Altered interactions between circulating and tissue-resident CD8 T cells with the colonic mucosa define checkpoint inhibitor colitis

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‡†

Author affiliations

  • 1 - Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
  • 2 - Massachusetts General Hospital, Cancer Center, Boston, MA, USA
  • 3 - Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
  • 4 - Harvard Medical School, Boston, MA, USA
  • 5 - Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
  • 6 - Division of Infectious Disease, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
  • 7 - Division of Rheumatology, North Shore Physicians Group, Department of Medicine, Mass General Brigham Healthcare Center, Lynn, MA, USA
  • 8 - Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
  • 9 - Clinical Research Center, Massachusetts General Hospital, Boston, MA, USA
  • 10 - Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
  • 11 - Current address: Genentech, 1 DNA Way, South San Francisco, CA, 94080

* 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

Nature Medicine 2024. doi: 10.1038/s41591-024-02895-x

Figure 1 from Thomas et al. 2021.

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.

🔬 View the data

On this website, we provide interactive data browsers to view all of the transcriptomics data for each of the manually curated cell clusters.

Cell Clusters

Metadata variables and gene expression in two-dimensional embeddings.

Tissue immune cells:

  • CD8 T cells, CD4 T cells, Myeloid cells, B cells

Tissue epithelial and mesenchymal nuclei:

  • 23 types of epithelial and mesenchymal nuclei
Blood immune cells:
  • CD8 T cells, CD4 T cells, Myeloid cells, B cells
View Cell Clusters

Gene Contrasts

Differential expression statistics for all genes:

  • 3 contrasts
    • irColitis Case vs Control
    • Case PD1/CTLA4 vs Case PD1
    • Control PD1 vs Control None
  • 9 major cell lineages
  • 105 cell clusters
View Gene Contrasts

📝 Cite our work

Here is the how you should cite this work:

BibTeX

@ARTICLE{Thomas2024-lk,
  title     = "{Single-cell transcriptomic analyses reveal distinct immune cell
               contributions to epithelial barrier dysfunction in checkpoint
               inhibitor colitis}",
  author    = "Thomas, Molly Fisher and Slowikowski, Kamil and
               Manakongtreecheep, Kasidet and Sen, Pritha and Samanta, Nandini
               and Tantivit, Jessica and Nasrallah, Mazen and Zubiri, Leyre and
               Smith, Neal P and Tirard, Alice and Ramesh, Swetha and Arnold,
               Benjamin Y and Nieman, Linda T and Chen, Jonathan H and
               Eisenhaure, Thomas and Pelka, Karin and Song, Yuhui and Xu,
               Katherine H and Jorgji, Vjola and Pinto, Christopher J and
               Sharova, Tatyana and Glasser, Rachel and Chan, Puiyee and
               Sullivan, Ryan J and Khalili, Hamed and Juric, Dejan and Boland,
               Genevieve M and Dougan, Michael and Hacohen, Nir and Li, Bo and
               Reynolds, Kerry L and Villani, Alexandra-Chloé",
  journal   = "Nature Medicine",
  publisher = "Nature Publishing Group",
  pages     = "1--14",
  abstract  = "Immune checkpoint inhibitor (ICI) therapy has revolutionized
               oncology, but treatments are limited by immune-related adverse
               events, including checkpoint inhibitor colitis (irColitis).
               Little is understood about the pathogenic mechanisms driving
               irColitis, which does not readily occur in model organisms, such
               as mice. To define molecular drivers of irColitis, we used
               single-cell multi-omics to profile approximately 300,000 cells
               from the colon mucosa and blood of 13 patients with cancer who
               developed irColitis (nine on anti-PD-1 or anti-CTLA-4 monotherapy
               and four on dual ICI therapy; most patients had skin or lung
               cancer), eight controls on ICI therapy and eight healthy
               controls. Patients with irColitis showed expanded mucosal Tregs,
               ITGAEHi CD8 tissue-resident memory T cells expressing CXCL13 and
               Th17 gene programs and recirculating ITGB2Hi CD8 T cells.
               Cytotoxic GNLYHi CD4 T cells, recirculating ITGB2Hi CD8 T cells
               and endothelial cells expressing hypoxia gene programs were
               further expanded in colitis associated with anti-PD-1/CTLA-4
               therapy compared to anti-PD-1 therapy. Luminal epithelial cells
               in patients with irColitis expressed PCSK9, PD-L1 and
               interferon-induced signatures associated with apoptosis,
               increased cell turnover and malabsorption. Together, these data
               suggest roles for circulating T cells and epithelial–immune
               crosstalk critical to PD-1/CTLA-4-dependent tolerance and barrier
               function and identify potential therapeutic targets for
               irColitis. Single-cell multi-omic analysis of 300,000 cells from
               29 patients representing peripheral immune cells and colon
               mucosal immune, epithelial and mesenchymal cells reveals
               crosstalk between circulating and tissue-resident immune cells
               with epithelial cells in checkpoint inhibitor colitis and
               identifies potential therapeutic targets.",
  month     =  may,
  year      =  2024,
  doi       = "10.1038/s41591-024-02895-x",
  issn      = "1546-170X,1546-170X",
  language  = "en"
}
            

💾 Download the data

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

💻 Read the source code

The code for our analysis and for this website is available at GitHub: github.com/villani-lab/ircolitis

✉ Contact us

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