Baseline mucosal transcriptomic endotypes stratify healing capacity and biologic therapy outcomes in ulcerative colitis: an integrative multi-cohort study
- 1School of Medicine, Quanzhou Medical College
- 2Key Laboratory of Screening and Control of Infectious Diseases (Quanzhou Medical College)
Abstract
Background: Numerous baseline mucosal transcriptomic signatures have been proposed to stratify therapeutic outcomes in ulcerative colitis (UC), but cross-cohort transferability is frequently undermined by platform heterogeneity, endpoint/timepoint differences, and drug-specific biases. The resulting lack of a biologic-agnostic molecular baseline has limited clinical translation and prospective trial design.
Methods: We integratively re-analyzed endpoint-linked baseline mucosal transcriptomes from seven public UC GEO series (778 unique baseline samples), with three additional public accessions used for disease-activity and contextual analyses. The primary response/healing synthesis used five study slices spanning anti-TNF, anti-integrin, and etrolizumab-treated cohorts. Unsupervised decomposition identified baseline endotypes, and endotype-outcome associations were estimated within each cohort (OR per 1-SD increase) and summarized by random-effects cross-cohort pooling with heterogeneity reporting, rank/seed sensitivity analyses, endpoint-restricted summaries, and negative controls.
Results: Across five primary response/healing study slices, an epithelial barrier endotype (EPITHELIAL_BARRIER/NMF_C3) was associated with higher odds of response/healing (random-effects cross-cohort pooling OR = 3.171, 95% CI 1.491–6.744), whereas macrophage-inflammation and lymphoid/complement-stromal axes (MACROPHAGE_INFLAMMATION/NMF_C1 and LYMPHOID_COMPLEMENT_STROMAL/NMF_C2) were associated with lower odds of response/healing (OR = 0.359, 0.175–0.735; OR = 0.378, 0.220–0.651). The epithelial estimate was largest in GSE73661 but remained significant in the five-study leave-one-out summary after excluding that cohort (OR = 2.547, 95% CI 1.271–5.105). Cross-mechanism evaluation included UNIFI ustekinumab week-8 mucosal healing (UST arm n = 358; EPITHELIAL_BARRIER OR = 4.483, 2.263–8.881) and directionally consistent effects in etrolizumab. Endotype axes were supported by independent single-cell localization (FDR = 0.0026). Treatment-interaction tests were imprecise and did not establish drug-class-specific prediction. In cohort-heldout prediction, AUC ranged from 0.717 to 0.758, but calibration was variable. A network-based therapeutic prioritization was enriched for UC-approved agents (AUC = 0.741; permutation p = 6.0 × 10 ⁻ ⁴ ) and is presented as hypothesis-generating.
Conclusion: Baseline mucosal endotypes stratify healing capacity and therapeutic outcomes across public cohorts, with orthogonal support from single-cell localization. These findings support prospective evaluation as biologic-agnostic outcome stratifiers rather than established drug-specific predictive biomarkers.
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BibTeX
@article{chen2026baseline,
title = {{Baseline mucosal transcriptomic endotypes stratify healing capacity and biologic therapy outcomes in ulcerative colitis: an integrative multi-cohort study}},
author = {Wenbiao Chen and Shiyong Zeng},
journal = {Frontiers in Pharmacology},
year = {2026},
month = oct,
doi = {10.3389/fphar.2026.1931118},
url = {https://www.frontiersin.org/articles/10.3389/fphar.2026.1931118/full},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Baseline mucosal transcriptomic endotypes stratify healing capacity and biologic therapy outcomes in ulcerative colitis: an integrative multi-cohort study
AU - Wenbiao Chen
AU - Shiyong Zeng
PY - 2026
DA - 2026/10/23
JO - Frontiers in Pharmacology
DO - 10.3389/fphar.2026.1931118
UR - https://www.frontiersin.org/articles/10.3389/fphar.2026.1931118/full
AB - Background: Numerous baseline mucosal transcriptomic signatures have been proposed to stratify therapeutic outcomes in ulcerative colitis (UC), but cross-cohort transferability is frequently undermined by platform heterogeneity, endpoint/timepoint differences, and drug-specific biases. The resulting lack of a biologic-agnostic molecular baseline has limited clinical translation and prospective trial design. Methods: We integratively re-analyzed endpoint-linked baseline mucosal transcriptomes from seven public UC GEO series (778 unique baseline samples), with three additional public accessions used for disease-activity and contextual analyses. The primary response/healing synthesis used five study slices spanning anti-TNF, anti-integrin, and etrolizumab-treated cohorts. Unsupervised decomposition identified baseline endotypes, and endotype-outcome associations were estimated within each cohort (OR per 1-SD increase) and summarized by random-effects cross-cohort pooling with heterogeneity reporting, rank/seed sensitivity analyses, endpoint-restricted summaries, and negative controls. Results: Across five primary response/healing study slices, an epithelial barrier endotype (EPITHELIAL_BARRIER/NMF_C3) was associated with higher odds of response/healing (random-effects cross-cohort pooling OR = 3.171, 95% CI 1.491–6.744), whereas macrophage-inflammation and lymphoid/complement-stromal axes (MACROPHAGE_INFLAMMATION/NMF_C1 and LYMPHOID_COMPLEMENT_STROMAL/NMF_C2) were associated with lower odds of response/healing (OR = 0.359, 0.175–0.735; OR = 0.378, 0.220–0.651). The epithelial estimate was largest in GSE73661 but remained significant in the five-study leave-one-out summary after excluding that cohort (OR = 2.547, 95% CI 1.271–5.105). Cross-mechanism evaluation included UNIFI ustekinumab week-8 mucosal healing (UST arm n = 358; EPITHELIAL_BARRIER OR = 4.483, 2.263–8.881) and directionally consistent effects in etrolizumab. Endotype axes were supported by independent single-cell localization (FDR = 0.0026). Treatment-interaction tests were imprecise and did not establish drug-class-specific prediction. In cohort-heldout prediction, AUC ranged from 0.717 to 0.758, but calibration was variable. A network-based therapeutic prioritization was enriched for UC-approved agents (AUC = 0.741; permutation p = 6.0 × 10 ⁻ ⁴ ) and is presented as hypothesis-generating. Conclusion: Baseline mucosal endotypes stratify healing capacity and therapeutic outcomes across public cohorts, with orthogonal support from single-cell localization. These findings support prospective evaluation as biologic-agnostic outcome stratifiers rather than established drug-specific predictive biomarkers.
SN - 1663-9812
ER -