates the generation of antibodies with enhanced effector function and the production of cell lines with elevated levels of antibody production. Other advantages of the present invention are described in the examples and figures described herein.
SUMMARY OF THE INVENTION
The invention provides methods for generating genetically altered antibodies (including single chain molecules) and antibody producing cell hosts in vitro and in vivo, whereby the antibody possesses a desired biochemical property(s), such as, but not limited to, increased antigen binding, increased gene expression, enhanced effector function and/or enhanced extracellular secretion by the cell host. One method for identifying antibodies with increased binding activity or cells with increased antibody production is through the screening of MMR defective antibody producing cell clones that produce molecules with enhanced binding properties, enhanced effector function such as (but not limited to) antibody-dependent cellular cytotoxicity (ADCC), or clones that have been genetically altered to produce enhanced amounts of antibody product.
The antibody producing cells suitable for use in the invention include, but are not limited to rodent, primate, or human hybridomas or lymphoblastoids; mammalian cells transfected with and expressing exogenous Ig subunits or chimeric single chain molecules; plant cells, yeast or bacteria transfected with and expressing exogenous Ig subunits or chimeric single chain molecules.
Thus, the invention provides methods for making hypermutable antibody-producing cells by introducing a polynucleotide comprising a dominant negative allele of a mismatch repair gene into cells that are capable of producing antibodies. The cells that are capable of producing antibodies include cells that naturally produce antibodies, and cells that are engineered to produce antibodies through the introduction of immunoglobulin encoding sequences. Conveniently, the introduction of polynucleotide sequences into cells is accomplished by transfection.
The invention also provides methods of making hypermutable antibody producing cells by introducing a dominant negative mismatch repair (MMR) gene such as PMS2 (preferably human PMS2), MLH1, PMS1, MSH1, or MSH2 into cells that are capable of producing antibodies. The dominant negative allele of a mismatch repair gene may be a truncation mutation of a mismatch repair gene (preferably a truncation mutation at codon 134, or a thymidine at nucleotide 424 of wild-type PMS2). The invention also provides methods in which mismatch repair gene activity is suppressed. This may be accomplished, for example, using antisense molecules directed against the mismatch repair gene or transcripts.
Other embodiments of the invention provide methods for making a hypermutable antibody producing cells by introducing a polynucleotide comprising a dominant negative allele of a mismatch repair gene into fertilized eggs of animals. These methods may also include subsequently implanting the eggs into pseudo-pregnant females whereby the fertilized eggs develop into a mature transgenic animal. The mismatch repair genes may include, for example, PMS2 (preferably human PMS2), MLH1, PMS1, MSH1, or MSH2. The dominant negative allele of a mismatch repair gene may be a truncation mutation of a mismatch repair gene (preferably a truncation mutation at codon 134, or a thymidine at nucleotide 424 of wild-type PMS2).
The invention further provides homogeneous compositions of cultured, hypermutable, mammalian cells that are capable of producing antibodies and contain a dominant negative allele of a mismatch repair gene. The mismatch repair genes may include, for example, PMS2 (preferably human PMS2), MLH1, PMS1, MSH1, or MSH2. The dominant negative allele of a mismatch repair gene may be a truncation mutation of a mismatch repair gene (preferably a truncation mutation at codon 134, or a thymidine at nucleotide 424 of wild-type PMS2). The cells of the culture may contain PMS2, (preferably human PMS2), MLH1, or PMS1; or express a human mutL homolog, or the first 133 amino acids of hPMS2.
The invention further provides methods for generating a mutation in an immunoglobulin gene of interest by culturing an immunoglobulin producing cell selected for an immunoglobulin of interest wherein the cell contains a dominant negative allele of a mismatch repair gene. The properties of the immunoglobulin produced from the cells can be assayed to ascertain whether the immunoglobulin gene harbors a mutation. The assay may be directed to analyzing a polynucleotide encoding the immunoglobulin, or may be directed to the immunoglobulin polypeptide itself.
The invention also provides methods for generating a mutation in a gene affecting antibody production in an antibody-producing cell by culturing the cell expressing a dominant negative allele of a mismatch repair gene, and testing the cell to determine whether the cell harbors mutations within the gene of interest, such that a new biochemical feature (e.g., over-expression and/or secretion of immunoglobulin products) is generated. The testing may include analysis of the steady state expression of the immunoglobulin gene of interest, and/or analysis of the amount of secreted protein encoded by the immunoglobulin gene of interest. The invention also embraces prokaryotic and eukaryotic transgenic cells made by this process, including cells from rodents, non-human primates and humans.
Other aspects of the invention encompass methods of reversibly altering the hypermutability of an antibody producing cell, in which an inducible vector containing a dominant negative allele of a mismatch repair gene operably linked to an inducible promoter is introduced into an antibody-producing cell. The cell is treated with an inducing agent to express the dominant negative mismatch repair gene (which can be PMS2 (preferably human PMS2), MLH1, or PMS1). Alternatively, the cell may be induced to express a human mutL homolog or the first 133 amino acids of hPMS2. In another embodiment, the cells may be rendered capable of producing antibodies by co-transfecting a preselected immunoglobulin gene of interest. The immunoglobulin genes of the hypermutable cells, or the proteins produced by these methods may be analyzed for desired properties, and induction may be stopped such that the genetic stability of the host cell is restored.
The invention also embraces methods of producing genetically altered antibodies by transfecting a polynucleotide encoding an immunoglobulin protein into a cell containing a dominant negative mismatch repair gene (either naturally or in which the dominant negative mismatch repair gene was introduced into the cell), culturing the cell to allow the immunoglobulin gene to become mutated and produce a mutant immunoglobulin, screening for a desirable property of said mutant immunoglobulin protein, isolating the polynucleotide molecule encoding the selected mutant immunoglobulin possessing the desired property, and transfecting said mutant polynucleotide into a genetically stable cell, such that the mutant antibody is consistently produced without further genetic alteration. The dominant negative mismatch repair gene may be PMS2 (preferably human PMS2), MLH1, or PMS1. Alternatively, the cell may express a human mutL homolog or the first 133 amino acids of hPMS2.
The invention further provides methods for generating genetically altered cell lines that express enhanced amounts of an antigen binding polypeptide. These antigen-binding polypeptides may be, for example, immunoglobulins. The methods of the invention also include methods for generating genetically altered cell lines that secrete enhanced amounts of an antigen binding polypeptide. The cell lines are rendered hypermutable by dominant negative mismatch repair genes that provide an enhanced rate of genetic hypermutation in a cell producing antigen-binding polypeptides such as antibodies. Such cells include, but are not limited to hybridomas. Expression of enhanced amounts of antigen binding polypeptides may be through enhanced transcription or translation of the polynucleotides encoding the antigen binding polypeptides, or through the enhanced secretion of the antigen binding polypeptides, for example.
Methods are also provided for creating genetically altered antibodies in vivo by blocking the MMR activity of the cell host, or by transfecting genes encoding for immunoglobulin in a MMR defective cell host.
Antibodies with increased binding properties to an antigen due to genetic changes within the variable domain are provided in methods of the invention that block endogenous MMR of the cell host. Antibodies with increased binding properties to an antigen due to genetic changes within the CDR regions within the light and/or heavy chains are also provided in methods of the invention that block endogenous MMR of the cell host.
The invention provides methods of creating genetically altered antibodies in MMR defective Ab producer cell lines with enhanced pharmacokinetic properties in host organisms including but not limited to rodents, primates, and man.
These and other aspects of the invention are provided by one or more of the embodiments described below. In one embodiment of the invention, a method for making an antibody producing cell line hypermutable is provided. A polynucleotide encoding a dominant negative allele of a MMR gene is introduced into an antibody-producing cell. The cell becomes hypermutable as a result of the introduction of the gene.
In another embodiment of the invention, a method is provided for introducing a mutation into an endogenous gene encoding for an immunoglobulin polypeptide or a single chain antibody. A polynucleotide encoding a dominant negative allele of a MMR gene is introduced into a cell. The cell becomes hypermutable as a result of the introduction and expression of the MMR gene allele. The cell further comprises an immunoglobulin gene of interest. The cell is grown and tested to determine whether the gene encoding for an immunoglobulin or a single chain antibody of interest harbors a mutation. In another aspect of the invention, the gene encoding the mutated immunoglobulin polypeptide or single chain antibody may be isolated and expressed in a genetically stable cell. In a preferred embodiment, the mutated antibody is screened for at least one desirable property such as, but not limited to, enhanced binding characteristics.
In another embodiment of the invention, a gene or set of genes encoding for Ig light and heavy chains or a combination therein are introduced into a mammalian cell host that is MMR defective. The cell is grown, and clones are analyzed for antibodies with enhanced binding characteristics.
In another embodiment of the invention, a method is provided for producing new phenotypes of a cell. A polynucleotide encoding a dominant negative allele of a MMR gene is introduced into a cell. The cell becomes hypermutable as a result of the introduction of the gene. The cell is grown. The cell is tested for the expression of new phenotypes where the phenotype is enhanced secretion of a polypeptide.
The invention also provides antibodies having increased affinity for antigen comprising immunoglobulin molecules wherein a substitution has been made for at least one amino acid in the variable domain of the heavy and/or light chain. In some embodiments, the substitution is in a position wherein the parental amino acid in that position is an amino acid with a non-polar side chain. In some embodiments the parental amino acid is substituted with a different amino acid that has a non-polar side chain. In other embodiments, the parental amino acid is replaced with a proline or hydroxyproline. In some embodiments, the substitution(s) are made in the framework regions of the heavy and/or light chain variable domains. In some embodiments, the substitution(s) are made within the first framework region of the heavy chain. In some embodiments, the substitution(s) are made within the second framework region of the light chain. In some embodiments, the substitutions are made within the first framework region of the heavy chain and the second framework region of the light chain. In some embodiments, a substitution is made at position 6 of the first framework region of the heavy chain as shown in SEQ ID NO: 18. In some embodiments a substitution is made at position 22 of the second framework region of the light chain as shown in SEQ ID NO:21. For the specific position mutations, in some embodiments the amino acid substitution is a proline or hydroxyproline.
The invention also provides methods for increasing the affinity of an antibody for an antigen comprising substituting an amino acid within the variable domain of the heavy or light chain of the subject antibody with another amino acid having a non-polar side chain. In some embodiments, a proline is substituted for the original amino acid at the position. In some embodiments, proline is used to substitute for another amino acid having a non-polar side chain. In some embodiments alanine and/or leucine is replaced by proline. In certain embodiments, the amino acid in position 6 of the first framework region of the heavy chain of the antibody as shown in SEQ ID NO: 18 is replaced with a proline. In other embodiments, the amino acid in position 22 of the second framework region of the light chain variable domain as shown in SEQ ID NO:21 is replaced with proline. The invention also provides antibodies produced by these methods.
The antibodies produced in the invention may be made using the process of the invention wherein a dominant negative allele of a mismatch repair gene is introduced into the antibody producing cell and the cell becomes hypermutable as described more fully herein. Alternatively, one may disrupt mismatch repair using chemical inhibitors of mismatch repair, such as using anthracene and/or its derivatives as described in PCT Publication No. WO 02/054856, published Jul. 18, 2002, which is specifically incorporated herein in its entirety. The cells treated with the chemicals that disrupt mismatch repair or which express a dominant negative mismatch repair gene become hypermutable. The antibodies produced by the hypermutable cells are screened for increased affinity, and those antibodies comprising the amino acid substitutions described above display increased affinity for antigen. The cells producing the antibodies which have the increased affinity and the molecular characteristics described herein may be rendered genetically stable again by withdrawing the chemical inhibitor, or by rendering the cells genetically stable through the inactivation of the expression of the dominant negative allele. For example, a dominant negative allele that it under the control of an inducible promoter may be inactivated by withdrawing the inducer. Alternatively, the dominant negative allele may be knocked out, or a CRE-LOX expression system may be used whereby the dominant negative allele is spliced from the genome once the cells containing a genetically diverse immunoglobulin has been established.
In other embodiments, one of skill in the art may use any known method of introducing mutations into proteins and selecting for antibodies having higher affinity with the amino acid substitutions described above. Methods of introducing mutations may be random, such as chemical mutagenesis, or may be specific, such as site-directed mutagenesis. Methods for random and specific mutagenesis are well-known in the art and include, but are not limited to, for example, chemical mutagenesis (e.g., using such chemicals as methane sulfonate, dimethyl sulfonate, 06-methyl benzadine, methylnitrosourea (MNU), and ethylnitrosourea (ENU)); oligonucleotide-mediated site-directed mutagenesis; alanine scanning; and PCR mutagenesis (see, for example, Kunkel et al. (1991) Methods Enzymol. 204:125-139), site-directed mutagenesis; Crameri et al. (1995) BioTechniques 18(2):194-196, cassette mutagenesis; and Haught et al. (1994) BioTechniques 16(1):47-48, restriction selection mutagenesis).
These and other embodiments of the invention provide the art with methods that can generate enhanced mutability in cells and animals as well as providing cells and animals harboring potentially useful mutations for the large-scale production of high affinity antibodies with beneficial pharmacokinetic profiles.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1. Hybridoma cells stably expressing PMS2 and PMS134 MMR genes. Shown is steady state mRNA expression of MMR genes transfected into a murine hybridoma cell line. Stable expression was found after 3 months of continuous growth. The (−) lanes represent negative controls where no reverse transcriptase was added, and the (+) lanes represent samples reverse transcribed and PCR amplified for the MMR genes and an internal housekeeping gene as a control.
FIG. 2. Creation of genetically hypermutable hybridoma cells. Dominant negative MMR gene alleles were expressed in cells expressing a MMR-sensitive reporter gene. Dominant negative alleles such as PMS134 and the expression of MMR genes from other species results in antibody producer cells with a hypermutable phenotype that can be used to produce genetically altered immunoglobulin genes with enhanced biochemical features as well as lines with increased Ig expression and/or secretion. Values shown represent the amount of converted CPRG substrate which is reflective of the amount of function of β-galactosidase contained within the cell from genetic alterations within the pCAR-OF reporter gene. Higher amounts of β-galactosidase activity reflect a higher mutation rate due to defective MMR.
FIG. 3. Screening method for identifying antibody-producing cells containing antibodies with increased binding activity and/or increased expression/secretion
FIG. 4. Generation of a genetically altered antibody with an increased binding activity. Shown are ELISA values from 96-well plates, screened for antibodies specific to hIgE. Two clones with a high binding value were found in HB134 cultures.
FIG. 5A illustrates sequence alteration within the variable chain of an antibody (a mutation within the light chain variable region in MMR-defective HB134 antibody producer cells). Arrows indicate the nucleotide at which a mutation occurred in a subset of cells from a clone derived from HB134 cells. The HB134 sequence (SEQ ID NO:25), the consensus sequence (SEQ ID NO:26), and the parental H36 sequence (SEQ ID NO:27) are shown. The change results in a Thr to Ser change within the light chain variable region. The coding sequence is in the antisense direction. FIG. 5B illustrates sequence alteration within the variable chain of an antibody (a mutation within the light chain variable region in MMR-defective HB134 antibody producer cells). The HB134 sequence (SEQ ID NO:28) is shown above and below the tracing for the HB134 sequence, and the parental H36 sequence (SEQ ID NO:29) is shown above and below the H36 sequence tracing. A consensus sequence (SEQ ID NO:30) is shown at the bottom of the figure. Arrows indicate the nucleotide at which a mutation occurred in a subset of cells from a clone derived from HB134 cells. The change results in a Pro to Leu change within the light chain variable region.
FIG. 6. Generation of MMR-defective clones with enhanced steady state Ig protein levels. A Western blot of heavy chain immunoglobulins from HB134 clones with high levels of MAb (>500 ngs/ml) within the conditioned medium shows that a subset of clones express higher steady state levels of immunoglobulins (Ig). The H36 cell line was used as a control to measure steady state levels in the parental strain. Lane 1: fibroblast cells (negative control); Lane 2: H36 cell; Lane 3: HB134 clone with elevated MAb levels; Lane 4: HB134 clone with elevated MAb levels; Lane 5: HB134 clone with elevated MAb levels.
FIG. 7. MORAb-003 is able to induce cytotoxicity in human ovarian tumor cells mediated by normal human PBMCs.



DETAILED DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS
Methods have been discovered for developing hypermutable antibody-producing cells by taking advantage of the conserved mismatch repair (MMR) process of host cells. Dominant negative alleles of such genes, when introduced into cells or transgenic animals, increase the rate of spontaneous mutations by reducing the effectiveness of DNA repair and thereby render the cells or animals hypermutable. Hypermutable cells or animals can then be utilized to develop new mutations in a gene of interest. Blocking MMR in antibody-producing cells such as but not limited to: hybridomas; mammalian cells transfected with genes encoding for Ig light and heavy chains; mammalian cells transfected with genes encoding for single chain antibodies; eukaryotic cells transfected with Ig genes, can enhance the rate of mutation within these cells leading to clones that have enhanced antibody production and/or cells containing genetically altered antibodies with enhanced biochemical properties such as increased antigen binding. The process of MMR, also called mismatch proofreading, is carried out by protein complexes in cells ranging from bacteria to mammalian cells. A MMR gene is a gene that encodes for one of the proteins of such a mismatch repair complex. Although not wanting to be bound by any particular theory of mechanism of action, a MMR complex is believed to detect distortions of the DNA helix resulting from non-complementary pairing of nucleotide bases. The non-complementary base on the newer DNA strand is excised, and the excised base is replaced with the appropriate base, which is complementary to the older DNA strand. In this way, cells eliminate many mutations that occur as a result of mistakes in DNA replication.
Dominant negative alleles cause a MMR defective phenotype even in the presence of a wild-type allele in the same cell. An example of a dominant negative allele of a MMR gene is the human gene hPMS2-134, which carries a truncating mutation at codon 134 (SEQ ID NO: 15). The mutation causes the product of this gene to abnormally terminate at the position of the 134th amino acid, resulting in a shortened polypeptide containing the N-terminal 133 amino acids. Such a mutation causes an increase in the rate of mutations, which accumulate in cells after DNA replication. Expression of a dominant negative allele of a mismatch repair gene results in impairment of mismatch repair activity, even in the presence of the wild-type allele. Any allele which produces such effect can be used in this invention. Dominant negative alleles of a MMR gene can be obtained from the cells of humans, animals, yeast, bacteria, or other organisms. Such alleles can be identified by screening cells for defective MMR activity. Cells from animals or humans with cancer can be screened for defective mismatch repair. Cells from colon cancer patients may be particularly useful. Genomic DNA, cDNA, or mRNA from any cell encoding a MMR protein can be analyzed for variations from the wild type sequence. Dominant negative alleles of a MMR gene can also be created artificially, for example, by producing variants of the hPMS2-134 allele or other MMR genes. Various techniques of site-directed mutagenesis can be used. The suitability of such alleles, whether natural or artificial, for use in generating hypermutable cells or animals can be evaluated by testing the mismatch repair activity caused by the allele in the presence of one or more wild-type alleles, to determine if it is a dominant negative allele.
A cell or an animal into which a dominant negative allele of a mismatch repair gene has been introduced will become hypermutable. This means that the spontaneous mutation rate of such cells or animals is elevated compared to cells or animals without such alleles. The degree of elevation of the spontaneous mutation rate can be at least 2-fold, 5-fold, 10-fold, 20-fold, 50-fold, 100-fold, 200-fold, 500-fold, or 1000-fold that of the normal cell or animal. The use of chemical mutagens such as but limited to methane sulfonate, dimethyl sulfonate, 06-methyl benzadine, MNU, ENU, etc. can be used in MMR defective cells to increase the rates an additional 10 to 100 fold that of the MMR deficiency itself.
According to one aspect of the invention, a polynucleotide encoding for a dominant negative form of a MMR protein is introduced into a cell. The gene can be any dominant negative allele encoding a protein, which is part of a MMR complex, for example, PMS2, PMS1, MLH1, or MSH2. The dominant negative allele can be naturally occurring or made in the laboratory. The polynucleotide can be in the form of genomic DNA, cDNA, RNA, or a chemically synthesized polynucleotide.
The polynucleotide can be cloned into an expression vector containing a constitutively active promoter segment (such as but not limited to CMV, SV40, Elongation Factor or LTR sequences) or to inducible promoter sequences such as the steroid inducible pIND vector (Invitrogen), where the expression of the dominant negative MMR gene can be regulated. The polynucleotide can be introduced into the cell by transfection.
According to another aspect of the invention, an immunoglobulin (Ig) gene, a set of Ig genes or a chimeric gene containing whole or parts of an Ig gene can be transfected into MMR-deficient cell hosts, the cell is grown and screened for clones containing genetically altered Ig genes with new biochemical features. MMR defective cells may be of human, primates, mammals, rodent, plant, yeast or of the prokaryotic kingdom. The mutated gene encoding the Ig with new biochemical features may be isolated from the respective clones and introduced into genetically stable cells (i.e., cells with normal MMR) to provide clones that consistently produce Ig with the new biochemical features. The method of isolating the Ig gene encoding Ig with new biochemical features may be any method known in the art. Introduction of the isolated polynucleotide encoding the Ig with new biochemical features may also be performed using any method known in the art, including, but not limited to transfection of an expression vector containing the polynucleotide encoding the Ig with new biochemical features. As an alternative to transfecting an Ig gene, a set of Ig genes or a chimeric gene containing whole or parts of an Ig gene into an MMR deficient host cell, such Ig genes may be transfected simultaneously with a gene encoding a dominant negative mismatch repair gene into a genetically stable cell to render the cell hypermutable.
Transfection is any process whereby a polynucleotide is introduced into a cell. The process of transfection can be carried out in a living animal, e.g., using a vector for gene therapy, or it can be carried out in vitro, e.g., using a suspension of one or more isolated cells in culture. The cell can be any type of eukaryotic cell, including, for example, cells isolated from humans or other primates, mammals or other vertebrates, invertebrates, and single celled organisms such as protozoa, yeast, or bacteria.
In general, transfection will be carried out using a suspension of cells, or a single cell, but other methods can also be applied as long as a sufficient fraction of the treated cells or tissue incorporates the polynucleotide so as to allow transfected cells to be grown and utilized. The protein product of the polynucleotide may be transiently or stably expressed in the cell. Techniques for transfection are well known. Available techniques for introducing polynucleotides include but are not limited to electroporation, transduction, cell fusion, the use of calcium chloride, and packaging of the polynucleotide together with lipid for fusion with the cells of interest. Once a cell has been transfected with the MMR gene, the cell can be grown and reproduced in culture. If the transfection is stable, such that the gene is expressed at a consistent level for many cell generations, then a cell line results.
An isolated cell is a cell obtained from a tissue of humans or animals by mechanically separating out individual cells and transferring them to a suitable cell culture medium, either with or without pretreatment of the tissue with enzymes, e.g., collagenase or trypsin. Such isolated cells are typically cultured in the absence of other types of cells. Cells selected for the introduction of a dominant negative allele of a mismatch repair gene may be derived from a eukaryotic organism in the form of a primary cell culture or an immortalized cell line, or may be derived from suspensions of single-celled organisms.
A polynucleotide encoding for a dominant negative form of a MMR protein can be introduced into the genome of an animal by producing a transgenic animal. The animal can be any species for which suitable techniques are available to produce transgenic animals. For example, transgenic animals can be prepared from domestic livestock, e.g., bovine, swine, sheep, goats, horses, etc.; from animals used for the production of recombinant proteins, e.g., bovine, swine, or goats that express a recombinant polypeptide in their milk; or experimental animals for research or product testing, e.g., mice, rats, guinea pigs, hamsters, rabbits, etc. Cell lines that are determined to be MMR defective can then be used as a source for producing genetically altered immunoglobulin genes in vitro by introducing whole, intact immunoglobulin genes and/or chimeric genes encoding for single chain antibodies into MMR defective cells from any tissue of the MMR defective animal.
Once a transfected cell line or a colony of transgenic animals has been produced, it can be used to generate new mutations in one or more gene(s) of interest. A gene of interest can be any gene naturally possessed by the cell line or transgenic animal or introduced into the cell line or transgenic animal. An advantage of using such cells or animals to induce mutations is that the cell or animal need not be exposed to mutagenic chemicals or radiation, which may have secondary harmful effects, both on the object of the exposure and on the workers. However, chemical mutagens may be used in combination with MMR deficiency, which renders such mutagens less toxic due to an undetermined mechanism. Hypermutable animals can then be bred and selected for those producing genetically variable B-cells that may be isolated and cloned to identify new cell lines that are useful for producing genetically variable cells. Once a new trait is identified, the dominant negative MMR gene allele can be removed by directly knocking out the allele by technologies used by those skilled in the art or by breeding to mates lacking the dominant negative allele to select for offspring with a desired trait and a stable genome. Another alternative is to use a CRE-LOX expression system, whereby the dominant negative allele is spliced from the animal genome once an animal containing a genetically diverse immunoglobulin profile has been established. Yet another alternative is the use of inducible vectors such as the steroid induced pIND (Invitrogen) or pMAM (Clonetech) vectors which express exogenous genes in the presence of corticosteroids.
Mutations can be detected by analyzing for alterations in the genotype of the cells or animals, for example by examining the sequence of genomic DNA, cDNA, messenger RNA, or amino acids associated with the gene of interest. Mutations can also be detected by screening for the production of antibody titers. A mutant polypeptide can be detected by identifying alterations in electrophoretic mobility, spectroscopic properties, or other physical or structural characteristics of a protein encoded by a mutant gene. One can also screen for altered function of the protein in situ, in isolated form, or in model systems. One can screen for alteration of any property of the cell or animal associated with the function of the gene of interest, such as but not limited to Ig secretion.
Cells expressing the dominant negative alleles can be “cured” in that the dominant negative allele can be turned off, if inducible, eliminated from the cell, and the like such that the cells become genetically stable once more and no longer accumulate mutations at the abnormally high rate. The polynucleotide can be cloned into an expression vector containing constitutively active promoter segment (such as but not limited to CMV, SV40, Elongation Factor or LTR sequences) or to inducible promoter sequences such as the steroid inducible pIND vector where the expression of the dominant negative mismatch repair gene can be regulated. The cDNA is introduced into the cell by transfection. Upon identification of the desired phenotype or trait the organism can then be genetically stabilized.
Examples of mismatch repair proteins and nucleic acid sequences include mouse PMS2 (SEQ ID NOs:5 and 6), human PMS2 (SEQ ID NOs:7 and 8), human PMS1 (SEQ ID NOs:9 and 10), human MSH2 (SEQ ID NOs: 11 and 12), human MLH1 (SEQ ID NOs: 13 and 14), and human PMS2-134 (SEQ ID NOs:15 and 16).
Mutant antibodies showing increased affinity for antigen were sequenced and compared to the sequence of the wild-type (WT) H36 parental antibody. It has been discovered that alterations of amino acids to proline has the effect of increasing affinity for antigen when introduced into the variable region of either the light chain or heavy chain of the immunoglobulin molecule. While not wishing to be bound by any particular theory of operation, it is believed that the prolines introduce a localized area of rigidity and lend stability to the immunoglobulin molecule, particularly to the regions around the antigen combining sites.
Thus, the invention provides for a method to increase the affinity of antibodies comprising replacing amino acids of the variable domain heavy and/or light chain with proline or hydroxyproline (collectively referred to as “proline”). In some embodiments, the substitution of prolines is in the heavy chain variable domain. In some embodiments, the substitution of prolines is in the light chain variable domain. In other embodiments, the substitution of proline is in both the heavy chain and the light chain of the variable domain of the immunoglobulin molecule. In some embodiments, the proline substitutes for another amino acid having a non-polar sidechain (e.g., glycine, alanine, valine, leucine, isoleucine, phenylalanine, methionine, tryptophan and cysteine). In some embodiments, further exchanges of amino acids having non-polar sidechains with other amino acids having non-polar sidechains may also confer increased affinity of the antibody for the antigen. In some embodiments, the amino acid substitutions are in a framework region of the heavy chain. In other embodiments, the amino acid substitutions are in a framework region of the light chain.
In other embodiments, the amino acid substitutions are in a framework region of both the heavy and light chain. In some embodiments, the amino acid substitutions are in the first framework region (FR1) of the heavy chain. In other embodiments, the amino acid substitution is in the second framework region (FR2) of the heavy chain. In other embodiments, the amino acid substitution is in the third framework region (FR3) of the heavy chain. In other embodiments, the amino acid substitution is in the fourth framework region (FR4) of the heavy chain. In some embodiments, the amino acid substitutions are in the first framework region (FR1) of the light chain. In other embodiments, the amino acid substitution is in the second framework region (FR2) of the light chain. In other embodiments, the amino acid substitution is in the third framework region (FR3) of the light chain. In other embodiments, the amino acid substitution is in the fourth framework region (FR4) of the light chain.
In certain embodiments of the invention, a proline substitutes for an alanine at position 6 of SEQ ID NO: 18. In other embodiments, proline substitutes for alanine at position 6 of SEQ ID NO: 18 and the glycine at position 9 of SEQ ID NO: 18, and/or the lysine at position 10 of SEQ ID NO: 18 is substituted with an amino acid having a non-polar side chain (preferably, valine and arginine, respectively). In other embodiments, proline substitutes for leucine at position 22 of SEQ ID NO:21.
The recent clinical and commercial success of anticancer antibodies, such as rituximab (Rituxan) and trastuzumab (Herceptin) and small molecule signal transduction inhibitors such as imatinib mesylate, (Gleevec or STI-571), has created great interest in “targeted” therapeutics for hematopoietic malignancies and solid tumors. In comparison to small molecule cytotoxic agents it is hoped that these approaches will result in lower toxicity while maintaining or increasing the therapeutic efficacy.
Antibodies conjugated to radionuclides, drugs or toxins have intrinsic specificity due to their specific antigen binding. The degree of specificity is dependent on the relative specificity of the antigen on the targeted tumor. The conjugated toxic component complicates the approach since the radionuclide is irradiating normal tissues during the duration of its circulation (prolonged for a humanized antibody) and drugs and toxins can be detached from the antibody by enzymatic and non-enzymatic mechanism, thus delivering the toxin to normal tissue. In addition, the presence of the conjugate can result in the body recognizing the complex as foreign with the resulting uptake into organs of clearance such as the liver.
Previous attempts at maximizing the therapeutic potential of monoclonal antibodies have mostly focused on improving the affinity and avidity of binding to the targeted antigen. The method of the invention allows for the maximization of efficacy of an unconjugated antibody. It is an object of the invention to generate improved monoclonal antibodies (e.g., humanized antibodies) by producing and assaying molecules with increases in the effector function (Fc) of the protein, regardless of the mechanisms behind the increases. These new molecules could then target human tumors and have enhanced potency for tumor cell killing. The resulting product would be expected to function at a lower dose, without an increase in toxicity, thus increasing its therapeutic window. In addition, many previous studies have shown that the accretion of an antibody into a tumor is relatively low (Sands, H. Cancer Research (Suppl) 1990, 50: 809s-813s). An increase in effector function could result in an increased therapeutic efficacy thus allowing a humanized monoclonal antibody to have a therapeutic effect at the accretion rates found in human tumors.
The method of the invention can enhance the effector function of monoclonal antibodies, including, but not limited to those currently in development for the treatment of cancer. Glycosylation is only one of many ways in which antibody effector function can be manipulated. The technology is ideally suited for this study since it can yield a more potent antibody that has minimal changes in amino acid sequence, in the glycosylation pattern and/or in other known and unknown mechanisms. These changes may arise due to genetic changes in the DNA resulting in the amino acid sequence of the immunoglobulin molecule itself, or in the cellular machinery that controls the sequence or nature of the post translational pattern.
The method of the invention may be used to enhance properties of antibodies, including, but not limited to, rodent antibodies against therapeutic targets, and chimerized and humanized versions thereof. One such antibody, referred to as MORAb-03, binds to a cell surface adult-type, high-affinity folate-binding glycoprotein antigen (designated MORAb-03 antigen) of normal placenta and gestational choriocarcinomas. Expression profiles show that MORAb-03 antigen has a restricted distribution in normal tissues, being expressed primarily in a subset of simple epithelia (Rettig W J, Cordon-Cardo C, Koulos J P, Lewis J L Jr, Oettgen H F, Old U. Int J. Cancer. 1985 Apr. 15; 35(4):469-75; Coney L R, Tomassetti A, Carayannopoulos L, Frasca V, Kamen B A, Colnaghi M I, Zurawski V R Jr. Cancer Res. 1991 Nov. 15; 51(22):6125-32) and fresh frozen sections of human pancreas, proximal kidney tubules, and bronchi. The distribution of MORAb-03 antigen was further determined by immunohistochemical analysis of 150 tumor cell lines and normal cell cultures as well as on primary tumor tissues using a MORAb-03-antigen specific mouse derived monoclonal antibody (L-26). MORAb-03 antigen was found expressed on all cultured choriocarcinomas and teratocarcinomas. Immunohistochemistry of primary tumors found MORAb-03 antigen expression in a significant number of ovarian tumors and over 400 tumors of other histological types (Garin-Chesa P, Campbell I, Saigo P E, Lewis J L Jr, Old U, Rettig W J. Am J Pathol. 1993 February; 142(2):557-67). Ovarian carcinomas derived from coelomic epithelium showed the most consistent and strongest immunostaining with the MORAb-03 antibody, with 52 of 56 cases being MORAb-03 positive. MORAb-03 antigen was not detected in normal fetal or adult ovary; however, it was found present in the lining epithelia in a subset of benign ovarian cysts.
The method of the invention may be used to develop a production line that produces an antibody that can meet the therapeutic and manufacturing requirements (i.e., high affinity and production) specified by the current industry standards. The method of the invention is suitable for application to mAbs generated using standard murine hybridoma techniques. In some embodiments, murine complementary determining regions (CDRs) are grafted into a human IgG1k backbone, and the light and heavy chain cDNAs are transfected into NSO cells, resulting in the generation of an antibody production system known in the industry as “transfectoma.” The process of grafting the CDRs into a human immunoglobulin sequence is called “humanization.” Unfortunately, the transfectoma line produced the MORAb-03 at a rate of less than 1 pg/cell/day and the humanization process had led to a reduction of the affinity, now in the micromolar range. The method of the invention enabled successful production of an optimized, humanized MORAb-03 antibody with acceptable antigen binding activity (low nanomolar dissociation constant) and production rates (>10 pg/cell/day). ADCC assays using human ovarian cancer cells as target and peripheral blood mononuclear cells (PBMCs) as effector cells showed that 200 ng/ml of MORAb-03 produced in NSO cells was able to mediate the lysis of 44% of target cells, whereas lysis mediated by the control IgG1 antibody was only 6% (FIG. 7). In contrast, the same concentration of MORAb-03 produced in CHO cells mediated the lysis of 32% of target cells, a reduction of 27% (paired T test=0.0008) (FIG. 4). Multiple independent ADCC assays have shown a similar trend, where MORAb-03 CHO produced in cells showed a reduction in activity as high as 50% compared to MORAb-03 produced in NSO cells. CHO is a standard host cell line recognized by the FDA and is well characterized by contract manufacturing organizations. Among its strengths are the robustness and stability of its growth, its adaptability to different manufacturing schemes and serum-free media, and its high efficiency and reproducibility of antibody production. A CHO line producing MORAb-03 with ADCC activity similar to or higher than NSO cell-produced MORAb-03 will be an extremely valuable manufacturing asset for the production of a therapeutic anti-cancer biologic. The method of the invention may be applied to the cell lines producing MORAb-03 in order to identify variants producing antibodies with enhanced ADCC activity.
In summary, the MORAb-03 antigen is a glycoprotein whose expression is highly restricted in normal tissues and highly expressed in a large portion of ovarian tumors. The antibody is capable of inducing ADCC thus making it an excellent drug candidate for the treatment of ovarian of cancer.
For further information on the background of the invention the following references may be consulted, each of which is incorporated herein by reference in its entirety:

    
    
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The above disclosure generally describes the present invention. A more complete understanding can be obtained by reference to the following specific examples which are provided herein for purposes of illustration only, and are not intended to limit the scope of the invention.
EXAMPLE I
Stable Expression of Dominant Negative MMR Genes in Hybridoma Cells
It has been previously shown by Nicolaides et al. (Nicolaides et al. (1998) A Naturally Occurring hPMS2 Mutation Can Confer a Dominant Negative Mutator Phenotype Mol. Cell. Biol. 18:1635-1641) that the expression of a dominant negative allele in an otherwise MMR proficient cell could render these host cells MMR deficient. The creation of MMR deficient cells can lead to the generation of genetic alterations throughout the entire genome of a host organisms offspring, yielding a population of genetically altered offspring or siblings that may produce biochemicals with altered properties. This patent application teaches of the use of dominant negative MMR genes in antibody-producing cells, including but not limited to rodent hybridomas, human hybridomas, chimeric rodent cells producing human immunoglobulin gene products, human cells expressing immunoglobulin genes, mammalian cells producing single chain antibodies, and prokaryotic cells producing mammalian immunoglobulin genes or chimeric immunoglobulin molecules such as those contained within single-chain antibodies. The cell expression systems described above that are used to produce antibodies are well known by those skilled in the art of antibody therapeutics.
To demonstrate the ability to create MMR defective hybridomas using dominant negative alleles of MMR genes, we first transfected a mouse hybridoma cell line that is known to produce an antibody directed against the human IgE protein with an expression vector containing the human PMS2 (cell line referred to as HBPMS2), the previously published dominant negative PMS2 mutant referred herein as PMS134 (cell line referred to as HB134), or with no insert (cell line referred to as HBvec). The results showed that the PMS134 mutant could indeed exert a robust dominant negative effect, resulting in biochemical and genetic manifestations of MMR deficiency. Unexpected was the finding that the full length PMS2 also resulted in a lower MMR activity while no effect was seen in cells containing the empty vector. A brief description of the methods is provided below.
The MMR proficient mouse H36 hybridoma cell line was transfected with various hPMS2 expression plasmids plus reporter constructs for assessing MMR activity. The MMR genes were cloned into the pEF expression vector, which contains the elongation factor promoter upstream of the cloning site followed by a mammalian polyadenylation signal. This vector also contains the NEOr gene that allows for selection of cells retaining this plasmid. Briefly, cells were transfected with 1 μg of each vector using polyliposomes following the manufacturer's protocol (Life Technologies). Cells were then selected in 0.5 mg/ml of G418 for 10 days and G418 resistant cells were pooled together to analyze for gene expression. The pEF construct contains an intron that separates the exon 1 of the EF gene from exon 2, which is juxtaposed to the 5′ end of the polylinker cloning site. This allows for a rapid reverse transcriptase polymerase chain reaction (RT-PCR) screen for cells expressing the spliced products. At day 17, 100,000 cells were isolated and their RNA extracted using the trizol method as previously described (Nicolaides N. C., Kinzler, K. W., and Vogelstein, 8. (1995) Analysis of the 5′ region of PMS2 reveals heterogeneous transcripts and a novel overlapping gene. Genomics 29:329-334). RNAs were reverse transcribed using Superscript II (Life Technologies) and PCR amplified using a sense primer located in exon 1 of the EF gene (5′-ttt cgc aac ggg ttt gcc g-3′) (SEQ ID NO:23) and an antisense primer (5′-gtt tca gag tta agc ctt cg-3′) (SEQ ID NO:24) centered at nt 283 of the published human PMS2 cDNA, which will detect both the full length as well as the PMS134 gene expression. Reactions were carried out using buffers and conditions as previously described (Nicolaides, N. C., et al. (1995) Genomic organization of the human PMS2 gene family. Genomics 30:195-206), using the following amplification parameters: 94° C. for 30 sec, 52° C. for 2 min, 72° C. for 2 min, for 30 cycles. Reactions were analyzed on agarose gels. FIG. 1 shows a representative example of PMS expression in stably transduced H36 cells.
Expression of the protein encoded by these genes were confirmed via western blot using a polyclonal antibody directed to the first 20 amino acids located in the N-terminus of the protein following the procedures previously described (data not shown) (Nicolaides et al. (1998) A Naturally Occurring hPMS2 Mutation Can Confer a Dominant Negative Mutator Phenotype. Mol. Cell. Biol. 18:1635-1641).
EXAMPLE 2
hPMS134 Causes a Defect in MMR Activity and Hypermutability in Hybridoma Cells
A hallmark of MMR deficiency is the generation of unstable microsatellite repeats in the genome of host cells. This phenotype is referred to as microsatellite instability (MI) (Modrich, P. (1994) Mismatch repair, genetic stability, and cancer. Science 266:1959-1960; Palombo, F., et al. (1994) Mismatch repair and cancer. Nature 36:4 17). MI consists of deletions and/or insertions within repetitive mono-, di-, and/or tri-nucleotide repetitive sequences throughout the entire genome of a host cell. Extensive genetic analyses of eukaryotic cells have found that the only biochemical defect that is capable of producing MI is defective MMR (Strand, M., et al. (1993) Destabilization of tracts of simple repetitive DNA in yeast by mutations affecting DNA mismatch repair. Nature 365:274-276; Perucho, M. (1996) Cancer of the microsatellite mutator phenotype. Biol Chem. 377:675-684; Eshleman J. R., and Markowitz, S. D. (1996) Mismatch repair defects in human carcinogenesis. Hum. Mol. Genet. 5:1489-494). In light of this unique feature that defective MMR has on promoting MI, it is now used as a biochemical marker to survey for lack of MMR activity within host cells (Perucho, M. (1996) Cancer of the microsatellite mutator phenotype. Biol Chem. 377:675-684; Eshleman J. R., and Markowitz, S. D. (1996) Mismatch repair defects in human carcinogenesis. Hum. Mol. Genet. 5:1489-494; Liu, T., et al. (2000) Microsatellite instability as a predictor of a mutation in a DNA mismatch repair gene in familial colorectal cancer. Genes Chromosomes Cancer 27:17-25).
A method used to detect MMR deficiency in eukaryotic cells is to employ a reporter gene that has a polynucleotide repeat inserted within the coding region that disrupts its reading frame due to a frameshift. In the case where MMR is defective, the reporter gene will acquire random mutations (i.e., insertions and/or deletions) within the polynucleotide repeat yielding clones that contain a reporter with an open reading frame. We have employed the use of an MMR-sensitive reporter gene to measure for MMR activity in HBvec, HBPMS2, and HBPMS134 cells. The reporter construct used the pCAR-OF, which contains a hygromycin resistance (HYG) gene plus a β-galactosidase gene containing a 29 bp out-of-frame poly-CA tract at the 5′ end of its coding region. The pCAR-OF reporter would not generate β-galactosidase activity unless a frame-restoring mutation (i.e., insertion or deletion) arose following transfection. HBvec, HBPMS2, and HB134 cells were each transfected with pCAR-OF vector in duplicate reactions following the protocol described in Example 1. Cells were selected in 0.5 mg/ml G418 and 0.5 mg/ml HYG to select for cells retaining both the MMR effector and the pCAR-OF reporter plasmids. All cultures transfected with the pCAR vector resulted in a similar number of HYG/G418 resistant cells. Cultures were then expanded and tested for β-galactosidase activity in situ as well as by biochemical analysis of cell extracts. For in situ analysis, 100,000 cells were harvested and fixed in 1% gluteraldehyde, washed in phosphate buffered saline solution and incubated in 1 ml of X-gal substrate solution [0.15 M NaCl, 1 mM MgCl2, 3.3 mM K4Fe(CN)6, 3.3 mM K3Fe(CN)6, 0.2% X-Gal] in 24 well plates for 2 hours at 37° C. Reactions were stopped in 500 mM sodium bicarbonate solution and transferred to microscope slides for analysis. Three fields of 200 cells each were counted for blue (β-galactosidase positive cells) or white (β-galactosidase negative cells) to assess for MMR inactivation. Table 1 shows the results from these studies. While no β-galactosidase positive cells were observed in HBvec cells, 10% of the cells per field were β-galactosidase positive in HB134 cultures and 2% of the cells per field were β-galactosidase positive in HBPMS2 cultures.
Cell extracts were prepared from the above cultures to measure β-galactosidase using a quantitative biochemical assay as previously described (Nicolaides et al. (1998) A Naturally Occurring hPMS2 Mutation Can Confer a Dominant Negative Mutator Phenotype Mol. Cell. Biol. 18:1635-1641; Nicolaides, N. C., et al. (1992) The Jun family members, c-JUN and JUND, transactivate the human c-myb promoter via an Ap1 like element. J. Biol. Chem. 267:19665-19672). Briefly, 100,000 cells were collected, centrifuged and resuspended in 200 uls of 0.25M Tris, pH 8.0. Cells were lysed by freeze/thawing three times and supernatants collected after microfugation at 14,000 rpms to remove cell debris. Protein content was determined by spectrophotometric analysis at OD280. For biochemical assays, 20 μg of protein was added to buffer containing 45 mM 2-mercaptoethanol, 1 mM MgCl2, 0.1 M NaPO4 and 0.6 mg/ml Chlorophenol red-β-D-galactopyranoside (CPRG, Boehringer Mannheim). Reactions were incubated for 1 hour, terminated by the addition of 0.5 M Na2CO3, and analyzed by spectrophotometry at 576 nm. H36 cell lysates were used to subtract out background. FIG. 2 shows the β-galactosidase activity in extracts from the various cell lines. As shown, the HB134 cells produced the highest amount of β-galactosidase, while no activity was found in the HBvec cells containing the pCAR-OF. These data demonstrate the ability to generate MMR defective hybridoma cells using dominant negative MMR gene alleles.







TABLE 1







β-galactosidase expression of HBvec, HBPMS2 and HB134 cells


transfected with pCAR-OF reporter vectors. Cells were transfected


with the pCAR-OF β-galactosidase reporter plasmid. Transfected


cells were selected in hygromycin and G418, expanded and stained


with X-gal solution to measure for β-galactosidase activity


(blue colored cells). 3 fields of 200 cells each were analyzed


by microscopy. The results below represent the mean +/− standard


deviation of these experiments.










Cell line
Number Blue Cells







HBvec
0 +/− 0



HBPMS2
4 +/− 1



HB134
20 +/− 3 










EXAMPLE 3
Screening Strategy to Identify Hybridoma Clones Producing Antibodies with Higher Binding Affinities and/or Increased Immunoglobulin Production
An application of the methods presented within this document is the use of MMR deficient hybridomas or other immunoglobulin producing cells to create genetic alterations within an immunoglobulin gene that will yield antibodies with altered biochemical properties. An illustration of this application is demonstrated within this example whereby the HB134 hybridoma (Example 1), which is a MMR-defective cell line that produces an anti-human immunoglobulin type E (hIgE) MAb, is grown for 20 generations and clones are isolated in 96-well plates and screened for hIgE binding. FIG. 3 outlines the screening procedure to identify clones that produce high affinity MAbs, which is presumed to be due to an alteration within the light or heavy chain variable region of the protein. The assay employs the use of a plate Enzyme Linked Immunosorbant Assay (ELISA) to screen for clones that produce high-affinity MAbs. 96-well plates containing single cells from HBvec or HB134 pools are grown for 9 days in growth medium (RPMI 1640 plus 10% fetal bovine serum) plus 0.5 mg/ml G418 to ensure clones retain the expression vector. After 9 days, plates are screened using an hIgE plate ELISA, whereby a 96 well plate is coated with 50 uls of a 1 μg/ml hIgE solution for 4 hours at 4° C. Plates are washed 3 times in calcium and magnesium free phosphate buffered saline solution (PBS−/−) and blocked in 100 μls of PBS−/− with 5% dry milk for 1 hour at room temperature. Wells are rinsed and incubated with 100 μls of a PBS solution containing a 1:5 dilution of conditioned medium from each cell clone for 2 hours. Plates are then washed 3 times with PBS−/− and incubated for 1 hour at room temperature with 50 μls of a PBS−/− solution containing 1:3000 dilution of a sheep anti-mouse horse radish peroxidase (HRP) conjugated secondary antibody. Plates are then washed 3 times with PBS−/− and incubated with 50 μls of TMB-HRP substrate (BioRad) for 15 minutes at room temperature to detect amount of antibody produced by each clone. Reactions are stopped by adding 50 μls of 500 mM sodium bicarbonate and analyzed by OD at 415 nm using a BioRad plate reader. Clones exhibiting an enhanced signal over background cells (H36 control cells) are then isolated and expanded into 10 ml cultures for additional characterization and confirmation of ELISA data in triplicate experiments. ELISAs are also performed on conditioned (CM) from the same clones to measure total Ig production within the conditioned medium of each well. Clones that produce an increased ELISA signal and have increased antibody levels are then further analyzed for variants that over-express and/or over-secrete antibodies as described in Example 4. Analysis of five 96-well plates each from HBvec or HB134 cells have found that a significant number of clones with a higher Optical Density (OD) value is observed in the MMR-defective HB134 cells as compared to the HBvec controls. FIG. 4 shows a representative example of HB134 clones producing antibodies that bind to specific antigen (in this case IgE) with a higher affinity. FIG. 4 provides raw data from the analysis of 96 wells of HBvec (left graph) or HB134 (right graph) which shows 2 clones from the HB134 plate to have a higher OD reading due to 1) genetic alteration of the antibody variable domain that leads to an increased binding to IgE antigen, or 2) genetic alteration of a cell host that leads to over-production/secretion of the antibody molecule. Anti-Ig ELISA found that the two clones, shown in FIG. 4 have Ig levels within their CM similar to the surrounding wells exhibiting lower OD values. These data suggest that a genetic alteration occurred within the antigen binding domain of the antibody which in turn allows for higher binding to antigen.
Clones that produced higher OD values as determined by ELISA were further analyzed at the genetic level to confirm that mutations within the light or heavy chain variable region have occurred that lead to a higher binding affinity hence yielding a stronger ELISA signal. Briefly, 100,000 cells are harvested and extracted for RNA using the Trizol® method as described above. RNAs are reverse transcribed using SuperScript® II as suggested by the manufacturer (Invitrogen Corp.) and PCR amplified for the antigen binding sites contained within the variable light and heavy chains. Because of the heterogeneous nature of these genes, the following degenerate primers are used to amplify light and heavy chain alleles from the parent H36 strain.










Light chain sense:









(SEQ ID NO:1)











5′-GGA TTT TCA GGT GCA GAT TTT CAG-3′




 



Light chain antisense:








(SEQ ID NO:2)











5′-ACT GGA TGG TGG GAA GAT GGA-3′




 



Heavy chain sense:








(SEQ ID NO:3)











5′-A(G/T) GTN (A/C)AG CTN CAG (C/G)AG TC-3′




 



Heavy chain antisense:








(SEQ ID NO:4)











5′-TNC CTT G(A/G)C CCC AGT A(G/A)(A/T)C-3′







PCR reactions using degenerate oligonucleotides are carried out at 94° C. for 30 sec, 52° C. for 1 mm, and 72° C. for 1 min for 35 cycles. Products are analyzed on agarose gels. Products of the expected molecular weights are purified from the gels by Gene Clean (Bio 101), cloned into T-tailed vectors, and sequenced to identify the wild type sequence of the variable light and heavy chains. Once the wild type sequence has been determined, nondegenerate primers were made for RT-PCR amplification of positive HB134 clones. Both the light and heavy chains were amplified, gel purified and sequenced using the corresponding sense and antisense primers. The sequencing of RT-PCR products gives representative sequence data of the endogenous immunoglobulin gene and not due to PCR-induced mutations. Sequences from clones were then compared to the wild type sequence for sequence comparison. An example of the ability to create in vivo mutations within an immunoglobulin light or heavy chain is shown in FIG. 5, where HB134 clone 92 was identified by ELISA to have an increased signal for hIgE. The light chain was amplified using specific sense and antisense primers. The light chain was RT-PCR amplified and the resulting product was purified and analyzed on an automated ABI377 sequencer. As shown in clone A, a residue −4 upstream of the CDR region 3 had a genetic change from ACT to TCT, which results in a Thr to Ser change within the framework region just preceding the CDR#3. In clone B, a residue −6 upstream of the CDR region had a genetic change from CCC to CTC, which results in a Pro to Leu change within framework region preceding CDR#2.
The ability to generate random mutations in immunoglobulin genes or chimeric immunoglobulin genes is not limited to hybridomas. Nicolaides et al. (Nicolaides et al. (1998) A Naturally Occurring hPMS2 Mutation Can Confer a Dominant Negative Mutator Phenotype Mol. Cell. Biol. 18:1635-1641) has previously shown the ability to generate hypermutable hamster cells and produce mutations within an endogenous gene. A common method for producing humanized antibodies is to graft CDR sequences from a MAb (produced by immunizing a rodent host) onto a human Ig backbone, and transfection of the chimeric genes into Chinese Hamster Ovary (CHO) cells which in turn produce a functional Ab that is secreted by the CHO cells (Shields, R. L., et al (1995) Anti-IgE monoclonal antibodies that inhibit allergen-specific histamine release. Int Arch. Allergy Immunol. 107:412-413). The methods described within this application are also useful for generating genetic alterations within Ig genes or chimeric Igs transfected within host cells such as rodent cell lines, plants, yeast and prokaryotes (Frigerio L, et al. (2000) Assembly, secretion, and vacuolar delivery of a hybrid immunoglobulin in plants. Plant Physiol. 123:1483-1494).
These data demonstrate the ability to generate hypermutable hybridomas, or other Ig producing host cells that can be grown and selected, to identify structurally altered immunoglobulins yielding antibodies with enhanced biochemical properties, including but not limited to increased antigen binding affinity. Moreover, hypermutable clones that contain missense mutations within the immunoglobulin gene that result in an amino acid change or changes can be then further characterized for in vivo stability, antigen clearance, on-off binding to antigens, etc. Clones can also be further expanded for subsequent rounds of in vivo mutations and can be screened using the strategy listed above.
The use of chemical mutagens to produce genetic mutations in cells or whole organisms is limited due to the toxic effects that these agents have on “normal” cells. The use of chemical mutagens such as MNU in MMR defective organisms is much more tolerable yielding to a 10 to 100 fold increase in genetic mutation over MMR deficiency alone (Bignami M, (2000) Unmasking a killer: DNA O(6)-methylguanine and the cytotoxicity of methylating agents. Mutat. Res. 462:71-82). This strategy allows for the use of chemical mutagens to be used in MMR-defective Ab producing cells as a method for increasing additional mutations within immunoglobulin genes or chimeras that may yield functional Abs with altered biochemical properties such as enhanced binding affinity to antigen, etc.
EXAMPLE 4
Generation of Antibody Producing Cells with Enhanced Antibody Production
Analysis of clones from H36 and HB134 following the screening strategy listed above has identified a significant number of clones that produce enhanced amounts of antibody into the medium. While a subset of these clones gave higher Ig binding data as determined by ELISA as a consequence of mutations within the antigen binding domains contained in the variable regions, others were found to contain “enhanced” antibody production. A summary of the clones producing enhanced amounts of secreted MAb is shown in TABLE 2, where a significant number of clones from HB134 cells were found to produce enhanced Ab production within the conditioned medium as compared to H36 control cells.







TABLE 2







Generation of hybridoma cells producing high levels of antibody.


HB134 clones were assayed by ELISA for elevated Ig levels. Analysis


of 480 clones showed that a significant number of clones had


elevated MAb product levels in their CM. Quantification showed


that several of these clones produced greater than 500 ngs/ml


of MAb due to either enhanced expression and/or secretion as


compared to clones from the H36 cell line.











Cell Line
% clones > 400 ng/ml
% clones > 500 ng/ml







H36
  1/480 = 0.2%
0/480 = 0%  



HB134
50/480 = 10%
8/480 = 1.7%










Cellular analysis of HB134 clones with higher MAb levels within the conditioned medium (CM) were analyzed to determine if the increased production was simply due to genetic alterations at the Ig locus that may lead to over-expression of the polypeptides forming the antibody, or due to enhanced secretion due to a genetic alteration affecting secretory pathway mechanisms. To address this issue, three HB134 clones that had increased levels of antibody within their CM were expanded. 10,000 cells were prepared for western blot analysis to assay for intracellular steady state Ig protein levels (FIG. 6). In addition, H36 cells were used as a standard reference (Lane 2) and a rodent fibroblast (Lane 1) was used as an Ig negative control. Briefly, cells were pelleted by centrifugation and lysed directly in 300 μl of SDS lysis buffer (60 mM Tris, pH 6.8, 2% SDS, 10% glycerol, 0.1 M 2-mercaptoethanol, 0.001% bromophenol blue) and boiled for 5 minutes. Lysate proteins were separated by electrophoresis on 4-12% NuPAGE gels (for analysis of Ig heavy chain). Gels were electroblotted onto Immobilon-P (Millipore) in 48 mM Tris base, 40 mM glycine, 0.0375% SDS, 20% methanol and blocked at room temperature for 1 hour in Tris-buffered saline (TBS) plus 0.05% Tween-20 and 5% condensed milk. Filters were probed with a 1:10,000 dilution of sheep anti-mouse horseradish peroxidase conjugated monoclonal antibody in TBS buffer and detected by chemiluminescence using Supersignal substrate (Pierce). Experiments were repeated in duplicates to ensure reproducibility. FIG. 6 shows a representative analysis where a subset of clones had enhanced Ig production which accounted for increased Ab production (Lane 5) while others had a similar steady state level as the control sample, yet had higher levels of Ab within the CM. These data suggest a mechanism whereby a subset of HB134 clones contained a genetic alteration that in turn produces elevated secretion of antibody.
The use of chemical mutagens to produce genetic mutations in cells or whole organisms is limited due to the toxic effects that these agents have on “normal” cells. The use of chemical mutagens such as MNU in MMR defective organisms is much more tolerable, yielding a 10 to 100 fold increase in genetic mutation over MMR deficiency alone (Bignanii M, (2000) Unmasking a killer: DNA O(6)-methylguanine and the cytotoxicity of methylating agents. Mutat. Res. 462:71-82). This strategy allows for the use of chemical mutagens to be used in MMR-defective Ab producing cells as a method for increasing additional mutations within immunoglobulin genes or chimeras that may yield functional Abs with altered biochemical properties such as enhanced binding affinity to antigen, etc.
EXAMPLE 5
Establishment of Genetic Stability in Hybridoma Cells with New Output Trait
The initial steps of MMR are dependent on two protein complexes, called MutSα and MutLα (Nicolaides et al. (1998) A Naturally Occurring hPMS2 Mutation Can Confer a Dominant Negative Mutator Phenotype. Mol. Cell. Biol. 18:1635-1641). Dominant negative MMR alleles are able to perturb the formation of these complexes with downstream biochemicals involved in the excision and polymerization of nucleotides comprising the “corrected” nucleotides. Examples from this application show the ability of a truncated MMR allele (PMS134) as well as a full length human PMS2 when expressed in a hybridoma cell line to block MMR resulting in a hypermutable cell line that gains genetic alterations throughout its entire genome per cell division. Once a cell line is produced that contains genetic alterations within genes encoding for an antibody, a single chain antibody, overexpression of immunoglobulin genes and/or enhanced secretion of antibody, it is desirable to restore the genomic integrity of the cell host. This can be achieved by the use of inducible vectors whereby dominant negative MMR genes are cloned into such vectors and introduced into Ab producing cells. The cells are cultured in the presence of inducer molecules and/or conditions. Inducible vectors include but are not limited to chemical regulated promoters such as the steroid inducible MMTV, tetracycline regulated promoters, temperature sensitive MMR gene alleles, and temperature sensitive promoters.
The results described above lead to several conclusions. First, expression of hPMS2 and PMS134 results in an increase in microsatellite instability in hybridoma cells. That this elevated microsatellite instability is due to MMR deficiency was proven by evaluation of extracts from stably transduced cells. The expression of PMS134 results in a polar defect in MMR, which was only observed using heteroduplexes designed to test repair from the 5′ direction (no significant defect in repair from the 3′direction was observed in the same extracts) (Nicolaides et al. (1998) A Naturally Occurring hPMS2 Mutation Can Confer a Dominant Negative Mutator Phenotype. Mol. Cell. Biol. 18:1635-1641). Interestingly, cells deficient in hMLH1 also have a polar defect in MMR, but in this case preferentially affecting repair from the 3′ direction (Drummond, J. T, et al. (1996) Cisplatin and adriamycin resistance are associated with MutLa and mismatch repair deficiency in an ovarian tumor cell line. J. Biol. Chem. 271:9645-19648). It is known from previous studies in both prokaryotes and eukaryotes that the separate enzymatic components mediate repair from the two different directions. Our results, in combination with those of Drummond et al. (Shields, R. L., et al. (1995) Anti-IgE monoclonal antibodies that inhibit allergen-specific histamine release. Int. Arch Allergy Immunol. 107:412-413), strongly suggest a model in which 5′ repair is primarily dependent on hPMS2 while 3′ repair is primarily dependent on hMLH1. The dimeric complex between PMS2 and MLH1 sets up this directionality. The combined results also demonstrate that a defect in directional MMR is sufficient to produce a MMR defective phenotype and suggests that any MMR gene allele is useful to produce genetically altered hybridoma cells, or a cell line that is producing Ig gene products. Moreover, the use of such MMR alleles will be useful for generating genetically altered Ig polypeptides with altered biochemical properties as well as cell hosts that produce enhanced amounts of antibody molecules.
Another method that is taught in this application is that any method used to block MMR can be performed to generate hypermutability in an antibody-producing cell that can lead to genetically altered antibodies with enhanced biochemical features such as but not limited to increased antigen binding, enhanced pharmacokinetic profiles, etc. These processes can also to be used to generate antibody producer cells that have increased Ig expression as shown in Example 4, FIG. 6 and/or increased antibody secretion as shown in Table 2.
In addition, we demonstrate the utility of blocking MMR in antibody producing cells to increase genetic alterations within Ig genes that may lead to altered biochemical features such as, but not limited to, increased antigen binding affinities (FIGS. 5A and 5B). The blockade of MMR in such cells can be through the use of dominant negative MMR gene alleles from any species including bacteria, yeast, protozoa, insects, rodents, primates, mammalian cells, and man. Blockade of MMR can also be generated through the use of antisense RNA or deoxynucleotides directed to any of the genes involved in the MMR biochemical pathway. Blockade of MMR can be through the use of polypeptides that interfere with subunits of the MMR complex including but not limited to antibodies. Finally, the blockade of MMR may be through the use of chemicals such as but not limited to nonhydrolyzable ATP analogs, which have been shown to block MMR (Galio, L, et al. (1999) ATP hydrolysis-dependent formation of a dynamic ternary nucleoprotein complex with MutS and MutL. Nucl. Acids Res. 27:2325-2331).
EXAMPLE 6
Analysis of Genetic Sequence of Mutant H36 Cell Lines Producing High Affinity Antibodies
The nucleic acid sequence of the light and heavy chains of the antibodies produced by the H36 mutant cell lines were examined for mutations within the immunoglobulin coding sequence that contribute to the increased affinity of the antibodies as compared to the parent clone. The results are shown in Table 3. The data show that proline substitutions in both the heavy and light chain variable domains contribute to increased affinity of the antibodies to antigen. A particular hot spot appears to be amino acid position 6 of SEQ ID NO:6 in which an amino acid substitution occurred changing the parental alanine to proline for HB91-47, HB134DRMA13, and HB134DRMA55. These three clones also had mutations at positions 9 and 10. In position 9, the parental valine was changed to glycine or arginine, while at position 10 of SEQ ID NO:6, the parental arginine was changed to lysine in both cases.












TABLE 3







Sequence
Amino acid
Mean



Clones
Chain
Change
Change
ELISA
Affinity




















H36

WT
None
0.542
4.80E−08


HB-134a1
L
A > T
Thr > Ser
1.632
nd


HB91-34
H
C
Frameshift
0
0




insertion


HB91-37
L
T > C
Leu > Pro
1.743
1.40E−09


HB91-38
H
T > A
Ser > Ser
1.641
nd


HB91-40
H
A > G
Ala > Thr
1.333
nd


HB91-47
H
Multiple
Ala > Pro,
1.979
3.12E−09





Val > Gly,





Arg > Lys


HB91-53
H
TT > AA
Phe > Lys
1.144
nd


HB91-62
H
A > G
Met > Gly
0.218
6.60E−07


HB91-71
H
T > G
Met > Gly
0.186
nd


HB134DRMA13
H
Multiple
Ala > Pro,
2.041
nd





Val > Gly,





Arg > Lys,





Thr > Ala


HB134DRMA14
H
G > A,
Arg > Lys,
1.211
nd




A > G
Thr > Ala


HB134DRMA55
H
Multiple
Ala > Pro,
2.012
nd





Val > Arg,





Arg > Lys,





Thr > Glu,





Ser > Thr









The genetically altered antibodies show the following sequence differences and consensus sequence:
Amino Acid Alignment of Morphogenic HB91-47 Heavy Chain (SEQ ID NO:17), Parental H36 Heavy Chain (SEQ ID NO:18), and Consensus Heavy Chain Sequence (SEQ ID NO:19)












                                 35



Morphogenic
(1)
LQQSGPELGKPGTSVKISCKASGYTFTNYGMNWVK


 


H36 parental
(1)
LQQSGAELVRPGTSVKISCKASGYTFTNYGMNWVK


 


Consensus
(1)
LQQSG-EL--PGTSVKISCKASGYTFTNYGMNWVK




|    FR1                |CDR1  |


 




36                                 70


Morphogenic
(36)
QAPGKGLKWMGWINTYTGEPTYADDFKGRFAFSLE


 


H36 parental
(36)
QAPGKGLKWMGWINTYTGEPTYADDFKGRFAFSLE


 


Consensus
(36)
QAPGKGLKWMGWINTYTGEPTYADDFKGRFAFSLE




     FR2   |   CDR2         | FR3






Amino acid alignment of morphogenic HB91-37 light chain (SEQ ID NO:20), parental H36 light chain (SEQ ID NO:21), and consensus light chain sequence (SEQ ID NO:22)












1                                 35



Morphogenic
(1)
SASSSVSSSYFHWYQQKSGASPKPLIHRTSNLASG


 


H36 parental
(1)
SASSSVSSSYFHWYQQKSGASLKPLIHRTSNLASG


 


Consensus
(1)
SASSSVSSSYFHWYQQKSGAS-KPLIHRTSNLASG




     CDR1   |  FR2         |CDR2  |


 




36       45


Morphogenic
(36)
VPARFSGSGS


H36 parental
(36)
VPARFSGSGS


Consensus
(36)
VPARFSGSGS




   FR3






The data shows that, for the light chain, a substitution in the second framework region (FR2) of the light chain at position 22 of SEQ ID NO:21 to a proline increased the binding affinity of the antibody.
EXAMPLE 7
An Efficient Screening System for Determining the Effector Function
Increased antibody dependent cellular cytotoxicity (ADCC) elicited by antibody clone variants generated using the method of the invention maybe detected as follows: In one embodiment, human peripheral blood mononuclear cells (PBMCs), isolated from healthy donors are used as effector cells. Briefly, 400 ml of whole blood is diluted 1:1 (volume:volume) with phosphate buffer saline (PBS), laid onto Ficoll-Paque (Amersham) solution, and centrifuged at 2,000 RPM, 18° C., for 30 minutes. The interphase containing the mononuclear cells is recovered and transferred into a fresh tube and cells are washed with PBS. Red blood cells are then lysed using ACK lysing buffer (150 mM NH4Cl, 10 mM KHCO3, and 0.1 mM Na2EDTA) for 5 minutes at room temperature. PBMCs are washed again and their number and viability determined via trypan blue exclusion. Typically, greater than 2×108 cells are recovered using this method, of which 60% endure the cryo-preservation and subsequent culturing (see below). PBMCs are then suspended in complete high glucose RMPI-1640 (Invitrogen), containing 10% fetal bovine serum (FBS) (Invitrogen), 2 mM L-glutamine (Invitrogen), 5% DMSO (Sigma), at a cell density of 20×106/ml. Cells are transferred into cryovials, 1 ml/vial, and stored at −80° C. until use. Cells are quickly brought to 37° C., washed once using pre-warmed compete RPMI, re-suspended at a cell density of 2.5×106/ml in complete RPMI containing 10 ng/ml human recombinant interleukin 2 (hIL-2) (R&D Systems), and grown for 3 days at 37° C., 5% CO2. At the end of this incubation, PBMC viability is typically >85%, and the expected yield will allow the screening of greater than 600 antibody producing clones, assuming an effector:target cell ratio of 5:1. Before the assay, cells are washed once with PBS buffer, counted via trypan blue exclusion, suspended in CD-CHO serum-free medium (Invitrogen) and used for ADCC assay. The isolation of PBMCs from about ten donors will be required to screen 5,000 clones. In the past this number has been sufficient for the isolation of clones with desired characteristics. PBMCs from each donor will be used for separate runs of screening and never mixed with PBMCs of other donors.
In another embodiments, the use of human stable lines are used as an alternate source of effector cells. It has been reported that U937 and HL-60 cells (ATCC CRL-1593.2 and CCL-2, respectively) are capable of effector function (Sarmay G, Lund J, Rozsnyay Z, Gergely J, Jefferis R.). Mol. Immunol. 1992 May; 29(5):633-9). This approach tests whether these cells elicit a cytolytic response against the target cells opsonized by the test antibody (e.g., an antibody against a tumor antigen applied to a tumor cell). Briefly, U937 or HL-60 cells will be cultured at 37° C., 5% CO2, in complete RPMI and stimulated with either 10 ng/ml recombinant human interferon gamma (INF, R&D Systems) or with 100 ng/ml of phorbol 12-myristate 13-acetate (PMA, Sigma). After a 2-day incubation, cells are washed once with PBS buffer, counted via trypan blue exclusion, suspended in CD-CHO serum-free medium (Invitrogen) and used for ADCC assay.
EXAMPLE 8
Production of Cell Lines that Produce Improved Antibodies
To generate phenotypically diversified cells for the selection of clones producing antibodies with increased ADCC activity, mAb-producing cells will be transfected with the vector p0124 (pEF1-hPMS2-134-IRES-TK) for the expression of the hPMS-134 gene, to inhibit mismatched DNA repair, using the Fugene reagent as described above. After selection using G41 8 (0.75 mg/ml), cells will be subcloned to isolate antibody producing clones concomitantly expressing hPMS-134 protein, as assessed by ELISA and western blotting, respectively. Cells will be allowed to expand for greater than 20 generations and then frozen and stored in liquid nitrogen until use.
EXAMPLE 9
Screening Cells for the Production of Antibodies with Enhanced Effector Function
The mAb-producing cells expressing the hPMS-134 will be subcloned by liming dilution and seeded in a flat-bottom 96-well plate. Seeding density will be determined empirically in order to obtain 40 single-cell colonies per plate to approximate monoclonality.
The clones will be allowed to grow for a number of days, which will be empirically determined, after which a sufficient amount of antibody, capable of mediating ADCC activity, is produced. Because the parental antibody can elicit ADCC activity at concentrations as low as 100 ng/ml, we predict that incubating the single cell-derived clones for 10-15 days should result in the production of sufficient antibodies to support effector function. At the end of this incubation period, 50 ul of conditioned medium from each clone/well will be used to assess concentration of antibodies by ELISA, while another 50 ul of conditioned medium from the same well/clone will be utilized in the ADCC assay. Briefly, for example, an anti-ovarian cancer mAb are used in conjunction with the target cells, SKOV3 (passage 1 to 20, obtained from ATCC), which are seeded the day before the assay in a flat-bottom 96-well microplate at a density of 30,000 cell/well in complete growth medium (RPMI-1640 containing 10% FBS, 2 mM L-glutamine). The following day, the complete medium is replaced with 100 ul of CHO-CD serum-free medium and 50 ul of antibody-containing conditioned medium will be added to target cells and incubated for 20 minutes at 37° C. Subsequently, 100 ul of serum-free medium containing 2×105 of effector cells are added to each well and cells are incubated for 5-6 hours at 37° C., 5% CO2. Plates are then briefly centrifuged and 100 ul of supernatant is collected from each well and transferred into ELISA plates (Nunc). One hundred ul of LDH substrate (Roche) is added to supernatants and incubated for 10 minutes at ambient temperature. LDH activity will be proportional to the extent of the LDH enzyme released from lysed target cells. Optical density at 490 um (OD490) is obtained spectrophotometrically and percent of cytotoxicity is determined with the formula: (sample OD490−spontaneous OD490)/(max OD490−spontaneous OD490)×100%, where ‘spontaneous’=target cells lysis in absence of effector cells or antibody, and ‘max’=target cells lysis in the presence of 2% Triton. Cytotoxicity elicited by 100 ng/ml of a reference antibody (protein A purified, parental antibody) will be used as positive control. Non-specific cytotoxicity will be monitored using 100 mg/ml of normal human IgG1. The ratio obtained by dividing the % cytotoxicity by the concentration of the antibody for each well/clone (i.e., ratio=50(%)/100(ng/ml)=0.5) will be set as the criterion for selecting lead clones with potentially enhanced effector function. Lead clones will be expanded to 50 ml cultures and antibody will be purified from their conditioned media by protein-A affinity column as described. ADCC activities of the antibodies produced by the lead clones will be compared to the parental antibody using concentrations ranging from 10-1000 ng/ml.
EXAMPLE 10
Correlating Effector Function and Receptor Binding Activity
One of the major modes of action of unconjugated therapeutic monoclonal antibodies directed against tumor antigens is through recruitment of immune effector populations to the tumor cells (Clynes R, Takechi Y, Moroi Y, Houghton A, Ravetch J V. Proc. Natl. Acad. Sci. U.S.A. 1998 Jan. 20; 95(2):652-6; Clynes R A, Towers T L, Presta L G, Ravetch J V. Nat. Med. 2000 April; 6(4):443-6). It is presumed that the efficiency with which a given antibody can recruit immune effector cells to a tumor cell is influenced by the affinity of the antibody for its cognate antigen on the tumor cell surface, such that a high affinity antibody will display more efficient recruitment of immune effectors to the tumor cell than a lower affinity counterpart recognizing the same antigen. Limited reports have attempted to demonstrate this relation in vitro (Alsmadi, O. and Tilley, S A. J. Virol. 1998 January; 72(1):286-293; McCall, A M., Shahied, L., Amoroso, A R., Horak, E M., Simmons, R H., Nielson, U., Adams, G P., Schier, R., Marks, J D., Weiner, L M. J. Immunol. 2001 May 15; 166(10):6112-7, as well as in vivo (Velders, M P, van Rhijn, C M., Oskam, G J., Warnaar, S O. and Litvinov, S V. J. Cancer 1998; 78(4):476-483). In order to determine if such a correlation exists, in vitro ADCC activity of enhanced mAbs, and the affinity of these antibodies may be compared for their relevant antigen by surface plasmon resonance spectroscopy.
Surface plasmon resonance spectroscopy relies on the short range (150 nm) interaction of the electrical field (evanescent wave) generated by photons under conditions of total internal reflection (TIR) with electrons (surface plasmons) in a conductive film at the boundary between two media of differing refractive indices, whereby one of the media is a thin gold layer (conductive film) coated with an alkane linker coupled to CM-dextran. The CM-dextran surface, which forms an extended hydrogel in solution, projecting roughly 100-150 nm into the flowcell, may be derivatized further with a ligand of choice by covalent immobilization to the carboxyl groups present on the CM-dextran layer. The angle necessary to allow the evanescent wave to interact with the gold layer will depend on the angle necessary to observe TIR, which in turn depends on the thickness or mass at the surface of the chip. The instrument thus allows for observation of the change in mass at the surface of the chip over time, as would be observed when an analyte which interacts with the immobilized ligand is injected into the flowcell. If injection of analyte is followed by injection of buffer, one can follow both the association (during injection of the analyte) and dissociation phases (during buffer injection) of the binding. Kinetic on-rates (ka) and off-rates (kd), as well as steady-state equilibrium constants (Ka and Kd) can thus be extrapolated.
The soluble, secreted form of the antigen will be purified from the serum-free culture supernatant of target cells by chromatography through Phenyl Sepharose (high sub), followed by ion exchange on S Sepharose Fast Flow. Briefly, culture supernatant containing secreted antigen will be loaded onto the Phenyl Sepharose (high sub) column in the absence of additional salts. Unbound proteins will be removed by extensive washing in HIC A (20 mM K phosphate pH 7.2), followed by elution of bound antigen using a linear gradient of 0-20 mM CHAPS in HIC buffer. Peak MORAb-03-containing fractions will be pooled, acidified (pH 5.5) with 1 M citrate, then applied to a S Sepharose cation exchange column. After washing with IEX buffer (20 mM K phosphate, pH 5.5), bound antigen will be eluted using a linear gradient of 0-1 M NaCl in IEX buffer. Peak fractions will be pooled, concentrated using a Centricon centrifugal concentration device (Millipore), and dialyzed against PBS. Based on the purity of the antigen preparation, an additional affinity chromatography step on covalently coupled folate Sepharose resin may be necessary (Sadasivan, E., da Costa, M., Rothenberg, S P. and Brink, L. Biochim. Biophys. Acta 1987; (925):36-47).
The mAb to be assayed will be purified in one step by affinity chromatography on recombinant protein A Sepharose resin (RPA-Sepharose, Amersham Biosciences). Immunoglobulin (Ig) containing tissue culture supernatants will be loaded onto RPASepharose columns by gravity, at a Ig/ml resin value of 10 mg/mL of resin. Unbound proteins will be removed by extensive washing with PBS, followed by elution using 0.1 M glycine-HCl pH 2.6. Fractions will be neutralized with 1 M Tris. Peak fractions will be pooled, and dialyzed against 1000 volumes of PBS. Ig concentration will be determined by BCA protein assay (Pierce Chemical Co.) and Ig-specific ELISA.
Purified antigen will be diluted into coupling buffer (10 mM NaOAc pH 5.0), and immobilized onto the flowcell of a CM5 sensor chip (Biacore) by amine coupling, using a mixture of N-hydroxysuccinimide (NHS) and 1-ethyl-3-[dimethylaminopropyl]carbodiimide hydrochloride (EDC) to activate carboxyl groups in the CM-Dextran hydrogel attached to the surface of the CM5 sensor chip. Activated, underivatized carboxyl groups will be quenched with 1 M ethanolamine. A reference flowcell, consisting of the quenched CMDextran surface, activated in the absence of antigen, will be used to normalize all measurements. Crude, mAb-containing culture supernatants, or purified mAb preparations will be injected at flow rates of 30 ul/min for kinetic assays, and 5 ul/mm for steady-state affinity ranking experiments, using HBS-EP (20 mM HEPES-OH, 150 mM NaCl, 3 mM EDTA, 0.005% Surfactant P-20, pH 7.4) as running buffer. Purified mAb preparations will be dialyzed against HBS-EP, using 10K MWCO Slide-A-Lyzer dialysis cassettes (Pierce) prior to their use in Biacore analysis. For samples containing tissue culture supernatant, BSA and soluble CM-Dextran will be added to final concentrations of 1% and 1 mg/ml, respectively. Regeneration of the surface will be accomplished by 30 second injection of 50 mM NaOH, at a flow rate of 100 ul/min. Data analysis will be performed using Bia Evaluation software (Biacore). Kinetic data will be fitted to a simple 1:1 (Langmuir) binding model. For ranking experiments, rank will be determined by KD values obtained from plots of Req versus C at different concentrations of sample.

## Claims

1. A method of producing an antibody with increased antibody-dependent cytotoxicity activity as compared with that of an antibody produced by an antibody-producinq cell comprising: inhibiting mismatch repair in said antibody-producing cell by introducing into said antibody-producing cell a dominant negative allele of a PMS2 gene encoding a truncated PMS2 polypeptide comprising the amino acid sequence of SEQ ID NO: 15, whereby said antibody-producing cell becomes hypermutable; allowing said hypermutable antibody-producing cell to grow, thereby generating a population of hypermutable antibody-producing cells; and screening said hypermutable antibody-producing cells for cells that produce antibodies with increased antibody-dependent cytotoxicity activity, which retain the antigen binding specificity of the antibody produced by said antibody-producinq cells, and optionally isolating said antibodies with increased antibody-dependent cytotoxicity activity.

2. The method of claim 1 wherein said dominant negative allele of a PMS2 gene comprises a truncation mutation at codon 134 of a wild-type PMS2 gene comprising the nucleotide sequence of SEQ ID NO: 8.

3. The method of claim 2 wherein said truncation mutation is a substitution of cytidine by thymidine at nucleotide 424 of the wild-type PMS2 gene.

4. The method of claim 1 wherein said dominant negative allele of said PMS2 gene encodes the first 133 amino acids of a wild-type PMS2 polypeptide comprising the amino acid sequence of SEQ ID NO: 7.

5. The method of claim 1 wherein the PMS2 gene is a human PMS2 gene encoding a PMS2 polypeptide comprising the amino acid sequence of SEQ ID NO: 7.

6. The method of claim 1 further comprising restoring mismatch repair to said hypermutable antibody-producing cell.

7. The method of claim 1 further comprising exposing said hypermutable antibody-producing cell to a chemical mutagen.