bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single cell transcriptomic changes of CD8T cells in male and female patients with coronary artery disease and diabetes
Authors: Iqneibi Shahad , Saigusa Ryosuke , Suthahar Sujit Silas Armstrong , Khan Amir , Oliaeimotlagh Mohammad , Gulati Rishab , Suryawanshi Vasantika , Alimadadi Ahmad , Pandori William , Makings Jeff , Durant Christopher , Ghosheh Yanal , Durant Fabrizio , McNamara Coleen , Shemesh Avishai , Lanier Lewis L , Hedrick Catherine , Ley Klaus 
Published: August 2023

Abstract

Objective
The objective of this study was to determine the role of CD8+ T cells in subjects with coronary artery disease (CAD) with and without diabetes (DM).

Methods
PBMCs of 60 men and women who underwent cardiac catheterization were interrogated by single cell RNA sequencing combined with 49 protein markers (CITE-Seq). Four pairs of groups were matched for all clinical and demographic parameters.

Results
140,610 single cell transcriptomes were successfully analyzed. Among them, 17,349 CD8+ T cells were identified as CD19− CD3+ CD4− CD8+, yielding 17 clusters. The proportion of cells in the CD137+ effector memory (EM) cluster were significantly decreased in CAD+ subjects when compared to matched CAD− subjects. This same cluster was significantly decreased in DM+ CVD− groups when compared to the matched DM− CVD− group. The NK-like Emra1 group was significantly more abundant in CVD+ subjects and in females compared to males. One of the regulatory CD8 T cell clusters was significantly reduced in diabetics. 30 genes were significantly upregulated in both CAD and DM. The DM gene signature was partially additive to the CAD gene signature. IFTM3 and RUNX3 showed more importance in females, TCF7 and LTB in males.

Conclusions
We conclude that CAD is clearly reflected in PBMC transcriptomes and that significant differences exist in immune cell transcriptomes between women and men and between diabetic and non-diabetic subjects.

Support by the NIH P01 HL 136275
Regulatory T cells in the fibrotic milieu: ontological characterization from initiation through remodeling in a murine model of spontaneous pulmonary fibrosis
Authors: Murthy Aditi , Rodriguez Luis , Tomer Yaniv , Iyer Swati , Chavez Katrina , Dimopoulos Thalia , Katzen Jeremy , Beers Michael 
Published: August 2023

Abstract
Using exogenous injury models, regulatory T cells (Tregs) have been shown to have both tissue protective (immunosuppressive) as well as deleterious (pro-fibrotic) effects on the lung. The goal of this study was to define the ontogeny of Tregs in a disease relevant preclinical model of spontaneous pulmonary fibrosis (PF). Transgenic Treg reporter and delete mouse lines were generated by crossing the published PF model, IER-SP-CI73T, to Foxp3-GFP or Foxp3-DEREG lines. Tamoxifen induction in IER-SP-CI73T mice resulted in a disease phenotype characterized by 3 phases of disease development corresponding to early initiation (7d), peak inflammation (14–21d) and fibrogenesis (28–42d). During resolution of inflammation and transition to fibrogenesis, we noted an increase in Tregs measured as either expression of CD25hiFoxP3+ or CD4+GFP+T cells at 21–28 days after Sftpc induction in either model. IHC demonstrated FoxP3+ cells localized to perivascular regions. Administration of diphtheria toxin to IER-SP-CI73T/Foxp3-DEREG mice at 17 days resulted in systemic loss of Tregs and increases in morbidity (weight loss), BALF cell counts, and tissue neutrophils accompanied by reduced lung compliance. RNA-seq of bulk isolated GFP+ (Treg) cells from the fibrotic phase (Day 21) identified enhanced proliferation signals. Collectively, the data demonstrate a clear pattern of Treg recruitment coinciding with the transition of inflammation resolution to fibrogenesis and suggest an essential protective role for Tregs through a dampening of underlying inflammation in pulmonary fibrosis.
Supported by NIH 2R01 HL 095993-10
Identified the pathogenic effects of GM-CSF autoantibodies in different diseases
Authors: Lo Yu-Fang , Wang Shang-Yu , Shih Han-Po , Chung Pei-Han , Ku Cheng-Lung 
Published: August 2023

Abstract
Pathogenic GM-CSF autoantibodies are found in over 90% of people with pulmonary alveolar proteinosis (PAP), a rare pulmonary autoimmune disease with surfactant lipoprotein accumulating in alveoli spaces. However, more and more people with GM-CSF autoantibodies have also been identified without PAP phenotype but underlying severe central nervous system (CNS)-involved Cryptococcus gattii or Nocardia spp. infection since 2013, highlighting the pathogenic mechanisms that might differ between individual diseases.
We developed single B cell cloning to isolate GM-CSF monoclonal antibodies from cryptococcosis patients aiming to investigate the pathogenic effects. GM-CSF autoantibodies in cryptococcosis bound GM-CSF through three non-overlapping epitopes, and formed a high-molecular-weight immune complex similar to the research of GM-CSF mAbs in PAP patients. Surprisingly, GM-CSF mAbs isolated from cryptococcosis revealed potentially binding to GM-CSF when the V gene reversed to the germline. GM-CSF autoantibodies underwent somatic hypermutation to enhance their binding ability and neutralizing activities. We analyzed whether the mAbs binding sites interfere with cytokine-specific receptor interaction, and only one epitope showed the receptor blockade. The GM-CSF mAbs from the other two epitopes remained inhibition effects, indicating another neutralizing mechanism independent of interfering receptor binding. The neutralizing pathway and biological impact of GM-CSF autoantibodies from cryptococcosis is still worthy of further investigation. These works might help know the anti-GM-CSF autoantibodies cause different clinical manifestations and find a novel pave for better diagnosis and treatments.
The effects of S100A8/A9 blockade in experimental Myocardial Infarction detected by CITE-seq RNA sequencing
Authors: Vallejo Jenifer , Jakobsson Gabriel , Ljungcrantz Irena , Schiopu Alexandru 
Published: August 2023

Abstract

Background
The alarmin S100A8/A9, is released from neutrophils in response to inflammatory stimuli, but monocytes, and macrophages can also secrete extracellular S100A8/A9. During the acute phase of myocardial infarction (MI), S100A8/A9 is released from the site of the ischemic injury and increases in the coronary and systemic circulation. We have previously shown that S100A8/A9 plays an important role in the inflammatory and reparatory immune responses in MI, and that S100A8/A9 blockade improves cardiac function post-MI.

Methods
In the present study we aimed to understand, on local and systemic level, the influence of S100A8/A9 blockade, by sequencing 30,000 cells by single-cell RNA (scRNA-Seq) and CITE-Seq. MI mice were induced by permanent coronary artery ligation, followed by the S100A8/A9 blocker ABR-238901 or PBS for 3 days. CD45+ cells were isolated from blood, heart, and bone marrow.

Results
Cell populations in blood generally reflected the changes induced by MI in the bone marrow and heart, but we also detected important shifts specific for the MI. ABR-238901 reduced the expression of pro-inflammatory genes and limited inflammatory neutrophil and monocyte sub-populations in blood and heart. In bone marrow the treatment inhibited the expression of genes involved in proliferation and differentiation of hematopoietic stem cells.

Conclusions
S100A8/A9 blockade has potent immunomodulatory effects in MI through inhibition of myelopoiesis and population shifts from pro-inflammatory to reparatory neutrophils, monocytes and macrophages in blood and heart. We have also identified pathogenic sub-populations in the ischemic heart that could be therapeutically targeted to reduce myocardial inflammation and damage.
CCR10 promotes blood pressure elevations and renal damage in a mouse model of hypertension
Authors: Nguyen Bianca A , Chen Ziche , Fehrenbach Daniel J , Zhong Xue , Xiong Na , Madhur Meena , Alexander Matthew R 
Published: August 2023

Abstract
Hypertension is the leading cause of morbidity and mortality worldwide. Emerging evidence suggests that pro-inflammatory immune cells play a central role in hypertension and its associated end-organ damage. Regulatory T cells (Tregs) are immunosuppressive, however their role in hypertension remains unclear. Interestingly, Tregs can be pathogenic in some disease states by limiting angiogenesis. We recently identified a selective decrease in circulating CCR10+ Tregs in hypertensive humans. CCR10 is a chemokine receptor important for recruitment of immune cells, particularly Tregs, to the skin. Prior studies have demonstrated skin microvascular rarefaction in hypertension as a mechanism to raise blood pressure (BP). We hypothesized that CCR10+ Tregs promote hypertension through skin infiltration leading to enhanced microvascular rarefaction. We demonstrate that mice with angiotensin II (Ang II) infusion to induce hypertension have an increased abundance of CCR10+ Tregs in the skin compared to normotensive controls. In addition, mice with CCR10 deficiency exhibit increased CD31+ endothelial cells in the skin after Ang II infusion compared to wild type controls, consistent with reduced cutaneous microvascular rarefaction. Moreover, CCR10-deficient mice have lower Ang II-induced increases in systolic BP and lower levels of albuminuria. Finally, using PrediXcan, we demonstrate that higher genetically predicted levels of CCR10 are associated with increased risk of hypertension in humans. Taken together, our data suggest that CCR10 promotes Ang II-induced BP elevations and renal damage in mice at least in part by promoting Treg recruitment to the skin leading to microvascular rarefaction.
Tunable dynamics of B cell selection in gut germinal centers
Authors: Nowosad Carla R , Mesin Luka , de Castro Tiago Rezende , Wichmann Christopher , Donaldson Gregory , Lockhart Ainsley , Bilate Angelina , Mucida Daniel , Victora Gabriel 
Published: August 2023

Abstract
B lymphocytes are central to maintaining balanced enteric responses through production of immunoglobulins (Igs). A large fraction of Igs are produced in germinal center (GC) responses, which form upon immunization or infection in the majority of secondary lymphoid organs, but are constitutively present in gut-associated lymphoid tissue. However, the ontogeny and antigenic drivers of constitutive gut-associated GCs were poorly understood. Using a multicolor fate-mapping approach with the Confetti fluorescent allele to visualize GC clonal expansions, we observed single-color GCs in the steady state intestine, suggestive of strong selection events. By coupling fate-mapping, gnotobiotics and Ig sequencing, we showed affinity-driven selection occurring in gut-associated GCs in response to members of the microbiome. We observed that these GCs persist even in the absence of microbiota, although their isotype distribution and clonal composition are altered. Furthermore, we identified several prominent public Ig clonotypes in intestinal GCs, whose presence were tuned by microbial diversity.
IgA deficient mice develop a gluten sensitive enteropathy specifically in the ileum
Authors: Ball Ryan A , Mohamed Ahmed , Kubinak Jason 
Published: August 2023

Abstract
Secretory IgA is the most abundant antibody in the intestinal mucosa and functions as the first line of defense against pathogens and micro-organisms in the gut. Selective IgA deficiency is the most common form of antibody deficiency. Clinically, IgA deficient patients are largely asymptomatic, they are however at a higher risk of developing inflammatory conditions like Celiac disease; an SI-specific enteropathy triggered by exposure to dietary gluten. Interestingly, celiac patients are 10–15 times more likely to have an IgA deficiency. Recent studies have shown that IgA−/− mice develop enteropathy specifically in the ileum. We confirmed this phenotype in our IgA−/− mice and then asked the question; are IgA−/− mice sensitive to gluten? To answer this question, we singly housed IgA−/− mice on a gluten free or nutritionally matched gluten rich diet for 4 weeks and quantitatively assessed their small intestine for histopathological changes. We found that IgA−/− mice on a gluten rich diet develop a significant shortening of villi in their ileum compared to mice on a gluten free diet. Next, in order to exacerbate the phenotype, we developed a line of IgA−/− mice which had never been exposed to gluten and After 8 weeks of age, challenged these mice with 10 mg of concentrated gluten or sterile water every other day for 3 weeks. We found that mice challenged with gluten developed significant shortening of their villi compared to the control. We then used high parametric flow cytometry to compare these findings to shifts in the immunological tone of the SI. Results from our experiments indicate that IgA−/− mice will be a useful model for downstream studies on the mechanisms driving enhanced risk for developing gluten sensitivity in IgA-deficient humans.
Premature Treg induction in early life results in FoxP3 instability post-weaning
Authors: Cheifetz Talia Raitt , Greenfield Kara G , Knoop Kathryn A 
Published: August 2023

Abstract
Peripherally-derived RORγt+ regulatory T cells (Tregs) induced in early life are crucial for maintaining oral tolerance later in life, and the loss of these long-lived cells is associated with increased allergic and inflammatory phenotypes in several animal models. We have identified a predominant pathway of luminal antigen delivery that is associated with Treg development. Around weaning, microbial and dietary proteins are delivered to the colonic lamina propria via goblet cell-associated antigen passages (GAPs) and taken up by antigen presenting cells. GAP formation is inhibited by breastmilk-derived epidermal growth factor (EGF) which is highest in maternal milk at parturition and is diminished by weaning. We have previously shown that disruption of this process – via EGF receptor inhibition (EGFRi) day of life (DOL)4–8 or by conditional deletion of EGFR from goblet cells – results in premature antigen delivery. Consequently, this results in an early initial increase in FoxP3 expression in the colon that is unstable and, ultimately, lost by Tregs primed pre-weaning; this suggests that earlier education of T cells is incompatible with regulatory T cell differentiation in early life. EGFRi-treated FoxP3eGFP-Cre-ERT2ROSAlsl-YFP mice, whose FoxP3+ cells were YFP-labeled at DOL21, had a larger number of YFP+ T cells that lost FoxP3 expression than that of control mice, by DOL28. Further, compared to controls, wild-type mice treated with EGFRi DOL4–8 had increased IFNγ, TNFα, and IL-17a-expressing CD4 T cells when challenged with DSS colitis later in life. This suggests that early antigen delivery-associated FoxP3 instability may contribute to an increased propensity toward an inflammatory phenotype later in life.
Regulating the Regulators: determinants of lineage- and tissue-specific Il10 expression in CD4+ T cells
Authors: Hegner Courtney Lynn , Chen Mei Lan , Sundrud Mark S 
Published: August 2023

Abstract
IL-10 is an essential anti-inflammatory cytokine involved in mucosal immune regulation. Whereas many lineages of innate and adaptive immune cells can produce IL-10, a comprehensive understanding of the common, lineage-specific and tissue-specific regulatory mechanisms underlying Il10 transcriptional regulation has remained elusive. Our lab recently identified the constitutive androstane receptor (CAR; encoded by Nr1i3)—a xenobiotic-sensing nuclear receptor (NR) with no previously known function in immune cells—as a selective regulator of Il10 gene expression in small intestinal (SI) type 1 regulatory (Tr1) cells. CAR induction of IL-10 expression in SI Tr1 cells stands in direct contrast with orthogonal mechanisms that underlie Il10 gene regulation in large intestinal (LI) Foxp3+ T regulatory (Treg) cells, and that involve other nuclear receptors, such as vitamin D receptor (VDR). By using a combination of next-generation sequencing techniques (ATAC-seq, CITE-seq, ChIP-seq), I am assessing how, where and in which cell types CAR most prominently regulates Il10 expression in vitro and in vivo. Our results are generating high resolution maps of Il10 transcriptional regulatory networks that are differentially called upon in different cell types and discrete mucosal tissues to achieve the complex and dynamic regulation of Il10 expression that is observed in vivo.
Supported by grants from NIH (RO1 AI143821-03)
Defining the abundance, fate, and function of secondary lymphoid organ resident memory T cells
Authors: O’Flanagan Stephen D , Künzli Marco , Scott Milcah , Gavil Noah Veis , Quarnstrom Clare F , Smith Olivia , Jackson Julia , Vezys Vaiva , Masopust David 
Published: August 2023

Abstract
For sixty years we have understood that lymphocytes recirculate through blood and secondary lymphoid organs (SLO). Recently, it has been observed that SLOs contain resident populations of memory T cells. Here, we show that conventional isolation techniques grossly underestimate the proportion of SLO CD8+ TRM, and resident cells constitute a substantial fraction of regionalized immunity within LNs. We found that SLO TRM are very long-lived in mice and persist for &gt;500 days after a single infection with LCMV Armstrong. Using a variety of infection models, we observed that the location of primary infection biased the density of SLO TRM to specific draining LNs. Moreover, SLO TRM expressed a phenotypic relationship with TRM in specific upstream nonlymphoid tissues, and remarkably, retained durable expression of regional homing markers. Upon reactivation, mesenteric LN derived SLO TRM preferentially homed to the small intestine compared to TCM. Thus, TRM comprise a substantial fraction of LN memory CD8+ T cells, are refractory to isolation, can be remarkably durable, retain tissue-specific homing potential in the event of reactivation, and likely comprise an underappreciated and underestimated contributor to LN immune surveillance and regional anamnestic immune responses.
Supported by fellowship from the University of Minnesota - Department of Microbiology and Immunology Dennis W. Watson Fellowship
Adaptive immunity to ancient retroelements controls the skin tissue threshold of activation
Authors: Wells Alexandria , Lima-Junior Djalma S , Link Verena M , Krishnamurthy Siddarth R , Belkaid Yasmine 
Published: August 2023

Abstract
A symbiotic dialogue between the microbiota and host is essential to promote protective immune responses in the skin. Integrated retroviral elements, or retrotransposons (RTNs), comprise up to 45% of the human genome. We previously found that immune responses to the skin microbiota are dependent on the reactivation and keratinocyte-intrinsic sensing of RTNs. Here, we explored the possibility that RTNs may also represent a source of antigens recognized by the skin adaptive immune system. We first established a model of sterile injury, where topical application of a mild detergent reactivated RTNs, and recruited CD8 T cells to the skin in an RTN-dependent manner. RNAseq analysis of RTN expression revealed Langerhans cells (LCs) have the most abundant RTN expression amongst skin dendritic cells. Our work demonstrated that CD8 T cell responses to sterile injury were entirely dependent on LCs, supporting the idea that LCs could present RTN antigens to CD8 T cells. To identify RTN-specific T cells, we selected peptides that were uniquely expressed in LCs, but not in thymic epithelial cells which mediate negative selection. Several peptides promoted cytokine production from injury-elicited CD8 T cells, confirming the presence of RTN-reactive CD8 T cells in the skin. RNA-seq analysis suggests RTN-specific CD8 T cells may contribute to wound repair and immunoregulation. Thus, mild stress, such as that induced by mild detergent, is sufficient to promote adaptive immunity to defined antigens derived from RTNs. Our work also proposes that homeostatic immunity to ancient retroviruses promotes a defined class of T cells responses aimed at maintaining barrier integrity in response to daily stressors encountered by the skin.
Cancer Research Institute, Irvington Postdoctoral Fellowship
C. difficile infection induces toxin A specific responses
Authors: Maslanka Jeffrey , Denny Joshua E , Alam M D Z , Alameh Mohamad-Gabriel , Zackular Joseph P , Abt Michael C 
Published: August 2023

Abstract
The nosocomial pathogen Clostridioides difficile colonizes the gastrointestinal tract of patients following microbiome disruption and secretes two major virulence factors toxin A (TcdA) and toxin B (TcdB). Approximately 25% of patients infected with C. difficile experience recurrent infection, and the rate of recurrence increases with each subsequent infection. The quality and protective capacity of the adaptive immune response generated following infection is not well defined. Using a mouse model, we saw high IgG and IgA antibody titers in the serum and stool to TcdA following C. difficile infection. Further, to identify toxin specific CD4+ T cells, a peptide library was generated from the amino acid sequence of TcdA and subsequently used to test for peptide reactive T cells. CD4+ T cells from infected mice produced IL-17a following restimulation with TcdA peptides, with the number of peptide reactive CD4+ T cells correlating with TcdA specific antibody titers. Furthermore, cellular responses were confined to the gastrointestinal tract, with expansion of germinal center B cells, T follicular helper cells, and TcdA specific CD4+ T cells in the lamina propria and mesenteric lymph nodes, but not the spleen. Further characterization of the TcdA response led to identification of a major peptide of interest that will aid in future investigation of the adaptive immune response following C. difficile infection.
Supported by grants from NIH (R01 AI158830-01, R21 AI164385)
The emergence of SARS-CoV-2 lineages and associated antibody responses among asymptomatic individuals in a large university community
Authors: Merling Marlena Rae , Mahfooz Najmus , Robinson Richard T 
Published: August 2023

Abstract
SARS-CoV-2 (CoV2) infected, asymptomatic individuals are an important contributor to COVID transmission. CoV2-specific immunoglobulin (Ig)—as generated by the immune system following natural infection or vaccination—has helped limit CoV2 transmission from asymptomatic individuals to more susceptible populations. The emergence of new Omicron lineages with extensive Spike and Nucleocapsid (N) mutations threatens our reliance on natural and vaccine-initiated Ig responses to limit COVID transmission; therefore, it is important to understand the relationships between CoV2 lineage emergence, CoV2-specific Ig levels, and their cross-neutralization capacity in asymptomatic individuals. Here, we describe the relationships between COVID incidence and CoV2 viral load, lineage, and CoV2-specific Ig levels (IgM, IgA, and IgG) in the saliva of asymptomatic individuals between Jan 2021 and May 2022. These data were generated as part of a large university COVID monitoring program and demonstrate that COVID incidence among asymptomatic individuals occurred in waves which mirrored those in surrounding regions, with saliva CoV2 viral loads becoming progressively higher until vaccine requirements were established. Among the unvaccinated, infection with each CoV2 lineage (pre-Omicron) resulted in Spike-specific IgM, IgA, and IgG responses, with Spike-specific IgG increasing significantly post-infection and being more pronounced than N-specific IgG responses. Among the vaccinated, saliva from those with breakthrough Delta infections had Spike-specific IgG levels that were comparable to those who were uninfected; their capacity to inhibit Spike function, however, was diminished relative to those who were uninfected.
The Ohio State University