GART expression is associated with a proliferative and purine-metabolic ISC-like epithelial state in ulcerative colitis

Abstract

To characterize the epithelial state associated with GART expression in ulcerative colitis (UC) and determine whether this association reflects a GART-specific program or a broader proliferative and purine-metabolic phenotype. Four independent bulk transcriptomic cohorts were analyzed and synthesized by random-effects meta-analysis. Human colonic scRNA-seq datasets (GSE214695 and SCP259) were integrated, with principal comparisons repeated using donor-aware pseudobulk or mixed-effects approaches and adjustment for sequencing depth, gene detection, and cell-cycle covariates. GART detection was defined from raw counts and tested using alternative thresholds. Pseudotime, scTenifoldKnk, CellChat/LIANA, and transcriptional-network analyses were used as exploratory analyses. Spatial transcriptomics (GSE189184), human colonic multiplex immunofluorescence, and acute DSS-induced colitis tissues were used for tissue-level localization. Across the four bulk cohorts, GART expression showed an overall increase in UC (pooled Hedges’ g = 0.743, 95% CI 0.239–1.248; P = 0.0183). In the single-cell atlas, GART detection localized preferentially to an ISC-like epithelial compartment, although the magnitude of the UC-associated detection difference varied between cohorts. Within UC ISC-like cells, donor-paired pseudobulk analyses identified proliferative and nucleotide-metabolic transcriptional differences associated with GART detection. Across the broader ISC-like epithelial atlas, donor-aware module analyses showed positive associations of GART detection with purine-biosynthesis, DNA-replication, DNA-repair, and mitotic programs, and these associations remained positive within cell-cycle strata. Comparison with other de novo purine-synthesis enzymes did not support a uniquely GART-specific alteration. Exploratory network analyses linked the GART-associated state to proliferative and nucleotide-metabolic programs but did not establish functional dependence. In seven independent spatial donors, the single-cell-derived epithelial program was consistently higher in GART-detected than GART-undetected epithelial regions (mean within-donor difference = 0.0262, 95% CI 0.0140–0.0407; exact P = 0.0156). Human tissue immunofluorescence further showed co-enrichment of GART with OLFM4-positive ISC-like, MYBL2/Ki67-positive proliferative, and MIF/CD74-associated inflammatory regions across the corresponding panel-specific participant sets. GART identifies a proliferative and purine-metabolic ISC-like epithelial state in UC but is not established as a specific driver of epithelial regeneration. The findings support an association between GART detection, nucleotide-demand programs, proliferative epithelial activity, and the inflammatory tissue context, providing a framework for future direct functional studies.