2022-Jun-Buquicchio

A unique epigenomic landscape defines CD8+ tissue-resident memory T cells
Buquicchio, F. et al. (BioRxiv) doi: 10.1101/2022.05.04.490680

Keywords

Epigenomics
CD8 T cells
Single-cell sequencing

Main Findings

Memory CD8+ T cells are phenotypically and transcriptionally parsed into heterogeneous subsets with specialized functions and recirculation patterns, including central memory T (TCM), effector memory T (TEM), and tissue-resident T (TRM) cells. In this preprint, Buquicchio et al. utilized the single-cell transposase-accessible chromatin with sequencing(scATAC-seq) to examine epigenetic changes over the course of the CD8+ T cell response in the mouse models of acute and chronic systemic (lymphocytic choriomeningitis virus, LCMV), or local (herpes simplex virus type 1, HSV-1) viral infections.

Based on scATAC-seq and flow cytometry analysis, they first studied memory CD8+ T cell development in the spleen and liver of acute LCMV infected mice at different time points and naive CD8+ P14 cells from non-infected mice. Whereas minor distinctions were observed between the chromatin states of TCM and TEM cells, regardless of tissue origin, a cluster of epigenetically distinct liver TRM cells was positioned separately from the circulatory T cell populations (TCIRC; including TCM and TEM). Clustering and trajectory analysis also indicated an early divergence of TRM and TCIRC precursors from effector CD8+ T cells. The authors uncovered retained differential expression of FcgRIIB between TRM and TCIRC cells and decreased accessibility of Fcgr2b (or lack of FcgRIIB expression), preferentially giving rise to TRM cells in the liver. In addition, an increase in the gene score of Hic1 was observed for TRM cells. Hic1, a known important gene for the accumulation of intraepithelial lymphocytes in the small intestine (IELs), was recently shown to be highly expressed in IELs, but not in the liver by single-cell RNA sequencing (scRNA-seq) [1]. To further investigate the functional relevance of HIC1 in liver TRM cell development, the authors used CRISPR-Cas9 to ablate HIC1 in P14 cells, then subsequently transferred these cells into LCMV-infected mice and found a significant reduction and depletion of CD69+ T cells in the liver after 9 and 30 days, respectively. These data suggest that HIC1 plays a critical regulatory role in TRM cell differentiation.

To define epigenetic features that are conserved between liver and skin TRM cells, the authors next utilized the HSV-1 infection mouse model to induce a skin TRM cell population. Using scATAC-seq, they found that liver and skin TRM cells clustered separately. Both possessed n=64 genes with differential accessibility that did not appear in any other memory cluster. TRM cells shared a core epigenetic signature across tissues, including the loss in the accessibility of Klf2 and S1pr1, which functionally antagonize TRM development, and increased Xcl1 and Chn2 gene scores.

Molecular signature analysis of enriched motifs (MSigDB) in skin versus liver TRM cells indicated enriched signatures for TGF-β signaling in skin TRM cells. In contrast, liver TRM cell motifs displayed enrichment in pathways related to IFN signaling, suggesting tissue-specific changes in the chromatin landscapes between TRM cells from different organs. By combining transcriptional data from a gene set (GSE70813), the authors found that skin TRM cells had increased expression and accessibility in AP-1 family members, including Fos, Fosb, Fosl1, and Fosl2, compared to liver TRM cells. In contrast, no significant differential gene expression was observed for Bach2 between the TRMsubsets. The specific roles of Fos, Fosb, Fosl1, and Bach2 in skin T cell formation were further validated using CRISPR-Cas9 to ablate them in effector P14 cells, followed by transferring these cells to LCMV-infected Dinitrofluorobenzene-treated mice. These data demonstrate the utility of integrating transcriptional and epigenetic analysis to identify major regulators of tissue-specific T cell development and highlight the utility of scATAC-seq in identifying novel transcriptional regulators.

To directly compare exhausted T (TEX) cells and TRM cells, the authors finally performed flow cytometry and scATAC-seq on T cells from the liver, skin, and spleen of acute and chronic LCMV and HSV-1-infected mice. These data revealed that TEX cells could be separated into 3 stages, including stem-like, intermediate, and terminal TEX cells based on Havcr2, Cx3cr1, Pdcd1, and Tcf7 gene scores. The TEX cells in all stages separated from T cells derived from acute LCMV infected mice, highlighting distinct chromatin states for TRM and TEX cells. By comparing the significant peak sets between T cell populations in each tissue, the authors found that TRM and TEX cells may share phenotypic similarities in expressing some co-inhibitory receptors, such as PD-1. Still, most accessible gene changes throughout TEX cell development were not present in TRM cells.

Limitations

The preprint shows the chromatin state characteristics of TRM cells in the liver and skin. It would be interesting to understand how the chromatin landscape of TRM cells is impacted in other organs, such as the small intestine, salivary glands, etc.
The study used pathogen-specific free animals infected with different viruses. These results may be representable for viral infections but not other diseases such as bacteria and parasites.
The work takes place in mice with no translational work done in humans. We suggest a change in the title to impress the unique chromatin state of mouse CD8+ T cells in viral infections.

Significance/Novelty

The data reinforce the concept that TRM cell fate may be imprinted early post-T cell activation. Integrating transcriptional and epigenetic analyses identified tissue-specific TRM cell regulators, including HIC1 and BACH2, and showed distinct epigenetic features of TRM and TEX cells. Overall, this preprint provides critical insight into the biology of TRM cell formation and indicates that local environmental cues shape T cell functions.

Additional Reading

[1] Crowl, J.T., Heeg, M., Ferry, A. et al. Tissue-resident memory CD8+ T cells possess unique transcriptional, epigenetic and functional adaptations to different tissue environments. Nat Immunol (2022). https://doi.org/10.1038/s41590-022-01229-8

Credit

Reviewed by Thi My Hanh Luong as part of the cross-institutional journal club of the Immunology Institute of the Icahn School of Medicine, Mount Sinai, the Kennedy Institute of Rheumatology and the Oxford Centre for Immuno-Oncology (OXCIO) (University of Oxford, GB) and Karolinska Institute’s Center for Infectious Medicine (CIM) & Center for Molecular Medicine (CMM).