WO2014194213A1 - Specific complement proteins and efficacy of antibody therapy - Google Patents

Abstract

Disclosed are methods, kits, and compositions for treating, diagnosing, and/or prognosing diseases based on immunotherapy. The methods, kits, and compositions may utilize at least one of complement factor H-related protein 1 (CFHR1), complement factor H-related protein 3 (CFHR3), and/or variants thereof for treating a patient in need thereof in conjunction with a therapeutic antibody or antigen-binding fragment. The methods, kits, and compositions may utilize diagnostic antibodies to CFHR1 and/or diagnostic antibodies to CFHR3 for diagnosing or prognosing a patient prior to treatment with a therapeutic antibody. The methods, kits, and compositions also may utilize reagents for detecting a polymorphism in rs3766404.

Description

SPECIFIC COMPLEMENT PROTEINS AND EFFICACY OF ANTIBODY THERAPY

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR

DEVELOPMENT

[0001] This invention was made with government support under P50 C A97274 and ROI

CA 137198 awarded by the National Institutes of Health. The government has certain rights in the invention.

CROSS-REFERENCE TO RELATED PATENT APPLICATIONS

[0002] The present application claims the benefit of priority under 35 U.S.C. § 119(e) to

U.S. Provisional Pa tent Application No. 61/829,011, filed on May 30. 2013, the content of which is incorporated herein by reference in its entirety.

BACKGROUND

[0003] The field of the invention relates to immunotherapy. In particular, the field of the invention relates to the role of complement iactors such as complement factor H-related protein 1 (CFHR1) and complement factor H-related protein 3 (CFHR3) in antibody-mediated inununotherapies.

SUMMARY

[0004] Disclosed are methods, kits, and compositions for treating, diagnosing, and/or prognosing diseases based on immunotherapy. The methods, kits, and compositions may utilize at least one of complement factor H-related protein (CFHR1), complement factor H-related protein 3 (CFHR3), and/or variants thereof for treating a patient in need thereof in conjunction with a therapeutic antibody or antigen-binding fragment. The methods, kits, and compositions may utilize diagnostic antibodies to CFHRl and/or diagnostic antibodies to CFHR3 for diagnosing/prognosing a patient prior to treatment with a therapeutic antibody. The methods, kits, and compositions may utilize reagents for detecting polymorpliisms associated with the genes for CFHRl and/or CFHR3, such, as rs3766404. for chagnosuig/prognosiiig a patient prior to treatment with a therapeutic antibody.

[0005] The disclosed methods may include methods of treatment having the following steps: (a) administering a first pharmaceutical composition comprising a therapeutic antibody or antigen-binding fragment to a patient in need thereof; and (b) administering a second pharmaceutical composition comprising at least one of CFHRl, CFHR3, and or a variant thereof to the patient. Suitable therapeutic antibodies may include monoclonal antibodies (mAbs) (e.g., Rituximab).

[0006] In the disclosed methods, the patient in need thereof typically is amenable to treatment with a therapeutic antibody or antigen-binding fragment. Suitable patients may include patients having or at risk for developing a disease or disorder selected from cardiovascular disease, auto-immune disorders a cell proliferative disease or disorder (e.g., cancer), transplant rejection, age-related macular degeneration, cryopyrin-associated periodic syndrome (CAPS), Crohn's disease, postmenopausal osteoporosis, paroxysmal nocturnal hemoglobinuria, psoriasis, rheumatoid arthritis, psoriatic arthritis, ankylosing spondylitis, multiple sclerosis, allergy-related asthma, and infection by a microbe or virus.

[0007] In some embodiments of the disclosed methods, the first pharmaceutical composition may be administered prior to or after the second pharmaceutical composition. Γη other embodiments, the fust pharmaceutical composition and the second pharmaceutical composition are administered concurrently. In even further embodiments, the first pharmaceutical composition and the second pharmaceutical may be combined prior to administration.

[0008] The dose of CFHRl, CFHR3, and/or a variant thereof administered in the disclosed methods or present in the second pharmaceutical composition may be modified according to the dose of the therapeutic antibody or antigen-binding fragment administered in the disclosed niethods or present in the first pharmaceutical composition. In some embodiments. the dose of CFHRl, CFHR3, and/or a variant thereof administered in the disclosed methods or present in the second pharmaceutical coniposition is an equimolar amount relative to the dose of the therapeutic antibody or antigen-binding fragment administered in the disclosed methods or present in the first pharmaceutical composition, in oilier embodiments, the molar ratio of the dose of CFHRl, CFHR3, and/or a variant thereof administered in the disclosed methods or present hi the second pharmaceutical coniposition to the dose of the therapeutic antibody or antigen-binding fragment adniiiiistered in the disclosed methods or present in the first pharmaceutical composition is selected from the following ratios; 1:10, 1.5, 1:2, 1 : 1 , 2:1 , 5:1, 10: 1 and ranges thereof.

[0009] Variants and derivatives of CFHR1 and CFHR3 may include fusion proteins that comprise CFHRl, CFHR3 or a fragment thereof fused to another protein. Such fusion proteins and methods utilizing and compositions comprising such fusion proteins are contemplated herein. In some embodiments, a fusion protein as contemplated herein may comprise: (a) a therapeutic antibody or antigen-binding fragment fused at its N-terniinus, C-ierminus, or both tennini, to (b) at least one of CFHRl, CFHR3, and or a variant thereof. T!ie therapeutic antibody or antigen-binding fragment and CFHRl , CFHR3, and/or a variant thereof may be directly fused. Alternatively, the therapeutic antibody or antigen-binding fragment and CFHRl, CFHR3, and/or a variant thereof may be fused indirectly via a peptide linker (e.g., a linker of 5- 10 amino acids which optionally is flexible and which optionally has o e or more glycine or serine residues or any other compatible amino acid sequence).

|0010] The disclosed methods may include adniimstering a pharmaceutical composition comprising the fusion protein to a patient in need thereof. For example, hi some embodiments of the disclosed methods, rather than adniimstering a therapeutic antibody or antigen-binding fragme t, the method comprising administering a fusion protein comprising: (a) a therapeutic antibody or antigen-binding fragment fused at its N-tenninus, C-temiiiius. o both termini, to (b) at least one of CFHRl , CFHR3. and/or a variant thereof. In other embodiments of the disclosed methods, rather than administering: (a) a first pharmaceutical composition comprising a therapeutic antibody or antigen-binding fragment and (b) a second pharmaceutical coniposition comprising CFH l, CFHR3, and^'or a variant thereof to the patient; instead the method comprises administering a fusion protein comprising; (a) a therapeutic antibody or antigen- binding fragment fused at its N-tenninus, C-temiimis, or both iennini, to (b) at least one of CFHRl, CFHR3, and/or a variant thereof.

[0011] The methods may include additional steps. For example, the methods may include administering an additional agent that modifies the complement system (e.g. , an inhibitor of C3b other than CFHRl, CFHR3, and or a variant thereof).

[0012] The disclosed methods may include methods having diagnostic steps and treatment steps. In some embodiments, the methods include: (a) reacting a patient sample with a diagnostic antibody that detects CFHRl and/or a diagnostic antibody that detects CFHR3; and (b) administering a pharmaceutical composition comprising a therapeutic antibody or antigen- binding fragment to the patient based on the detected CFHRl and/or detected CFHR3. Optionally, the methods may include administering a second pharmaceutical composition comprising CFHRl, CFHR3, and or a variant thereof based on the detected CFHRl and/or detected CFHR3.

[0013] hi other embodiments, the methods include: (a) reacting a patient sample comprising nucleic acid with a reagent that detects a polymorphism in rs3766404 (e.g., a C/C polymorphism in rs3766404, a T/C polymorphism in rs3766404, or a T/T polymorphism in rs3766404); and (b) administering a pharmaceutical composition comprising a therapeutic antibody or antigen-binding fragment to the patient based on the detected polymorphism in rs3766404. The disclosed methods may include amplifying nucleic acid in the patient sample and sequencing the amplified nucleic acid. Optionally, the methods may include adnrinistermg a second pharmaceutical composition comprising CFHRl, CFHR3, and/or a variant thereof based on the detected polymorphism in rs3766404.

[0014] Also disclosed are kits and compositions for perfomiing the disclosed treatment methods. In some embodiments, the kits include; (a) a first pharmaceutical composition comprising an antibody or antigen-binding fragment; and (b) a second pharmaceutical composition comprising at least one of CFHRl, CFHR3, and/or a variant thereof.

[0015] Also disclosed are kits and compositions for performing the disclosed diagnostic/prognostic methods and treatment methods, hi some embodiments, the kits include: a composition comprising a diagnostic antibody for detecting CFHRl and or a diagnostic antibody for detecting CFHR3; and a pharmaceutical composition comprising a therapeutic antibody or antigen-binding fragment, hi other embodiments, the kits include: (a) a reagent that detects a polymorphism in rs3766404 (e.g., a C/C polymorphism in rs3766404, a T/C polymorphism in rs3766404, or a T/T polymorphism in rs3766404); and (b) a pharmaceutical composition comprising a therapeutic antibody or antigen-binding fragment. Optionally, the kits include a second pharmaceutical composition comprising CFHRl, CFHR3, and/or a variant thereof.

BRIEF DESCRIPTION OF THE FIGURES

[0016] Figure 1 provides an illustration of a model for antibody-dependent cellular cytotoxicity (ADCC) by a natural killer (NK) cell.

[0017] Figure 2 provides an illustration of a model whereby C3b blocks aniibody- dependent activation and cellular cytotoxicity by a natural killer (NK) cell.

[0018] Figure 3 provides an illustration of a model whereby CFHRl improves the efficacy of antibody therapy for antibodies that mediate ADCC.

[0019] Figure 4 provides a graphical illustration of the correlation between the CHF polymorphism at rs3766404 (i.e., either TT or TC) and the response to Rituximab therapy.

[0020] Figure 5 provides a Western blot for CFH, CFHRl a and CRHRlb in patient samples for patients having one of the C/C, T/T, or C/T polymorphisms at rs376640.

[0021] Figure 6 provides a graphical illustration of me band intensities for the bands in the Western blot of Figure 5. DETAILED DESCRIPTION

[0022] The disclosed subject matter further may be described utilizing terms as defined below.

[0023] Unless otherwise specified or indicated by context, the terms "a", "an", and "the" mean "one or more." For example, a "protein," "polypeptide," or "antibody' should be interpreted to mean "one or more proteins," "one or more polypeptides;' or "one or more antibodies," respectively.

[0024] As used herein, "about", "approximately," "substantially," and "significantly" will be understood by persons of ordmary skill in the art and will vary to some extent on the context in which they are used. If there are uses of the term which are not clear to persons of ordinary skill in the art given the context in which it is used, "about" and "approximately" will mean plus or minu <I0% of the particular term and "substantially" and "significantly" will mean plus or minus >10% of the particula term.

[0025] As used herein, the terms "include" and "including" have the same meaning as the terms "comprise" and "comprising" in that these latter terms are "open" transitional terms that do not limit claims only to the recited elements succeeding these transitional terms. The term "consisting of," while encompassed by the term "comprising," should be interpreted as a "closed" transitional term that limits claims only to the recited elements succeeding this transitional term. The term "consisting essentially of " while encompassed by the term "comprising," should be interpreted as a "partially closed" transitional term which permits additional elements succeeding this transitional term, but only if those additional elements do not materially affect the basic and novel characteristics of the claim.

[0026] As used herein, the term "patient" may be used interchangeably with the term

"subject" or "individual" and may include an "animal" and in particular a "mammal." Mammalian subjects may include humans and other primates, domestic animals, farm animals. and companion animals such as dogs, cats, guinea pigs, rabbits, rats, mice, horses, cattle, cows, and Hie like.

[0027] A "patient in need thereof is intended to include a patient having or at risk for developing diseases and disorders such as diseases and disorders treated by adininistering a pharmaceutical composition comprising an antibody such as a monoclonal antibody or an antigen-binding fragment. Diseases and disorders may include, but are not limited to, cardiovascular disease, auto-immune disorders {e.g., systemic lupus erythematosus), a cell proliferative disease or disorder {e.g.. chronic lymphocytic leukemia, colorectal cancer, anaplastic large cell lymphoma (ALCL), Hodgkin lymphoma, head and neck cancer, solid tumor bony metasteses, acute myelogenous leukemia non-Hodgkin lymphoma, melanoma, breast cancer), transplant rejection, age-related macular degeneration, cryopyrin-associated periodic syndrome (CAPS), Crohn's disease, postmenopausal osteoporosis, paroxysmal nocturnal hemoglobinuria, psoriasis, rheumatoid armritis, psoriatic arthritis, ankylosing spondylitis, multiple sclerosis, allergy-related asthma, and infection by a microbe or virus (e.g., infection by respirator syncytial virus).

[0028] The disclosed methods typically include administering a composition comprising an antibody or an antigen-binding fragment. Suitable antibodies may include monoclonal antibodies (mAb), such as, Abciximab, Adalimiimab, Alemtuzumab, Basiiiximab, Belimiimab, Bevacizumab, Brentuximab vedotin, Canakinuniab, Cetuximab, Certolizumab pegol, Daclizumab, Denosumab. Eculizmiiab, Efalizumab, Gemtuzumab, Golmiimiab, Ibritumomab tiuxetan. Infliximab, Ipilimumab (MDX-101), Muromonab-CD3, Natalizumab, Obinutuzumab, Ofatuiiimnab, Omalizimiab, Palivizmiiab, Panitumumab, Ranibizimiab, Rituximab, Tocilizumab, Tositumomab, Trastuzumab, and antigen-binding fragments thereof. As contemplated herein, the antibody or antigen-binding fragment may be fused at its N-terminus, C-terminus, or both termini to a CFHR1 protein, a CFHR3 protein, or a variant thereof.

[0029] As used herein, the terms "protein" or "polypeptide" or ''peptide" may be used interchangeable to refer to a polymer of amino acids. Typically, a "polypeptide" or "protein" is defined as a longer polymer of amino acids, of a length typically of greater than 50, 60, 70, 80, 90, or 100 amino acids. A "peptide" is defined as a short polymer of amino acids, of a length typically of 50, 40, 30, 20 or less amino acids.

[0030] A 'protein," 'polypeptide," or "peptide" as contemplated herein typically comprises a polymer of naturally occurring amino acids (e.g. , alanine, arginme, asparagine, aspartic acid, cysteine, gmtamine, glutamic acid, glycine, liistidine, isoleiicine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, and valine). The proteins, polypeptides, and peptides contemplated herein may be modified in vitro or in vivo to include non-arnino acid moieties. These modifications may include but are not limited to acylation (e.g., O-acyiation (esters), N-aeylation (amides), S-acylation (thioesters)), acetylation (e.g., the addition of an acetyl group, eithe at the N-tenninus of the protein or at lysine residues), fonnylation lipoylation (e.g., attachment of a lipoate, a C8 functional group), myiistoylation (e.g. , attachment of myristate, a C14 saturated acid), palmitoylation (e.g., attachment of paimitate, a C16 saturated acid), alkylation (e.g., the addition of an aifcyl group, such as an methyl at a lysine or arginine residue), isoprenylation or prenylation (e.g., the addition of an isoprenoid group such as farnesol or geranylgeraniol), aniidation at C,~ -terminus, glyeosylation (e.g. , the addition of a glycosyl group to either asparagine, hydroxylysme. serine, or threonine, resulting in a glycoprotein). Distinct from glycation, which is regarded as a nonenzymatic attachment of sugars, polysiaMation (e.g., the addition of polysialic acid), glypiation (e.g., glycosylphosphatidylmositol (GPI) anchor formation, nydroxylation, iodination (e.g. , of thyroid hormones), and phosphorylation (e.g. , the addition of a phosphate group, usually to serine, tyrosine, threonine or histidine). Tlie proteins contemplated herein may include in particular modifications that increase the stability of the proteins in serum (e.g., after the proteins are administered to a patient in need thereof).

[0031] The CFHR1 and/or CFHR3 proteins contemplated herein may include "wild type" CFHR1 and/or CFHR3 proteins and variants, mutants, and derivatives thereof. As used herein the term "wild type" is a term of the art understood by skilled persons and means the typical form of an organism, strain, gene or characteristic as it occurs in nature as distinguished from .mutant or variant forms. As used herein, a 'Variant, ''mutant," or "derivative" refers to a protein molecule having an amino acid sequence that differs from a reference protem or polypeptide molecule. A variaiit or mutant may have one or more insertions, deletions, or substitutions of an amino acid residue relative to a. reference molecule. A variant or mutant may include a fragment of a reference molecule. For example, a CFHRl and/or CFHR3 mutant or variant molecule may one or more insertions, deletions, or substitution of at least one amino acid residue relative to the CFHRl and/or CFHR3 full-length polypeptide. Exemplary amino acid sequences of CFHRl and/or CFHR3 proteins are presented as SEQ ID NOs:l-6 and may be used as a reference in this regard. Regarding proteins, a ''deletion" refers to a change in the amino acid sequence that results in the absence of one or more amino acid residues. A deletion may remove at least 1, 2. 3, 4, 5, 10, 20, 50, 100, 200. or more amino acids residues. A deletion may include an internal deletion and/ or a terminal deletion (e.g. , an N-terminal truncation, a C- terminal truncation or bo ill of a reference polypeptide).

[0032] Regarding proteins, "fragment" is a portion of an amino acid sequence which is identical in sequence to but shorter in length than a reference sequence. A fragment may comprise up to the entire length of the reference sequence, minus at least one amino acid residue. Fo example, a fragment may comprise from 5 to 1000 contiguous amino acid residues of a reference polypeptide, respectively, hi some embodiments, a fragment may comprise at least 5, 10, 15, 20, 25, 30, 40, 50, 60, 70, 80, 90, 100, 1 0, 250, or 500 contiguous ammo acid residues of a reference polypeptide. Fragments may be preferentially selected from certain regions of a molecule. The term "at least a fragment" encompasses the full length polypeptide. A fragment of a CFHR l and^'or CFHR3 protein may comprise o consist essentially of a contiguous portion of an amino acid sequence of the full-length CFHRl and/or CFHR3 protein (e.g. , any contiguous portion of any of SEQ ID NOs: l-6). A fragment may include an N-terminal truncation, a C- terramal truncation, or both truncations relative to a CFHRl and/or CFHR3 protein.

[0033] Regarding proteins, the words "insertion" and "addition" refer to changes in an amino acid sequence resulting in the addition of one or more amino acid residues. An insertion or addition may refer to 1, 2, 3, 4, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, or more amino acid residues. A variant of a CFHR1 and/or CFHR3 protein may have N-feonmal insertions, C-temiinal insertions, internal insertions, or any combination of N-terrninal insertions, C-terminai insertions,, and internal insertions. Variants and derivatives of CFHR^'l and/or CFHR3 may include fusion proteins tliat comprise at least a fragment of CFHR1 and/or CFHR3 fused to another heterologous protein or polypeptide. The term "heterologous* as applied to a protein or polypeptide, means that the protein or polypeptide is derived from a genotypically distinct entity from thai of the rest of the entity to which it is being compared.

[0034] Regarding proteins, the phrases "percent identity" and "% identity," refer to the percentage of residue matches between at least two amino acid sequences aligned using a standardized algorithm. Methods of amino acid sequence alignment are well-known. Some alignment methods take into account conservative amino acid substitutions. Such conservative substitutions, explained in more detail below, generally preserve the charge and hydrophobicity at the site of substitution, thus preserving the structure (and therefore function) of the polypeptide. Percent identity for amino acid sequences may be determined as understood in the art. (See, e.g.„ U.S. Patent No. 7,396,664, which is incorporated herein by reference in its entirety). A suite of commonly used and freely available sequence comparison algorithms is provided by the National Center for Biotechnology Information (NCBI) Basic Local Aligmnent Search Tool (BLAST), which is available from several sources, including the NCBI, Bethesda, M&, at its website. The BLAST software suite includes various sequence analysis programs including "blastp," that is used to align a known amino acid sequence with other amino acids sequences from a variety of databases. Other publicly available software includes ALIGN or Megalign (DNASTAR) software. As described herein, variants, mutants, or fragments (e.g., a CFHR1 and/or CFHR3 protein variant, mutant, or fragment thereof) may have 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, 90%, 80%, 70%, 60%, or 50% amino acid sequence identity relative to a reference molecule (e.g., relative to any of SEQ ID NOs:l-6).

[0035] Regarding proteins, percent identity may be measur ed over the length of an entire defined polypeptide sequence, for example, as defined by a particular SEQ ID number, or may be measured over a shorter length, for example, over the length of a fragment taken from a larger, defined polypeptide sequence, for instance, a fragment of at least 15, at least 20, at least 30, at least 40. at least 50. at least 70 or at least 150 contiguous residues. Suck lengths are exemplary only, and it is understood that, any fragment length supported by the sequences shown herein, in the tables, figures or Sequence Listing, may be used to describe a length over which percentage identity may be measured.

[0036] Regarding proteins, the amino acid sequences of valiants, mutants, or derivatives as contemplated herein may include conservative amino acid substitutions relative to a reference amino acid sequence. For example, a variant, mutant, or derivative protein may include conservative amino acid substitutions relative to a reference molecule. "Conservative amino acid substitutions" are those substitutions that are a substitution of an amino acid for a different amino acid where the substitution is predicted to interfere least with the properties of the reference polypeptide. In other words, conservative amino acid substitutions substantially conserve the structure and the function of the reference polypeptide. The following table provides a list of exemplary conservative amino acid substitutions winch are contemplated herein:

Ai:¾ Gly, Se?

Mis

lis

A¾ Gin, Ghi

et

PJhfc !lis, xsf, Im, Tip, Ivr

Sc r (As, T¾r

?he_s Tyr

TVs- His, >κ·. Τ

Ik, a, thr Conservative amino acid substitutions generally maintain (a) the structure of the polypeptide backbone in the area of the substitution, for example, as a beta sheet or alpha helical conformation, (b) the charge or hydrophobicity of the molecule at the site of the substitution, and/or (e) the bulk of the side chain.

[0037] Hie disclosed proteins, mutants, variants, or described herein may have one or more functional or biological activities exhibited by a reference polypeptide (e.g. , one or more functional or biological activities exhibited by wild-type CFHRI and or CFHR3 protein). For example, the disclosed CFHRI and/or CFHR3 proteins, mutants, variants, or derivatives thereof may have one or more biological activities that include: binding to C3b and/or inducing degradation of C3b.

[0038] The disclosed CFHRI and/or CFHR3 proteins, mutants, variants, or derivatives thereof may be substantially isolated or purified. The term "substantially isolated or purified" refers to amino acid sequences that are removed from their natural environment, and are at least 60% free, preferably at least 75% tree, and more preferably at least 90% free, even more preferably at least 95% free from other components with which they are naturally associated.

[0039] The disclosed methods may include administering a composition comprising at least one of CFHRI, CFHR3, and or a variant thereof. Human CFHRI is expressed as a precursor protein having 330 amino acids. (See SEQ ID NO: !). Amino acids 1-18 are cleaved to provide the processed precursor having 312 amino acids (See SEQ ID NO:2). Human CFHR3 may be expresses as Isofonn 1 or Isofomi 2, which both are encompassed by the presently disclosed methods, kits, and compositions. Human CFHR3 Isofonn 1 is expressed as a precursor protein having 330 amino acids. (See SEQ ID NO:3). Amino acids 1-18 are cleaved to provide the processed precursor having 312 amino acids (See SEQ ID NO:4). Human CFHR2 Isofomi 2 is expressed as a precursor protein having 269 amino acids, (See SEQ ID NO: 5). Amino acids 1-18 are cleaved to provide the processed precursor having 251 amino acids (See SEQ ID NO:6). Variants of CFHRI and/or variants of CFHR3 may include polypeptides having an amino acid sequence having at least about 80%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity with any of SEQ ID NOs.1-6. Variants may include fragments of CFRH1 and or fragment of CFHR3 (e.g., fragments of any of SEQ ID NOs;i -6 having a .. -teiminal deletion, a C-teiininal deletion, botli of a N-terarinal deletion and a C-teiiniiial deletion, or an internal deletion) where the fragment optionally has at least about .80%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity- with any of SEQ ID KOs:^"l-6. Preferably, the variant of CFHR1 and/or variant of CFHR3 has one or more biological activities associated with CFHR1 and/or CFHR3, for example, binding to C3b and or inducing degradation of C3b.

[0040] As utilized herein, the term "antibody" should be interpreted to include "antigen- binding fragments" thereof. The term "antigen-binding fragment" of an antibody (or simply "antibody portion" or "fragment"), as used herein, refers to one or more fragments of a full- length antibody that retain the ability to specifically bind to the corresponding antigen. Examples of antigen-binding fi agments of the disclosed antibodies include, but are not limited to: (i) an Fab fragment or a monovalent fragment consisting of the VL, VH, CL and CH^'l domains; (ii) an F(ab')₂ fragment or a bivalent fragment comprising two Fab fiagments linked by a disulfide bridge at the hinge region; (iii) an Fd fragment consisting of the VH and CHI domains; (iv) a Fv fragment consisting of the VL and VH domains of a single arm of an antibody, (v) a dAb fragment (Ward e.g., (1989) Nature 341:544 546), which consists of a VH domain; and (vi) an isolated complementarity determining region (CDR). Even though the two domains of the Fv fragment, VL and VH, are coded for by separate genes, they can be joined, using recombinant methods, by a synthetic linker that enables them to be made as a single protein chain in which the VL and VH regions pair to form monovalent molecules (known as single chain Fv or "scFv." (See, e.g.. Bird e.g. (1988) Science 242:423 426; and Huston e.g. (1988) Proc. Natl. Acad. Sci. USA 85:5879 5883). Single chain Fv or "scFv" are encompassed within the term "antigen -binding fragment" of an antibody.

[0041] The disclosed antibodies can be full-length (e.g., an IgG (e.g., an IgGi, IgG2,

IgG3, IgG4), IgM, IgA (e.g., IgAl , IgA2), IgD, and IgE) or can include only an antigen-binding fragment (e.g., a Fab, F(ab¾ or scFV fragment, or one or more CDRs). The antibodies disclosed herein may be a polyclonal or monoclonal antibodies. The disclosed antibodies may be monospecific, (e.g. , a monoclonal antibody, or an antigen-binding fragment thereof), or may be inultispeeiiic (e.g.. bispecific recombinant diabodies). hi some embodiments, the antibody can be recombinant!)? produced (e.g., produced by phage display or by combinatorial methods), hi some embodiments, the antibodies (or fragments thereof) are recombinant or modified antibodies (e.g., a chimeric, a humanized, a . deimmunized, or an in vitro generated antibody).

[0042] The presently disclosed compositions may be administered in methods in order to enhance the ability of a monoclonal antibody to kill tumor cells via antibody-dependent cellular cytotoxicity or other mechanisms. The methods may enhance killing of target cells by natural killer (NK) cells.

[0043] The compositions disclosed herein may be formulated as pharmaceutical composition for administration to a subject in need thereof. Such compositions can be formulated and/or administered in dosages and by techniques well known to those skilled hi the medical arts taking into consideration such factors as the age, sex, weight, and condition of the particular patient, and the route of admhiistration. The compositions may include pharmaceutically acceptable carriers, diluents, or excipients as known in the art. A "phamiaceutically acceptable" carrier, excipient, diluent, or stabilizer typically is not biologically or otherwise undesirable, i.e., the carrier, excipient, diluent, or stabilizer may be administered to a subject, along with an antibody and at least one of CFHR1, CFHR3, and/or a variant thereof, hi some embodiments, the carrier, excipient, diluent, or stabilizer may be selected to mhiiiiiize any degradation of the antibody and at least one of CFHR1, CFHR3, and/or a variant thereof or to mmimize any adverse side effects in a patient to which the compositions are administered. Suitable earners, excipients, or diluents for the compositions utilized in the disclosed methods may include, but are not limited to, fillers such as saccharides (e.g._., lactose or sucrose, mannitol or sorbitol), cellulose preparations and/or calcium phosphates (e.g., fricalcium phosphate or calcium hydrogen phosphate), as well as binders (e.g., starch paste, using, for example, maize starch, wheat starch, rice starch, potato starch, gelatin, tragacanth, methyl cellulose, hydroxypropylmefhylcellulose, sodium carboxy-inethylcellulose, or polyvinyl pyrrolidone). Further, the compositions may include preservatives (e.g. , aiiti-mierobial or antibacterial agents such as benzalkonium chloride) or adjuvants.

[0044] The pharmaceutical composition disclosed herein may be delivered via a variety of routes including but not limited to intravenous and parenteral routes (e.g., intradermal, intramuscular or subcutaneous delivery)- Suitable formulations of the pharmaceutical compositions may include liquid formulations or solid formulations (e.g. , powders), which may be reconstituted as liquid formulations.

[0045] Methods contemplated herein include methods of diagnosis and prognosis. As used herein the terms "diagnose" or "diagnosis" or "diagnosing" refer to distinguisliiiig or identifying a disease, syndrome or condition or distinguishing or identifying a person having or at risk for developing a particular disease, syndrome or condition. As used herein the terms "prognose'^* or "prognosis" or "prognosing" refer to predicting an outcome of a disease, syndrome or condition.

[0046] The diagnostic/prognostic methods may be performed on a patient sample. The term ''sample" or "patient sample" is meant to include biological samples such as tissues and bodily fluids. "Bodily fluids" may include, but are not limited to, blood, serum, plasma, saliva, cerebral spinal fluid, pleural fluid, tears, lacfal duct fluid, lymph, sputum, and semen. A sample may include nucleic acid, protein, or both. A biological sample may include biological molecules such as biological proteins or nucleic acid (e.g., genomic DNA and/or RNA).

[0047] The term "nucleic acid" or "nucleic acid sequence" refers to an oligonucleotide, nucleotide or polynucleotide, and fragments or portions thereof which may be single or double stranded, and represents the sense or antisense strand. A nucleic acid may include DNA or RNA, and may be of natural or synthetic origin. For example, a nucleic acid may include niR A or cD A. Nucleic acid may include nucleic acid thai has been amplified (e.g., using polymerase chain reaction). [0048] As used herein the term "sequencing." as in determining the sequence of a polynucleotide, refers to methods that determine fee base identity at multiple base positions or that determine the base identity at_. a single position. The term "amplification" or "amplifying" refers to fee production of additional copies of a nucleic acid sequence. Amplification is generally carried out using polymerase chain reaction (PCR) technologies known in^' the art^'.

[0049] The present methods and kits may utilize nucleotide reagents for detecting a nucleic sequence. Nucleotid reagents may include primers, probes, or both. The term "primer" refers to an oligonucleotide that hybridizes to a target nucleic acid and is capable of acting as a point of initiation of synthesis when placed under conditions in which primer extension is initiated (e.g., primer extension associated with an application such as PCR). For example, primers contemplated herein may hybridize to one or more polynucleotide sequences that encode CFHR1 and/or CFHR3 and i particular a polymorphism at rs3766404 (i.e. T T, T/C, or C/C). A "probe" refers to an oligonucleotide that interacts with a target nucleic acid via hybridization. A primer or probe may be fully complementary to a target nucleic acid sequence or partially complementary. The level of complementarity will depend on many factors based, in general, on the function of the primer or probe. A primer or probes can be used, for example to detect the presence or absence of a mutation in a nucleic acid sequence by virtue of the sequence characteristics of the target. Primers and probes can be labeled (e.g., with a fluorophore, a radiolabel, an enzyme, a particulate label, or the like) or unlabeled, or modified in any of a number of ways well known in the art. A primer or probe may specifically hybridize to a target nucleic acid (e.g. , hybridize under stringent conditions as discussed herein).

[0050] The term "oligonucleotide" is understood to be a molecule that has a sequence of bases on a backbone comprised mainly of identical monomer units at defined intervals. The bases are arranged on the backbone in such a way that they can enter into a bond with a nucleic acid having a sequence of bases that ar e complementary to the bases of the oligonucleotide. The most common oligonucleotides have a backbone of sugar phosphate units. Oligonucleotides of the method which function as primers or probes are generally at least about 10-15 nucleotides long and more preferably at least about 15 to 25 nucleotides long, although shorter or longer oligonucleotides may he used i the method. The exact size will depend on many factors, which in turn depend on the ultimate function or use of the oligonucleotide. An oligonucleotide (e.g., a probe or a primer) that is specific for a target nucleic acid will "hybridize" to the target nucleic acid under suitable conditions. As used herein, "hybridization" or "hybridizing" refers to the process by which an oligonucleotide single strand anneals with a complementary strand through base pairing under defined hybridization conditions. Oligonucleotides used as primers or probes for specifically amplifying (i.e., amplifying a particular target nucleic acid sequence) or specifically detecting (i.e. , detecting a particular target nucleic acid sequence) a target nucleic acid generally are capable of specifically hybridizing to the target nucleic acid.

[0051] The present methods may be performed to detect the presence or absence of the disclosed polymorphisms (e.g., rs3766404). Methods of determining the presence or absence of a polymorphism may include a variety of steps known in the art, including one or more of the following steps: amplifying nucleic acid that comprises the polymorphism (e.g., amplifying genomic DN A thai comprises the polymorphism), hybridizing a probe or a primer to nucleic acid that comprises the poljmorphism (e.g., hybridizing a probe to oiRNA, cD A, or amplified genomic DNA that comprises the polymorphism), sequencing nucleic acid that comprises the polymorphism (e.g., sequencing cDNA or amplified DNA that comprises the polymorphism), and reverse transcribing niRNA thai comprises the polymorphism to cDNA.

[0052] The term "heterozygous" refers to having different alleles at one or more genetic loci in homologous chromosome segments. As used herein "heterozygous" may also refer to a sample, a cell, a cell population or a patient in which different alleles at one or more genetic loci may be detected (e.g. T/C at the rs3766404 polymorphism). Heterozygous samples may also be determined via methods known in the art such as, for example, nucleic acid sequencing.

[0053] As used herein, the term "homozygous" refers to having identical alleles (e.g. T/T or C/C at the rs3766404 polyniorphism) at one or more genetic loci in homologous chromosome segments. "Homozygous" may also refer to a sample, a cell, a cell population, or a patient in which the same alleles at one or more genetic loci may be detected. Homozygous samples may be determined via methods known in the art. such as, for example, nucleic acid sequencing.

[0054] As used herein, the term "specific hybridization" indicates that two nucleic acid sequences share a high degree of complementarity. Specific hybridization complexes form under stringent annealing conditions and remain hybridized after any subsequent washing steps. Stringent conditions for annealing of nucleic acid sequences are routinely determinable by one of ordinary skill in the art and may occur, for example, at 65° C. in the presence of about 6xSSC. Stringency of hybridization may be expressed, in part, with reference to the temperature under which the wash steps are earned out. Such temperatures are typically selected to be about 5° C. to 20° C. lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. The Tm is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. Equations for calculating Tm and conditions for nucleic acid hybridization are known in the art.

[0055] As used herein, a "target nucleic acid" refers to a nucleic acid molecule containing a sequence that has at least partial complementarity with a probe oligonucleotide, a primer oligonucleotide, or both. A primer or probe may specifically hybridize to a target nucleic acid. A target nucleic acid may comprise the rs3766404 polymorphism.

[0056] A "polymorphism" refers to the occurrence of two or more alternative genomic sequences or alleles between or among different genomes or individuals. "Polymorphic" refers to the condition in which two or more variants of a specific genomic sequence can be found in a population. A "polymorphic site" is the locus at which the variation occur s. A single nucleotide polymorphism is the replacement of one nucleotide by another nucleotide at the polymorphic site. Deletion of a single nucleotide or insertion of a single nucleotide also gives rise to single nucleotide polymorphisms. "Single nucleotide polymorphism" preferably refers to a single nucleotide substitution. Typically, between different individuals, the polymorphic site can be occupied by two different nucleotides. An individual may be homozygous or heterozygous for the single nucleotide polymorphism. "Mutation" as utilized herein, is intended to encompass a single nucleotide substitution, which is observed to be a single nucleotide polymorphism.

EXAMPLES

[0058] The following example is illustrative and is not intended to limit the scope of the claimed subject matter.

[0059] Title: Complement Factor H-Related Protein 1 (CFHRl). Complement Factor H-

Related Protein 3 (CFHR3) and the Efficacy of Antibody Therapy

[0060] Abstract

[0061] This example describes the diagnostic and therapeutic implications resulting from our identification of a protein that appears to explain why immunotherapy using Monoclonal Antibodies (mAbs) is effective in some patients and not effective in others. This example is based on evidence that Complement Factor H Related Protein 1 (CFHRl ), complement factor H- related protein 3 (CFHR3) or other members of this family of proteins, is necessary for rituximab, the most extensively studied niAb, to mediate its anti-cancer effects. It is likely that CFHRl or CFHR3 is important for the efficacy of oilier niAb immunotherapies as well. CFHRl and CFHR3 have been previously described but little is known about their activities, and identification of their role in mediating the therapeutic effects of niAb therapy is entirely novel .

[0062] Rituximab and other mAb have had a major impact on our ability to treat a variety of cancers and oilier diseases. MAbs are among the most costly drugs currently approved by the FDA. Understanding factors that contribute to the sensitivity' or resistance to niAb therapy could have major medical and cost implications in two ways: (1) Measurement of CFHRl, CFHR3 or related proteins (or genetic mutations associated therewitli) could be applied as an assay to predict which patients will respond to niAb therapy; (2) Treatment with CFHRl, CFHR3 or related proteins could be used to enhance the efficacy ofmAb therapy. Therefore, the present invention could lead to a diagnostic test and/or treatment method that could have a major impact on the use ofniAbs for heating a variety of diseases.

[0063] Background

[0064] Tliis example describes a potential new approach to improving the clinical efficacy of mAb therapy, and to predicting which patients are most likely to respond to mAb therapy, Rimximab and other mAbs have had a major impact on our ability to treat a variety of cancers and other diseases as well. However, clinical response to mAb therapy is inconsistent, and the majority of patients relapse and eventually become resistant to mAb therapy. Several mechanisms of action have been identified that can contribute to the efficacy of mAb therapy. These include antibody dependent cellular cytotoxicity (ADCC) (see Figure 1) and complement mediated cytotoxicity (CMC). The strongest evidence at the present time points to ADCC as being the primary mechanism of action for many (but not all) mAb therapies.

[0065] Over the past few years we have published a series of papers demonstrating the apparent paradox that complement, if it does not kill the target cell, can block cellular killing by blocking NK cell activation and ADCC. (See Wang et al 2008; and Wang et al. 2009). Thus, complement can enhance or reduce killing of target cells by mAb. Clinically, complement could enhance the therapeutic efficacy of mAb by mediating CMC, or complement could limit therapeutic efficacy by blocking ADCC. Mechanistically, complement can reduce the efficacy of mAb when the C3b component of complement binds to mAb and blocks interaction between the mAb and NK cell, thereby limiting NK cell activation and preventing ADCC (see Figure 2).

[0066] Results and Discussion

[0067] The need to better understand the role of complement in mAb therapy led us to explore the effect of complement genetics on rituximab therapy at the population level. The following information is known or has now been discovered about this family of proteins: (1) CFH and the CFH family of proteins can degrade C3b; (2) C3b can block NK cell activation and ADCC of rituximab-coated cancer cells; (3) Polymorphisms in CFH are correlated with outcome in subjects treated with tituximab; (4) CFHRl and C3FH 3 play an important role in complement-mediated autoimmunity and (5) individuals with a mutation that results in loss of CFHRl and CFHR3 develop hemolytic uremic syndrome that is mediated by complement mediated lysis of red blood cells.

[0068] Our studies, outlined below, have revealed important and unexpected findings that pointed towards the CFHRl and CFHR3 proteins as playing a critical role in the efficacy of mAb therapy. These results provide indirect but convincing evidence that higher levels of CFHRl and CFHR3 result in more rapid degr adation of C3b on niAb-coated target cells, thereby resulting in enhanced N activation and ADCC, and a better clinical outcome (see Figure 3). Conversely, C3b remains on mAb of individuals lacking CFHRl and CFHR3. This blocks NK activation, prevents killing of the targeted cells, and results in an inferior outcome.

[0069] From the point of view of application of this discovery, it could lead to testing for

CFHRl or CFHR3 to determine the likelihood that a given patient will respond to iiiAb therapy. It also suggests that treatment with CFHRl and CFHR3 could enhance the efficacy of mAb therapy.

[0070] In collaboration with our colleagues from the Mayo Clinic, we evaluated whether there was a correlation between polymorphisms in the complement pathway and the outcome for patients having lymphoma and undergoing treatment with riraxirnab. (See Charboimeau et al. Am J Hematol. 2012;87(9):880-5, incorporated herein by reference in its entirety). In this study, we identified single nucleotide polymorphisms (SNPs) in Complement Factor H (CFH) that correlated with outcome in follicular lymphoma patients treated with Riiuximab but not in observed follicular lymphoma patients (i.e., patients who received no therapy). This suggests that the complement pathway has a greater impact on a patient's response to rituximab therapy than on the natural history of the disease. The greatest statistical significance was found at an intronic SNP in CFH (rs3766404). Subjects with T T at rs3766404 had better outcome than subjects with T/C or C/C at this position (p=.0007). (See Table 1 and Figure 4). Table L

§¾¾¾-*.δ« ΤΤ :¾fi *SS ί ίί« rsrssss

TO >·* r.caa

CO

Other CFH SNPs revealed a trend towards better outcome in riroximab-treated subjects, as did SNPs in other CFH family members including rs436719 in CFHR1 (P=O.O90

[0058] CFH is found in high concentration in the serum and has a broad variety of effects on the complement system including degradation of C3b. Increased CFH activity could degrade C3b more effectively and so reduce CMC. Based on our work outlined above, I hypothesized that increased CFH activity could degrade C3b and so enhance ADCC. Thus, differences in CFH levels or function could enhance ADCC and improve the efficacy of niAb therapy.

[0059] Experiments were designed to evaluate this hypothesis. In orde to evaluate the relationship between CFH genetics and CFH function further, I obtained serum from subjects who had been genotyped for the CFH rs3766404 polymorphisms. These samples came from Iowa lymphoma subjects that are part of the Iowa/Mayo Lymphoma SPORE, and from normal subjects irom the Mayo Clinic.

[0060] There was considerable variation in overall CFH levels, but this variation did not correlate statistically with the rs3766404 polymorphism. We also evaluated CFH by Western Blot. CFH was probed using an antibody that recognize both CFH and CFHRl, a smaller member of the CFH family. The rs3766404 polymorphism had no significant impact on. the CFH band. Unexpectedly, CRHR1 was absent in the vast majority of samples from subjects with the C/C -genotype, was present in T/C heterozygotes, and was highest in subjects with the T/T genotype. In addition, we evaluated whether the polymorphism in rs37660404 correlated with the deletion in CFHRl and CFHR3 that has been described as associated with aiitoiimnmiity. We found CFHRl and CFHR3 was deleted in all three samples from subjects with the C/C genotype - the subjects with the worst outcome (see Figures 5 and 6). These results initially were observed in the Iowa samples from lymphoma patients, and confirmed on Mayo samples from normal subjects.

[0061 ] Summary

[0062] We found that polymorphisms in rs3766404 are associated with the clinical outcome in lymphoma patients undergoing immunotherapy with Rituximab. A polymorphism that was associated with a better clinical outcome (T/T), also was correlated with higher semm levels of CFHRl, a complement protein found on the same region of chromosome Iq32 as the polymorphisms. The subjects with the worst clinical outcome had a deletion in the CFHRl and CFHR3 genes. Thus, taken together, these results indicate that the T/T polymorphism in rs3766404 that correlates with a better clinical outcome also correlates with higher serum levels of CFHRl , and suggests that the absence of CFHRI and/or CFHR3, or at least lower levels of CFHRl and/or CFHR3, could be responsible for the poor outcome in this subset of patients.

[0063] References

[0064] 1. Charbonneau B, Maurer MJ, Fredericksen ZS, Zent CS, Link B , Novak

AJ, et al. Germ-line variation in complement genes and event-free survival in follicular and diffuse large Β-ςχΆ lymphoma. Am J Hematol. 2012;87( ):8S0-5.

[0065] 2. Wang SY, Racila E, Taylor RP, Weiner GJ. NK-cell activation and antibody-dependent cellula cytotoxicity induced by riraximab-coated target cells is inhibited by the C3b component of complement. Blood. 2008;! 11(3): 1456-63. [0066] 3. Wang SY, Veeramani S, Racila E, Cagtey J, Fritzinger DC, Vogel. CW. et al. Depletion of the C3 component of complement enhances fee ability of rimxiinab-coated target cells to activate human NK cells and improves fee efficacy of monoclonal antibody therapy in an in vivo model. Blood. 2009;! 14(26):5322-3G.

[0067] 4. de Cordoba SR, de Jorge EG. Translational mini-review series on complement factor H; genetics and disease associations of human complement factor H. Clin Exp Immunol. 2008;151(I):1-13.

[0068] In fee foregoing description, it will be readily apparent to one skilled in the art that varying substitutions and modifications may be made to the invention disclosed herein without departing from the scope and spirit of the invention. The invention illustratively described herein suitably may be practiced in the absence of any element or elements, limitation or limitations which is not specifically disclosed herein. The terms and expressions which have been employed are used a terms of description and not of limitation, and there is no intention that in the use of such terms and expressions of excluding any equivalents of the features shown and described or portions thereof, but it is recognized that various modifications are possible within the scope of the invention. Thus, it should be imderstood that although the present invention has been illustrated by specific embodiments and optional features, modification and/or variation of the concept herein disclosed may be resorted to by those skilled in the art, and that such modifications and variations are considered to be within the scope of this invention.

[0069] Citations to a number of references are made herein. The cited references are incorporated by reference herein in their entireties. In the event that there is an inconsistency between a definition of a term in the specification as compared to a definition of the term in a cited reference, the term should be interpreted based on the definition in fee specification.

Claims

CLAIMS We claim:

1. A method comprising:

(a) administering a first pharmaceutical composition comprising a therapeutic antibody or an antigen-binding fiagment to a patient in need thereof; and

(b) admiiiisiering a second phamiaceiitical composition comprising at least one of complement factor H-related protein 1 (CFHR1), complement factor H-related protein 3 (CFHR3), and/or a variant thereof to the patient.

2. The method of claim 1, wherein the patient has a C/C polymorphism in rs3766404 or a T/C polymorphism in rs3766404.

3. The method of claim 1 or 2, wherein the therapeutic antibody is a monoclonal antibody.

4. The method of claim 3. wherein the monoclonal antibody is selected from a group consisting of Abciximab, Adalimumab, Alemtuzumab, Basiliximab, Belimumab, Bevacizumab, Brentuximab vedotin, Canakinumab, C^'emximab, Certo!izumab pegol, Daclizumab, Denosumab, Eciiliziimab, Efalizumab, Gemhizumab, Golimumab, Ifaritumomah tiuxetan. Infliximab, Ipilmmmab (MDX-101), Muromonab-CD3, Natalizumab, Oiatimmmab, Omalizumab, Palivizumab, Panitumumab. Ranibizumab, Rituximab, Tocilizumab, Tositumomab, and Trastuziimab.

5. The method of claim 4, wherein the antibody is Rituximab.

6. The method of any of the preceding claims, wherein the patient has or is at risk for developing a disease or disorder selected from cardiovascular disease, auto-immune disorders (e.g. , systemic lupus erythematosus), a cell proliferative disease or disorder (e.g.. chronic lymphocytic leukemia, colorectal cancer, anaplastic large cell lymphoma (ALCL), Hodgkin lymphoma, head and neck cancer, solid tumor bony metasteses, acute myelogenous leukemia non-Hodgkin lymphoma, melanoma, breast cancer), transplant rejection, age-related macular degeneration, eiyopyrin-assGeiated periodic syndrome (CAPS), Crohn's disease, postmenopausal osteoporosis, paroxysmal nocturnal hemoglobinuria, psoriasis, rheumatoid arthritis, psoriatic arthritis, ankylosing spondylitis, multiple sclerosis, allergy-related asthma, and infection by a microbe or virus (e.g., infection by respiratory syncytial virus).

7. Tlie method of any of the preceding claims, wherein the CFHR1 , CFHR3, and/or variant thereof has an amino acid sequence comprising at least one of SEQ ID NOs: l-6.

8. The method of any of claims 1-6, wherein the variant of CFHR1 and/or variant of CFHR3 has an amino acid sequence having at least about 80% sequence identity to at least one of SEQ ID NO: 1-6.

9. The method of claim 8, wherein the variant of CFHR1 and/or variant of CFHR3 exhibits C3b binding activity.

10. The method of claim 8 or 9, wherein the variant induces degradation of

C3b.

11. Tlie method of any of the preceding claims, wherein the first pharmaceutical composition is aciministered prior to the second pharmaceutical composition.

12. The method of any of claims 1-10, wherein the second pharmaceutical composition is administered prior to the first pharmaceutical composition.

13. The method of any of claims 1-10, wherein the first pharmaceutical composition and the second pharmaceutical composition are administered concurrently.

14. The method of any of the preceding claims further comprising administering an additional agent that modifies the complement system.

15. A kit comprising:

(a) a first pharmaceutical composition comprising an antibody or antigen-hmding fragment; and

(b) a second pharmaceutical composition comprising at least one of complement factor H-related protein 1 (CFHRl), complement factor H-related protein 3 (CFHR3), and or a variant thereof.

16. The kit of claim 15, wherein the antibody is a monoclonal antibody.

17. The kit of claim 15, wherein the monoclonal antibody is selecied from a group consisting of Abciximab, Adaliinurnab, Alemtuzumab, Basiliximab, Belimumab, Bevacizuinab, Brentuximab vedotin, Canakimmiab, Cetiiximab, Certolizumab pegol, Daclizumab, Denosuinab, Eciiliziiniab, Efalizumab, Geaituzumab, Golimumab, Ibritumomah tiuxetan. Infliximab, Ipiliinuinab (MDX-101), Muronionab-CD3, Natalizumab, Ofatumumab, Omalizuniab, Palivizumab, Paninmmmab, Ranibizumab, Rituximab, Tocilizumah, Tositumomab, and Trastuzumab.

18. T!ie kit of any of claims 5-17, wherein the CFHR1, CFHR3, and/or variant thereof has an amino acid sequence comprising a t least one of SEQ II) NOs:l-6.

19. The kit of any of claims 15-17, wherein the variant of CFHR1 and/or variant of CFHR3 has an amino acid sequence having at least about 80% sequence identity to at least one of SEQ ID NO: 1-6.

20. The kit of claim 19, wherein the variant of CFHRl and or variant of CFHR3 exhibits C3b binding activity.

21. The kit of claim 1 or 20, wherein the variant induces degradation of C3b.

22. A method comprising:

(a) reacting a patient sample with a diagnostic antibody that detects CFHRl and/or a diagnostic antibody that detects CFHR3; and (b) administering a pharmaceutical composition comprising a therapeutic antibody or antigen-binding fragment to the patient based on the detected CFHR1 and/or detected CFHR3.

23. The method of claim 22, wherein the therapeutic antibody is a monoclonal antibody.

24. The method of claim 23, wherein the monoclonal antibody is selected from a group consisting of Abciximab, Adalimumab, Alemtuzumab, Basiliximab, Belimumab, Bevaciziimab, Brentiiximab vedotin, Canakinumab, Cetuximah, Certolizumab pegoL Daclizumab, Denosuniab, Ecul unab, Efalizumab, Gemtuzumab, Golimumab, Ibntumomab tiuxetan, infliximab, Ipilimumab (MDX-101), Muromonab-CD3, Natalizumab. Ofatumumab, Omalizumab, Palivizuinab, Panitumumab, Ranibizumab, Ritiiximab, Toeilizumab, Tositumomab, and Trastuzumab.

25. The method of claim 24, wherein the therapeutic antibody is Rituximab.

2Ci The method of any of claims 22-25 further comprising adimnistering a second pharmaceutical composition comprising CFHRI, GFHR3, and/or variant thereof having an amino acid sequence with at least about 80% sequence identity to at least one of SEQ ID NO: 1-6 based on the detected CFHRI and/or the detected CFHR3.

27. The method of any of claims 26, wherein the CFHRI, CFHR3, and or variant thereof has an amino acid sequence comprising a t least one of SEQ∑D NOs:l-6.

28. The method of claim 26 or 27, wherein the variant of CFHRI and/or variant of CFHR3 exhibits C3b binding activity.

29. The method of any of claims 26-28, wherein the variant induces degradation of C3b.

30. The method of any claims 26-29, further comprising administering an additional agent thai modifies the complement system.

31. The method of any of claims 22-30, wherein the patient has or is at risk for developing a diseas or disorder selected from cardiovascular disease, auto-immune disorders (e.g. , systemic lupus erythematosus), a ceil proliferative disease or disorder (e.g. , chronic lymphocytic leukemia, colorectal cancer, anaplastic large cell lymphoma (ALCL), Hodgkin lymphoma, head and neck cancer, solid tumor bony metasteses, acute myelogenous leukemia non-Hodgkin lymphoma, melanoma, breast cancer), transplant rejection, age-related macular degeneration, cryopyrin-associated periodic syndrome (CAPS), Crohn's disease, postmenopausal osteoporosis, paroxysmal nocturnal hemoglobinuria, psoriasis, rheumatoid arthritis, psoriatic arthritis, ankylosing spondylitis, multiple sclerosis, allergy-related astlmia, and infection by a microbe or vims {e.g., infection by respiratory syncytial virus).

32. A kit comprising :

(a) a composition comprising a diagnostic antibody for detecting CFHR1 and/or a diagnostic antibody for detecting CFHR3; and

(b) a pharmaceutical composition comprising a therapeutic antibody or antigen-binding fragment.

33. The kit of claim 32, wherein the therapeutic antibody is a monoclonal antibody.

34. The kit of claim 33, wherein the monoclonal antibody is selected from a group consisting of Abciximab, Adalimmnab, Alemtuzumab, Basiliximab, Belimumab, Bevacizmnab, Brentuximab vedotin, Canakimmiab, Cetuximab, Certolizumab pegol, Daclizumab. Denosumab, Eculizimiab, Efalizumab, Gemtuzumab, Golimumab, Ibritumomab tiuxetan. Infliximab, Ipilimumab (MDX-lOi), Muromonah-CD3, Nataliznmab, Obinutuzumah, Ofarumumab, Omalizumab, Palivizimiab, Pamtimiimiab, Ranibizumab, Rituximab, Tocilizumab, Tositumomab, and Trastuzumab.

35. A method comprising:

(a) reacting a patient sample with a reagent that detects a CYC polymorphism in rs3766404 or a T/C polymorphism in rs3766404; and

(b) admiiiisiering a pharmaceutical composition comprising a therapeutic antibody or antigen-binding fragment to the patient based on the detected C/C polymorphism in rs3766404 or the detected T/C polymorphism in rs3766404.

36. The method of claim 35, wherein ste (a) comprises amplifying nucleic acid in the patient sample and sequencing the amplified nucleic acid.

37. The method of claim 35 or 36, wherein the therapeutic antibody is a monoclonal antibody.

38. The method of claim 37, wherein the monoclonal antibody is selected from a group consisting of Ahciximab, Adalimumab, Alemtuzumab, Basilixiniah, Belimumah, BevacizuHiab, Brentuximab vedotin, Canakinumab, C^'emximab, Certolizomab pegoL Daclizumab, Denosumab, Eculiziimab, Efalizumab, Gemhizumab, Golimumab, Ibritumomab tiuxetan. Infliximab, Ipiliinuinab (MDX-101), Muromonab-CD3, Natalizumab, Ofatumumab, Omalizuinab. Palivizumab, Panmmiuinab. Ranibizumab, Rituxiniab, Tocilizumab, Tosimmomab, and Trastuzumab.

39. The method of claim 38, wherein the therapeutic antibody is Rituxiniab.

40. The method of any of claims 35-39 further comprising administering a second pharmaceutical composition comprising CFHR1, CFHR3, and or vaiiant thereof having an amino acid sequence with at least about 80% sequence identity to at least one of SEQ ID NO: 1-6 based on the detected C/C polymorphism in rs3766404 or the detected T/C polymorphism in rs3766404.

41. The method of any of claims 40, wherein the CFHRI, CFHR3, and/or variant thereof has an amino acid sequence comprising at least one of SEQ ID NOs: 1-6.

42. The method of claim 40 or 41, wherein the variant of CFHRI and or variant of CFHR3 exhibits C3b binding activity.

43. T!ie method of any of claims 40-42, wherein the variant induces degradation of C3b.

44. The method of any claims 40-43, further comprising administering an additional agent that modifies the complement system.

45. The method of any of claims 35-45, wherein the patient has or is at risk for developing a disease or disorder selected from cardiovascular disease, auto-immune disorders ( .g., systemic lupus erythematosus), a cell proliferative disease or disorder (e.g., chronic lymphocytic leukemia, colorectal cancer, anaplastic large cell lymphoma (ALCL), Hodgkin lymphoma, head and neck cancer, solid tumor bony nietasieses, acute myelogenous leukemia nou-Hodgkin lymphoma, melanoma, breast cancer), transplant rejection, age-related macular degeneration, cryopyrin-associated periodic syndrome (CAPS). Crohn's disease, postmenopausal osteoporosis, paroxysmal nocturnal hemoglobinuria, psoriasis, rheimiatoid arthritis, psoriatic arthritis, ankylosing spondylitis, multiple sclerosis, allergy-related asthma, and infection by a microbe or vims (e.g., infection by respiratory syncytial virus).

46. A kit comprising:

(a) a reagent for detecting a C/C polymorphism in rs3766404 or a T C polymorphism in rs3766404; and

(b) a pharmaceutical composition comprising a therapeutic antibody or antigen-binding fragment.

47. The kit of claim 46, wherein the therapeutic antibody is a monoclonal antibody.

48. The kit of claim 47, wherein the nionocloiial antibody is selecied from a group consisting of Abciximab, Adalirmunab, Aleitttuzomab, Basiliximab, Belimumab, Bevacizumab, Brenfuximab vedotin, Canakinumab, Ceftiximab, Cer olizumab pegol, Daclizumab, Denosumab, Eculizumab. Efalizumab, Gemtuzumab, Golim iiiiab, Ibriramomah thixetan. Infliximab, Ipilimiimab (MDX-101). Muromonab-CDS, Natabzuinab, Obinutuzumab. Oiaftmiumab, Omalizraiiab, Palivizumab, Pamtumumab, Ranibizumab, Rituximab, Tocilizuinab, Tositumomab, and Trastuzumab.

49. A fusion protein comprising:

(a) an antibody or antigen-binding fragment fused to

(b) CFHRI, CFHR3, and/or variant thereof.

50. A pharmaceutical composition comprising the fusion protein of claim 49.