bluuebunny/crossref_metadata_2025_split huggingface dataset:
Frequency and phenotype of SARS-CoV-2-specific CD8+ T cells in healthy and convalescent COVID-19 individuals
Authors: Choy Cecily , Lu Jian , Li Jiangyuan , Dunn Christopher , Wallace Tonya , Nguyen Cuong , McKelvey Julia , Melvin Denise , Egan Josephine , Weng Nan-Ping 
Published: February 2023

Abstract
COVID-19, an infectious disease caused by SARS-CoV-2, has caused the current global pandemic. Despite the number of infections nearing 100 million people worldwide, the CD8+ T cells against SARS-CoV-2 in healthy adults as well as in convalescent COVID-19 patients are not fully characterized. Here, we report an analysis of the frequency and phenotype of circulating CD8+ T cells recognizing seventeen epitopes from three SARS-CoV-2 proteins (S, N, and M) in HLA-A2+ healthy adults and COVID-19 convalescent patients by multi-color flow cytometry with antigen-specific tetramers. Through the analysis of 65 healthy adults ranging between 17 to 98 years of age, we found that the frequencies of CD8+ T cells recognizing SARS-CoV-2 ranged from 10−2 to undetectable. We did not find a generalized age-related change in the frequency of SARS-CoV-2-recognizing CD8+ T cells. Interestingly, we also did not find increased frequencies of SARS-CoV-2-recognizing CD8+ T cells from convalescent patients compared to the healthy controls. Phenotypical analysis showed that SARS-CoV-2-recognizing CD8+ T cells had a mixed naive and memory phenotype in healthy adults whereas convalescent patients mainly had a memory phenotype. Currently, we are identifying the TCRs of these SARS-CoV-2-recognizing CD8+ T cells. Taken together, our findings have identified the frequency and phenotype of CD8+ T cells which recognize SARS-CoV-2-specific epitopes in humans, and future TCR research will further reveal the binding specificity and functionality of these SARS-CoV-2-specific CD8+ T cells.
Concurrent microglial activation in CD8 T cell-mediated CNS vasculature permeability during Theiler’s virus infection
Authors: Khadka Roman , Zheng Jiaying , Ayasoufi Katayoun , Fain Cori E. , Jin Fang , Hansen Michael , Wu LongJun , Johnson Aaron J 
Published: February 2023

Abstract
Immune-mediated blood brain barrier (BBB) disruption is a prominent feature of various neurological conditions for which an emerging role of CD8 T cells is being realized. Our group has developed a unique model of CD8 T cell-mediated BBB disruption which employs Theiler’s murine encephalomyelitis virus (TMEV) infection. Upon intravenous administration of VP2121–130 viral peptide during the peak antiviral adaptive response, Db:VP2121–130 epitope specific CD8 T cells induce BBB disruption in a perforin dependent manner. In this model, we addressed the role of microglia in relation to antigen specific CD8+ T cells and permeable cerebral vessels. Using real time two-photon in vivo imaging, we demonstrate that microglia adopt distinct morphological features, including enlarged cell body and fewer ramified processes as early as 6 hours post administration of VP2 peptide. Notably, microglial population exhibit robust down-regulation of homeostatic markers including CX3CR1 during BBB disruption. This study demonstrates CD8 T cells can promote microglia activation in a perforin-dependent manner during BBB disruption. Importantly, microglial activation occurs concurrently with the onset of vascular permeability and could serve as a critical cell type in this process.
Skin-derived alternatively spliced IL-15 isoform-producing cells impair the generation of anti-viral effector CD8+ T cells in HSV-1 zosteriform mouse model
Authors: Ku ChiaChi , Wu Kwan-Lun , Chien Po-Ya 
Published: February 2023

Abstract
We previously reported a Pedigree 191 (P191) of N-ethyl-N-nitrosourea (ENU) mutagenized mice that highly expressed an alternatively spliced IL-15 isoform with deletion of the first 16 amino acids in exon 7 (IL-15ΔE7). Infection of P191 mice with herpes simplex virus-1 (HSV-1) via flank skin generated a prolonged and early re-emerged HSV-1 zosteriform rash compared to wild type (WT) C57BL/6 mice. Using Kb/gB498–505 MHC Class I tetramer provided by NIH Tetramer Core Facility, we found that the numbers of gB-specific CD8+ T cells generated in draining lymph nodes (dLN) of P191 mice were greatly reduced over 10-day course after HSV-1 flank infection compared with WT mice. As expressions of IFN-γ, granzyme B and perforin were induced in WT CD8+ T cells by in vitro restimulation with gB peptides, they were poorly expressed in P191 CD8+ T cells. While HSV-1 skin infection induced migration of Langerhans cells into dLNs accompanied with increased IL-15 expression in WT mice, the number of migrated Langerhans cells was less in P191 and they preferentially expressed IL-15ΔE7 rather than IL-15. The reverse relationship between the cell number of Langerhans cells and the increased expression of IL-15ΔE7 mRNA in dLN of P191 mice suggested that the influx of skin-derived IL-15ΔE7 expressing cells plays an important role in influencing the quantity and quality of anti-HSV-1 CD8+ T cells generated in P191 mice. More experiments will be carried out to understand how the alternatively cytokine splicing mechanism regulates a long term and effective CD8+ T cell immunity against virus infection.
Defining cellular correlates of protection and vaccine failure to influenza across two human cohorts
Authors: Mettelman Robert C , Souquette Aisha , Van de Velde Lee-Ann , Allen E. Kaitlynn , Wood Timothy , Krammer Florian , Petrie Joshua G , Martin Emily T , Monto Arnold S , Huang Q. Sue , Thomas Paul Glyndwr 
Published: February 2023

Abstract
Influenza viruses are endemic viral pathogens causing mild to severe respiratory illness in humans. Immunologic protection against influenza is determined by immune correlates of protection– factors associated with reduced infection or severe disease. While antibodies specific to viral surface proteins are known correlates, waning seasonal vaccine efficacy and reported infection of patients despite elevated antibody titers suggest that humoral responses alone do not provide complete protective immunity. Indeed, evidence points to a larger role for cell-mediated immunity (CMI; innate cells and antigen-specific T cells) in conferring protection. CMI correlates, which act independently from humoral responses, have yet to be identified. Here, we analyzed samples from adult human subjects across two influenza infection and vaccination cohorts to identify distinct CMI correlates of protection to influenza. We profiled CMI responses using high-dimension flow cytometry from PBMCs collected pre- and post-exposure to influenza infection or vaccination. Statistical comparison of cell frequency and infection status identified candidate CMI correlates, which were validated using logistic regression accounting for vaccination, demographic (age, sex, BMI), and serologic (antibody) covariates. We identified 9 individual and 6 cell clusters across myeloid and lymphoid compartments associated with protection. The strongest correlations were observed in Th17, cTfh, and subsets of NK and dendritic cells. Further, AUROC models identified 3 baseline CMI infection classifiers. Lastly, our study identified correlates of vaccine failure– pre-exposure CMI profiles correlated with positive infection status despite vaccination.
Analyses of the interactions of tapasin and ERp57-tapasin proteins with PaSTa 1 and PaSTa 2 antibodies and MHC-I molecules
Authors: Taylor Daniel Kyle , Boyd Lisa F , Jiang Jiansheng , Mage Mike M , Cresswell Peter , Margulies David H , Natarajan Kannan 
Published: February 2023

Abstract
The intracellular loading of major histocompatibility complex class I (MHC-I) molecules with high affinity peptides is a pre-requisite for their cell surface display as ligands for T and NK cells. Peptide acquisition occurs in the ER within the peptide loading complex (PLC) and is accomplished through the concerted action of several proteins, most notably tapasin. In the absence of tapasin, peptide loading is compromised, resulting in decreased cell surface expression of some, though not all, MHC-I allelomorphs. In order to gain a mechanistic understanding of tapasin function as well as its apparent allelomorph specificity we have produced recombinant Fab fragments of two anti-tapasin antibodies, PaSTa 1 and PaSTa 2, and investigated their binding to human recombinant soluble tapasin and ERp57/tapasin by SPR methods. Both antibody Fabs bind with nanomolar affinities characterized by slow off rates. Based on these results we developed an MHC-I binding assay employing PaSTa 1-captured tapasin or ERp57/tapasin which reveals affinities in the micromolar range for selected MHC-I alleles. These affinities are notably weaker than those obtained for the structurally related but PLC-independent chaperone, TAPBPR (TAP-binding protein, related), and may reflect distinct evolutionarily derived functions for the two related molecules.
Penalized regression analysis identifies features of the peptide:MHC class I interaction and mRNA expression as key to prioritizing neoantigen immunogenicity
Authors: Borden Elizabeth S , Phung Tanya N , Buetow Kenneth H , Lafleur Bonnie , Wilson Melissa A , Hastings Karen Taraszka 
Published: February 2023

Abstract
Current approaches to prioritization of tumor-specific neoantigens have low sensitivity and specificity, directly impacting the development of personalized vaccines and the prediction of immunotherapy efficacy. Many biological features have been suggested to contribute to accurate neoantigen prioritization. We calculated predictors for a comprehensive set of biological features for presentation and recognition of neoantigens on a validated neoantigen dataset. One thousand random, evenly-split combinations of immunogenic and non-immunogenic neoantigens were analyzed using penalized regression (lasso) for variable selection. This analysis isolated the peptide:MHC class I dissociation constant, binding stability, and mRNA expression as the key predictive variables of tumor-specific neoantigens. Based on these results, we fit a logistic regression model and tested its performance on three independent datasets. We compared our results to the models by Wells et al., Łuksza et al., and Zhou et al. Our model has improved performance as measured by the area under the receiver operator curve (AUC) compared to Łuksza and Zhou et al. Our model selects the same terms as Wells et al. and performs equivalently. However, it has the advantage of providing a predicted immunogenicity score for each individual neoantigen. Individual antigen approaches are useful for prioritizing vaccine candidates and predicting response to immunotherapy. Future work will focus on the application of this predictor to patient response to immunotherapy.
Kidney function, age, and education as contributors to depression and anxiety in juvenile systemic lupus erythematosus
Authors: Poole Brian D , Figueiredo-Braga Margarida , Silva Beatriz , Ganhão Sara , Aguiar Francisca , Cornaby Caleb , Brito Iva 
Published: February 2023

Abstract

Background:
Juvenile systemic lupus erythematosus (JSLE) is diagnosed in children younger than 18 years of age. Depression and anxiety are common, but not well understood in JSLE. We investigated the clinical and psychological factors associated with the psychological manifestations of JSLE.

Methods:
Twenty-nine JSLE patients were recruited for the study. They responded to surveys testing their psychological status and perceptions about their health, including the Hospital Anxiety and Depression scale, the Fatigue Severity Scale, and a Medical outcomes questionnaire (the SF-36). Clinical lab results were obtained from the patients’ medical records. Univariate and multivariate analyses were used to compare the patient populations with adult-onset SLE (ASLE) patients and unaffected controls, finding indicators that correlated with depression and anxiety in JSLE patients.

Results:
Kidney disease was associated with depression in the JSLE patients. The BUN levels, BUN/creatinine ratio, and leukocyturia were all significantly associated with depressive symptoms. The BUN/creatinine ratio was the most predictive laboratory value for both depression and anxiety.
The JSLE patients had less depression than the ASLE, although not less anxiety. JSLE patients had comparable levels of fatigue and pain to the adult-onset SLE patients. Age and education were protective against depression in the JSLE patients.

Conclusions:
Kidney function correlated with symptoms of depression and anxiety. This may mean that symptomatology is an important indicator of whether the patient needs psychiatric care. Age and education were likely protective against depression in the JSLE population.
Androgen-associated increases in Bacteroides abundance correlate with enhanced immunoregulation and suppression of lupus in BWF1 mice.
Authors: Ma Jing , Harder James W , Alard Pascale , Kosiewicz Michele M 
Published: February 2023

Abstract
Similar to humans, lupus incidence is higher in female than male NZBxNZW1(BWF1) mice, and castration abolishes male protection implicating androgens in disease suppression. Gut microbiota and metabolite compositions differ between female and male BWF1 mice; males have higher abundance of Bacteroides and the metabolites, phytol and phytanic acid (RXR agonists that can increase retinoic acid, RA). Male cecal transfers into females suppress disease which correlates with an increase in Bacteroides in recipients. In addition, female gut CD103+ dendritic cells (CD103+DC) have decreased ability to induce pTreg due to an RA deficiency (decreased RALDH2) that can be restored by male cecal transfer. The goal of this project was to study androgen effects on these processes. We found that male castration altered microbiota and metabolite compositions similarly to those found in female mice, e.g., reduced Bacteroides, and phytol and phytanic acid abundance. Castrated male cecal transfer did not suppress disease or increase Bacteroides abundance in recipients. As in females, castrated male CD103+DC had decreased ability to induce pTreg (decreased RALDH2) but induced high levels of IFNγ. And although androgen receptor mRNA was undetectable in CD103+DC, male mice treated with androgen receptor inhibitor (flutamide) had the same negative effect on CD103+DC function as castration, suggesting androgens affect CD103+DC indirectly. Interestingly, flutamide-treated and castrated male microbiota looked very similar, e.g., reduced Bacteroides. These data suggest that androgens in males increase Bacteroides abundance via receptor signaling in host cells that may in turn play a role in enhancing immunoregulation and suppressing lupus.
Regulators of Type III Cytokines in Type III Innate lymphoid Cells Identified by CRISPR Activation and Inhibition Screens
Authors: Brown Rachel Anne , Dangel Andrew W , Saini Ankita , Oltz Eugene M 
Published: February 2023

Abstract
Type III cytokines interleukin (IL)-22 and IL-17 are expressed by both innate and adaptive immune cells to defend against extracellular pathogens, yet their dysregulation contributes to autoimmunity and malignancy. A deeper knowledge of IL-22/17 regulation is warranted to understand physiologic processes as well as disease pathogenesis, thereby elucidating druggable targets. Toward this goal, we applied genome-wide CRISPR activation (CRISPRa) and CRISPR inhibition (CRISPRi) screens to identify the collection of factors that positively or negatively regulate IL-17/22 expression in a murine type III innate lymphoid cell (ILC3) model. Following lentiviral transduction of a CRISPRi or CRISPRa guide RNA (gRNA) library, cells were stimulated and sorted by levels of intracellular IL-22/17 protein expression. Relative gRNA frequencies in each sequenced population revealed enrichment and depletion of potential regulators (“hits”), which were then tested with gene-specific gRNAs to validate or exclude them from further study. These genome-wide screens have illuminated hits from several biological pathways, ranging from transmembrane channels to RNA splicing. We identify previously known regulators, including IL23R, STAT3, and ZFP36, as well as novel potential regulators, including SLC family members and a nuclear protein called SON. Our screens provide a diverse array of candidate factors that govern expression of type III cytokines by ILC3s, with potential for extrapolation to other cytokine-expressing cells. Genome-wide gain and loss of function screens are powerful, complementary tools to facilitate regulatory pathway discovery.
IL-27 enhances cytokine secretion by TIGIT+ HIVGag-specific T cells
Authors: Cheng Jie , Myers Timothy G. , Kumar Princy , Kumar Jai , Goshu Bruktawit A , Catalfamo Marta 
Published: February 2023

Abstract
In chronic HIV infection, HIV-specific T cells have diminished effector function and fail to control/eliminate the viral reservoirs. HIV-specific T cells and latently HIV infected T cells express checkpoint receptors suggesting that therapeutic strategies improving T cell function and targeting the reservoir will be required to treat HIV infection. IL-27, a member of the IL-6/IL-12 cytokine superfamily, can be considered as such agent because of its anti-viral properties and immune modulatory functions. IL-27 signaling activates mainly Signal Transducer and Activator of Transcription (STAT) 1 and 3. IL-27 can inhibit HIV replication, however, its immunomodulatory functions in T cells are largely unknown. In this study, we hypothesized that IL-27 promotes pro-inflammatory properties enhancing HIV-specific T cell immunity. We found that IL-27 enhanced STAT1 activation in T cell subsets from people living with HIV (PLWH). Moreover, the RNA-Seq analysis showed that IL-27 stimulation induced global transcriptional changes that overlapped with both IFNα and IL-6 signaling. We also determined that the T cells response to IL-27 stimulation were enriched in genes associated with IFN/STAT1 signaling pathways in PLWH and healthy donors. In addition, overnight in vitro stimulation with IL-27 upregulated expression of CD69 and T-bet in CD4 and CD8 T cells. Accordingly, IL-27 increased IFN-ɣ and TNF-αsecretion by TIGIT+ HIVGag specific CD4 and CD8 T cells. The previously described anti-viral properties and these newly immunomodulatory features of IL-27 in HIV-specific T cell function suggest its potential therapeutic use in HIV cure strategies.
Systematic dissection of cytokine responses in vivo at single-cell resolution
Authors: Cui Ang , Huang Teddy , Li Shuqiang , Ma Aileen , Perez Jorge , Keskin Derin , Sander Chris , Wu Catherine J. , Fraenkel Ernest , Hacohen Nir 
Published: February 2023

Abstract
Cytokines mediate a highly complex intercellular signaling network in health and disease. While many individual cytokines have been studied in-depth, we do not have a systems-level view of cell-type-specific responses to each cytokine and do not yet understand how cytokines orchestrate cell-cell communication networks in a complex immune response. To address these two gaps in cytokine biology, we performed single-cell RNA sequencing to measure gene expression profiles of over 20 mouse lymph node cell populations in response to over 80 cytokines in vivo. We first investigated how distinct cell types respond to the same cytokine and found that while some pathways are activated across multiple cell types, many cytokines induced cell-type-specific gene expression signatures. Next, we compared responses across cytokines and found that cytokines induced both unique and shared biological processes. For example, in NK cells, we found that IL-2/7/12/15/27/33/36a, IFN-a1/b/g/e/k, LIF, CT-1, and NP each induced a cytolytic program, but also cytokine-specific gene expression programs involved in antigen presentation, NF-kB activation, and mRNA splicing. Finally, based on our compendium of cytokine signatures, we created an algorithm to assess the level of cytokine responses and reconstruct cell-cell communication networks, and used this approach to uncover cytokine mediators in checkpoint blockade cancer immunotherapy treatment. Our study provides a global view of cell-type specific cytokine responses in vivo. The framework can be readily applied to other transcriptomic datasets for assessing the roles of cytokines and cell-cell communication networks in any immune response.
BATF regulates innate lymphoid cell hematopoiesis and homeostasis
Authors: Liu Qingyang , Kim Myung H. , Friesen Leon , Kim Chang H 
Published: February 2023

Abstract
Early hematopoietic progenitors undergo sophisticated developmental processes to become committed progenitors for innate lymphoid cells (ILC) in hematopoietic tissues, which ultimately become mature ILC subsets in the periphery. Basic leucine zipper ATF-like transcription factor (Batf) plays important roles in lymphocyte biology. We report that Batf regulates the production of bone marrow ILC progenitors and maintenance of peripheral ILCs. Batf is most highly expressed in ILCs among all lymphocytes. Data from in vivo and in vitro ILC differentiation experiments revealed that the expression of Batf is induced in early ILC progenitors at the α-lymphoid progenitor stage in response to the cytokine IL-7. Our Chromatin immunoprecipitation and retroviral gene transfer experiments revealed that up-regulated Batf binds and activates transcription of the Nfil3 gene to promote ILC hematopoiesis. Data from bone marrow chimera and parabiosis experiments support that Batf is intrinsically necessary to maintain normal numbers of early and late ILC progenitors in the bone marrow and mature ILC1, ILC2, ILC3, and NK cells in most peripheral tissues. Batf-deficient mice have ILC3 lymphopenia and fail to control Citrobacter rodentium infection. Moreover, ILC2 responses to cytokines were defective in Batf-deficient mice. Thus, Batf is required for normal ILC responses to inflammatory cytokines and bacterial infection. These data suggest that Batf plays fairly comprehensive roles in supporting bone marrow hematopoiesis, maintenance, and effector functions of ILCs.
Exploring the B cell microenvironment in von-Hippel Lindau (Vhl) Dmp1-specific knockout mice
Authors: Chicana Betsabel J , Abbasizadeh Nastaran , Burns Christian , Spencer Joel , Manilay Jennifer 
Published: February 2023

Abstract
Osteoblasts (OBs) and osteocytes (OCYs) have been shown to support B cell development. The von-Hippel Lindau protein (VHL) regulates hypoxia-inducible factor degradation and is involved in responses to low oxygen environments. We utilized Dmp1-Cre;Vhl conditional knockout mice (cKO), in which Vhl is deleted in OBs and OCYs. The cKO display dysregulated bone growth, high bone density, smaller bone marrow (BM) cavity volume, and overall decrease in BM cellularity compared to wild-type (WT) mice. B cell progenitors were significantly increased in frequency and numbers whereas Hardy Fractions B, C, D, E and F were significantly decreased in the cKO BM. cKO Fraction B-C cells showed an increase in apoptosis and decreased proliferation. Reciprocal BM chimeras showed significant reduction in Fractions B-C and later Fractions in the WT→cKO, while B cell development was normal in the cKO→WT chimeras, indicating a cell-extrinsic effect of Vhl on B cells within the cKO BM microenvironment. We hypothesize that B cell development is not supported due to reduction of key niche cells such as stromal cells, OBs, mesenchymal stem cells and decreased production of key cytokines. In preliminary studies, we found that CXCL12 and SCF, key cytokines for B cell development, were reduced in the cKO BM serum. We have begun longitudinal studies using intravital and ex vivo imaging of the cKO BM to identify temporally dependent changes in oxygenation, blood vessel type, structure, permeability, and location of stromal cells. Ex vivo long bone imaging of cKO BM in 6-month-old mice revealed an increase in blood vessel diameter compared to WT. These studies will reveal details and novel molecular mechanisms by which Vhl in Dmp1 expressing cells may serve as a B cell niche.