Integrated Single-Cell and Bulk Transcriptomics Reveal Myeloid-Cell Heterogeneity in Ulcerative Colitis

Background: Ulcerative colitis (UC) is a chronic relapsing inflammatory bowel disease closely linked to dysregulation of the intestinal mucosal immune microenvironment. However, myeloid cell heterogeneity and related diagnostic biomarkers in UC remain incompletely defined. Methods: UC-related single-cell RNA sequencing and bulk transcriptomic datasets were integrated to characterize intestinal mucosal myeloid cell heterogeneity. Weighted gene co-expression network analysis (WGCNA), machine learning, consensus clustering, immune infiltration, and pathway enrichment analyses were performed to identify and characterize candidate diagnostic genes. Their expression was further examined by quantitative real-time PCR (qRT-PCR) in whole-colon tissue from a dextran sulfate sodium (DSS)-induced mouse model of colitis, followed by in silico gene perturbation analysis to investigate their potential functional roles. Results: A total of 65,148 single cells were classified into nine major cell populations. Compared with controls, UC samples showed a significantly higher proportion of myeloid cells and enrichment of MARCO+ macrophages. The BACH1 regulon showed relatively high activity and specificity in MARCO+ macrophages across myeloid subsets. Integrated WGCNA and machine-learning analyses identified basic helix–loop–helix family member e40 (BHLHE40) and serpin family A member 1 (SERPINA1) as candidate diagnostic genes, both distinguishing UC from healthy controls in the analyzed training and validation cohorts. qRT-PCR confirmed increased Bhlhe40 and Serpina1a expression in whole-colon tissue from DSS-treated mice. Virtual knockout and functional enrichment analyses suggested distinct potential downstream effects, with SERPINA1 associated with inflammatory responses and myeloid immune functions. Conclusions: These findings characterize myeloid-cell heterogeneity in UC and support further investigation of BHLHE40 and SERPINA1 as candidate biomarkers associated with intestinal inflammation.