Spatially Resolved Insights Into Fistulating Crohn's Disease Pathogenesis - bulk RNA-Seq

The aim of this study was to investigate how over expression of transcription factors alters the gene expression program of primary human colonic fibroblasts. Fibroblasts isolated from healthy donor biopsies were transduced with lentiviral vectors to over-express TWIST1 or OSR2, or with empty vector as a control, followed by bulk RNA sequencing. The goal was to identify transcriptional pathways and effector genes regulated by these factors, with a focus on extracellular matrix organization, morphogen signaling, and fibroblast functional states. Overall design: Primary human colonic fibroblasts were isolated from endoscopic biopsies of healthy donors and expanded in vitro. Cells were transduced with lentiviral vectors to over-express TWIST1 or OSR2, or with empty vector as a control, followed by puromycin selection. Total RNA was extracted from each condition using the RNeasy Plus Micro kit (Qiagen). Bulk RNA sequencing libraries were prepared by Novogene and sequenced on an Illumina platform to a depth of approximately 50 million paired-end reads per sample.