Concerted changes in the pediatric single-cell intestinal ecosystem before and after anti-TNF blockade

Crohn’s disease is an inflammatory bowel disease (IBD) commonly treated through anti-TNF blockade. However, most patients still relapse and inevitably progress. Comprehensive single-cell RNA-sequencing (scRNA-seq) atlases have largely sampled patients with established treatment-refractory IBD, limiting our understanding of which cell types, subsets, and states at diagnosis anticipate disease severity and response to treatment. Here, through combining clinical, flow cytometry, histology, and scRNA-seq methods, we profile diagnostic human biopsies from the terminal ileum of treatment-naive pediatric patients with Crohn’s disease (pediCD; n = 14), matched repeat biopsies (pediCD-treated; n = 8) and from non-inflamed pediatric controls with functional gastrointestinal disorders (FGIDs; n = 13). To resolve and annotate epithelial, stromal, and immune cell states among the 201,883 baseline single-cell transcriptomes, we develop a principled and unbiased tiered clustering approach, ARBOL. Through flow cytometry and scRNA-seq, we observe that treatment-naive pediCD and FGID have similar broad cell type composition. However, through high-resolution scRNA-seq analysis and microscopy, we identify significant differences in cell subsets and states that arise during pediCD relative to FGID. By closely linking our scRNA-seq analysis with clinical meta-data, we resolve a vector of T cell, innate lymphocyte, myeloid, and epithelial cell states in treatment-naive pediCD (pediCD-TIME) samples, which can distinguish patients along the trajectory of disease severity and anti-TNF response. By using ARBOL with integration, we position repeat on-treatment biopsies from our patients between treatment-naive pediCD and on-treatment adult CD. We identify that anti-TNF treatment pushes the pediatric cellular ecosystem toward an adult, more treatment-refractory state. Our study jointly leverages a treatment-naive cohort, high-resolution principled scRNA-seq data analysis, and clinical outcomes to understand which baseline cell states may predict Crohn’s disease trajectory.

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Publication Details

Journal
eLife
Published
2026-09-01
DOI
https://doi.org/10.7554/elife.91792.3
Primary Topic
Single-cell and spatial transcriptomics
Type
article
Field-Weighted Citation Impact
0.00

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article

Concerted changes in the pediatric single-cell intestinal ecosystem before and after anti-TNF blockade

Matthew F. Wipperman, Victor Tkachev, Brandi Bratrude, Kayla Cribbin et al.
eLife
Single-cell and spatial transcriptomics
article

Concerted changes in the pediatric single-cell intestinal ecosystem before and after anti-TNF blockade

Matthew F. Wipperman, Victor Tkachev, Brandi Bratrude, Kayla Cribbin, George D. Kalliolias, Gail H. Deutsch, Yoko Yabe, Sara Hamon, Leslie S. Kean, Andrew C. Kwong, Xuemei Deng, Vanessa Mitsialis, Alison Yu, Michael Dobosz, Conner Kummerlowe, Ruben van Esch, Alexandre Albanese, David L. Suskind, Veronika Niederlová, Scott B. Snapper, Baijun Kou, Madeline Ford, Lusine Ambartsumyan, Paula Keskula, Hengqi Zheng, José Ordovás-Montañés, Sumreen Jalal, Benjamin A. Doran, Faith Taliaferro, Nathalie Fiaschi, Joshua de Sousa Casal, Alex K. Shalek, Sandra Coetzee, Lauren V. Collen, Wei Keat Lim, Lorenzo Cagnin, Ryan Fleming, Andrea Hooper, Ghassan Wahbeh, Dale Lee, Maria Sacta, Yi Wei, Kyle Kimler, Connor McGuckin, Kayla Betz, Sokol Haxhinasto
article en

Abstract

Crohn’s disease is an inflammatory bowel disease (IBD) commonly treated through anti-TNF blockade. However, most patients still relapse and inevitably progress. Comprehensive single-cell RNA-sequencing (scRNA-seq) atlases have largely sampled patients with established treatment-refractory IBD, limiting our understanding of which cell types, subsets, and states at diagnosis anticipate disease severity and response to treatment. Here, through combining clinical, flow cytometry, histology, and scRNA-seq methods, we profile diagnostic human biopsies from the terminal ileum of treatment-naive pediatric patients with Crohn’s disease (pediCD; n = 14), matched repeat biopsies (pediCD-treated; n = 8) and from non-inflamed pediatric controls with functional gastrointestinal disorders (FGIDs; n = 13). To resolve and annotate epithelial, stromal, and immune cell states among the 201,883 baseline single-cell transcriptomes, we develop a principled and unbiased tiered clustering approach, ARBOL. Through flow cytometry and scRNA-seq, we observe that treatment-naive pediCD and FGID have similar broad cell type composition. However, through high-resolution scRNA-seq analysis and microscopy, we identify significant differences in cell subsets and states that arise during pediCD relative to FGID. By closely linking our scRNA-seq analysis with clinical meta-data, we resolve a vector of T cell, innate lymphocyte, myeloid, and epithelial cell states in treatment-naive pediCD (pediCD-TIME) samples, which can distinguish patients along the trajectory of disease severity and anti-TNF response. By using ARBOL with integration, we position repeat on-treatment biopsies from our patients between treatment-naive pediCD and on-treatment adult CD. We identify that anti-TNF treatment pushes the pediatric cellular ecosystem toward an adult, more treatment-refractory state. Our study jointly leverages a treatment-naive cohort, high-resolution principled scRNA-seq data analysis, and clinical outcomes to understand which baseline cell states may predict Crohn’s disease trajectory.

eLifeVol. 12
Broad Institute (US), Brigham and Women's Hospital (US), Boston Children's Hospital (US), Harvard University (US), Regeneron (United States) (US), Ragon Institute of MGH, MIT and Harvard (US), University Medical Center Utrecht (NL), Seattle Children's Hospital (US), Dana-Farber Cancer Institute (US), Institute of Molecular Genetics (RU), Harvard Stem Cell Institute (US), Massachusetts Institute of Technology (US)
Food Allergy Science Initiative, Pew Charitable Trusts, Alfred P. Sloan Foundation, Arnold and Mabel Beckman Foundation, Richard and Susan Smith Family Foundation, New York Stem Cell Foundation, AGA Research Foundation, Leona M. and Harry B. Helmsley Charitable Trust, Broad Institute, Searle Scholars Program, Manton Foundation, National Institutes of Health, Harvard Digestive Diseases Center, Harvard University, National Heart, Lung, and Blood Institute
Openalex Percentile: Top 18%
Single-cell and spatial transcriptomics
DOIOpen Access PDFOpenAlex
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