Short-lived Effector Cells Research Articles

InVivo CRISPR Screening Reveals CHD7 as a Positive Regulator of Short-lived Effector Cells.

CD8+ T cells differentiate into two subpopulations in response to acute viral infection: memory precursor effector cells (MPECs) and short-lived effector cells (SLECs). MPECs and SLECs are epigenetically distinct; however, the epigenetic regulators required for formation of these subpopulations are mostly unknown. In this study, we performed an invivo CRISPR screen in murine naive CD8+ T cells to identify the epigenetic regulators required for MPEC and SLEC formation, using the acute lymphocytic choriomeningitis virus Armstrong infection model. We identified the ATP-dependent chromatin remodeler CHD7 (chromodomain-helicase DNA-binding protein 7) as a positive regulator of SLEC formation, as knockout (KO) of Chd7 reduced SLECs numerically. In contrast, KO of Chd7 increased the formation of central memory T cells following pathogen clearance yet attenuated memory cell expansion following a rechallenge. These findings establish CHD7 as a novel positive regulator of SLEC and a negative regulator of central memory T cell formation.

CD39 Is Expressed on Functional Effector and Tissue-resident Memory CD8+ T Cells.

The ecto-ATPase CD39 is expressed on exhausted CD8+ T cells in chronic viral infection and has been proposed as a marker of tumor-specific CD8+ T cells in cancer, but the role of CD39 in an effector and memory T cell response has not been clearly defined. We report that CD39 is expressed on Ag-specific CD8+ short-lived effector cells, while it's co-ectoenzyme, CD73, is found on memory precursor effector cells (MPECs) invivo. Inhibition of CD39 enzymatic activity during invitro T cell priming enhances MPEC differentiation invivo after transfer and infection. The enriched MPEC phenotype is associated with enhanced tissue resident memory T cell (TRM cell) establishment in the brain and salivary gland following an acute intranasal viral infection, suggesting that CD39 ATPase activity plays a role in memory CD8+ T cell differentiation. We also show that CD39 is expressed on human and murine TRM cells across several nonlymphoid tissues and melanoma, whereas CD73 is expressed on both circulating and resident memory subsets in mice. In contrast to exhausted CD39+ T cells in chronic infection, CD39+ TRM cells are fully functional when stimulated ex vivo with cognate Ag, further expanding the identity of CD39 beyond a T cell exhaustion marker.

BRD7 as key factor in PBAF complex assembly and CD8+ T cell differentiation.

Upon infection, naive CD8+ T cells differentiate into cytotoxic effector cells to eliminate the pathogen-infected cells. Although many mechanisms underlying this process have been demonstrated, the regulatory role of chromatin remodeling system in this process remains largely unknown. Here we show that BRD7, a component of the polybromo-associated BAF complex (PBAF), was required for naive CD8+ T cells to differentiate into functional short-lived effector cells (SLECs) in response to acute infections caused by influenza virus or lymphocytic choriomeningitis virus (LCMV). BRD7 deficiency in CD8+ T cells resulted in profound defects in effector population and functions, thereby impairing viral clearance and host recovery. Further mechanical studies indicate that the expression of BRD7 significantly turned to high from naive CD8+ T cells to effector cells, which bridged BRG1 and PBRM1 to the core module of PBAF complex, consequently facilitating the assembly of PBAF complex rather than BAF complex in the effector cells. The PBAF complex changed the chromatin accessibility at the loci of Tbx21 gene and upregulated its expression, leading to the maturation of effector T cells. Our research demonstrates that BRD7 and the PBAF complex are key in CD8+ T cell development and present a significant target for advancing immune therapies.

Sustained AhR activity programs memory fate of early effector CD8+ T cells

Identification of mechanisms that program early effector T cells to either terminal effector T (Teff) or memory T (Tm) cells has important implications for protective immunity against infections and cancers. Here, we show that the cytosolic transcription factor aryl hydrocarbon receptor (AhR) is used by early Teff cells to program memory fate. Upon antigen engagement, AhR is rapidly up-regulated via reactive oxygen species signaling in early CD8+ Teff cells, which does not affect the effector response, but is required for memory formation. Mechanistically, activated CD8+ T cells up-regulate HIF-1α to compete with AhR for HIF-1β, leading to the loss of AhR activity in HIF-1αhigh short-lived effector cells, but sustained in HIF-1αlow memory precursor effector cells (MPECs) with the help of autocrine IL-2. AhR then licenses CD8+ MPECs in a quiescent state for memory formation. These findings partially resolve the long-standing issue of how Teff cells are regulated to differentiate into memory cells.

Emergence and fate of stem cell–like Tcf7 + CD8 + T cells during a primary immune response to viral infection

In response to infection, naïve CD8 + T (T N ) cells yield a large pool of short-lived terminal effector (T TE ) cells that eliminate infected host cells. In parallel, a minor population of stem cell–like central memory (T CM ) cells forms, which has the capacity to maintain immunity after pathogen clearance. It has remained uncertain whether stem-like T CM cells arise by dedifferentiation from a subset of cytolytic T TE cells or whether priming generates stem-like cells capable of seeding the T CM compartment and, if so, when cytolytic T TE cells branch off. Here, we show that CD8 + T cells with stem-like properties, which are identified by the expression of TCF1 (encoded by Tcf7 ), are present across the primary response to infection. Priming programs T N cells to undergo multiple cell divisions, over the course of which TCF1 expression is maintained. These TCF1 + cells further expand relatively independently of systemic inflammation, antigen dose, or affinity, and they quantitatively yield TCF1 + T CM cells after pathogen clearance. Inflammatory signals suppress TCF1 expression in early divided TCF1 + cells. TCF1 down-regulation is associated with the irreversible loss of self-renewal capacity and the silencing of stem/memory genes, which precedes the stable acquisition of a T TE state. TCF1 expression restrains cell cycling, explaining in part the limited expansion of TCF1 + relative to TCF1 − cells during the primary response. Thus, our data are consistent with terminal differentiation of effector cells being a step-wise process that is initiated by inflammation in primed stem-like cells, which would otherwise become central memory cells by default.

Novel neoantigen peptides and tumor regression in the MC38 colorectal cancer model.

28 Background: Neoantigen vaccine is an emerging modality to treat cancer by unleashing cytotoxic T cells against tumor-specific mutant antigens. Neoantigens are de-novo changes in tumor cells and are hence more immunogenic and less susceptible to off-target toxicities. In building our own pipeline for neoantigen discovery, we used the mouse colon adenocarcinoma cell line MC38 as a validation model. Methods: We sequenced MC38 cells by whole exome and RNA sequencing to shortlist variants. Candidates were confirmed by sanger sequencing, then analyzed for binding affinity to MHC class I H2-Kb and H2-Db. We selected top 10 epitopes for facile modification to maximize immunogenicity by taking into account peptide characteristics, such as hydrophobicity. In-vivo immunogenicity was tested by subcutaneous injections of pooled peptides in C57BL/6J mice. Amongst the 10 peptides tested, we picked five that elicited greatest IFNγ secretion in re-stimulated splenocytes. Predicted binding affinity did not correlate with in-vivo immunogenicity. We inoculated MC38 cells into the left flank of C57BL/6J mice and started treatment four days later. Mice were injected twice weekly with PBS (group 1), CpG only (group 2), anti-PDL1 only (group 3), Peptide pool + CpG (group 4) and Peptide pool + CpG + anti-PDL1 (group 5) (n=8 per group). CpG ODN 1826 is a TLR9 agonist and acts as an adjuvant, while anti-PDL1 is an immune checkpoint inhibitor. We monitored tumor size, animal weights and food intake every 2-3 days. Results: In control group 1, tumor size exponentially increased by 36 folds on the 18th day of treatment. Groups 2, 3, 4 and 5 saw 16, 13, 8 and 5-fold increases in tumor size respectively, 21 days post-treatment. No tumors were found in 3/7 mice in group 5 upon sacrifice, suggesting tumor regression. Tumor control in groups 4 and 5 corroborated with significant IFNγ secretion from neoantigen re-stimulated splenocytes. We observed 38-45 fold expansion in the number of CD8+ KLRG1+ short-lived effector cells and significant increase in PD-1+ TIM3+ exhausted T cells in group 4 and 5 relative to control. Reps1 and Adpgk neoantigen peptides are widely reported and used in MC38 syngenic model. However, they were not included because both were undetected by sequencing. Cell line authentication by STR profiling confirmed that our cells matched that of MC38 from Kerafast. Conclusions: Using an in-house pipeline, we derived a set of novel neoantigen peptides that robustly controlled tumor growth in the MC38 tumor challenge model. In-silico binding predictions did not correlate with in-vivo patterns of IFNγ secretion. In-vivo tests for IFNγ induction after peptide vaccination is a better measure for potential in tumor control. Upregulation of T-cell exhaustion markers after peptide vaccination explains the improved response with anti-PDL1. Reps1 and Adpgk mutations were absent in our cells, which calls caution to researchers conducting similar research.

Vaccine adjuvant-elicited CD8+ T cell immunity is co-dependent on T-bet and FOXO1

T-bet and FOXO1 are transcription factors canonically associated with effector and memory Tcell fates, respectively. During an infectious response, these factors direct the development of CD8+ Tcell fates, where T-bet deficiency leads to ablation of only short-lived effector cells, while FOXO1 deficiency results in selective loss of memory. In contrast, following adjuvanted subunit vaccination in mice, both effector- and memory-fated Tcells are compromised in the absence of either T-bet or FOXO1. Thus, unlike responses to challenge with Listeria monocytogenes, productive CD8+ Tcell responses to adjuvanted vaccination require coordinated regulation of FOXO1 and T-bet transcriptional programs. Single-cell RNA sequencing analysis confirms simultaneous T-bet, FOXO1, and TCF1 transcriptional activity in vaccine-elicited, but not infection-elicited,Tcells undergoing clonal expansion. Collectively, our data show that subunit vaccine adjuvants elicit Tcell responses dependent on transcription factors associated with effector and memory cell fates.

Translation inhibitor PDCD4 promotes CD8+ T cell proliferation during antiviral response

Abstract CD8+ T cell clonal expansion is critical for controlling intracellular infections and tumors. Thus, unravelling the mechanisms that regulate CD8+ T cell proliferation are imperative to improve vaccine design and immunotherapy. However, the molecular mechanisms that govern CD8+ T cell proliferation are still not fully understood. PDCD4 (Programmed cell death 4) was shown to inhibit translation by sequestering mRNA helicase eIF4A, which leads to translation inhibition of genes involved in cell proliferation. Despite the well-characterized anti-proliferative role of PDCD4, our studies suggest that PDCD4 promotes CD8+ T cell proliferation during the expansion phase of acute LCMV infection. We find that PDCD4 over-expressed Ag-specific CD8+ T cells have higher proliferation rate which leads to increased cell number compared to control Ag-specific CD8+ T cells. Consistent with the over-expression results, PDCD4 knocking-down Ag-specific CD8+ T cells undergo less cell proliferation, resulting in reduced clonal expansion compared to controls. Interestingly, contrary to the paradigm that increased proliferation generates more short-lived effector cells, CD8+ T cell proliferation mediated by PDCD4 does not skew the differentiation of short-lived and memory precursor effector cells. This PDCD4 mediated CD8+ T cell proliferation is also confirmed by over-expression of a constitutively active form of PDCD4 which resists degradation by CD8+ T cell endogenous ubiquitin pathway. In conclusion, our work has identified a novel pro-proliferative role of PDCD4 during CD8+ T cell response. Supported by grants from NIH (R01 AI139675)

Dynamic single cell lineage recording of endogenous viral specific CD8 T cells reveals multiple potential cell fate pathways

Abstract In response to viral infection, antigen specific naïve CD8 T cells expand to give rise to a heterogenous pool of effector cells consisting of short-lived effector cells (SLECs) and memory precursor effector cells (MPECs). While these effector populations are phenotypically and functionally well characterized, we still don’t fully understand how they arise from antigen responsive naïve CD8 T cells. We have combined progressive lineage recording with single-cell RNA sequencing and T cell receptor sequencing to delineate the early differentiation of OVA-specific endogenous CD8 T cells in response to acute VSV infection. Transcriptional profiling of CD8 T cells captured at the peak of T cell response confirmed 8 distinct T cell states including a unique interferon responsive cluster. RNA Velocity trajectory analysis supported an asymmetric model of CD8 T cell differentiation where early effector cells gave rise to SLECs while MPECs differentiated into further memory precursors. Moreover, our CRISPR/Cas9-based lineage recorder uncovered T cell clones of various sizes and allowed us to follow up to 5 generations of differentiating CD8 T cells. We observed that expanded clones comprised of memory and effector CD8 T cells while medium size clones preferred memory or effector fate, suggesting that different clones follow different differentiation models. Thus, using RNA-seq based trajectory analyses and a dynamic lineage recorder we uncovered potential differentiation pathways taken by early viral specific CD8 T cells. Our single cell full length TCR-seq will further add to our current models and highlight TCR sequences with better memory potential in response to infection. Supported by grants from NIH (R01 AI089805, R01 CA254042) and a training fellowship from the Burroughs Wellcome Fund.

Neutrophil diversity in inflammation and cancer.

Neutrophils are the most abundant circulating leukocytes in humans and the first immune cells recruited at the site of inflammation. Classically perceived as short-lived effector cells with limited plasticity and diversity, neutrophils are now recognized as highly heterogenous immune cells, which can adapt to various environmental cues. In addition to playing a central role in the host defence, neutrophils are involved in pathological contexts such as inflammatory diseases and cancer. The prevalence of neutrophils in these conditions is usually associated with detrimental inflammatory responses and poor clinical outcomes. However, a beneficial role for neutrophils is emerging in several pathological contexts, including in cancer. Here we will review the current knowledge of neutrophil biology and heterogeneity in steady state and during inflammation, with a focus on the opposing roles of neutrophils in different pathological contexts.

Themis suppresses the effector function of CD8+ T cells in acute viral infection.

CD8+ T cells play a central role in antiviral immune responses. Upon infection, naive CD8+ T cells differentiate into effector cells to eliminate virus-infected cells, and some of these effector cells further differentiate into memory cells to provide long-term protection after infection is resolved. Although extensively investigated, the underlying mechanisms of CD8+ T-cell differentiation remain incompletely understood. Themis is a T-cell-specific protein that plays critical roles in T-cell development. Recent studies using Themis T-cell conditional knockout mice also demonstrated that Themis is required to promote mature CD8+ T-cell homeostasis, cytokine responsiveness, and antibacterial responses. In this study, we used LCMV Armstrong infection as a probe to explore the role of Themis in viral infection. We found that preexisting CD8+ T-cell homeostasis defects and cytokine hyporesponsiveness do not impair viral clearance in Themis T-cell conditional knockout mice. Further analyses showed that in the primary immune response, Themis deficiency promoted the differentiation of CD8+ effector cells and increased their TNF and IFNγ production. Moreover, Themis deficiency impaired memory precursor cell (MPEC) differentiation but promoted short-lived effector cell (SLEC) differentiation. Themis deficiency also enhanced effector cytokine production in memory CD8+ T cells while impairing central memory CD8+ T-cell formation. Mechanistically, we found that Themis mediates PD-1 expression and its signaling in effector CD8+ T cells, which explains the elevated cytokine production in these cells when Themis is disrupted.

Memory Precursors and Short-Lived Effector T cell Subsets Have Different Sensitivities to TGFβ.

After exposure to an antigen, CD8 T cells reach a decision point about their fate: to become either short-lived effector cells (SLECs) or memory progenitor effector cells (MPECs). SLECs are specialized in providing an immediate effector function but have a shorter lifespan and lower proliferative capacity compared to MPECs. Upon encountering the cognate antigen during an infection, CD8 T cells rapidly expand and then contract to a level that is maintained for the memory phase after the peak of the response. Studies have shown that the contraction phase is mediated by TGFβ and selectively targets SLECs, while sparing MPECs. The aim of this study is to investigate how the CD8 T cell precursor stage determines TGFβ sensitivity. Our results demonstrate that MPECs and SLECs have differential responses to TGFβ, with SLECs being more sensitive to TGFβ than MPECs. This difference in sensitivity is associated with the levels of TGFβRI and RGS3, and the SLEC-related transcriptional activator T-bet binding to the TGFβRI promoter may provide a molecular basis for increased TGFβ sensitivity in SLECs.

Chronic lymphocytic leukemia presence impairs antigen-specific CD8+ T-cell responses through epigenetic reprogramming towards short-lived effectors.

T-cell dysregulation in chronic lymphocytic leukemia (CLL) associates with low response rates to autologous T cell-based therapies. How CLL affects antigen-specific T-cell responses remains largely unknown. We investigated (epi)genetic and functional consequences of antigen-specific T-cell responses in presence of CLL in vitro and in an adoptive-transfer murine model. Already at steady-state, antigen-experienced patient-derived T cells were skewed towards short-lived effector cells (SLEC) at the expense of memory-precursor effector cells (MPEC). Stimulation of these T cells in vitro showed rapid induction of effector genes and suppression of key memory transcription factors only in presence of CLL cells, indicating epigenetic regulation. This was investigated in vivo by following antigen-specific responses of naïve OT-I CD8+ cells to mCMV-OVA in presence/absence of TCL1 B-cell leukemia. Presence of leukemia resulted in increased SLEC formation, with disturbed inflammatory cytokine production. Chromatin and transcriptome profiling revealed strong epigenetic modifications, leading to activation of an effector and silencing of a memory profile through presence of CLL cells. Secondary challenge in vivo confirmed dysfunctional memory responses by antigen-experienced OT-I cells generated in presence of CLL. Altogether, we show that presence of CLL induces a short-lived effector phenotype and impaired memory responses by epigenetic reprogramming during primary responses.

The aryl hydrocarbon receptor cell intrinsically promotes resident memory CD8+ T cell differentiation and function

The Aryl hydrocarbon receptor (Ahr) regulates the differentiation and function of CD4+ Tcells; however, its cell-intrinsic role in CD8+ Tcells remains elusive. Herein we show that Ahr acts as a promoter of resident memory CD8+ Tcell (TRM) differentiation and function. Genetic ablation of Ahr in mouse CD8+ Tcells leads to increased CD127-KLRG1+ short-lived effector cells and CD44+CD62L+ T central memory cells but reduced granzyme-B-producing CD69+CD103+ TRM cells. Genome-wide analyses reveal that Ahr suppresses the circulating while promoting the resident memory core gene program. A tumor resident polyfunctional CD8+ Tcell population, revealed by single-cell RNA-seq, is diminished upon Ahr deletion, compromising anti-tumor immunity. Human intestinal intraepithelial CD8+ Tcells also highly express AHR that regulates invitro TRM differentiation and granzyme B production. Collectively, these data suggest that Ahr is an important cell-intrinsic factor for CD8+ Tcell immunity.

Regulatory T-cell-derived interleukin-15 shapes cytotoxic T cell memory.

It is well known that regulatory T-cells (Tregs) are required to prevent autoimmunity, but they may also have some less-well understood immune-stimulatory effects. In particular, in CD8+ T-cell responses Tregs select high-affinity clones upon priming and promote memory by inhibiting inflammation-dependent generation of short-lived effector cells. In the current issue of the European Journal of Immunology [Eur. J. Immunol. 2023. 53: 2149400], Madi etal. report the surprising finding that human and murine FOXP3+ Tregs are a physiologically relevant source of IL-15, a homeostatic cytokine that promotes antigen-independent maintenance of CD8+ memory T-cells. In mice that lack IL-15 selectively in FOXP3+ Tregs the authors show that the composition of the CD8+ T-cell memory pool is altered in the absence of Treg-derived IL-15, since a subset of terminally effector memory cells is drastically reduced. Otherwise Treg-derived IL-15 is dispensable for antiviral immune responses and the generation of anti-viral CD8+ memory T-cells. These findings add to our understanding of the multifaceted role of Tregs in immune responses, and how IL-15 derived from different cellular sources maintains anti-viral T-cell memory.

Manipulation of diacylglycerol and ERK-mediated signaling differentially controls CD8+ T cell responses during chronic viral infection.

Activation of T cell receptor (TCR) signaling is critical for clonal expansion of CD8+ T cells. However, the effects of augmenting TCR signaling during chronic antigen exposure is less understood. Here, we investigated the role of diacylglycerol (DAG)-mediated signaling downstream of the TCR during chronic lymphocytic choriomeningitis virus clone 13 (LCMV CL13) infection by blocking DAG kinase zeta (DGKζ), a negative regulator of DAG. We examined the activation, survival, expansion, and phenotype of virus-specific T cell in the acute and chronic phases of LCMV CL13-infected in mice after DGKζ blockade or selective activation of ERK. Upon LCMV CL13 infection, DGKζ deficiency promoted early short-lived effector cell (SLEC) differentiation of LCMV-specific CD8+ T cells, but this was followed by abrupt cell death. Short-term inhibition of DGKζ with ASP1570, a DGKζ-selective pharmacological inhibitor, augmented CD8+ T cell activation without causing cell death, which reduced virus titers both in the acute and chronic phases of LCMV CL13 infection. Unexpectedly, the selective enhancement of ERK, one key signaling pathway downstream of DAG, lowered viral titers and promoted expansion, survival, and a memory phenotype of LCMV-specific CD8+ T cells in the acute phase with fewer exhausted T cells in the chronic phase. The difference seen between DGKζ deficiency and selective ERK enhancement could be potentially explained by the activation of the AKT/mTOR pathway by DGKζ deficiency, since the mTOR inhibitor rapamycin rescued the abrupt cell death seen in virus-specific DGKζ KO CD8+ T cells. Thus, while ERK is downstream of DAG signaling, the two pathways lead to distinct outcomes in the context of chronic CD8+ T cell activation, whereby DAG promotes SLEC differentiation and ERK promotes a memory phenotype.

Crossover behavior of the Zika virus infection and the delayed immune response

The control of the transmission of viruses is really challenging. Zika virus is the twentieth among the most deadly viruses in world’s history. With the advancement in research and technology several epidemiological issues are controlled, yet the vector borne diseases have remained a great challenge and the most effective approach to control its spread is to strictly adhere to the precautionary measures. Computational framework is ideal to forecast the impact of precautionary measures on the crossover behavior of the Zika virus and the delay in population growth, caused by such viruses. During this research, a delayed computational model is studied and the dynamical analysis with useful thresholds are reported. The compartmental model is comprised of the interactions of Zika virus infected cells and the short lived effector cells. Based on the fetal abnormalities, associated with the Zika virus infection, delayed pregnancy is recommended by WHO. The impact of the Zika virus to the delayed pregnancies, to avoid such fetal complications is demonstrated with the aid of dynamical analysis of interactions with delay at the inter-cellular levels. The dynamics are depicted numerically relative to key parameters and useful conclusions are drawn.

The generation of stem cell-like memory cells early after BNT162b2 vaccination is associated with durability of memory CD8+ Tcell responses.

COVID-19 vaccines elicit humoral and cellular immune responses. Durable maintenance of vaccine-induced immunity is required for long-term protection of the host. Here, we examine activation and differentiation of vaccine-induced CD8+ T cells using MHC class I (MHC-I) multimers and correlations between early differentiation and the durability of CD8+ T cell responses among healthcare workers immunized with two doses of BNT162b2. The frequency of MHC-I multimer+ cells is robustly increased by BNT162b2 but decreases 6 months post-second vaccination to 2.4%–65.6% (23.0% on average) of the peak. MHC-I multimer+ cells dominantly exhibit phenotypes of activated effector cells 1–2 weeks post-second vaccination and gradually acquire phenotypes of long-term memory cells, including stem cell-like memory T (TSCM) cells. Importantly, the frequency of TSCM cells 1–2 weeks post-second vaccination significantly correlates with the 6-month durability of CD8+ T cells, indicating that early generation of TSCM cells determines the longevity of vaccine-induced memory CD8+ T cell responses.

Abstract 2529: T-cell phenotype and differentiation vary in the tumor microenvironment of follicular lymphoma and are associated with patient outcome

Abstract Previous studies have found that the prevalence of subtypes of T cells may be associated with patient outcomes, but a comprehensive analysis of the immune profile in the TM of FL has not been done. In the present study, we identified groups of FL patients with discretely unique TMEs and determined whether the T-cell phenotypes in the TME differed among groups. Using a cohort of 82 FL patients with biopsy specimens collected before treatment, we defined the type of TME based on the content of major lineages (T, B, monocytes/macrophages and NK cells) determined by CyTOF analysis. Hierarchical clustering of this cohort stratified patients into 4 groups with different TME: group 1 (G1) included patients with a high percentage of monocyte/macrophages/NK cells; patients from G2 and G3 were enriched for intratumoral T and B cells, respectively. Patients with intermediate numbers of T and B cells were included in G4. CITRUS analysis revealed that T-cell clusters with phenotypes expressing KLRG1, CD57, PD-1dim and rich in TEMRA cells were significantly more abundant in G1 when compared to G2, G3 or G4. In contrast, T-cell clusters with phenotypes containing CD127, CD45RA, CCR7 or PD-1high cells were significantly less abundant in G1 when compared to other groups. When compared to G3 or G4, 2 classes of T cell clusters, all from CD4+ T cells, were significantly more (CD127+KLRG1-) or less (CD57+PD-1high) abundant in G2, respectively. Clusters with a phenotype rich in short-lived effector cells (SLEC) (from CD8+) were upregulated in G3 when compared to G4. These results suggest that patient groups with distinct TME exhibited variable T-cell phenotypes. To determine the role of T-cell differentiation in predicting patient outcome in FL, we identified T-cell subsets using tSNE plots based on the expression of T-cell maturation markers. We identified 18 subsets (S1-S18) of T cells (11 from CD4, 6 from CD8 and 1 from CD4-CD8-) in each sample. Four subsets - S4 (CD4+TN), S5 (CD4+TCM), S7 (CD8+TN) and S10 (CD8+MEPCs) - were considered to be naïve cells or cells in the early stages of differentiation. Four additional subsets - S8 (CD57+TFH), S9 (CD4+TEXH), S13 (CD8+SLECs) and S17 (CD4+PD-1+Treg) - were memory cells with expression of surface markers indicting late-stage differentiation. We found that the 4 subsets (S4: p=0.08, S5: p=0.01, S7: p=0.04 and S10: p<0.01) with an early-stage phenotype were associated with a favorable clinical outcome. In contrast, subsets (S8: p=0.02, S9: p=0.04, S13: p=0.07 and S17: p=0.06) with a late-stage differentiation phenotype had an unfavorable survival. Supporting this finding, we observed that increased numbers of CD45RA+ T cells correlated with a favorable survival. These results indicate that the differentiation stage may determine the role of T cells in predicting patient outcome in FL. Citation Format: Zhi-Zhang Yang, Hyo Jin Kim, Hongyan Wu, Xinyi Tang, Jordan Krull, Patrizia Mondello, Jose Villasboas, Anne Novak, Stephen Ansell. T-cell phenotype and differentiation vary in the tumor microenvironment of follicular lymphoma and are associated with patient outcome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2529.

The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression.

During an immune response to microbial infection, CD8+ T cells give rise to short-lived effector cells and memory cells that provide sustained protection. Although the transcriptional programs regulating CD8+ T cell differentiation have been extensively characterized, the role of long noncoding RNAs (lncRNAs) in this process remains poorly understood. Using a functional genetic knockdown screen, we identified the lncRNA Malat1 as a regulator of terminal effector cells and the terminal effector memory (t-TEM) circulating memory subset. Evaluation of chromatin-enriched lncRNAs revealed that Malat1 grouped with trans lncRNAs that exhibit increased RNA interactions at gene promoters and gene bodies. Moreover, we observed that Malat1 was associated with increased H3K27me3 deposition at a number of memory cell-associated genes through a direct interaction with Ezh2, thereby promoting terminal effector and t-TEM cell differentiation. Our findings suggest an important functional role of Malat1 in regulating CD8+ T cell differentiation and broaden the knowledge base of lncRNAs in CD8+ T cell biology.