Concerted changes in the pediatric single-cell intestinal ecosystem before and after anti-TNF blockade
Hengqi Betty Zheng, Benjamin A. Doran, Kyle Kimler, Alison Yu, Victor Tkachev, Veronika Niederlova, Kayla Cribbin, Ryan Fleming, Brandi Bratrude, Kayla Betz, Lorenzo Cagnin, Connor McGuckin, Paula Keskula, Alexandre Albanese, Maria Sacta, Joshua de Sousa Casal, Ruben van Esch, Andrew C. Kwong, Conner Kummerlowe, Faith Taliaferro, Nathalie Fiaschi, Baijun Kou, Sandra Coetzee, Sumreen Jalal, Yoko Yabe, Michael Dobosz, Matthew F. Wipperman, Sara Hamon, George D. Kalliolias, Andrea Hooper, Wei Keat Lim, Sokol Haxhinasto, Yi Wei, Madeline Ford, Lusine Ambartsumyan, David L. Suskind, Dale Lee, Gail Deutsch, Xuemei Deng, Lauren V. Collen, Vanessa Mitsialis, Scott B. Snapper, Ghassan Wahbeh, Alex K. Shalek, Jose Ordovas-Montanes, Leslie S. Kean
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-naïve 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 (FGID; 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-naïve 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-naïve 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-naïve pediCD and on-treatment adult CD. We identify that anti-TNF treatment pushes the pediatric cellular ecosystem towards an adult, more treatment-refractory state. Our study jointly leverages a treatment-naïve cohort, high-resolution principled scRNA-seq data analysis, and clinical outcomes to understand which baseline cell states may predict Crohn’s disease trajectory.
Datasets
1. 3-prime FGID data
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Source data
https://cellxgene.cziscience.com/collections/a064d795-3b77-44ae-9fb5-beb57c567443
Alias names
SCP1422
Cite this study
Zheng, H.B., Doran, B.A., Kimler, K., Yu, A., Tkachev, V., Niederlova, V., Cribbin, K., Fleming, R., Bratrude, B., Betz, K. and Cagnin, L., 2021. Concerted changes in the pediatric single-cell intestinal ecosystem before and after anti-TNF blockade. medRxiv, pp.2021-09. https://doi.org/10.1101/2021.09.17.21263540