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-tumor necrosis factor alpha (TNF or TNF) treatment to assess 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-TNF treatment.

Claims

1. A method for diagnosing whether an individual suffering from rheumatoid arthritis will be responsive to an anti-TNF treatment, comprising: (i) obtaining a biological sample from the individual; (ii) providing a surface comprising one or more biomarker proteins attached to said surface, wherein the biomarker protein(s) comprises one or more sequences selected from the group consisting of SEQ ID NO:119, SEQ ID NO:120 and SEQ ID NO:121 (iii) incubating said surface with said biological sample; (iv) washing the product of step (iii) and incubating with an antibody that binds an IgG isotype, wherein the presence of IgG isotype immunoglobulin(s) that bind to one or more of said biomarker proteins classifies the individual as a responder to anti-TNF treatment.

2. The method according to claim 1, wherein the biomarkers attached to said surface comprise at least one expression product encoded by a gene selected from the group consisting of PSCD2L and PPIA, wherein the expression product comprises a sequence selected from the group consisting of SEQ ID NO:115, SEQ ID NO:116, and SEQ ID NO:117.

3. The method according to claim 1, wherein the surface is part of an immunoassay.

4. The method according to claim 1, wherein the surface is part of a composition selected from the group consisting of a strip test, a radioimmunoassay, a chemiluminescence immunoassay, a fluorescence immunoassay, a immunoblot assay, an Enzyme-linked Immunoassay (ELISA), a Luminex-based bead arrays, and a protein microarray assay.

5. The method according to claim 1, wherein the biological sample is selected from the group consisting of blood, saliva, tears, synovial and spinal fluid, plasma, urine and stool.

Description

FIGURE DESCRIPTION

(1) FIG. 1 shows SEQ ID No. 1 which is a DNA sequence of the gene RAB11B (Table 1, No. 1)

(2) FIG. 2 shows SEQ ID No. 2 which is a DNA sequence of the gene PPP2R1A (Table 1, No. 2)

(3) FIG. 3 shows SEQ ID No. 3 which is a DNA sequence of the gene PPP2R1A (Table 1, No. 2)

(4) FIG. 4 shows SEQ ID No. 4 which is a DNA sequence of the gene KPNB1 (Table 1, No. 3)

(5) FIG. 5 shows SEQ ID No. 5 which is a DNA sequence of the gene COG4 (Table 1, No. 4)

(6) FIG. 6 shows SEQ ID No. 6 which is a DNA sequence of the gene COG4 (Table 1, No. 4)

(7) FIG. 7 shows SEQ ID No. 7 which is a DNA sequence of the gene COG4 (Table 1, No. 4)

(8) FIG. 8 shows SEQ ID No. 8 which is a DNA sequence of the gene COG4 (Table 1, No. 4)

(9) FIG. 9 shows SEQ ID No. 9 which is a DNA sequence of the gene FDFT1 (Table 1, No. 5)

(10) FIG. 10 shows SEQ ID No. 10 which is a DNA sequence of the gene PECI (Table 1, No. 6)

(11) FIG. 11 shows SEQ ID No. 11 which is a DNA sequence of the gene PECI (Table 1, No. 6)

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

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

(14) FIG. 14 shows SEQ ID No. 14 which is a DNA sequence of the gene PECI (Table 1, No. 6)

(15) FIG. 15 shows SEQ ID No. 15 which is a DNA sequence of the gene CTNND2 (Table 1, No. 7)

(16) FIG. 16 shows SEQ ID No. 16 which is a DNA sequence of the gene CTNND2 (Table 1, No. 7)

(17) FIG. 17 shows SEQ ID No. 17 which is a DNA sequence of the gene NSMCE1 (Table 1, No. 8)

(18) FIG. 18 shows SEQ ID No. 18 which is a DNA sequence of the gene NSMCE1 (Table 1, No. 8)

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

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

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

(22) FIG. 22 shows SEQ ID No. 22 which is a DNA sequence of the gene ARMC6 (Table 1, No. 11)

(23) FIG. 23 shows SEQ ID No. 23 which is a DNA sequence of the gene ARMC6 (Table 1, No. 11)

(24) FIG. 24 shows SEQ ID No. 24 which is a DNA sequence of the gene ARMC6 (Table 1, No. 11)

(25) FIG. 25 shows SEQ ID No. 25 which is a DNA sequence of the gene ARMC6 (Table 1, No. 11)

(26) FIG. 26 shows SEQ ID No. 26 which is a DNA sequence of the gene TH1L (Table 1, No. 12)

(27) FIG. 27 shows SEQ ID No. 27 which is a DNA sequence of the gene PSME1 (Table 1, No. 13)

(28) FIG. 28 shows SEQ ID No. 28 which is a DNA sequence of the gene PSME1 (Table 1, No. 13)

(29) FIG. 29 shows SEQ ID No. 29 which is a DNA sequence of the gene GPC1 (Table 1, No. 14)

(30) FIG. 30 shows SEQ ID No. 30 which is a DNA sequence of the gene EDC4 (Table 1, No. 15)

(31) FIG. 31 shows SEQ ID No. 31 which is a DNA sequence of the gene EDC4 (Table 1, No. 15)

(32) FIG. 32 shows SEQ ID No. 32 which is a DNA sequence of the gene PRC1 (Table 1, No. 16)

(33) FIG. 33 shows SEQ ID No. 33 which is a DNA sequence of the gene PRC1 (Table 1, No. 16)

(34) FIG. 34 shows SEQ ID No. 34 which is a DNA sequence of the gene PRC1 (Table 1, No. 16)

(35) FIG. 35 shows SEQ ID No. 35 which is a DNA sequence of the gene NAT6 (Table 1, No. 17)

(36) FIG. 36 shows SEQ ID No. 36 which is a DNA sequence of the gene NAT6 (Table 1, No. 17)

(37) FIG. 37 shows SEQ ID No. 37 which is a DNA sequence of the gene NAT6 (Table 1, No. 17)

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

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

(40) FIG. 40 shows SEQ ID No. 40 which is a DNA sequence of the gene PLXNA2 (Table 1, No. 20)

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

(42) FIG. 42 shows SEQ ID No. 42 which is a DNA sequence of the gene ELMO2 (Table 1, No. 21)

(43) FIG. 43 shows SEQ ID No. 43 which is a DNA sequence of the gene ELMO2 (Table 1, No. 21)

(44) FIG. 44 shows SEQ ID No. 44 which is a DNA sequence of the gene ELMO2 (Table 1, No. 21)

(45) FIG. 45 shows SEQ ID No. 45 which is a DNA sequence of the gene ELMO2 (Table 1, No. 21)

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

(47) FIG. 47 shows SEQ ID No. 47 which is a DNA sequence of the gene NDUFS2 (Table 1, No. 22)

(48) FIG. 48 shows SEQ ID No. 48 which is a DNA sequence of the gene IRAK1 (Table 1, No. 23)

(49) FIG. 49 shows SEQ ID No. 49 which is a DNA sequence of the gene IRAK1 (Table 1, No. 23)

(50) FIG. 50 shows SEQ ID No. 50 which is a DNA sequence of the gene IRAK1 (Table 1, No. 23)

(51) FIG. 51 shows SEQ ID No. 51 which is a DNA sequence of the gene IRAK1 (Table 1, No. 23)

(52) FIG. 52 shows SEQ ID No. 52 which is a DNA sequence of the gene IRAK1 (Table 1, No. 23)

(53) FIG. 53 shows SEQ ID No. 53 which is a DNA sequence of the gene C20orf149 (Table 1, No. 24)

(54) FIG. 54 shows SEQ ID No. 54 which is a DNA sequence of the gene C20orf149 (Table 1, No. 24)

(55) FIG. 55 shows SEQ ID No. 55 which is a DNA sequence of the gene C20orf149 (Table 1, No. 24)

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

(57) FIG. 57 shows SEQ ID No. 57 which is a DNA sequence of the gene PCSD2L (Table 1, No. 25)

(58) FIG. 58 shows SEQ ID No. 58 which is a DNA sequence of the gene PPIA (Table 1, No. 26)

(59) FIG. 59 shows SEQ ID No. 59 which is a Protein sequence of the gene RAB11B (Table 1, No. 1)

(60) FIG. 60 shows SEQ ID No. 60 which is a Protein sequence of the gene PPP2R1A (Table 1, No. 2)

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

(62) FIG. 62 shows SEQ ID No. 62 which is a Protein sequence of the gene KPNB1 (Table 1, No. 3)

(63) FIG. 64 shows SEQ ID No. 64 which is a Protein sequence of the gene COG4 (Table 1, No. 4)

(64) FIG. 65 shows SEQ ID No. 65 which is a Protein sequence of the gene COG4 (Table 1, No. 4)

(65) FIG. 66 shows SEQ ID No. 66 which is a Protein sequence of the gene COG4 (Table 1, No. 4)

(66) FIG. 67 shows SEQ ID No. 67 which is a Protein sequence of the gene COG4 (Table 1, No. 4)

(67) FIG. 68 shows SEQ ID No. 68 which is a Protein sequence of the gene FDFT1 (Table 1, No. 5)

(68) FIG. 69 shows SEQ ID No. 69 which is a Protein sequence of the gene PECI (Table 1, No. 6)

(69) FIG. 70 shows SEQ ID No. 70 which is a Protein sequence of the gene PECI (Table 1, No. 6)

(70) FIG. 71 shows SEQ ID No. 71 which is a Protein sequence of the gene PECI (Table 1, No. 6)

(71) FIG. 72 shows SEQ ID No. 72 which is a Protein sequence of the gene PECI (Table 1, No. 6)

(72) FIG. 73 shows SEQ ID No. 73 which is a Protein sequence of the gene PECI (Table 1, No. 6)

(73) FIG. 74 shows SEQ ID No. 74 which is a Protein sequence of the gene CTNND2 (Table 1, No. 7)

(74) FIG. 75 shows SEQ ID No. 75 which is a Protein sequence of the gene CTNND2 (Table 1, No. 7)

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

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

(77) FIG. 78 shows SEQ ID No. 78 which is a Protein sequence of the gene NSMCE1 (Table 1, No. 8)

(78) FIG. 79 shows SEQ ID No. 79 which is a Protein sequence of the gene KTELC1 (Table 1, No. 9)

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

(80) FIG. 81 shows SEQ ID No. 81 which is a Protein sequence of the gene ARMC6 (Table 1, No. 11)

(81) FIG. 82 shows SEQ ID No. 82 which is a Protein sequence of the gene ARMC6 (Table 1, No. 11)

(82) FIG. 83 shows SEQ ID No. 83 which is a Protein sequence of the gene ARMC6 (Table 1, No. 11)

(83) FIG. 84 shows SEQ ID No. 84 which is a Protein sequence of the gene ARMC6 (Table 1, No. 11)

(84) FIG. 85 shows SEQ ID No. 85 which is a Protein sequence of the gene TH1L (Table 1, No. 12)

(85) FIG. 86 shows SEQ ID No. 86 which is a Protein sequence of the gene PSME1 (Table 1, No. 13)

(86) FIG. 87 shows SEQ ID No. 87 which is a Protein sequence of the gene PSME1 (Table 1, No. 13)

(87) FIG. 88 shows SEQ ID No. 88 which is a Protein sequence of the gene GPC1 (Table 1, No. 14)

(88) FIG. 89 shows SEQ ID No. 89 which is a Protein sequence of the gene EDC4 (Table 1, No. 15)

(89) FIG. 90 shows SEQ ID No. 90 which is a Protein sequence of the gene EDC4 (Table 1, No. 15)

(90) FIG. 91 shows SEQ ID No. 91 which is a Protein sequence of the gene PRC1 (Table 1, No. 16)

(91) FIG. 92 shows SEQ ID No. 92 which is a Protein sequence of the gene PRC1 (Table 1, No. 16)

(92) FIG. 93 shows SEQ ID No. 93 which is a Protein sequence of the gene PRC1 (Table 1, No. 16)

(93) FIG. 94 shows SEQ ID No. 94 which is a Protein sequence of the gene NAT6 (Table 1, No. 17)

(94) FIG. 95 shows SEQ ID No. 95 which is a Protein sequence of the gene NAT6 (Table 1, No. 17)

(95) FIG. 96 shows SEQ ID No. 96 which is a Protein sequence of the gene NAT6 (Table 1, No. 17)

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

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

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

(99) FIG. 100 shows SEQ ID No. 100 which is a Protein sequence of the gene PLXNA2 (Table 1, No. 20)

(100) FIG. 101 shows SEQ ID No. 101 which is a Protein sequence of the gene ELMO2 (Table 1, No. 21)

(101) FIG. 102 shows SEQ ID No. 102 which is a Protein sequence of the gene ELMO2 (Table 1, No. 21)

(102) FIG. 103 shows SEQ ID No. 103 which is a Protein sequence of the gene ELMO2 (Table 1, No. 21)

(103) FIG. 104 shows SEQ ID No. 104 which is a Protein sequence of the gene ELMO2 (Table 1, No. 21)

(104) FIG. 105 shows SEQ ID No. 105 which is a Protein sequence of the gene NDUFS2 (Table 1, No. 22)

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

(106) FIG. 107 shows SEQ ID No. 107 which is a Protein sequence of the gene IRAK1 (Table 1, No. 23)

(107) FIG. 108 shows SEQ ID No. 108 which is a Protein sequence of the gene IRAK1 (Table 1, No. 23)

(108) FIG. 109 shows SEQ ID No. 109 which is a Protein sequence of the gene IRAK1 (Table 1, No. 23)

(109) FIG. 110 shows SEQ ID No. 110 which is a Protein sequence of the gene IRAK1 (Table 1, No. 23)

(110) FIG. 111 shows SEQ ID No. 111 which is a Protein sequence of the gene IRAK1 (Table 1, No. 23)

(111) FIG. 112 shows SEQ ID No. 112 which is a Protein sequence of the gene C20orf149 (Table 1, No. 24)

(112) FIG. 113 shows SEQ ID No. 113 which is a Protein sequence of the gene C20orf149 (Table 1, No. 24)

(113) FIG. 114 shows SEQ ID No. 114 which is a Protein sequence of the gene C20orf149 (Table 1, No. 24)

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

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

(116) FIG. 117 shows SEQ ID No. 117 which is a Protein sequence of the gene PPIA (Table 1, No. 26)

(117) FIG. 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)

(118) FIG. 119 shows SEQ ID No. 119 which is a Protein sequence derived from an incorrect reading frame of the gene IRAK1 (Table 1, No. 23)

(119) FIG. 120 shows SEQ ID No. 120 which is a Protein sequence derived from an incorrect reading frame of the gene C20orf149 (Table 1, No. 24)

(120) FIG. 121 shows SEQ ID No. 121 which is a Protein sequence derived from an incorrect reading frame of the gene C20orf149 (Table 1, No. 24)

(121) FIG. 122 shows SEQ ID No. 122 which is a Protein sequence derived from an incorrect reading frame of the gene HS6ST1 (Table 1, No. 10)

(122) The invention also relates to the following items:

(123) Item 1:

(124) A method for diagnosing an individual who is to be subjected to or is being subjected to an anti-TNF treatment to assess the responsiveness to an anti-TNF treatment prior to anti-TNF treatment which comprises: (a) Detection of immunoglobulin(s) against one or more biomarker proteins in a bodily fluid or an excrement of said patient, wherein the one or more biomarker is indicative for the responsiveness to an anti-TNF treatment prior to anti-TNF treatment, (b) Sorting the individual into responder or NON-responder based on detection of said immunoglobulin(s).

(125) Item 2:

(126) A method for diagnosing an individual who is to be subjected to or is being subjected to an anti-TNF treatment to assess the responsiveness to an anti-TNF treatment prior, during and/or after anti-TNF treatment which comprises: (a) Detection of immunoglobulin(s) against at least two biomarker proteins in a bodily fluid or an excrement of said patient, wherein the at least two biomarker are indicative for the responsiveness to an anti-TNF treatment prior to anti-TNF treatment, (b) Sorting the individual into responder or NON-responder based on detection of said immunoglobulin(s).
wherein the at least two biomarker proteins are selected from the group comprising RAB11B, PPP2R1A, KPNB1, COG4, FDFT1, PECI, CTNND2, NSMCE1, KTELC1, HS6ST1, ARMC6, TH1L, PSME1, GPC1, EDC4, PRC1, NAT6, EEF1AL3, NP_612480.1, PLXNA2, ELMO2 and NDUFS2.

(127) Item 3:

(128) A method for diagnosing an individual who is to be subjected to or is being subjected to an anti-TNF treatment to assess the responsiveness to an anti-TNF treatment which 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 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.

(129) Item 4:

(130) A method for diagnosing an individual who is to be subjected to or is being subjected to an anti-TNF treatment according to item 1 to 3, wherein 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, PRC1, NAT6, EEF1AL3, NP_612480.1, PLXNA2, ELMO2 and NDUFS2.

(131) Item 5:

(132) A method for diagnosing an individual who is to be subjected to or is being subjected to an anti-TNF treatment according to any of items 1 to 4, wherein the immunoglobulin(s) is IgA and/or IgG.

(133) Item 6:

(134) A method for diagnosing an individual who is to be subjected to or is being subjected to an anti-TNF treatment according any of items 1 to 5, wherein the bodily fluid and/or excrement may be selected from a group comprising: blood, saliva, tears, synovial and spinal fluid, plasma, urine and stool.

(135) Item 7:

(136) A method for diagnosing an individual who is to be subjected to or is being subjected to an anti-TNF treatment according any of items 1 to 6, wherein the individual suffers from rheumatoid arthritis.

(137) Item 8:

(138) A kit for diagnosing an individual who is to be subjected to or is being subjected to an anti-TNF treatment to assess the responsiveness to an 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.

(139) Item 9:

(140) A kit according to item 8 wherein 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, PRC1, NAT6, EEF1AL3, NP_612480.1, PLXNA2, ELMO2 and NDUFS2.

(141) Item 10

(142) A kit for diagnosing an individual who is to be subjected to or is being subjected to an anti-TNF treatment to assess 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 RAB11B, PPP2R1A, KPNB1, COG4, FDFT1, PECI, CTNND2, NSMCE1, KTELC1, HS6ST1, ARMC6, TH1L, PSME1, GPC1, EDC4, PRC1, NAT6, EEF1AL3, NP_612480.1, PLXNA2, ELMO2 and NDUFS2.

(143) Item 11:

(144) A method for diagnosing an individual who is to be subjected to or is being subjected to an anti-TNF treatment to assess the responsiveness to an anti-TNF treatment which 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 the group comprising IRAK1 and C20orf149, wherein an individual positive for at least one of said immunoglobulin(s) is classified as responder.

(145) Item 12:

(146) A method for diagnosing an individual who is to be subjected to or is being subjected to an anti-TNF treatment according to item 11, wherein the biomarker protein group additionally comprises at least one other expression product encoded by a gene selected from the group comprising PSCD2L and PPIA.

(147) Item 13:

(148) A method for diagnosing an individual who is to be subjected to or is being subjected to an anti-TNF treatment according to any of items 11 to 12, wherein the immunoglobulin(s) is IgA and/or IgG.

(149) Item 14:

(150) A method for diagnosing an individual who is to be subjected to or is being subjected to an anti-TNF treatment according any of items 11 to 13, wherein the bodily fluid and/or excrement may be selected from a group comprising: blood, saliva, tears, synovial and spinal fluid, plasma, urine and stool.

(151) Item 15:

(152) A method for diagnosing an individual who is to be subjected to or is being subjected to an anti-TNF treatment according any of items 11 to 14, wherein the individual suffers from rheumatoid arthritis.

(153) Item 16:

(154) A kit for diagnosing an individual who is to be subjected to or is being subjected to an anti-TNF treatment to assess the responsiveness to an anti-TNF treatment which 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 the group comprising IRAK1 and C20orf149.

(155) Item 17:

(156) A kit according to items 8 to 10, wherein the biomarker protein group additionally comprises at least one other expression product encoded by a gene selected from the group comprising PSCD2L and PPIA.

(157) Item 18:

(158) The use of a kit according to any of items 8 to 10, 16 and 17 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-TNF treatment.

EXAMPLES

(159) 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 >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; Bssow K, et al. Nucleic Acids Res. 1998 Nov. 1; 26(21):5007-8. PMID: 9776767; Bssow 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 January; 6(2):605-13. PMID: 16419013; Lueking A, et al. Mol Cell Proteomics. 2005 September; 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 isotypes such as IgG, IgA, IgM and IgD as described beneath:

(160) 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 320 min. in TBST, followed by a second incubation for 1 h at room temperature with anti human IgG or anti human IgA secondary antibody (mouse) conjugated with alkaline 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 information of the insert, and hence the gene fragment of which the translation product is recognised by the patient sera. These fragments can be full length proteins and fragments thereof, as well as artificial peptides resulting from out-of frame-translation products.

(161) The protein macroarrays were screened with pools of anti-TNF treatment (Adalimumab; Humira) responder and non-responder patient sera before and after therapy. Responder and non-responder patients were categorised according to the clinical response evaluated after 1 year (or 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 A M et al. Arthritis Rheum 1996; 39:34-40. PMID:

(162) 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 sedimentation rate (ESR; first hour), which are also part of the American College of Rheumatology (ACR) response criteria.

(163) Description of the used patient sera:

(164) 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. RA cohort 1 (RA1) consisted of therapy responder patients and the RA cohort 2 (RA2) consisted of 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 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 DAS28 in the non responder group.

(165) 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 translation products in the incorrect reading frame found to be predictive for responsiveness to anti-TNF antibody treatment (Adalimumab; Humira) of the patient groups described above having been subjected to an anti-TNF treatment.

(166) TABLE-US-00001 TABLE 1A List of candidate genes encoding a biomarker set detected by immunoglobulins of TNF inhibitor therapy NON-RESPONDER patients frame ENSEMBL HGNC No. Importance offset gene identifier gene symbol gene description and alternative identifiers 1 1: High 0 ENSG00000185236 RAB11B Ras-related protein Rab-11B (GTP-binding protein YPT3). [Source: Uniprot/SWISSPROT; Acc: Q15907] 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) (Importin 90). [Source: Uniprot/SWISSPROT; 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) (Farnesyl-diphosphate farnesyltransferase) (FPP: FPP farnesyltransferase). [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)-enoyl-CoA isomerase) (D3,D2- enoyl-CoA isomerase) (DBI-related protein 1) (DRS-1) (Hepatocellular carcinoma- associated antigen 88) (Renal carcinoma antige 7 2: Medium 0 ENSG00000169862 CTNND2 Catenin delta-2 (Delta-catenin) (Neural plakophilin-related ARM- repeat protein) (NPRAP) (Neurojungin) (GT24). [Source: Uniprot/SWISSPROT; Acc: Q9UQB3] chromosome_NCBI36: 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-sulfotransferase 1 (EC 2.8.2.) (HS6ST-1). [Source: Uniprot/SWISSPROT; Acc: O60243] 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). [Source: Uniprot/SWISSPROT; Acc: Q8IXH7] 13 2: Medium 0 ENSG00000092010 PSME1 Proteasome activator complex subunit 1 (Proteasome activator 28-alpha subunit) (PA28alpha) (PA28a) (Activator of multicatalytic protease subunit 1) (11S regulator complex subunit alpha) (REG-alpha) (Interferon gamma up-regulated I-5111 protein) (IGUP I-51 14 2: Medium 0 ENSG00000063660 GPC1 Glypican-1 precursor. [Source: Uniprot/SWISSPROT; 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. [Source: Uniprot/SWISSPROT; Acc: O43663] chromosome_NCBI36: 15: 89310279-89338808: 1 17 3: Low 0 ENSG00000186792 NAT6 Hyaluronidase-3 precursor (EC 3.2.1.35) (Hyal-3) (Hyaluronoglucosaminidase-3) (LUCA-3). [Source: Uniprot/SWISSPROT; Acc: O43820] chromosome_NCBI36: 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_NCBI36: 11: 63337436-63351727: 1 20 3: Low 0 ENSG00000076356 PLXNA2 Plexin-A2 precursor (Semaphorin receptor OCT). [Source: Uniprot/SWISSPROT; Acc: O75051] chromosome_NCBI36: 1: 206262210-206484288: 1 21 3: Low 0 ENSG00000062598 ELMO2 Engulfment and cell motility protein 2 (CED-12 homolog A) (hCED-12A). [Source: Uniprot/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: O75306]

(167) TABLE-US-00002 TABLE 1B List of candidate genes encoding a biomarker set detected by immunoglobulins of TNF inhibitor therapy RESPONDER patients HGNC frame ENSEMBL gene No. Importance offset gene identifier symbol gene description and alternative identifiers 23 1: High 1 ENSG00000184216 IRAK1 Interleukin-1 receptor-associated kinase 1 (EC 2.7.11.1) (IRAK-1). [Source: Uniprot/SWISSPROT; Acc: P51617] 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_NCBI36: 19: 53664424-53674457: 1 26 3: Low 0 ENSG00000198618 PPIA Peptidyl-prolyl cis-trans isomerase A (EC 5.2.1.8) (PPlase A) (Rotamase A) (Cyclophilin A) (Cyclosporin A-binding protein). [Source: Uniprot/SWISSPROT; Acc: P62937] chromosome_NCBI36: 21: 19151917-19152651: 1