Exploration of potential immune mechanisms in cervical dystonia

BACKGROUND

Although there are many possible causes for cervical dystonia (CD), a specific etiology cannot be identified in most cases. Prior studies have suggested a relationship between autoimmune disease and some cases of CD, pointing to possible immunological mechanisms.

OBJECTIVE

The goal was to explore the potential role of multiple different immunological mechanisms in CD.

METHODS

First, a broad screening test compared neuronal antibodies in controls and CD. Second, unbiased blood plasma proteomics provided a broad screen for potential biologic differences between controls and CD. Third, a multiplex immunoassay compared 37 markers associated with immunological processes in controls and CD. Fourth, relative immune cell frequencies were investigated in blood samples of controls and CD. Finally, sequencing studies investigated the association of HLA DQB1 and DRB1 alleles in controls versus CD.

RESULTS

Screens for anti-neuronal antibodies did not reveal any obvious abnormalities. Plasma proteomics pointed towards certain abnormalities of immune mechanisms, and the multiplex assay pointed more specifically towards abnormalities in T lymphocytes. Abnormal immune cell frequencies were identified for some CD cases, and these cases clustered together as a potential subgroup. Studies of HLA alleles indicated a possible association between CD and DRB1*15:03, which is reported to mediate the penetrance of autoimmune disorders.

CONCLUSIONS

Altogether, the association of CD with multiple different blood-based immune measures point to abnormalities in cell-mediated immunity that may play a pathogenic role for a subgroup of individuals with CD.

Prevention of respiratory virus transmission by resident memory CD8+ T cells

An ideal vaccine both attenuates virus growth and disease in infected individuals and reduces the spread of infections in the population, thereby generating herd immunity. Although this strategy has proved successful by generating humoral immunity to measles, yellow fever and polio, many respiratory viruses evolve to evade pre-existing antibodies1. One approach for improving the breadth of antiviral immunity against escape variants is through the generation of memory T cells in the respiratory tract, which are positioned to respond rapidly to respiratory virus infections2-6. However, it is unknown whether memory T cells alone can effectively surveil the respiratory tract to the extent that they eliminate or greatly reduce viral transmission following exposure of an individual to infection. Here we use a mouse model of natural parainfluenza virus transmission to quantify the extent to which memory CD8+ T cells resident in the respiratory tract can provide herd immunity by reducing both the susceptibility of acquiring infection and the extent of transmission, even in the absence of virus-specific antibodies. We demonstrate that protection by resident memory CD8+ T cells requires the antiviral cytokine interferon-γ (IFNγ) and leads to altered transcriptional programming of epithelial cells within the respiratory tract. These results suggest that tissue-resident CD8+ T cells in the respiratory tract can have important roles in protecting the host against viral disease and limiting viral spread throughout the population.

CRISPR/Cas9 editing reveals IRF8 regulated gene signatures restraining plasmablast differentiation

The transcription factor Interferon regulatory factor 8 (IRF8) is involved in maintaining B cell identity. However, how IRF8 regulates T cell independent B cell responses are not fully characterized. Here, an in vivo CRISPR/Cas9 system was optimized to generate Irf8-deficient murine B cells and used to determine the role of IRF8 in B cells responding to LPS stimulation. Irf8-deficient B cells more readily formed CD138⁺ plasmablasts in response to LPS with the principal dysregulation occurring at the activated B cell stage. Transcriptional profiling revealed an upregulation of plasma cell associated genes prematurely in activated B cells and a failure to repress the gene expression programs of IRF1 and IRF7 in Irf8-deficient cells. These data expand on the known roles of IRF8 in regulating B cell identity by preventing premature plasma cell formation and highlight how IRF8 helps evolve TLR responses away from the initial activation towards those driving humoral immunity.

The 'omics of obesity in B-cell acute lymphoblastic leukemia

The obesity pandemic currently affects more than 70 million Americans and more than 650 million individuals worldwide. In addition to increasing susceptibility to pathogenic infections (eg, SARS-CoV-2), obesity promotes the development of many cancer subtypes and increases mortality rates in most cases. We and others have demonstrated that, in the context of B-cell acute lymphoblastic leukemia (B-ALL), adipocytes promote multidrug chemoresistance. Furthermore, others have demonstrated that B-ALL cells exposed to the adipocyte secretome alter their metabolic states to circumvent chemotherapy-mediated cytotoxicity. To better understand how adipocytes impact the function of human B-ALL cells, we used a multi-omic RNA-sequencing (single-cell and bulk transcriptomic) and mass spectroscopy (metabolomic and proteomic) approaches to define adipocyte-induced changes in normal and malignant B cells. These analyses revealed that the adipocyte secretome directly modulates programs in human B-ALL cells associated with metabolism, protection from oxidative stress, increased survival, B-cell development, and drivers of chemoresistance. Single-cell RNA sequencing analysis of mice on low- and high-fat diets revealed that obesity suppresses an immunologically active B-cell subpopulation and that the loss of this transcriptomic signature in patients with B-ALL is associated with poor survival outcomes. Analyses of sera and plasma samples from healthy donors and those with B-ALL revealed that obesity is associated with higher circulating levels of immunoglobulin-associated proteins, which support observations in obese mice of altered immunological homeostasis. In all, our multi-omics approach increases our understanding of pathways that may promote chemoresistance in human B-ALL and highlight a novel B-cell-specific signature in patients associated with survival outcomes.

A transcriptionally distinct subset of influenza-specific effector memory B cells predicts long-lived antibody responses to vaccination in humans

Seasonal influenza vaccination elicits hemagglutinin (HA)-specific memory B (Bmem) cells, and although multiple Bmem cell populations have been characterized, considerable heterogeneity exists. We found that HA-specific human Bmem cells differed in the expression of surface marker FcRL5 and transcriptional factor T-bet. FcRL5+T-bet+ Bmem cells were transcriptionally similar to effector-like memory cells, while T-betnegFcRL5neg Bmem cells exhibited stem-like central memory properties. FcRL5+ Bmem cells did not express plasma-cell-commitment factors but did express transcriptional, epigenetic, metabolic, and functional programs that poised these cells for antibody production. Accordingly, HA+ T-bet+ Bmem cells at day 7 post-vaccination expressed intracellular immunoglobulin, and tonsil-derived FcRL5+ Bmem cells differentiated more rapidly into antibody-secreting cells (ASCs) in vitro. The T-bet+ Bmem cell response positively correlated with long-lived humoral immunity, and clonotypes from T-bet+ Bmem cells were represented in the secondary ASC response to repeat vaccination, suggesting that this effector-like population predicts influenza vaccine durability and recall potential.

Distinct transcriptomic and epigenomic modalities underpin human memory T cell subsets and their activation potential

Human memory T cells (MTC) are poised to rapidly respond to antigen re-exposure. Here, we derived the transcriptional and epigenetic programs of resting and ex vivo activated, circulating CD4+ and CD8+ MTC subsets. A progressive gradient of gene expression from naïve to TCM to TEM is observed, which is accompanied by corresponding changes in chromatin accessibility. Transcriptional changes suggest adaptations of metabolism that are reflected in altered metabolic capacity. Other differences involve regulatory modalities comprised of discrete accessible chromatin patterns, transcription factor binding motif enrichment, and evidence of epigenetic priming. Basic-helix-loop-helix factor motifs for AHR and HIF1A distinguish subsets and predict transcription networks to sense environmental changes. Following stimulation, primed accessible chromatin correlate with an augmentation of MTC gene expression as well as effector transcription factor gene expression. These results identify coordinated epigenetic remodeling, metabolic, and transcriptional changes that enable MTC subsets to ultimately respond to antigen re-encounters more efficiently.

Aiolos represses CD4+ T cell cytotoxic programming via reciprocal regulation of TFH transcription factors and IL-2 sensitivity

During intracellular infection, T follicular helper (TFH) and T helper 1 (TH1) cells promote humoral and cell-mediated responses, respectively. Another subset, CD4-cytotoxic T lymphocytes (CD4-CTLs), eliminate infected cells via functions typically associated with CD8+ T cells. The mechanisms underlying differentiation of these populations are incompletely understood. Here, we identify the transcription factor Aiolos as a reciprocal regulator of TFH and CD4-CTL programming. We find that Aiolos deficiency results in downregulation of key TFH transcription factors, and consequently reduced TFH differentiation and antibody production, during influenza virus infection. Conversely, CD4-CTL programming is elevated, including enhanced Eomes and cytolytic molecule expression. We further demonstrate that Aiolos deficiency allows for enhanced IL-2 sensitivity and increased STAT5 association with CD4-CTL gene targets, including Eomes, effector molecules, and IL2Ra. Thus, our collective findings identify Aiolos as a pivotal regulator of CD4-CTL and TFH programming and highlight its potential as a target for manipulating CD4+ T cell responses.

Deletion of histone demethylase Lsd1 (Kdm1a) during retinal development leads to defects in retinal function and structure

Purpose

The purpose of this study was to investigate the role of Lysine specific demethylase 1 (Lsd1) in murine retinal development. LSD1 is a histone demethylase that can demethylate mono- and di-methyl groups on H3K4 and H3K9. Using Chx10-Cre and Rho-iCre75 driver lines, we generated novel transgenic mouse lines to delete Lsd1 in most retinal progenitor cells or specifically in rod photoreceptors. We hypothesize that Lsd1 deletion will cause global morphological and functional defects due to its importance in neuronal development.

Methods

We tested the retinal function of young adult mice by electroretinogram (ERG) and assessed retinal morphology by in vivo imaging by fundus photography and SD-OCT. Afterward, eyes were enucleated, fixed, and sectioned for subsequent hematoxylin and eosin (H&E) or immunofluorescence staining. Other eyes were plastic fixed and sectioned for electron microscopy.

Results

In adult Chx10-Cre Lsd1fl/fl mice, we observed a marked reduction in a-, b-, and c-wave amplitudes in scotopic conditions compared to age-matched control mice. Photopic and flicker ERG waveforms were even more sharply reduced. Modest reductions in total retinal thickness and outer nuclear layer (ONL) thickness were observed in SD-OCT and H&E images. Lastly, electron microscopy revealed significantly shorter inner and outer segments and immunofluorescence showed modest reductions in specific cell type populations. We did not observe any obvious functional or morphological defects in the adult Rho-iCre75 Lsd1fl/fl animals.

Conclusion

Lsd1 is necessary for neuronal development in the retina. Adult Chx10-Cre Lsd1fl/fl mice show impaired retinal function and morphology. These effects were fully manifested in young adults (P30), suggesting that Lsd1 affects early retinal development in mice.

IL-6/STAT3 Signaling Axis Enhances and Prolongs Pdcd1 Expression in Murine CD8 T Cells

CD8 cytotoxic T cells are a potent line of defense against invading pathogens. To aid in curtailing aberrant immune responses, the activation status of CD8 T cells is highly regulated. One mechanism in which CD8 T cell responses are dampened is via signaling through the immune-inhibitory receptor Programmed Cell Death Protein-1, encoded by Pdcd1. Pdcd1 expression is regulated through engagement of the TCR, as well as by signaling from extracellular cytokines. Understanding such pathways has influenced the development of numerous clinical treatments. In this study, we showed that signals from the cytokine IL-6 enhanced Pdcd1 expression when paired with TCR stimulation in murine CD8 T cells. Mechanistically, signals from IL-6 were propagated through activation of the transcription factor STAT3, resulting in IL-6-dependent binding of STAT3 to Pdcd1 cis-regulatory elements. Intriguingly, IL-6 stimulation overcame B Lymphocyte Maturation Protein 1-mediated epigenetic repression of Pdcd1, which resulted in a transcriptionally permissive landscape marked by heightened histone acetylation. Furthermore, in vivo-activated CD8 T cells derived from lymphocytic choriomeningitis virus infection required STAT3 for optimal Programmed Cell Death Protein-1 surface expression. Importantly, STAT3 was the only member of the STAT family present at Pdcd1 regulatory elements in lymphocytic choriomeningitis virus Ag-specific CD8 T cells. Collectively, these data define mechanisms by which the IL-6/STAT3 signaling axis can enhance and prolong Pdcd1 expression in murine CD8 T cells.

Persistent Antigen Harbored by Alveolar Macrophages Enhances the Maintenance of Lung-Resident Memory CD8+ T Cells

Lung tissue-resident memory T cells are crucial mediators of cellular immunity against respiratory viruses; however, their gradual decline hinders the development of T cell-based vaccines against respiratory pathogens. Recently, studies using adenovirus (Ad)-based vaccine vectors have shown that the number of protective lung-resident CD8+ TRMs can be maintained long term. In this article, we show that immunization of mice with a replication-deficient Ad serotype 5 expressing influenza (A/Puerto Rico/8/34) nucleoprotein (AdNP) generates a long-lived lung TRM pool that is transcriptionally indistinct from those generated during a primary influenza infection. In addition, we demonstrate that CD4+ T cells contribute to the long-term maintenance of AdNP-induced CD8+ TRMs. Using a lineage tracing approach, we identify alveolar macrophages as a cell source of persistent NP Ag after immunization with AdNP. Importantly, depletion of alveolar macrophages after AdNP immunization resulted in significantly reduced numbers of NP-specific CD8+ TRMs in the lungs and airways. Combined, our results provide further insight to the mechanisms governing the enhanced longevity of Ag-specific CD8+ lung TRMs observed after immunization with recombinant Ad.

Adipocyte-mediated epigenomic instability in human T-ALL cells is cytotoxic and phenocopied by epigenetic-modifying drugs

The world’s population with obesity is reaching pandemic levels. If current trends continue, it is predicted that there will be 1.5 billion people with obesity by 2030. This projection is alarming due to the association of obesity with numerous diseases including cancer, with recent studies demonstrating a positive association with acute myeloid leukemia (AML) and B cell acute lymphoblastic leukemia (B-ALL). Interestingly, several epidemiological studies suggest the converse relationship may exist in patients with T cell acute lymphoblastic leukemia (T-ALL). To determine the relationship between obesity and T-ALL development, we employed the diet-induced obesity (DIO) murine model and cultured human T-ALL cells in adipocyte-conditioned media (ACM), bone marrow stromal cell-conditioned media, stromal conditioned media (SCM), and unconditioned media to determine the functional impact of increased adiposity on leukemia progression. Whereas only 20% of lean mice transplanted with T-ALL cells survived longer than 3 months post-inoculation, 50%–80% of obese mice with leukemia survived over this same period. Furthermore, culturing human T-ALL cells in ACM resulted in increased histone H3 acetylation (K9/K14/K18/K23/K27) and methylation (K4me3 and K27me3) posttranslational modifications (PTMs), which preceded accelerated cell cycle progression, DNA damage, and cell death. Adipocyte-mediated epigenetic changes in human T-ALL cells were recapitulated with the H3K27 demethylase inhibitor GSK-J4 and the pan-HDAC inhibitor vorinostat. These drugs were also highly cytotoxic to human T-ALL cells at low micromolar concentrations. In summary, our data support epidemiological studies demonstrating that adiposity suppresses T-ALL pathogenesis. We present data demonstrating that T-ALL cell death in adipose-rich microenvironments is induced by epigenetic modifications, which are not tolerated by leukemia cells. Similarly, GSK-J4 and vorinostat treatment induced epigenomic instability and cytotoxicity profiles that phenocopied the responses of human T-ALL cells to ACM, which provides additional support for the use of epigenetic modifying drugs as a treatment option for T-ALL.

Germline ETV6 mutation promotes inflammation and disrupts lymphoid development of early hematopoietic progenitors

Germline mutations in ETV6 are associated with a syndrome of thrombocytopenia and leukemia predisposition, and ETV6 is among the most commonly mutated genes in leukemias, especially childhood B-cell acute lymphoblastic leukemia. However, the mechanisms underlying disease caused by ETV6 dysfunction are poorly understood. To address these gaps in knowledge, using CRISPR/Cas9, we developed a mouse model of the most common recurrent, disease-causing germline mutation in ETV6. We found defects in hematopoiesis related primarily to abnormalities of the multipotent progenitor population 4 (MPP4) subset of hematopoietic progenitor cells and evidence of sterile inflammation. Expression of ETV6 in Ba/F3 cells altered the expression of several cytokines, some of which were also detected at higher levels in the bone marrow of the mice with Etv6 mutation. Among these, interleukin-18 and interleukin-13 abrogated B-cell development of sorted MPP4 cells, but not common lymphoid progenitors, suggesting that inflammation contributes to abnormal hematopoiesis by impairing lymphoid development. These data, along with those from humans, support a model in which ETV6 dysfunction promotes inflammation, which adversely affects thrombopoiesis and promotes leukemogenesis.

The Regulation of Immunity

In their AAI President's Addresses reproduced in this issue, Jeremy M. Boss, Ph.D. (AAI '94; AAI president 2019–2020), and Jenny P.-Y. Ting, Ph.D. (AAI '97; AAI president 2020–2021), welcomed attendees to the AAI annual meeting, Virtual IMMUNOLOGY2021™. Due to the SARS-CoV-2 pandemic and the cancellation of IMMUNOLOGY2020™, Dr. Boss and Dr. Ting each presented their respective president's address to open the meeting.

Epigenome accessibility changes before and after activation reveal distinct and progressive differentiation for human memory T cell subsets

Memory T cells (MTC), an indispensable part of adaptive immune memory, have historically been categorized by the cell surface proteins CCR7 and CD45RA into specialized subtypes (TCM, TEM, and TEMRA), each with unique functions. However, the epigenetic characteristics that distinguish the MTC subsets as well as the gene regulatory networks governing each MTC subsets’ response to activation remain poorly understood. Here we define and categorize the transcriptional and epigenetic differences of MTC and their respective primary subsets found in human blood, both in a resting state and after ex-vivo stimulation. Resting TCM were found to be relatively more similar to naïve cells in both CD4 and CD8 lineages, while TEM exhibited greater numbers of differentially expressed genes (DEG) and alterations to chromatin accessibility. Differentially accessible regions (DAR) discerning memory subsets contained binding motifs for factors thought to regulate memory formation from the bZIP, T-box and HMG families, as well as sites for novel bHLH factors MSC and AHR that may function in MTC development. Examining the effect of stimulation on MTC gene expression and chromatin identified unique DAR and DEG modules, some of which may have initially been primed by previous activation events in naive progenitors. Primed DAR were correlated with augmented expression of important genes in MTC after stimulation, suggesting an epigenetic mechanism of regulation. Ultimately these results describe the accumulation of epigenetic alterations during primary activation and during memory development that distinguish MTC from naïve T cells, enable differentiation into distinct subsets, and influence how MTC respond to secondary activation.

Supported by grants from NIH (RO1 AI113021,T32 GM0008490)

Somatic Diversification of Rearranged Antibody Gene Segments by Intra- and Interchromosomal Templated Mutagenesis

The ability of the humoral immune system to generate Abs capable of specifically binding a myriad of Ags is critically dependent on the somatic hypermutation program. This program induces both templated mutations (i.e., gene conversion) and untemplated mutations. In humans, somatic hypermutation is widely believed to result in untemplated point mutations. In this study, we demonstrate detection of large-scale templated events that occur in human memory B cells and circulating plasmablasts. We find that such mutations are templated intrachromosomally from IGHV genes and interchromosomally from IGHV pseudogenes as well as other homologous regions unrelated to IGHV genes. These same donor regions are used in multiple individuals, and they predominantly originate from chromosomes 14, 15, and 16. In addition, we find that exogenous sequences placed at the IgH locus, such as LAIR1, undergo templated mutagenesis and that homology appears to be the major determinant for donor choice. Furthermore, we find that donor tracts originate from areas in proximity with open chromatin, which are transcriptionally active, and are found in spatial proximity with the IgH locus during the germinal center reaction. These donor sequences are inserted into the Ig gene segment in association with overlapping activation-induced cytidine deaminase hotspots. Taken together, these studies suggest that diversity generated during the germinal center response is driven by untemplated point mutations as well as templated mutagenesis using local and distant regions of the genome.

Defining the cis- and trans-regulatory architecture for human PD-1 in T Follicular Helper Cells

The surface immune checkpoint inhibitor Programed Death-1 (PD-1), encoded by PDCD1, is expressed throughout the immune system. Notably, PD-1 expression is amongst its highest in a specialized subset of CD4+ T follicular helper (TFH) cells. TFH cells primarily function by engaging with cognate B cells, facilitating the generation of high affinity vaccine- and pathogen-specific antibodies. Despite the proven clinical benefit of therapies targeting the PD-1 pathway, very little is known regarding the mechanisms by which human PDCD1 is transcriptionally regulated in humans. Here, we seek to elucidate both the cis- and trans-regulatory mechanisms that govern PDCD1 expression in TFH cells. Human TFH cells were sourced from discarded tonsil tissue, circulating blood, or through an ex vivo differentiation model to generate ‘TFH-like’ cells. RNA-seq analysis revealed that ex vivo-derived ‘TFH-like’ cells resembled bona-fide in vivo TFH cells, including induction of PDCD1. Furthermore, ATAC-sequencing experiments identified 8 conserved regions in the PDCD1 locus that exhibited altered accessibility in TFH cells. These cis-regulatory elements were determined to have distinct functions in controlling PDCD1 expression. Additionally, bioinformatic analysis revealed a core TFH gene program, implicating the transcription factors BCL-6, ASCL2, TOX, TOX2, and AIOLOS as regulators of PDCD1 and TFH fate. Taken together, these findings uncover the molecular mechanisms that control PDCD1 expression, informing the design of future therapies aimed at manipulating PD-1.

Supported by National Institute of Health grants: RO1 AI113021 to J.M.B, F32 AI161857 to M.D.P

Memory B cells are a heterogenous population regulated by epigenetic programming

Memory B cells (MBC) are a heterogenous population that consist of immunoglobin class switched and non-class switched MBC, and these populations can arise via germinal center dependent or independent mechanisms. The timing of MBC development influences the fate outcome of MBC populations. These different populations of MBC are regulated by cell signaling, but it is not clearly defined what epigenetic factors influence MBC differentiation. EZH2 is an important histone methyltransferase that catalyzes H3K27me3 resulting in gene repression. EZH2 has been shown to regulate B cell differentiation into germinal centers and plasma cells; however, it is unknown if EZH2 regulates MBC development. To address this, a knockout model has been established where EZH2 is conditionally deleted using the CD19 and AICDA driven CRE expression. Here we used the influenza PR8 model to ascertain the kinetics of MBC differentiation and formation in the spleen, dLN, and lungs following a live infection in wild-type and EZH2-KO cohorts. Using B cell tetramers, antigen-specific MBC will be analyzed to define the kinetics of MBC development and determine the similarities and differences between the different populations of MBC. Overall, these data define the early kinetics of MBC establishment and the developmental timing that EZH2-dependent H3K27me3 remodeling is required for MBC formation.

Supported by NIH/NIAID to CDS (R01 AI148471)

H3K27me3 Demethylase UTX Restrains Plasma Cell Formation

B cell differentiation is associated with substantial transcriptional, metabolic, and epigenetic remodeling, including redistribution of histone 3 lysine 27 trimethylation (H3K27me3), which is associated with a repressive chromatin state and gene silencing. Although the role of the methyltransferase EZH2 (Enhancer of zeste homolog 2) in B cell fate decisions has been well established, it is not known whether H3K27me3 demethylation is equally important. In this study, we showed that simultaneous genetic deletion of the two H3K27 demethylases UTX and JMJD3 (double-knockout [Utx ^fl/fl Jmjd3 ^fl/fl Cd19 ^cre/+] [dKO]) led to a significant increase in plasma cell (PC) formation after stimulation with the T cell-independent Ags LPS and NP-Ficoll. This phenotype occurred in a UTX-dependent manner as UTX single-knockout mice, but not JMJD3 single-knockout mice, mimicked the dKO. Although UTX- and JMJD3-deficient marginal zone B cells showed increased proliferation, dKO follicular B cells also showed increased PC formation. PCs from dKO mice upregulated genes associated with oxidative phosphorylation and exhibited increased spare respiratory capacity. Mechanistically, deletion of Utx and Jmjd3 resulted in higher levels of H3K27me3 at proapoptotic genes and resulted in reduced apoptosis of dKO PCs in vivo. Furthermore, UTX regulated chromatin accessibility at regions containing ETS and IFN regulatory factor (IRF) transcription factor family motifs, including motifs of known repressors of PC fate. Taken together, these data demonstrate that the H3K27me3 demethylases restrain B cell differentiation.

Generation of human long-lived plasma cells by developmentally regulated epigenetic imprinting

Antibody secreting cells (ASCs) circulate after vaccination and infection and migrate to the BM where a subset known as long-lived plasma cells (LLPCs) persists and secrete antibodies for a lifetime. The mechanisms by which circulating ASCs become LLPCs are not well elucidated. Here, we show that human blood ASCs have distinct morphology, transcriptomes, and epigenetics compared with BM LLPCs. Compared with blood ASCs, BM LLPCs have decreased nucleus/cytoplasm ratio but increased endoplasmic reticulum and numbers of mitochondria. LLPCs up-regulate pro-survival genes MCL1, BCL2, and BCL-XL while simultaneously down-regulating pro-apoptotic genes HRK1, CASP3, and CASP8 Consistent with reduced gene expression, the pro-apoptotic gene loci are less accessible in LLPCs. Of the pro-survival genes, only BCL2 is concordant in gene up-regulation and loci accessibility. Using a novel in vitro human BM mimetic, we show that blood ASCs undergo similar morphological and molecular changes that resemble ex vivo BM LLPCs. Overall, our study demonstrates that early-minted blood ASCs in the BM microniche must undergo morphological, transcriptional, and epigenetic changes to mature into apoptotic-resistant LLPCs.

Inhibition of H3K27me3 Demethylases Promotes Plasmablast Formation

B cell differentiation into Ab-secreting plasma cells requires transcriptional, metabolic, and epigenetic remodeling. Histone H3 lysine 27 trimethylation (H3K27me3), a histone modification associated with gene silencing, is dynamically regulated during B cell differentiation. Although several studies have focused on mechanisms involving the gain of this modification in plasmablasts (PB), the role of active demethylation of H3K27me3 by ubiquitously transcribed tetratricopeptide repeat, X chromosome (UTX) and Jumonji domain-containing protein 3 (JMDJ3) during B cell differentiation has not been examined. In this study, this process was assessed using a pharmacological inhibitor of UTX and JMJD3, GSK-J4. Treatment of ex vivo stimulated mouse B cells with GSK-J4 led to an increase in PB frequency without affecting the ability of the newly formed PB to secrete Abs. Consistent with the role of UTX and JMJD3 in promoting gene expression, the majority of differentially expressed were downregulated upon GSK-J4 treatment. GSK-J4-treated cells downregulated genes associated with signaling and P53 pathways. Inhibitor treated cells upregulated genes associated with cell cycle and proliferation, which correlated with an increase in actively proliferating cells. Unexpectedly, a majority of the downregulated transcripts corresponded to genes that in the wild-type setting were genes that gain H3K27me3 and downregulated in PB. Together, our results show that UTX and JMDJ3 are required to restrain B cell differentiation and suggest that they function as a rheostat for H3K27me3 to control this process.

An IRF4-MYC-mTORC1 Integrated Pathway Controls Cell Growth and the Proliferative Capacity of Activated B Cells during B Cell Differentiation In Vivo

Cell division is an essential component of B cell differentiation to Ab-secreting plasma cells, with critical reprogramming occurring during the initial stages of B cell activation. However, a complete understanding of the factors that coordinate early reprogramming events in vivo remain to be determined. In this study, we examined the initial reprogramming by IRF4 in activated B cells using an adoptive transfer system and mice with a B cell-specific deletion of IRF4. IRF4-deficient B cells responding to influenza, 4-hydroxy-3-nitrophenylacetyl-Ficoll, and LPS divided but stalled during the proliferative response. Gene expression profiling of IRF4-deficient B cells at discrete divisions revealed IRF4 was critical for inducing MYC target genes, oxidative phosphorylation, and glycolysis. Moreover, IRF4-deficient B cells maintained an inflammatory gene expression signature. Complementary chromatin accessibility analyses established a hierarchy of IRF4 activity and identified networks of dysregulated transcription factor families in IRF4-deficient B cells, including E-box binding bHLH family members. Indeed, B cells lacking IRF4 failed to fully induce Myc after stimulation and displayed aberrant cell cycle distribution. Furthermore, IRF4-deficient B cells showed reduced mTORC1 activity and failed to initiate the B cell activation unfolded protein response and grow in cell size. Myc overexpression in IRF4-deficient cells was sufficient to overcome the cell growth defect. Together, these data reveal an IRF4-MYC-mTORC1 relationship critical for controlling cell growth and the proliferative response during B cell differentiation.

Cohesin Core Complex Gene Dosage Contributes to Germinal Center Derived Lymphoma Phenotypes and Outcomes

The cohesin complex plays critical roles in genomic stability and gene expression through effects on 3D architecture. Cohesin core subunit genes are mutated across a wide cross-section of cancers, but not in germinal center (GC) derived lymphomas. In spite of this, haploinsufficiency of cohesin ATPase subunit Smc3 was shown to contribute to malignant transformation of GC B-cells in mice. Herein we explored potential mechanisms and clinical relevance of Smc3 deficiency in GC lymphomagenesis. Transcriptional profiling of Smc3 haploinsufficient murine lymphomas revealed downregulation of genes repressed by loss of epigenetic tumor suppressors Tet2 and Kmt2d. Profiling 3D chromosomal interactions in lymphomas revealed impaired enhancer-promoter interactions affecting genes like Tet2, which was aberrantly downregulated in Smc3 deficient lymphomas. Tet2 plays important roles in B-cell exit from the GC reaction, and single cell RNA-seq profiles and phenotypic trajectory analysis in Smc3 mutant mice revealed a specific defect in commitment to the final steps of plasma cell differentiation. Although Smc3 deficiency resulted in structural abnormalities in GC B-cells, there was no increase of somatic mutations or structural variants in Smc3 haploinsufficient lymphomas, suggesting that cohesin deficiency largely induces lymphomas through disruption of enhancer-promoter interactions of terminal differentiation and tumor suppressor genes. Strikingly, the presence of the Smc3 haploinsufficient GC B-cell transcriptional signature in human patients with GC-derived diffuse large B-cell lymphoma (DLBCL) was linked to inferior clinical outcome and low expression of cohesin core subunits. Reciprocally, reduced expression of cohesin subunits was an independent risk factor for worse survival int DLBCL patient cohorts. Collectively, the data suggest that Smc3 functions as a bona fide tumor suppressor for lymphomas through non-genetic mechanisms, and drives disease by disrupting the commitment of GC B-cells to the plasma cell fate.

Extrafollicular IgD+ B cells generate IgE antibody secreting cells in the nasal mucosa

Increased IgE is a typical feature of allergic rhinitis. Local class-switch recombination has been intimated but B cell precursors and mechanisms remain elusive. Here we describe the dynamics underlying the generation of IgE-antibody secreting cells (ASC) in human nasal polyps (NP), mucosal tissues rich in ASC without germinal centers (GC). Using VH next generation sequencing, we identified an extrafollicular (EF) mucosal IgD+ naïve-like intermediate B cell population with high connectivity to the mucosal IgE ASC. Mucosal IgD+ B cells, express germline epsilon transcripts and predominantly co-express IgM. However, a small but significant fraction co-express IgG or IgA instead which also show connectivity to ASC IgE. Phenotypically, NP IgD+ B cells display an activated profile and molecular evidence of BCR engagement. Transcriptionally, mucosal IgD+ B cells reveal an intermediate profile between naïve B cells and ASC. Single cell IgE ASC analysis demonstrates lower mutational frequencies relative to IgG, IgA, and IgD ASC consistent with IgE ASC derivation from mucosal IgD+ B cell with low mutational load. In conclusion, we describe a novel mechanism of GC-independent, extrafollicular IgE ASC formation at the nasal mucosa whereby activated IgD+ naïve B cells locally undergo direct and indirect (through IgG and IgA), IgE class switch.

Epigenetic gene regulation in plasma cells

Humoral immunity provides protection from pathogenic infection and is mediated by antibodies following the differentiation of naive B cells (nBs) to antibody-secreting cells (ASCs). This process requires substantial epigenetic and transcriptional rewiring to ultimately repress the nB program and replace it with one conducive to ASC physiology and function. Notably, these reprogramming events occur within the framework of cell division. Efforts to understand the relationship of cell division with reprogramming and ASC differentiation in vivo have uncovered the timing and scope of reprogramming, as well as key factors that influence these events. Herein, we discuss the unique physiology of ASC and how nBs undergo epigenetic and genome architectural reorganization to acquire the necessary functions to support antibody production. We also discuss the stage-wise manner in which reprogramming occurs across cell divisions and how key molecular determinants can influence B cell fate outcomes.

IRF4 regulates the proliferative capacity of activated B cells during B cell differentiation

Cell division is essential for B cell differentiation to a plasma cell (PC). While the cell division coupled changes in the expression of transcription factors that coordinate the PC program have been described, it is unclear how these factors coordinate the proliferative program. To address this, we used an adoptive transfer system and monitored the cell division/differentiation kinetics in response to LPS, NP-ficoll, and X31 influenza. In this system, wild-type (WT) B cells undergo at least 8 cell divisions before differentiating into PC. In contrast, Interferon Regulatory Factor 4-null (IRF4−/−) B cells began dividing normally but stalled during the proliferative response. To assess the scope of IRF4-dependent reprogramming, WT and IRF4−/− B cells in divisions 0, 1, and 3–6 were sorted for ATAC- and RNA-seq. RNA-seq data revealed hundreds of differentially expressed genes (DEG) when IRF4 was deleted that encompassed a number of gene sets critical for B cell reprogramming, including glycolysis, OXPHOS, and mTORC1 signaling. Further, MYC target genes became progressively dysregulated across divisions. Indeed, IRF4−/− cells failed to fully upregulate MYC compared to WT cells and consequently, we observed aberrant cell cycle distribution, cell growth defects, and fewer actively proliferating cells. Overexpressing MYC in IRF4−/− B cells rescued cell growth and significantly improved proliferation. ATAC-seq data also exposed hundreds of differentially accessible regions, the majority of which contained a known IRF4 binding motif and mapped to a corresponding DEG. Together, these data create a road map defining the role of IRF4 throughout differentiation, revealing a critical function in coordinating the proliferative response.

T-bet expression marks a transcriptionally and functionally distinct population of memory B cells

Memory B cells (Bmem) rapidly differentiate and mount antibody (Ab) responses to previously encountered antigen (Ag). Mouse Bmem can be subdivided using BCR isotype or expression of CD73, CD80, and PD-L2. Many of these Bmem populations were discovered following vaccination with alum-adjuvanted Ag, which drives a distinct immune response from those generated after infection with IFN-inducing viruses. We previously demonstrated that the IFNγ-inducible transcription factor T-bet is required for Bmem recall responses to influenza but not nematode infections, suggesting that T-bet might regulate anti-viral Bmem. Therefore, we hypothesized that the anti-viral Bmem compartment likely contained cells that were distinct from the established subpopulations. Here, we show that T-bet expression within the flu-specific Bmem is heterogeneous and not restricted to any of the previously described Bmem subsets. Furthermore, B cell-intrinsic T-bet ablation caused the loss of one of these Bmem subpopulations, and inducible deletion of T-bet in Bmem caused the loss of the same subpopulation. To determine how T-bet regulates the Bmem compartment, we performed single-cell RNAseq and CITEseq on flu infection-induced Bmem. We identified numerous transcriptionally distinct clusters of Bmem, several of which express T-bet as well as genes associated with plasma cell function. Consistent with this, in vitro assays show that T-bet+ Bmem differentiate more robustly than T-betneg Bmem. These data show that the anti-viral Bmem compartment is heterogeneous and includes a T-bet expressing subpopulation that appears poised for rapid Ab responses. Thus, T-bet appears to be important for the maintenance and function of some, but not all, Bmem.

Cell-intrinsic MAVS promotes antigen specific CD8+ T cell proliferation and mitochondrial metabolism

Mitochondrial antiviral signaling protein (MAVS), the central adaptor protein for RIG-I like receptor (RLR) signaling, is essential for promoting innate immunity against RNA virus infections. MAVS is ubiquitously expressed, however its function in T cells is less clear. Using a mouse model of West Nile virus (WNV) infection, we find that MAVS is required in a cell-intrinsic manner for promoting antigen-specific CD8+ T cell accumulation. Through adoptive transfer experiments, we find that MAVS positively regulates cell cycle genes and promotes entry into proliferation in antigen-specific CD8+ T cells. Mechanistically, knockout of MAVS leads to dysregulated metabolic transcriptional profiles and decreased mitochondrial potential in vivo. Furthermore, we determined that CD8+ T cell receptor stimulation promotes oxidative phosphorylation in a MAVS-dependent manner to facilitate entry into proliferation. Our findings identify a non-canonical role for MAVS as a positive regulator of mitochondrial respiration and proliferation in CD8+ T cells during viral infection.

H3K27me3 demethylases restrict the magnitude of PC formation

Robust differentiation of naïve B cell into antibody secreting plasma cells (PC) in response to foreign antigens is a cornerstone of the humoral immune response. PC formation is highly regulated and requires substantial epigenetic remodeling, including redistribution of histone modification H3 lysine 27 trimethylation (H3K27me3), which is associated with a repressive chromatin state and gene silencing. However, little is known about the role of the two demethylases, UTX and JMDJ3, that remove H3K27me3 in B cells. To examine whether these enzymes module PC formation, we generated mice with B cell specific deletion of UTX and JMDJ3 (dKO; Utxfl/flJmjd3fl/fl Cd19Cre/+). Stimulation of B cells with T cell independent antigens, LPS or NP-Ficoll, led to a significant increase in PC in dKO mice compared to CreCtrl mice (Cd19Cre/+). This phenotype was attributed to enhanced proliferation and differentiation of marginal zone (MZ), but not follicular B cells (FoB). dKO PC upregulated genes associated with oxidative phosphorylation metabolism and exhibited higher spare respiratory capacity. Furthermore, deletion of UTX and JMJD3 led to significant redistribution of accessible chromatin and H3K27me3. Regions with reduced chromatin accessibility in dKO PC were enriched for transcription factor motifs of known PC repressors suggesting a potential mode of regulation. Additionally, we demonstrated that UTX is the primary H3K27me3 demethylase regulating B cell differentiation and evaluated whether its demethylase activity is required to augment PC formation. Taken together, H3K27me3 demethylases are critical epigenetic regulators necessary restrain B cell differentiation.

Genomic Screening of B cell differentiation by using CRIPSR/Cas9

The differentiation of naïve B cells to antibody secreting plasma cells plays a crucial role in humoral immunity. This process is regulated by multiple factors including, transcription factors and epigenetic modifiers. Type II, clustered, regularly interspaced, short palindromic repeats (CRISPR)–CRISPR-associated (Cas) systems can be used to identify genes that influence a phenotype of interest. Herein, we established this system to identify novel regulators of plasma cell differentiation. To accomplish this, we transduced hematopoietic stem cells derived from mice expressing Cas9 specifically in B cells (Rosa26-Cas9, Cd19-Cre) with lentiviral based gRNAs targeting Ptprc (CD45), Irf8 and Bach2 and transplanted the stem cells into congenically disparate hosts. Hematopoietic stem cells are enriched with lineage depletion kit and then sorted by C-kit and Sca-1, followed by culture for 24 hours and spin-infection with corresponding lentivirus. After another 24-hour recovery, these cells are transferred to radioactively immune system destroyed hosts. Following immune constitution, B cells were isolated and the deletion of CD45, IRF8 and BACH2 was confirmed. Consistent with previous findings, deletion of IRF8 and BACH2 augmented plasma cell formation in ex vivo differentiation assays. Additionally, we used a genome-wide CRISPR gRNA lentiviral library targeting 18,424 genes to screen for factors that influenced B cell differentiation to LPS, IL-2 and IL-5. In conclusion, the CRISPR/Cas9 system allows us to rapidly generate genetic deletions to explore B cell differentiation in vivo and to discover novel factors that regulate plasma cell formation.

H3K9 dimethyltransferase G9a deficiency modulates B-cell response to LPS

B cell differentiation is a tightly regulated process coordinated by the timed expression of various transcription factors and chromatin accessibility changes mediated by histone modifying enzymes. The histone methyltransferase (HMT) G9a, dimethylates histone H3 lysine 9 (H3K9) at promoters and inhibits gene expression through recruitment of proteins that impair chromatin accessibility. HMTs are expressed ubiquitously but display distinct enzymatic activities and patterns of chromosomal localization. G9a is most known for co-localizing with Blimp-1 to silence genes associated with the B cell phenotype in plasma cells. However, our findings show a constitutive expression of G9a during B-cell division. In addition, B cell processes that are modulated by G9a mediated dimethylation remain to be elucidated. To study G9a’s involvement at various stages of B-cell differentiation, we crossed G9afl/fl mice onto the CD19Cre/+ background (G9aKO mice). Phenotypic characterization of these mice identified a skewing within the mature B cell population towards marginal zone (MZ) B cells in G9aKO mice. Upon challenge with LPS significantly elevated activated B-cell and plasmablast frequencies were observed in G9aKO mice. Regions with chromatin accessibility and expression changes identified by ATAC-Seq and RNA-Seq elucidated the B cell processes that are modulated in G9a deficient mice. B cell processes that are subject to direct modulation by G9a will be elucidated using CUT&Tag. Together, our data shows the importance of G9a in epigenetic modulation required for B cell function.

Unique abilities of human memory T cell subsets are associated with both specialized gene expression modules and epigenetic priming

Memory T cells are a diverse set of cells that respond to immunologic challenge more quickly and with greater efficacy than their naïve counterparts. Their potential in the resting and stimulated state has not been explored for each of the subsets. To define their capabilities, RNA-seq and ATAC-seq data assessing the transcriptome and chromatin accessibility potential of both resting and activated human memory T cells was analyzed. Clustering gene expression modules identified a core set of genes highly expressed in both resting central memory and effector memory cells (but not in naïve or terminally differentiated effector cells). Memory subsets also expressed unique gene modules enabling specialized functions such as cell cytotoxicity, migration, or self-renewal. Subset differences in gene expression were reflected in differentiated chromatin accessibility and enhanced variation around binding motifs for key T cell differentiation transcription factors such as Tbet, EOMES, and LEF1. Upon activation memory T cells showed substantial rapid upregulation of genes including cytokines which were absent in activated naïve T cells. These differences in gene expression from naïve T cells were often preceded by areas of open chromatin in a resting memory state, suggesting mechanisms of epigenetic priming for rapid recall or augmentation of effector T cell function in memory. In summary, memory T cell subsets are distinct in both resting gene expression functionalities and differentiated epigenetic landscape—both of which enable unique, rapid, and effective response to antigen.

Exploring Mechanisms of Human PD-1 Gene Regulation in T Follicular Helper Cells

Programed Cell death (PD-1), encoded by Pdcd1, is an immune inhibitory receptor expressed on the surface of lymphocytes. Surface PD-1 expression is amongst its highest in a subset of CD4+ T cells called T follicular helper cells (TFH). TFH cells are pivotal for optimal germinal center formation and subsequent generation of pathogen- and vaccine-induced antibodies by B cells. Despite the clear connection to human health, the majority of previous work has centered on elucidating the mechanisms surrounding murine Pdcd1 regulation. Surprisingly, there is almost nothing known about how human Pdcd1 (hPdcd1) is regulated! Here we seek to close this gap in knowledge by identifying the cis-, trans-, and epigenetic pathways that regulate hPdcd1 in TFH cells. To this end, human TFH cells were sourced from both discarded tonsil tissue as well as from a recently described model to generate ex vivo human TFH cells through treatment with the cytokines Activin A, IL-12 and TGFβ. RNA-sequencing demonstrated that ex vivo TFH cells exhibit characteristics of bona-fide tonsillar TFH cells, including increased expression of PD-1. Furthermore, ATAC-seq and H3K27Ac Hi-ChIP experiments revealed the presence of 7 conserved accessible regions within the hPdcd1 locus that exhibit unique looping characteristics and potential enhancer properties. Functionality of each regulatory element was further defined through promoter reporter assays. Additionally, PAGE-RANK analysis elucidated transcription factors that may play a role in the induction of hPdcd1 expression. Collectively, these findings begin to unearth the mechanisms that control hPdcd1, informing the design of future therapeutics aimed at precisely manipulating human PD-1 expression.

Identifying mechanisms that enhance the longevity of tissue-resident memory CD8+ T cells in the lung

Lung tissue-resident memory CD8+ T cells (TRM) are crucial mediators of cellular immunity against influenza viruses, but the number of these cells in the lung tissue gradually declines in the months following influenza infection. Recently, we showed that intranasal immunization with a replication-deficient adenovirus that expresses the nucleoprotein from influenza A virus (AdNP) results in long-term maintenance of lung CD8+ TRM for up to 1-year post-immunization. However, the mechanism(s) that promote this enhanced longevity of FluNP-specific CD8+ lung TRM remain unknown. Using a combination of mouse infection models, flow cytometry, and RNA-sequencing, we compared CD8+ T cells from the airways, lungs, and spleen of AdNP-immunized or influenza x31-infected mice. We found that CD8+ TRM in the lungs of AdNP-immunized mice show increased homeostatic turnover and hallmarks of persistent antigen stimulation in the lung. However, RNA-sequencing analysis comparing lung CD8+ TRM from AdNP-immunized and x31-infected mice at 1-month and 1-year post-immunization showed only minor variations that did not fully explain the differences in lung TRM persistence. Lineage tracing experiments using a Cre recombinase-expressing Adenovirus (AdCre) identified alveolar macrophages as the primary cell type harboring persistent antigen in the lung. Together, these results define one mechanism for enhancing the durability of lung TRM, which is an important consideration for the design of future cell-mediated influenza vaccines

The Murine MHC Class II Super Enhancer IA/IE-SE Contains a Functionally Redundant CTCF-Binding Component and a Novel Element Critical for Maximal Expression

In both humans and mice, CTCF-binding elements form a series of interacting loops across the MHC class II (MHC-II) locus, and CTCF is required for maximal MHC-II gene expression. In humans, a CTCF-bound chromatin insulator termed XL9 and a super enhancer (SE) DR/DQ-SE situated in the intergenic region between HLA-DRB1 and HLA-DQA1 play critical roles in regulating MHC-II expression. In this study, we identify a similar SE, termed IA/IE-SE, located between H2-Eb1 and H2-Aa of the mouse that contains a CTCF site (C15) and a novel region of high histone H3K27 acetylation. A genetic knockout of C15 was created and its role on MHC-II expression tested on immune cells. We found that C15 deletion did not alter MHC-II expression in B cells, macrophages, and macrophages treated with IFN-γ because of functional redundancy of the remaining MHC-II CTCF sites. Surprisingly, embryonic fibroblasts derived from C15-deleted mice failed to induce MHC-II gene expression in response to IFN-γ, suggesting that at least in this developmental lineage, C15 was required. Examination of the three-dimensional interactions with C15 and the H2-Eb1 and H2-Aa promoters identified interactions within the novel region of high histone acetylation within the IA/IE-SE (termed N1) that contains a PU.1 binding site. CRISPR/Cas9 deletion of N1 altered chromatin interactions across the locus and resulted in reduced MHC-II expression. Together, these data demonstrate the functional redundancy of the MHC-II CTCF elements and identify a functionally conserved SE that is critical for maximal expression of MHC-II genes.

Conserved Epigenetic Programming and Enhanced Heme Metabolism Drive Memory B Cell Reactivation

Memory B cells (MBCs) have enhanced capabilities to differentiate to plasma cells and generate a rapid burst of Abs upon secondary stimulation. To determine if MBCs harbor an epigenetic landscape that contributes to increased differentiation potential, we derived the chromatin accessibility and transcriptomes of influenza-specific IgM and IgG MBCs compared with naive cells. MBCs possessed an accessible chromatin architecture surrounding plasma cell-specific genes, as well as altered expression of transcription factors and genes encoding cell cycle, chemotaxis, and signal transduction processes. Intriguingly, this MBC signature was conserved between humans and mice. MBCs of both species possessed a heightened heme signature compared with naive cells. Differentiation in the presence of hemin enhanced oxidative phosphorylation metabolism and MBC differentiation into Ab-secreting plasma cells. Thus, these data define conserved MBC transcriptional and epigenetic signatures that include a central role for heme and multiple other pathways in augmenting MBC reactivation potential.

Selective DNA Demethylation Accompanies T Cell Homeostatic Proliferation and Gene Regulation in Lupus-Prone lpr Mice

Systemic lupus erythematosus (SLE) is characterized by increased DNA demethylation in T cells, although it is unclear whether this occurs primarily in a subset of SLE T cells. The process driving the DNA demethylation and the consequences on overall gene expression are also poorly understood and whether this represents a secondary consequence of SLE or a primary contributing factor. Lupus-prone lpr mice accumulate large numbers of T cells with age because of a mutation in Fas (CD95). The accumulating T cells include an unusual population of CD4-CD8-TCR-αβ+ (DN) T cells that arise from CD8+ precursors and are also found in human SLE. We have previously observed that T cell accumulation in lpr mice is due to dysregulation of T cell homeostatic proliferation, which parallels an increased expression of numerous genes in the DN subset, including several proinflammatory molecules and checkpoint blockers. We thus determined the DNA methylome in lpr DN T cells compared with their CD8+ precursors. Our findings show that DN T cells manifest discrete sites of extensive demethylation throughout the genome, and these sites correspond to the location of a large proportion of the upregulated genes. Thus, dysregulated homeostatic proliferation in lpr mice and consequent epigenetic alterations may be a contributing factor to lupus pathogenesis.

Transcriptomic and epigenomic dynamics associated with development of human iPSC-derived GABAergic interneurons

GABAergic interneurons (GINs) are a heterogeneous population of inhibitory neurons that collectively contribute to the maintenance of normal neuronal excitability and network activity. Identification of the genetic regulatory elements and transcription factors that contribute toward GIN function may provide new insight into the pathways underlying proper GIN activity while also indicating potential therapeutic targets for GIN-associated disorders, such as schizophrenia and epilepsy. In this study, we examined the temporal changes in gene expression and chromatin accessibility during GIN development by performing transcriptomic and epigenomic analyses on human induced pluripotent stem cell-derived neurons at 22, 50 and 78 days (D) post-differentiation. We observed 13 221 differentially accessible regions (DARs) of chromatin that associate with temporal changes in gene expression at D78 and D50, relative to D22. We also classified families of transcription factors that are increasingly enriched at DARs during differentiation, indicating regulatory networks that likely drive GIN development. Collectively, these data provide a resource for examining the molecular networks regulating GIN functionality.

Antibody-secreting cell destiny emerges during the initial stages of B-cell activation

Upon stimulation, B cells assume heterogeneous cell fates, with only a fraction differentiating into antibody-secreting cells (ASC). Here we investigate B cell fate programming and heterogeneity during ASC differentiation using T cell-independent models. We find that maximal ASC induction requires at least eight cell divisions in vivo, with BLIMP-1 being required for differentiation at division eight. Single cell RNA-sequencing of activated B cells and construction of differentiation trajectories reveal an early cell fate bifurcation. The ASC-destined branch requires induction of IRF4, MYC-target genes, and oxidative phosphorylation, with the loss of CD62L expression serving as a potential early marker of ASC fate commitment. Meanwhile, the non-ASC branch expresses an inflammatory signature, and maintains B cell fate programming. Finally, ASC can be further subseted based on their differential responses to ER-stress, indicating multiple development branch points. Our data thus define the cell division kinetics of B cell differentiation in vivo, and identify the molecular trajectories of B cell fate and ASC formation.

Defining altered regulome structured in response to antigen co-receptors, toll-like receptors, and cytokine receptors stimuli to predispose early developing B cells for pathogenic fate in Systemic lupus erythematosus

A TLR7-IFNg driven IL-21 mediated unique extra-follicular pathway of ASC differentiation of activated naïve B cells through an intermediary DN2 B cell subset has been characterized in pathogenesis of SLE. It has been correlated to distinct priming of naïve B cells characterized by the presence of SLE disease signatures which indicates towards the convergence of TLR, and cytokine signaling along with BCR signaling in the expansion and differentiation of peripheral B cells in SLE. Thus, we hypothesize that distinct combinations of innate, cytokines and antigen driven stimuli cause pathogenesis of SLE by maneuvering disease-related epigenetic programs and molecular networks during B cell development resulting in perturbed activation and differentiation. Indeed, initial data from bulk RNA-seq show enrichment of Type I interferon production and signature genes in HSCs to transitional B cells in SLE BM. Confounded by scRNA-seq, these populations also show profound type II interferon signature genes in SLE BM. Interestingly, BCR devoid Pro-B cells show reduced expression of BCR signaling intermediates with enhanced proliferation. However, expression of Pre-BCR or BCR on the surface of Pre-B cells or Immature B cells respectively are accompanied by increased expression of BCR co-receptors in SLE BM. On the other hand, metabolically SLE early BM B cells are less dependent on oxidative phosphorylation with reduced protein synthesis and processing. Together, these initial findings provide evidence that the proinflammatory microenvironment in SLE BM exerts its effect by differentially regulating BCR signaling factors and co-receptors in early B cell populations and thereby could define the pathogenic fate of B cell in periphery in SLE.

IRF4 regulates the proliferative capacity of activated B cells during B cell differentiation

Cell division is essential for B cell differentiation to a plasma cell (PC). While the cell division coupled changes in the expression of transcription factors that coordinate the PC program have been described, little is known regarding how these factors coordinate the proliferative program. To address this, we exploited an adoptive transfer system and monitored the cell division/differentiation kinetics in response to lipopolysaccharide (LPS). In this system, wildtype (WT) B cells undergo at least 8 cell divisions before differentiating into PC, and the same requirement is also observed following NP-ficoll or influenza immune challenge. Modeling division rates over time identified a proliferative burst between 48 and 60 hours following LPS injection. In contrast, Interferon Regulatory Factor 4-deficient (IRF4−/−) B cells divided but failed to undergo the proliferative burst, stalling at divisions 2–6. To assess the scope of IRF4-dependent reprogramming, WT and IRF4−/− B cells at divisions 0, 1, and 3–6 were sorted for ATAC- and RNA-seq. RNA-seq data revealed hundreds of differentially expressed genes (DEGs) when IRF4 was deleted, a subset of which included MYC target genes. Indeed, IRF4−/− cells failed to upregulate MYC compared to WT cells and consequently, we observed little increase in cell size following immune challenge. Furthermore, IRF4−/− B cells exhibited aberrant cell cycle distribution when compared to WT cells at the same timepoint and division. ATAC-seq data also exposed hundreds of differentially accessible regions, the majority of which contained a known IRF4 binding motif and mapped to a corresponding DEG. Together, these data reveal a critical role for IRF4 in maintaining the proliferative response.

CD8+ T cell intrinsic MAVS promotes antigen-specific responses and mitochondrial metabolism during West Nile Virus neuroinvasive disease

West Nile Virus (WNV) is an arbovirus of the Flaviviridae family that causes annual outbreaks of encephalitis across North America. RIG-I like receptor (RLR) signaling through the central adaptor Mitochondrial antiviral signaling protein (MAVS) is essential for promoting immunity against WNV infection. While MAVS has been associated with type I interferon (IFN) induction during virus infection, here we describe a novel, cell-intrinsic role for MAVS in regulating antigen-specific CD8+ T cell responses. MAVS is expressed in CD8+ T cells and remains constant during the differentiation of CD8+ T cells. Generation of an effective CD8+ T cell response against WNV is essential for limiting virus replication in neurons, mitigating pathology in the brain, and protecting against lethal outcome. To understand how MAVS impacts CD8+ T cell responses during WNV infection, we utilized the WNV mouse model and adoptively co-transferred WT and Mavs−/− CD8+ T cells into congenically marked WT mice. We found that compared to WT cells, Mavs−/− antigen-specific CD8+ T cells displayed reduced accumulation of antigen-specific CD8+ T cells, reduced IFN-γ production and reduced formation of memory precursor cells during virus infection. At the peak of brain infection, Mavs−/− antigen-specific CD8+ T cells displayed highly divergent transcriptomes, including altered metabolic profiles, compared to WT CD8+ T cells. Further mechanistic studies found that after TCR stimulation of CD8+ T cells, MAVS promotes oxidative respiration and remodeling of mitochondrial morphology. Our findings identify a novel, non-canonical role for MAVS in the regulation of antigen-specific CD8+ T cell responses and mitochondrial function during neuroinvasive viral infection.

Interferon gamma signaling regulates the generation of influenza-specific memory B cells

Memory B cells(Bmem), which can rapidly differentiate into antibody secreting cells (ASC) upon secondary challenge, are key mediators of humoral immunity. However, the signals that govern the formation and function of these cells remain poorly understood. To date, most Bmem studies have been performed with alum-adjuvanted proteins that induce type 2 immune responses. This differs significantly from the type I and II interferon (IFN) response generated after viral infection. Using a murine model of influenza, we showed that Bmem cell intrinsic expression of the IFNγ-inducible transcription factor (TF) T-bet was required for Bmem secondary ASC responses following viral challenge. Here, we demonstrate that B cell-specific deletion of the IFNγR and the IFNg-induced TF STAT1 also affects the flu-specific Bmem compartment and greatly diminishes Bmem recall responses. We demonstrate that T-bet is expressed by a subset of all flu-specific Bmem, including those expressing IgG1 and IgM receptors. Therefore, we hypothesized that T-bet expression could be used to subset the Bmem cells into those that did or did not receive prior IFNg and STAT1 programming signals. Sorting Bmem from flu-infected mice, we show that Bmem cells with the highest levels of T-bet differentiate quickly and robustly following ex vivo stimulation. By contrast, those Bmem expressing lower levels of T-bet differentiate with delayed kinetics. Taken together, these data support the notion that B cell intrinsic IFNγR signaling, mediated by STAT1, drives formation of a distinct population of T-bet expressing effector memory B cells that are programmed to rapidly differentiate following re-exposure to antigen.

Templated mutagenesis in B cell non-Ig genes

The immunoglobulin genes of germinal center B cells (GCB) undergo somatic hypermutation in order to generate antibody diversity. Additionally, several non-immunoglobulin (non-Ig) genes are known to accumulate mutations in the germinal center. There are two methods by which mutations are introduced at the Ig and non-Ig loci. The first is through the accumulation of pseudorandom point mutations as a result of activation-induced cytidine deaminase (AID)-dependent double stranded breaks (DSB). The second is through the process of gene conversion, which involves the use of a template sequence to repair a DSB resulting in the template being copied at the site of repair. Findings from our lab suggest that some mutations in the non-Ig genes of human GCB arise through a gene conversion-like mechanism, referred to as templated mutagenesis. We sorted 4 B cell populations, including light zone and dark zone GCB from a young human tonsil and sequenced ~500bp sections from non-Ig genes including FAS, RHOH, and BTG1 via Illumina MiSeq. Previously, our lab has developed a computational pipeline called TRACE, that is able to match mutation clusters within an input sequence to partially homologous donor templates elsewhere in the genome. TRACE-identified donor templates are statistically likely to have been used in a templated mutagenesis event which led to the mutation of the gene. Through this analysis, we found that unlike gene conversion observed in chickens, human templated mutagenesis occurs between sequences on different chromosomes. Furthermore, donor template sequences tend to originate in introns and intergenic regions, not exons. These findings have opened an avenue into the study of non-Ig templated mutagenesis in human B cells.

H3K27me3 demethylases are important epigenetic regulators of B cell differentiation

The humoral immune response relies on robust differentiation of naïve B cells into antibody secreting plasma cells (PC) in response to foreign, but not self-antigens. To ensure proper immune responses, B cell differentiation is regulated through processes that remodel the epigenome. The histone modification H3 lysine 27 trimethylation (H3K27me3) is associated with a repressive chromatin state and gene silencing. This histone modification is deposited by EZH2, which has been shown to regulate all stages of B cell differentiation leading to PC. However, a role for the two demethylases UTX and JMJD3 that remove H3K27me3 in B cells is still to be elucidated. To determine how these enzymes modulate B cell differentiation, we crossed Utxfl/flJmjd3fl/flmice onto the Cd19Cre/+background (dKO mice). Stimulation of Cd19Cre/+(CreCtrl) and dKO mice with the T cell independent antigen LPS led to a significant increase in PC in dKO mice. This phenotype was attributed to enhanced differentiation of marginal zone (MZ), but not follicular B cells (FoB). UTX- and JMJD3-deficient PC unregulated genes associated with oxidative phosphorylation metabolism and resulted in a significantly higher spare respiratory capacity. In response to infection with influenza virus, we observed a significant increase in GC B cells in UTX- and JMJD3-deficient mice. Taken together, our data place H3K27me3 demethylases as critical epigenetic regulators that restrict B cell responses to T cell dependent and independent stimuli.

Single cell transcriptomics of in vivo differentiating antibody-secreting cells reveals a divergent activated B cell program dependent on IRF4

The generation of antibody-secreting cells (ASC) requires reprogramming the B cell transcriptome, epigenome, and metabolic potential to support the processes necessary to synthesize and secrete antibodies. These molecular changes have largely been studied at defined stages representing naive B cells, activated B cells, and ASC. To further refine when ASC fate decisions occur, we adoptively transferred CTV labeled B cells and monitored differentiation to both type I and II T cell independent antigens. At the peak of ASC responses, transferred cells were phenotyped by flow cytometry and isolated for single-cell RNA-seq. These data captured a continuum of responding B cells representing all stages of differentiation, with the largest heterogeneity observed among actB. Computationally ordering cells along differentiation trajectories, revealed divergent actB differentiation paths, with one branch leading to ASC formation that was dependent on IRF4. Moreover, cells that followed this trajectory downregulated the surface marker L-selectin and could be separated from cells that followed the alternative non-ASC differentiation branch. Indeed, isolation of actB by L-selectin status confirmed that L-selectin negative cells were ten times more likely to form ASC in culture. In summary these data provide insights into the cell division kinetics, molecular heterogeneity, and differentiation paths that lead to ASC formation.

Murine gammaherpesvirus infection is skewed toward Igλ+ B cells expressing a specific heavy chain V-segment

One of the defining characteristics of the B cell receptor (BCR) is the extensive diversity in the repertoire of immunoglobulin genes that make up the BCR, resulting in broad range of specificity. Gammaherpesviruses are B lymphotropic viruses that establish life-long infection in B cells, and although the B cell receptor plays a central role in B cell biology, very little is known about the immunoglobulin repertoire of gammaherpesvirus infected cells. To begin to characterize the Ig genes expressed by murine gammaherpesvirus 68 (MHV68) infected cells, we utilized single cell sorting to sequence and clone the Ig variable regions of infected germinal center (GC) B cells and plasma cells. We show that MHV68 infection is biased towards cells that express the Igλ light chain along with a single heavy chain variable gene, IGHV10-1*01. This population arises through clonal expansion but is not viral antigen specific. Furthermore, we show that class-switching in MHV68 infected cells differs from that of uninfected cells. Fewer infected GC B cells are class-switched compared to uninfected GC B cells, while more infected plasma cells are class-switched compared to uninfected plasma cells. Additionally, although they are germinal center derived, the majority of class switched plasma cells display no somatic hypermutation regardless of infection status. Taken together, these data indicate that selection of infected B cells with a specific BCR, as well as virus mediated manipulation of class switching and somatic hypermutation, are critical aspects in establishing life-long gammaherpesvirus infection.

Environmental cues regulate epigenetic reprogramming of airway-resident memory CD8+ T cells

Tissue-resident memory T cells (TRM cells) are critical for cellular immunity to respiratory pathogens and reside in both the airways and the interstitium. In the present study, we found that the airway environment drove transcriptional and epigenetic changes that specifically regulated the cytolytic functions of airway TRM cells and promoted apoptosis due to amino acid starvation and activation of the integrated stress response. Comparison of airway TRM cells and splenic effector-memory T cells transferred into the airways indicated that the environment was necessary to activate these pathways, but did not induce TRM cell lineage reprogramming. Importantly, activation of the integrated stress response was reversed in airway TRM cells placed in a nutrient-rich environment. Our data defined the genetic programs of distinct lung TRM cell populations and show that local environmental cues altered airway TRM cells to limit cytolytic function and promote cell death, which ultimately leads to fewer TRM cells in the lung.

Abstract A74: Loss of L-selectin distinguishes activated B cells destined to differentiate to plasma cells

Plasma cells engineered to produce and secrete de novo proteins have the potential to be used as biologic therapeutics for the treatment of cancer and other diseases. Genetic manipulation, expansion, and differentiation of naive B cells has been performed in vitro, and significant efforts have been made to understand and model the mechanisms that govern B cell fate decisions. Collectively, these studies indicated B-cell differentiation occurred across all cell divisions and that considerable cell fate heterogeneity exists between responding B cells within the same cell division. However, the differences in transcriptional programming that drive these differences and whether the same kinetics of cell division and differentiation are observed in vivo remain unknown, leaving a gap in our knowledge that may be critical for the efficacy of future therapeutic applications. To begin to address this, we employed an in vivo murine adoptive transfer system and monitored the kinetics of cell division and differentiation in response to lipopolysaccharide. We report that in vivo B cell differentiation requires a minimum of eight cell divisions, which corresponded to peak IRF4 expression and Blimp-1-mediated reprogramming. However, only a fraction of the cells that divided eight times differentiated, indicating that additional guidance cues ultimately decide cell fate decisions. To resolve B-cell differentiation at finer molecular resolution, we performed single-cell RNA sequencing. These data captured a continuum of LPS-responding B cells representing all stages of differentiation, with the majority of heterogeneity observed among activated B cells (actB). Computationally ordering cells along differentiation, or pseudotime, revealed divergent actB trajectories, with one branch leading to plasma cell formation that was dependent on IRF4. Cells along this branch upregulated genes associated with MYC activation and oxidative phosphorylation, both of which are important for achieving the metabolic and catabolic requirements to support plasma cell functions. Moreover, cells that followed this trajectory downregulated the surface marker L-selectin and could be separated from cells that followed the alternative non-plasma cell differentiation branch. Indeed, isolation of actB that had divided eight times and by L-selectin status confirmed that L-selectin-negative cells were ten times more likely to form plasma cells in culture. In summary, these data provide insight into the cell division kinetics of B-cell differentiation in vivo, highlight an IRF4-dependent bifurcation event that occurs early during actB reprogramming, and specify a strategy to identify actB that preferentially differentiate to plasma cells. Together, these data may be leveraged to improve desired immune outcomes by forcing cells down a path to a plasma cell or by identifying and expanding cells that are more prone to differentiate.

Citation Format: Dillon G. Patterson, Christopher D. Scharer, Tian Mi, Madeline J. Price, Sakeenah L. Hicks, Jeremy M. Boss. Loss of L-selectin distinguishes activated B cells destined to differentiate to plasma cells [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2019 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(3 Suppl):Abstract nr A74.

A super enhancer controls expression and chromatin architecture within the MHC class II locus

Super enhancers (SEs) play critical roles in cell type-specific gene regulation. The mechanisms by which such elements work are largely unknown. Two SEs termed DR/DQ-SE and XL9-SE are situated within the human MHC class II locus between the HLA-DRB1 and HLA-DQA1 genes and are highly enriched for disease-causing SNPs. To test the function of these elements, we used CRISPR/Cas9 to generate a series of mutants that deleted the SE. Deletion of DR/DQ-SE resulted in reduced expression of HLA-DRB1 and HLA-DQA1 genes. The SEs were found to interact with each other and the promoters of HLA-DRB1 and HLA-DQA1. DR/DQ-SE also interacted with neighboring CTCF binding sites. Importantly, deletion of DR/DQ-SE reduced the local chromatin interactions, implying that it functions as the organizer for the local three-dimensional architecture. These data provide direct mechanisms by which an MHC-II SE contributes to expression of the locus and suggest how variation in these SEs may contribute to human disease and altered immunity.

Signaling through the Inhibitory Fc Receptor FcγRIIB Induces CD8+ T Cell Apoptosis to Limit T Cell Immunity

Effector CD8+ T cells are important mediators of adaptive immunity, and receptor-ligand interactions that regulate their survival may have therapeutic potential. Here, we identified a subset of effector CD8+ T cells that expressed the inhibitory fragment crystallizable (Fc) receptor FcγRIIB following activation and multiple rounds of division. CD8+ T cell-intrinsic genetic deletion of Fcgr2b increased CD8+ effector T cell accumulation, resulting in accelerated graft rejection and decreased tumor volume in mouse models. Immunoglobulin G (IgG) antibody was not required for FcγRIIB-mediated control of CD8+ T cell immunity, and instead, the immunosuppressive cytokine fibrinogen-like 2 (Fgl2) was a functional ligand for FcγRIIB on CD8+ T cells. Fgl2 induced caspase-3/7-mediated apoptosis in Fcgr2b+, but not Fcgr2b-/-, CD8+ T cells. Increased expression of FcγRIIB correlated with freedom from rejection following withdrawal from immunosuppression in a clinical trial of kidney transplant recipients. Together, these findings demonstrate a cell-intrinsic coinhibitory function of FcγRIIB in regulating CD8+ T cell immunity.