bluuebunny/crossref_metadata_2025_split huggingface dataset:
FCRL1 inhibits ERK: Implications on B cell homeostasis and humoral immunity.
Authors: DeLuca Jenna M , Murphy Maegan K , Wilson Timothy J 
Published: February 2023

Abstract
FCRL1 is a tyrosine-phosphorylated receptor found on the surface of B cells and some dendritic cells. FCRL1 co-localizes with BCR signaling complexes following BCR engagement and augments BCR-induced calcium flux. By examination of phosphotyrosine-dependent interactions of FCRL1 with intracellular signaling partners, we have identified interactions between FCRL1-Tyr281 and GRAP, GRB2, SHIP-1, and SOS1, with a requirement for GRB2 to mediate binding of FCRL1 to SHIP-1 and SOS1. Examination of MAP kinase signaling downstream of FCRL1 revealed that FCRL1 suppresses ERK phosphorylation in B cells at a resting state and following BCR engagement. In vivo, naïve FCRL1 knockout mice accumulate more B cells in the spleen, including immature, follicular and marginal zone cells, implicating a potential role for FCRL1 in B cell selection and maturation. By contrast, after immunization with thymus-dependent and independent antigens, FCRL1 knockout mice show impaired production of antigen-specific antibodies indicating an essential role for FCRL1 in humoral immune responses.
Genomic Screening of B cell differentiation by using CRIPSR/Cas9
Authors: Zuo Zhihong , Kania Anna K. , Patterson Dillon G. , Scharer Christopher D. , Boss Jeremy M. 
Published: February 2023

Abstract
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.
Stroma-derived Notch signals drive transdifferentiation of follicular B cells into marginal zone B cells during lymphopenia
Authors: Atria Daniela Gomez , Londregan Jennifer , Gaudette Brian T. , Perkey Eric , Kelly Samantha , Ludewig Burkhard , Siebel Christian W. , Ryan Russell J. H. , Pear Warren S. , Allman David , Maillard Ivan 
Published: February 2023

Abstract
In lymphopenic environments, secondary lymphoid organs regulate the size of B and T cell compartments by supporting homeostatic proliferation of mature lymphocytes. The molecular mechanisms underlying these responses and their functional consequences remain poorly understood. To evaluate the homeostasis of the mature B cell pool during lymphopenia, we developed an adoptive transfer model of follicular B (FoB) cells into Rag2−/− mouse recipients. We report that highly purified FoB cells transdifferentiate into marginal zone (MZ)-like B cells when transferred into Rag2−/− lymphopenic hosts, but not into wild type hosts. In lymphopenic spleens, transferred B cells gradually lost their FoB phenotype and acquired multiple characteristics of MZ B cells, as judged by their cell surface phenotype (sIgMhi sIgDlow CD21hi CD1dhi CD23low), expression of integrins and chemokine receptors, positioning close to the marginal sinus, and functional ability to rapidly generate plasma cells. Initiation of FoB to MZ B cell transdifferentiation preceded proliferation. Furthermore, the transdifferentiation process was dependent on Notch2 receptors in B cells and expression of Delta-like 1 Notch ligands by Ccl19-Cre+ fibroblastic stromal cells, a pathway also required for MZ B cell development in steady-state conditions. We postulate that stromal Notch ligands are critical to regulate the size and composition of the splenic B cell pool via interactions with Notch2 receptors in B cells. Thus, FoB cells are not locked in their FoB cell fate, but are are endowed with plastic transdifferentiation potential in response to increased stromal Dll1 availability in lymphopenic environments.
Redox regulation of autophagy in thymic stromal cell function.
Authors: Semwal Manpreet Kaur , Hester Allison K , Cepeda Sergio , Xiao Yangming , Udeaja Chioma , Griffith Ann V. 
Published: February 2023

Abstract
T lymphocytes develop in the thymus, where mutually inductive signaling between lymphoid progenitors and thymic stromal cells (TSCs) directs the progenitors along a well-characterized program of differentiation. However, the biology of the TSCs comprising the lymphopoietic thymic microenvironment remains relatively under-characterized because stromal cells are rare and difficult to isolate. Using a deconvolution technique to study gene expression essentially in situ, we previously identified a deficiency in the H202 quenching enzyme catalase (CAT) in TSCs, and found that CAT deficiency results in high H202 levels in this population, eventually leading to thymic atrophy. Our current studies address the possibility that high H202 levels serve physiological functions in TSCs in the young, steady state thymus. TSCs exhibit high basal levels of autophagy at the steady state, which is critical for self-antigen presentation and T cell selection. The mechanisms governing high basal autophagy in TSCs are unknown, however autophagy is induced by many stressors, including high H202 levels. Our data indicates that catalase overexpression targeted to mitochondria in transgenic mice (mCAT Tg) results in diminished autophagy in TSCs and causes diminished negative selection in the thymus, eventually leading to autoimmunity. The effects on negative selection in mCAT Tg mice are rescued by increased basal autophagy on the beclin 1 knock-in (Becn1F121A/F121A) background. Our results suggest that the high basal autophagy level required in TSCs for T cell negative selection is promoted by physiologically low levels of catalase expression in the steady state thymus.
Influence of Lymph Node Microenvironment on Naive T cell Aging
Authors: Gustafson Claire E , Liu Jie Yu , Colville Alex J , Cao Wenqiang , Zhang Huimin , Weyand Cornelia M , Goronzy Jorg J 
Published: February 2023

Abstract
Although the loss of naive CD8 T cells is a hallmark of immune aging, naïve CD4 T cells appear to be more resilient, demonstrating less numerical loss and fewer transcriptional and epigenetics changes with age. That said, naïve CD4 T cells still display altered antigen-specific responses and subset polarization with age, implying that although numerically robust, the composition of the naïve CD4 T cell population may differ with age. Thus, we examined the compositional heterogeneity of naïve CD4 T cell compartment using mass cytometry during human aging. We found that a unique CD45RAhigh population was lost with age, converting to a CD45RA+/low population in older individuals. In young adults, CD45RAhigh naïve T cells were found highly enriched in the lymph nodes (LN). To determine the role of the LN microenvironment in the maintenance of CD45RAhigh population, we developed bioengineered human LN-like organoids that actively maintained this cell type, requiring both fibroblastic reticular cells (FRCs) and a 3D structure. Notably, within these LN-like organoids, CD45RA+/low naïve CD4 T cells from older individuals were able to convert back to a CD45RAhigh phenotype, implying cell extrinsic influences mediate naïve T cell aging. However, neither aging nor cellular senescence of FRCs caused the conversion of naive T cells to an aged CD45RA+/low phenotype. Together, these data suggest that naïve T cell aging is not directly mediated by intrinsic age-related defects in stromal FRCs but instead may be linked with structural changes within the LN microenvironment of older individuals.
Unbiased Identification of Novel Plasma Cell Markers Across Mouse and Man
Authors: Rothrauff Abigail E , Liu Ailing , Borghesi Lisa A 
Published: February 2023

Abstract
Naïve B cells differentiate into short-term and long-lived plasma cells (PCs) following pathogen exposure, contributing to the overall humoral immune response. However, an extensive comparison of murine and human antibody secreting cells (ASCs) that integrates surface phenotype and intracellular function is lacking. Mapping B cell lineage populations across diverse tissues in mouse and man is important for vaccine efficacy and clinical immuno-monitoring. In this study, we interrogated relatively unattainable tissues from normal donors such as BM, LN, and gut through LEGENDScreen and exploited an unbiased algorithmic pipeline to visualize broader population structure. We found similarities across species with potential novelty in PC surface markers including CD134/OX40, CD172/Sirpa, CD180/RP105, CD28, CD88/C5aR, CD79b/IgBeta, CD162/PSGL1, CD74/CLIP, CD7, CD360/IL-21R, and CD220/Insr. Expression of these markers are being validated through conventional flow cytometry and scRNA-sequencing, and we are assessing functionality of novel PC subsets in vivo and in vitro. Exposing the distribution of PC subsets and functional diversity in different tissue sites across human and murine models will help validate survival pathways, and provide new insights on the subsets that support long-lived humoral immune responses throughout the body.
Ets1 governs the differential formation of circulating and tissue-resident memory CD8 T cells
Authors: Tsuda Shanel M , Diao Huitian , Getzler Adam , Milner Justin , Goldrath Ananda W , Crotty Shane , Pipkin Matthew E. 
Published: February 2023

Abstract
During infections, naive CD8 T cells differentiate into terminal effector cells (TE) and long-lived memory CD8 T cells that recirculate through lymphoid organs using the vasculature (TCIRC), and tissue resident memory (TRM) cells that do not recirculate. The transcriptional control that delineates differentiation of TE cells from memory cell subsets is still unclear. DNA motifs recognized by ETS-family transcription factors (TFs) are highly frequent in cis-regulatory regions that become chromatin accessible in naïve CD8 T cells 24 hours after TCR stimulation, and in mature memory T cell subsets. The ETS-family is encoded by 27 genes, and expression analyses revealed Ets1 is the most highly expressed member. Ets1 is transiently downregulated during activation and is re-expressed in TCIRC cells, but remains lower in intestinal TRM cells. P14 CD8 T cells responding to acute LCMV infection that were depleted of Ets1 using retrovirally-delivered shRNAmirs preferentially became KLRG1hi CD127lo TE-like cells, and their numbers in the circulation rapidly declined, resulting in an absence of long-lived effector cells and residual numbers of central memory-like cells. Concomitantly, Ets1-depleted cells re-distributed into the gut TRM compartment and had increased fractions of CD69hi CD103hi cells. Early after infection in the spleen, a larger fraction of Ets1-depleted P14 cells express CCR9 and α4β7. Depletion or overexpression of Ets1 in P14 cells both indicate it negatively regulates CD25 and Prdm1 expression, and promotes Tcf7 and Bcl6 expression. These results suggest that Ets1 functions early during CD8 T cell activation to establish the normal pattern of TCIRC and TRM cell differentiation during acute viral infection.
Multi-omics analyses of radiation survivors identify radioprotective microbes and metabolites
Authors: Guo Hao , Chou Wei-Chun , Lai Yunjia , Liang Kaixin , Tam Jason , Brickey W. June , Chen Liang , Montgomery Nathan D. , Li Xin , Bohannon Lauren M. , Sung Anthony D. , Chao Nelson J. , Peled Jonathan U. , Gomes Antonio L.C. , van den Brink Marcel R.M. , French Matthew J. , Macintyre Andrew N. , Sempowski Gregory D. , Tan Xianming , Sartor R. Balfour , Lu Kun , Ting Jenny P.Y. 
Published: February 2023

Abstract
Ionizing-radiation causes acute radiation syndrome leading to hematopoietic, gastrointestinal and cerebrovascular injuries. Substantial federal efforts have been made to develop therapeutic radioprotectants for routine clinical use, however it remains a long-standing and unresolved problem.
We investigated a population of mice that recovered from high-dose radiation to live normal lifespans. These elite-survivors harbored distinct gut microbiota that developed post-radiation and protected against radiation-induced damage and death in germ-free and conventionally housed recipients. Elevated abundances of members of the bacterial taxa Lachnospiraceae and Enterococcaceae were associated with post-radiation restoration of hematopoiesis and gastrointestinal repair. These bacteria were also found to be more abundant in leukemia patients undergoing radiotherapy who also displayed milder gastrointestinal dysfunction. Metabolomics revealed increased fecal concentrations of microbially derived propionate and tryptophan metabolites in elite-survivors. The concentrations of these metabolites correlated with long-term radioprotection, mitigation of hematopoietic and gastrointestinal syndromes, and a reduction in pro-inflammatory responses.
The novelty of our work lies in the first identification of gut microbiota and downstream metabolites in providing protection against lethal radiation. Furthermore, our work provides a comprehensive omics dataset at the bacteria and metabolite levels that is of broad interest and serves as a powerful resource and example for the identification of actionable therapeutic targets derived from microbiome studies.
Effective clearance of Chlamydia from the female reproductive tract in the absence of T-bet+ Th1 cells
Authors: Rixon Jordan , McSorley Stephen J 
Published: February 2023

Abstract
Protective immune responses to Chlamydia infection within the female reproductive tract (FRT) are incompletely understood. MHC class II-restricted CD4 Th1 responses are thought to be vital for bacterial clearance, due to their capacity to secrete IFN-γ, but Th1 responses as defined by the master transcription factor T-bet had not yet been fully interrogated in primary infection. Here, we investigated T-bet and IFN-γ involvement in primary infection clearance. We found that IFN-γ producing CD4+ T cells from the FRT exhibited surprisingly low levels of T-bet throughout primary infection, indicating low involvement of classical T-bet+ Th1 cells. Mice deficient for T-bet either globally or specifically in CD4+ cells both competently cleared infection along wild-type kinetics. T-bet-deficient mice also showed significant skewing towards Th17 responses, indicating potential compensation pathways through alternate Th fates. On the other hand, IFN-γ-, and IFN-γR-deficient mice resolved much of FRT infection, but experienced systemic dissemination and 100% mortality with an average median survival of approximately 4 weeks. Together, this indicates that while IFN-γ is important to protect mice from death, classical T-bet+ Th1 cells are ultimately not required for primary clearance. Studies are underway to examine which alternative CD4 T cell mechanisms contribute to bacterial clearance within the FRT. Supported by grants from NIH (RO1 A1103422, T32 AI060555)
A blend of broadly-reactive and pathogen-selected Vγ4Vγδ1 T cell receptors confer broad bacterial reactivity of resident memory γδ T cells
Authors: Khairallah Camille F , Bettke Julie A , Gorbatsevych Oleksandr , Qiu Zhijuan , Zhang Yue , Cho Kyungjin , Kim Kwang Soon , Chu Timothy H , Imperato Jessica N , Hatano Shinya , Yoshikai Yasanobu , Puddington Lynn , Surh Charles D , Bliska James , Van der Velden Adrianus WM , Sheridan Brian S 
Published: February 2023

Abstract
γδ T cells are pleiotropic sentinels involved in immune defense at barrier tissues. While most γδ T cell subsets are associated with innate-like responses, foodborne Listeria monocytogenes (Lm) infection elicits a substantial resident memory Vγ4Vδ1 T cell response that appears specific to the priming pathogen despite limited T cell receptor (TCR) diversity. As our understanding of memory γδ T cells remains elusive, memory γδ T cells were examined using heterologous challenge infections coupled with TCRδ sequencing to reveal an unanticipated complexity in this memory compartment. CDR3δ sequence analysis revealed that a subset of non-canonical Vδ1 clones expanded during primary and secondary Lm infection but contracted at memory, consistent with antigen-specific clonal expansion. Additionally, canonical clones comprised most of the response, suggesting that some cells may not be Lm-restricted. Indeed, ex vivo stimulation of Lm-elicited memory γδ T cells with Salmonella enterica serovar typhimurium (STm), Yersinia pseudotuberculosis, and Citrobacter rodentium (Cr) induced a robust multifunctional response. Furthermore, heterologous STm-induced colitis infection and intraperitoneal Cr infection of Lm-immune mice led to the TCR-dependent recall of memory γδ T cells, demonstrating their broad reactivity in vivo. Interestingly, most of the non-canonical Vγ4Vδ1 T cell clones that expanded in an antigen-specific manner after Lm infection did not respond after STm infection, suggesting some level of specificity. These findings underscore the complex and promiscuous nature of memory γδ T cells and suggest that pathogen-elicited memory γδ T cells are potential targets for broad-spectrum anti-infective vaccines.
Memory-like innate immunity following infection with Pneumocystis murina
Authors: Samet Shelly , Bishop Lisa , Kovacs Joseph 
Published: February 2023

Abstract
Pneumocystis pneumonia (PCP) continues to be a life-threatening infection in HIV-infected patients, renal transplant patients, and other immunocompromised individuals. Dendritic cells are key antigen presenters to CD4+ T cells, which are critical to controlling Pneumocystis infection. b-1,3 glucans are found in the cell wall of the cyst form of Pneumocystis and are a known activator of innate immune cells via the dectin-1 receptor. b-glucans derived from other fungi have been shown to induce an enhanced “memory-like” immune response, termed trained immunity, in innate cells, including monocytes, macrophages, and dendritic cells. Therefore, we explored if Pneumocystis infection can induce an enhanced innate immune response in mice following exposure via a natural route of infection. We conducted mixing experiments using purified CD4+ T cells and dendritic cells from unexposed C57BL/6 mice and mice that spontaneously cleared infection. We found that CD4+ T cells from naïve mice exhibited a significantly greater proliferation after 5-day cultures when a crude Pneumocystis antigen was presented by CD11c+ dendritic cells from exposed mice compared to unexposed mice. In support of this, CD4+ T cells from C57BL/6 mice that were immunized with Freund’s adjuvant alone exhibited significantly greater proliferation when a crude Pneumocystis antigen was presented by either CD11c+ dendritic cells or CD11b+macrophages from mice immunized with Pneumocystis antigen mixed with Freund’s adjuvant vs. adjuvant alone. These results suggest that Pneumocystis infection stimulates a memory-like innate immune response which may be important in controlling subsequent exposure to Pneumocystis, as well as exposure to other pulmonary pathogens.
Understanding immunological memory in the lung microenvironment during Coccidioidomycosis
Authors: Miranda Nadia Esmeralda , Diep Anh L. , Tejeda-Garibay Susana , Hoyer Katrina K. 
Published: February 2023

Abstract
Valley fever is caused by unknowingly inhaling the fungal pathogen Coccidioides. Coccidioides grows in the soil as mycelia segments into arthroconidia (spores) and when the soil is disrupted and aerosolized, it can be inhaled and cause lung infections. Due to global warming, spread has increased into non-endemic areas and is predicted to spread further. 60% of patients are asymptomatic or display minimal disease. Meanwhile, 40% of symptomatic patients may develop deteriorating health complications for months to years after diagnosis. Researchers have tried to develop a human vaccine for Valley fever but very little is known about how the fungus interacts with the immune system and the lung microenvironment. There is a critical need to identify which immune cells are interacting with the fungus in the lungs and how these cells control infection. It is known that the immune system partially controls the infection through TH1 and TH17 responses. T cell memory functionally determines how the immune system responds upon antigen reencounter. We do not know how the immune system develops memory in response to Coccidioides and if the fungus influences differentiation in the memory environment. There has been no human vaccine. Prior translational attempts from mouse to human have been unsuccessful due to the lack of knowledge of how memory responses are being shaped in this disease. We are assessing the durability, types of memory, and how memory changes with repeated exposure in the patient blood via flow cytometry. These experiments have allowed us to investigate which cells participate in recall immunity in animal models and patients of Valley fever.
Exposure to host inflammation in vivo induces rapid transcriptomic change and impaired maturation in malaria parasites.
Authors: Lansink Lianne I.M. , Engel Jessica A. , Lee Hyun Jae , Soon Megan S.F. , Williams Cameron G. , Aogo Rosemary A. , Cromer Deborah , Davenport Miles P. , Khoury David S. , Haque Ashraful 
Published: February 2023

Abstract
We previously reported slowing of the Plasmodium life-cycle in acutely-infected wild-type but not immune-deficient mice, suggesting a role for host responses in mediating this effect. Here, we hypothesized that parasites sense and rapidly adapt to host inflammation in vivo. We tested this in mice using a combination of immunological, metabolomic and parasite single-cell RNA-sequencing (scRNA-seq) approaches. Firstly, systemic treatment with LPS, but not CpG or Poly I:C, impaired in vivo maturation of parasites, the magnitude of which correlated with plasma TNF/IFNγ levels. This supported our idea that a systemic inflammatory response alone could impair malaria parasite maturation. Metabolomic analysis of plasma indicated host inflammation was associated with substantial changes to the external environment in which parasites circulated. Subsequent in vitro culture confirmed this plasma directly impaired maturation, and moreover, suggested the presence of inhibitory factor(s) within it. scRNAseq conducted on asynchronous parasites exposed to host-inflammation in vivo, suggested a global down-regulation of transcription, specifically in mid-stage of the blood-cycle – also confirmed by flow-cytometric analysis. In addition, we noted specific down-regulation of protein translation associated genes. Thus, malaria parasites in the mid-stages of their blood-stage cycle actively sense systemic host inflammation, and respond by slowing down gene transcription and protein translation, resulting in slowed maturation. Our work suggests systemic inflammatory responses may control malaria parasites not via their clearance, nor directly killing, but by slowing down the rate of parasite maturation and replication.