Gene expression profile predicting the response to anti-TNF antibodies therapy in patients with inflammatory bowel disease: analyses of GEO datasets

Anti-tumor necrosis factor (anti-TNF) antibodies therapy is a new choice for patients with inflammatory bowel disease (IBD). However, not all patients show favorable response to anti-TNF therapy. Our aim of this study is to identify differentially expressed genes (DEGs) that could predict the response to anti-TNF antibodies therapy in IBD patients. We selected microarray datasets that examined response to anti-TNF therapy in IBD patients from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO). A meta-analysis of these datasets was performed using LIMMA package. Our analysis included 4 microarray datasets containing 56 responders and 50 non-responders. We identified 621 DEGs (adjusted P value < 0.05), 23 up-regulated and 598 down-regulated. Among these DEGs, IL13RA2 had the lowest adjusted P value (adjusted P=6.19E-08). In addition, the DEGs were enriched in 78 GO terms. The GO term "response to wounding" had the lowest FDR value (FDR=1.00E-38). CXCR2, SELE, CXCL6, OSM, TNFAIP6, IL6, S100A8 and S100A9 were on the list of top 40 DEGs. Meanwhile, these genes were also enriched in the GO term "immune response" or "inflammatory response". Our findings provide a possibility of these genes play a role in predicting the response to anti-TNF therapy in IBD patients.