{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T14:34:04Z","timestamp":1790087644223,"version":"4.0.1"},"reference-count":69,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T00:00:00Z","timestamp":1774915200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Immunol."],"abstract":"<jats:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>Ulcerative colitis (UC) is driven by mucosal inflammation and epithelial injury. Single cell RNA sequencing (scRNA-seq) enables high resolution profiling of immune, stromal and epithelial compartments in UC, whilst spatial transcriptomic (ST) and proteomic (SP) enable interrogation of cell-cell interactions, niche-specific expression profiles, and spatially restricted pathological processes. Although scRNA-seq, ST, and SP technologies have been rapidly evolved in the past ten years, relatively limited clinical applications have been demonstrated. This systematic review aims at comprehensively analysing current evidence in UC studies as an approach to identifying key limitations and proposing recommendations for strengthening future spatial research towards translations into clinics.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>A comprehensive search of Embase, Medline, and grey literature was conducted to identify studies using scRNA-seq or spatial transcriptomic or proteomic technologies in adult UC cohorts. Outcomes of interest included insights into disease pathogenesis or treatment response.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>scRNA-seq studies revealed alterations across the innate and adaptive immune systems, as well as stromal and epithelial compartments in UC colonic tissue. Spatial studies provided insights into: (i) cellular composition of the UC microenvironment; (ii) inflammatory features in treatment responders versus non-responders; and (iii) ligand-receptor interactions as potential spatial biomarkers and therapeutic targets.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>Overall, single-cell and spatial studies are deepening our understanding of UC pathogenesis and treatment response. However, they are often limited by small sample sizes and heterogeneous UC phenotypes. Future studies should prioritise robust cohort design and careful sample stratification. This will be critical to generating mechanistically precise, reproducible, and clinically meaningful insights into the heterogeneity of UC pathogenesis and treatment response.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Systematic Review Registration<\/jats:title>\n                    <jats:p>\n                      <jats:ext-link>https:\/\/www.crd.york.ac.uk\/PROSPERO\/<\/jats:ext-link>\n                      , identifier CRD42024601628.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fimmu.2026.1794207","type":"journal-article","created":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T05:34:45Z","timestamp":1774935285000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":3,"title":["Understanding heterogeneity in the pathogenesis and drug responses of ulcerative colitis through single-cell and spatial transcriptomics"],"prefix":"10.3389","volume":"17","author":[{"given":"Jennifer","family":"Phillips","sequence":"first","affiliation":[{"name":"Department of Gastroenterology and Hepatology, Inflammatory Bowel Disease Unit, Royal Brisbane and Women\u2019s Hospital","place":["Brisbane, QLD, Australia"]},{"name":"The Faculty of Medicine, University of Queensland","place":["Brisbane, QLD, Australia"]},{"name":"Queensland Institute for Medical Research (QIMR) Berghofer","place":["Brisbane, QLD, Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"George","family":"Tambakis","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology and Hepatology, Inflammatory Bowel Disease Unit, Royal Brisbane and Women\u2019s Hospital","place":["Brisbane, QLD, Australia"]},{"name":"The Faculty of Medicine, University of Queensland","place":["Brisbane, QLD, Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rina","family":"Kumar","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology and Hepatology, Inflammatory Bowel Disease Unit, Royal Brisbane and Women\u2019s Hospital","place":["Brisbane, QLD, Australia"]},{"name":"Queensland Institute for Medical Research (QIMR) Berghofer","place":["Brisbane, QLD, Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anthony","family":"Croft","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology and Hepatology, Inflammatory Bowel Disease Unit, Royal Brisbane and Women\u2019s Hospital","place":["Brisbane, QLD, Australia"]},{"name":"The Faculty of Medicine, University of Queensland","place":["Brisbane, QLD, Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ian","family":"Brown","sequence":"additional","affiliation":[{"name":"Envoi Specialist Pathologists","place":["Kelvin Grove, QLD, Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christophe","family":"Rosty","sequence":"additional","affiliation":[{"name":"The Faculty of Medicine, University of Queensland","place":["Brisbane, QLD, Australia"]},{"name":"Envoi Specialist Pathologists","place":["Kelvin Grove, QLD, Australia"]},{"name":"Colorectal Oncogenomic Group, Department of Clinical Pathology, The University of Melbourne","place":["Parkville, VIC, Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"Anderson","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology, Mackay Base Hospital","place":["Mackay, QLD, Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabrielle","family":"Belz","sequence":"additional","affiliation":[{"name":"The University of Queensland Frazer Institute, University of Queensland","place":["Brisbane, QLD, Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amanda J.","family":"Oliver","sequence":"additional","affiliation":[{"name":"Queensland Institute for Medical Research (QIMR) Berghofer","place":["Brisbane, QLD, Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Albert","family":"Xiong","sequence":"additional","affiliation":[{"name":"Queensland Institute for Medical Research (QIMR) Berghofer","place":["Brisbane, QLD, Australia"]},{"name":"National Centre for Spatial Tissue and AI Research (NCSTAR)","place":["Brisbane, Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Quan","family":"Nguyen","sequence":"additional","affiliation":[{"name":"Queensland Institute for Medical Research (QIMR) Berghofer","place":["Brisbane, QLD, Australia"]},{"name":"National Centre for Spatial Tissue and AI Research (NCSTAR)","place":["Brisbane, Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Graham","family":"Radford-Smith","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology and Hepatology, Inflammatory Bowel Disease Unit, Royal Brisbane and Women\u2019s Hospital","place":["Brisbane, QLD, Australia"]},{"name":"The Faculty of Medicine, University of Queensland","place":["Brisbane, QLD, Australia"]},{"name":"Queensland Institute for Medical Research (QIMR) Berghofer","place":["Brisbane, QLD, Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gareth J.","family":"Walker","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology and Hepatology, Inflammatory Bowel Disease Unit, Royal Brisbane and Women\u2019s Hospital","place":["Brisbane, QLD, Australia"]},{"name":"The Faculty of Medicine, University of Queensland","place":["Brisbane, QLD, Australia"]},{"name":"Queensland Institute for Medical Research (QIMR) Berghofer","place":["Brisbane, QLD, Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,3,31]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"139","DOI":"10.21203\/rs.3.rs-4810674\/v1","article-title":"Global, regional, and national burden of inflammatory bowel disease, 1990-2021: Insights from the global burden of disease 2021","volume":"39","author":"Lin","year":"2024","journal-title":"Int J Colorectal Dis"},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.1038\/nature10209","article-title":"Genetics and pathogenesis of inflammatory bowel disease","volume":"474","author":"Khor","year":"2011","journal-title":"Nature"},{"key":"B3","doi-asserted-by":"publisher","first-page":"1493","DOI":"10.1038\/s41467-024-45665-6","article-title":"Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis","volume":"15","author":"Mennillo","year":"2024","journal-title":"Nat Commun"},{"key":"B4","doi-asserted-by":"publisher","first-page":"1526","DOI":"10.3390\/ijms24021526","article-title":"Pathophysiology of inflammatory bowel disease: Innate immune system","volume":"24","author":"Saez","year":"2023","journal-title":"Int J Mol Sci"},{"key":"B5","doi-asserted-by":"publisher","DOI":"10.1016\/s2468-1253(21)00377-0","article-title":"Efficacy and safety of biologics and small molecule drugs for patients with moderate-to-severe ulcerative colitis: a systematic review and network meta-analysis","volume":"7","author":"Lasa","year":"2022","journal-title":"Lancet Gastroenterol Hepatol"},{"key":"B6","doi-asserted-by":"publisher","DOI":"10.1097\/mog.0000000000000449","article-title":"Approach to treatment failure in inflammatory bowel disease","volume":"18","author":"Moss","year":"2022","journal-title":"Gastroenterol Hepatol (N Y)"},{"key":"B7","doi-asserted-by":"publisher","DOI":"10.1053\/j.gastro.2021.09.078","article-title":"Breaking through the therapeutic ceiling: What will it take","volume":"162","author":"Raine","year":"2022","journal-title":"Gastroenterology"},{"key":"B8","doi-asserted-by":"publisher","DOI":"10.1053\/j.gastro.2021.09.077","article-title":"The future of precision medicine to predict outcomes and control tissue remodeling in inflammatory bowel disease","volume":"162","author":"Lamb","year":"2022","journal-title":"Gastroenterology"},{"key":"B9","doi-asserted-by":"publisher","DOI":"10.1136\/egastro-2023-100006","article-title":"Pathogenesis and precision medicine for predicting response in inflammatory bowel disease: advances and future directions","volume":"2","author":"Little","year":"2024","journal-title":"eGastroenterology"},{"key":"B10","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0076235","article-title":"Identification of novel predictor classifiers for inflammatory bowel disease by gene expression profiling","volume":"8","author":"Montero-Mel\u00e9ndez","year":"2013","journal-title":"PLoS One"},{"key":"B11","doi-asserted-by":"publisher","DOI":"10.1002\/ibd.20342","article-title":"Activation of an IL-6:STAT3-dependent transcriptome in pediatric-onset inflammatory bowel disease","volume":"14","author":"Carey","year":"2007","journal-title":"Inflammatory Bowel Dis"},{"key":"B12","doi-asserted-by":"publisher","DOI":"10.1136\/gut.2008.148395","article-title":"Regional variation in gene expression in the healthy colon is dysregulated in ulcerative colitis","volume":"57","author":"Noble","year":"2008","journal-title":"Gut"},{"key":"B13","doi-asserted-by":"publisher","DOI":"10.1038\/s41368-021-00146-0","article-title":"From bulk, single-cell to spatial RNA sequencing","volume":"13","author":"Li","year":"2021","journal-title":"Int J Oral Sci"},{"key":"B14","doi-asserted-by":"publisher","first-page":"1335","DOI":"10.1136\/gutjnl-2024-334165","article-title":"Single-cell omics in inflammatory bowel disease: recent insights and future clinical applications","volume":"74","author":"Gudi\u00f1o","year":"2025","journal-title":"Gut"},{"key":"B15","doi-asserted-by":"publisher","DOI":"10.1016\/j.csbj.2024.07.011","article-title":"Decoding the mosaic of inflammatory bowel disease: Illuminating insights with single-cell RNA technology","volume":"23","author":"Liu","year":"2024","journal-title":"Comput Struct Biotechnol J"},{"key":"B16","doi-asserted-by":"publisher","DOI":"10.1152\/ajpgi.00191.2022","article-title":"Spatial transcriptomics add a new dimension to our understanding of the gut","volume":"324","author":"Danan","year":"2023","journal-title":"Am J Physiol Gastrointest Liver Physiol"},{"key":"B17","doi-asserted-by":"publisher","first-page":"98","DOI":"10.1038\/s44320-023-00006-5","article-title":"Identifying spatial co-occurrence in healthy and inflamed tissues (ISCHIA)","volume":"20","author":"Lafzi","year":"2024","journal-title":"Mol Syst Biol"},{"key":"B18","doi-asserted-by":"publisher","DOI":"10.1136\/bmj.i4919","article-title":"ROBINS-I: a tool for assessing risk of bias in non-randomised studies of interventions","volume":"355","author":"Sterne","year":"2016","journal-title":"Bmj"},{"key":"B19","doi-asserted-by":"publisher","first-page":"699","DOI":"10.1038\/s41586-024-07571-1","article-title":"Single-cell integration reveals metaplasia in inflammatory gut diseases","volume":"635","author":"Oliver","year":"2024","journal-title":"Nature"},{"key":"B20","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1038\/s41576-020-00292-x","article-title":"Deciphering cell\u2013cell interactions and communication from gene expression","volume":"22","author":"Armingol","year":"2021","journal-title":"Nat Rev Genet"},{"key":"B21","doi-asserted-by":"publisher","DOI":"10.21203\/rs.3.rs-4376986\/v2","article-title":"Spatial single-cell transcriptomic analysis in breast cancer reveals potential biomarkers for PD1 blockade therapy","author":"Wang","year":"2024"},{"key":"B22","doi-asserted-by":"publisher","first-page":"714","DOI":"10.1016\/j.cell.2019.06.029","article-title":"Intra- and inter-cellular rewiring of the human colon during ulcerative colitis","volume":"178","author":"Smillie","year":"2019","journal-title":"Cell"},{"key":"B23","doi-asserted-by":"publisher","DOI":"10.1038\/s41590-024-01994-8","article-title":"A longitudinal single-cell atlas of anti-tumour necrosis factor treatment in inflammatory bowel disease","volume":"25","author":"Thomas","year":"2024","journal-title":"Nat Immunol"},{"key":"B24","doi-asserted-by":"publisher","first-page":"567","DOI":"10.1186\/s12967-025-06565-5","article-title":"Unveiling the hidden dance: SPP1\u2009+\u2009macrophages identified in ulcerative colitis reveal crosstalk with CHI3L1\u2009+\u2009fibroblasts","volume":"23","author":"Zhou","year":"2025","journal-title":"J Transl Med"},{"key":"B25","doi-asserted-by":"publisher","first-page":"591","DOI":"10.1053\/j.gastro.2020.04.074","article-title":"Single-cell analyses of colon and blood reveal distinct immune cell signatures of ulcerative colitis and Crohn's disease","volume":"159","author":"Mitsialis","year":"2020","journal-title":"Gastroenterology"},{"key":"B26","doi-asserted-by":"publisher","first-page":"2023.06.02.542863","DOI":"10.1101\/2023.06.02.542863","article-title":"Myeloid cell influx into the colonic epithelium is associated with disease severity and non-response to anti-Tumor Necrosis Factor Therapy in patients with Ulcerative Colitis","volume":"5","author":"Jha","year":"2023","journal-title":"bioRxiv"},{"key":"B27","doi-asserted-by":"publisher","DOI":"10.1136\/gutjnl-2015-310187","article-title":"Development and validation of the Nancy histological index for UC","volume":"66","author":"Marchal-Bressenot","year":"2017","journal-title":"Gut"},{"key":"B28","doi-asserted-by":"publisher","DOI":"10.1136\/gut.47.3.404","article-title":"A reproducible grading scale for histological assessment of inflammation in ulcerative colitis","volume":"47","author":"Geboes","year":"2000","journal-title":"Gut"},{"key":"B29","doi-asserted-by":"publisher","DOI":"10.1136\/gutjnl-2015-310393","article-title":"Development and validation of a histological index for UC","volume":"66","author":"Mosli","year":"2017","journal-title":"Gut"},{"key":"B30","doi-asserted-by":"publisher","first-page":"eabb4432","DOI":"10.1126\/sciimmunol.abb4432","article-title":"Heterogeneity and clonal relationships of adaptive immune cells in ulcerative colitis revealed by single-cell analyses","volume":"5","author":"Boland","year":"2020","journal-title":"Sci Immunol"},{"key":"B31","doi-asserted-by":"publisher","first-page":"e20220538","DOI":"10.1084\/jem.20220538","article-title":"Remodeling of colon plasma cell repertoire within ulcerative colitis patients","volume":"220","author":"Scheid","year":"2023","journal-title":"J Exp Med"},{"key":"B32","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-022-01680-y","article-title":"Ulcerative colitis is characterized by a plasmablast-skewed humoral response associated with disease activity","volume":"28","author":"Uzzan","year":"2022","journal-title":"Nat Med"},{"key":"B33","doi-asserted-by":"publisher","DOI":"10.3389\/fmolb.2022.859645","article-title":"Mass cytometry and single-cell transcriptome analyses reveal the immune cell characteristics of ulcerative colitis","volume":"9","author":"Luo","year":"2022","journal-title":"Front Mol Biosci"},{"key":"B34","doi-asserted-by":"publisher","DOI":"10.1136\/gut.2010.225482","article-title":"Randomised placebo-controlled trial of rituximab (anti-CD20) in active ulcerative colitis","volume":"60","author":"Leiper","year":"2011","journal-title":"Gut"},{"key":"B35","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMc2508023","article-title":"CD19 CAR T-cell therapy in multidrug-resistant ulcerative colitis","volume":"393","author":"M\u00fcller","year":"2025","journal-title":"N Engl J Med"},{"key":"B36","doi-asserted-by":"publisher","first-page":"3675","DOI":"10.1038\/s41467-023-39173-2","article-title":"Selective oxidative protection leads to tissue topological changes orchestrated by macrophage during ulcerative colitis","volume":"14","author":"Du","year":"2023","journal-title":"Nat Commun"},{"key":"B37","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1016\/j.jcmgh.2021.01.020","article-title":"Identification of novel population-specific cell subsets in Chinese ulcerative colitis patients using single-cell RNA sequencing","volume":"12","author":"Li","year":"2021","journal-title":"Cell Mol Gastroenterol Hepatol"},{"key":"B38","doi-asserted-by":"publisher","DOI":"10.1093\/ecco-jcc\/jjac190.0900","article-title":"P770 Autologous regulatory T cell transfer in patients with refractory ulcerative colitis: Interim report of a phase 1, dose-escalation trial","volume":"17","author":"Voskens","year":"2023","journal-title":"J Crohn's Colitis"},{"key":"B39","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1186\/s12935-021-01763-9","article-title":"Monoclonal antibodies and chimeric antigen receptor (CAR) T cells in the treatment of colorectal cancer","volume":"21","author":"Jin","year":"2021","journal-title":"Cancer Cell Int"},{"key":"B40","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-020-1003-4","article-title":"Single-cell atlas of colonic CD8(+) T cells in ulcerative colitis","volume":"26","author":"Corridoni","year":"2020","journal-title":"Nat Med"},{"key":"B41","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1038\/s41586-019-0992-y","article-title":"Colonic epithelial cell diversity in health and inflammatory bowel disease","volume":"567","author":"Parikh","year":"2019","journal-title":"Nature"},{"key":"B42","doi-asserted-by":"publisher","DOI":"10.1016\/j.phrs.2020.105040","article-title":"Targeting T cells in inflammatory bowel disease","volume":"159","author":"Giuffrida","year":"2020","journal-title":"Pharmacol Res"},{"key":"B43","doi-asserted-by":"publisher","DOI":"10.1016\/j.ard.2025.05.482","article-title":"POS0094 Pharmacodynamic activity of JNJ-67484703 in rheumatoid arthritis, ulcerative colitis and Sjogren's disease (PARIS): Results of a phase II proof of biology trial","volume":"84","author":"Fisher","year":"2025","journal-title":"Ann Rheumatic Dis"},{"key":"B44","doi-asserted-by":"publisher","DOI":"10.1111\/imr.12039","article-title":"CD4+ T-cell subsets in intestinal inflammation","volume":"252","author":"Shale","year":"2013","journal-title":"Immunol Rev"},{"key":"B45","doi-asserted-by":"publisher","DOI":"10.1053\/j.gastro.2020.12.076","article-title":"Inflamed ulcerative colitis regions associated with MRGPRX2-mediated mast cell degranulation and cell activation modules, defining a new therapeutic target","volume":"160","author":"Chen","year":"2021","journal-title":"Gastroenterology"},{"key":"B46","doi-asserted-by":"publisher","first-page":"372","DOI":"10.1016\/j.cell.2018.08.067","article-title":"Structural remodeling of the human colonic mesenchyme in inflammatory bowel disease","volume":"175","author":"Kinchen","year":"2018","journal-title":"Cell"},{"key":"B47","doi-asserted-by":"publisher","first-page":"481","DOI":"10.1016\/j.medj.2022.05.002","article-title":"Cross-tissue, single-cell stromal atlas identifies shared pathological fibroblast phenotypes in four chronic inflammatory diseases","volume":"3","author":"Korsunsky","year":"2022","journal-title":"Med"},{"key":"B48","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajhg.2021.07.013","article-title":"Stratification of risk of progression to colectomy in ulcerative colitis via measured and predicted gene expression","volume":"108","author":"Mo","year":"2021","journal-title":"Am J Hum Genet"},{"key":"B49","doi-asserted-by":"publisher","first-page":"4506","DOI":"10.1038\/s41467-023-40156-6","article-title":"Macrophage and neutrophil heterogeneity at single-cell spatial resolution in human inflammatory bowel disease","volume":"14","author":"Garrido-Trigo","year":"2023","journal-title":"Nat Commun"},{"key":"B50","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-021-01520-5","article-title":"IL-1-driven stromal-neutrophil interactions define a subset of patients with inflammatory bowel disease that does not respond to therapies","volume":"27","author":"Friedrich","year":"2021","journal-title":"Nat Med"},{"key":"B51","doi-asserted-by":"publisher","DOI":"10.1093\/ibd\/izad084","article-title":"Responsiveness to vedolizumab therapy in ulcerative colitis is associated with alterations in immune cell-cell communications","volume":"29","author":"Hsu","year":"2023","journal-title":"Inflammation Bowel Dis"},{"key":"B52","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2022.893803","article-title":"Identification of a disease-associated network of intestinal immune cells in treatment-naive inflammatory bowel disease","volume":"13","author":"van Unen","year":"2022","journal-title":"Front Immunol"},{"key":"B53","doi-asserted-by":"publisher","DOI":"10.1002\/ueg2.70002","article-title":"Serum collagen biomarkers are reflective of tissue specific fibroblasts associated with ulcerative colitis activity and treatment response to ustekinumab","volume":"13","author":"Venkat","year":"2025","journal-title":"United Eur Gastroenterol J"},{"key":"B54","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.add1166","article-title":"A tissue atlas of ulcerative colitis revealing evidence of sex-dependent differences in disease-driving inflammatory cell types and resistance to TNF inhibitor therapy","volume":"9","author":"Mayer","year":"2023","journal-title":"Sci Adv"},{"key":"B55","doi-asserted-by":"publisher","DOI":"10.1093\/ecco-jcc\/jjae190.0023","article-title":"OP23 neutrophil niches and therapy resistance in ulcerative colitis: Spatial atlas insights","volume":"19","author":"Holman","year":"2025","journal-title":"J Crohn's Colitis"},{"key":"B56","doi-asserted-by":"publisher","DOI":"10.1093\/ecco-jcc\/jjad212.0021","article-title":"OP21 spatial transcriptomics of pre-treatment biopsies revealing molecular maturation state and chronic crypt damage, reflecting histological severity, as predictors of primary responsiveness to TNF-\u03b1 inhibitors in bio-naive ulcerative colitis patients","volume":"18","author":"Kim","year":"2024","journal-title":"J Crohn's Colitis"},{"key":"B57","doi-asserted-by":"publisher","first-page":"77","DOI":"10.3390\/pharmaceutics13010077","article-title":"Whole transcription profile of responders to anti-TNF drugs in pediatric inflammatory bowel disease","volume":"13","author":"Salvador-Mart\u00edn","year":"2021","journal-title":"Pharmaceutics"},{"key":"B58","doi-asserted-by":"publisher","DOI":"10.1093\/ecco-jcc\/jjac190.0033","article-title":"OP33 results of a randomised controlled trial to evaluate interleukin 1 blockade with anakinra in patients with acute severe ulcerative colitis (IASO)","volume":"17","author":"Raine","year":"2023","journal-title":"J Crohn's Colitis"},{"key":"B59","doi-asserted-by":"publisher","first-page":"i478","DOI":"10.1093\/ecco-jcc\/jjad212.0302","article-title":"P172 spatial transcriptomics characterization of S1P pathway genes in ulcerative colitis and Crohn\u2019s disease colon tissues","volume":"18","author":"Zhang","year":"2024","journal-title":"J Crohn's Colitis"},{"key":"B60","doi-asserted-by":"publisher","DOI":"10.1053\/j.gastro.2020.12.031","article-title":"STRIDE-II: An update on the selecting therapeutic targets in inflammatory bowel disease (STRIDE) initiative of the International Organization for the Study of IBD (IOIBD): Determining therapeutic goals for treat-to-target strategies in IBD","volume":"160","author":"Turner","year":"2021","journal-title":"Gastroenterology"},{"key":"B61","doi-asserted-by":"publisher","DOI":"10.1038\/s41596-024-00967-3","article-title":"Stress-free single-cell transcriptomic profiling and functional genomics of murine eosinophils","volume":"19","author":"Borrelli","year":"2024","journal-title":"Nat Protoc"},{"key":"B62","doi-asserted-by":"publisher","DOI":"10.1016\/j.heliyon.2024.e28358","article-title":"Comparative analysis of 10X Chromium vs. BD Rhapsody whole transcriptome single-cell sequencing technologies in complex human tissues","volume":"10","author":"Salcher","year":"2024","journal-title":"Heliyon"},{"key":"B63","doi-asserted-by":"publisher","DOI":"10.2174\/1389202921999200625220812","article-title":"The comparison of two single-cell sequencing platforms: BD Rhapsody and 10x Genomics Chromium","volume":"21","author":"Gao","year":"2020","journal-title":"Curr Genomics"},{"key":"B64","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1186\/s13073-022-01075-1","article-title":"An introduction to spatial transcriptomics for biomedical research","volume":"14","author":"Williams","year":"2022","journal-title":"Genome Med"},{"key":"B65","doi-asserted-by":"publisher","first-page":"597","DOI":"10.1038\/s41575-023-00784-1","article-title":"A roadmap for the human gut cell atlas","volume":"20","author":"Zilbauer","year":"2023","journal-title":"Nat Rev Gastroenterol Hepatol"},{"key":"B66","doi-asserted-by":"publisher","first-page":"2303.16725v1","DOI":"10.1007\/978-3-031-01526-7_4","article-title":"Machine learning for uncovering biological insights in spatial transcriptomics data","author":"Lee","year":"2023","journal-title":"ArXiv"},{"key":"B67","doi-asserted-by":"publisher","first-page":"4452","DOI":"10.1038\/s41467-025-58989-8","article-title":"Combining spatial transcriptomics with tissue morphology","volume":"16","author":"Chelebian","year":"2025","journal-title":"Nat Commun"},{"key":"B68","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-025-08668-x","article-title":"Spatial immune scoring system predicts hepatocellular carcinoma recurrence","volume":"640","author":"Jia","year":"2025","journal-title":"Nature"},{"key":"B69","doi-asserted-by":"publisher","DOI":"10.3389\/fcell.2022.841090","article-title":"Digital spatial profiling reveals functional shift of enterochromaffin cell in patients with ulcerative colitis","volume":"10","author":"Lyu","year":"2022","journal-title":"Front Cell Dev Biol"}],"container-title":["Frontiers in Immunology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fimmu.2026.1794207\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T05:34:46Z","timestamp":1774935286000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fimmu.2026.1794207\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3,31]]},"references-count":69,"alternative-id":["10.3389\/fimmu.2026.1794207"],"URL":"https:\/\/doi.org\/10.3389\/fimmu.2026.1794207","relation":{},"ISSN":["1664-3224"],"issn-type":[{"value":"1664-3224","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,3,31]]},"article-number":"1794207"}}