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The genomic loci associated with B cell differentiation that are subject to transcriptional and epigenetic regulation in vivo are not well defined, leaving a gap in our understanding of the development of humoral immune responses. Here, using an in vivo T cell independent B cell differentiation model, we define a cellular division-dependent cis -regulatory element road map using ATAC-seq. Chromatin accessibility changes correlate with gene expression and reveal the reprogramming of transcriptional networks and the genes they regulate at specific cell divisions. A subset of genes in naive B cells display accessible promoters in the absence of transcription and are marked by H3K27me3, an EZH2 catalyzed repressive modification. Such genes encode regulators of cell division and metabolism and include the essential plasma cell transcription factor Blimp-1. Chemical inhibition of EZH2 results in enhanced plasma cell formation, increased expression of the above gene set, and premature expression of Blimp-1 ex vivo. These data provide insights into cell-division coupled epigenetic and transcriptional processes that program plasma cells. During B cell differentiation, the role of different genomic loci in transcriptional and epigenetic regulation in vivo is not well defined. Here the authors use an in vivo B cell differentiation model to map cellular division-dependent cis -regulatory element road map with ATAC-seq.

B cells provide humoral immunity by differentiating into antibody-secreting plasma cells, a process that requires cellular division and is linked to DNA hypomethylation. Conversely, little is known about how de novo deposition of DNA methylation affects B cell fate and function. Here we show that genetic deletion of the de novo DNA methyltransferases Dnmt3a and Dnmt3b (Dnmt3-deficient) in mouse B cells results in normal B cell development and maturation, but increased cell activation and expansion of the germinal center B cell and plasma cell populations upon immunization. Gene expression is mostly unaltered in naive and germinal center B cells, but dysregulated in Dnmt3-deficient plasma cells. Differences in gene expression are proximal to Dnmt3-dependent DNA methylation and chromatin changes, both of which coincide with E2A and PU.1-IRF composite-binding motifs. Thus, de novo DNA methylation limits B cell activation, represses the plasma cell chromatin state, and regulates plasma cell differentiation. DNA methylation is known to contribute to B cell differentiation, but de novo methylation has not been studied in this context. Here the authors use a conditional Dnmt3a/b knockout mouse to map the function of de novo DNA methylation in B cell differentiation and the development of humoral immunity.

PD-1 is a key negative regulator of CD8 + T cell activation and is highly expressed by exhausted T cells in cancer and chronic viral infection. Although PD-1 blockade can improve viral and tumor control, physiological PD-1 expression prevents immunopathology and improves memory formation. The mechanisms driving high PD-1 expression in exhaustion are not well understood and could be critical to disentangling its beneficial and detrimental effects. Here, we functionally interrogated the epigenetic regulation of PD-1 using a mouse model with deletion of an exhaustion-specific PD-1 enhancer. Enhancer deletion exclusively alters PD-1 expression in CD8 + T cells in chronic infection, creating a ‘sweet spot’ of intermediate expression where T cell function is optimized compared to wild-type and Pdcd1 -knockout cells. This permits improved control of chronic infection without additional immunopathology. Together, these results demonstrate that tuning PD-1 via epigenetic editing can reduce CD8 + T cell dysfunction while avoiding excess immunopathology. PD-1 is a critical modulator of CD8 + T cell activation and exhaustion. Sen and colleagues show that a cell-state-specific enhancer tunes PD-1 expression exclusively in exhaustion and that deletion of this enhancer improves CD8 + T cell function.

Boss and colleagues provide mechanistic insight into cell-division-coupled transcriptional and epigenetic reprogramming events during plasma cell differentiation. The epigenetic processes that regulate antibody-secreting plasma cells are not well understood. Here, analysis of plasma cell differentiation revealed DNA hypomethylation of 10% of CpG loci that were overrepresented at enhancers. Inhibition of DNA methylation enhanced plasma cell commitment in a cell-division-dependent manner. Analysis of B cells differentiating in vivo stratified by cell division revealed a fivefold increase in mRNA transcription coupled to DNA hypomethylation. Demethylation occurred first at binding motifs for the transcription factors NF-κB and AP-1 and later at those for the transcription factors IRF and Oct-2 and was coincident with activation and differentiation gene-expression programs in a cell-division-dependent manner. These data provide mechanistic insight into cell-division-coupled transcriptional and epigenetic reprogramming and suggest that DNA hypomethylation reflects the cis-regulatory history of plasma cell differentiation.

The receptor PD-1 drives immune cell inhibition and exhaustion upon up-regulation. Blockade of this receptor has been shown to be an effective way to restore the function of cells during chronic inflammation, and has been employed therapeutically to that end in cancer patients. Here, systems and regulomes that drive PD-1 expression were studied across multiple cell types and in response to various immune stimuli. A novel driver of PD-1 expression (NF-κB) was identified as the primary driver of PD-1 expression in macrophages. This transcription factor, similarly to the previously identified NFATc1 and STAT3 activators and the repressor FoxO1, binds to the CR-C region of the Pdcd1 locus. The function of this cis-element was found to be involved in driving early changes to PD-1 expression, but not necessary for the prolonged expression of PD-1 during chronic inflammation. Abrogating early PD-1 expression through deletion of CR-C, without altering later modalities of expression, resulted in a shift away from effector cell formation towards a stronger memory cell formation. Furthermore, the histone modifier LSD1 was shown to bind to and regulate the PD-1 locus on an epigenetic level, enforcing a silenced profile following the transient expression seen in the late stages of an acute infection. This partially accounts for the differential expression of PD-1 seen in acute compared to chronic inflammatory settings. In further analysis of the epigenetics of immune responses, distinct chromatin accessibility profiles were identified for naive, effector, exhausted, and memory T cells during viral infection, and correlated with changes in mRNA expression. Specifically, a set of loci that remains accessible during the effector to memory transition identifies drivers of improved memory functionality compared to naive cells. In addition to providing an understanding of which active immune environments may induce and be affected by PD-1's function, knowledge of both the molecular mechanisms regulating PD-1, as well as the dynamic epigenetics of the immune response, may help tailor future immunotherapies for fighting cancer, chronic HIV and HCV infections, or prevention of allergic responses, transplant rejection, and autoimmunity as well as improving durable responses to vaccines.

During prolonged exposure to antigens, such as chronic viral infections, sustained T cell receptor (TCR) signaling can result in T cell exhaustion mediated in part by expression of Programmed cell death-1 (PD-1) encoded by the Pdcd1 gene. Here, dynamic changes in histone H3K4 modifications at the Pdcd1 locus during ex vivo and in vivo activation of CD8 T cells, suggested a potential role for the histone H3 lysine 4 demethylase LSD1 in regulating PD-1 expression. CD8 T cells lacking LSD1 expressed higher levels of Pdcd1 mRNA following ex vivo stimulation, as well as increased surface levels of PD-1 during acute but not chronic infection with lymphocytic choriomeningitis virus (LCMV). Blimp-1, a known repressor of PD-1, recruited LSD1 to the Pdcd1 gene during acute but not chronic LCMV infection. Loss of DNA methylation at Pdcd1’s promoter proximal regulatory regions is highly correlated with its expression. However, following acute LCMV infection where PD-1 expression levels return to near base line, LSD1-deficient CD8 T cells failed to remethylate the Pdcd1 locus to the levels of wild-type cells. Finally, in a murine melanoma model, the frequency of PD-1 expressing tumor infiltrating LSD1-deficient CD8 T cells was greater than wild-type. Thus, LSD1 is recruited to the Pdcd1 locus by Blimp-1, downregulates PD-1 expression by facilitating the removal of activating histone marks, and is important for remethylation of the locus. Together, these data provide insight into the complex regulatory mechanisms governing T cell immunity and the regulation of a critical T cell checkpoint gene. LSD1 suppress PD-1 expression following acute infection or transient induction. Blimp-1 binding to the Pdcd1 locus is required to recruit LSD1. LSD1 is required to fully remethylate the PD-1 proximal promoter region.

IntroductionApproximately 30% of somatic hospital inpatients experience psychosocial distress, contributing to increased (re-)hospitalisation rates, treatment resistance, morbidity, and direct and indirect costs. However, such distress often remains unrecognised and unaddressed. We established ‘SomPsyNet’, a ‘stepped and collaborative care model’ (SCCM) for somatic hospital inpatients, aiming at alleviating this issue through early identification of distress and provision of appropriate care, providing problem-focused pathways and strengthening collaborative care. We report the protocol of the ‘SomPsyNet’ study, aiming to evaluate implementation and impact of the SCCM on distressed patients’ health-related quality of life. Secondary objectives include assessing efficacy of the screening procedures, influence of SCCM on other health outcomes and associated costs.Methods and analysisOur stepped wedge cluster randomised trial conducted at three tertiary hospitals comprises three conditions: treatment as usual (TAU) without screening for distress (phase 0), TAU with screening but without consequences (phase I, main comparator) and TAU with screening and psychosomatic-psychiatric consultations for those distressed (phase II). The time-of-transition between phases I and II was randomised. Sample size target is N=2200–2500 participants, with 6 month follow-up for distressed (anticipated n=640–700) and a subsample of non-distressed (anticipated n=200) patients. Primary outcome is mental health-related quality of life (SF-36 ‘Mental Health Component Summary score’); secondary outcomes include psychosocial distress, anxiety, depressive and somatic symptoms, symptom burden and distress, resilience, social support and qualitative of life, assessed by internationally accepted instruments, with good psychometric properties. Further, health claims data will be used to assess SCCM’s impact on direct and indirect costs.Ethics and disseminationSomPsyNet adheres to the Helsinki Declaration and is approved by the ‘Ethikkommission Nordwest- und Zentralschweiz’ (2019–01724). Findings will be published in peer-reviewed journals and communicated to participants, healthcare professionals and the public.Trial registration numberSwiss National Clinical Trials Portal; ClinicalTrials.gov (NCT04269005, updated 19.09.2023).