bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-cell characterization of circulating and synovial immune cells reveals a unique dendritic cell landscape and enrichment of granzyme K+ T cells in Psoriatic Arthritis
Authors: Mullins Briana J , Herrera Alberto , Chang Anthony , Yang Katharine Lu , Girija Parvathy V , Hernandez Anthony Jimenez , Alvarado Luz , Medina Rhina , Scher José , Koralov Sergei B 
Published: August 2023

Abstract
Psoriatic Arthritis (PsA) is an immune mediated disease of the joint. It typically develops within 10 years after the onset of psoriasis, with ~30% of individuals progressing to joint disease. The progression of disease from skin to joint is not fully understood, although it is thought to be orchestrated by T helper 17 immune responses. To understand the immune landscape of PsA, we isolated immune cells from four matched PsA patient blood and synovium samples and performed multimodal single-cell sequencing (ExCITE-seq), which captures surface epitope information and T and B cell receptor rearrangement in addition to transcriptional profile. Our preliminary analysis revealed an enrichment of CD1c+/CD141+ dendritic cells (DCs) in synovium compared to the blood of PsA patients. Differential gene expression of these DC populations showed increased expression of CXCL16 in synovium derived DCs, while analysis of synovial fluid revealed high levels of CXCL10. Differential gene expression of CD8 and CD4 T cells across blood and synovium revealed increased granzyme K (GZMK) in the synovium. Further analyses comparing the GZMK+ T cell populations to their negative counterparts revealed upregulation of CXCR3, suggesting that CXCR3-CXCL10 axis may be responsible for recruitment and/or retention of T cells in the synovium. Pathway analysis for GZMK+ T cells revealed increased cytotoxicity and granulitic activity. Together this data suggests that GZMK+ T cells may contribute to inflammation in the joint of PsA patients, after recruitment to the site of inflammation by CD1c+/CD141+ DCs. Further characterization of additional PsA patients and psoriasis patients at risk for developing PsA is ongoing and will provide insight into PsA pathogenesis.
Supported by a grant from the NIH (I&I Schwab T32) and funding from the National Psoriasis Foundation and the Colton Center for Autoimmunity.
SARS-CoV-2 RBD-specific atypical memory B cells exhibit effector memory-like features in multi-dose mRNA vaccination
Authors: Lee Jeongsoo , Kim Sung-Han , Shin Eui-Cheol , Park Su-Hyung 
Published: August 2023

Abstract
Memory B cell is a heterogenous population and such heterogeneity is a focus of active investigation. How distinct subsets of memory B cells respond to repeated novel antigen challenges such as SARS-CoV-2 in human remains a subject of vigorous research. We employed fluorochrome-conjugated streptavidin tetramers bound with RBD of wild-type and omicron variant (B.1.1.529), respectively, to sort RBD-specific B cells and performed CITE-seq to investigate detailed dynamics of transcriptomes, surface phenotyes and clonality in healthy mRNA vaccination cohort. PBMC samples of 8 BNT162b2 vaccine recipients from 7 consecutive timepoints, before and after each dose of 3-times vaccination, were analyzed. We found pulsating, yet with increasing trend, frequency of atypical memory B cells among tetramer-binding B cells after each dose of vaccine. SCENIC analysis of tetramer-binding memory B cells to find subset-specific regulatory gene networks revealed atypical memory B cells have distinct regulons of genes related to activation such as receptor clustering, signaling and calcium-dependent activation compared with classical memory B cells and found only one shared clone between atypical and classical tetramer-binding memory B cells, suggesting infrequent interconversion between the two subsets. Furthermore, in-vitro polyclonal stimulation of atypical memory B cells showed higher frequency of antibody-secreting cells (ASC) and pre-plasmablasts in flow cytometry and wild-type RBD-specific ASCs in IgG ELISPOT assay, compared with classical memory B cells. These findings highlight effector memory-like features of atypical memory B cells in viral antigen challenge and a potential target of future vaccine design.
Critical COVID-19 disease explained by type I interferon autoantibodies found in patients within the Military Health System
Authors:   EPICC Study Group, Leondaridis Maria A , Yee Debra , Tso Marana , Shaw Elana , Rosen Lindsey B , Samuels Emily , Bastard Paul , Casanova Jean-Laurent , Holland Steven M , Su Helen C , Richard Stephanie , Mende Katrin , Lalani Tahaniyat , Lindholm David , Berjohn Catherine M , Maves Ryan , Colombo Rhonda , Colombo Christopher , Larson Derek , Ewers Evan , Ganesan Anuradha , Huprikar Nikhil , Mody Rupal M , Jones Milissa U , Simons Mark P , Tribble David , Laing Eric , Agan Brian , Pollett Simon , Burgess Timothy , Snow Andrew L 
Published: August 2023

Abstract
Neutralizing auto-antibodies (auto-Abs) that target type I interferons (IFN), a group of cytokines that induce innate immune responses upon viral infection, are found within approximately 10–20% of patients with critical COVID-19. We sought to determine if neutralizing type I IFN auto-Abs contribute to severe COVID-19 in patients within the Military Health System (MHS). The Epidemiology, Immunology, and Clinical Characteristics of Emerging Infectious Diseases with Pandemic Potential (EPICC) cohort collected demographic data, clinical data and sera from SARS-CoV-2 infected patients enrolled across 10 U.S. military treatment facilities. We screened sera collected &lt;21 days post-symptom onset from 214 COVID-19 inpatients and 312 COVID-19 outpatients for IFN auto-Ab positivity and neutralizing activity using Luminex and intracellular flow cytometry, respectively. Similar to previous reports, we detected neutralizing auto-Abs against IFN-α and/or IFN-ω in a significantly higher frequency of inpatients (9 total, 4.2%) versus outpatients (1, 0.32%) (p=0.009). Remarkably, IFN auto-Abs persisted 6–12 months post-infection in most inpatients, including several with a prior history of autoimmune disease. Among inpatients, multivariate logistic regression analyses demonstrated that type I IFN auto-Abs were associated with a greater risk of severe and critical COVID-19 (adjusted odds ratio (aOR) = 16.40 and 6.44, respectively) after adjusting for age, sex and comorbidity burden. Our results confirm a robust association between critical COVID-19 and the presence of type I IFN auto-Abs, which may predispose to other severe respiratory viral infections that cause substantial morbidity and mortality in the MHS.
This work was supported by awards from the Defense Health Program (HU00012020067) and the National Institute of Allergy and Infectious Disease (HU00011920111). The protocol was executed by the Infectious Disease Clinical Research Program (IDCRP), a Department of Defense (DoD) program executed by the Uniformed Services University of the Health Sciences (USUHS) through a cooperative agreement by the Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. (HJF).
Single cell mapping identifies expansion of Cytotoxic CD4 T cells in the atherosclerotic plaque of subjects with Type 2 Diabetes
Authors: Das Dayasagar , Gildea Michael , Eberhardt Natalia , Kaur Ravneet , Fernandez Dawn , Amadori Letizia , Sajja Swathy , Shamailova Roza , Goldberg Ira J , Maldonado Thomas , Rockman Caron B , Berger Jeffrey , Fisher Edward A , Giannarelli Chiara 
Published: August 2023

Abstract
Patients with Type 2 diabetes (T2D) are at greater risk of atherosclerotic cardiovascular disease (ASCVD) and fail to fully respond to standard lipid lowering drugs. While the role of macrophages in T2D plaque pathology has been investigated, no studies have systematically investigated the heterogeneity of CD4 T cells in human plaques and how they respond to cholesterol reduction. To identify the specific T cell alterations in plaques from patients with T2D, we performed scRNAseq of human carotid plaques from 22 subjects (54.5% T2D) were being treated with cholesterol lowering drugs (average LDL cholesterol of 1.2 mmol/L) undergoing carotid endarterectomy. Data were processed and integrated using Seurat and Slingshot algorithms. We identified a total of 24 immune cell clusters by unbiased clustering of CD45+ cells, including CD4 T cells that presented similar frequencies between T2D (~11%) and non-T2D patients (~10%). CD4 T cells comprised of 13 sub clusters: naïve, central memory (CM), effector memory (EM), T regulatory (Tregs), cytotoxic (CTL), and gamma delta (γδ) T cells. One cluster of CD4 CTLs (cluster 5) expressing TRDC and TRGC2 surface markers along with cytotoxicity markers GZMB, GNLY, and PRF1 was significantly expanded in T2D plaques (p=0.032). This CD4CTL expressed high levels of transcription factors (TFs) involved in T cell differentiation such as RUNX3 and ZEB2 and contained sets of genes involved in cytotoxicity, chemotaxis and IL-1 signaling. Trajectory analysis using Slingshot inferred that CD4 CTLs clusters in the plaques differentiate from CD4 EM T cells. Plaques from patients with T2D are highly enriched in CTL/γδ T cells and suggest that their cytotoxic potential contributes to the increased cardiovascular risk.
This Work is supported by AHA SFRN 20SFRN35210252 and the AHA-SFRN Training Program.
Using novel diagnostic antibodies to identify lymphocyte markers of rheumatic fever and heart disease
Authors: Euler Chad W , Fischetti Vincent A 
Published: August 2023

Abstract
Acute rheumatic fever (ARF) is an autoimmune disease that occurs in a subset of patients as a delayed complication of an improperly treated throat infection with a rheumatogenic strain of Streptococcus pyogenes. ARF / Rheumatic heart disease is a leading cause of preventable cardiovascular morbidity and mortality in children worldwide, affecting &gt;33 million people. A method of detecting children susceptible to ARF (3–5% of the total population) would have major global health and economic benefits.
One potential ARF diagnostic is the IgM antibody, D8/17, which binds B cells from ARF patients of diverse ethnic groups and geographical locations at a higher % versus matched controls. While this antibody has had mixed results in the past, no group has identified the antigen that D8/17 binds. To aid in this endeavor, we used recombinant antibody engineering to produce new IgM and IgG1 versions of D8/17 that give more consistent results in our in vitro diagnostic tests.
These new derivatives were then utilized in a multi-omics approach to characterize the differences between immortalized B cell lines of ARF patients and controls. Western blot and MS/MS proteomic analyses of lymphocyte lysates identified cytoskeletal proteins from ARF B cells that cross-react more readily with our recombinant D8/17. RNA sequencing and microarray analysis of B cells from ARF patients versus controls confirmed our proteomic results. Further, we discovered differences in the gene expression of other cell surface proteins, kinases and signaling pathways in ARF B cells that bind these antibodies. We hope our analyses will help identify markers or genetic factors related to ARF development and pathogenesis, or aid in designing diagnostic assays for ARF susceptibility.
Supported by a grant from the NIH /NIAD (SC2 1SC2AI134947-01)
Role of cholinergic anti-inflammatory pathway in the regulation of vascular endothelial permeability and inflammation in type 2 diabetes
Authors: Fazal Nadeem , Tauseef Mohammad 
Published: August 2023

Abstract
Despite tremendous advancement in glycemic control, anti-diabetic medications have failed to revert vascular impairment once triggered by the metabolic disorder. The cholinergic anti-inflammatory pathway (CAP) is a neurophysiological mechanism that regulates the immune system. Studies show that the CAP inhibits inflammation by suppressing cytokine synthesis via release of acetylcholine in organs of the reticuloendothelial system, including the heart, lungs and gastrointestinal tract. Upon release, acetylcholine interacts with α7 nicotinic acetylcholine receptors (α7nAChR), down-regulate pro-inflammatory cytokine synthesis and prevent tissue damage and inflammation. Although a CAP modulated the response to severe inflammation during sepsis, the role of this pathway in the regulation of type-2 diabetes (T2D)-induced increase in endothelial permeability is completely unknown. Our data showed that human coronary artery endothelial cells (HCAECs) from T2D displayed increased endothelial permeability and enhanced pro-inflammatory signaling in response to pro-coagulant thrombin and endotoxin lipopolysaccharide (LPS), respectively. We also found increased expression and activity of acetylcholinesterase enzyme, and no change in expression of α7nAChR in T2D endothelial cells (ECs) compared to ECs from normal subjects. Our research findings showed that the T2D increased the expression and activity of AChE enzyme in HCAECs, and thereby decreasing the availability of ACh at α7nAChR. In summary, our work offered novel insights and therapeutic targets that we think will lead to the development of more effective treatments with improved outcomes.
Grant from CTRE Chicago State University, Chicago, IL
Characterization of Lung Eosinophil Subsets During Respiratory Viral Infection in Mice with Pre-Existing Immunity
Authors: Chang Lauren A , Choi Angela , Rathnasinghe Raveen , Warang Prajakta , Noureddine Moataz , Jangra Sonia , García-Sastre Adolfo , Schotsaert Michael 
Published: August 2023

Abstract
Eosinophils are critical cells in Type 2 immune responses and mucosal tissue homeostasis. Historically, lung eosinophilia has been linked to aberrant Th2 responses in response to inhaled allergens or as a consequence of vaccine-associated enhanced respiratory disease in viral infection. In some animal models of respiratory viral infection, lung eosinophilia has been observed in the absence of overt pathology. Here, we interrogated the phenotype and function of eosinophil subsets recruited to the lung after a sublethal, vaccine-matched intranasal challenge, modeling breakthrough infection. We observed an enrichment for eosinophils in the lungs of TIV-vaccinated mice post-challenge that were phenotypically similar to that of OVA-sensitized allergic mice, but with a marked absence of strong inflammatory cytokine signatures, detectable viral titers, and enhanced morbidity. Moreover, we did not observe an influx of eosinophils in the lungs of challenged unvaccinated mice, which were unable to control viral replication and had strong pro-inflammatory cytokine profiles. This suggests that vaccine-matched viral infection of the respiratory mucosa after priming with antigen in the periphery can result in lung eosinophilia that is neither pathological nor disease-enhancing, but correlates more so with clearance during a breakthrough infection. We longitudinally discerned the differential cellular kinetics of lung eosinophils and the lung microenvironment after breakthrough influenza infection or OVA sensitization across multiple parameters, including pathology. We are further analyzing the eosinophil compartment via RNA-seq, imaging, and spectral flow cytometry for in-depth characterization of this phenomenon.
Supported by NIH Public Health Service Institutional Research T32 Training Award (AI07647) and Centers of Excellence for Influenza Research and Response (CEIRR) contract (75N93021C00014-0-9999-1).
Reduction of cell fusion by deletion in the hypervariable region of the spike protein of mouse hepatitis virus
Authors: Shin Hyun-Jin 
Published: August 2023

Abstract
Deletions in the spike gene of mouse hepatitis virus (MHV) produce several variants with diverse biological characteristics, highlighting the significance of the spike gene in viral pathogenesis. In this study, we characterized the JHM-X strain, which has a deletion in the hypervariable region (HVR) of the spike gene, compared with the cl-2 strain, which has a full spike gene. Cytopathic effects (CPEs) induced by the two strains revealed that the size of the CPE produced by cl-2 is much greater than that produced by JHM-X in delayed brain tumor (DBT) cells. Thus, this finding explains the greater fusion activity of cl-2 than JHM-X in cultured cells, and we speculate that the deletion region of the spike protein is involved in the fusion activity differences. In contrast with the fusion activity, comparison of the virus growth kinetics revealed that the titer of JHM-X was approximately 100 times higher than that of cl-2. We found that the deletion region of the spike protein was involved in fusion activity differences, whereas cl-2 produced significantly higher luciferase activity than JHM-X upon similar expression levels of the spike protein. However, the reason behind the growth difference is still unknown. Overall, we discovered that deletion in the HVR of the spike gene could be involved in the fusion activity differences between the two strains.
Definition and mapping of Cmv5 interval associated effects on the innate immune response to acute Murine Cytomegalovirus infection
Authors: Annis Jessica L , Crittenden Rowena B , Brown Michael G 
Published: August 2023

Abstract
MHC-I molecule H-2Dk confers resistance to acute murine cytomegalovirus (MCMV) infection in both C57L and MA/My mice. M.H2k/b mice are MA/My background aside from a C57L-derived region within the MHC (Cmv5), which diminishes this resistance. Thus M.H2k/b mice lose more weight during infection and present with increased viral load. Additionally, M.H2k/b mice have fewer, more activated NK cells and significant spleen histopathology measured by decreased white pulp area, loss of marginal zone definition, and increasing red pulp acellularity. To better understand how the Cmv5 interval regulates the response to MCMV, we generated several Cmv5 recombinant mouse strains and screened them in vivo, allowing us to narrow the phenotype-associated interval as much as 14 times from the original size of 23.08 Mb. In addition, we sought to further characterize the Cmv5-associated phenotypes in their temporal appearance and potential direct relation to viral load. To this end, we found that many Cmv5 phenotypes could not be fully mirrored in the MA/My mice with increased viral dose, and that marginal zone disruption was one of the first Cmv5 phenotypes to appear, being reliably quantified as early as 2 days post infection (dpi) in the M.H2k/bmice. This suggests that splenic tissue disruption, occurring prior to increase in weight loss or NK cell activation, may be a primary target of the Cmv5 genetic interval and its impact on the response to MCMV. In conclusion, we verified and defined the Cmv5-associated susceptibility to MCMV infection, generated and tested several Cmv5 recombinant strains resulting in a substantially reduced interval size, and determined that the full Cmv5 phenotype is unlikely to be a direct result of increased viral load.
NIH NIAID R01AI50072, Department of Medicine/Nephrology, Center for Immunity Inflammation and Regenerative Medicine, Beirne B Carter Center for Immunology Research.
Gp120 envelope glycoproteins of HIV-1 Group M Subtype A and Subtype B differentially affect gene expression in human vascular endothelial cells
Authors: Suh Andrew J , Suzuki Dante I , Brelidze Tinatin I , Suzuki Yuichiro J 
Published: August 2023

Abstract
While HIV-1 Group M Subtype B is the most prevalent subtype in western countries, the majority of HIV-1 infections in eastern Africa and former Soviet Union countries are caused by Subtype A. However, most of the research on HIV has focused on Subtype B and information on the molecular mechanisms of Subtype A is virtually non-existent. The lack of such knowledge results in health disparities for the development of therapeutic strategies to prevent/treat HIV-associated complications. The present study examined envelope glycoprotein (gp120) of HIV-1 Group M Subtypes A and B. The amino acid sequence alignment analysis determined that gp120 proteins of A and B subtypes are 76% identical and share 86% similarity. The treatment of human vascular endothelial cells with the two gp120 proteins exhibited differential gene expression changes as determined by Proteome Profiler Arrays. Subtype A more potently downregulated prostasin, matrix metalloproteinase-2 (MMP-2), and receptor tyrosine-protein kinase erbB-3/Her3 than did Subtype B, while Subtype B was more effective in downregulating monocyte chemoattractant proteins (MCP-2 and MCP-3). Further, epidermal growth factor (EGF), a mediator of vascular complications, was found to be upregulated by gp120 of Subtype A, but not Subtype B. This is the first report of gp120 proteins affecting human host cells in an HIV subtype-specific manner, opening up the possibility that complications may occur differently in HIV patients throughout the world.
Supported by grants from NIH (R21 AG73919, R03 AG71596)
IL-33 promotes inflammatory responses and exacerbates lung pathology in a mouse model of SARS-CoV-2 infection
Authors: Liang Yuejin , Wang Hui , Hosakote Yashoda Madaiah , Gonzales Casey , Xie Xuping , Shi Pei-Yong , Sun Keer , Soong Lynn , Sun Jiaren 
Published: August 2023

Abstract
The ongoing COVID-19 pandemic caused by SARS-CoV-2 has resulted in more than 6.6 million deaths worldwide as of the end of 2022. Clinical data revealed that dysregulated host immune responses may contribute to disease severity and poor recovery outcomes; however, the mechanisms that underlie immune dysregulation and disease severity are relatively unknown. Interleukin-33 (IL-33), a damage-associated molecular pattern (DAMP) molecule, is mainly expressed in nucleus of epithelial and endothelial cells. Elevated serum IL-33 levels have been recently reported in COVID-19 patients and might be associated with adverse outcomes. In this study, we infected B6 mice with a mouse-adapted SARS-CoV-2 MA10 and found that IL-33 was significantly increased in the lungs at day 2 post-infection, accompanied by highly upregulated inflammatory chemokines CXCL1, CXCL2 and CCL2. Next, we used IL-33−/− mice and demonstrated that IL-33 deficiency resulted in less bodyweight loss at days 2 and 3 and decreased viral burden at day 4. Flow cytometry analyses showed that IL-33−/− mice had reduced numbers of innate immune cells at day 2, including neutrophils, macrophages and NK cells. At day 4, IL-33−/− mice displayed reduced activated T cells in the lungs as compared to WT mice. Lung tissue RNAseq transcriptomics revealed that IL-33 signals contributed to several inflammatory pathways, including type II interferon signaling, pathogen phagocytosis, macrophage activation, cytokine/chemokine and inflammatory responses and oxidative damage. Overall, these data uncover a detrimental role of the DAMP IL-33 in the lungs following SARS-CoV-2 infection and provide new insights to support the development of effective therapeutic strategies for COVID-19.
Supported by grants from NIH (R21 AI153586)