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Single-Cell Transcriptomic Analysis of the Pediatric Gut in Crohn's Disease Reveals Compositional Remodeling toward an Inflammatory Cellular Landscape

Author(s)

Bingyao Chen

Affiliation(s)

Xi'an Jiaotong-Liverpool University, Suzhou, China

Abstract

Crohn's disease is a chronic inflammatory disorder of the gut. It often begins in childhood, and its cellular basis in young patients is still not fully understood. Bulk gene expression studies report average changes in tissue, but they cannot show which cell types drive disease. In this work we reanalyze a public single-cell RNA sequencing atlas of the pediatric human gut and compare children with Crohn's disease to healthy controls. After quality control we studied 17,965 cells from 15 donors, grouped into 31 cell types that span the epithelial, stromal, vascular, and immune compartments. We used a standard and open pipeline that includes quality control, normalization, batch integration with Harmony, graph based clustering, and marker based validation of cell identity. We then measured how the cell type composition differs between disease and control tissue. Crohn's disease tissue showed a clear shift toward an inflammatory landscape. Inflammatory monocytes, IgG plasma cells, fibroblasts, and blood vessel cells all increased in disease, while mature B cells and absorptive enterocytes decreased. The expansion of IgG plasma cells, monocytes, and stromal cells matches a known pathogenic module that is linked to poor drug response in adult Crohn's disease. The results give a clear, cell level picture of pediatric Crohn's disease and provide a reproducible base for biomarker work and for future spatial and predictive studies.

Keywords

RNA Sequencing; Crohn's Disease; Inflammatory Bowel Disease; Pediatric; Cell Type Composition; Gut Mucosa; Transcriptomics.

References

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