ArticleScience advances2023
A tissue atlas of ulcerative colitis revealing evidence of sex-dependent differences in disease-driving inflammatory cell types and resistance to TNF inhibitor therapy.
Article in Science advances, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers, 1 of them a synthesis that pooled it.
What it found
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Who cites it
29 citing papers in PubMed, 1 synthesis or guideline pooled it, 39 citations in OpenAlex.
- Understanding heterogeneity in the pathogenesis and drug responses of ulcerative colitis through single-cell and spatial transcriptomics.Frontiers in immunology · 2026Pooled it
- Accurate and well-powered case-control analysis of spatial molecular data.Nature methods · 2026Article
- Flexible discovery of disease-associated tissue structures.Nature methods · 2026Article
- Spotlight on challenges and novel methods in highly multiplexed tissue imaging-based spatial proteomics.Journal of translational medicine · 2026Review
- Current Methods in CODEX High-Multiplex Microscopy to Describe Spatial Relationships in the Tissue Microenvironment.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Spatial multi-omics-guided drug development in inflammatory bowel disease: from mucosal immune niches to precision therapy.Frontiers in immunology · 2026Review
- Ulcerative colitis, but not Crohn's disease, displays demographically and clinically driven mucosal immune heterogeneity: implications for patient stratification.Frontiers in immunology · 2026Article
- Tumor Development in Ulcerative Colitis: Perspectives From Biomechanical Characteristics.Development, growth & differentiation · 2025Review
- Sexual dimorphism in colon is mediated by an androgen-IL33Cell & bioscience · 2025Article
- Sex-Specific Real-Life Profiling in Vedolizumab, Ustekinumab, and Tofacitinib Effectiveness in Ulcerative Colitis.Journal of clinical medicine · 2025Article
- The Immune Microenvironment of Transplant Glomerulitis.Kidney international reports · 2025Article
- Spatial Omics in Clinical Research: A Comprehensive Review of Technologies and Guidelines for Applications.International journal of molecular sciences · 2025Review
- Relating the molecular phenotype of ulcerative colitis to the clinical course.Scientific reports · 2025Article
- Spatial-Omics Methods and Applications.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Unraveling the complexity of ulcerative colitis: insights into cytokine dysregulation and targeted therapies.EXCLI journal · 2025Review
- Spatial profiling of the mouse colonic immune landscape associated with colitis and sex.Communications biology · 2024Article
- A longitudinal single-cell atlas of anti-tumour necrosis factor treatment in inflammatory bowel disease.Nature immunology · 2024Article
- Answering open questions in biology using spatial genomics and structured methods.BMC bioinformatics · 2024Review
- Safety and effectiveness of tofacitinib in Korean adult patients with ulcerative colitis: post-marketing surveillance study.BMC gastroenterology · 2024Observational
- Automated spatial omics landscape analysis approach reveals novel tissue architectures in ulcerative colitis.Scientific reports · 2024Article
Corrections and comments
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Authors and funding
21 authors at 3 institutions in 1 country.
Funding
Abstract
Although literature suggests that resistance to TNF inhibitor (TNFi) therapy in patients with ulcerative colitis (UC) is partially linked to immune cell populations in the inflamed region, there is still substantial uncertainty underlying the relevant spatial context. Here, we used the highly multiplexed immunofluorescence imaging technology CODEX to create a publicly browsable tissue atlas of inflammation in 42 tissue regions from 29 patients with UC and 5 healthy individuals. We analyzed 52 biomarkers on 1,710,973 spatially resolved single cells to determine cell types, cell-cell contacts, and cellular neighborhoods. We observed that cellular functional states are associated with cellular neighborhoods. We further observed that a subset of inflammatory cell types and cellular neighborhoods are present in patients with UC with TNFi treatment, potentially indicating resistant niches. Last, we explored applying convolutional neural networks (CNNs) to our dataset with respect to patient clinical variables. We note concerns and offer guidelines for reporting CNN-based predictions in similar datasets.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.