bluuebunny/crossref_metadata_2025_split huggingface dataset:
Landscape of bone marrow T cells in acquired aplastic anaemia revealed by single-cell sequencing
Authors: LIU YAN , Wang Shuwen , Zuo Xinyi , Peng Jun 
Published: January 2023

Abstract

Objective
Acquired aplastic anaemia (AA) is a T-cell-mediated autoimmune disease characterized by hematopoietic stem cell destruction in the bone marrow (BM). The aim of our study is to explore the cellular heterogeneity, lineage and functional states of T cells involved in the pathogenesis of AA.

Methods
CD3+CD4+ and CD3+CD8+ mature T cells, isolated from BM of five newly diagnosed severe AA patients and two healthy controls by FACS, were subjected to single-cell RNA sequencing (ScRNA-seq) and T cell receptor (TCR) sequences using 10X Genomics Chromium Single Cell 5′ and Single-Cell V(D)J protocols. Libraries were sequenced on Illumina NovaSeq platforms.

Results
We obtained transcriptome data for 47,508 cells from severe AA patients and 20,758 cells from controls. Bioinformatic analysis of the transcriptional profiles and TCR sequences revealed their molecular and functional properties and developmental trajectory. All clusters are not library specific, but consisted of cells from 7 different donors. We identified all major cell types and signature genes for each subset. We discovered a marked decrease of three heat shock protein family A (Hsp70) members (HSPA6, HSPA1A and HSPA1B) as a signature of AA patients. Interestingly, this phenomenon occurred for all T cell subpopulations. GO annotations related to these genes included response to temperature stimulus, unfolded protein binding and protein folding. We suspected these Hsp70 members were closely related to the pathogenesis of AA.

Conclusions
Our results establish a reference map of human BM T cells in health and AA patients. and demonstrate that T cells have unique characteristics in AA patients, which may represent a pathogenesis of this autoimmune disease.
IFNγ Contributes to Splenic B and T cell Activation and Cytopenia in STING Gain-of-Function Autoinflammation
Authors: Gao Kevin MingJie , Motwani Mona , Marshak-Rothstein Ann , Fitzgerald Kate A. 
Published: January 2023

Abstract
cGAS-STING is a cytosolic dsDNA sensing pathway whose regulation is vital to immune homeostasis. Constitutively active STING mutations cause an autoinflammatory syndrome known as STING Associated Vasculopathy with onset in Infancy (SAVI). Pediatric SAVI patients develop treatment resistant lung fibrosis associated with immune abnormalities, including lymphopenia with hyperactivity of remaining lymphocytes and an interferon-stimulated gene signature. Unlike other cGAS-STING driven autoinflammatory syndromes in which Type 1 interferons (T1IFNs) mediate pathology, loss of the T1IFN receptor fails to prevent disease in mice expressing the STINGV154M SAVI (VM) mutation. Instead, lymphocytes play a critical role in SAVI, as VM Rag1−/− mice fail to develop lung disease. Thus, we sought to test whether T cell production of IFNγ (Type 2 IFN) could be a causal mechanism of disease in SAVI, and predicted that IFNγR1 and TCRβ deficiency ought to rescue SAVI disease in a similar fashion. In alignment with our expectations, we found that B cell lymphopenia and hyperactivity were equally rescued in VM IFNγR1−/− and VM TCRβ−/− mice. Moreover, IFNγR1 deficiency also led to improvements in thymic development, T lymphopenia, and hyperactivity. However, despite resolution of splenic lymphocyte defects in VM IFNγR1−/− and VM TCRβ−/− mice, these mice continued to develop fibrotic lung disease. This finding indicates a T cell and IFNγ independent process in SAVI lung disease pathogenesis. In concordance with this, we have recently found that B cells accumulate in the VM lung with a highly activated phenotype independent of αβ T cells, suggesting a potential role for B cells in the etiology of SAVI fibrotic lung disease which we are actively investigating.
Immunodietica: towards a data-driven approach to dissect interactions between diet and autoimmune disease
Authors: Ferreira Leonardo , Burov Andrey A. , Miao Brenda Y. , Morais Vasco H. , Gershteyn Iosif M. 
Published: January 2023

Abstract
50 Million people in the United States are estimated to suffer from an autoimmune disease, and this number is predicted to continue growing. Up to 70% of cases could be due to environmental factors. Therefore, an understanding of how diet, likely a major component of the environmental factors described, impacts the immune system merits exploration. We sought to develop a system of comparison between human epitopes implicated in seventy autoimmune diseases and the overlap between them and epitopes found in various commonly consumed animals and plants. The aim of the comparison was to construct a comprehensive database of overlap to provide an index, the Gershteyn-Ferreira index, of potential auto-immunogenicity of various diet-derived proteins. The construction of the database utilized the automation of querying and recording the epitopes with the IEDB (Immune Database and Analysis Resource) system. We created a comprehensive index for twenty-four organisms. Of note, our system personalizes the epitope overlap of the organisms per individual by integrating the human leukocyte antigen (HLA) alleles of the subject and re-running the overlapping epitopes to filter for in silico HLA binding. In addition, we mapped the tissue expression pattern of each epitope to gauge the risk of being exposed to it in the diet. With this new system, Immunodietica, we can determine exact diet-derived epitopes that could be responsible for the pathogenesis or symptom severity of autoimmunity, as well as generate a personalized ‘heat-map’ of potential triggers, the Gershteyn-Ferreira sensitivity passport, for use by autoimmune disease patients.
An amino acid change in IRF7 increases SLE risk through transcriptional regulation of type I interferons
Authors: Javier Ellen F , Dunn Katelyn , Donmez Omer , Forney Carmy , Roe Margaret , Rowden Hope , Miller Daniel , Javier Jose , McDaniel Margaret M , Pasare Chandrashekhar , Waggoner Stephen N , Weirauch Matthew T , Kottyan Leah C 
Published: January 2023

Abstract
Systemic Lupus Erythematosus (SLE) is an incurable, debilitating autoimmune disease characterized by widespread inflammation and rampant production of autoantibodies. The most prominent and highly replicated set of genes up-regulated in the immune cells of patients with SLE are the type I interferons (IFN-I) and IFN-responsive genes. IFN-I are predominantly made by plasmacytoid dendritic cells (pDCs), and their expression is directly regulated by the transcription factor interferon regulatory factor 7 (IRF7). While IRF7 is an established SLE risk locus, the variants responsible for disease pathology remain unknown. We hypothesize that an amino-acid changing SLE risk variant in IRF7 (rs1131665) alters expression of disease-relevant IFN-I in clinically-relevant cells to increase SLE risk. The functional genomic consequences of the SLE-associated variant were assessed in human cell lines and in genome-edited mice with an introduced SLE-risk variant at Irf7. Our data demonstrate greater than 2-fold genotype-dependence in IFN-stimulated response element-driven luciferase activity and inflammatory cytokine secretion detected in supernatant after toll-like receptor-7 stimulation. Gene expression differences in cells with IRF7/Irf7 risk variants are consistent with those dysregulated in SLE patients. In the present study, we demonstrate the functional consequences of an amino acid substitution in a critical type I interferon regulator. Understanding these mechanisms will enhance development of more effective clinical practices for autoimmune patients expressing the risk variant for IRF7.
Understanding human Crohn’s disease: T cell immunoprofiling and in vitro primary intestinal epithelial monolayer models
Authors: Kemp Roslyn , Angus Hamish , Fan Lisa , Butt Grant , Schultz Michael 
Published: January 2023

Abstract
Crohn’s disease (CD) is a type of inflammatory bowel disease caused by uncontrolled inflammation and is associated with loss of tolerance to commensal bacteria. There is no current consensus on how CD forms; however, four susceptibility criteria are required for disease: a microbial presence, an immune response, an environmental trigger, and genetic susceptibility.
We investigated the peripheral and intestinal immune response of people with CD compared to healthy people. CD peripheral blood (PBMC) contained higher baseline frequencies of pro-inflammatory Th17 cells compared to those from healthy controls, and regulatory T cells from CD patients increased in frequency in response to the commensal Faecalibacterium prausnitzii, whereas those from healthy controls did not. CD patient PBMCs secreted higher concentrations of the pro-inflammatory cytokines: IL-6, TNF, and IL-17A, compared to healthy controls.
We developed a human 2-dimensional large intestine organoid monolayer transwell model that replicates the in vivo intestinal epithelial barrier as the cells of the epithelial monolayer are arranged into a selectively semi-permeable polarised membrane, separating the apical and basal regions of the system, emulating the luminal and lamina propria intestinal regions. Co-culture of CD patient-derived monolayers with patient PBMCs and heat-killed F. prausnitzii caused disruption of monolayer integrity, whereas control patient monolayers were unaffected. IL-6 was present in control monolayer supernatants but not those from CD patients. We hypothesise that CD patient PBMCs have inherent abnormal responses to commensal bacteria, and in the context of this model, IL-6 may be required for maintenance of monolayer integrity.
Role of eosinophils and MMP-9 in autoimmune blistering disease bullous pemphigoid
Authors: Liu Zhi , Burette Susan , Diaz Luis , Li Ning 
Published: January 2023

Abstract
Bullous pemphigoid (BP) is an autoimmune inflammatory subepidermal blistering disease associated with autoantibodies against two hemidesmosomal components, the BP230 and BP180 and an inflammatory infiltrate including eosinophils and neutrophils. BP180-specific IgG autoantibodies from BP patients induce BP-like skin lesions in BP180 humanized mice (hBP180 mice). Subepidermal blistering induced by anti-BP180 IgG depends on complement, mast cells, and neutrophils. Since mouse eosinophils lack IgE receptors for human IgE, we generated a humanized IgE receptor FceRI mouse strain (hFceRI) and crossed hFceRI mice onto hBP180 mice to generate hFceRI/hBP180 mice. Anti-BP180 IgE, when injected i.d. into hFceRI/hBP180 mice, trigger infiltration of dominant eosinophils and minor neutrophils and subsequent subepidermal blistering 48 h post IgE injection. In this study, we tested if anti-BP180 IgE-induced BP depends on eosinophils, neutrophils or both. We found that anti-BP180 IgE induce BP in hFceRI/hBP180 mice and neutrophil-deficient but not eosinophil-deficient hFceRI/hBP180 mice. Eosinophil-deficient hFceRI/hBP180 mice reconstituted with eosinophils but not neutrophils from hFceRI/hBP180 mice became susceptible to anti-BP180 IgE-induced BP. Increased MMP-9 was present in diseased mouse blister fluid. MMP-9-deficient and eosinophil-deficient hFceRI/hBP180 mice reconstituted with MMP-9-sufficient but not MMP-9-deficient eosinophils when injected with anti-BP180 IgE developed BP. These data suggest that eosinophils and MMP-9 are critical for BP and could be therapeutic targets for BP treatment.
Telomere length predicts mortality in the Black Women’s Experiences Living with Lupus (BeWELL) Study
Authors: Chae David H. , Chung Kara , Martz Connor D. , Drenkard Cristina M. , Lim S. Sam , Lin Jue , Epel Elissa S. 
Published: January 2023

Abstract
Systemic lupus erythematosus (SLE) is a chronic autoimmune disease marked by inflammation that disproportionately impacts Black women. Telomeres are repetitive sequences of DNA capping the ends of chromosomes that shorten more rapidly in response to inflammation. Studies suggest that the telomere maintenance system may be disrupted in those with SLE, who have been shown to have shorter telomeres compared to healthy controls. Among those with SLE, Blacks have been found to experience more accelerated telomere shortening compared to those of other race groups. We examined the relationship between telomere length (TL) and mortality using data from the Black Women’s Experiences Living with Lupus (BeWELL) Study. Participants were 438 Black women with a validated diagnosis of SLE living in the Atlanta, Georgia metropolitan area, recruited between April 2015 and May 2017 predominantly from a large population-based registry. TL was assayed from dried blood spots collected at baseline and measured as the relative telomere to single copy gene (T/S) ratio. Mortality was assessed prospectively through April 2019. A total of 24 participants died during this time period. There was a negative association between TL and mortality, with shorter TL being associated with greater mortality risk (hazard ratio = 0.01, p=0.02). This relationship remained statistically significant after controlling for age and years since diagnosis, and further adjustment for a range of socio-demographic and health-related factors, including SLE damage and activity. Findings suggest that TL may forecast mortality among Black women with SLE. The association between TL and mortality among people with SLE should be further explored.
Similar cardiovascular disease histopathology and macrophages in heart tissues of younger adult SIV-infected and uninfected aged rhesus macaques
Authors: Kuroda Marcelo J , Petkov Daniel I , Liu David , Allers Carolina , Didier Peter J , Didier Elizabeth S 
Published: January 2023

Abstract
Cardiovascular disease is a major cause of morbidity in aging and in HIV-infected individuals despite efficacy of cART, and furthermore, is associated with macrophage activation and inflammation. Nonhuman primates simulate human disease, and we previously reported that distinct macrophage populations play different roles in the pathogenesis of disease during SIV infection in rhesus macaques. For example, in the lung, short-lived macrophages were more readily destroyed by SIV and contributed to AIDS pathogenesis. Long-lived alveolar macrophages on the other hand were not easily destroyed by virus and thus may contribute to a long-term virus reservoir that also promotes chronic inflammation. The present studies extend this work to characterize macrophages in heart and skeletal muscles affecting cardiomyopathy observed during SIV/HIV infection as well as in heart tissues of uninfected younger and older macaques. The results demonstrated that macrophages are distributed uniformly throughout the heart tissues in animals of all age groups. Increased percentages of macrophages, however, were observed in hearts of aged macaques with similar increased percentages of macrophages in SIV-infected younger adult macaques. Interestingly, the increased macrophages of both aged uninfected and younger SIV-infected macaques was not due to increases in the absolute numbers of macrophages but rather to decreased heart muscle cellularity. This suggested that cardiovascular disease observed in aged as well as HIV-infected individuals may be due to similar mechanisms of decreased number of heart muscle cells and dysfunctional inflammatory long-lived macrophages of the heart.
Single cell transcriptomics of the T cell response to Mycobacterium Tuberculosis reveals phenotypic diversity within and between infected individuals
Authors: Kirschman Junghwa Choi , Ogongo Paul , Ernst Joel , Altin John 
Published: January 2023

Abstract
Tuberculosis (TB) is an airborne infectious disease and caused by Mycobacterium Tuberculosis (MTB) and the leading infectious cause of adult mortality in the world. Despite its high transmission rate and high fatality in untreated individuals, currently there is only one widely-used vaccine and it does not protect adults from TB. The development of a more efficacious vaccine has been hampered by limitations in our understanding of the type of immunity required to protect against TB. Using single cell transcriptomics, we have developed a method of identifying Mtb-reponsive T cell clones and performing deep phenotyping on them. Our study of circulating cells in latently-infected individuals reveal robust differences in the transcriptional phenotypes of Mtb-responsive CD4 T cells, both within and between individuals. We expect that this transcriptome-wide view of Mtb-specific cells, and a simultaneous view of the inciting antigens at peptide resolution, will enable a next-generation studies of the response to Mtb in natural history and vaccine trial cohorts, with the potential to reveal correlations of protection and therefore new vaccine targets and mechanisms.
Prognostic value of autophagy markers in sepsis- a clinical case report
Authors: Mallarpu Chandra Shekar , Ponnana Meenakshi , Prasad Sudhir , Singarapu Maneendra , Chelluri Lakshmi Kiran , Madiraju Charitha 
Published: January 2023

Abstract
Sepsis is characterized by a dysregulated response to infection that is initiated by recognition of pathogen-associated molecular patterns from invasive microorganisms by pathogen recognition receptors to trigger an immune response. The goal is to establish regulatory mechanisms governing sepsis-induced cell death and correlate cell death mechanisms with clinical biochemistry pre- and post- antibiotic treatment. Towards this end, we present a case report of a 48-year-old male patient with a clinical history of adenocarcinoma, colostomy, chronic kidney disease and suspected sepsis admitted to emergency department. Patient was on an antibiotic treatment regimen (Monocef 1 g single dose and Flucloxacillin 1 g single dose for three days). Among several promising biomarkers for sepsis, the role of cell death marker p62/SQSTM1 was evaluated for its prognostic role in this particular case of sepsis. Flow cytometry and ELISA analysis of septic patient’s peripheral blood mononuclear cells (PBMCs) and serum samples were performed and correlated with serum electrolyte and serum biochemistry values pre- and post- antibiotic dose. Flow cytometry data analysis of PBMC samples from septic patient showed significantly lower p62 post- antibiotic when compared to pre- antibiotic dose [p &lt; 0.05]. Notably, comparison of pre- and post- antibiotic treatment regimen showed significant modulation of serum ELISA levels of autophagy marker, p62/SQSTM1, that correlated with alteration in serum potassium levels [p &lt; 0.05]. Our current study demonstrates the impact of serum potassium levels on autophagy in a patient’s case of sepsis.
Activation of the innate immune response by IL-36 mediated inflammation during active ticks mediated ehrlichial transmission in mice
Authors: Kempaiah Kempaiah Rayavara , Harrison Mack , Saito Tais B. 
Published: January 2023

Abstract
Tick borne ehrlichiosis is a life-threatening disease affecting humans and animals worldwide. Early host response to pathogen-tick interaction at the site of transmission has not been well studied due to difficulties associated with natural model of infection. To study the host immune interaction with Ehrlichia muris eauclarensis (EME), a human pathogen, we compare tick transmission of EME in C57Bl/6 mice with needle inoculation. Our objective was to analyze the local and systemic infection to identify the immune pathways involved in the pathogenesis of tick borne ehrlichiosis. As previously reported, our studies show inflammatory infiltration of neutrophils and eosinophils at the site of infection within 24–48h of tick infestation. Further evaluation of the site of tick transmission demonstrated increased expression of IL36α, IL36γ, IL1β and IL18 cytokines during initial ehrlichial infection. Our analysis of the peak of infection identified an increased epidermal thickening, massive inflammatory infiltration at the site of infection and systemically, and increased levels of proinflammatory cytokines in serum. The disease progression is associated with increased bacterial load in lungs, spleen, liver and other tissues tested, with increased liver ANG-2 and apoptosis, suggesting acute vascular dysfunction and liver injury. These results demonstrate that ehrlichial transmission by ticks causes severe inflammation with up-regulation of IL36 group of cytokines, potentially activating innate immune system to facilitate bacterial dissemination and severity of the disease. Understanding the key determinants of tick mediated ehrlichiosis will enable us to identify susceptibility markers and new therapeutic targets.
SIV and CD4 depletion distinctly reactivate latent Mycobacterium. tuberculosis infection
Authors: Diedrich Collin R , Rutledge Tara , Maiello Pauline , Baranowski Tonilynn , White Alex , Borish H. Jacob , Karell Paul , Hopkins Forrest , Brown Jessica , Fortune Sarah , Flynn JoAnne L , Ambrose Zandrea , Lin Philana Ling 
Published: January 2023

Abstract
Human immunodeficiency virus infection is the most common risk factor for severe forms of tuberculosis (TB) regardless of CD4 T cell count. Using a well-characterized cynomolgus macaque model, we compared reactivation of latent M. tuberculosis (Mtb) infection induced by simian immunodeficiency virus (SIV) or anti-CD4 antibody (αCD4). Reactivation, as defined by the appearance of a new lung lesion by PET CT, occurred in 5 of 7 αCD4 treated animals compared to 4 of 8 SIV infected animals within 2 months of treatment. αCD4 animals had significantly fewer CD4 T cells within granulomas compared to SIV/Mtb infected animals. However, compared to αCD4 groups, SIV infection caused more dissemination of lung granulomas and higher granuloma bacterial burdens. Within the granulomas, SIV replication was associated with greater Mtb growth and reduced Mtb killing. Granulomas from SIV/Mtb animals displayed a distinctly different profile of T cell cytokine and granzyme B expression compared to αCD4 animals and controls. PET CT imaging prior to treatment could predict reactivation in αCD4-treated animals, but not in SIV/Mtb animals. These data suggest that SIV infection disrupts protective immune responses against Mtb infection beyond the loss of CD4 T cells, and that synergy between SIV and Mtb occurs within granulomas.
Regulation of Id2 gene expression in plasmacytoid dendritic cells
Authors: Babcock Rachel Lauren , Li Haiyan S , Zhou Yifan , Chrisikos Taylor T , Watowich Stephanie S 
Published: January 2023

Abstract
Plasmacytoid dendritic cells (pDCs) are specialized type I interferon (IFN-I) producing cells that mediate anti-viral responses, anti-tumor immunity, and autoimmunity. When exposed to Toll-like receptor 7 (TLR7)- and TLR9-ligands, pDCs mature and produce IFN-Is; pDCs also acquire conventional DC (cDC)-like morphology and features, including the cell surface expression of antigen presentation and co-stimulatory molecules, secretion of additional cytokines, and ability to activate adaptive T cell responses. Yet, the transcriptional pathways regulating TLR-induced pDC maturation are poorly characterized. We found the mRNA and protein expression of the inhibitor of DNA binding protein 2 (Id2) was induced in TLR7/9-stimulated pDCs, and Id2 expression correlated with greater cDC-like features. Id2 normally blocks pDC development by antagonizing the pDC-master regulator, E2-2, while E2-2 suppresses Id2 transcription. Thus, we hypothesize TLR-activated signaling pathways in pDCs control the abundance of transcriptional regulators (e.g., E2-2) at the Id2 promoter as well as the promoter chromatin state, leading to induction of Id2 transcription during pDC maturation. Using genetic knockout mouse models, we found Id2 induction was independent of interferon alpha receptor and nuclear factor kappa beta signaling pathways. Chromatin-immunoprecipitation assays suggested E2-2 abundance at the Id2 promoter decreased following TLR stimulation, while activating histone modifications increased. These data are consistent with transcriptional induction of Id2 upon TLR stimulation. Future work will investigate the effect of additional regulators and TLR-regulated pathways on Id2 induction in TLR7/9-stimulated pDCs.