CD19-CAR T Cells Develop Exhaustion Epigenetic Programs During a Clinical Response

The goal of this study was to determine the epigenetic landscape of CD19-CAR T cells pre and post infusion in leukemia patients as an initial step to elucidate intrinsic mechanisms that limit CAR T-cell effector functions in humans. A longitudinal analysis of CD8+ CD19-CAR T cell epigenetic changes was performed by whole-genome DNA methylation profiling of CAR T cells during manufacturing and from peripheral blood mononuclear cells (PBMCs) of 15 patients enrolled on our institutional, autologous CD19-CAR T cell therapy study (NCT03573700). CAR T cell expansion and persistence were determined by measuring vector copy numbers in the PBMCs of treated patients. We had previously established novel exhaustion DNA methylation datasets that delineate between progenitor and fully exhausted T cells. These datasets served as a guide for stratifying our post-infusion CAR T cells along the exhaustion developmental trajectory. Our data show that CD19-CAR T cells lose repressive DNA methylation at effector loci (e.g. PRF1, TBET) while gaining methylation at genes associated with memory potential (e.g. LEF1, TCF7). We confirmed these epigenetic changes are coupled to endogenous human T cell effector and memory differentiation by cross-referencing our epigenetic data with publicly available transcriptional profiles for antigen-specific effector and long-lived memory CD8 T cells from individuals vaccinated for yellow fever. Furthermore, we show that CAR T cells were unable to mount an in vivo recall response after relapse of antigen-positive disease or recovery of endogenous B cells. These observations support the conclusion that CD19-CAR T cells acquire stable epigenetic exhaustion programs that limit their protective capacity.

This work was supported by the National Institutes of Health (1R01AI114442 to BY and LRP to CCZ), the National Comprehensive Cancer Network Young Investigator Award (to CZ), Alex’s Lemonade Stand Foundation Young Investigator Grant (to CZ), Stand Up to Cancer- SU2C (to BY), the American Lebanese Syrian Associated Charities (ALSAC) to BY, and Assisi foundation to BY.

HIV-specific CD8 T cells from elite controllers have an epigenetic imprint that preserves effector functions

CD8 T cells from HIV infected ‘elite controllers’ maintain long-lived protective properties including enhanced cytokine production and proliferative capacity over many years. With the advent of adoptive cellular therapy to treat chronic diseases it has become even more vital to understand the intrinsic cellular mechanisms of elite controller HIV specific CD8 T cells that enable lasting antiviral functionality. To identify epigenetic programs that regulate their functional capacity we performed genome-wide DNA methylation analysis of MHC Class I multimer+ CD8 T cells sorted from aviremic elite controllers compared to aviremic non-controllers on suppressive ART. Principle component analysis of the CpG sites broadly distinguished EC and ART HIV specific CD8 T cells, while deeper investigation of the differentially methylated region analysis revealed enrichment of pathways that support a multipotent differentiation state, cytokine signaling, and a long-lived effector cell fate in HIV-specific CD8 T cells from elite controllers. We also observed DNA methylation programs at the transcription factor binding sites of the stem-associated factors TCF-1 and LEF1 that delineate HIV-specific CD8 T cells from elite controllers versus ART-treated individuals. These findings show that HIV-specific CD8 T cells from elite controllers have DNA methylation programs that maintain developmental potential and in turn enable long-term survival, proliferative potential, and effector capacity. These data also provide new insights into the relationship between stem-associated transcription factors and stable epigenetic restriction of T cell developmental capacity.

Supported by grants from NIH (R01AI114442 and R01CA237311 to BY, K23AI134327 to RLR), loan repayment program and National comprehensive Cancer Network Young Investigator Award (CZ), ASSISI foundation support (BY) and American Lebanese Syrian Associated Charities (ALSAC to BY)

De novo DNA methylation programs regulate T cell exhaustion and limit T cell-based immunotherapies

T cell-based immunotherapies have emerged as one of the most promising frontiers in the fight against cancer and chronic infections. However, it has become clear that prolonged exposure of T cells to their cognate antigen drives them toward a terminally differentiated state, limiting their capacity to mount an effector response. The commitment of T cells to this “exhausted” fate is currently a major barrier in the advancement of T cell immunotherapy efforts. To better understand mechanisms that reinforce the T cell exhaustion gene expression program, we investigated the role of de novo epigenetic programming in establishing exhausted T cells that are non-responsive during immune checkpoint blockade (ICB) therapy. Using mouse models of tumor and chronic viral infection, we observed that genetic deletion of the de novo DNA methyltransferase, Dnmt3a, in antigen-specific T cells that are chronically stimulated allowed them to remain highly functional despite expressing high levels of the checkpoint inhibitory receptor PD-1. Furthermore, PD-1 blockade treatment resulted in massive expansion of PD-1+ Dnmt3a-deficient antigen-specific T cells. Building upon the findings from our murine studies, we have generated whole-genome DNA methylation profiles of human CD8 T cells from a wide array of differentiation states, and established an epigenetic-based human T cell multipotency index. Using this index, we report that tumor-associated PD-1hi CD8 T cells from pediatric solid tumors acquire an epigenetically reinforced terminal differentiation program. Collectively, these data establish Dnmt3a-mediated de novo DNA methylation programming as a key factor in limiting CD8 T cell-based immunotherapuetic approaches.

De novo DNA methylation programs restrain T cell rejuvenation during immune checkpoint blockade therapy

Immune-checkpoint blockade (ICB)-mediated rejuvenation of CD8 T cell effector functions has emerged as one of the most promising frontiers for treating cancer and chronic infections. However, antigen-specific T cells that have experienced prolonged antigen exposure are often terminally differentiated, and have a limited capacity to mount an effector response during ICB treatment. Such exhaustion of effector potential is a major impediment of current T cell based immunotherapy efforts. Using in vivo mouse models of tumor and chronic viral infection, we assessed the role of de novo epigenetic programming in establishing ICB-refractory exhausted T cells. We observed that genetic deletion of Dnmt3a in T cells at the effector stage of an immune response to chronic lymphocytic choriomeningitis virus (LCMV) infection allowed antigen-specific T cells to remain highly functional despite expressing high levels of PD-1 and having prolonged exposure to antigen. Quite strikingly, PD-1 blockade treatment of chronically infected animals resulted in massive expansion of PD-1+ Dnmt3a-deficient antigen-specific T cells. Whole-genome methylation profiling of WT and Dnmt3a-deficient LCMV-specific CD8 T cells identified de novo DNA methylation programs that are coupled to development of ICB-nonresponsive virus and tumor-specific T cells. Building upon these findings, we have identified de novo epigenetic programs acquired in human tumor-associated PD-1hi CD8 T cells. Collectively, these data establish Dnmt3a-mediated de novo DNA methylation programming as a key regulator in establishing ICB-refractory exhausted CD8 T cells and highlights epigenetic reprogramming of T cells as a novel approach to enhance T cell-based cancer therapies.

Maintenance of PD-1 on brain-resident memory CD8 T cells is antigen independent

Infection of the central nervous system (CNS) by murine polyomavirus (MuPyV), a persistent natural mouse pathogen, establishes brain‐resident memory CD8 T cells (bT_RM) that uniformly and chronically express programmed cell death protein 1 (PD‐1) irrespective of the expression of α_E integrin CD103, a T_RM cell marker. In contrast, memory antiviral CD8 T cells in the spleen are PD‐1⁻, despite viral loads being similar in both the brain and spleen during persistent infection. Repetitive antigen engagement is central to sustained PD‐1 expression by T cells in chronic viral infections; however, recent evidence indicates that expression of inhibitory receptors, including PD‐1, is part of the T_RM differentiation program. Here we asked whether PD‐1 expression by CD8 bT_RM cells during persistent MuPyV encephalitis is antigen dependent. By transferring MuPyV‐specific CD8 bT_RM cells into the brains of naive mice and mice infected with cognate epitope‐sufficient and ‐deficient MuPyVs, we demonstrate that antigen and inflammation are dispensable for PD‐1 maintenance. In vitro and direct ex vivo analyses indicate that CD103⁻ MuPyV‐specific CD8 bT_RM retain functional competence. We further show that the Pdcd‐1 promoter of anti‐MuPyV bT_RM cells is epigenetically fixed in a demethylated state in the brain. In contrast, the PD‐1 promoter of splenic antiviral memory CD8 T cells undergoes remethylation after being demethylated during acute infection. These data show that PD‐1 expression is an intrinsic property of brain T_RM cells in a persistent CNS viral infection.

Tumor infiltrating T cells acquire exhaustion-associated epigenetic programs

Antigen-specific CD8 T cells play a critical role in controlling chronic infections and cancer, but progressively lose their effector functions during prolonged antigen exposure. Repression of CD8 T cell effector functions, commonly referred to as T cell exhaustion, limits the ability of the immune system to purge the chronic pathogen from the host. It has recently become recognized that CD8 T cell exhaustion programs can be reinforced and heritably maintained. Therefore in order to develop and/or improve current therapeutic approaches that utilize host antigen-specific T cells to treat chronic infections or cancer a major challenge for the field is to identify mechanisms that stabilize T cell exhaustion. Using the LCMV model system of chronic viral infection we determined that Dnmt3a mediated de novo DNA methylation plays a causal role in establishing CD8 T cell exhaustion. We then performed whole-genome methylation profiling of WT and Dnmt3a cKO CD8 T cells from chronically infected animals and identified Dnmt3a-dependent DNA methylation programs in genes, including interferon gamma and Tcf7, that are coupled to the progressive decline in effector function and developmental plasticity of the antigen specific cell. Lastly, we extended these findings to the tumor setting using a syngeneic mouse tumor model. We found that tumor-infiltrating PD-1hi CD8 T cells acquire exhaustion-associated de novo DNA methylation programs. These results have significant implications for therapeutic strategies that utilize reactivation of host pathogen-specific CD8 T cells to control chronic viral infections or cancer and provide a nucleotide-resolution map of epigenetic programs progressively acquired during T cell exhaustion.

Cognate epitope is dispensable in maintenance of PD-1 expression on tissue-resident CD8+ cells

Persistent CNS infection by mouse polyomavirus (MuPyV) establishes a tissue-resident memory (TRM) CD8+ T cell population possessing higher TCR affinity than the memory cells in spleen. This necessitates a mechanism to regulate the functions of a non-replenished TRM population. Here, we report that virus-specific CD8+ T cells express PD-1 during acute infection and remain PD-1hion brain-infiltrating T cells. In contrast, antiviral memory CD8+ T cells in the spleen downregulate PD-1 expression during persistent infection, despite having similar viral load as the brain. The Pdcd1 promoter was found to be partially remethylated following its downregulation in the splenic population while the locus remained unmethylated in the brain-resident cells. Antiviral TRM cells purified from infected brain when transferred into a naïve mouse via intracerebral route, remained PD-1hi. Thus, epitope as well as inflammation are dispensable for maintenance of PD-1 expression. Absence of PD-1 signaling in an in vitro peptide stimulation assay resulted in augmented IFN-γ production and in vivo absence of PD-1 or PD-L1 resulted in increased IFN-γ-dependent microglial activation, indicating that PD-1 operates to limit CD8+ T cell-dependent neuroinflammation. PD-L1 was found to be expressed on infiltrating myeloid cells and astrocytes; astrocytes were also found to support productive MuPyV infection. PD-L1−/− mice had fewer anti-MuPyV brain-TRM cells, but increased proportion of the cells that were CD103hi, an αE integrin expressed by TRM cells. In summary, our data shows that PD-1 plays an important role in maintenance of antiviral CD8+ TRM cells in the brain and its expression is independent of the cognate epitope.

Cell-Intrinsic Barriers of T Cell-Based Immunotherapy

Prolonged exposure of CD8⁺ T cells to their cognate antigen can result in exhaustion of effector functions enabling the persistence of infected or transformed cells. Recent advances in strategies to rejuvenate host effector function using Immune Checkpoint Blockade have resulted in tremendous success towards the treatment of several cancers. However, it is unclear if T cell rejuvenation results in long-lived antitumor functions. Emerging evidence suggests that T cell exhaustion may also represent a significant impediment in sustaining long-lived antitumor activity by chimeric antigen receptor T cells. Here, we discuss current findings regarding transcriptional regulation during T cell exhaustion and address the hypothesis that epigenetics may be a potential barrier to achieving the maximum benefit of T cell-based immunotherapies.

T cell exhaustion is Reinforced by Progressive De novo DNA Methylation Programming

Antigen-specific CD8 T cells play a critical role in controlling chronic infections and cancer, but progressively lose their effector functions during prolonged antigen exposure. Repression of CD8 T cell effector functions, commonly referred to as T cell exhaustion, limits the ability of the immune system to purge the chronic pathogen from the host. It has recently become recognized that CD8 T cell exhaustion programs can be reinforced and heritably maintained. Therefore in order to develop and/or improve current therapeutic approaches that utilize host antigen-specific T cells to treat chronic infections or cancer a major challenge for the field is to identify mechanisms that stabilize T cell exhaustion. We have recently found that epigenetic modifications acquired in pathogen-specific CD8 T cells during prolonged antigen exposure reinforce T cell exhaustion. Using the LCMV model system of chronic viral infection we investigated the role of Dnmt3a mediated de novo DNA methylation in regulating CD8 T cell exhaustion. Strikingly, conditional deletion of Dnmt3a in activated CD8 T cells blocked the cells from becoming exhausted. Longitudinal analysis of whole-genome methylation programming of WT and Dnmt3a cKO CD8 T cells from chronically infected animals reveals progressive acquisition of Dnmt3a-dependent DNA methylation programs in genes, including interferon gamma, that are coupled to the progressive decline of effector functions. These results have significant implications for therapeutic strategies that utilize reactivation of host pathogen-specific CD8 T cells to control chronic viral infections or cancer and provide a nucleotide-resolution map of epigenetic programs progressively acquired during T cell exhaustion.