Single Cell and Bulk RNA Data of IBD patient

Fibrosis, a common complication in Crohn’s disease (CD), frequently leads to intestinal strictures resistant to biologic therapies, necessitating surgical intervention. This study explores the transcriptomic signature of fibrostenotic ileal CD to better understand the biological and cellular mechanisms driving intestinal fibrosis.Resected ileal specimens from nine CD patients undergoing surgery were analyzed using bulk transcriptomics and single-cell RNA sequencing (scRNA-seq). Differential gene expression and pathway enrichment analyses identified 81 differentially expressed genes (DEGs), with 64 up-regulated and 17 down-regulated in strictures compared to non-strictured margins. Up-regulated genes were linked to inflammation, matrix remodeling, adipogenesis, and cellular stress, while down-regulated genes were associated with epithelial barrier integrity. Machine learning and random forest models highlighted key predictive genes, including LY96, GREM1, and FGF2, which were validated via qPCR.scRNA-seq localized GREM1 to fibroblasts, while EHD2 and FGF2 were expressed in fibroblasts and endothelial cells. Endothelial cells in strictures showed unexpected expression of smooth muscle-related genes, suggesting a mechanistic link between endothelial cells and smooth muscle hyperplasia.This study provides a comprehensive characterization of CD-associated ileal strictures, identifying dysregulated pathways, potential biomarkers, and therapeutic targets for intestinal fibrosis.

搜集汇总

背景与挑战

背景概述

该数据集包含克罗恩病患者的单细胞和批量RNA测序数据，重点研究肠道纤维化的分子机制。通过对9名手术患者的回肠样本分析，发现了81个差异表达基因，并确定了与疾病相关的关键生物标志物和治疗靶点。