bluuebunny/crossref_metadata_2025_split huggingface dataset:
HIV-specific CD8 T cells from elite controllers have an epigenetic imprint that preserves effector functions
Authors: Frias Adolfo B , Rutishauser Rachel L , Sharma Ashish Arunkumar , Mi Tian , Abdelsamed Hossam Aly , Zebley Caitlin , Constantz Christian M , Stone Mars , Busch Michael , Deeks Steven , Sekaly Rafick , Youngblood Ben A 
Published: January 2023

Abstract
CD8 T cells from HIV infected ‘elite controllers’ maintain long-lived protective properties including enhanced cytokine production and proliferative capacity over many years. With the advent of adoptive cellular therapy to treat chronic diseases it has become even more vital to understand the intrinsic cellular mechanisms of elite controller HIV specific CD8 T cells that enable lasting antiviral functionality. To identify epigenetic programs that regulate their functional capacity we performed genome-wide DNA methylation analysis of MHC Class I multimer+ CD8 T cells sorted from aviremic elite controllers compared to aviremic non-controllers on suppressive ART. Principle component analysis of the CpG sites broadly distinguished EC and ART HIV specific CD8 T cells, while deeper investigation of the differentially methylated region analysis revealed enrichment of pathways that support a multipotent differentiation state, cytokine signaling, and a long-lived effector cell fate in HIV-specific CD8 T cells from elite controllers. We also observed DNA methylation programs at the transcription factor binding sites of the stem-associated factors TCF-1 and LEF1 that delineate HIV-specific CD8 T cells from elite controllers versus ART-treated individuals. These findings show that HIV-specific CD8 T cells from elite controllers have DNA methylation programs that maintain developmental potential and in turn enable long-term survival, proliferative potential, and effector capacity. These data also provide new insights into the relationship between stem-associated transcription factors and stable epigenetic restriction of T cell developmental capacity.
Supported by grants from NIH (R01AI114442 and R01CA237311 to BY, K23AI134327 to RLR), loan repayment program and National comprehensive Cancer Network Young Investigator Award (CZ), ASSISI foundation support (BY) and American Lebanese Syrian Associated Charities (ALSAC to BY)
A unique gammadelta T cell population in the brain during viral infection
Authors: Berger Jennifer , Monogue Brendan , Beckham J David , Berg Leslie 
Published: January 2023

Abstract
Historically, the central nervous system (CNS) was considered to be an immune privileged site with limited immune responses. Now, it is known that the CNS presents a unique immunological environment with restricted infiltration by immune cells from the periphery or meningeal compartments. There remains limited understanding of which peripheral cells enter the brain during infection, how these cells enter the brain, and whether their function is detrimental or vital to eliminating infectious insult. Here, we utilize the attenuated Venezuelan equine encephalitis virus vaccine strain TC83 (VEEV-TC83) to study neuroimmunology during viral infection. Intracranial (IC) infection with VEEV-TC83 results in high viral titers in the brains of wild-type mice, without lethality, enabling study of immune responses in the brain. During CNS VEEV-TC83 infection, a large number of T cells infiltrate the brain rapidly after infection and, are thus, not antigen-specific T cells. After five days of infection, we found unusually high levels of infiltrating gammadelta T cells (γδ T cells) into VEEV-TC83-infected brains (upwards of 40% of the CNS-infiltrating T cells). The infiltrating γδ T cells express the uncommon surface markers CD11b and IL-23R. In this study we investigated the role of this unique γδ T cell population how these cells infiltrate the brain during viral infection. We found that the γδ T cells in infected brains are a unique subset expressing noncanonical surface markers and cytokines.
Supported by the Training Program in Immunology T32 AI007405
HSV-2 increases replication of HIV in human T cells
Authors: Pierce Carl A , Preston-Hurlburt Paula , Loh Lip Nam , Steach Holly , Sidoli Simone , Zhang Fengrui , Philbrick William , Nassar Michel , Krishnaswamy Smita , Herold Kevan C , Herold Betsy C 
Published: January 2023

Abstract
Herpes simplex virus 2 (HSV-2) infection is a major factor driving the global HIV epidemic, leading to increased HIV plasma viral loads (PVLs) and transmission. Previous studies which focused on mucosal responses cannot explain the observed effects of HSV-2 on HIV PVLs. We sought to determine mechanisms by which HSV-2 increases HIV PVLs. CD4 T cells are recruited to sites of HSV-2 lesions and HSV-2 can infect these cells. Phenotyping of CD4 cells infected with HSV-2 in vitro suggested a preference for T follicular helper cells, an HIV latent reservoir. HSV infection of latently infected Jurkat-2D10 cells resulted in a 10-fold increase in HIV ltr expression. After exposing CD4 cells from HIV+ donors to HSV-2, HIV p24 was detected only in cells expressing HSV-2 glycoprotein B (gB), a marker of productive HSV-2 infection. Bulk and single cell RNAseq on FACS-purified, HSV-infected and uninfected CD4 cells demonstrated reduced expression of HIV restriction factors in HSV+ cells; HSV exposed but uninfected cells exhibited higher expression of interferon response genes, potentially explaining their resistance to HIV reactivation. HSV+ cells exhibited increased expression of the lncRNA MALAT1, which may promote HIV reactivation through epigenetic modification, and HSV infection of 2D10 and CD4 cells led to decreased histone deacetylase activity. Transfection of 2D10 cells with HSV protein VP16 resulted in significantly increased HIV ltr and MALAT1 gene expression, and reduced epigenetic silencing marks. HIV proteins were also increased by proteomic analyses. These findings identify several mechanisms by which HSV-2 directly triggers HIV reactivation, such as the up-regulation of the lncRNA MALAT1.
Supported by grants from the NIH (R01 AI134367, T32 AI007501, T32 GM007288)
IL-27 signaling contributes to pathogenic T cells in a mouse model of Sjögren’s
Authors: Debreceni Ivy L , Chen Yi-Guang , Lieberman Scott M 
Published: January 2023

Abstract
Sjögren’s is an autoimmune disease with limited therapies due to an incomplete understanding of the immunological mechanisms that contribute to disease. Non-obese diabetic (NOD) mice spontaneously develop lacrimal gland inflammation dominated by early T cell infiltration, mirroring human disease. IL-27 is elevated in serum and saliva of Sjögren’s patients and is required for disease development in NOD mice.
Here, we define the requirements of IL-27 signaling in effector T cell subsets in the context of lacrimal gland autoimmunity. We utilized IL-27Rα KO NOD mice and an adoptive transfer model to determine which T cell subsets require IL-27 signaling to mediate lacrimal gland inflammation in NOD-SCID recipients. Both CD4 and CD8 T cells require IL-27Rα to transfer disease. Through co-transferring different combinations of KO and WT effector T cells, we found significantly decreased disease development when CD4 effector T cells did not express IL-27Rα. The role of IL-27 signaling in CD4 T cells is further supported by co-transfers of bulk lymphocytes from WT and KO mice which implicate IL-27 in driving the imbalance of CD4 effector T cells to Tregs in lacrimal glands. Additionally, Nanostring analyses performed on whole lacrimal glands from WT and KO mice support a role for IL-27 in driving pathogenic T cell infiltration. Together, these data demonstrate a pathogenic role for IL-27 in the T cell dysregulation in Sjögren’s.
Supported by grants from NIH (2T32 AI007485, DK121747 and EY027731)
Investigating immune tolerance: characterization of immunoregulatory DN T cells
Authors: Pasquin Sarah , Pelletier Adam-Nicolas , Lombard-Vadnais Félix , Chabot-Roy Geneviève , Collin Roxanne , Coderre Lise , Lesage Sylvie 
Published: January 2023

Abstract
Autoimmunity results from defects in immune tolerance pathways that impair the capacity of immune cells to distinguish between self and non-self. One of these immune tolerance processes involves immunoregulatory TCRαβ+ CD4− CD8− double negative T cells (DN T). Indeed, DN T cells protect from autoimmune pathologies and graft rejection in mice. Similarly, high DN T cell numbers correlate with a low incidence of chronic graft-versus-host disease in humans, an autoimmune-like pathology. While the thymic differentiation process of DN T cells was recently described, the function of these unconventional T cells is still poorly documented. To characterize DN T cells, we performed bulk RNA sequencing on CD4, CD8, γδ and DN T cells isolated from mouse spleen. Comparison of the transcriptome profiles revealed that DN T cells express a unique signature. Moreover, following in vitro stimulation, we find that DN T cells also present a distinct cytokine secretion pattern. Interestingly, we observed a lower induction of CD69, LAG-3 and PD-1 on DN T cells in comparison to CD4 and CD8 T cells, whereas LCK phosphorylation is unabated. DN T cell proliferation in mixed lymphocyte reactions is also lower than that of CD4 and CD8 T cells. Overall, our transcriptomic and cytokine analyses clearly identify DN T cells as a unique T cell subset. Moreover, while DN T cells do not express an exhaustion profile, they are more refractory to in vitro T cell stimulation than conventional T cells. A better characterization of DN T cell function will help conceive novel immunotherapies to treat autoimmune diseases.
Supported by the Canadian Institutes of Health Research - PJT 159603. S.P. was supported by a postdoctoral CIHR fellowship
The X-linked gene for the helicase DDX3X is required for lymphoid differentiation and MYC-driven lymphomagenesis
Authors: Lacroix Marion , Beauchemin Hugues , Ross Julie , Fraszczak Jennifer , Shooshtarizadeh Peiman , Chen Riyan , Moroy Tarik 
Published: January 2023

Abstract
The X-linked gene DDX3X encodes an RNA helicase and is mutated at high frequencies in several types of human B-cell lymphoma. Females have two active DDX3X alleles and males carry a DDX3Y homolog on the Y chromosome. We show here that pan-hematopoietic, homozygous deletion of Ddx3x in female mice perturbs erythropoiesis causing early developmental arrest. However, both hemizygous male and heterozygous female embryos develop normally, suggesting that one Ddx3x allele is sufficient for fetal hematopoietic development in females and that the Ddx3y allele can compensate for the loss of Ddx3x in males. In adult mice, loss of DDX3X affects hematopoietic progenitors, early lymphoid development, marginal zone and germinal center B-cells and lymphomagenesis driven by an Em-Myc transgene in a sex-dependent manner. Loss of one Ddx3x allele slightly accelerated MYC-driven lymphomagenesis in female mice, while male Em-Myc mice lacking Ddx3x remained almost lymphoma-free. However, the few tumors that appeared in male mice showed upregulated expression of DDX3Y indicating a minimal requirement for DDX3 activity for lymphomagenesis. Our data reveal sex specific roles of DDX3X in erythro- and lymphopoiesis as well as in MYC-driven lymphomagenesis, which are important when considering inhibition of DDX3 as a treatment of B-cell lymphoma.
Tarik Möröy holds a Canada Research Chair (Tier 1), a Foundation grant from the CIHR (FDN-148372) and support from the Cancer Research Society (CRS). Marion Lacroix is supported by fellowships from the Cole Foundation and the IRCM.
Epithelial mesenchymal transition of epithelial cells induced by TGF-β signaling in lymphedema
Authors: Park Hyeung Ju , Kataru Raghu P , Shin Jinyeon P , Mehrara Babak J 
Published: January 2023

Abstract
TGF-β driven fibrosis of the skin is a key pathologic feature of secondary lymphedema. However, the cellular mechanisms that regulate this process remain unknown. Epithelial mesenchymal transition (EMT) is a mechanism by which TGF-β induces fibrosis in other skin diseases. This process is characterized by loss of epithelial cell markers and polarity and increased migratory capacity and invasiveness. Therefore, the purpose of this study was to determine if EMT of skin keratinocytes is activated in lymphedema and if this process is mediated by TGF-β.
Using clinical lymphedema biopsy specimens and mouse models of lymphedema, we found that lymphedema results in fibrosis in the papillary dermis and a greater number of rete ridges in the basal layer of epithelium. Keratinocytes in the basal layer of lymphedematous skin express EMT markers (vimentin, fsp1, itgb4, slug, mmp9, twist) and fail to express epithelial markers (keratin14, E-cadherin). Interestingly, we found psamd3 expression in these EMT-like epithelial cells with accumulated TGF-β in papillary dermis by immunohistochemistry. Inhibition of TGF-β signaling markedly decreased EMT and prevented development of fibrosis in a mouse model. To determine if EMT of epithelial cells is induced by lymphedema fluid in skin, we treated keratinocytes with lymph fluid obtained from patients with lymphedema and analyzed in cultures with or without TGF-β inhibitors. We found that keratinocytes cultured with arm fluid only rapidly underwent EMT. In contrast, inhibition of TGF-β signaling prevented this response. Taken together, our findings show for the first time that EMT is activated by TGF-β signaling in lymphedema and that this process plays an important role in the pathology of this disease.
Supported by grants from NIH (R01HL111130).
The contribution of fetal-derived tissue resident macrophages to cytomegalovirus-associated sensorineural hearing loss
Authors: Otsuka Kelly , Nielson Chris , Suarez Daniel , Park Albert , Beaudin Anna E 
Published: January 2023

Abstract
Cytomegalovirus (CMV) is the most common congenital viral infection in the developed world and the leading cause of non-genetic sensorineural hearing loss (SNHL) in children. Congenital CMV causes progressive SNHL long after acute infection has resolved, suggesting a lasting effect on the developing host immune response within the cochlea and surrounding temporal bone marrow (TB). Using fate-mapping models, we have investigated the contribution of fetal-derived tissue resident macrophages (TRMs) to normal cochlear development and function, and their role in mediating CMV-associated SNHL. Our analysis defined two distinct myeloid population within the inner ear: 1) classical tissue resident macrophages (F4/80hi CD11blo) that highly express CD64 and are found exclusively in cochlear tissue; and 2) transitional monocytes (F4/80mid CD11bhi) that express both CD64 and Ly6C and are found in cochlea and TB. Fate mapping of these populations uncovered dual contribution of fetal-derived cochlear TRMs from yolk sac (YS) and fetal liver (FL) hematopoiesis. Transitional monocytes increase during acute CMV infection, acting as drivers of expanded lymphoid populations after CMV resolves. Importantly, analysis of Flt3-Cre labeling within myeloid populations suggests that TRMs are replaced by BM-derived populations at later postnatal stages following CMV infection, coinciding with SNHL. Ongoing work examines spatial distribution of distinct fetal-derived TRMs along cochlear architecture, defining transcriptional regulation differences between YS-, FL-, and adult-derived TRMs in response to CMV, and examining how replacement of fetal-derived TRMs with adult-derived TRMs affects tissue function and response to infection.
Supported by grants from University of Utah Molecular Medicine and Immunology, Inflammation and Infectious Disease (3i) Initiative and NIAID (T32 5T32AI138945)
Identification of a Novel Protein Interactions that Elucidates the Mechanism of Hydatidiform Molar Pregnancies in Women with NLRP2 and NLRP7 Mutations
Authors: Son Nayeon , So Matthew , Lupfer Christopher R 
Published: January 2023

Abstract
Mutations in NLRP2 and NLRP7 genes result in genetic maternal imprinting disorders. These genes have been identified to be maternal effect genes regulating early embryo development in idiopathic recurrent miscarriage. Previous research suggests that NLRP2 and NLRP7 regulate DNA methylation and immune signaling through inflammasome formation. However, the exact mechanisms underlying recurrent miscarriages are not known. In this study, we report a novel protein interaction of Human proliferation-associated 2G4 (PA2G4, aka: EBP1) with NLRP2 and NLRP7 through an unbiased yeast 2-hybrid screen of a human HeLa cell cDNA library. Protein interactions were confirmed by co-immunoprecipitation and confocal microscopy. Furthermore, global DNA methylation decreased in cells that overexpressed NLRP2/7 and EBP1. Our results further support the role for NLRP2/7 in regulating DNA methylation as a mechanism for recurrent miscarriages. Since EBP1 is implicated in apoptosis, cell proliferation, and differentiation, our discovery significantly advances our understanding of NLR biology and helps to explain the cellular pathways involved in idiopathic recurrent miscarriages.
Supported by grants from Beta Beta Beta Biological Honor Society
Epithelial C15ORF48/miR-147 is an essential regulator of gut inflammation and microbiome homeostasis
Authors: Xiong Min , Liu Ze , Graham Natalie Marie , Sokolich Thomas , Boldin Mark P 
Published: January 2023

Abstract
Aberrant inflammation plays an important role in the pathogenesis of several gastrointestinal diseases, including inflammatory bowel disease (IBD) and colorectal cancer (CRC). Insufficient understanding of the molecular mechanisms that control gut inflammation is one of the critical barriers to effective IBD and CRC therapies. To this end, we have uncovered C15ORF48/miR-147 as a novel negative regulator of gut inflammation. The C15ORF48/miR-147 gene encodes a small protein (C15ORF48) and a microRNA (miR-147-3p). Both molecular products are expressed predominantly in the large intestine, and their genetic ablation significantly exacerbates dextran sodium sulfate (DSS)-induced colitis in mice. The fulminant DSS-induced colitis phenotype in C15ORF48/miR-147−/− mice is driven by a cell-autonomous defect in gut epithelial cells and is mediated by gut dysbiosis. miR-147-3p and C15ORF48 synergize to silence the expression of NDUFA4, an accessory subunit of complex IV (CIV) in the mitochondrial electron transport chain. Our findings suggest that NDUFA4 plays an essential role in the activation of NF-kB signaling and the downstream inflammatory responses. Furthermore, C15ORF48, being an NDUFA4 structural paralog, can replace NDUFA4 in CIV and thus attenuate CIV activity and mitochondrial respiration, which may subsequently impact gut microbiome homeostasis. Collectively, our findings have established the C15ORF48/miR-147-NDUFA4 molecular axis as a novel, indispensable regulator of gut inflammation and a critical mediator between gut epithelial cells and microbiota.
CD300e Acts As A Ligand To Inhibit T Cell Immunity
Authors: Wang Jinghua , Manick Brian , Li Jun , Bi Ming , Kalabokis Vassilios , Person Anthony , Wu Guoping 
Published: January 2023

Abstract
CD300e has been reported as either an activating or inhibitory receptor and is involved in the tuning of immune responses. In this study, we demonstrate that CD300e acts as a ligand through an unknown receptor to inhibit T cell immunity. In PBMCs, CD300e protein is expressed on the cell surface of CD14+ monocytes, but not on T and B cells. CD300e-Fc fusion protein significantly reduced the expression of CD69 and CD25 on T cells, which suggest that CD300e inhibits the activation of T cells. Furthermore, CD300e-Fc fusion protein significantly inhibited TCR-mediated T cell proliferation and cytokine production including IL-2, IFN-gamma, IL-17, TNF-alpha, IL-8 and IP-10/CXCL10. Florescent conjugated CD300e-Fc fusion protein significantly bound to activated T cells and weakly to inactive T cells, suggesting that the putative CD300e counter-receptor is expressed on the cell surface of T cells, and the expression levels are upregulated upon T cell activation. CD300e-Fc fusion protein inhibited TCR-mediated p38 MAPK phosphorylation which indicates that CD300e negatively regulates T cell activation by impairing the p38 MAPK dependent antigen presentation. Moreover, our results support the notion that CD300e might be a new player in the regulation of the expansion of T cell-mediated responses. This CD300e novel T cell inhibitory pathway may provide a new strategy to modulate T cell-mediated immunity to treat immune-related diseases.
Metabolic fuel choices control MAIT cell functions at homeostasis and after infection
Authors: Riffelmacher Thomas , Paynich Mallory Murray , Chandra Shilpi , Wientjens Chantal , Seumois Gregory , Vijayanand Pandurangan , Kronenberg Mitchell 
Published: January 2023

Abstract
Mucosal-associated-invariant-T (MAIT) cells are an innate-like T cell subset that recognizes microbial-derived vitamin B metabolites. In contrast to conventional T cells, MAIT cells have an antigen-experienced phenotype and express memory markers by default. When activated, MAIT cells rapidly produce copious amounts of cytokines, resembling IFNg+ Th1- or IL-17+ Th17 effectors cells. While memory-like vs effector-like states in conventional CD4 and CD8 T cells are controlled by mutually exclusive metabolic states, the question remains as to which metabolic programs MAIT cells adopt at steady-state and after infection. Here we integrate scRNA-seq analysis with single-cell metabolic characterization of MAIT cells from humans and mice. We discovered a memory-like metabolic program that is acquired in the thymus and at steady state in the periphery. We identify a novel cluster of circulatory MAIT cells which is metabolically similar to IFNg+ MAIT1-like cells and preferentially consumes glucose. MAIT17 clusters, most prevalent in mice, uniquely engage in fatty acid uptake and mitochondrial metabolism. Following exposure to bacteria, mouse MAIT cells expand as CD127− KLRG1+ and CD127+ KLRG1− populations that adopt divergent transcriptomic and metabolic profiles with enhanced functionality. They remain altered long-term. CD127+, but not KLRG1+ MAIT cells engage in MAIT17-like metabolic and effector pathways and protect mice from lung infection with Streptococcus pneumoniae. In contrast, KLRG1+ MAIT cells depend on Hif1a-driven glycolysis and remain metabolically dormant but ready to respond, more rapidly engaging multiple metabolic programs to protect from viral infection.
Supported by R01AI137230 (MK), R01AI71922 (MK), Wellcome Trust 210842_Z_18_Z (TR)