Single-cell RNA sequencing platform for identifying anti-fibrotic siRNA therapies in Crohn's disease

Overview

This research program leverages single-cell RNA sequencing (scRNA-seq) combined with machine learning and virtual screening to identify novel siRNA candidates for anti-fibrotic therapies, with a primary focus on Crohn's disease. By analyzing the cellular heterogeneity of intestinal fibrosis in the SAMP1/YitFc murine model, the project aims to uncover key mRNA targets involved in fibrosis genesis. The integration of structure-based and ligand-based virtual screening enables efficient sampling of chemical diversity while significantly reducing the time and costs associated with traditional wet high-throughput screening methods.

The approach addresses a critical unmet need in Crohn's disease treatment, where intestinal fibrosis remains a major complication lacking effective therapeutic options. By focusing on tissue-specific endpoints and clinically feasible siRNA applications, this research seeks to translate molecular insights into actionable therapeutic candidates.

Technical specifications

Key methodological components:

• Animal model: SAMP1/YitFc mice exhibiting spontaneous ileocolitis at 10–20 weeks and fibrosis at 30 weeks, with extracellular matrix accumulation in small and large bowel
• Disease assessment: Endoscopic evaluation of macroscopic colitis progression and histological assessment of tissue samples
• Cell isolation: Intestinal epithelial cells, fibroblasts, endothelial epithelial cells, and mesenchymal stem cells isolated from experimental groups
• Single-cell sequencing: BD Rhapsody Scanner for scRNA-seq, Illumina NovaSeq for sequencing, and SeqGeq for gene expression data analysis
• Virtual screening pipeline: Structure-based VS utilizing 3D target structures for docking experiments, combined with ligand-based VS leveraging similarity to known active compounds
• Machine learning integration: Tools applied to identify siRNA candidates involved in fibrosis genesis from scRNA-seq data

Technology readiness level

The project is in an active research phase with a planned one-year timeline. The validation procedures draw upon established single-cell sequencing methodologies that have demonstrated utility in understanding Crohn's disease heterogeneity, including prior studies showing increased fibroblast heterogeneity in stricturing disease. The SAMP1/YitFc mouse model provides a well-characterized platform for studying spontaneous ileocolitis and fibrosis progression. The research team is seeking partnership support for scRNA-seq experiments and virtual screening analysis to advance candidate identification toward therapeutic development.