RNA sequencing shows transcriptomic changes in rectosigmoid mucosa in patients with irritable bowel syndrome-diarrhea: a pilot case-control study.
Our aim was to conduct a pilot case-control study of RNA expression profile using RNA sequencing of rectosigmoid mucosa of nine females with -diarrhea-predominant irritable bowel syndrome (IBS-D) with accelerated colonic transit and nine female healthy controls. Mucosal total RNA was isolated and purified, and next-generation pair-end sequencing was performed using Illumina TruSeq. Analysis was carried out using a targeted approach toward 12 genes previously associated with IBS and a hypothesis-generating approach. Of the 12 targeted genes tested, patients with IBS-D had decreased mRNA expression of TNFSF15 (fold change controls to IBS-D: 1.53, P = 0.01). Overall, up- and downregulated mRNA expressions of 21 genes (P = 10(-5) to 10(-8); P values with false detection rates are shown) were potentially relevant to IBS-D including the following: neurotransmitters [P2RY4 (P = 0.001), vasoactive intestinal peptide (VIP, P = 0.02)]; cytokines [CCL20 (P = 0.019)]; immune function [C4BPA complement cascade (P = 0.0187)]; interferon-related [IFIT3 (P = 0.016)]; mucosal repair and cell adhesion [trefoil protein (TFF1, P = 0.012)], retinol binding protein [RBP2 (P = 0.017)]; fibronectin (FN1, P = 0.009); and ion channel functions [guanylate cyclase (GUCA2B, P = 0.017), PDZ domain-containing protein 3 (PDZD3, P = 0.029)]. Ten genes associated with functions related to pathobiology of IBS-D were validated by RT-PCR. There was significant correlation in fold changes of the selected genes (Rs = 0.73, P = 0.013). Up- or downregulation of P2RY4, GUC2AB, RBP2, FNI, and C4BPA genes were confirmed on RT-PCR, which also revealed upregulation of farnesoid X receptor (FXR) and apical sodium-coupled bile acid transporter (IBAT/ASBT). RNA-Seq and RT-PCR analysis of rectosigmoid mucosa in IBS-D show transcriptome changes that provide the rationale for validation studies to explore the role of mucosal factors in the pathobiology of IBS-D.
Clinical Enteric Neuroscience Translational and Epidemiological Research (C.E.N.T.E.R.) and camilleri.michael@mayo.edu.
Michael
M
Camilleri
Clinical Enteric Neuroscience Translational and Epidemiological Research (C.E.N.T.E.R.) and.
Paula
P
Carlson
Clinical Enteric Neuroscience Translational and Epidemiological Research (C.E.N.T.E.R.) and.
Andres
A
Acosta
Clinical Enteric Neuroscience Translational and Epidemiological Research (C.E.N.T.E.R.) and.
Irene
I
Busciglio
Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota.
Asha A
AA
Nair
Clinical Enteric Neuroscience Translational and Epidemiological Research (C.E.N.T.E.R.) and.
Simon J
SJ
Gibbons
Clinical Enteric Neuroscience Translational and Epidemiological Research (C.E.N.T.E.R.) and.
Gianrico
G
Farrugia
Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota.
Eric W
EW
Klee
D000328:Adult; D001483:Base Sequence; D016022:Case-Control Studies; D003106:Colon / Q000378:metabolism*; D016207:Cytokines / Q000378:metabolism; D003967:Diarrhea / Q000235:genetics* / Q000378:metabolism; D005260:Female; D015870:Gene Expression / Q000235:genetics; D006801:Humans; D007413:Intestinal Mucosa / Q000378:metabolism*; D043183:Irritable Bowel Syndrome / Q000235:genetics*; D008875:Middle Aged; D010865:Pilot Projects; D012007:Rectum / Q000378:metabolism*; D017423:Sequence Analysis, RNA / Q000379:methods; D059467:Transcriptome
D016207:Cytokines
barrier; cytokines; ion channels; mucosal repair; neurotransmitters