bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unique Features of Immunity within the Immunoglobulin Heavy Chain Locus of Egyptian Rousette Bats
Authors: Bartlett Maggie , Larson Peter A. , Palacios Gustavo , Sanchez-Lockhart Mariano 
Published: January 2023

Abstract
The Egyptian fruit bat (Rousettus aegyptiacus, ERB) is reported to be the reservoir of Marburg virus (MARV). Indeed, MARV infection is almost completely asymptomatic in ERBs while eliciting a severe hemorrhagic fever in humans and non-humans primates (NHPs). To understand the biological mechanisms that explain these differential outcomes to MARV, we aim to investigate the differences between both animals’ immune systems. One of the antiviral mechanisms to control viruses is the humoral response. The B cell receptor (BCR) is composed of two heavy and two light chains heterodimers. Both immunoglobulin (Ig) chains undergo DNA rearrangement to generate a diverse repertoire, crucial for diverse antigenic recognition. The Ig heavy chain locus is comprised of the variable (V), diversity (D), joining (J), and constant (C) genes. Utilizing high throughput sequencing to resolve the V(D)J rearrangements we can characterize the BCR repertoire and define the clonotypes that are generated in response to vaccination or infection. To define the BCR repertoire with DNA sequencing, a thorough representation of the Ig heavy chain (IGH) locus is necessary. We were able to resolve on contiguous IGH locus containing all BCR genes that were previously on 21 different scaffolds. In addition, we identified a unexpected expansion of IgE genes not described in another species to date. We defined the tissue expression of these novel IgE genes as well as IgGs, IgA, and IgM. Finally, we predicted differential functions between subclasses in silico. These data support unique immune response capabilities of ERBs that may aid in their control of pathogenic human viruses.
Interleukin-6 induces immunometabolic reprogramming in human rheumatoid arthritis synovial fibroblasts to promote osteoclastogenesis
Authors: Ahmed Salah-Uddin , Singh Anil K , Haque Mahamudul , Basit Abdul , Shi Yuanyuan , Wildman Benjamin J , Prasad Bhagwat , Hassan Quamarul 
Published: January 2023

Abstract
Interleukin-6 (IL-6) plays an important role in progressive bone loss in rheumatoid arthritis (RA). However, the molecular mechanisms through which IL-6 propels RA synovial fibroblasts (RASFs) to contribute to bone loss are not fully understood. Treatment of human RASFs with IL-6 and IL-6 receptor (IL-6/IL-6R, 100 ng/ml each) alone or in combination with M-CSF (2 ng/ml) and RANKL (5 ng/ml) for 9 days resulted in the phenotypic changes to osteoclast-like features as determined by increase in TRAP staining and Dentin pit resorption area, which were comparable to M-CSF/RANKL group. IL-6/IL-6R induced a dose-dependent increase in the expression of transcription factor Ets2 and enhanced its nuclear translocation alone or combinatorially in M-CSF/RANKL-differentiated human RASFs. Chromatin immunoprecipitation (ChIP) analysis of Cathepsin K and B promoters showed Ets2 binding and transcriptional activation upon IL-6/IL-6R stimulation, which was further increased with M-CSF/RANKL. Interestingly, the untargeted proteomics analysis of the conditioned media from activated RASFs using Mass-Spectrometry (MS) technique and Trans-Proteomic Pipeline tool showed the production of 113 analytes unique to IL-6/IL-6R stimulation. Further analysis of the proteomics data using STRING database for pathway analysis showed the impact of IL-6/IL-6R on immunometabolic reprogramming of human RASFs towards osteoclast-like phenotype, which was partly mediated through Ets2. These preliminary studies identified a novel role of IL-6/IL-6R-mediated transsignaling in the metabolic reprogramming in RASFs that could potentially be targeted by inhibiting Ets2 to limit their role in bone resorption in RA.
Identifying innate immune receptors causing production of inflammatory cytokines by infection of Francisella tularensis
Authors: Gutierrez Stephanie K , Setzu Nicole R , Spencer Charles T 
Published: January 2023

Abstract
Francisella tularensis is a pathogenic species and a causative agent of tularemia. This bacterium is incredibly infectious and often lethal in that F. tularensis causes the overproduction of pro-inflammatory cytokines. The objective of this study is to identify the innate immune receptors responsible for the production of inflammatory cytokines in response to F. tularensis infection. The study uses an immortalized C57BL/6 Bone Marrow Macrophage (BMMac) cell line as the control and knockout BMMac that are deficient in various innate immune receptors. The cells are passaged and seeded before infecting them with F. tularensis for 2 hours. The cells are treated with a high dose of gentamicin for 2 hours followed by a low dose of gentamicin for an incubation period of 24 hours. The supernatant from these cells are then collected and analysis processed by ELISA, an enzyme-linked immunosorbent assay, to measure production of inflammatory cytokines. These data were compared with the positive control of wild type BMMac and the negative control of uninfected BMMac cells. Analysis of these mutants reveal the involvement of innate immune receptors in triggering the pro-inflammatory cytokine storm in response to F. tularensis infection that leads to death of the host.
C3 complement mediates neutrophil control of cryptococcal lung infection and dissemination
Authors: Ogbomo Henry , Li ShuShun , Stack Danuta , Chojnacki Andrew K , Wojcik Katarzyna , Polyak Maria J , Colarusso Pina , Kubes Paul , Mody Christopher H 
Published: January 2023

Abstract
The encapsulated budding yeast Cryptococcus neoformans causes meningitis and pneumonia particularly in immunocompromised individuals including HIV-infected patients. The organism is acquired by the pulmonary route where it disseminates via the bloodstream from the lung to the brain and causes meningitis. Since the lung vasculature is replete with several innate immune cells, it is conceivable that the host would mount an immune response in the pulmonary vasculature to prevent or at least limit the dissemination of C. neoformans to other sites of the body. Hence, we used intravital microscopy to study the host cell immune interactions that occur within the lung vasculature in a living mouse. We found that neutrophils, but not monocytes, interacted with and phagocytosed C. neoformans. Interestingly, additional neutrophils underwent accretion around the phagocytosed C. neoformans, forming a cast of the vasculature. Phagocytosis of C. neoformans was impaired by the presence of cryptococcal capsule, since acapsular strain of C. neoformans were rapidly phagocytosed by neutrophils compared with encapsulated strain. Neutrophil phagocytosis of C. neoformans and subsequent accretion was mediated by complement C3 in both acapsular and encapsulated strains. Mice deficient in C3 complement showed reduced clearance of C. neoformans from the lungs and brain, compared to C3 sufficient mice. These findings highlight the importance of neutrophils in the control of C. neoformans in the pulmonary vasculature and subsequent dissemination to the distal organs including the brain.
Age-related chromatin landscapes in mouse macrophages
Authors: Oh Kyu-Seon , Babagana Mahamat , Pacholewska Alicja , Chakraborty Sayantan , Ha Jisu , Baek Songjoon , Sung Myong-Hee 
Published: January 2023

Abstract
Aging is associated with changes in gene expression. Age-related changes in chromatin structure may contribute to alterations in gene expression and to aging phenotypes in human. Macrophages play essential roles in tissue homeostasis and repair. Macrophage activation by bacterial LPS leads to induction of a complex inflammatory gene program dependent on numerous transcription factor (TF) families. We previously showed that chromatin accessibility of macrophages is massively increased after LPS treatment. Similar programs may also contribute to the chronically elevated inflammatory state in aging. Therefore, it is important to understand how macrophages are epigenetically and functionally altered during aging. To address the age-associated differences in the transcriptome and chromatin landscape of macrophages, we have performed RNA-seq and ATAC-seq of tissue-resident macrophages in the presence or absence of LPS. Our results revealed that age effect in macrophages seems cell type-specific with the strongest effect in microglia. The majority of age-dependent TF footprints in macrophages showed reduced TF occupancy, but with either reduced or increased chromatin accessibility. We are investigating the functional relevance of the candidate TFs identified in our analysis. Our data highlight the tissue-specificity of aging features that occur in resident macrophages in vivo.
Macrophage-associated lipin-1 regulates lipid catabolism to promote effective efferocytosis
Authors: Schilke Robert Michael , Blackburn Cassidy M.R. , Rao Shashanka , Krzywanski David M. , Woolard Matthew D. 
Published: January 2023

Abstract
Failure to resolve inflammation leads to numerous chronic diseases. Disease resolution requires the effective removal of dead cells by macrophage-mediated efferocytosis. Excess lipid accumulation within macrophages can lead to dysfunction that promotes disease pathogenesis. Efferocytosis results in a significant accumulation of lipid inside the macrophage, yet macrophage continue to function. This suggest that during efferocytosis, macrophages have pathways to ameliorate the high lipid load. We have identified that lipin-1, a regulator of lipid metabolism, is critical to proper macrophage responses during efferocytosis. Lipin-1 is a phosphatidic acid phosphatase that also functions as a transcriptional coregulator. We used mice that lack either lipin-1 enzymatic activity or both functions in myeloid cells to define how lipin-1 regulates excess lipids during efferocytosis. We have demonstrated that mice lacking myeloid-associated lipin-1 have diminished apoptotic cell (AC) clearance in a zymozan model of efferocytosis. Clearance of lipids during efferocytosis is accomplished through beta-oxidation. Bone marrow derived macrophages lacking lipin-1 have reduced oxidative respiration in response to both AC and purified palmitate (lipid), indicating defective lipid catabolism. These data suggest that lipin-1 regulates mitochondrial lipid catabolism to reduce lipid burden during efferocytosis. These studies highlight regulation of lipid metabolic pathways in macrophages during efferocytosis that allow them to handle excess lipid burden and promote disease resolution.
Lipin-1 coordinates macrophage lipid metabolism to allow macrophage wound healing function
Authors: Woolard Matthew D , Blackburn Cassidy M.R. , Schilke Robert Michael , Chandran Sunitha , Vozenilek Aimee E 
Published: January 2023

Abstract
Excess lipid burden within macrophages disrupts cellular metabolism and alters their cellular function allowing these macrophages to contribute to both inappropriate and/or unresolving inflammation. The molecular mechanisms that align lipid metabolism to macrophage function are not well understood. Lipin-1 is a phosphatidic acid phosphatase that regulates the penultimate step of glycerolipid metabolism. Lipin-1 is also a transcriptional coregulator that regulates the expression of lipid catabolism genes including beta-oxidation. We and others have demonstrated that lipin-1 promotes macrophage pro-inflammatory responses. The objective of this study was to determine the contribution of lipin-1 transcriptional coregulator function within macrophages activity. We used mice that lack either lipin-1 enzymatic activity or both lipin-1 functions in myeloid cells to define how lipin-1 transcriptional coregulator function contributes to macrophage function. We demonstrated that lipin-1 transcriptional coregulator function is required for IL-4 mediated macrophage polarization and effective efferocytosis through the promotion of beta-oxidation/oxidative phosphorylation via activation of PPARγ. Loss of both lipin-1 activities from myeloid cells leads to increased atherosclerotic burden and reduction in wound closure. Furthermore, we observed enhanced pro-inflammatory responses both in the plaques and the serum of atherosclerotic mice lacking myeloid associated lipin-1. Our work provides evidence that lipin-1 aligns cellular lipid metabolism to promote effective macrophage responses.
Single-cell transcriptome profiling reveals heterogeneity of brain myeloid cells and unique subsets that regulate T cell immunity and cerebrovascular inflammation in diet-induced obesity
Authors: Yu I-Chen Ivorine , Paraiso Hallel C. , Kuo Ping-Chang , Furnas Destin J , Scofield Barbara A. , Weng Wen-Tsan , Sweazey Robert D , Chang Fen-Lei , Yen Jui-Hung 
Published: January 2023

Abstract
Midlife obesity and type 2 diabetes mellitus (T2DM) are linked to decreased cognition and strong risk for Alzheimer’s disease in late life. Previous studies show that obesity/T2DM is associated with a heightened state of neuroinflammation in aging mice. However, it remains unclear how diverse immune cell populations in the brain contribute to the cognitive decline. To address this, we fed middle-aged mice with high-fat diet (HFD) to induce visceral obesity and hyperglycemia. Chronic HFD consumption resulted in cognitive impairment and activation of brain resident microglia (MG). The CD45hiCD11b+ peripheral myeloid cells and CD3+ T cells were significantly increased in the brain of obese mice. Single-cell RNA sequencing was performed to characterize CD11b+ cells isolated from the brain. Unsupervised clustering singled out distinct myeloid cell clusters. Using Tmem119 and P2ry12 as markers to distinguish MG from infiltrating cells, we observed a 2-fold increase of peripheral myeloid cells, comprising distinct clusters in HFD-fed mice. Multiple subsets of MG were identified in HFD-fed mice, showing Ms4a, Apoe and gene signatures of perivascular macrophages. Notably, these subsets expressed high levels of MHC class-II-related molecules, H2-Eb1, H2-Ab1, and Cd74, and with special functions in lipid metabolism. These data suggested possible interactions between MG and T cells to potentiate neuroinflammation in HFD-fed mice. Overall, our results highlighted heterogeneity of brain myeloid cells in obesity during aging. The identified subsets of MG provide insights into brain MG controlling T cell immunity and cerebrovascular inflammation, which might lead to cognitive impairment associated with obesity and T2DM during aging.
A novel role for indoleamine 2,3-dioxygenase (IDO) in supporting the survival of long lived plasma cells (LLPC)
Authors: Lightman Shivana M , Carlson Louise M , Holling G. Aaron , Lee Kelvin P 
Published: January 2023

Abstract
Protective antibodies against diseases such as measles and polio primarily come from bone marrow (BM) resident long lived plasma cells (LLPC) and are a key component of durable humoral immunity. As LLPC are not innately long lived a major question remains about how these cells maintain survival. Our lab has previously demonstrated that the T cell receptor, CD28, is essential for the survival and function of LLPC. Here we further demonstrate that when CD28 on LLPC ligates with CD80/CD86 on DC, it induces upregulation and activation of indoleamine 2,3-dioxygenase (IDO). IDO’s primary action is catabolizing tryptophan into kynurenine, a well-known ligand of the aryl hydrocarbon receptor (AhR). A nuclear transcription factor, AhR is known to modulate immune responses and is expressed in PC. Unexpectedly we observed that IDO KO mice have significantly less long lived antigen specific antibody titers and a decrease in LLPC specifically in the BM post immunization. Specific deletion of IDO+DC also significantly decreases LLPC in vivo. Furthermore, treatment with kynurenine in LLPC causes upregulation of CYP1A1, the downstream target of AhR. Moreover, we see an increase in CD28 expression with kynurenine treatment in murine and human PC. We propose a model where the interaction of CD28 on LLPC with CD80/CD86 on DC activates IDO, producing kynurenine, which activates AhR to further regulate CD28 expression on LLPC. These findings challenge the traditional paradigm of IDO as immunosuppressive and uncover a novel role in promoting immunity. Filling this gap in knowledge furthers our understanding of diseases that involve LLPC, but also has direct implications in future vaccine and therapeutic drug development.
Support: T32 CA085183, R01CA121044
Solid micro particle mediated sterile type2 inflammation is mediated through cell death and A2b adenosine receptor signaling pathways
Authors: Mishra Pankaj Kumar , Davra Viralkumar , Palma Mark , Lothstein Katherine E , El-Naccache Darine W. , Benevenia Joseph , Beebe Kathleen , Hallab Nadim J , Hasko George , Birge Raymond B , Gause William 
Published: January 2023

Abstract
Sterile solid microparticles (MPs) trigger an innate type 2 inflammatory response dependent on a SYK-BTK-IL33 signaling axis (Nature Materials,18, 289,2019). Inoculation with MPs trigger innate inflammation with influx of neutrophils, eosinophils and alternatively activated macrophages (M2). MPs also trigger cell death in macrophages leading to release of IL33 and the development of a type 2 response with increased IL4,IL5 and IL13 and expression of M2 markers including Arg1, Relmα and Chil3. Blockade of cell death by inhibiting necroptosis (necrox-2) or apoptosis (ZVED-FMK) alone or in combination inhibited the MP mediated release of IL33 by macrophages ex vivo. We also examined the role of adenosine in MP-mediated IL-33 release by inoculating LysMCreA2bfl/flwith MP.MP induced inflammation was blocked in LysMCreA2bfl/fmice compared to LysMCre controls, with significant decreases in type 2 cytokines and IL33. Adoptive transfer of wild type macrophages to LysMCreA2bfl/flrestored the MP-mediated type 2 inflammation. These findings indicate that programmed cell death and A2b receptor signaling pathways play a major role in particulate induced sterile inflammation.
Degranulation-enhanced presynaptic membrane packing protects NK cells from perforin-mediated autolysis
Authors: Li Yu , Orange Jordan Scott 
Published: January 2023

Abstract
NK cells are resistant to autolysis when they kill a target cell using perforin secretion into the lytic immunological synapse. Perforin makes pores in target cell membranes allowing delivery of pro-apoptotic enzymes. Despite the fact that the perforin-containing organelles (lytic granules) are released in close range to both the NK and target cell, the NK cell membrane is protected. How NK cells avoid autolysis during degranulation is perplexing.
We demonstrate that NK cells are protected from perforin by their densely packed presynaptic membranes. When treated with 7-ketocholesterol lipid packing is reduced in NK cells, making them susceptible to perforin mediated autolysis after degranulation.
Using advanced imaging, we showed that lytic granules themselves have endogenously densely packed membranes. Importantly, during degranulation lytic granule-cell membrane fusion further reinforces local presynaptic membrane packing. This provides enhanced membrane protection at the specific sites of degranulation where NK cells face maximum local concentrations of secreted perforin.
Additionally, we found that an aggressive breast cancer cell line utilizes the same strategy to evade NK cellmediated killing. These cells are perforin-resistant owing to a densely packed postsynaptic membrane. By disrupting membrane packing, we effectively switched them to an NK-susceptible state.
Overall, we reveal an unexpected role for lipid membranes in NK cell functionality and that degranulation uses lytic granule membrane packing to create local “shields” against autolysis. Furthermore, lipid membrane modulation could alter the susceptibility of perforin-resistant cancer cells and should be considered in cytotoxic cell therapies.
Liver-derived mitochondria drive CD8 T-cell dysfunction, alter purinergic signaling and impair bacterial clearance in the lung in vivo
Authors: Tiwari-Heckler Silpa , Lee Ghee Rye , Harbison James , Csizmadia Eva , Ledderose Carola , Hauser Carl J , Otterbein Leo E , Longhi Maria Serena , Robson Simon C. 
Published: January 2023

Abstract
Trauma is the leading cause of death in young adults. The pathogenetic mechanisms resulting in posttraumatic immunosuppression with increased susceptibility to infection remain unclear. Mitochondria (MT) are released by cells after trauma and can generate danger molecules, such as extracellular ATP (eATP). The vascular and immune cell ectonucleotidase CD39 scavenges eATP to generate immunosuppressive derivatives such as adenosine. Here, we examined the role of eATP generated by exogenous mitochondria in modulating the immune response and provoking immunosuppression in the context of experimental pneumonia models. ATP probes and MitoSOX revealed that liver-derived MT generate ATP and ROS ex vivo. When injected into recipient mice, MT isolated from mouse liver induced upregulation of CD39 and CD73 expression on circulating CD8 T cells and promoted immune cell exhaustion. Next, wild-type mice were injected intraperitoneally with liver MT, followed by intratracheal instillation of pathogenic S. aureus. Mice receiving MT were unable to clear bacteria, as demonstrated by elevated CFU counts in the bronchoalveolar lavage, when compared to mice with bacterial instillation alone. Histological analysis confirmed more pronounced lung injury with infiltration of inflammatory neutrophils in mice administered both MT and bacteria, when compared to mice instilled only with bacteria. Lastly, the MT injection with concomitant bacteria administration resulted in loss of lung-derived CD8 T-cells.
Our data indicate that ATP generation by exogenous mitochondria boost CD39 expression in circulating CD8 T-cells and drive dysfunctional immune responses in mice that result in increased susceptibility to bacterial infection of the lungs.
Analysis of the role of helminth TGF-β mimic in tissue repair
Authors: Lothstein Katherine E , Smyth Danielle J , Maizels Rick , Gause William C 
Published: January 2023

Abstract
Intestinal parasites express excretory/secretory (ES) molecules, which modulate the type-2 immune response, including anti-inflammatory and tissue repair mechanisms. TGF-β mimic (TGM), an ES molecule secreted by H. polygyrus (Hp), binds TGF-β receptors yet lacks structural homology to TGF-β and exhibits distinct receptor interactions. Studies suggest TGM generates higher expression of immunoregulatory Foxp3+ Tregs and decreased fibrotic markers in vitro compared to TGF-β. Host TGF-β also influences wound healing. In cutaneous wounds, effective tissue repair requires rapid suppression of inflammation and local production of wound healing factors. We investigated whether TGM modulates wound healing using an in vivo wound biopsy model during which TGM is injected beneath a Tegaderm® layer to mimic cutaneous wound treatment. We showed that TGM accelerates wound healing when applied to the wound surface at multiple doses and modulates the associated inflammatory response. LC-MS/MS analysis of TGM-treated wound exudate revealed increases in proteins mediating leukocyte chemotaxis and proliferation, collagen deposition and fibrotic regulation. There was also enhanced immune cell infiltration of alternatively activated CD206+F4/80+ macrophages and epithelial cells concurrent with accelerated wound closure. These macrophages are CD301b+ and are essential for effective wound healing and potentially regulating fibrosis. Our findings indicate that TGM can enhance skin wound healing through enhanced production of proteins facilitating wound repair and through recruitment of specific macrophage subsets. This study will investigate TGM as a potential novel and effective therapeutic option for enhanced wound healing.