Introduction
Irritable bowel syndrome (IBS) is a chronic, relapsing disorder frequently associated with psychiatric and/or somatic comorbidities, including depression, anxiety, fibromyalgia, and chronic fatigue. Although its pathogenesis is multifactorial, dysfunction of the gut-brain axis is considered a key underlying mechanism. However, the specific molecular alterations and pathways involved remain poorly characterized.
Aims & Methods
We aimed to characterize the transcriptomic and proteomic profiles of colonic mucosa in irritable bowel syndrome (IBS) patients with or without mental and/or somatic comorbidities compared with healthy subjects. Methods: Within the European DISCOvERIE project, IBS patients and healthy volunteers (HV) were recruited across five European centers. Colonic biopsies and demographic and clinical variables, including symptom severity scores for IBS (IBS-SSS), depression (PHQ-9), anxiety (GAD-7), somatic symptoms (PHQ-15), fibromyalgia (FIQ), and fatigue (MFI) were collected. RNA was extracted and analyzed by RNA sequencing (RNA-seq). Libraries were prepared using TruSeq Stranded mRNA (Illumina) and sequenced on a NovaSeq 6000 platform. Differential gene expression (DE) analysis was performed using the DESeq2 package in R, with gene-level validation by qPCR. Proteomic analysis was performed through LC-MS/MS and quantified using Proteome Discoverer 2.5. Protein DE was assessed using the limma package in R.
Results
A total of 174 subjects (131 IBS patients and 43 HV) were included. For transcriptomic analysis, a subset was randomly selected comprising 20 HV (10 male/10 female) and 60 IBS patients (17 M/43 F), stratified into IBS without comorbidities (IBS-A: n=20), IBS with anxiety and/or depression (IBS-Co:N=20), and IBS with both mental and somatic comorbidities (IBS-MCo; N=20). Symptom severity scores for IBS, depression, anxiety, somatic symptoms, fibromyalgia, and fatigue increased progressively along with the number of comorbidities (p<0.001). In colonic mucosa, seven DE genes were identified between HV and IBS-MCo (FDR<0.1), two of which were related to barrier function and immune response. qPCR confirmed increased expression of both genes in IBS (p=0.023 and p=0.083). Proteomic analysis identified 271 DE proteins in IBS-MCo compared with HV. These proteins were enriched in pathways related to DNA/RNA processing and extracellular matrix-receptor interaction, oxidative phosphorylation, and thermogenesis. Additionally, 18, 12, and 3 DE proteins were identified in IBS-A, IBS-Co, and IBS-MCo, respectively. Interestingly, 46 DE proteins were identified in HV compared with IBS, of which 4 were consistently DE across all three IBS subgroups.
Conclusion
Integrated transcriptomic and proteomic analysis of colonic mucosa reveals distinct molecular alterations in IBS patients, depending on comorbidity burden. Several potential diagnostic biomarkers emerged from this analysis. Further validation studies are required to confirm these findings.
References
EU-FUNDED PROJECT Nº: 848228