Whole Transcription Profile of Responders to Anti-TNF Drugs in Pediatric Inflammatory Bowel Disease

Abstract

Background: Up to 30% of patients with pediatric inflammatory bowel disease (IBD) do not respond to anti-Tumor Necrosis Factor (anti-TNF) therapy. The aim of this study was to identify pharmacogenomic markers that predict early response to anti-TNF drugs in pediatric patients with IBD.

Methods: An observational, longitudinal, prospective cohort study was conducted. The study population comprised 38 patients with IBD aged < 18 years who started treatment with infliximab or adalimumab (29 responders and nine non-responders). Whole gene expression profiles from total RNA isolated from whole blood samples of six responders and six non-responders taken before administration of the biologic and after two weeks of therapy were analyzed using next-generation RNA sequencing. The expression of six selected genes was measured for purposes of validation in all of the 38 patients recruited using qPCR.

Results: Genes were differentially expressed in non-responders and responders (32 before initiation of treatment and 44 after two weeks, Log2FC (Fold change) >0.6 or <-0.6 and p value < 0.05). After validation, FCGR1A, FCGR1B, and GBP1 were overexpressed in non-responders two weeks after initiation of anti-TNF treatment (Log2FC 1.05, 1.21, and 1.08, respectively, p value < 0.05).

Conclusion: Expression of the FCGR1A, FCGR1B, and GBP1 genes is a pharmacogenomic biomarker of early response to anti-TNF agents in pediatric IBD.

Keywords: Crohn disease; adalimumab; biomarker; gene expression; inflammatory bowel disease; infliximab; ulcerative colitis.

Figure 1

Network of differentially expressed genes prior to initiation of anti-TNF therapy based on interactions using Ingenuity Pathway Analysis. Red, genes overexpressed in non-responders vs. responders; green, genes downregulated in non-responders vs. responders.

Figure 2

Network of differentially expressed genes after two weeks of anti-TNF treatment based on interactions using IPA. Red, genes overexpressed in non-responders vs. responders; green, genes downregulated in non-responders vs. responders.

Figure 3

Relative expression levels of the genes GBP1 (a,b), GBP5 (c,d), GNLY (e,f), BATF2 (g,h), IGHA1 (i,j), IGHG2 (k,l), FCGR1A (m,n), and FCGR1B (o,p) in responders (R, green) and non-responders (NR, orange) at time 0 (t = 0) and at two weeks (t = 2) after initiation of anti-TNF therapy. Expression values were normalized to the ACTB and RPL4 genes. Values are expressed as mean (horizontal line) and standard error of the mean (SEM); n, sample size; * p value < 0.05 vs. control (unpaired t test).

Figure 3

Relative expression levels of the genes GBP1 (a,b), GBP5 (c,d), GNLY (e,f), BATF2 (g,h), IGHA1 (i,j), IGHG2 (k,l), FCGR1A (m,n), and FCGR1B (o,p) in responders (R, green) and non-responders (NR, orange) at time 0 (t = 0) and at two weeks (t = 2) after initiation of anti-TNF therapy. Expression values were normalized to the ACTB and RPL4 genes. Values are expressed as mean (horizontal line) and standard error of the mean (SEM); n, sample size; * p value < 0.05 vs. control (unpaired t test).

Figure 4

Schematic representation of the ratio between relative expression levels at week 2 (T2) and week 0 (T0) (T2/T0) of the genes GBP1 (a), GBP5 (b), GNLY (c), BATF2 (d), IGHA1 (e), IGHG2 (f), FCGR1A (g), and FCGR1B (h) in responders (R) and non-responders (NR). Expression values were normalized to the ACTB and RPL4 genes. Values are expressed as mean (horizontal line) and standard error of the mean (SEM); n, sample size; * p value < 0.05 vs. control (unpaired t test).