Epigenetic scarring restricts the long-term function of exhausted CD8 T cells (TEX), impairing their ability to control chronic infections and tumors, or to respond effectively to immunotherapy. While our prior work established that de novo DNA methylation reinforces terminal exhaustion, how upstream histone modifications influence these methylation programs remains largely unknown. Defining these molecular mechanisms is essential for reversing exhaustion and enhancing the durability of T cell immunotherapies.
We employed a novel in vitro model of human CD8 T cell dysfunction alongside preclinical murine models of T cell exhaustion. Using integrative epigenomic approaches, we profiled H3K4 methylation states (H3K4me1/3) and DNA methylation signatures across distinct TEX subsets. To investigate functional relevance, we performed CRISPR/Cas9-gene editing, retroviral transduction, and pharmacological inhibition of histone demethylases to assess their impact on TEX functions, stemness, and response to immune checkpoint blockade (ICB).
While distinct histone and DNA methylation landscapes defined TEX subsets in both human and murine models, H3K4me1/3–histone marks that inhibit Dnmt3a-mediated DNA methylation–were enriched at effector/memory-associated genes in cytolytic/progenitor TEX but diminished in terminally exhausted cells. Genetic or therapeutic inhibition of specific H3K4 demethylases (KDM5A/B) improved effector function and cytotoxicity in dysfunctional human CD8 T cells. In vivo, KDM5A/B targeting enhanced TEX fitness and responsiveness to anti-PD-L1 therapy during chronic viral infection and cancer.
Our findings uncover a central histone—DNA methylation circuit, regulated by KDM5A/B and DNMT3A, that drives epigenetic scarring and terminal exhaustion in CD8 T cells. Therapeutic targeting of this circuit offers a novel approach to epigenetically reprogram TEX cells and enhance the efficacy of cancer immunotherapy.
R01AI170926 (NIH, NIAID)
Tumor Immunology: Checkpoints, Prevention, and Treatment (TIPT)
Hazem E. Ghoneim, Amira Yousif, Abbey A. Saadey et al.· Journal of Immunology· 0 citations
Exhaustion of CD8 T cells during cancer or chronic infections remains a significant barrier to T cell immunotherapies. Recent studies showed that distinct epigenetic changes drive exhaustion by silencing effector and memory-related genes, thereby establishing the dysfunctional state of exhausted T cells (TEX). Thus, targeting epigenetic regulation of exhaustion is crucial for restoring TEX cell function. Short-chain fatty acids (SCFAs) are emerging as key mediators linking cellular metabolism to gene regulation. Notably, certain SCFAs naturally produced by human microbiota have been shown to modulate host immune responses through epigenetic mechanisms.
To investigate their effects on TEX cell epigenetic programming, we utilized innovative in vitro T cell exhaustion models that generate stable terminal dysfunction in both human and mouse CD8 T cells. By inducing a state of exhaustion that recapitulates key molecular and functional features observed in cancer and chronic infections, these models enabled us to assess how SCFA treatment affects T cell function and memory-associated stemness features.
We discovered that a specific microbial SCFA triggered a significant recovery of polyfunctionality and memory programs within both human and mouse dysfunctional T cells. SCFA-treated TEX cells exhibited renewed effector capabilities, such as enhanced cytokine production, degranulation, and tumor-killing activity. The enhanced effector functions persisted even following termination of SCFA treatment, suggesting stable reprogramming of TEX cells.
These findings identify a novel microbial SCFA as a potential metabolic-epigenetic regulator, capable of reactivating effector programs in TEX cells while blocking terminal exhaustion. These results provide insights into developing new therapeutic approaches to reprogram TEX cells and enhance the efficacy of T cell immunotherapy.
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Tumor Immunology: Cellular Responses and Tumor Microevironment (TIME)
Asmaa M. Yousif, Amira Yousif, Ava Lowin et al.· Journal of Immunology· 0 citations