Biomarkers predictive of the responsiveness to tnfalpha inhibitors in autoimmune disorders

Abstract

The invention provides methods for predicting responsiveness to TNFα inhibitors in a subject suffering from an autoimmune disorder, such as rheumatoid arthritis. The methods involve assaying for expression of one or more biomarkers in the subject that are predictive of responsiveness to TNFα inhibitors. A preferred biomarker of the invention is CD11c. The methods can further comprise selecting a treatment regimen with a TNFα inhibitor in an autoimmune disorder subject based upon expression of the biomarker(s) in the subject. The methods can further comprise administering a TNFα inhibitor to the subject according to the selected treatment regimen. Kits that include means for measuring expression of one or more biomarkers that are predictive of responsiveness to TNFα inhibitors for an autoimmune disorder are also provided. Methods of preparing and using databases, and computer program products therefore, for selecting an autoimmune disorder subject for treatment with a TNFα inhibitor are also provided.

What is claimed is: 
     
         1 . A method for predicting responsiveness to a TNFα inhibitor in a subject having an autoimmune disorder, the method comprising: (i) assaying the subject for expression of one or more biomarkers predictive of responsiveness to a TNFα inhibitor in an autoimmune disorder, and (ii) predicting responsiveness of the subject to the TNFα inhibitor based on expression of the one or more biomarkers in the subject, wherein the one or more biomarkers is encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NO: 1-10, 12-28, 30-43, 45-61, 63, 64, 66-73, and 75-82,
 wherein decreased expression of the one or more biomarkers encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1-5, 8, 9, 12-14, 18, 20, 21, 23, 25, 26, 28, 30, 32, 33, 40-42, 48, 50, 52, 53, 56, 58, 60, 63, 66-69, 71-73, 76-78, 80 and 81 is predictive of responsiveness of the subject to a TNFα inhibitor; and/or 
 wherein increased expression of the one or more biomarkers encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6, 7, 10, 15-17, 19, 22, 24, 27, 31, 34-39, 43, 45-47, 49, 51, 54, 55, 57, 59, 61, 64, 70, 75, 79 and 82 is predictive of responsive of the subject to a TNFα inhibitor. 
 
     
     
         2 . A method for predicting responsiveness to a TNFα inhibitor in a subject having an autoimmune disorder, the method comprising:
 (i) assaying the subject for expression of one or more biomarkers predictive of responsiveness to a TNFα inhibitor in an autoimmune disorder, and 
 (ii) predicting responsiveness of the subject to the TNFα inhibitor based on expression of the one or more biomarkers in the subject, wherein the one or more biomarkers is selected from the group consisting of Aquaporin 3 (Genbank Accession No. NM — 004925); Similar to ribosomal protein S24, clone MGC:8595 (Genbank Accession No. NM — 033022); Transmembrane emp24 domain trafficking protein 2 (Genbank Accession No. NM — 006815); Superoxide dismutase 1, soluble (amyotrophic lateral sclerosis 1 (Genbank Accession No. NM — 000454); Calmodulin 1 (phosphorylase kinase, delta) (Genbank Accession No. NM — 006888); Guanine nucleotide binding protein (G protein), beta polypeptide 1 (Genbank Accession No. NM — 002074); Prothymosin, alpha (gene sequence 28) (Genbank Accession No. NM — 002823);  Homo sapiens  isocitrate dehydrogenase 1 (NADP + ) soluble (IDH1) (Genbank Accession No. NM — 005896); Tumor protein D52 (Genbank Accession Nos. NM — 001025252, NM — 001025253, NM — 005079); Early growth response 1 (Genbank Accession No. NM — 001964); Cytochrome c oxidase subunit VIIb (Genbank Accession No. NM — 001866); CUG triplet repeat, RNA binding protein 2 (Genbank Accession No. NM — 001025077, NM — 001025076, NM — 006561); Ubiquinol-cytochrome c reductase hinge protein (Genbank Accession No. NM — 006004);  Homo sapiens  leptin receptor gene-related protein (HS0BRGRP) (Genbank Accession No. NM — 017526); Wiskott-Aldrich syndrome protein interacting protein (Genbank Accession Nos. NM — 001077269, NM — 003387); CD97 antigen (Genbank Accession Nos. NM — 001025160, NM — 001784, NM — 078481); Glutamate-cysteine ligase, catalytic subunit (Genbank Accession No. NM — 001498); Crystallin, zeta (quinone reductase) (Genbank Accession No. NM — 001889); Rap guanine nucleotide exchange factor (GEF) 2 (Genbank Accession No. NM — 014247); Ataxin 1 (Genbank Accession No. NM — 000332); Adaptor-related protein complex 1, sigma 2 subunit (Genbank Accession No. NM — 003916); Ectonucleotide pyrophosphatase/phosphodiesterase 4 (Genbank Accession No. NM — 014936); Desmocollin 2 (Genbank Accession Nos. NM — 024422, NM — 004949); MAL, T-cell differentiation protein (Genbank Accession Nos. NM — 002371, NM — 022438, NM — 022439, NM — 022440); Glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase (Genbank Accession No. NM — 005476); Chemokine (C—C motif) ligand 3 (Genbank Accession Nos. NM — 001001437, NM — 021006); Carboxypeptidase A3 (Genbank Accession No. NM — 001870); NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 1, 7 kDa (Genbank Accession No. NM — 004545); Interleukin 8 receptor, beta (Genbank Accession No. NM — 001557); Platelet factor 4 variant 1 (Genbank Accession No. NM — 002620); Poly(A) binding protein interacting protein 1 (Genbank Accession No. NM — 006451); ATP-binding cassette, sub-family C (CFTR/MRP), member 3 (Genbank Accession No. NM — 003786); Actinin, alpha 1 (Genbank Accession No. NM — 001102); NAD kinase (Genbank Accession No. NM — 023018); Platelet/endothelial cell adhesion molecule (CD31 antigen) (Genbank Accession No. NM — 000442); Esterase D/formylglutathione hydrolase (Genbank Accession No. NM — 001984); Chromosome 20 open reading frame 111 (Genbank Accession No. NM — 016470); Sterol-C4-methyl oxidase-like (Genbank Accession Nos. NM — 001017369, NM — 006745); PIM-1 oncogene (Genbank Accession No. NM — 002648); GATA binding protein 2 (Genbank Accession No. NM — 032638); Cathepsin Z (Genbank Accession No. NM — 001336); Lectin, galactoside-binding, soluble, 8 (galectin 8) (Genbank Accession Nos. NM — 006499, NM — 201545); CD86 antigen (CD28 antigen ligand 2, B7-2 antigen) (Genbank Accession Nos. NM — 006889, NM — 175862); Interleukin 8 (Genbank Accession No. NM — 000584); Fc fragment of IgE, high affinity I, receptor for alpha polypeptide (Genbank Accession No. NM — 002001); Actin, gamma 1 (Genbank Accession No. NM — 001614); KIAA0746 protein (Genbank Accession No. NM — 015187); Glucosamine (N-acetyl)-6-sulfatase (Sanfilippo disease IIID) (Genbank Accession No. NM — 002076); Transcription factor 4 (Genbank Accession Nos. BF592782, CR612521); Major histocompatibility complex, class II, DQ alpha 1 (Genbank Accession Nos. NM — 002122, NM — 020056); Cell division cycle 2-like 6 (CDK8-like) (Genbank Accession No. NM — 015076); Major histocompatibility complex, class II, DQ beta 1 (Genbank Accession No. XM — 942240); Phospholipase C-like 2 (Genbank Accession No. NM — 015184); Coagulation factor II (thrombin) receptor-like 1 (Genbank Accession No. NM — 005242); TM2 domain containing 1 (Genbank Accession No. NM — 032027); Splicing factor 3b, subunit 1, 155 kDa (Genbank Accession No. NM — 012433); SUB1 homolog ( S. cerevisiae ) (Genbank Accession No. NM — 006713); MRNA, cDNA DKFZp564O0862 (Genbank Accession No. AI278204); Cytochrome b-5 (Genbank Accession Nos. NM — 001914, NM — 148923); Cold autoinflammatory syndrome 1 (Genbank Accession No. NM — 183395); Ribosomal protein S26, 40S ribosomal protein (Genbank Accession No. XM — 941927); CCR4-NOT transcription complex, subunit 6 (Genbank Accession No. NM — 015455); Ubiquinol-cytochrome c reductase complex (7.2 kD) (Genbank Accession Nos. NM — 013387, NM — 001003684); Hepatocellular carcinoma-associated antigen 112 (Genbank Accession No. NM — 018487); Kruppel-like factor 11 (Genbank Accession No. XM — 001129527); GGA binding partner (Genbank Accession No. NM — 018318); Cornichon homolog 4 (Drosophila) (Genbank Accession No. NM — 014184); Hypothetical protein FLJ21616 (Genbank Accession No. NM — 024567); Nuclear prelamin A recognition factor (Genbank Accession Nos. NM — 012336, NM — 001038618); Erythroblast membrane-associated protein (Genbank Accession Nos. NM — 018538, NM — 001017922); LR8 protein (Genbank Accession No. NM — 014020); Likely ortholog of mouse limb-bud and heart gene (LBH) (Genbank Accession No. NM — 030915); Calmin (calponin-like, transmembrane) (Genbank Accession No. NM — 024734); Chromosome 14 open reading frame 156 (Genbank Accession No. NM — 031210); Guanine nucleotide binding protein (G protein) alpha 12 (Genbank Accession No. NM — 007353); and SRY (sex determining region Y)-box 18 (Genbank Accession No. NR — 003287). 
 
     
     
         3 . A method for predicting responsiveness to a TNFα inhibitor, which TNFα inhibitor is adalimumab, in a subject having an autoimmune disorder, the method comprising:
 (i) assaying the subject for expression of one or more biomarkers predictive of responsiveness to adalimumab in an autoimmune disorder, and 
 (ii) predicting responsiveness of the subject to adalimumab based on expression of the one or more biomarkers in the subject, 
 wherein decreased expression of the one or more biomarkers encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1-5, 8, 9, 12-14, 18, 20, 21, 23, 25, 26, 28, 30, 32, 33, 40-42, 48, 50, 52, 53, 56, 58, 60, 63, 66-69, 71-73, 76-78, 80 and 81 is predictive of responsiveness of the subject to a TNFα inhibitor; and/or 
 wherein increased expression of the one or more biomarkers encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6, 7, 10, 15-17, 19, 22, 24, 27, 31, 34-39, 43, 45-47, 49, 51, 54, 55, 57, 59, 61, 64, 70, 75, 79 and 82 is predictive of responsive of the subject to a TNFα inhibitor. 
 
     
     
         4 . The method of any of  claims 1 - 3 , wherein a sample from the subject is assayed for expression of mRNA encoding the one or more biomarkers. 
     
     
         5 . The method of any of  claims 1 - 3 , wherein a sample from the subject is assayed for protein expression of the one or more biomarkers. 
     
     
         6 . The method of any of  claims 1 - 3 , which further comprises selecting a treatment regimen with the TNFα inhibitor based upon expression of the one or more biomarkers in the subject. 
     
     
         7 . The method of  claim 6 , which further comprises administering the TNFα inhibitor to the subject according to the treatment regimen such that the autoimmune disorder is inhibited in the subject. 
     
     
         8 . The method of any of  claims 1 - 3 , wherein the TNFα inhibitor is an anti-tumor necrosis factor-alpha (TNFα) antibody, or antigen-binding portion thereof. 
     
     
         9 . The method of  claim 8 , wherein the anti-TNFα antibody, or antigen-binding portion thereof, is a human antibody, a humanized antibody, a chimeric antibody or a multivalent antibody. 
     
     
         10 . The method of  claim 8 , wherein the anti-TNFα antibody, or antigen-binding portion thereof, is adalimumab. 
     
     
         11 . The method of  claim 9 , wherein the anti-TNFα antibody, or antigen-binding portion thereof, is selected from the group consisting of
 i) an isolated human antibody that dissociates from human TNFα with a Kd of 1×10 −8  M or less and a Koff rate constant of 1×10 −3  s −1  or less, both determined by surface plasmon resonance, and neutralizes human TNFα cytotoxicity in a standard in vitro L929 assay with an IC50 of 1×10 −7  M or less; 
 ii) an isolated human antibody with the following characteristics:
 a) dissociates from human TNFα with a Koff rate constant of 1×10-3 s-1 or less, as determined by surface plasmon resonance; 
 b) has a light chain CDR3 domain comprising the amino acid sequence of SEQ ID NO: 305, or modified from SEQ ID NO: 305 by a single alanine substitution at position 1, 4, 5, 7 or 8 or by one to five conservative amino acid substitutions at positions 1, 3, 4, 6, 7, 8 and/or 9; 
 c) has a heavy chain CDR3 domain comprising the amino acid sequence of SEQ ID NO: 306, or modified from SEQ ID NO: 306 by a single alanine substitution at position 2, 3, 4, 5, 6, 8, 9, 10 or 11 or by one to five conservative amino acid substitutions at positions 2, 3, 4, 5, 6, 8, 9, 10, 11 and/or 12; and 
 
 iii) an isolated human antibody with a light chain variable region (LCVR) comprising the amino acid sequence of SEQ ID NO: 303 and a heavy chain variable region (HCVR) comprising the amino acid sequence of SEQ ID NO: 304. 
 
     
     
         12 . The method of  claim 1 , wherein the TNFα inhibitor is etanercept. 
     
     
         13 . The method of any one of  claims 1 - 3 , wherein the subject is a human. 
     
     
         14 . The method of any one of  claims 1 - 3 , wherein the autoimmune disorder is rheumatoid arthritis. 
     
     
         15 . A kit for predicting responsiveness to a TNFα inhibitor in a subject having an autoimmune disorder, the kit comprising:
 a) means for isolating monocytes; 
 b) means for measuring expression in the subject of one or more biomarkers predictive of responsiveness to a TNFα inhibitor in an autoimmune disorder; 
 c) means for measuring expression of at least one housekeeping gene; and 
 d) instructions for use of the kit to predicting responsiveness to a TNFα inhibitor in a subject having an autoimmune disorder, wherein decreased expression of the one or more biomarkers encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1-5, 8, 9, 11-14, 18, 20, 21, 23, 25, 26, 28-30, 32, 33, 40-42, 48, 50, 52, 53, 56, 58, 60, 63, 65-69, 71-74, 76-78, 80 and 81 is predictive of responsiveness of the subject to a TNFα inhibitor and/or wherein increased expression of the one or more biomarkers encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 6, 7, 10, 15-17, 19, 22, 24, 27, 31, 34-39, 43, 44-47, 49, 51, 54, 55, 57, 59, 61, 62, 64, 70, 75, 79 and 82 is predictive of responsive of the subject to a TNFα inhibitor. 
 
     
     
         16 . A method of monitoring an autoimmune disorder in a subject having the autoimmune disorder, the method comprising: assaying the subject for expression of one or more biomarkers, wherein the one or more biomarkers is encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NO: 83-133, thereby monitoring the autoimmune disorder in the subject. 
     
     
         17 . A method of monitoring an autoimmune disorder in a subject having the autoimmune disorder, the method comprising: assaying the subject for expression of one or more biomarkers, wherein the one or more biomarkers is encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NO: 134-177, 110, 112, 118, 123 and 131, thereby monitoring the autoimmune disorder in the subject. 
     
     
         18 . A method of monitoring an autoimmune disorder in a subject having an autoimmune disorder, the method comprising: assaying the subject for expression of one or more biomarkers, wherein the one or more biomarkers is encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NO: 178-292, 91 and 97, thereby monitoring the autoimmune disorder in the subject. 
     
     
         19 . A method of monitoring an autoimmune disorder in a subject having the autoimmune disorder, the method comprising: assaying the subject for expression of one or more biomarkers, wherein the one or more biomarkers is encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NO: 87, 97, 101, 293, 92, 272, 93, 107, 108, 121 and 123, and wherein the subject is monitored prior to treatment with a TNFα inhibitor, thereby monitoring the autoimmune disorder in the subject. 
     
     
         20 . A method of monitoring an autoimmune disorder in a subject having the autoimmune disorder, the method comprising: assaying the subject for expression of one or more biomarkers, wherein the one or more biomarkers is encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NO: 290, 209, 98, 112, 116, 121, 130, 155, 92, 289, 216 and 131, and wherein the subject is monitored after treatment with a TNFα inhibitor, thereby monitoring the autoimmune disorder in the subject. 
     
     
         21 . A method of monitoring an autoimmune disorder in a subject having the autoimmune disorder, the method comprising: assaying the subject for expression of one or more biomarkers, wherein the one or more biomarkers is encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NO: 97, 102, 29, 294, 295, 91, 131, 290, 100, 134, 296, 297, 298, 299, 136, 174 and 300, thereby monitoring the autoimmune disorder in the subject. 
     
     
         22 . A method of selecting an autoimmune disorder subject for a treatment with a TNFα inhibitor, the method comprising:
 (i) identifying, in a database comprising a plurality of autoimmune disorder subjects, a subject whose database entry is associated with a biomarker expression pattern that is predictive of responsiveness to treatment with a TNFα inhibitor, and 
 (ii) selecting the subject for treatment with a TNFα inhibitor, wherein the biomarker expression pattern reports expression in the subject of one or more biomarkers encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NO: 1-82.