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Integrated Single Cell Spatial Analysis Reveals Dysregulated Basal Progenitor Cells in Ulcerative Colitis
Xiaopeng Chen1, Chuiguo Huang2, Zhuofeng Wen3
1Department of Hepatobiliary Surgery The Second Hospital of Longyan Longyan Fujian China.
Health Science Reports
|January 16, 2026
Summary
Altered basal progenitor cells (BPCs) show spatial dysfunction in ulcerative colitis (UC). Key genes like FABP1 are implicated in UC and colorectal cancer progression, suggesting BPC restoration as a therapeutic target.
Area of Science:
- Gastroenterology and Molecular Biology
- Inflammatory Bowel Disease Research
- Cancer Biomarker Discovery
Background:
- Ulcerative colitis (UC) involves chronic inflammation and epithelial dysfunction, impacting basal progenitor cells (BPCs) crucial for intestinal repair.
- The precise spatial dynamics and functional roles of BPCs in UC pathogenesis are not well understood, despite extensive research on immune dysregulation.
Purpose of the Study:
- To investigate the spatial dynamics and functional alterations of basal progenitor cells (BPCs) in ulcerative colitis (UC) using multi-omics and machine learning.
- To identify key genes and molecular pathways driving BPC dysfunction in UC and assess their prognostic potential for colorectal cancer (CRC).
Main Methods:
- Integrated multi-omics data, including single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST), to analyze BPC behavior in UC and healthy samples.
- Employed machine learning (ML) models to identify key genes associated with UC severity and utilized external survival data for colorectal cancer (CRC) prognostic assessment.
Main Results:
- Significant alterations in BPC differentiation pathways were observed in UC, driven by a FABP1-led gene matrix.
- Spatially distinct expression patterns of key genes (FABP1, CLCA1, ITLN1, MUC2, TFF1) were identified in UC BPCs, with FABP1 downregulation.
- Identified these genes as significant biomarkers for both UC and colorectal cancer (CRC) prognosis through external survival analyses.
Conclusions:
- Uncovered a novel role for spatially dysfunctional BPCs in UC pathogenesis, positioning them as potential therapeutic targets.
- The FABP1-led gene matrix provides new insights into epithelial dysregulation in UC and its link to colorectal cancer (CRC) development.
- Restoring BPC function presents a potential novel therapeutic strategy for ulcerative colitis and associated colorectal cancer risk.
Keywords:
basal progenitor cellsfunctional matriximmune diseasesingle‐cell sequencingulcerative colitis
