Genes predictive of anti-TNF response in inflammatory diseases

A biomarker, comprising:

• (a) a first primer pair capable of selectively amplifying a detectable portion of a nucleic acid selected from the group consisting of SEQ ID NO:20 and/or 21 (LYN), SEQ ID NO:1 (IL8), SEQ ID NO:18 and/or 19 (F3), SEQ ID NO:10 (CXCL1), SEQ ID NO:11 (IL6), SEQ ID NO:3 (S100A12), SEQ ID NO:4 (SELP), SEQ ID NO:2 (C3AR1), SEQ ID NO:5, 6, 7, and/or 8 (IL1RN), SEQ ID NO:9 (CCL2), and SEQ ID NO:12, 13, 14, 15, 16, and/or 17 (CLEC7A);
• and
• (b) a second primer pair capable of selectively amplifying a detectable portion of a nucleic acid selected from the group consisting of SEQ ID NO:20 and/or 21 (LYN), SEQ ID NO:1 (IL8), SEQ ID NO:18 and/or 19 (F3), SEQ ID NO:10 (CXCL1), SEQ ID NO:11 (IL6), SEQ ID NO:3 (S100A12), SEQ ID NO:4 (SELP), SEQ ID NO:2 (C3AR1), SEQ ID NO:5, 6, 7, and/or 8 (IL1RN), SEQ ID NO:9 (CCL2), and SEQ ID NO:12, 13, 14, 15, 16, and/or 17 (CLEC7A),
• wherein the first primer pair and the second primer pair do not selectively amplify the same nucleic acid.
• second primer pair, and the third primer pair selectively amplify the same nucleic acid.

A method for predicting anti-TNF therapy response in a patient with an inflammatory disease, comprising:

• (a) contacting a mRNA-derived nucleic acid sample obtained from a subject with an inflammatory disease for whom treatment with an anti-TNF therapeutic is being considered under hybridizing conditions with 2 or more probes sets, wherein at least a first probe set and a second probe set selectively hybridize under high stringency conditions to a nucleic acid target selected from the group consisting of SEQ ID NO:20 and/or 21 (LYN), SEQ ID NO:1 (IL8), SEQ ID NO:18 and/or 19 (F3), SEQ ID NO:10 (CXCL1), SEQ ID NO:11 (IL6), SEQ ID NO:3 (S100A12), SEQ ID NO:4 (SELP), SEQ ID NO:2 (C3AR1), SEQ ID NO:5, 6, 7, and/or 8 (IL1RN), SEQ ID NO:9 (CCL2), and SEQ ID NO:12, 13, 14, 15, 16, and/or 17 (CLEC7A);
• wherein the first probe set and the second probe set do not selectively hybridize to the same nucleic acid;
• and
• (b) detecting formation of hybridization complexes between the 2 or more probe sets and nucleic acid targets in the nucleic acid sample, wherein a number of such hybridization complexes provides a measure of gene expression of the nucleic acid targets;
• wherein the gene expression of the nucleic acid targets is predictive of anti-TNF therapy response in the subject.

A method for predicting anti-TNF therapy response in a patient with an inflammatory disease, comprising:

• (a) contacting a mRNA-derived nucleic acid sample obtained from a subject with an inflammatory disease for whom treatment with an anti-TNF therapeutic is being considered under amplifying conditions with 2 or more primer pairs, wherein at least a first primer pair and a second primer pair are capable of selectively amplifying a detectable portion of a nucleic acid target selected from the group consisting of SEQ ID NO:20 and/or 21 (LYN), SEQ ID NO:1 (IL8), SEQ ID NO:18 and/or 19 (F3), SEQ ID NO:10 (CXCL1), SEQ ID NO:11 (IL6), SEQ ID NO:3 (S100A12), SEQ ID NO:4 (SELP), SEQ ID NO:2 (C3AR1), SEQ ID NO:5, 6, 7, and/or 8 (IL1RN), SEQ ID NO:9 (CCL2), and SEQ ID NO:12, 13, 14, 15, 16, and/or 17 (CLEC7A);
• wherein the first primer pair and the second primer pair do not selectively amplify the same nucleic acid;
• and
• (b) detecting amplification products generated by amplification of nucleic acid targets in the nucleic acid sample by the two or more primer pairs, wherein the amplification products provide a measure of gene expression of the nucleic acid targets;
• wherein the gene expression of the nucleic acid targets is predictive of anti-TNF therapy response in the subject.