Spatiotemporal Imprinting of Tissue-Resident Memory CD8 T Cell Diversity

Rheumatology and Immunology Life Sciences Immunology Medicine
Tissue-resident memory T cells Small intestine Spatial transcriptomics Cell differentiation Immune response Cellular heterogeneity Cell localization

Spatiotemporal Imprinting of Tissue-Resident Memory CD8 T Cell Diversity

Background

Tissue-resident memory CD8 T cells (TRM cells) provide long-term immune protection at barrier sites such as the intestine. However, the heterogeneity of TRM cells and the mechanisms underlying their formation remain incompletely understood. Previous studies have identified at least two subsets of TRM cells in the small intestine: one with higher expression of effector molecules and another with greater memory potential. The origin of this heterogeneity is still unclear. This study aims to explore how different tissue microenvironments drive the phenotypic heterogeneity of TRM cells and reveal their spatiotemporal distribution patterns in the intestine.

Source of the Paper

This paper was co-authored by Miguel Reina-Campos, Alexander Monell, and others from institutions such as the University of California, San Diego and the La Jolla Institute for Immunology. It was published in Nature in 2024. The research combines spatial transcriptomics, mouse models, and novel optically encoded gene perturbation techniques to uncover the spatiotemporal distribution and regulatory mechanisms of TRM cells in the small intestine.

Research Process and Results

1. Application of Spatial Transcriptomics

The research team first utilized spatial transcriptomics to perform high-resolution analysis of the mouse small intestine. By designing a detection panel containing 350 genes, the team captured the gene expression profiles of TRM cells in different anatomical regions of the intestine, such as the villus tip and base. The experimental subjects were mice infected with lymphocytic choriomeningitis virus (LCMV), and samples were collected at various time points (6, 8, 30, and 90 days post-infection).

Experimental Results:

  • Spatiotemporal Distribution of TRM Cells: The study found that the distribution of TRM cells in the small intestine exhibits distinct regional characteristics. In the early stages of infection (6 and 8 days), TRM cells primarily accumulated at the base of the villus and the muscularis layer. By the later stages of infection (30 and 90 days), TRM cells differentiated into two spatially separated populations: one located at the villus tip, expressing high levels of effector molecules (e.g., GZMA, GZMB), and another located at the villus base, expressing genes associated with memory potential (e.g., TCF7, SLAMF6).
  • Spatiotemporal Imprinting of Gene Expression: By analyzing the gene expression of TRM cells, the study found that 46% of gene expression changes occurred along the crypt-villus axis, while 40% of gene expression changes occurred along the epithelial axis. This indicates that the functional state of TRM cells is closely related to their location in the small intestine.

2. Cellular Interactions and Cytokine Gradients

To further explore the mechanisms underlying TRM cell heterogeneity, the research team analyzed the interactions between TRM cells and surrounding cells, as well as the distribution of cytokine gradients.

Experimental Results:

  • Cellular Interactions: The study found that TRM cells located at the villus tip primarily interacted with epithelial cells and immune cells (e.g., mucosal-associated invariant T cells and natural killer cells), while TRM cells located at the villus base interacted more with B cells, CD4 T cells, and fibroblasts.
  • Cytokine Gradients: The study revealed the gradient distribution of various cytokines (e.g., TGFβ, IL-7, IL-15) in the small intestine. For example, TGFβ signaling was more active at the villus tip, while CXCL9 and CXCL10 signals were primarily expressed in fibroblasts at the base of the muscularis layer after infection.

3. Roles of TGFβ and CXCR3 Signaling

The research team validated the critical roles of TGFβ and CXCR3 signaling in the localization and differentiation of TRM cells through gene knockout experiments.

Experimental Results:

  • Role of TGFβ Signaling: Knockout of TGFβ receptor II (TGFβRII) resulted in TRM cells accumulating more at the villus base, with a significant reduction in the expression of core TRM cell markers (e.g., CD103). This indicates that TGFβ signaling is crucial for the localization and functional maintenance of TRM cells at the villus tip.
  • Role of CXCR3 Signaling: Using CRISPR-Cas9 technology to knockout the CXCR3 gene, the study found that CXCR3-deficient TRM cells accumulated more at the villus tip, with increased expression of effector molecules (e.g., GZMA). This suggests that CXCR3 signaling plays an important role in regulating the localization and functional state of TRM cells.

4. Study of TRM Cells in Human Small Intestine

To validate the universality of the findings from mouse studies, the research team also performed spatial transcriptomics analysis on human small intestine samples.

Experimental Results:

  • Heterogeneity of Human TRM Cells: The study found that CD8 T cells in the human small intestine exhibited heterogeneity similar to that observed in mice. CD8 T cells located at the villus tip expressed high levels of effector molecules (e.g., GZMA, ITGAE), while those located at the villus base expressed genes associated with memory potential (e.g., TCF7).
  • Cellular Signaling in Humans: Consistent with the mouse study results, TRM cells in the human small intestine were also regulated by local cytokines and cellular interactions.

Research Conclusions and Significance

1. Scientific Value

This study is the first to systematically reveal the spatiotemporal distribution patterns of TRM cells in the small intestine and the regulatory mechanisms underlying their functional states. The results demonstrate that the anatomical structure of the small intestine shapes TRM cell heterogeneity through regional signals, such as cytokine gradients and cellular interactions. This discovery provides new insights into the development and function of tissue-resident immune cells.

2. Application Value

The study highlights the critical roles of TGFβ and CXCR3 signaling in the localization and differentiation of TRM cells, offering potential targets for developing therapeutic strategies targeting tissue-resident immune cells. For example, modulating TGFβ or CXCR3 signaling could enhance the function of TRM cells in specific tissues, thereby improving vaccine efficacy or anti-tumor immune responses.

3. Research Highlights

  • High-Resolution Spatial Transcriptomics: The research team developed a novel computational framework to capture the spatiotemporal distribution of cell types and gene expression along the three-dimensional anatomical axes of the small intestine.
  • Optically Encoded Gene Perturbation Techniques: The study achieved multiplexed optically encoded CRISPR knockout experiments in vivo for the first time, providing a new tool for studying immune cell differentiation.
  • Cross-Species Validation: The study not only revealed TRM cell heterogeneity in mouse models but also validated its universality in human samples.

Summary

By combining spatial transcriptomics, gene perturbation techniques, and cross-species validation, this study systematically revealed the spatiotemporal distribution and regulatory mechanisms of TRM cells in the small intestine. The research not only deepens our understanding of tissue-resident immune cells but also provides a theoretical foundation and technical support for developing novel immunotherapeutic strategies.