Tracking In Situ Checkpoint Inhibitor-Bound Target T Cells in Patients with Checkpoint-Induced Colitis

Rheumatology and Immunology Gastroenterology Medicine Biochemistry Life Sciences Immunology
Checkpoint inhibitors T cells Colitis Single-cell transcriptomics Spatial transcriptomics Immune-related adverse events

Tracking In Situ Checkpoint Inhibitor-Bound Target T Cells

Title Page

Academic Background

Checkpoint inhibitors (CPIs) have revolutionized cancer treatment by blocking immune regulatory signals mediated by checkpoint molecules, restoring T cell-mediated tumor clearance. However, these therapies also lead to a range of immune-related adverse events (IRAEs), with gastrointestinal inflammation being the most common, affecting approximately 60% of patients. While IRAEs in the gut, skin, and joints have been associated with improved cancer survival rates, their severe side effects significantly increase the medical burden. Although the specific immune mechanisms leading to IRAEs remain unclear, they may be triggered by dysregulated activation of T cells responding to self-antigens or commensal microbes.

CTLA-4 (cytotoxic T-lymphocyte associated protein 4), PD-1 (programmed cell death protein 1), and its ligand PD-L1 are major immune checkpoints targeted by CPIs, whose expression on T cells increases with activation. CTLA-4 competes with CD28 for the co-stimulatory ligands CD80 and CD86, whereas PD-1 binds to its ligands PD-L1 and PD-L2 for inhibitory T cell receptor (TCR) signaling. These actions promote T cell exhaustion and suppress T cell-mediated tumor clearance. Anti-CTLA-4 and PD-1 reverse these effects, restoring T cell responsiveness to tumor antigens. CPI-mediated IRAEs are believed to be driven by similar principles.

Research Source

This paper, authored by Tarun Gupta, Agne Antanaviciute, Chloe Hyun-Jung Lee, and others from the Oxford University’s Molecular Medicine MRC Weatherall Institute and the Translational Immunology Discovery Unit at the Oxford University-affiliated John Radcliffe Hospital, was published in Cancer Cell on May 13, 2024. The paper is titled “Tracking in situ checkpoint inhibitor-bound target T cells in patients with checkpoint-induced colitis.”

Research Details

Research Process

In this study, the authors tracked CPI-bound T cells in the blood and intestinal tissues of patients who developed colitis after receiving CPIs, using multimodal single-cell RNA sequencing (scRNA-seq) and subcellular spatial transcriptomics (ST), to investigate their role in colitis.

  1. Building a Single-Cell Reference Atlas:
    • Samples included colonic and peripheral blood mononuclear cells (PBMCs) from patients who received mono- (anti-PD-1, nivolumab or pembrolizumab) and dual (anti-PD-1 and anti-CTLA-4, ipilimumab) CPI therapies, healthy controls, CPI patients who did not develop colitis, and non-CPI treated inflammatory controls (ulcerative colitis, UC).
    • The single-cell atlas covered samples from 72 donors containing 186,838 cells, encompassing subtypes of epithelial, stromal, and immune cells.
    • Clustering analysis identified various expected cell types in the colon, with specific “activated” stromal clusters and phenotypically transformed epithelial, glial, endothelial, and macrophage cells particularly in CPI-colitis samples.
  2. Conducting Spatial Transcriptomics Analysis:
    • Involving 18 tissue sections from 16 donors, integrating 25,672 spatial transcriptomics spots revealed 19 united spatial regions enriched by anatomical or representative cell types.
    • Identified co-existing cell types reflecting colonic structures, such as apex crypt cells and deep crypt cells.
    • High-resolution subcellular ST data further captured all key cell populations, including traditionally hard-to-capture neutrophils and subdivisions.
  3. Detecting CPI-Bound Single Cells:
    • Sequenced a total of 72,561 CD3+ T cells from colorectal biopsy and 36,176 matched PBMCs, allowing tracking of T cell clones in the colon and blood.
    • CITE-seq analysis showed reduced PD-1 antibody binding in most CPI-colitis samples compared to non-CPI treated controls, along with decreased correlation between PD-1 mRNA and protein detection.
    • Quantum regression random forest model predicted PD-1 expression in non-CPI treated samples, identifying potential CPI-bound cells.
  4. Comparing T Cell States in Colitis Samples:
    • Found CPI-bound cells mainly among CD4+ T cells (including Tregs, TFH, TH17, etc.) and specific CD8+ T cell subsets.

Main Findings

The study illustrated the distribution characteristics of CPI-bound target cells in inflammatory and non-inflammatory tissues, defining the pathogenic cellular niches contributing to colitis and their comparison with UC.

  1. Multimodal Analysis Identifies Pathogens and Pathways:
    • CPI-bound T cells mainly comprised CD4+ T cells (including peripheral helper T cells, follicular helper T cells, regulatory T cells).
    • IFN-γ CD8+ T cells derived from tissue-resident memory (TRM) and peripheral populations had more restricted target occupancy, colocating with damaged epithelial niches lacking effective regulatory signals.
    • CPI-bound CD4+ TH17 cells were primary IFN-γ sources in colitis.
  2. Revealed Specific Distribution of T Cell Subtypes in Different Tissues:
    • Observed T cell subtypes co-located with epithelial cells in colitis patient tissues, with increased non-CPI-bound T cells expressing macrophage-expressed Cxcl13.
  3. Spatial Analysis Refined Target Niche Characteristics:
    • High-resolution spatial transcriptomics with labeled CPI target cells detected increased proportion of CPI-bound cells in muscular and immune-infiltrated regions, enhancing understanding of CPI-induced T cell activation and migration patterns.

Conclusion

Utilizing multimodal single-cell RNA sequencing and spatial transcriptomics, the study comprehensively describes the distribution characteristics and pathogenic mechanisms of CPI-bound T cells in colitis. The research elucidates the roles of CPI-bound T cells in disease progression and contrasts these mechanisms with inflammatory control in non-CPI treatments. These findings not only provide deep insights into the pathology of CPI-associated colitis but also offer new perspectives for managing CPI therapy side effects in the future.

Research Highlights:

  1. Major Findings:
    • Identified specific CPI-bound T cell subpopulations and pathogenic niches in colitis.
  2. Innovative Research Methods:
    • Combined multimodal single-cell RNA sequencing and high-resolution spatial transcriptomics to reveal molecular mechanisms behind CPI treatment-related colitis.
  3. Scientific and Application Value:
    • Provides new targets and strategies for managing CPI therapy side effects in precision medicine.

The in-depth investigation and technological innovation of this study lay a vital foundation for understanding the mechanisms of side effects in cancer immunotherapy, potentially playing a crucial role in future clinical diagnosis and treatment optimization.