Single-Cell RNA Sequencing Reveals Disrupted Stromal-Epithelial Crosstalk Impairs Gut Barrier in Depression

Depressive disorder is commonly associated with gastrointestinal dysfunction, but the specific cellular and molecular alterations within the colonic mucosa remain poorly understood. The role of stromal-epithelial crosstalk in the colonic niche under depressive conditions is particularly unclear.

A chronic unpredictable mild stress (CUMS) mouse model of depression was established and validated behaviorally. Single-cell RNA sequencing (scRNA-seq) of colon tissues from CUMS and control mice was performed to define cellular composition and transcriptional changes. Pseudotime trajectory, Gene Set Variation Analysis (GSVA), and cell-cell interaction analyses were used to investigate differentiation pathways and functional states. Key findings were validated using intestinal organoid cultures and immunofluorescence staining.

The CUMS model successfully induced depression-like behaviors. scRNA-seq revealed a global reduction in colonic epithelial cells and a severely disrupted differentiation trajectory in depressed mice. The continuum from stem to terminally differentiated states was broken, with concomitant downregulation of the stem cell marker Lgr5 and key tight junction genes Ocln, Tjp1(encoding zonula occludens-1, ZO-1), and Cldn2. We identified a profound stromal remodeling, characterized by expansion of specific subsets: cCF1 (colonic crypt-bottom fibroblast 1, which support the stem cell niche) and CTF (crypt-top fibroblasts, which promote epithelial differentiation). CTF cells adopted a pro-inflammatory, oxidative stress phenotype, while cCF1 cells exhibited a pro-fibrotic signature involving enhanced TGF-β and suppressed Wnt/β-catenin signaling. Cell communication analysis demonstrated a globally enhanced interaction network between epithelial stem cells and the expanded cCF1/CTF subsets in depression. Functionally, intestinal organoids derived from depressed mice exhibited altered growth and regenerative capacity, as evidenced by reduced Ki67-positive proliferating cells and Lgr5-positive stem cells in immunofluorescence staining.

This study provides a single-cell transcriptomic atlas of the colon in depression, preliminary suggesting that disease pathology may involve functional reprogramming of the stromal niche. Expansion of disease-specific stromal populations cCF1 and CTF may disrupt epithelial homeostasis, suggesting a potential role in impaired stem cell function, dysregulated cellular differentiation, and compromised intestinal barrier integrity. These findings suggest a potential cellular mechanism for depression-associated gastrointestinal comorbidity and may provide a reference for the development of future treatment strategies.