AU2014277709B2 - Biomarker for the prediction of responsiveness to an anti-tumour necrosis factor alpha (TNF) treatment - Google Patents

Abstract

H:\mdt\Interwoven\NRPortbl\DCC\MIDT\7301984_.docx-16/12/2014 BIOMARKER FOR THE PREDICTION OF RESPONSIVENESS TO AN ANTI TUMOUR NECROSIS FACTOR ALPHA (TNF) TREATMENT Abstract The invention refers to a method for diagnosing an individual who is to be subjected to or is being subjected to an anti-tumour necrosis factor alpha (TNFa or TNF) treatment to asses the responsiveness to an anti-TNF treatment which comprises the detection of immunoglobulin(s) against one or more biomarker proteins in a bodily fluid or an excrement of said patient, and sorting the individual into one of two categories based on detection of said immunoglobulin(s), wherein individuals are classified as NON-responder or responder. The invention refers to diagnostic kits comprising said one or more biomarker proteins and the use of these kits for assessing the responsiveness to an anti TNF treatment of an individual who is to be subjected to or is being subjected to an anti TNFa treatment.

Description

WO 2009/056633 PCT/EP2008/064820 2014277709 17 Dec 2014 1

Biomarker for the prediction of responsiveness to an anti-Tumour Necrosis Factor alpha (TNF) Treatment 5 The invention refers to a method for diagnosing an individual who is to be subjected to or is being subjected to an anti-tumour necrosis factor alpha (TNFa or TNF) treatment to asses the responsiveness to an anti-TNF treatment which comprises the detection of immunoglobulin(s) against one or more biomarker proteins in a bodily fluid or an excrement of said patient, and sorting the individual into one of two categories based on detection of said immunoglobiilin(s), 10 wherein individuals are classified as NON-responder or responder. The invention refers to diagnostic kits comprising said one or more biomarker proteins and the use of these kits for assessing the responsiveness to an anti-TNF treatment of an individual who is to be subjected to or is being subjected to an anti-TNFa treatment. 15 Background

Rheumatic diseases are the most common chronic inflammatory disorders. In Germany alone, one million patients suffer from immunologically mediated rheumatic diseases including rheumatoid arthritis (RA), spondyloarthropathies (SpA) and systemic autoimmune diseases like 20 systemic lupus erythematosus (SLE), while additional five million individuals have osteoarthritis (OA), a primarily degenerative joint disease, which, however, in its active phases is also dominated by inflammatory processes. Rheumatoid arthritis leads to severe pain, loss of function and serious impairment of the quality of life. Besides these deleterious consequences for the individual patient, there is a striking socio-economic impact leading to direct and indirect costs 25 of about 20 billion Euros in Germany per year. The demographic development clearly indicates that rheumatic diseases will dramatically increase over the next decades and will be equal in importance to cardiovascular diseases and cancer. Already now, rheumatic disorders dominate the number of patient visits in the General Practitioner’s office and are the leading cause of absence from work and premature invalidity. In recognition of the tremendous impact of arthritic 2014277709 17 Dec 2014 WO 2009/056633 PCT/EP2008/064820 2 and bone diseases, the World Health Organization has announced the current decade as the "Decade of Bone and Joint Diseases". A range of therapies for rheumatoid arthritis is available based on standard disease-modifying 5 antirheumatic drugs (DMARDs), such as Methotrexate (MTX) and on biologicals, such as TNF inhibitors/antagonists. Chronically elevated levels of TNF have been implicated as a pathogenic component in rheumatoid arthritis, TNF inhibitors are biologicals which bind to soluble and cell membrane-associated form of TNFa and neutralise the proinflammatory effect of TNFa by preventing the binding of TNFa to die TNF-RI/II cell-surface receptors. TNFa-inhibiting 10 biological agents comprise e.g. therapeutic antibodies (Adalimumab® & Infliximab®) and soluble receptor constructs (Etanercept®). These biologicals are currently used to treat active rheumatoid arthritis, all of which effectively reduce the signs and symptoms of the disease and inhibit radiographic joint damage progression. Currently -10 % of patients in Germany, but up to 30% in Scandinavian countries are treated with TNF-α inhibitors and die numbers are 15 continuously growing. Anti-TNF-α antibodies (Adalimumab®; Humira) account for 90 % of all biologicals in current use of rheumatoid arthritis therapy.

However, only 70 % of rheumatoid arthritis patients benefit from a treatment with anti-TNFa, while 30% (~ 10.000 patients in Germany in 2006) remain non-responders. An anti-TNFa 20 therapy costs currently -20.000 € in Germany and hence, the costs of unsuccessful therapies account for 200 Mio €/ year in Germany alone.

Next to rheumatoid arthritis, chronically elevated levels of TNF have been implicated as a pathogenic component in a number of other disease states - primarily autoimmune conditions -25 such as psoriasis, psoriatic arthritis, ankylosing spondylitis, Crohn’s disease, ulcerative colitis, etc.

Currently, there are no biomarkers available, which can predict the outcome of a treatment with anti-TNF agents (e.g. TNF antagonists/inhibitors) prior treatment. Only reduction of all isotype 30 levels of rheumatoid factors during and after treatment is associated with a positive response and outcome of the treatment (van Laar JM. Nat Clin Pract Rheumatol. 2007 Oct; 3(10):544-5. PMID: 17726429). However, high level of IgA rheumatoid factor in sera of patients with rheumatoid arthritis has been suggested to identify a subgroup of patients at risk of a poor 2014277709 17 Dec 2014 WO 2009/056633 PCT/EP2008/064820 3 clinical response to treatment with anti-TNFa antibodies (Bobbio-Pallavicini F. et al. Ann Rheum Dis. 2007 Mar; 66(3):302-7. PMID: 17079248; Bobbio-Pallavicini F. et al. Ann N Y Acad Sci. 2007 Aug; 1109:287-95. PMID: 17785317; van Laar JM. Nat Clin Pract Rheumatol. 2007 Oct;3(l 0):544-5. PMID: 17726429). The nature of anti-CCP antibodies suggested as a 5 predictor for therapy efficacy is controversial (Braun-Moscovici Y et al. J Rheumatol. 2006 Mar;33(3):497-500. PMID: 16511906; Bobbio-Pallavicini F et al. Ann N Y Acad Sci. 2007 Aug; 1109:287-95. PMID: 17785317; van Laar JM. Nat Clin Pract Rheumatol. 2007 Oct; 3(10):544-5, PMID: 17726429). io Thus, there is a need in the art for markers, which can predict the outcome of an anti-TNFa therapy prior to and during treatment. There is a need for stratification of patients who are to be subjected to or are being subjected to an anti-TNFa treatment and distinguishing between anti-TNFa treatment responder and Non-responder patients. 15 Subject of the present invention is a method for diagnosing an individual who is to be subjected to or is being subjected to an anti-TNFa treatment to asses the responsiveness to an anti-TNF treatment prior, during and/or after anti-TNFa treatment which comprises: a. Detection of immunoglobulin(s) against one or more biomarker proteins in a bodily fluid or excrement of said patient, wherein the one or more biomarker is 20 indicative for the responsiveness to an anti-TNF treatment prior, during and after anti-TNFa treatment. b. Sorting the individual into responder or NON-responder based on detection of said immunoglobulin(s). 25 Thus, die invention provides for the first time marker which can predict the outcome of an anti-TNFa treatment prior to treatment in addition to during and/or after treatment. Anti-TNFalpha treatment may be conducted by administration of TNF inhibitors, e.g. TNF antagonists. These markers are not related to IgA rheumatoid factor. The marker according to the present invention can either be indicative of responder or of NON-responder as will be outlined below in detail. It 30 is preferred that the responsiveness is assessed prior to treatment. WO 2009/056633 PCT/EP2008/064820 4 2014277709 17 Dec 2014

Subject of the present invention is a method for diagnosing an individual who is to be subjected to or is being subjected to an anti-TNFa treatment to asses the responsiveness to an anti-TNF treatment which comprises:

Detection of immunoglobulin(s) against one or more biomarker proteins in a bodily s fluid or an excrement of said patient, wherein a biomarker protein is an expression product encoded by a gene selected from the group comprising RAB11B, PPP2R1A, KPNB1, COG4 and FDFT1, wherein an individual positive for at least one of said immunoglobulin(s) is classified as NON-responder. io In a preferred embodiment of the above-identified method the individual is sorted into one of two categories based on detection of said immunoglobulin(s), wherein an individual positive for at least one of said immunoglobulin(s) is classified as NON-responder and, wherein an individual negative for any of said detected immunoglobulin(s) is classified as responder. 15 In a preferred embodiment of the inventive method at least two of the biomarker proteins of the protein marker group are detected wherein a biomarker protein is an expression product encoded by a gene selected from the group comprising RAB1 IB, PPP2R1 A, KPNB1, COG4 and FDFT1 (Protein Set 1 = RAB11B, PPP2R1A, KPNB1, COG4 and FDFTI). In another preferred embodiment of the inventive method at least expression products encoded by genes RAB1 IB, 20 PPP2R1A, KPNB1, COG4 and FDFTI are detected, In another preferred embodiment only expression products encoded by genes RAB11B, PPP2R1A, KPNB1, COG4 and FDFTI are detected. In another preferred embodiment each and only the expression products encoded by genes RAB1 IB, PPP2R1A, KPNB1, COG4 and FDFTI are detected. 25 In another preferred embodiment of the method for diagnosing an individual who is to be subjected to or is being subjected to an anti-TNFa treatment according to the invention the biomarker protein group additionally comprises at least one other expression product encoded by a gene selected from the group comprising PECI, CTNND2, NSMCE1, KTELCI, HS6ST1, ARMC6, TH1L, PSME1, GPC1, EDC4 (Protein Set 2) and at least one of the proteins of the so entire group 1 and 2 (Protein Set 1 and 2) is detected. In a preferred embodiment of the invention at least one protein from Protein Set 1 is detected and additionally at least one of Protein Set 2 is detected. In another preferred embodiment at least two of the proteins of Protein Set 1 and additionally at least one of Protein Set 2 are detected. In another preferred embodiment Protein Set 1 and Protein Set 2 are detected. 5 2014277709 22 Aug 2017

In another preferred embodiment additionally to the above cited combinations of marker proteins a protein of Protein Set 3 is detected: the Protein Set 3 comprises the expression products encoded by genes PRC1, NAT6, EEF1 AL3, NP_612480.1, PLXNA2, ELM02 and NDUFS2. 5 In another preferred embodiment of the invention at least two marker proteins are selected from the group comprising the marker from protein sets 1, 2 and 3 for the method for diagnosing an individual who is to be subjected to or is being subjected to an anti-TNFa treatment to asses the responsiveness to an anti-TNF treatment prior, during and/or after anti-TNFa treatment. This means in this embodiment at least two marker are selected from the 0 group comprising RAB11B, PPP2R1A, KPNB1, COG4, FDFT1, PECI, CTNND2, NSMCE1, KTELC1, HS6ST1, ARMC6, TH1L, PSME1, GPC1, EDC4, PRC1, NAT6, EEF1AL3, NP_612480.1, PLXNA2, ELM02 andNDUFS2.

In another preferred embodiment at least three marker proteins are selected, more preferably four or five protein marker. 5 According to the present invention biomarker proteins of the present invention may be peptides, protein fragments, full length or splice variants or synthetically modified derivatives or post-translationally modified versions of the proteins encoded by aforementioned genes. Preferably, said protein fragments have a length of more than nine amino acids, more preferably at least twelve or more than twelve amino acids. Modification of proteins may be but are not limited to deimination, deamidation and/or transglutamination. Additionally, they can be artificial polypeptides being expression products derived from incorrect reading frames within the gene. An examples for such an expression product derived from incorrect reading frames within the gene is shown in Figure 122 which is a protein sequence derived from an incorrect reading frame of the gene HS6SP1. Another 25 example is shown in Figure 121 which is a protein sequence derived from an incorrect reading frame of the gene C20orfll49. Yet another example is shown in Figure 119 which is a protein sequence derived from an incorrect reading frame of the gene IRAKI.

This means when for example IRAKI is mentioned in the context of the present application it may concern the peptides, protein fragments, full length or splice variants or synthetically 30 modified derivatives and/or post-translationally modified versions of IRAKI and/or a protein sequence derived from an incorrect reading frame of the gene IRAKI. WO 2009/056633 PCT/EP2008/064820 6 2014277709 17 Dec 2014 A biomarker protein encompasses also variants thereof, such as peptides, protein fragments, artificial polypeptides, full length or splice variants, synthetically modified derivatives or post-translationally modified versions of the proteins encoded by aforementioned genes which are characterized in that these variants exhibit essentially the same ability to be recognized by the 5 respective immunoglobulin as the biomarker proteins that are subject of the invention.

In particular, according to the present inventions biomarker proteins are encompassed wherein the sequences involved in binding to the respective immunoglobulin exhibit at least 80 %, preferred at least 90 %, more preferred at least 95 % degree of sequence identity on the amino 10 acid level to the sequences involved in binding of the biomarker proteins defined in SEQ ID No.s 59-122 as well as peptides, protein fragments, full length or splice variants, synthetically modified derivatives or post-translationally modified versions thereof exhibiting the same ability.

In context of the present invention a DNA sequence of a gene is defined by comprising all exons 15 of a gene necessary to represent the protein coding sequence (CDS) or all splice variants thereof, as well as the exons representing the 5' untranslated region (UTR) and the 3' UTR.

According to the present invention all DNA sequences are encompassed which encode the before-mentioned biomarker proteins.

In particular, according to the present inventions furthermore DNA sequences are encompassed 20 which exhibit referred to the sequence encoding a stretch which is involved in the binding region at least 80 %, preferred at least 90 %, more preferred at least 95 % degree of sequence identity on the nucleic acid level to the DNA sequences encoding a stretch which is involved in the binding region defined in SEQ ID No.s 1-58 as well as fragments thereof encoding the biomarkers according to the present invention. 25 The before mentioned definitions for biomarker proteins and for genes encoding said biomarker proteins apply to every single embodiment of this inventions, any specific method, kit etc.

The determination of percent identity between two sequences is accomplished using the mathematical algorithm of Karlin and Altschul (1993) Proc. Natl. Acad. Sci. USA 90: 5873-30 5877. Such an algorithm is incorporated into the BLASTN and BLASTP programs of Altschul et al. (1990) J. Mol. Biol. 215: 403-410. BLAST nucleotide searches may be performed with the BLASTN program, score = 100, word length = 12, to obtain nucleotide sequences homologous to variant polypeptide encoding nucleic acids. BLAST protein searches are performed with the BLASTP program, score = 50, wordlength = 3, to obtain amino acid sequences homologous to 2014277709 17 Dec 2014 WO 2009/056633 PCT/EP2008/064820 7 the variant polypeptide, respectively. To obtain gapped alignments for comparative purposes, Gapped BLAST is utilized as described in Altschul et al. (1997) Nucleic Acids Res. 25: 3389-' 3402. When utilizing BLAST and Gapped BLAST programs, the default parameters of the respective programs are used. 5

The immunoglobulin(s) to be detected may be selected from IgA, IgD, IgG and IgM. In a preferred embodiment the immunoglobulin(s) to be detected is IgA or IgG. In the most preferred embodiment the immunoglobulin is IgA. The immunoglobulin(s) to be detected is not related to IgA rheumatoid factor. 10

In another preferred embodiment subsets of biomarker proteins may be used to asses the responsiveness to an anti-TNF treatment prior, during and/or after anti-TNFa treatment.

The respective set of proteins can not only predict responsiveness before, but also during 15 treatment. Thus, a diagnostic assay based on one or more protein of the set will help the clinician in treatment decisions and die identification of anti-TNF therapy responders and non- responders a priory.

The bodily fluid and/or excrement from the individual to be assessed may be selected from a 20 group comprising: blood, saliva, tears, synovial and spinal fluid, plasma, urine and stool.

An individual who is to be subjected to or is being subjected to an anti-TNFa treatment may suffer autoimmune conditions such as Crohn’s disease, ulcerative colitis, psoriasis, psoriatic arthritis, ankylosing spondylitis, spondyloarthropathies, rheumatoid arthritis etc. 25 The method of the invention is especially suited for individuals suffering from rheumatoid arthritis.

Subject of the present invention is furthermore a kit for diagnosing an individual who is to be subjected to or is being subjected to an anti-TNFa treatment to asses the responsiveness to an so anti-TNF treatment which comprises one or more biomarker proteins, wherein a biomarker protein is an expression product encoded by a gene selected from the group comprising RAB11B, PPP2R1A, KPNB1, COG4 and FDFT1. In a preferred embodiment the kit comprises 2014277709 17 Dec 2014 WO 2009/056633 PCT/EP2008/064820 8 at least those proteins encoded by a gene selected from the group comprising RAB11B, PPP2R1A, KPNB1, COG4 and FDFT1.

In a preferred embodiment of the inventive kit at least two of the biomarker proteins of the 5 protein marker group are detected wherein a biomarker protein is an expression product encoded by a gene selected from the group comprising RAB11B, PPP2R1A, KPNB1, COG4 and FDFT1 (Protein Set 1 = RAB11B, PPP2R1A, KPNB1, COG4 and FDFT1). In another preferred embodiment of the inventive kit at least one expression product encoded by genes RAB11B, PPP2R1A, KPNB1, COG4 and FDFT1 are detected. In another preferred embodiment only 10 expression products encoded by genes RAB11B, PPP2R1A, KPNB1, COG4 and FDFT1 are detected. In another preferred embodiment each and only the expression products encoded by genes RAB11B, PPP2R1A, KPNB1, COG4 and FDFT1 are detected.

In another preferred embodiment of the kit for diagnosing an individual who is to be subjected to 15 or is being subjected to an anti-TNFa treatment according to the invention the biomarker protein group additionally comprises at least one other expression product encoded by a gene selected from the group comprising PECI, CTNND2, NSMCE1, KTELC1, HS6ST1, ARMC6, TH1L, PSME1, GPC1, EDC4 (Protein Set 2) and at least one of the proteins of the entire group 1 and 2 (Protein Set 1 and 2) is detected. In a preferred embodiment of the invention at least one protein 20 from Protein Set 1 is detected and additionally at least one of Protein Set 2 is detected. In another preferred embodiment at least two of the proteins of Protein Set 1 and additionally at least one of Protein Set 2 are detected. In another preferred embodiment Protein Set 1 and Protein Set 2 are detected. 25 In another preferred embodiment additionally to the above cited combinations of marker proteins a protein of Protein Set 3 is detected: the Protein Set 3 comprises the expression products encoded by genes PRC1, NAT6, EEF1AL3, NP_612480.1, PLXNA2, ELM02 and NDUFS2.

In another preferred embodiment of the kit the biomarker protein group additionally comprises at 30 least one expression product encoded by genes PECI, CTNND2, NSMCE1, KTELC1, HS6ST1, ARMC6, TH1L, PSME1, GPC1, EDC4, PRC1, NAT6, EEF1AL3, NP_612480.1, PLXNA2, ELM02 and NDUFS2. 2014277709 17 Dec 2014 WO 2009/056633 PCT/EP2008/064820 9

Another preferred embodiment of the invention is a kit for diagnosing an individual who is to be subjected to or is being subjected to an anti-TNFa treatment to asses the responsiveness to an anti-TNF treatment which comprises at least two biomarker proteins, wherein a biomarker protein is an expression product encoded by a gene selected from the group comprising 5 RAB1 IB, PPP2R1A, KPNB1, COG4, FDFT1, PECI, CTNND2, NSMCE1, KTELC1, HS6ST1, ARMC6, TH1L, PSME1, GPC1, EDC4, PRC1, NAT6, EEF1AL3, NP 612480.1, PLXNA2, ELM02 and NDUFS2.

As outlined above subject of the present invention is a method, wherein markers are detected and 10 used to identify non-responder. A further embodiment of the present invention is the provision of marker(s), wherein the detection of those marker(s) is indicative for responder.

Thus, subject of the present invention is further a method for diagnosing an individual who is to be subjected to or is being subjected to an anti-TNFa treatment to asses the responsiveness to an 15 anti-TNF treatment which comprises:

Detection of immunoglobulin(s) against one or more biomarker proteins in a bodily fluid or excrement of said patient, wherein a biomarker protein is an artificial peptides deduced from an expression product in an incorrect reading frame of a gene selected from the group comprising IRAKI and C20orfl49, wherein an individual positive for 20 at least one of said hnmunoglobulin(s) is classified as responder.

In a preferred embodiment of the above-identified method the individual is sorted into one of two categories based on detection of said immunoglobulm(s), wherein an individual positive for at least one of said immunoglobulin(s) is classified as responder and, wherein an individual 25 negative for any of said detected immunoglobulin(s) is classified as NON-responder.

In a preferred embodiment of the present invention the method for diagnosing an individual who is to be subjected to or is being subjected to an anti-TNFa treatment the biomarker protein group additionally comprises at least one other expression product encoded by a gene selected from a so group comprising PSCD2L and PPIA.

In another preferred embodiment all members of the biomarker group are detected, the group comprising either artificial peptides deduced from an expression product in an incorrect reading 2014277709 17 Dec 2014 WO 2009/056633 PCT/EP2008/064820 10 frame of a gene or the expression products encoded by die following genes IRAKI and C20orfl49 as well as PSCD2L and PPIA.

The immunoglobulin(s) to be detected may be selected from IgA, IgD, IgG and IgM. In a 5 preferred embodiment the immunoglobulin(s) to be detected is IgA or IgG. In the most preferred embodiment the immunoglobulin is IgG. The immunoglobulin(s) to be detected is not related to IgA rheumatoid factor.

Subject of the method of the present invention is a method for diagnosing an individual who is to io be subjected to or is being subjected to an anti-TNFa treatment, wherein the immunoglobulin(s) is IgA and/or IgG. IgG is especially preferred in die context of a method for diagnosing an individual who is to be subjected to or is being subjected to an anti-TNFa treatment to asses the responsiveness to an anti-TNF treatment, wherein an individual positive for at least one of before said immunoglobulin(s) is classified as responder. 15

The respective set of proteins can not only predict responsiveness before, but also during treatment. Thus, a diagnostic assay based on one or more protein of the set will help the clinician in treatment decisions and the identification of anti-TNF dierapy responders and non- responders a priory. 20

The bodily fluid and/or excrement from the individual to be assessed may be selected from a group comprising: blood, saliva, tears, synovial and spinal fluid, plasma, urine and stool.

An individual who is to be subjected to or is being subjected to an anti-TNFa treatment may 25 suffer autoimmune conditions such as Crohn’s disease, ulcerative colitis, psoriasis, psoriatic arthritis, ankylosing spondylitis, spondyloarthropathies, rheumatoid arthritis etc.

The method of the invention is especially suited for individuals suffering from rheumatoid arthritis. 30 Subject of the present invention is also a kit for diagnosing an individual who is to be subjected to or is being subjected to an anti-TNFa treatment to asses the responsiveness to an anti-TNF treatment which comprises one or more biomarker proteins, wherein a biomarker protein is an 2014277709 17 Dec 2014 WO 2009/056633 PCT/EP2008/064820 11 artificial peptides deduced from an expression product in an incorrect reading frame of a gene selected from the group comprising IRAKI and C20orfI49.

In a preferred embodiment of the present invention the kit for diagnosing an individual who is to 5 be subjected to or is being subjected to an anti-TNFoc treatment the biomarker protein group additionally comprises at least one other expression product encoded by a gene selected from a group comprising PSCD2L and PPIA.

In another preferred embodiment all members of the biomarker group arc detected, the group 10 comprising either artificial peptides deduced from an expression product in an incorrect reading frame of a gene or the expression products encoded by the following genes IRAKI and C20orfl49 as well as PSCD2L and PPIA.

In another embodiment of the invention the kit and the method according to the present invention 15 may additionally comprise one or more known diagnostic markers e.g. for autoimmune disorders. In a preferred embodiment the kit may also comprise other known diagnostic markers for rheumatoid arthritis.

The proteins, protein sets / kits may be conducted in different assay types known to a person 20 skilled in the art.

The immunoglobulins to be detected are in or isolated from body fluids and excrements, such as blood, saliva, tears, synovial and spinal fluid, plasma, urine and stool, etc.

The diagnostic assay can be of any type applied in the field of diagnostics, including but not restricted to assays methods based on 25 - enzymatic reactions - luminescence - fluorescence radiochemicals

The preferred detection methods comprise strip tests, radioimmunoassay, chemiluminescence-30 and fluorescence- immunoassay, hnmunoblot assay, Enzyme-linked immunoassay (ELISA), Luminex-based bead arrays, and protein microarray assay.

The assay types can further be microtitre plate-based, chip-based, bead-based, wherein die biomarker proteins can be attached to the surface or in solution. 2014277709 17 Dec 2014 WO 2009/056633 PCT/EP2008/064820 12

The assays can be homogenous or heterogeneous assays, sandwich assays, competitive and non-competive assays (The Immunoassay Handbook, Ed. David Wild, Elsevier LTD, Oxford; 3rd ed. (May 2005), ISBN-13: 978-0080445267; Hultschig C et al., Curr Opin Chem Biol. 2006 Feb; 10(1):4-10. PMID: 16376134). 5 TNFa treatment is conducted by administration of a TNF inhibitor to an individual in need thereof. TNF inhibitors are biologicals which bind to soluble and cell membrane-associated form of TNFa and neutralise the proinflammatory effect of TNF by preventing the binding of TNFa to the TNF-RI/II cell-surface receptors. The TNF inhibitors can be anti-TNFa antibodies or io receptor molecules but also of other types. The essential of a TNF inhibitor according to the present invention is the ability to capture TNF before it binds to the TNF receptor on the cells.

Subject to the present invention is also the use of the biomarker proteins and/or protein sets and the kits comprising these biomarker proteins and/or protein sets according to the present 15 invention for assessing the responsiveness to an anti-TNFa treatment of an individual who is to be subjected to or is being subjected to an anti-TNFa treatment.

Figure Description 20 Figure 1 shows SEQ ID No. 1 which is a DNA sequence of die gene RAB1 IB (Table 1, No.l) Figure 2 shows SEQ ID No. 2 which is a DNA sequence of the gene PPP2R1A (Table 1, No. 2) Figure 3 shows SEQ ID No. 3 which is a DNA sequence of the gene PPP2R1A (Table 1, No. 2) Figure 4 shows SEQ ID No. 4 which is a DNA sequence of the gene KPNB1 (Table 1, No. 3) Figure 5 shows SEQ ID No. 5 which is a DNA sequence of the gene COG4 (Table 1, No. 4) 25 Figure 6 shows SEQ ID No. 6 which is a DNA sequence of the gene COG4 (Table 1, No. 4) Figure 7 shows SEQ ID No. 7 which is a DNA sequence of die gene COG4 (Table 1, No. 4) Figure 8 shows SEQ ID No. 8 which is a DNA sequence of the gene COG4 (Table 1, No. 4) Figure 9 shows SEQ ID No. 9 which is a DNA sequence of the gene FDFT1 (Table 1, No. 5) Figure 10 shows SEQ ID No. 10 which is a DNA sequence of the gene PECI (Table 1, No. 6) so Figure 11 shows SEQ ID No. 11 which is a DNA sequence of the gene PECI (Table 1, No. 6)

Figure 12 shows SEQ ID No. 12 which is a DNA sequence of the gene PECI (Table 1, No. 6)

Figure 13 shows SEQ ID No. 13 which is a DNA sequence of the gene PECI (Table 1, No. 6)

Figure 14 shows SEQ ID No. 14 which is a DNA sequence of the gene PECI (Table 1, No. 6) 2014277709 17 Dec 2014 WO 2009/056633 PCT/EP2008/064820 13

Figure 15 shows SEQ ID No. 15 which is a DNA sequence of the gene CTNND2 (Tablel, No. 7) Figure 16 shows SEQ ID No. 16 which is a DNA sequence of the gene CTNND2 (Tablel, No. 7) Figure 17 shows SEQ ID No. 17 which is a DNA sequence of the gene NSMCE1 (Table 1, No. 8) 5 Figure 18 shows SEQ ID No. 18 which is a DNA sequence of the gene NSMCE1 (Table 1, No. 8)

Figure 19 shows SEQ ID No. 19 which is a DNA sequence of the gene NSMCE1 (Table 1, No. 8)

Figure 20 shows SEQ ID No. 20 which is a DNA sequence of the gene KTELC1 (Table 1, No. io 9)

Figure 21 shows SEQ ID No. 21 which is a DNA sequence of the gene HS6ST1 (Table 1, No. 10)

Figure 22 shows SEQ ID No. 22 which is a DNA sequence of the gene ARMC6 (Tablel, No. 11) Figure 23 shows SEQ ID No. 23 which is a DNA sequence of the gene ARMC6 (Tablel, No. 11) 15 Figure 24 shows SEQ ID No. 24 which is a DNA sequence of the gene ARMC6 (Tablel, No. 11) Figure 25 shows SEQ ID No. 25 which is a DNA sequence of the gene ARMC6 (Tablel, No. 11) Figure 26 shows SEQ ID No. 26 which is a DNA sequence of the gene TH1L (Tablel, No. 12) Figure 27 shows SEQ ID No. 27 which is a DNA sequence of the gene PSME1 (Tablel, No. 13) Figure 28 shows SEQ ID No. 28 which is a DNA sequence of the gene PSME1 (Tablel, No. 13) 20 Figure 29 shows SEQ ID No. 29 which is a DNA sequence of the gene GPC1 (Tablel, No. 14)

Figure 30 shows SEQ ID No. 30 which is a DNA sequence of the gene EDC4 (Tablel, No. 15)

Figure 31 shows SEQ ID No. 31 which is a DNA sequence of the gene EDC4 (Tablel, No. 15)

Figure 32 shows SEQ ID No. 32 which is a DNA sequence of the gene PRC1 (Tablel, No. 16)

Figure 33 shows SEQ ID No. 33 which is a DNA sequence of the gene PR.C1 (Tablel, No. 16) 25 Figure 34 shows SEQ ID No. 34 which is a DNA sequence of the gene PRC1 (Tablel, No. 16)

Figure 35 shows SEQ ID No. 35 which is a DNA sequence of the gene NAT6 (Tablel, No. 17)

Figure 36 shows SEQ ID No. 36 which is a DNA sequence of the gene NAT6 (Tablel, No. 17)

Figure 37 shows SEQ ID No. 37 which is a DNA sequence of the gene NAT6 (Tablel, No. 17)

Figure 38 shows SEQ ID No. 38 which is a DNA sequence of the gene EEF1AL3 (Table 1, No. 30 18)

Figure 39 shows SEQ ID No. 39 which is a DNA sequence of the gene NP_612480.1 (Table 1, No. 19)

Figure 40 shows SEQ ID No. 40 which is a DNA sequence of the gene PLXNA2 (Table 1, No. 20) WO 2009/056633 PCT/EP2008/064820 14 2014277709 17 Dec 2014

Figure 41 shows SEQ ID No. 41 which is a DNA sequence of the gene PLXNA2 (Table 1, No. 20)

Figure 42 shows SEQ ID No. 42 which is a DNA sequence of the gene ELM02 (Table 1, No. 21) 5 Figure 43 shows SEQ ID No. 43 which is a DNA sequence of the gene ELM02 (Table 1, No. 21)

Figure 44 shows SEQ ID No. 44 which is a DNA sequence of the gene ELM02 (Table 1, No. 21)

Figure 45 shows SEQ ID No. 45 which is a DNA sequence of the gene ELM02 (Table 1, No. 10 21)

Figure 46 shows SEQ ID No. 46 which is a DNA sequence of the gene NDUFS2 (Table 1, No. 22)

Figure 47 shows SEQ ID No. 47 which is a DNA sequence of the gene NDUFS2 (Table 1, No. 22) 15 Figure 48 shows SEQ ID No. 48 which is a DNA sequence of the gene IRAKI (Table 1, No. 23) Figure 49 shows SEQ ID No. 49 which is a DNA sequence of the gene IRAKI (Table 1, No. 23) Figure 50 shows SEQ ID No. 50 which is a DNA sequence of the gene IRAKI (Table 1, No. 23) Figure 51 shows SEQ ID No. 51 which is a DNA sequence of the gene IRAKI (Table 1, No. 23) Figure 52 shows SEQ ID No. 52 which is a DNA sequence of the gene IRAKI (Table 1, No. 23) 20 Figure 53 shows SEQ ID No. 53 which is a DNA sequence of the gene C20orfl49 (Table 1, No. 24)

Figure 54 shows SEQ ID No. 54 which is a DNA sequence of the gene C20orfl49 (Table 1, No. 24)

Figure 55 shows SEQ ID No. 55 which is a DNA sequence of the gene C20orfl49 (Table 1, No. 25 24)

Figure 56 shows SEQ ID No. 56 which is a DNA sequence of the gene PCSD2L (Table 1, No. 25)

Figure 57 shows SEQ ID No. 57 which is a DNA sequence of the gene PCSD2L (Table 1, No. 25) 30 Figure 58 shows SEQ ID No. 58 which is a DNA sequence of the gene PPIA (Table 1, No. 26) Figure 59 shows SEQ ID No. 59 which is a Protein sequence of the gene RAB11B (Table 1, No.l)

Figure 60 shows SEQ ID No. 60 which is a Protein sequence of the gene PPP2R1A (Table 1, No. 2) 2014277709 17 Dec 2014 WO 2009/056633 PCT/EP2008/064820 15

Figure 61 shows SEQ ID No. 61 which is a Protein sequence of the gene PPP2R1A (Table 1, No. 2)

Figure 62 shows SEQ ID No. 62 which is a Protein sequence of the gene KPNB1 (Table 1, No. 3) s Figure 64 shows SEQ ID No. 64 which is a Protein sequence of the gene COG4 (Table 1, No. 4) Figure 65 shows SEQ ID No. 65 which is a Protein sequence of the gene COG4 (Table 1, No. 4) Figure 66 shows SEQ ID No. 66 which is a Protein sequence of the gene COG4 (Table 1, No. 4) Figure 67 shows SEQ ID No. 67 which is a Protein sequence of the gene COG4 (Table 1, No. 4) Figure 68 shows SEQ ID No. 68 which is a Protein sequence of the gene FDFTl (Table 1, No. 5) 10 Figure 69 shows SEQ ID No. 69 which is a Protein sequence of the gene PECI (Table 1, No. 6) Figure 70 shows SEQ ID No. 70 which is a Protein sequence of the gene PECI (Table 1, No. 6) Figure 71 shows SEQ ED No. 71 which is a Protein sequence of the gene PECI (Table 1, No. 6) Figure 72 shows SEQ ED No. 72 which is a Protein sequence of the gene PECI (Table 1, No. 6) Figure 73 shows SEQ ID No. 73 which is a Protein sequence of the gene PECI (Table 1, No. 6) is Figure 74 shows SEQ ID No. 74 which is a Protein sequence of the gene CTNND2 (Tablel, No. 7)

Figure 75 shows SEQ ID No. 75 which is a Protein sequence of the gene CTNND2 (Tablel, No. 7)

Figure 76 shows SEQ ID No. 76 which is a Protein sequence of the gene NSMCE1 (Table 1, No. 20 8)

Figure 77 shows SEQ ED No. 77 which is a Protein sequence of the gene NSMCE1 (Table 1, No. 8)

Figure 78 shows SEQ ID No. 78 which is a Protein sequence of tire gene NSMCE1 (Table 1, No. 8) 25 Figure 79 shows SEQ ID No. 79 which is a Protein sequence of the gene KTELC1 (Table 1, No. 9)

Figure 80 shows SEQ ID No. 80 which is a Protein sequence of the gene HS6ST1 (Table 1, No. 10)

Figure 81 shows SEQ ID No. 81 which is a Protein sequence of the gene ARMC6 (Tablel, No. 30 11)

Figure 82 shows SEQ ID No. 82 which is a Protein sequence of the gene ARMC6 (Tablel, No. 11)

Figure 83 shows SEQ ID No. 83 which is a Protein sequence of the gene ARMC6 (Tablel, No. 11) 2014277709 17 Dec 2014 WO 2009/056633 PCT/EP2008/064820 16

Figure 84 shows SEQ ID No. 84 which is a Protein sequence of the gene ARMC6 (Tablel, No. Π)

Figure 85 shows SEQ ID No. 85 which is a Protein sequence of the gene TH1L (Tablel, No. 12) Figure 86 shows SEQ ID No. 86 which is a Protein sequence of the gene PSME1 (Tablel, No. 5 13)

Figure 87 shows SEQ ID No. 87 which is a Protein sequence of the gene PSME1 (Tablel, No. 13)

Figure 88 shows SEQ ID No. 88 which is a Protein sequence of the gene GPC1 (Tablel, No. 14)

Figure 89 shows SEQ ID No. 89 which is a Protein sequence of the gene EDC4 (Tablel, No. 15) 10 Figure 90 shows SEQ ID No. 90 which is a Protein sequence of the gene EDC4 (Tablel, No. 15)

Figure 91 shows SEQ ID No. 91 which is a Protein sequence of the gene PRC1 (Tablel, No. 16)

Figure 92 shows SEQ ID No. 92 which is a Protein sequence of the gene PRC1 (Tablel, No. 16)

Figure 93 shows SEQ ID No. 93 which is a Protein sequence of the gene PRC1 (Tablel, No. 16)

Figure 94 shows SEQ ID No. 94 which is a Protein sequence of the gene NAT6 (Tablel, No. 17) 15 Figure 95 shows SEQ ID No. 95 which is a Protein sequence of the gene NAT6 (Tablel, No. 17)

Figure 96 shows SEQ ID No. 96 which is a Protein sequence of the gene NAT6 (Tablel, No. 17)

Figure 97 shows SEQ ID No. 97 which is a Protein sequence of the gene EEF1AL3 (Table 1, No. 18)

Figure 98 shows SEQ ID No. 98 which is a Protein sequence of the gene NP_612480.1 (Table 1, 20 No. 19)

Figure 99 shows SEQ ID No. 99 which is a Protein sequence of the gene PLXNA2 (Table 1, No. 20)

Figure 100 shows SEQ ID No. 100 which is a Protein sequence of the gene PLXNA2 (Table 1, No. 20) 25 Figure 101 shows SEQ ID No. 101 which is a Protein sequence of the gene ELM02 (Table 1, No. 21)

Figure 102 shows SEQ ID No. 102 which is a Protein sequence of the gene ELM02 (Table 1, No. 21)

Figure 103 shows SEQ ID No. 103 which is a Protein sequence of the gene ELM02 (Table 1, 30 No. 21)

Figure 104 shows SEQ ID No. 104 which is a Protein sequence of the gene ELM02 (Table 1, No. 21)

Figure 105 shows SEQ ID No. 105 which is a Protein sequence of the gene NDUFS2 (Table 1, No. 22) 2014277709 17 Dec 2014 WO 2009/056633 PCT/EP2008/064820 17

Figure 106 shows SEQ ID No. 106 which is a Protein sequence of the gene NDUFS2 (Table 1, No. 22)

Figure 107 shows SEQ ID No. 107 which is a Protein sequence of the gene IRAKI (Table 1, No. 23) 5 Figure 108 shows SEQ ID No. 108 which is a Protein sequence of the gene IRAKI (Table 1, No. 23)

Figure 109 shows SEQ ID No. 109 which is a Protein sequence of the gene IRAKI (Table 1, No. 23)

Figure 110 shows SEQ ID No. 110 which is a Protein sequence of the gene IRAKI (Table 1, No. 10 23)

Figure 111 shows SEQ ID No. Ill which is a Protein sequence of the gene IRAKI (Table 1, No. 23)

Figure 112 shows SEQ ID No. 112 which is a Protein sequence of the gene C20orfl49 (Table 1, No. 24) 15 Figure 113 shows SEQ ID No. 113 which is a Protein sequence of the gene C20orfl49 (Table 1, No. 24)

Figure 114 shows SEQ ID No. 114 which is a Protein sequence of the gene C20orfl49 (Table 1, No. 24)

Figure 115 shows SEQ ID No. 115 which is a Protein sequence of the gene PCSD2L (Table 1, 20 No. 25)

Figure 116 shows SEQ ID No. 116 which is a Protein sequence of the gene PCSD2L (Table 1, No. 25)

Figure 117 shows SEQ ID No. 117 which is a Protein sequence of the gene PPIA (Table 1, No. 26) 25 Figure 118 shows SEQ ID No. 118 which is a Protein sequence derived from an incorrect reading frame of the gene HS6ST1 (Table 1, No. 10)

Figure 119 shows SEQ ID No. 119 which is a Protein sequence derived from an incorrect reading frame of the gene IRAKI (Table 1, No. 23)

Figure 120 shows SEQ ID No. 120 which is a Protein sequence derived from an incorrect 30 reading frame of the gene C20orfl49 (Table 1, No. 24)

Figure 121 shows SEQ ID No. 121 which is a Protein sequence derived from an incorrect reading frame of the gene C20orfl49 (Table 1, No. 24)

Figure 122 shows SEQ ID No. 122 which is a Protein sequence derived from an incorrect reading frame of the gene HS6SP1 (Table 1, No. 10) 2014277709 17 Dec 2014 WO 2009/056633 PCT/EP2008/064820 18

Examples

The set of proteins which are subject of the present invention have been found by conducting serum screening experiments on protein macroarrays. The protein macroarrays consist of 5 >38.000 individual E. coli clones expressing human gene fragments cloned from a foetal brain cDNA library. These fragments can be full length proteins and fragments thereof, as well as artificial peptides resulting from translation products in the incorrect reading frame. The technology for screening was developed at the MPI for Molecular Genetics and constitutes prior art; Bussow K, et al. Nucleic Acids Res. 1998 Nov 1; 26(21):5007-8. PMID: 9776767; Biissow ίο K, et al. Genomics 2000 Apr 1; 65(1):1-8. PMID: 10777659) and has been applied since then in multiple scientific publications (e.g. Horn S, et al. Proteomics. 2006 Jan; 6(2):605-13. PMID: 16419013; Lueking A, et al. Mol Cell Proteomics. 2005 Sep; 4(9):1382-90. PMID: 15939964). The only amendment to the method described in the original paper is the incubation with patient serum and the use of specific secondary antibodies directed against different immunoglobulin 15 isotypes such as IgG, IgA, IgM and IgD as described beneath:

Patient serum was diluted 1:40 in blocking buffer (3 % Milk powder / TBST) and incubated overnight at room temperature, kept in slow motion on an orbital shaker. After incubation filters are washed 3x 20 min. in TBST, followed by a second incubation for lh at room temperature with anti human IgG or anti human IgA secondary antibody (mouse) conjugated with alkaline 20 phosphatase, 1:1000 in blocking buffer. Positive signals on the macroarray (PVDF filter) were recorded as described and correlated to the original E. coli clones stored in 384-well microtitre plates. E. coli clones corresponding with the signals on the macroarray were sequenced to obtain infonnation of the insert, and hence the gene fragment of which the translation product is recognised by die patient sera. These fragments can be full length proteins and fragments 25 thereof, as well as artificial peptides resulting from out-of frame-translation products.

The protein macroarrays were screened with pools of anti-TNFa treatment (Adalimumab®; Humira) responder and non-responder patient sera before and after therapy. Responder and nonresponder patients were categorised according to the clinical response evaluated after 1 year (or 30 at drop-out) in accordance with the European League Against Rheumatism criteria using the modified disease activity score that includes 28 joints (DAS 28). The DAS28 score and the European League Against Rheumatism (EULAR) response criteria are widely used to record disease activity and therapeutic response in patients with RA (Van Gestel AM et al. Arthritis Rheum 1996; 39:34-40. PMID: 19 2014277709 22 Aug 2017

The DAS28 was developed and validated for patients with RA, and in addition to disease activity it also reflects the patient's satisfaction with reasonable accuracy. This composite index comprises 4 items, namely, swollen joint count (SJC), tender joint count (TJC), a visual analog scale (VAS) of the patient's assessment of general health (GH), and erythrocyte 5 sedimentation rate (ESR; first hour), which are also part of the American College of

Rheumatology (ACR) response criteria.

Description of the used patient sera: DAS28 values from 2 RA patient cohorts comprising 3 patients each were compared and sera of these patients before and after therapy were used for screening the protein macroarrays. 0 RA cohort 1 (RA1) consisted of therapy responder patients and the RA cohort 2 (RA2) consisted of age- and sex-matched patients seen during the same period who were therapy non-responders. Item weighting, factor loading, and internal consistency were assessed by factor analysis, principal component analysis, and calculation of Cronbach's alpha. The range of DAS 28 scores in the responder group initially before treatment was from 4.4 - 6 with a 5 mean value of 4,83 and in the non responder group 4,1 - 8,6 with a mean value 6,2.

Responder had a mean change of 2,36 during therapy while there was no mean change in the DAS 28 in the non responder group.

Table 1 (consisting of Table 1 A and Table 1 B) shows a summary list of genes of which the expression products represent biomarker proteins and artificial peptides resulting from 0 translation products in the incorrect reading frame found to be predictive for responsiveness to anti-TNFa antibody treatment (Adalimumab; Humira) of the patient groups described above having been subjected to an anti-TNFa treatment.

Throughout this specification and the claims which follow, unless the context requires otherwise, the word "comprise", and variations such as "comprises" and "comprising", will 25 be understood to imply the inclusion of a stated integer or step or group of integers or steps but not the exclusion of any other integer or step or group of integers or steps.

The reference in this specification to any prior publication (or information derived from it), or to any matter which is known, is not, and should not be taken as an acknowledgment or admission or any form of suggestion that that prior publication (or information derived from 30 it) or known matter forms part of the common general knowledge in the field of endeavour to which this specification relates. 2014277709 17 Dec 2014 20 TABLE 1 A: List of candidate genes encoding a biomarker set detected by immunoglobulins of TNF inhibitor therapy NON-RESPONDER patients

No. Importance frame offset ENSEMBL gene identifier HGNC gene symbol gene description and alternative identifiers 1 1: High 0 ENSG00000185236 RAB11B Ras-re!ated protein Rab-11B {GTP-binding protein YPT3). fSource:Uniprot/SWISSPROT;Aoc:Q159071 2 1: High 0 ENSG00000105568 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform {PP2A, subunit A, PR65-alpha isoform) (PP2A, subunit A, R1-alpha isoform) (Medium tumor antigen-associated 61 kDa protein). [Source:Uniprot/SWiSSPROT;Acc:P30153] 3 1: High 0 ENSG00000108424 KPNB1 Importin beta-1 subunit (Karyopherin beta-1 subunit) (Nuclear factor P97) (Imporiin 90). [Source: Uniprot/SW ISS PROT ;Acc:Q14974] 4 1: High 0 ENSG00000103051 COG4 Conserved oligomeric Golgi complex component 4. [Source:Uniprot/SWISSPROT;Acc:Q9H9E3] 5 1: High 0 ENSG00000079459 FDFT1 Squalene synthetase (EC 2.5.1.21) (SQS) (SS) (Famesyl-dlphosphate famesyltransferase) (FPP:FPP famesyltransferase). [Source:Uniprot/SWISSPROT;Acc:P37268] 6 2: Medium 0 ENSG00000198721 PECI Peroxisomal 3,2-trans-enoyl-CoA isomerase (EC 5.3.3.8) (Dodecenoyl-CoA isomerase) (Delta(3),delta(2)-enoyI-CoA Isomerase) (D3,D2-enoyl-CoA isomerase) (DBI-related protein 1) (DRS-1) (Hepatocellular carcinoma- associated antigen 88) (Renal carcinoma anb'ge 7 2: Medium 0 ENSG00000169862 CTNND2 Catenin delta-2 (Delta-catenin) (Neural plakophilin-related ARM-repeat protein) (NPRAP) (Neurajungin) (GT24). [Source:Uniprof/SWISSPROT;Acc:Q9UGB3] chromosome NCBt36:5:11024952-11957110:-1 8 2: Medium 0 ENSG00000169189 NSMCE1 non-SMC element 1 homolog [Source:RefSeq_peptide;Acc:NP 659547] chromosome NCBI36:16:27143817-27187586:-1 9 2: Medium 0 ENSG00000163389 KTELC1 KTEL motif-containing protein 1 precursor (CAP10-like 46 kDa protein) (Myelodysplastic syndromes relative protein). [Source:Uniprot/SWISSPROT;Acc:Q8NBL1] 10 2: Medium -1 ENSG00000136720 HS6ST1 Heparan-sulfate 6-O-suIfotransferase 1 (EC 2.8.2.-) (HS6ST-1). rSource:Uniprot/SWISSPROT;Acc:O602431 11 2: Medium 0 ENSG00000105676 ARMC6 Armadillo repeat-containing protein 6. [Source:Uniprot/SWISSPROT;Acc:Q6NXE6] chromosome_NCBI36:19:19005538-19029985:1 12 2: Medium 0 ENSG00000101158 TH1L Negative elongation factor C/D (NELF-C/D) (TH1-like protein). FSource:Uniprot/SWlSSPROT;Acc:Q8!XH71 13 2: Medium 0 ENSG00000092010 PSME1 Proteasome activator complex subunit 1 (Proteasome activator 28-alpha subunit) (PA28alpha) (PA28a) (Activator of multicataiytic protease subunit 1) (11S regulator complex subunit alpha) (REG-alpha) (Interferon gamma up-regulated 1-5111 protein) (IGUP 1-51 14 2: Medium 0 ENSG00000063660 GPC1 Giypican-1 precursor. [Source:Uniprot/SWtSSPROT;Acc:P35052] 15 2: Medium 0 ENSG00000038358 EDC4 autoantigen RCD8 [Source:RefSeq_peptide;Acc:NP 055144] chromosome NCBI36:16:66464500-66475906:1 16 3: Low 0 ENSG00000198901 PRC1 Protein regulator of cytokinesis 1. [Souroe:Uniprot/SWISSPR0T;Acc:043663] chromosome_NCB136:15:89310279-B9338808:-1 WO 2009/056633 PCT/EP2008/064820 2014277709 17 Dec 2014 -21 - 17 3: Low 0 ENSG00000186792 NAT6 Hyaiuronidase-3 precursor (EC 3.2.1.35) (Hyal-3) (Hyaluronoglucosaminidase-3) (LUCA-3). [Source:Uniprot/SWISSPROT;Acc:O43B20] chromosome_NCB!36:3:50300178-50311903:-1 18 3: Low 0 ENSG00000185637 EEF1AL3 Eukaryotic translation elongation factor 1 alpha 1 (Fragment). [Source:Uniprot/SPTREMBL;Acc:Q5JR01] chromosome_NCBI36:9:134884631-134886374:1 19 3: Low 0 ENSG00000168005 NP_612480.1 chromosome_NCB!36:11:63337436-63351727:1 20 3: Low 0 ENSGQOQOQO76350 PLXNA2 Plexin-A2 precursor (Semaphortn receptor OCT). [Source:Uniprot/SWISSPROT;Acc:O75051] chromosome_NCBI36:1:206262210-206484288:-1 21 3: Low 0 ENSG00000062598 ELM02 Engulfment and cell motility protein 2 (CED-12 homolog A) (hCED-12A). [Source:Uniprat/SWISSPROT;Acc:Q96JJ3] chromosome_NCBI36:20:44428096-44468678:-1 22 3: Low 0 ENSG00000158864 NDUFS2 NADH-ubiquinone oxidoreductase 49 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (Complex I-49KD) (CI-49KD). [Source:Uniprot/SWISSPROT;Acc:075306] TABLE 1 B: List of candidate genes encoding a biomarker set detected by immunoglobulins of TNF inhibitor therapy RESPONDER patients No. Importance frame offset ENSEMBL gene identifier HGNC gene symbol gene description and alternative identifiers 23 1: High -1 ENSG00000184216 IRAKI lnterleukin-1 receptor-associated kinase 1 (EC 2.7.11.1) (IRAK-1). fSource:Uniprot/SWISSPROT;Acc:P516171 24 1: High -1 ENSG00000125534 C20orf149 UPF0362 protein C20orf149. [Source:Uniprot/SWISSPROT;Acc:Q9H3Y8] 25 2: Medium 0 ENSG00000105443 PSCD2L Cytohesin-2 (ARF nucleotide-binding site opener) (ARNO protein) (ARF exchange factor). [Source:Uniprot/SWISSPROT;Acc:Q99418] chromosome NCB136:19:53664424-53674457:1 26 3: Low 0 ENSG00000198618 PPIA Peptidyl-prolyl cis-trans isomerase A (EC 5.2.1.8) (PPIase A) (Rotamase A) (Cyclophilin A) (Cyclosporin A-binding protein). [Source:Uniprot/SWISSPROT;Acc:P629373 chromosome NCBI36:21:19151917-19152651:1 WO 2009/056633 PCT/EP2008/064820

Claims (10)

1. THE CLAIMS DEFINING THE INVENTION ARE AS FOLLOWS:

   1. A method for diagnosing an individual who is to be subjected to or is being subjected to an anti-TNFa treatment to assess the responsiveness to an anti-TNFa treatment, wherein the method comprises detection of immunoglobulin(s) against one or more biomarker proteins in a bodily fluid or an excrement of said patient, wherein a biomarker protein is an artificial peptide deduced from an expression product in an incorrect reading frame of a gene selected from IRAKI and C20orfl49, wherein the artificial peptide deduced from an expression product in an incorrect reading frame of IRAKI is SEQ ID NO: 119, wherein the artificial peptide deduced from an expression product in an incorrect reading frame of C20orfl49 is selected from SEQ ID NOs:120 or 121, and wherein an individual positive for at least one of said immunoglobulin(s) is classified as a responder.
2. 2. A method according to claim 1, wherein the one or more biomarker proteins additionally comprises at least one other expression product encoded by a gene selected from PSCD2L and PPIA.
3. 3. A method according to claim 1 or claim 2, wherein the immunoglobulin(s) is IgA and/or IgG.
4. 4. A method according to any one of claims 1 to 3, wherein the bodily fluid and/or excrement may be selected from the group consisting of: blood, saliva, tears, synovial fluid, spinal fluid, plasma, urine and stool.
5. 5. A method according to any one of claims 1 to 4, wherein the individual suffers from rheumatoid arthritis.
6. 6. A kit when used for diagnosing an individual who is to be subjected to or is being subjected to an anti-TNFa treatment to assess the responsiveness to an anti-TNFa treatment, wherein the kit comprises one or more biomarker proteins, wherein a biomarker protein is an artificial peptide deduced from an expression product in an incorrect reading frame of a gene selected from IRAKI and C20orfl49, wherein the artificial peptide deduced from an expression product in an incorrect reading frame of IRAKI is SEQ ID NO: 119, and wherein the artificial peptide deduced from an expression product in an incorrect reading frame of C20orfl49 is selected from SEQ ID NOs:120 or 121.
7. 7. A kit when used according to claim 6, wherein the one or more biomarker proteins additionally comprises at least one other expression product encoded by a gene selected from PSCD2L and PPIA.
8. 8. A kit when used according to claim 6 or claim 7, wherein the kit is for use in an assay selected from the group consisting of a strip test, radioimmunoassay, chemiluminescence immunoassay, fluorescence immunoassay, immunoblot assay, ELISA, T .um in ex based bead array, and protein microarray assay.
9. 9. A kit when used according to any one of claims 6 to 8, wherein the kit is for use in an assay selected from the group consisting of microtitre plate-based, chip-based, and bead based assays, wherein the one or more biomarker protein(s) are attached to the surface or are in solution.
10. 10. The use of a kit according to any one of claims 6 to 9 for assessing the responsiveness to an anti-TNFa treatment of an individual who is to be subjected to or is being subjected to an anti-TNFa treatment.