bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early AID expression in developing B cells marks a population with a restricted IgH repertoire favoring D-proximal VH gene usage
Authors: von Beck Troy Alexander , Dale Gordon , Jacob Joshy 
Published: January 2023

Abstract
Activation-induced cytidine deaminase (AID) is well characterized in germinal center reactions as a driver of secondary antibody diversification through the processes of somatic hypermutation and class-switch recombination, but recent reports from clinical and murine studies suggest an additional role during primary diversification. Specifically, inhibition or knockout of AID activity during B cell development results in increased IgM autoantibody production. Furthermore, the expression of AID during development appears to be driven by B cell receptor mediated recognition of autoantigens, including RNA and dsDNA. To examine the pattern of early AID expression, we used lineage tracing in an AID-Cre x R26R-EYFP mouse model to identify a subpopulation of AID experienced (AID-exp) pre-B cells. Sequencing of the IgH repertoire from the AID-exp subpopulation reveals a stark reduction in the diversity of VH gene usage compared to AID-naïve pre-B cells. The reduction in diversity is accompanied by enrichment for specific VH genes, including D-proximal elements associated with B1 cells and autoantibodies. Thus, we discern skewing within the AID-exp repertoire suggestive of antigen-dependent selection in the bone marrow compartment. Our results support the hypothesis that AID is induced in pre-B cells carrying an autoreactive heavy chain and effects tolerization to specific self-antigens.
Depletion of SCFA-fermenting gut bacteria alters the epigenome of hematopoietic stem and progenitor cells
Authors: Hughes Michael R , Cait Alissa , Bilenky Misha , Moksa Michelle M. , Yip William , Li Kristen , Canals-Hernaez Diana , Hirst Martin , Mohn William W , McNagny Kelly M 
Published: January 2023

Abstract
Gut dysbiosis alters the development and severity of atopic disease. We previously demonstrated that nursing dams and newborn mice treated with low-dose vancomycin alters gut microbial diversity with a marked loss of bacteria that produce short-chain fatty acids (including butyrate). Vancomycin-induced gut dysbiosis enhances the TH2 response to lung allergens due to altered dendritic cell trafficking and activation in addition to modifying the behavior of other mature leukocyte lineages. Butyrate supplementation reverses the vancomycin-induced TH2 pro-inflammatory phenotype.
Butyrate is known to exert some of its effects on target cells by inhibiting histone deacetylases (HDACs) with consequent effects on gene expression. Consistent with a role for epigenetic skewing of the hematopoietic compartment, we found that engraftment of total bone marrow from dysbiotic mice transferred enhanced TH2 proclivity in normobiotic recipients. Strikingly, we found unique regulatory states (H3K27ac marks) in purified hematopoietic stem and progenitor cells (HSPC) of TH2-skewed recipient mice. Single cell RNA sequence analyses identified a distinct transcriptomic signature in HSPC of dysbiotic mice that was reversed by butyrate supplementation. Together, these data suggest that the gut microbiome alters gene expression in blood progenitor cells with long term consequences on the immune response to peripheral allergens.
A single-cell multiomics approach to study tumor-driven perturbations during hematopoiesis in mice
Authors: Kara Nihan , Shi Xiaoshan , Samusik Nikolay , Widmann Stephanie , Tyznik Aaron J 
Published: January 2023

Abstract
Cancer is associated with concomitant myeloid cell responses that are characterized by an expansion of tumor associated myeloid cells, including myeloid derived suppressor cells, tumor associated macrophages and neutrophils. The prevailing paradigm is that cancer interferes with normal hematopoiesis by skewing the generation of myeloid cells with tumor promoting functions and promoting extramedullary hematopoiesis in organs such as the spleen. Advances in single cell multiomic technologies now enable the analysis of high dimensional protein and mRNA expression from thousands of cells simultaneously. Using the power of the BD Rhapsody™ Single-Cell Analysis System, we have carefully investigated melanoma associated extramedullary hematopoiesis in mice. To do this, we isolated 4 hematopoietic stem and progenitor cell populations simultaneously, including Lin− Sca-1+ c-Kit+, common myeloid progenitor, granulocyte-macrophage progenitor, and megakaryocyte-erythrocyte progenitor cells from the spleen and bone marrow of melanoma bearing mice using the BD FACSMelody™ cell sorter in combination with a multiplex BD® AbSeq Oligos panel for surface protein expression and a single-cell whole transcriptome analysis. Using advanced analysis plugins in SeqGeq™ software, we were able to delineate the developmental trajectories of these hematopoietic stem and progenitor cells in this systemic immuno-suppressive myeloid environment. These advanced technologies are critical to uncover tumor mediated abnormalities in hematopoiesis.
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Metabolic pathways that mediate expansion and homeostasis of hematopoietic lineages
Authors: Pizzato Hannah A , Wang Yahui , Lam Wing Y. , Wolfgang Michael J. , Finck Brian N. , Patti Gary J. , Bhattacharya Deepta 
Published: January 2023

Abstract
Due to the rarity of hematopoietic stem cells, their differentiation into progenitors then on to mature cells must occur with proliferation, leading to an expansion of each downstream population. This process, called transit amplification, is required to produce a sufficient mature cell population and must be balanced with survival to maintain homeostasis and prevent hematological malignancies. How transit amplification and subsequent homeostasis is controlled is not well understood but may involve metabolic switches. Various groups have demonstrated that hematopoietic expansion requires a switch from glycolysis to oxidative phosphorylation, but what induces this switch and the specific carbon sources that fuel it remain unclear. To address these questions, we employed mice conditionally deficient in mitochondrial pyruvate import, fatty acid oxidation, or glutamine hydrolysis and examined the requirements of these pathways in hematopoietic homeostasis. Ablation of carnitine palmitoyltransferase II (Cpt2) or glutaminase (Gls) had no effect on lineages examined, suggesting fatty acid oxidation and glutaminolysis are not required for the production or survival of various immune cells. In contrast, upon deletion of mitochondrial pyruvate carrier 2 (Mpc2), peripheral myeloid cell numbers declined dramatically. Over time after Mpc2 ablation, a recovery of myeloid cells was observed. This recovery was associated with increased proliferation of Mpc2-deficient progenitors relative to wild type counterparts immediately following genetic deletion. Further studies are being done to elucidate what metabolic pathway may allow myeloid progenitors to rapidly proliferate and recover after mitochondrial pyruvate ablation.
Human TLR8 Adversely Affects Placental Development and Induces Spontaneous Pregnancy Loss in a model of Systemic Lupus Erythematosus
Authors: Maria Naomi I. , Martinez Shani , Raparia Chirag , Diadhiou Catherine M.M. , Davidson Anne 
Published: January 2023

Abstract
SLE is associated with adverse pregnancy outcomes, particularly in the presence of antiphospholipid antibodies (aPL). Pathogenic mechanisms damaging the fetal-maternal unit, however, remain poorly understood. A role for endosomal TLR8 was recently hypothesized in aPL induced placental damage. The role of TLR8 in systemic autoimmunity has remained elusive as TLR8 function differs from mouse to man. We investigated the effect of human (hu)TLR8 expression on pregnancy outcomes in Sle1 mice that develop aPL antibodies.
huTLR8 transgenic(tg) Sle1 mice were generated and huTLR8 DNA copy number and mRNA expression was confirmed by qDigital- and qRT-PCR. Pregnancies were closely followed and terminal C-sections performed at signs of dystocia/prolonged labor. Pup and placental weight was assessed. Placental tissues were characterized by H&E and Myeloperoxidase (MPO) staining and inflammatory cytokine expression was assessed in placental tissue. Splenic and bone marrow immune populations were analyzed using flow cytometry.
Female Sle1.huTLR8tg mice developed aPL and sm/RNP autoantibodies earlier than Sle1 controls and ±50% loss of litters was observed, compared to 0% in controls. IL-6, TNFa and MPO mRNA expression was significantly increased in placentas of affected litters and negatively correlated with placental weight. Abnormal placental morphology included placental infarcts, loss of placental lakes, arterial wall thickening and increased netting neutrophils.
Here we identify a new model to study adverse pregnancy complications in SLE. In the presence of both Sle1 and huTLR8, we observed early onset of aPS autoantibodies and pregnancy loss attributed to placental developmental abnormalities, infarcts and inflammation.
Pro-fibrotic Activation of Human Macrophages in Systemic Sclerosis
Authors: Bhandari Rajan , Ball Michael S. , Martyanov Viktor , Popovich Dillon , Schaafsma Evelien , Han Saemi , Eltanbouly Mohamed , Carns Mary , Arroyo Esperanza , Aren Kathleen , Hinchcliff Monique , Whitfield Michael L , Pioli Patricia A 
Published: January 2023

Abstract
Genome-wide gene expression studies implicate macrophages as mediators of fibrosis in Systemic sclerosis (SSc), and we have shown that macrophages constitute the dominant inflammatory signature in SSc tissue. However, little is known about how these cells contribute to fibrotic activation in SSc. Using a bioinformatics approach, we show that the gene expression profile of blood-derived human SSc macrophages is significantly enriched in SSc patient skin. We characterize the immunophenotype of human SSc macrophages as pro-fibrotic, demonstrating that these cells are activated under basal conditions, expressing elevated levels of surface markers associated with activation and releasing CCL2, IL-6, and TGF-beta. We also show that STAT3 is phosphorylated in macrophage from SSc patient compared to the healthy donor, and the phosphorylation is attenuated after IL-6 blockade, suggesting that increased expression of IL-6 by SSc macrophages accounts, at least in part, for increased signaling. Moreover, our results suggest that activation of SSc macrophages arises from soluble factors, as differentiation of healthy donor monocytes in SSc patient-derived plasma confers the immunophenotype of SSc patient macrophages. For the first time, we show that co-culture of human SSc macrophages with SSc fibroblasts induces fibroblast activation. Collectively, these studies implicate macrophages as likely drivers of fibrosis in SSc and suggest therapeutic targeting of these cells may be beneficial in ameliorating disease in SSc patients.
Connecting metabolism to inflammation: the role of LACC1 in inflammatory diseases
Authors: Li Yingcong , Chandra Vivek , Vijayanand Pandurangan , Kronenberg Mitchell 
Published: January 2023

Abstract
Genome wide association studies (GWAS) identified several single nucleotide polymorphisms (SNPs) in inflammatory diseases. However, it is difficult to determine the gene that GWAS identified SNPs affect and in which cell type(s). RNA-seq analysis of immune cells from 89 healthy humans, led to the identification of the gene laccase domain containing 1 (LACC1), as one of the most promising targets for investigating the role of human gene polymorphisms in inflammatory bowel disease (IBD). LACC1 is a critical immunometabolic mediator in macrophages that drives fatty-acid oxidation. Surprisingly, we found that polymorphisms near LACC1 that have been linked to IBD correlated with significantly lower LACC1 expression in naïve and activated CD4 and CD8 T cells. No difference in expression was observed in macrophages, where it’s highly expressed and has been shown to influence macrophage function. Thus, we hypothesized that these polymorphisms contribute to the genetic risk for IBD by reducing LACC1 expression and, subsequently, inducing T cell dysfunction. As LACC1 plays an important role in macrophage fatty acid metabolism, we tested if this held true in T cells. In our study, knockdown of LACC1 in human CD4 T cells increased mitochondrial mass and lipid droplet formation. This change in metabolism was associated with a significantly reduced production of several cytokines, including IL-2 and IFNg, following anti-CD3/CD28 stimulation. Further, levels of expression of the T cell activation marker CD25 were also attenuated. In summary, our studies provide insights into new mechanisms controlling T cell metabolism and suggest that LACC1 may provide a target for regulating T cell function to prevent inflammatory and autoimmune diseases.
Genetic immunodeficiency and autoimmune disease reveals a WRC-independent role for Hem1 in mTORC2 regulation
Authors: Cook Sarah 
Published: January 2023

Abstract
Inborn errors of immunity (IEI) are genetic disorders that cause life-threatening infections, lymphoproliferation, autoimmunity, or combinations of these features. We describe five patients from four families with a novel IEI characterized by recurrent infections, atopic disease, lymphoproliferation, cytokine overproduction, and autoimmunity. All patients harbored loss-of-function (LOF) variants in the gene NCKAP1L, which encodes the hematopoietic-specific Hem1 protein. Hem1 is a required component of the WAVE regulatory complex (WRC), a critical mediator of Arp2/3-dependent actin polymerization. Three LOF mutations impair interactions between Hem1 and other WRC components, resulting in degradation of the complex. A fourth mutation in Hem1 (M371V) abrogates activation of the WRC by Arf1 GTPase, resulting in WRC deficiency. Loss of Hem1 function disrupts Arp2/3-dependent actin polymerization, immune synapse formation, lamellipodia formation, and migration. Diminished cortical actin barriers in Hem1-deficient cells enable increased degranulation, cytokine secretion, and immune hyperresponsiveness leading to lymphoproliferation. Surprisingly, Hem1 deficiency causes reduced mTORC2-mediated AKT phosphorylation independently of its role in the actin polymerization. Dysregulation of the mTORC2/AKT axis leads to impaired T cell proliferation and effector cytokine production upon T cell activation. Our data show that Hem1 governs two key regulatory complexes, the WRC and mTORC2, and provide a cellular explanation for the combined immunodeficiency and immune hyperresponsiveness observed in Hem1-deficient patients. This research was supported by the Intramural Research Program of the NIH, NIAID.
Intestinal commensal bacteria promote AT2 self-renewal and AT1 differentiation in an IL-22 dependent fashion and prepare the newborn to fight potentially fatal respiratory pathogens
Authors: Nadeem Amraha , Deshmukh Hitesh , Gray Jerilyn , Wang Timothy 
Published: January 2023

Abstract
We demonstrated that disruption of intestinal commensal bacteria with antibiotics (ABX) severely diminished the levels of cytokine interleukin (IL)-22 in the newborn lung and rendered the ABX-exposed newborn mice susceptible post challenge with Streptococcus pneumoniae (S. pneumoniae). These experimental data suggest that colonization by intestinal commensal bacteria is vital for newborn’s lung defense against respiratory pathogens. Pregnant mouse dams were treated with ABX, and newborn mice were challenged with intratracheal S. pneumoniae (on postnatal day 5). Lungs were harvested and stained. AT2 cells and fibroblast harvested from ABX-treated or ABX-free newborn mice were cultured in matrigel to generate alveolar organoids. After harvest, the organoids were stained. To test the role of IL-22 signaling, Il22rafl/fl mice were bred with SftpcCreERT2 mice. The progeny was treated with tamoxifen and then challenged with S. pneumoniae. We found increased alveolar injury, loss of AT1 cells and reduced the frequency of proliferating AT2 cells in ABX-treated newborn mice compared to ABX-free newborn mice post-challenge with S. pneumoniae. Reconstitution of intestinal commensal bacteria or treatment with recombinant IL-22 restored the numbers of proliferating AT2 cells, reduced the injury score, and improved survival in ABX-treated newborn mice. Organoids derived ABX-exposed newborns demonstrated reduced growth and diminished AT1 differentiation. Using a developmentally appropriate and clinically relevant model, we report that intestinal commensal bacteria promote AT2 self-renewal and AT1 differentiation in an IL-22 dependent fashion, thus preparing the newborn to fight potentially fatal respiratory pathogens.
Cytomegalovirus coinfection is associated with increased vascular-homing CD57+ CD4 T cells in HIV infection
Authors: Freeman Michael L , Chen Bonnie , Morris Stephen R , Panigrahi Soumya , Michaelson Gillian M , Wyrick Jonathan M , Komissarov Alexey A , Potashnikova Daria , Lebedeva Anna , Younes Souheil Antoine , Harth Karem , Kashyap Vikram S , Vasilieva Elena , Margolis Leonid , Zidar David A , Sieg Scott F , Shive Carey L , Funderburg Nicholas T , Gianella Sara , Lederman Michael M 
Published: January 2023

Abstract
Cytotoxic CD4 T cells are linked to cardiovascular morbidities and accumulate in both human immunodeficiency virus (HIV) and cytomegalovirus (CMV) infections, both of which are associated with increased risk of cardiovascular disease. Here we identify CMV coinfection as a major driver of the cytotoxic phenotype – characterized by elevated CD57 expression and reduced CD28 expression – in circulating CD4 T cells from people living with HIV infection (PLWH). We find that CD57+ CD4 T cells express high levels of the costimulatory receptor CD2 and that CD2/LFA-3 costimulation results in a more robust and polyfunctional effector response to T cell receptor (TCR) signals, compared to CD28-mediated costimulation. CD57+ CD4 T cells also express the vascular endothelium-homing receptor CX3CR1 and migrate toward CX3CL1-expressing endothelial cells in vitro. IL-15 promotes the cytotoxic phenotype, elevates CX3CR1 expression, and enhances the trafficking of CD57+ CD4 T cells, and may therefore be important in linking these cells to cardiovascular complications. Finally, we demonstrate the presence of CD57+ CD4 T cells and expression of IL-15, CX3CL1, and LFA-3 in atherosclerotic plaque tissues from HIV-uninfected donors. Our findings are consistent with a model in which cytotoxic CD4 T cells contribute to cardiovascular disease in HIV/CMV coinfection and in atherosclerosis via CX3CR1-mediated trafficking and CD2-mediated costimulation, and may help bridge the gap in understanding how CMV infection and immunity are linked to increased cardiovascular risk in PLWH.
Defects in the Macrophage Galactose-type Lectin Pathway due to HIV Infection
Authors: Bharaj Preeti , Lisinicchia Joshua , Naqvi Kubra Fatima , Fan Xiuzhen , Huante Matthew B. , Chahuan Sadhana , Martinez Yazmin , Endsley Mark , Endsley Janice , Gelman Benjamin 
Published: January 2023

Abstract
In the era of highly active antiretroviral therapy, HIV infection still produces 800,000 deaths and 1.2 million new infections per year. People living with HIV (PLWH) are vulnerable to several co-morbidities and co-infections, due to depletion of CD4+T cells and other incompletely characterized immune disturbances. To address the mechanisms involved, lung mRNAs from humanized mice co-infected with HIV and Mycobacterium tuberculosis (Mtb) were screened. Macrophage Galactose-type Lectin (MGL) was differentially regulated in co-infected animals. When MGL protein was quantified in biobanked frozen human lung specimens from 47 HIV-infected decedents, it was lower in the lung specimens with actively replicating HIV-1, as compared to those lacking detectable viral load. Lung MGL levels were negatively correlated with HIV RNA copies in the lung, and in the spleen, which is a key lymphoid organ that influences systemic immunity. Peripheral blood leukocytes from HIV infected patients showed that MGL activation was abnormal in those cells; comparable results were obtained in cultured HIV-infected macrophages. Molecular silencing of MGL in human monocyte-derived macrophages in vitro produced increased growth of Mtb, suggesting that lower MGL expression in PLWH could compromise their innate immunity to opportunistic pathogens such as Mtb. Macrophage MGL is a novel target to elucidate how HIV infection disrupts innate immunity and increases vulnerability to tuberculosis.
A host innate immune circuit licenses downregulation of Salmonella flagellin expression inside macrophages
Authors: Akhade Ajay Suresh , Atif Shaikh M , Lakshmi Bhavna S , Dikshit Neha , Qadri Ayub , Subramanian Naeha 
Published: January 2023

Abstract
While the effect of bacterial molecules on host immune system is well studied, how host factors affect expression of bacterial molecules is not understood in great detail. Inflammasomes are instrumental in detection and clearance of bacterial pathogens, but little is known about whether there is an active cross-talk between the host sensing mechanism and the expression of stimulatory ligands by the pathogen. We used Salmonella-macrophage infection model to assess the impact of inflammasome activation on the expression of flagellin as a candidate Salmonella protein. We discovered that early during infection, host lysophospholipids released upon rapid NLRC4-mediated pyroptosis of macrophages increase flagellin expression by extracellular bacteria which leads to even greater pyroptosis when these bacteria infect healthy macrophages, thus facilitating NLRC4-mediated detection and clearance of Salmonella. A TLR-dependent host response, however, later inhibits expression of NLRC4 and the lysophospholipid biosynthetic enzyme iPLA2, causing a decline in intracellular lysophospholipids pool that permits downregulation of flagellin by intracellular Salmonella. Our findings reveal a novel mode of host-pathogen cross-talk wherein expression of a bacterium-derived inflammasome ligand is temporally controlled by the very process of inflammasome activation, and identify a host mechanism that controls switching of Salmonella to a flagellin-low phenotype inside macrophages with important implications for bacterial pathogenesis and immunity. Future investigations will utilize dual RNA-Seq studies to understand how Salmonella gene expression networks rewire to adapt to different host intracellular microenvironments.