Molly Fisher Thomas1-5*†, Kamil Slowikowski1-4*†, Kasidet Manakongtreecheep1-3, Pritha Sen1-4,6, Nandini Samanta1-3, Jessica Tantivit1-3, Mazen Nasrallah1-4,7, Leyre Zubiri2,4, Neal P. Smith1-3, Alice Tirard1-3, Swetha Ramesh1-3, Benjamin Y. Arnold1-3, Linda T. Nieman2, Jon athan H. Chen2-4,8, Thomas Eisenhaure3, Karin Pelka2-4, Yuhui Song2, Katherine H. Xu2, Vjola Jorgji2,8, Christopher J. Pinto2,9, Tatyana Sharova9, Rachel Glasser5, PuiYee Chan2,4, Ryan J. Sullivan2,4, Hamed Khalili3-5, Dejan Juric2-4, Genevieve M. Boland2,4,10, Michael Dougan4-5, Nir Hacohen2-4, Bo Li1,3,11, Kerry L. Reynolds2,4‡, and Alexandra-Chloé Villani1-4,7‡†
* These authors contributed equally: Molly Fisher Thomas, Kamil Slowikowski
‡These authors contributed equally: Kerry Reynolds, Alexnandra-Chloé Villani
† Correspondence to: mfthomas@partners.org; kslowikowski@mgh.harvard.edu; avillani@mgh.harvard.edu
bioRxiv 2021. doi: 10.1101/2021.09.17.460868
Abstract
Therapeutic immune checkpoint blockade has revolutionized oncology, but treatments are limited by immune-related adverse events, including checkpoint inhibitor colitis (irColitis). To define molecular drivers of irColitis, we profiled ~300,000 cells from the colon mucosa and blood of 29 patients and controls. Patients with irColitis showed expanded mucosal Tregs, ITGAEHi CD8 tissue-resident memory T cells expressing CXCL13 and Th17 gene programs, and circulating ITGB2Hi CD8 T cells recruited by ICAM and CXCR3 ligands. Cytotoxic GNLYHi CD4 T cells, ITGB2Hi CD8 T cells from circulation, and endothelial cells associated with hypoxia gene programs were further expanded in colitis associated with anti-PD-1/CTLA-4 compared to anti-PD-1 therapy. Luminal epithelial cells in irColitis patients expressed PD-L1 and interferon-induced signatures associated with apoptosis, increased cell turnover, and malabsorption. Together, we highlight novel roles for circulating T cells and epithelial-immune crosstalk critical to PD-1/CTLA-4-dependent tolerance and barrier function and nominate novel irColitis therapeutic targets.
On this website, we provide interactive data browsers to view all of the transcriptomics data for each of the manually curated cell clusters.
Metadata variables and gene expression in two-dimensional embeddings.
Tissue immune cells:
Tissue epithelial and mesenchymal nuclei:
Differential expression statistics for all genes:
Here is the original preprint we posted to bioRxiv in 2021:
@UNPUBLISHED{Thomas2021,
title = "{Altered interactions between circulating and tissue-resident CD8
T cells with the colonic mucosa define colitis associated with
immune checkpoint inhibitors}",
author = "Thomas, Molly Fisher and Slowikowski, Kamil and
Manakongtreecheep, Kasidet and Sen, Pritha and Tantivit, Jessica
and Nasrallah, Mazen and Smith, Neal P and Ramesh, Swetha and
Zubiri, Leyre and Tirard, Alice and Arnold, Benjamin Y and
Nieman, Linda T and Chen, Jonathan H and Eisenhaure, Thomas and
Pelka, Karin and Xu, Katherine H and Jorgji, Vjola and Pinto,
Christopher J and Sharova, Tatyana and Glasser, Rachel and Chan,
Elaina Puiyee and Sullivan, Ryan J and Khalili, Hamed and Juric,
Dejan and Boland, Genevieve M and Dougan, Michael and Hacohen,
Nir and Reynolds, Kerry L and Li, Bo and Villani,
Alexandra-Chlo{\'e}",
journal = "bioRxiv",
pages = "2021.09.17.460868",
month = sep,
year = 2021,
language = "en",
doi = "10.1101/2021.09.17.460868"
}
Analysis result files are available at Zenodo: 10.5281/zenodo.8088435
Single-cell expression data files are available at NCBI GEO: GSE206301
Sequencing reads are available at dbGAP: phs003418.v1.p1
The code for our analysis and for this website is available at GitHub: github.com/villani-lab/ircolitis
Please contact us with any questions or comments.
The data presented here comes from the laboratory of Dr. Alexandra-Chloé Villani.
This site was made by Kamil Slowikowski