Expression Levels of 4 Genes in Colon Tissue Might Be Used to Predict Which Patients Will Enter Endoscopic Remission After Vedolizumab Therapy for Inflammatory Bowel Diseases

Abstract

Background & aims: We aimed to identify biomarkers that might be used to predict responses of patients with inflammatory bowel diseases (IBD) to vedolizumab therapy.

Methods: We obtained biopsies from inflamed colon of patients with IBD who began treatment with vedolizumab (n = 31) or tumor necrosis factor (TNF) antagonists (n = 20) and performed RNA-sequencing analyses. We compared gene expression patterns between patients who did and did not enter endoscopic remission (absence of ulcerations at month 6 for patients with Crohn's disease or Mayo endoscopic subscore ≤1 at week 14 for patients with ulcerative colitis) and performed pathway analysis and cell deconvolution for training (n = 20) and validation (n = 11) datasets. Colon biopsies were also analyzed by immunohistochemistry. We validated a baseline gene expression pattern associated with endoscopic remission after vedolizumab therapy using 3 independent datasets (n = 66).

Results: We identified significant differences in expression levels of 44 genes between patients who entered remission after vedolizumab and those who did not; we found significant increases in leukocyte migration in colon tissues from patients who did not enter remission (P < .006). Deconvolution methods identified a significant enrichment of monocytes (P = .005), M1-macrophages (P = .05), and CD4+ T cells (P = .008) in colon tissues from patients who did not enter remission, whereas colon tissues from patients in remission had higher numbers of naïve B cells before treatment (P = .05). Baseline expression levels of PIWIL1, MAATS1, RGS13, and DCHS2 identified patients who did vs did not enter remission with 80% accuracy in the training set and 100% accuracy in validation dataset 1. We validated these findings in the 3 independent datasets by microarray, RNA sequencing and quantitative PCR analysis (P = .003). Expression levels of these 4 genes did not associate with response to anti-TNF agents. We confirmed the presence of proteins encoded by mRNAs using immunohistochemistry.

Conclusions: We identified 4 genes whose baseline expression levels in colon tissues of patients with IBD associate with endoscopic remission after vedolizumab, but not anti-TNF, treatment. We validated this signature in 4 independent datasets and also at the protein level. Studies of these genes might provide insights into the mechanisms of action of vedolizumab.

Keywords: Endoscopic Remisison; IBD; Personalised Medicine; Precision Medicine; Vedolizumab.

Figure 1

Top 5 differentially expressed genes. Visual representation of the top differentially expressed genes in mucosal biopsies of patients responding and not responding to vedolizumab. FDR, false discovery rate–corrected P value; logFC, log fold change. Top 5 differentially expressed genes: (A) KRT23, (B) TMEM35, (C) DCHS2, (D) CLDN8, and (E) IFI6.

Figure 2

Cellular deconvolution. Visual representation of the enrichment scores for the individual cells types identified being differentially represented between vedolizumab (A) nonremitters and (B) remitters, according to deconvolution techniques on the baseline transcriptome. T regs, regulatory T cells; T em, effector memory cells.

Figure 3

Receiver-operating characteristic statistics predicting vedolizumab-induced endoscopic remission based on the colonic 4-gene predictive panel in an independent Belgian-Spanish validation cohort. AUC, area under the curve.

Figure 4

(A) Immunohistochemical PIWIL1 staining in inflamed inflammatory bowel disease (IBD) colon (original magnification [OM] ×100). (B) Immunohistochemical MAATS1 staining in inflamed IBD colon (OM ×100). (C) Immunohistochemical DCHS2 staining in inflamed IBD colon (OM ×200). (D) Immunohistochemical RGS13 staining in inflamed IBD colon (OM ×200).

Supplementary Figure S1

Gene set enrichment analysis enrichment of the Gene Ontology (GO) leukocyte migration gene set in the colonic transcriptomic dataset. The bar-code plot indicates the position of the genes on the expression data rank, sorted by its association with vedolizumab-induced endoscopic remission (P < .001).

Supplementary Figure S2

Differential expression of the 4 genes in the predictive panel. Visual representation of the differential gene expression in mucosal biopsies of patients responding and not responding to vedolizumab therapy of the 4 genes included in the predictive panel. FDR P value, false discovery rate corrected P value; logFC, log fold change. Differential expression of the 4 genes in the predictive panel: (A) PIWIL1, (B) MAATS1, (C) RGS13, and (D) DCHS2.

Supplementary Figure S3

Immunohistochemical PIWIL1 staining in regenerating colonic epithelium (original magnification ×50).