ArticleCell2019
Single-Cell Analysis of Crohn's Disease Lesions Identifies a Pathogenic Cellular Module Associated with Resistance to Anti-TNF Therapy.
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In one paragraph
Article in Cell, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 561 papers, 1 of them a synthesis that pooled it.
0numbers the graph read from it
0cells of the map it votes in
561citing papers in PubMed, 1 pooled it
32.7field-weighted citation impact, top 1% of its field
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
561 citing papers in PubMed, 1 synthesis or guideline pooled it, 866 citations in OpenAlex.
- Multi-Omics Biomarkers for Predicting Efficacy of Biologic and Small-Molecule Therapies in Adults With Inflammatory Bowel Disease: A Systematic Review.United European gastroenterology journal · 2025Pooled it
- Serum Collagen Biomarkers Are Reflective of Tissue Specific Fibroblasts Associated With Ulcerative Colitis Activity and Treatment Response to Ustekinumab.United European gastroenterology journal · 2025Trial
- Metabolism and response to stress gene signatures reveal ulcerative colitis heterogeneity and identify patients with increased response to therapy.Journal of Crohn's & colitis · 2025Trial
- Trial
- Gut Microbial Species and Endotypes Associate with Remission in Ulcerative Colitis Patients Treated with Anti-TNF or Anti-integrin Therapy.Journal of Crohn's & colitis · 2024Trial
- A Modelling Approach to Resolve Gene Temporal Dynamics in Intestinal Inflammation.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Crosstalk between the microbiota and intestinal γδ T cell compartments in health and IBD.Gut microbes · 2026Review
- Enhanced therapeutic efficacy of granulocyte/monocyte adsorption in rats with drug-induced colitis : Insights from a downsized bead column and newly formed B cells.Therapeutic apheresis and dialysis : official peer-reviewed journal of the International Society for Apheresis, the Japanese Society for Apheresis, the Japanese Society for Dialysis Therapy · 2026Article
- Engineering immune cell therapies for inflammatory bowel disease: from stem cells to CAR T cells.Nature reviews. Gastroenterology & hepatology · 2026Review
- Assembled Hyaluronic Acid Therapeutics for Targeting M1 Macrophages and Regulating Immune Homeostasis for Ulcerative Colitis Treatment.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Single-cell immune repertoire atlas maps coordinated circulating adaptive immune states in inflammatory bowel disease.bioRxiv : the preprint server for biology · 2026Article
- Persistence of mucosal CAR-T cells and inflammatory remodeling in enterocolitis associated with BCMA CAR-T cell therapy.Nature medicine · 2026Article
- Systemic reprogramming of monocytes in Crohn's disease promotes their intestinal inflammatory function.JCI insight · 2026Article
- Uninflamed colonic tissue harbors humoral activity linked to anti-TNF therapy non-response in ulcerative colitis.iScience · 2026Article
- Identification of Ferro-Aging-Related Biomarkers for Ulcerative Colitis Through Integrated Machine Learning, Single-Cell Analysis, and Spatial Transcriptomics.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026Article
- IL1B-high macrophages promote ferroptosis-like lipid peroxidation injury in Crohn's disease intestinal epithelium.Redox biology · 2026Article
- Macrophage heterogeneity in human secondary lymphoid organs.Clinical science (London, England : 1979) · 2026Review
- Concerted changes in the pediatric single-cell intestinal ecosystem before and after anti-TNF blockade.eLife · 2026Article
- Epigenetic modulation of stromal cell states underpins pathological tissue niches in Crohn's disease.Nature immunology · 2026Article
- Review
501 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
31 authors at 6 institutions in 1 country.
Jerome C MartinPrecision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Christie ChangPrecision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Gilles BoschettiPrecision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Ryan UngaroThe Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA.
Mamta GiriCharles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
John A GroutPrecision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Kyle GettlerCharles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Ling-Shiang ChuangCharles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Shikha NayarCharles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Alexander J GreensteinDepartment of Colorectal Surgery, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Marla DubinskyDepartment of Pediatrics, Susan and Leonard Feinstein IBD Clinical Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Laura WalkerHuman Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Andrew LeaderPrecision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Jay S FineBoehringer Ingelheim Pharmaceuticals, Immunology and Respiratory Diseases Research, Ridgefield, CT 06877, USA.
Charles E WhitehurstBoehringer Ingelheim Pharmaceuticals, Immunology and Respiratory Diseases Research, Ridgefield, CT 06877, USA.
M Lamine MbowBoehringer Ingelheim Pharmaceuticals, Immunology and Respiratory Diseases Research, Ridgefield, CT 06877, USA.
Subra KugathasanDivision of Pediatric Gastroenterology, Emory University School of Medicine, Atlanta, GA, USA.
Lee A DensonDivision of Pediatric Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH, USA.
Jeffrey S HyamsDivision of Digestive Diseases, Hepatology, and Nutrition, Connecticut Children's Medical Center, Hartford, CT, USA.
Joshua R FriedmanJanssen Research and Development, Spring House, PA, USA.
Prerak T DesaiJanssen Research and Development, Spring House, PA, USA.
Huaibin M KoThe Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA; Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Ilaria LafacePrecision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Guray AkturkPrecision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Eric E SchadtDepartment of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Helene SalmonPrecision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Sacha GnjaticPrecision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Division of Hematology Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Adeeb H RahmanPrecision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Miriam MeradPrecision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Electronic address: miriam.merad@mssm.edu.
Judy H ChoCharles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Electronic address: judy.cho@mssm.edu.
Ephraim KenigsbergPrecision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Electronic address: ephraim.kenigsberg@mssm.edu.
Icahn School of Medicine at Mount Sinai · USBoehringer Ingelheim (United States) · USJanssen (United States) · USCincinnati Children's Hospital Medical Center · USConnecticut Children's Medical Center · USEmory University · US
Funding
Viral Assays CoreU19AI128949 · NIAID · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI Donna L. Farber, Peter Alan Sims · 2017 to 2026
$26.4MHigh-Dimensional Immune Monitoring of NCI-Supported Immunotherapy TrialsU24CA224319 · NCI · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI Sacha Gnjatic, Seunghee Kim-Schulze · 2017 to 2026
$21.5MInflammatory Bowel Disease Genetics Consortium Data Coordinating CenterU01DK062429 · NIDDK · YALE UNIVERSITY · PI CHO, JUDY H. · 2002 to 2016
$16.8MPrecision IBD via genetics and genomics: integrating International and multi-omic datasets, expanding studies in diverse populations, and defining mechanisms of unmet clinical needs in IBDU24DK062429 · NIDDK · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI Ling-shiang Chuang, Ron Do · 2017 to 2026
$13.9MTRAINING PROGRAM IN CANCER THERAPYT32CA078207 · NCI · MOUNT SINAI SCHOOL OF MEDICINE OF NYU · PI James J Manfredi · 1999 to 2026
$11.6MYale University Inflammatory Bowel Disease Genetics Research CenterU01DK062422 · NIDDK · YALE UNIVERSITY · PI Ling-shiang Chuang · 2002 to 2026
$10.8MIntegrative Genomic Analyses of Macrophages in Crohns DiseaseR01DK106593 · NIDDK · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI CHO, JUDY H. · 2016 to 2020
$3.8MNovel tools to maximize profiling of tissue and antigen specific immune dysregulation in allergy and inflammatory bowel disesaseU24AI118644 · NIAID · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI BERIN, CECILIA, MERAD, MIRIAM · 2015 to 2020
$2.4MThe Immune Cell Atlas â A Robust Framework to Map the Entire Human Immune SystemR56AI137244 · NIAID · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI BENOIST, CHRISTOPHE O., HACOHEN, NIR · 2018 to 2018
$2.0MTransforming Genomics with 5 PB Big Omics Data Engine Cray CS300-AC SupercomputerS10OD018522 · OD · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI KOVATCH, PATRICIA · 2014 to 2014
$1.9MHarnessing Csf-2 compartmentalized role on tissue resident phagocytes to uncouple anti-tumoral from pathological immunity induced by checkpoint inhibitorsR01CA190400 · NCI · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI MERAD, MIRIAM · 2015 to 2019
$1.9MAssessing Predictors of Response to Anti-Tumor Necrosis Alpha Therapy in Early Crohns DiseaseK23DK111995 · NIDDK · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI UNGARO, RYAN · 2019 to 2023
$948kNCI NIH HHS R01 CA190400NCI NIH HHS T32 CA078207NCI NIH HHS U24 CA224319NIAID NIH HHS R56 AI137244NIAID NIH HHS U19 AI128949NIAID NIH HHS U24 AI118644NIDDK NIH HHS K23 DK111995NIDDK NIH HHS R01 DK106593NIDDK NIH HHS U01 DK062422NIDDK NIH HHS U01 DK062429NIDDK NIH HHS U24 DK062429NIH HHS S10 OD018522NIH HHS S10 OD023547
Abstract
Clinical benefits of cytokine blockade in ileal Crohn's disease (iCD) are limited to a subset of patients. Here, we applied single-cell technologies to iCD lesions to address whether cellular heterogeneity contributes to treatment resistance. We found that a subset of patients expressed a unique cellular module in inflamed tissues that consisted of IgG plasma cells, inflammatory mononuclear phagocytes, activated T cells, and stromal cells, which we named the GIMATS module. Analysis of ligand-receptor interaction pairs identified a distinct network connectivity that likely drives the GIMATS module. Strikingly, the GIMATS module was also present in a subset of patients in four independent iCD cohorts (n = 441), and its presence at diagnosis correlated with failure to achieve durable corticosteroid-free remission upon anti-TNF therapy. These results emphasize the limitations of current diagnostic assays and the potential for single-cell mapping tools to identify novel biomarkers of treatment response and tailored therapeutic opportunities.
Indexed as
Crohn DiseaseCytokinesHumansImmunotherapyIntestinesPhagocytesSingle-Cell AnalysisStromal CellsT-LymphocytesTumor Necrosis Factor-alphaCytokinesTumor Necrosis Factor-alphaCrohn’s diseasehigh-dimensional profilinginflammatory bowel diseasemolecular classificationsingle-cell RNA sequencing
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