ArticleCell2024
Charting the cellular biogeography in colitis reveals fibroblast trajectories and coordinated spatial remodeling.
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Article in Cell, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 84 papers.
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84citing papers in PubMed
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84 citing papers in PubMed, 85 citations in OpenAlex.
- Serum Collagen Biomarkers Are Reflective of Tissue Specific Fibroblasts Associated With Ulcerative Colitis Activity and Treatment Response to Ustekinumab.United European gastroenterology journal · 2025Trial
- ResolVI: addressing noise and bias in spatial transcriptomics.Nature methods · 2026Article
- Cellular crosstalk of fibroblast-myofibroblast transition in intestinal homeostasis and disease.Biomarker research · 2026Review
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- RNA-aware tissue preservation workflows for high-quality spatial transcriptomics.bioRxiv : the preprint server for biology · 2026Article
- A spatial and temporal transcriptomic atlas of mouse intestinal regeneration in the jejunum.Nature communications · 2026Article
- scDiagnostics: systematic assessment of cell type annotation in single-cell transcriptomics data.Briefings in bioinformatics · 2026Article
- Epigenetic modulation of stromal cell states underpins pathological tissue niches in Crohn's disease.Nature immunology · 2026Article
- Multi-omics-driven precision medicine.iMeta · 2026Review
- Integrated inference of cellular compositions and gene expression programs by deconvolution.Cell regeneration (London, England) · 2026Article
- Chrono-atlas of cell-type specific daily gene expression rhythms in the regenerating colon.Nature communications · 2026Article
- hoodscanR: profiling single-cell neighborhoods in spatial transcriptomics data.Bioinformatics (Oxford, England) · 2026Article
- Single-cell spatial transcriptomics of formalin-fixed, paraffin-embedded biopsies reveals colitis-associated cell networks.The Journal of clinical investigation · 2026Article
- Intestinal muscularis in health and disease.Communications biology · 2026Review
- Article
- Dermal fibroblasts attenuate osteoarthritis by restoring synovial fibroblast homeostasis.Journal of orthopaedic translation · 2026Article
- Spatial co-expression and cell-cell communication inference from spatially resolved transcriptomics with CONCISE.bioRxiv : the preprint server for biology · 2026Article
- Article
- Targeted and quantitatively modeled biologic delivery via dual-functional probiotic yeast in inflammatory bowel disease.Journal of controlled release : official journal of the Controlled Release Society · 2026Article
- Multi-omics reveals fibroblast subtypes with distinct roles in inflammatory bowel disease.Biology direct · 2026Article
24 more citing papers are in PubMed but not listed here.
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Authors and funding
21 authors at 7 institutions in 1 country.
Paolo CadinuProgram in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
Kisha N SivanathanGene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
Aditya MisraGene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
Rosalind J XuProgram in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
Davide ManganiGene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA.
Evan YangProgram in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
Joseph M RoneGene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
Katherine TooleyGene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA.
Yoon-Chul KyeGene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA.
Lloyd BodGene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA.
Ludwig GeistlingerCenter for Computational Biomedicine, Harvard Medical School, Boston, MA 02115, USA.
Tyrone LeeCenter for Computational Biomedicine, Harvard Medical School, Boston, MA 02115, USA.
Randall T MertensGene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
Noriaki OnoUniversity of Texas Health Science Center at Houston School of Dentistry, Houston, TX 77030, USA.
Gang WangDepartment of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
Liliana SanmarcoGene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA.
Francisco J QuintanaGene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
Ana C AndersonGene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
Vijay K KuchrooGene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
Jeffrey R MoffittProgram in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. Electronic address: jeffrey.moffitt@childrens.harvard.edu.
Roni NowarskiGene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. Electronic address: rnowarski@bwh.harvard.edu.
Harvard University · USBrigham and Women's Hospital · USMassachusetts General Hospital · USBoston VA Research Institute · USBoston Children's Hospital · USBroad Institute · USThe University of Texas Health Science Center at Houston · US
Funding
STRUCTURE-FUNCTION RELATIONSHIPS IN THE ALIMENTARY TRACTP30DK034854 · NIDDK · HARVARD UNIVERSITY (MEDICAL SCHOOL) · PI JONATHAN C KAGAN · 1986 to 2026
$32.4MSystematic dissection of gut cellular circuits [at single cell resolution]RC2DK114784 · NIDDK · BROAD INSTITUTE, INC. · PI ASHENBERG, ORR, GRAHAM, DANIEL BARTHOLOMEW · 2017 to 2021
$9.0MNeuroimmune interactions regulate development of allergic inflammationR01AI139536 · NIAID · BRIGHAM AND WOMEN'S HOSPITAL · PI KUCHROO, VIJAY K. · 2018 to 2022
$2.9MMetabolic regulators of Treg/Th17 balance in CNS autoimmunityR01AI169075 · NIAID · BRIGHAM AND WOMEN'S HOSPITAL · PI VIJAY K. KUCHROO · 2022 to 2026
$2.8MMechanisms of Tissue Immune Regulation in Sepsis and Local InfectionR35GM133800 · NIGMS · BRIGHAM AND WOMEN'S HOSPITAL · PI Roni Nowarski · 2019 to 2026
$2.6MRole of Tim-l in B Cells in regulating autoimmunity in the CNSR01AI185514 · NIAID · BRIGHAM AND WOMEN'S HOSPITAL · PI VIJAY K. KUCHROO · 2024 to 2026
$1.9MRapid, Robust, and Routine: Multiplexed Microscopy for Spatially Resolved Whole-Transcriptomic Single-Cell Profiling and the Construction of Cell Atlases of all Tissues and in all OrganismsR01GM143277 · NIGMS · BOSTON CHILDREN'S HOSPITAL · PI MOFFITT, JEFFREY · 2021 to 2024
$1.6MNIAID NIH HHS R01 AI139536NIAID NIH HHS R01 AI169075NIAID NIH HHS R01 AI185514NIDDK NIH HHS P30 DK034854NIDDK NIH HHS RC2 DK114784NIGMS NIH HHS R01 GM143277NIGMS NIH HHS R35 GM133800
Abstract
Gut inflammation involves contributions from immune and non-immune cells, whose interactions are shaped by the spatial organization of the healthy gut and its remodeling during inflammation. The crosstalk between fibroblasts and immune cells is an important axis in this process, but our understanding has been challenged by incomplete cell-type definition and biogeography. To address this challenge, we used multiplexed error-robust fluorescence in situ hybridization (MERFISH) to profile the expression of 940 genes in 1.35 million cells imaged across the onset and recovery from a mouse colitis model. We identified diverse cell populations, charted their spatial organization, and revealed their polarization or recruitment in inflammation. We found a staged progression of inflammation-associated tissue neighborhoods defined, in part, by multiple inflammation-associated fibroblasts, with unique expression profiles, spatial localization, cell-cell interactions, and healthy fibroblast origins. Similar signatures in ulcerative colitis suggest conserved human processes. Broadly, we provide a framework for understanding inflammation-induced remodeling in the gut and other tissues.
Indexed as
ColitisColitis, UlcerativeAnimalsCell CommunicationFibroblastsGastrointestinal TractHumansInflammationIn Situ Hybridization, FluorescenceMice
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