Stat5 opposes the transcription factor Tox and rewires exhausted CD8+ T cells toward durable effector-like states during chronic antigen exposure

Rewiring exhausted CD8+ T (Tex) cells toward functional states remains a therapeutic challenge. Tex cells are epigenetically programmed by the transcription factor Tox. However, epigenetic remodeling occurs as Tex cells transition from progenitor (Texprog) to intermediate (Texint) and terminal (Texterm) subsets, suggesting development flexibility. We examined epigenetic transitions between Tex cell subsets and revealed a reciprocally antagonistic circuit between Stat5a and Tox. Stat5 directed Texint cell formation and re-instigated partial effector biology during this Texprog-to-Texint cell transition. Constitutive Stat5a activity antagonized Tox and rewired CD8+ T cells from exhaustion to a durable effector and/or natural killer (NK)-like state with superior anti-tumor potential. Temporal induction of Stat5 activity in Tex cells using an orthogonal IL-2:IL2Rβ-pair fostered Texint cell accumulation, particularly upon PD-L1 blockade. Re-engaging Stat5 also partially reprogrammed the epigenetic landscape of exhaustion and restored polyfunctionality. These data highlight therapeutic opportunities of manipulating the IL-2-Stat5 axis to rewire Tex cells toward more durably protective states.

Serotonin reduction in post-acute sequelae of viral infection

Post-acute sequelae of COVID-19 (PASC, "Long COVID") pose a significant global health challenge. The pathophysiology is unknown, and no effective treatments have been found to date. Several hypotheses have been formulated to explain the etiology of PASC, including viral persistence, chronic inflammation, hypercoagulability, and autonomic dysfunction. Here, we propose a mechanism that links all four hypotheses in a single pathway and provides actionable insights for therapeutic interventions. We find that PASC are associated with serotonin reduction. Viral infection and type I interferon-driven inflammation reduce serotonin through three mechanisms: diminished intestinal absorption of the serotonin precursor tryptophan; platelet hyperactivation and thrombocytopenia, which impacts serotonin storage; and enhanced MAO-mediated serotonin turnover. Peripheral serotonin reduction, in turn, impedes the activity of the vagus nerve and thereby impairs hippocampal responses and memory. These findings provide a possible explanation for neurocognitive symptoms associated with viral persistence in Long COVID, which may extend to other post-viral syndromes.

Cancer cells resistant to immune checkpoint blockade acquire interferon-associated epigenetic memory to sustain T cell dysfunction

Prolonged interferon (IFN) signaling in cancer cells can promote resistance to immune checkpoint blockade (ICB). How cancer cells retain effects of prolonged IFN stimulation to coordinate resistance is unclear. We show that, across human and/or mouse tumors, immune dysfunction is associated with cancer cells acquiring epigenetic features of inflammatory memory. Here, inflammatory memory domains, many of which are initiated by chronic IFN-γ, are maintained by signal transducer and activator of transcription (STAT)1 and IFN regulatory factor (IRF)3 and link histone 3 lysine 4 monomethylation (H3K4me1)-marked chromatin accessibility to increased expression of a subset of IFN-stimulated genes (ISGs). These ISGs include the RNA sensor OAS1 that amplifies type I IFN (IFN-I) and immune inhibitory genes. Abrogating cancer cell IFN-I signaling restores anti-programmed cell death protein 1 (PD1) response by increasing IFN-γ in immune cells, promoting dendritic cell and CD8⁺ T cell interactions, and expanding T cells toward effector-like states rather than exhausted states. Thus, cancer cells acquire inflammatory memory to augment a subset of ISGs that promote and predict IFN-driven immune dysfunction.

MicroRNA-29a attenuates CD8 T cell exhaustion and induces memory-like CD8 T cells during chronic infection

CD8 T cells mediate protection against intracellular pathogens and tumors. However, persistent antigen during chronic infections or cancer leads to T cell exhaustion, suboptimal functionality, and reduced protective capacity. Despite considerable work interrogating the transcriptional regulation of exhausted CD8 T cells (TEX), the posttranscriptional control of TEX remains poorly understood. Here, we interrogated the role of microRNAs (miRs) in CD8 T cells responding to acutely resolved or chronic viral infection and identified miR-29a as a key regulator of TEX. Enforced expression of miR-29a improved CD8 T cell responses during chronic viral infection and antagonized exhaustion. miR-29a inhibited exhaustion-driving transcriptional pathways, including inflammatory and T cell receptor signaling, and regulated ribosomal biogenesis. As a result, miR-29a fostered a memory-like CD8 T cell differentiation state during chronic infection. Thus, we identify miR-29a as a key regulator of TEX and define mechanisms by which miR-29a can divert exhaustion toward a more beneficial memory-like CD8 T cell differentiation state.

NFAT-dependent and -independent exhaustion circuits program maternal CD8 T cell hypofunction in pregnancy

Pregnancy is a common immunization event, but the molecular mechanisms and immunological consequences provoked by pregnancy remain largely unknown. We used mouse models and human transplant registry data to reveal that pregnancy induced exhausted CD8 T cells (Preg-TEX), which associated with prolonged allograft survival. Maternal CD8 T cells shared features of exhaustion with CD8 T cells from cancer and chronic infection, including transcriptional down-regulation of ribosomal proteins and up-regulation of TOX and inhibitory receptors. Similar to other models of T cell exhaustion, NFAT-dependent elements of the exhaustion program were induced by fetal antigen in pregnancy, whereas NFAT-independent elements did not require fetal antigen. Despite using conserved molecular circuitry, Preg-TEX cells differed from TEX cells in chronic viral infection with respect to magnitude and dependency of T cell hypofunction on NFAT-independent signals. Altogether, these data reveal the molecular mechanisms and clinical consequences of maternal CD8 T cell hypofunction and identify pregnancy as a previously unappreciated context in which T cell exhaustion may occur.

Distinct mechanisms govern populations of myeloid-derived suppressor cells in chronic viral infection and cancer

Myeloid-derived suppressor cells (MDSCs) are major negative regulators of immune responses in cancer and chronic infections. It remains unclear if regulation of MDSC activity in different conditions is controlled by similar mechanisms. We compared MDSCs in mice with cancer and lymphocytic choriomeningitis virus (LCMV) infection. Chronic LCMV infection caused the development of monocytic MDSCs (M-MDSCs) but did not induce polymorphonuclear MDSCs (PMN-MDSCs). In contrast, both MDSC populations were present in cancer models. An acquisition of immune-suppressive activity by PMN-MDSCs in cancer was controlled by IRE1α and ATF6 pathways of the endoplasmic reticulum (ER) stress response. Abrogation of PMN-MDSC activity by blockade of the ER stress response resulted in an increase in tumor-specific immune response and reduced tumor progression. In contrast, the ER stress response was dispensable for suppressive activity of M-MDSCs in cancer and LCMV infection. Acquisition of immune-suppressive activity by M-MDSCs in spleens was mediated by IFN-γ signaling. However, it was dispensable for suppressive activity of M-MDSCs in tumor tissues. Suppressive activity of M-MDSCs in tumors was retained due to the effect of IL-6 present at high concentrations in the tumor site. These results demonstrate disease- and population-specific mechanisms of MDSC accumulation and the need for targeting different pathways to achieve inactivation of these cells.

Epigenetic scarring of exhausted T cells hinders memory differentiation upon eliminating chronic antigenic stimulation

Exhausted CD8 T cells (T_EX) are a distinct state of T cell differentiation associated with failure to clear chronic viruses and cancer. Immunotherapies like PD-1 blockade can re-invigorate T_EX cells, but re-invigoration is not durable. A major unanswered question is whether T_EX cells differentiate into functional durable memory T cells (T_MEM) upon antigen clearance. Here, using a mouse model, we found that upon eliminating chronic antigenic stimulation, T_EX cells partially (re)acquire phenotypic and transcriptional features of T_MEM cells. These “recovering” T_EX cells originated from the T-cell factor (TCF-1⁺) T_EX progenitor subset. Nevertheless, the recall capacity of these recovering-T_EX cells remained compromised compared to T_MEM cells. Chromatin-accessibility profiling revealed failure to recover core memory epigenetic circuits and maintenance of a largely exhausted open chromatin landscape. Thus, despite some phenotypic and transcriptional recovery upon antigen clearance, exhaustion leaves durable epigenetic scars constraining future immune responses. These results support epigenetic remodeling interventions for T_EX cell targeted immunotherapies.

A role for the transcription factor STAT5 in antagonizing CD8+ T cell exhaustion

Exhaustion gradually establishes in chronically stimulated CD8s and this process is not reverted by current therapeutic approaches due to establishment of a stable epigenetic program. Recent advances have informed on the developmental process of exhaustion and highlighted TOX as a key lineage-defining TF in the process. Yet, little remains known on molecular pathways capable of antagonizing the TOX-dependent exhaustion program. By depicting transcriptional changes at key developmental steps of exhaustion, we demonstrate an antagonistic role for the TF STAT5 in the development of CD8 T cell exhaustion. STAT5 transcriptional network is heavily silenced upon chronic antigenic stimulation in a TOX-dependent manner which allows initiation of the exhaustion lineage. Increasing STAT5 activity abrogates establishment of the exhaustion lineage leading to the development of effector-like CD8s that acquire a unique transcriptional identity, distinct from exhausted cells, persist throughout chronicity and demonstrate higher protective capacity. Using temporal loss and gain of function approaches, we show that STAT5 triggers loss of progenitor identity by exhausted CD8s (Tex) and subsequent differentiation into the recently identified effector-like intermediate Tex subset. Temporal increase in STAT5 activity also robustly synergizes with PD-L1 blockade by further fostering intermediate Tex cells accumulation. Together, we show that modulating STAT5 activity may counteract the exhaustion process and favor instigation of effector-like characteristic in Tex cells suitable for optimal therapeutic efficacy.

This work is supported by the Parker Institute for Cancer Immunotherapy (PICI). JC-Beltra is a PICI scholar awardee.

Inhibitory signaling sustains a distinct early memory CD8+ T cell precursor that is resistant to DNA damage

The developmental origins of memory T cells remain incompletely understood. During the expansion phase of acute viral infection, we identified a distinct subset of virus-specific CD8⁺ T cells that possessed distinct characteristics including expression of CD62L, T cell factor 1 (TCF-1), and Eomesodermin; relative quiescence; expression of activation markers; and features of limited effector differentiation. These cells were a quantitatively minor subpopulation of the TCF-1⁺ pool and exhibited self-renewal, heightened DNA damage surveillance activity, and preferential long-term recall capacity. Despite features of memory and somewhat restrained proliferation during the expansion phase, this subset displayed evidence of stronger TCR signaling than other responding CD8⁺ T cells, coupled with elevated expression of multiple inhibitory receptors including programmed cell death 1 (PD-1), lymphocyte activating gene 3 (LAG-3), cytotoxic T-lymphocyte-associated protein 4 (CTLA-4), CD5, and CD160. Genetic ablation of PD-1 and LAG-3 compromised the formation of this CD62L^hi TCF-1⁺ subset and subsequent CD8⁺ T cell memory. Although central memory phenotype CD8⁺ T cells were formed in the absence of these cells, subsequent memory CD8⁺ T cell recall responses were compromised. Together, these results identify an important link between genome integrity maintenance and CD8⁺ T cell memory. Moreover, the data indicate a role for inhibitory receptors in preserving key memory CD8⁺ T cell precursors during initial activation and differentiation. Identification of this rare subpopulation within the memory CD8⁺ T cell precursor pool may help reconcile models of the developmental origin of long-term CD8⁺ T cell memory.

Developmental Relationships of Four Exhausted CD8+ T Cell Subsets Reveals Underlying Transcriptional and Epigenetic Landscape Control Mechanisms

CD8⁺ T cell exhaustion is a major barrier to current anti-cancer immunotherapies. Despite this, the developmental biology of exhausted CD8⁺ T cells (Tex) remains poorly defined, restraining improvement of strategies aimed at "re-invigorating" Tex cells. Here, we defined a four-cell-stage developmental framework for Tex cells. Two TCF1⁺ progenitor subsets were identified, one tissue restricted and quiescent and one more blood accessible, that gradually lost TCF1 as it divided and converted to a third intermediate Tex subset. This intermediate subset re-engaged some effector biology and increased upon PD-L1 blockade but ultimately converted into a fourth, terminally exhausted subset. By using transcriptional and epigenetic analyses, we identified the control mechanisms underlying subset transitions and defined a key interplay between TCF1, T-bet, and Tox in the process. These data reveal a four-stage developmental hierarchy for Tex cells and define the molecular, transcriptional, and epigenetic mechanisms that could provide opportunities to improve cancer immunotherapy.

Developmental relationships of four exhausted CD8 T cell subsets reveals underlying transcriptional and epigenetic control mechanisms

Exhausted CD8 T cells (TEX) are essential during chronic viral infections and cancer. Two TEX subpopulations including a progenitor and a more terminally exhausted subset cooperate to maintain an active immune response during antigen persistence. However, non-overlapping delineations of these populations have suggested a more complex developmental biology. Here, using the LCMV mouse model of chronic viral infection, we identify four distinct TEX subsets based on Ly108 (Slamf6) and CD69 expression revealing a novel stepwise developmental framework. We reveal the transcriptional and epigenetic control mechanisms and associated biological changes underlying each TEX subset transition. Two TCF1+ progenitors were identified along with a novel TCF1-intermediate subset that re-engaged some aspects of effector biology. This subset depended on T-bet and was re-invigorated upon PD-L1 blockade. Ultimately, Tox coordinated loss of T-bet and differentiation into a fourth, terminally exhausted subset. These data define a new developmental hierarchy of TEX and reveal distinct biological properties with direct relevance to immunotherapy. Defining the control mechanisms of this TEX subset hierarchy provides novel opportunities to manipulate TEX biology for clinical goals.

Common gamma chain cytokines and CD8 T cells in cancer

Overcoming exhaustion-associated dysfunctions and generating antigen-specific CD8 T cells with the ability to persist in the host and mediate effective long-term anti-tumor immunity is the final aim of cancer immunotherapy. To achieve this goal, immuno-modulatory properties of the common gamma-chain (γ_c) family of cytokines, that includes IL-2, IL-7, IL-15 and IL-21, have been used to fine-tune and/or complement current immunotherapeutic protocols. These agents potentiate CD8 T cell expansion and functions particularly in the context of immune checkpoint (IC) blockade, shape their differentiation, improve their persistence in vivo and alternatively, influence distinct aspects of the T cell exhaustion program. Despite these properties, the intrinsic impact of cytokines on CD8 T cell exhaustion has remained largely unexplored impeding optimal therapeutic use of these agents. In this review, we will discuss current knowledge regarding the influence of relevant γ_c cytokines on CD8 T cell differentiation and function based on clinical data and preclinical studies in murine models of cancer and chronic viral infection. We will restate the place of these agents in current immunotherapeutic regimens such as IC checkpoint blockade and adoptive cell therapy. Finally, we will discuss how γ_c cytokine signaling pathways regulate T cell immunity during cancer and whether targeting these pathways may sustain an effective and durable T cell response in patients.

TCF-1-Centered Transcriptional Network Drives an Effector versus Exhausted CD8 T Cell-Fate Decision

TCF-1 is a key transcription factor in progenitor exhausted CD8 T cells (Tex). Moreover, this Tex cell subset mediates responses to PD-1 checkpoint pathway blockade. However, the role of the transcription factor TCF-1 in early fate decisions and initial generation of Tex cells is unclear. Single-cell RNA sequencing (scRNA-seq) and lineage tracing identified a TCF-1+Ly108+PD-1+ CD8 T cell population that seeds development of mature Tex cells early during chronic infection. TCF-1 mediated the bifurcation between divergent fates, repressing development of terminal KLRG1Hi effectors while fostering KLRG1Lo Tex precursor cells, and PD-1 stabilized this TCF-1+ Tex precursor cell pool. TCF-1 mediated a T-bet-to-Eomes transcription factor transition in Tex precursors by promoting Eomes expression and drove c-Myb expression that controlled Bcl-2 and survival. These data define a role for TCF-1 in early-fate-bifurcation-driving Tex precursor cells and also identify PD-1 as a protector of this early TCF-1 subset.

Abstract A166: Reprogramming of exhausted T-cells following cure of chronic viral infection

T-cell exhaustion is a hallmark of immunologic failure in chronic infections and cancer. Blocking immune inhibitory receptors such as programmed death-1 (PD-1) can re-invigorate exhausted T-cells (Tex), but many patients fail to achieve durable disease control. Thus, a deeper understanding of molecular pathways underlying reversal of T-cell exhaustion is needed. Little is known about “reprogramming” of Tex into recovered T-cells (Trecov) with better functionality and durable memory properties following cure of chronic disease. Here, we aim to determine the molecular program and underlying mechanisms of Trecov. We used the well-defined LCMV mouse model of T-cell exhaustion. To achieve “cure” of chronic infection, we adoptively transferred Tex from mice chronically infected with LCMV clone 13 into antigen-free mice and interrogated changes in Tex as they recovered, including testing the recall capacity of Trecov, a quintessential memory T-cell (Tmem) property. These studies revealed some recovery of phenotypic markers of T-cell memory, but also demonstrated that “scars” of chronic infection persisted. For example, although expression of the IL-7R was increased and PD-1 expression was lower, consistent with differentiation toward memory, the frequency of IL-7R+ cells was lower and PD-1 expression was still higher when compared to bona fide memory T-cells. These changes were accompanied by partial recovery from dysfunction, where Trecov displayed a moderate improvement in effector function. Consistent with this partial recovery, single-cell RNA sequencing (scRNAseq) indicated that the gene-expression profile of Trecov resembles Tmem in some respects, but other features were still more similar to Tex cells. To test how this collection of changes impacted a key property of Tmem, the ability to mount a recall response, we designed a series of challenge experiments. These studies revealed that although Trecov responded better than Tex, recall capacity was still inferior on a per cell basis compared to true Tmem. Together, these results suggest that following elimination of persistent antigenic stimulation and inflammation, previously exhausted T-cells are able to recover some properties of Tmem, while other aspects remain “scarred” from their history of exhaustion. These studies will enhance our understanding of immunologic and molecular mechanisms of Tex recovery, and have the potential to identify novel therapeutic strategies for recovery of more durable functional T-cells in the treatment of cancer and chronic infection.

Citation Format: Mohamed S. Abdel-Hakeem, Jean-Christophe Beltra, Zeyu Chen, John Johnson, Saskinath Manne, Mohammed-Alkhatim Ali, E. John Wherry. Reprogramming of exhausted T-cells following cure of chronic viral infection [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr A166.

IL-2 and IL-15 on CD8 T cells during chronic viral infection: The exhaustion program awakens

CD8 T cell exhaustion is an immunosuppressive mechanism by which chronic viruses escape adaptive immune response. Yet, the direct implication of cytokines as well as the precise candidates involved in this process have remained elusive. Here we demonstrate the direct contribution of IL-2 and IL-15 on several aspects of CD8 T cell exhaustion. Using a mouse model of chronic viral infection (LCMV clone-13), we show that IL2Rβ (CD122; the receptor chain common to IL-2 and IL-15) is maintained on CD8 T cells during chronicity. Its expression correlates with deeper exhaustion and selectively marks terminally exhausted CD8 T cells in mice and humans. Adoptive transfer of IL2Rβ−/− P14 CD8 T cells (unresponsive to combined IL-2 and IL-15-dependent signals) revealed that IL-2 and IL-15 directly control the expression of a specific pattern of inhibitory receptors and are mandatory for the development of PD-1hi effectors. Further, IL-2 and IL-15 instigate the arrested development of central memory cells seen during antigen persistence and preclude responsiveness to IL-7-dependent signals. Together, we ascribe a novel role to IL-2 and IL-15 as instigators of CD8 T cell exhaustion during chronic viral infection.

IL-2 and IL-15 regulate CD8+ memory T-cell differentiation but are dispensable for protective recall responses

The ability to mount effective secondary responses is a cardinal feature of memory CD8(+) T cells. An understanding of the factors that regulate the generation and recall capacities of memory T cells remains to be ascertained. Several cues indicate that two highly related cytokines, IL-2 and IL-15, share redundant functions in this process. To establish their combined roles in memory CD8(+) T-cell development, maintenance, and secondary responses, we compared the outcome of adoptively transferred IL2Rβ(+/-) or IL2Rβ(-/-) CD8(+) T cells after an acute viral infection in mice. Our results demonstrate that both IL-2 and IL-15 signals condition the differentiation of primary and secondary short-lived effector cells by altering the transcriptional network governing lineage choices. These two cytokines also regulate the homeostasis of the memory T-cell pool, with effector memory CD8(+) T cells being the most sensitive to these two interleukins. Noticeably, the inability to respond to both cytokines limits the proliferation and survival of primary and secondary effectors cells, whereas it does not preclude potent cytotoxic functions and viral control either initially or upon rechallenge. Globally, these results indicate that lack of IL-2 and IL-15 signaling modulates the CD8(+) T-cell differentiation program but does not impede adequate effector functions.

Chronic viral infection: the perfidious role of IL-2 and IL-15 on CD8 T cell exhaustion (IRM4P.500)

CD8 T cell exhaustion is a major immuno-regulatory mechanism by which chronic viruses escape the immune response. However, little is known on the factors regulating the unresponsiveness of CD8 T cells is this context. Here, we investigated the combined role of IL-2 and IL-15, two common gamma chain-dependent cytokines, on CD8 T cell differentiation and exhaustion during a chronic viral infection. We performed adoptive transfer of WT or IL-2RβKO P14 CD8 T cells (unresponsive to both IL-2 and IL-15 signals) in mice challenged with LCMV clone 13. Initially, IL-2Rβ-signals were critical for short-lived effector cell differentiation. IL-2 and IL-15 conditioned optimal proliferation of early effector CD8 T cells and promoted their cytotoxic functions. Interestingly, over the chronic phase, IL-2Rβ-signals dramatically worsened CD8 T cell exhaustion. IL-2 and IL-15 sustained the expression of several inhibitory receptors and fostered the development of the highly exhausted PD-1hi progeny population. Finally, IL-2Rβ-signals precluded central memory CD8 T cell differentiation capable of homeostatic proliferation and robust secondary expansion. Altogether, these data demonstrated for the first time an important deleterious effect of IL-2 and IL-15 on the CD8 T cell response to a chronic viral infection. Reconsidering their role in this context may provide new insights for therapeutic regimens against chronic viruses.