bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of cellular subpopulations and their gene expression by single-cell RNA sequencing in canine atopic dermatitis
Authors: Drechsler Yvonne , Sparling Brandi Ann Terrance Elize , Moss Nicholas Grimm , Kaur Gagandeep , Hawkins R David 
Published: January 2023

Abstract
Atopic Dermatitis (AD) is the most common, chronic, and inflammatory allergic skin disease worldwide, with a high prevalence both in children and adults, particularly in developed countries. There are limited effective treatments for severe allergic skin diseases available, thus, there is an unmet need of better understanding the molecular mechanisms and cellular populations involved in AD. Since AD in canines closely resembles the disease in humans, they are an attractive animal model for further studies.
Leveraging single-cell RNA sequencing, we identified the cellular composition and shifts in cell populations in canine epidermis of atopic dogs compared to the epidermis from healthy controls. Fibroblasts and keratinocytes represented the largest cell populations, with fibroblasts decreasing in the atopic epidermis. Other populations such as endothelial vascular cells showed differences as well. Shifts in immune cell distribution included changes in subpopulations of dendritic cells and monocytes in the atopic skin. NK and T cells, particularly CD8 T cells were increased. Subclustering revealed specific cellular changes in AD dogs. We found signifiant changes in gene expression in most cell populations, with some genes differentially expressed across cells, while others were expressed in a cell specific manner. We also observed subtle differences between samples from animals with different disease progression, identifying gene expression markers changing with AD severity.
Here we show that single-cell sequencing is a useful tool to define the cellular composition in canine atopic dermatitis, resolving changes in gene expression at the cellular level to advance our understanding of disease development and progression.
Supported by intramural funds from Western University of Health Sciences
Changes of small non-coding RNAs by severe acute respiratory syndrome coronavirus 2 infection
Authors: Wu Wenzhe , Zhang Ke , Choi Eunjin , Buck Darby , Wang Binbin , Adam Awadalkareem , Huang Gengming , Lee Inhan , Dong Jianli , Wang Tian , Bao Xiaoyong 
Published: January 2023

Abstract
The ongoing pandemic of coronavirus disease 2019 (COVID-19), which results from the rapid spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a significant global public health threat. In the context of viral infections, sncRNAs have been shown to regulate the host responses, viral replication, and host-virus interaction. Compared with other subfamilies of sncRNAs, including microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs), tRNA-derived RNA fragments (tRFs) are relatively new and emerge as a significant regulator of host-virus interactions. Using T4 PNK-RNA-seq, a modified next-generation sequencing (NGS), we found that nasopharyngeal swabs (NPS) samples from SARS-CoV-2 positive and negative subjects show a significant difference in sncRNA profiles. There are about 166 impacted sncRNAs. Among them, tRFs are the most significantly affected and almost all impacted tRFs are derived from the 5′-end of tRNAs (tRF5). Using qRT-PCR, we validated that tRF5s derived from tRNA GluCTC (tRF5-GluCTC), LysCTT (tRF5-LysCTT), ValCAC (tRF5-ValCAC), CysGCA (tRF5-CysGCA) and GlnCTG (tRF5-GlnCTG) are enhanced in NPS samples of SARS-CoV2 patients and SARS-CoV2-infected airway epithelial cells. In addition to host-derived ncRNAs, we also identified several sncRNAs derived from the virus (svRNAs), among which a svRNA derived from CoV2 genomic site 346 to 382 (sv-CoV2-346) has the highest expression. The induction of both tRFs and sv-CoV2-346 has not been reported previously, as the lack of the 3′-OH ends of these sncRNAs prevents them to be detected by routine NGS. In summary, our studies demonstrated the involvement of tRFs in COVID-19 and revealed new CoV2 svRNAs
Maternal and Neonatal Antibody And T Cell Responses To SARS-CoV-2 Following Maternal Infection And/Or Vaccination
Authors: Trinh Ivy , Eyoh Enwono , Murrell Amelie , Desai Srushti , Lauritsen Cody , Rambaran Saraswatie , Stone Addison , Agbodji Ayitevi , Chandra Sruti , Elliott Debra , Smira Ashley , Dugas Courtney , Satou Ryosuke , Pridjian Gabriella , Longo Sherri , Robinson James , Piedimonte Giovanni , Gunn Bronwyn M , Norton Elizabeth B 
Published: January 2023

Abstract
Pregnant women and neonates are at risk for adverse SARS CoV-2 infection outcomes, but few studies have evaluated this population for adaptive immunity. Here, we utilized samples collected from pregnant women 18 years or older reporting two or more respiratory symptoms. Information about trimester of COVID positive test or history of vaccination was also collected. Maternal blood (MB) samples were collected at prenatal clinic visits, or at delivery together with the fetal cord blood (CB)(n=70 dyads). Groups were selected based on trimester of infection, vaccination only, or no history of vaccination or infection (n=9–24) and compared with banked samples from a non-pregnant, age-matched woman from the same time period (n=7–12). Data shows IgG transfer to baby irrespective of trimester of infection (n=9–24 per group). Highest levels of antibodies were observed with vaccinated, uninfected women. Functional antibodies are transferred from mother to fetus following infection and vaccination. CD4 and CD8 T-cell activation and cytokine secretion were detected in maternal PBMCs, with highly variable expression between subjects. In at least one dyad with a PCR-confirmed infection during second trimester, both maternal and cord blood samples had low level expression of anti-S, N, RBD antibodies at delivery and the cord blood mononuclear cells showed CD4 T cell activation (CD134+) and cytokine secretion (IL-2, IL-6, TNFalpha) to spike antigens. These results indicate the unusual immunity to SARS CoV-2 infection during pregnancy and suggest at least one case of a neonate with anti-viral cellular immunity. Ongoing analyses and surveillance for perinatal outcomes may reveal how these immune responses impact infant respiratory outcomes.
Multi-functional HCV-specific CD4+ T cells associated with viral control during the postpartum period express Th1- and Tfh-biasing transcription factors
Authors: Phelps Christopher , Walker Christopher M , Honegger Jonathan R 
Published: January 2023

Abstract
Chronic hepatitis C virus (HCV) infection is characterized by dysfunctional HCV-specific CD8+ T cells, rare CD4+ T responses, and stable high-level viremia. Recovered CD4+ T cell function and unusual declines in viremia have been observed in some women after childbirth. Whether recovered CD4+ T cells are of lineages to help B cells or CD8 T cells is unknown. Preliminary studies suggest both may be true. In 7 women with postpartum viral suppression (&gt;= 1 log10 by 3 months postpartum, “controllers”), and 7 women with more stable viral levels, “non-controllers”, circulating HCV-tetramer+ (tet+) CD4+ T cells expressed chemokine receptors associated with two predominate populations, Th1-biased Tfh (cTfh1) cells and Th1 cells – with a higher cTfh1/Th1 ratio linked to viral control. Here we assessed HCV-specific cTfh1 and Th1 functional responses by combined surface chemokine receptor and intracellular cytokine staining (ICS) after HCV peptide stimulation, and we also assessed expression of lineage-defining transcription factors on HCV-tet+ cells. HCV-specific cytokine+ cells were predominantly cTfh1 or Th1 populations, and multi-functionality correlated with viral control. HCV-tet+ CD4+ T cell Tbet and BCL6 expression levels did not differ by degree of viral control, but both were enhanced in tet+ cTfh1 cells relative to bulk cTfh1 cells, and tet+ Th1 cells expressed significantly more BCL6 than bulk Th1 cells. Together, these data point to a postpartum CD4+ T cell recovery driven by transcription factors favoring cTfh1/Th1-biased phenotypes. Understanding how these cells interact with CD8+ T cells and B cell will be vital for understanding this unique instance of natural control of a chronic viral infection.
Supported by a grant from the NIH (R01 AI096882).
Evidence for metabolic disturbances in the pathogenesis of immune-mediated disease in SAMP1/YitFcs Mice
Authors: Campillo-Gimenez Laure , Drygiannakis Ioannis , Yazgan Ayca Sayi , Rivera-Nieves Jesus , Vera David , Ernst Peter B 
Published: January 2023

Abstract

Background
Inflammatory bowel diseases (IBD), including ulcerative colitis (UC) and Crohn’s disease (CD), affect ~1% of the people in the United States. SAMP1/YitFcs mice are a model of CD with terminal ileitis which is rare in other animal models of IBD. Switch of cell energy metabolism towards aerobic glycolysis is a hallmark of inflammation and has been implicated in immune-mediated diseases. Thus, we sought to determine how energy metabolism is altered in the SAMP mice.

Methods
Glucose metabolism in vivo was determined by 18F-fluorodeoxyglucose (FDG) positron emission tomography (PET). Tissue taking up the 18F-FDG were collected for histology. Metabolic phenotype of activated B and CD4+ T lymphocytes isolated from mesenteric lymph nodes of control and SAMP mice was evaluated by extracellular flux analysis (SeaHorse). To relate the SAMP model to human disease, normal and inflamed ileum from mice and humans were assayed by RNAseq focusing on metabolism-related genes.

Results
PET scans showed a varying tissue distribution of 18F-FDG uptake in SAMP mice, including ileum, salivary glands and kidneys which all had histological evidence of inflammation. Compared to control, both SAMP B and T cells displayed an increase in glycolysis and oxidative phosphorylation (OXPHOS) rates which is supported by an overall increase in genes related to glucose metabolism, TCA cycle, OXPHOS and fatty acid oxidation in the ileum.

Conclusion
SAMP mice have a multi-organ immune-mediated disease relying on an increase in cell energy metabolism. Therefore, targeting aerobic glucose metabolism to limit inflammation emerges as a new strategy for CD treatment.
Correlation between acute and chronic inflammatory states, a case control study
Authors: Mahesh Seema , Mallappa Mahesh , Vacaras Vitalie , Shah Viraj , Belagaje Amritha , Dhamodar Pooja , Serzhantova Elena , Kubasheva Nadezhda , Chabanov Dmitriy , Tsintzas Dionysios , Jaggi Latika , Jaggi Atul , Vithoulkas George 
Published: January 2023

Abstract

Objective
Suppression of efficient acute inflammation may be one of the mechanisms behind the onset of chronic low-grade inflammation. Efficient acute inflammatory response to pathogenic stimulus may not be possible in the presence of chronic inflammation. We investigated if a correlation exists between chronic and efficient acute inflammation.

Methods

Design
Case control study.

Setting
Homeopathic medical practices in 4 countries Patients with definite improvement in chronic inflammatory conditions with at least 6 months of follow up were selected as cases. Age matched controls involved those who did not improve.

Event of interest
Occurrence of common acute infectious diseases with fever during the follow up period.

Statistical analysis
Odds Ratio of improvement in the chronic condition, with development of acute infectious diseases with fever was calculated. Graphs were plotted to study this correlation in individual cases.

Results
20 cases and 20 age matched controls were selected. Average age was 28.4 and 27.9 years respectively. 18/20 cases and 4/20 controls developed common infectious diseases with fever during the follow up period. Odds Ratio of the chronic condition improving, with development of acute infectious diseases with fever was 36 (95 %, CI: 5.7973 to 223.5513), z statistic: 3.846 and significance level was p = 0.0001. Graphs of individual cases showed distinct patterns confirming the same.

Conclusions
In this case control study, appearance of common acute infectious diseases with fever during treatment was strongly associated with improvement in the chronic inflammatory conditions. Larger studies are needed to further establish the correlation.
Supported by Nil
COVID-19 patients are characterized by increased levels of immune cell membrane-bound and soluble CD48
Authors: Pahima Hadas Tamar , Zaffran Ilan , Jarjoui Amir , Orenbuch-Harroch Efrat , Gaur Pratibha , Puxeddu Ilaria , Zinner Carl , Ben-Chetrit Eli , Tzankov Alexandar , Levi-Schaffer Francesca 
Published: January 2023

Abstract
COVID-19 is a respiratory-centered systemic disorder caused by the severe acute respiratory syndrome (SARS-CoV-2) virus. The disease can progress into a severe form causing acute lung injury (ALI), mainly diffuse alveolar damage (DAD) with thromboinflammation, immunopathology, and cytokine storm. CD48 is an activating/co-activating receptor expressed on most hematopoietic cells, existing as both membrane-bound (mCD48) and soluble (sCD48) forms. Its high-affinity ligand is 2B4 (CD244). We previously found the mCD48 and sCD48 levels are dysregulated in asthma patients regardless of their atopic status. Therefore, we reasoned that CD48 could be dysregulated in COVID-19 ALI too.
CD48 expression was evaluated in tissue sections collected at autopsies of lethal COVID-19 at the first wave (patients not being exposed to high dose dexamethasone), and on peripheral blood leukocytes and in sera of COVID-19 patients by gene expression profiling (autoimmune panel pf HTG), IHC, flow-cytometry and ELISA. Lung tissue of COVID-19 patients showed significantly increased CD48 mRNA expression and infiltration of CD48+ lymphocytes in comparison to other inflammatory conditions (influenza-virus and pneumococcal pneumonia, and non-COVID-19 DAD). In the peripheral blood mCD48 was significantly increased on all the evaluated cells and, additionally, sCD48 levels were significantly higher in COVID-19 patients independent of disease severity. Positive correlation was found between mCD48 levels on monocytes and sCD48 release.
Since both mCD48 and sCD48 are significantly increased in COVID-19, a specific a role for CD48 in COVID-19 can be assumed, suggesting it as a potential target for therapy.
Supported by Israel Science Foundation Grant no. 3933/19 the Aimwell Charitable Trust (UK), Emalie Gutterman Memorial Endowed Fund for COPD related research (USA)
Circulating Monocytes Co-expressing Surface ACE2 and TMPRSS2 upon TLR4/7/8 Activation Are Susceptible to SARS-CoV-2 Infection
Authors: Yao Yi , Subedi Kalpana , Sexton Jonathan Z , Liu Tingting , Khalasawi Namir , Pretto Carla , Wotring Jesse W , Wang Jie , Yin Congcong , Jiang Aimin , Li Jia , Zhou Li , McKinnon John , Mi Qing-Sheng 
Published: January 2023

Abstract
Angiotensin-converting enzyme 2 (ACE2) receptor is required for SARS-CoV-2 entry into human cells. However, emerging evidence shows SARS-CoV-2 infected lung monocytes/macrophages from COVID-19 patients barely express ACE2 mRNA, raising a question how SARS-CoV-2 penetrates macrophages. It’s also under debating whether the peripheral blood cells (HPBCs) can be infected by SARS-CoV-2 that may facilitate viral spread from circulation to other organs besides lung. Herein we demonstrate that resting primary HPBCs harbor abundant cytoplasmic ACE2, regardless of COVID-19 status, and that surface translocation is necessary for viral infection. Upon ex vivo TLR4/7/8 stimulation of HPBCs, ACE2 translocated to the cell surface independent of ACE2 transcription, and this translocation was blocked by an endosomal trafficking inhibitor, suggesting the putative source as ACE2-containing exosomes. However, only stimulated monocytes concurrently expressing ACE2 and cell surface transmembrane serine protease type 2 (TMPRSS2) were efficiently infected by SARS-CoV-2, which was significantly mitigated by remdesivir. Furthermore, ACE2 surface translocation in peripheral myeloid cells from patients with severe COVID-19 correlated with their proinflammatory cytokine production. Collectively, TLR4/7/8-induced ACE2 translocation with TMPRSS2 expression is indispensable for SARS-CoV-2 infection of circulating monocytes. Our work not only provides a new mechanism for the pathogenesis of SARS-CoV-2 and a potential path for its systemic infection, but also unveils a prospective therapeutic strategy by targeting ACE2 trafficking for preventing monocyte/macrophage infection.
This study is partially supported by National Institutes of Health grants R61AR076803, R01AR063611, R01AI119041, and R01AR069681 (Q-S. M.), R01AR072046 (L.Z.), R01DK120623 (J.Z.S.), Henry Ford Immunology Program grants (T71016, Q-S. M.; T71017, L. Z.), and funding for the U-M Center for Drug Repurposing - NCATS CTSA UL1TR002240 (J.Z.S.).
Osteoclast differentiation alters monocyte inflammatory responses to Staphylococcus aureus
Authors: Petronglo Jenna Rose , Eichelberger Kara Rose , Cassat Jim 
Published: January 2023

Abstract
Staphylococcus aureus is the major causative agent of bacterial osteomyelitis, an invasive infection of bone. Osteomyelitis is associated with significant bone destruction, bone-resorbing osteoclasts have been implicated in this process. Osteoclasts differentiate from monocyte precursors in response to the canonical osteoclastogenic cytokine RANKL, or receptor activator of (NF)-κB ligand. The process of osteoclastogenesis involves significant transcriptional reprogramming, thereby altering inflammatory responses of osteoclasts, relative to inflammatory monocytes or macrophages. In this study, we sought to elucidate mechanisms of infection-associated bone loss by defining how RANKL shapes osteoclast responses to S. aureus secreted virulence factors and pathogen-associated molecular patterns. We found that, whereas RANKL-naïve monocytes produce significant amounts of IL-1β in response to priming with S. aureus supernatants, differentiated osteoclasts do not. Osteoclasts instead undergo enhanced caspase-dependent cell death, relative to RANKL-naïve monocytes, without associated IL-1β release. This cell death occurs in response to virulence factors regulated by the S. aureus accessory gene regulator (Agr) quorum-sensing system. These results suggest that RANKL alters monocyte-lineage inflammatory responses to microbial pathogens, that osteoclasts have enhanced susceptibility to S. aureus cytotoxins. In parallel studies, we also found that S. aureus supernatants promote osteoclast differentiation of RANKL-primed monocytes in a TLR-dependent manner. Collectively, these studies contribute to the mechanistic understanding of dysregulated bone homeostasis and bone loss during infection.
Supported by R01AI161022, R01AI145992, R01AI132560, Burroughs Wellcome Fund and T32AR059039.
Tissue resident lung natural killer (NK) cells demonstrate enhanced responses to IL-15 compared to peripheral populations
Authors: Sholevar Cyrus , Judge Sean J , Nielsen Ryan , Farley Lauren E , Dunai Cordelia , Razmara Aryana M , Cooke David T , Brown Erin G , Rebhun Robert B , Murphy William J , Canter Robert J 
Published: January 2023

Abstract
Tissue resident NK cells with unique phenotype and function have been identified in organs such as the lung and liver. We have shown that inhaled (IH) rhIL-15 can lead to durable clinical responses in dogs with naturally occurring osteosarcoma or melanoma lung metastases, suggesting that lung NK populations can be targeted therapeutically. Thus, we set out to evaluate the phenotype of resting and rhIL-15-stimulated lung NK cells isolated from murine and human lung. C57BL/6 and BALB/c mice were exposed to IH or systemic IL-15 at escalating doses, and NK cells were isolated by negative selection from lungs and spleen of wild type mice for co-culture. In human patients undergoing surgery for malignancy, non-tumor lung tissue was isolated for flow cytometry and ex vivo stimulation with IL-15. Using mouse spleen or human blood as controls, we observed a higher proportion of lung NK cells per live CD45+ cells in baseline mouse and human samples. Lung NK also had higher expression of activation markers CD69 and HLA-DR (human), but lower expression of the inhibitory receptor TIGIT. Ex vivo culture with IL-15 also resulted in greater upregulation of Ki67 on lung NK cells. Compared to systemic delivery of IL-15, IH IL-15 resulted in greater upregulation of Ki67 and lower upregulation of TIGIT in lung NK cells. Subset analysis of CD49a+ lung NK cells showed similar results in both mouse and human models for activation marker and Ki67 expression after IL-15. Taken together, our results suggest that lung NK cells possess a more active baseline phenotype and exhibit preferential stimulation in response to rhIL-15 compared to circulating NK cells. Ultimately, targeting of lung resident NK cells may be a viable therapeutic strategy in patients with lung metastases.
Supported by NIH/ NCI 1R03CA252793 NIH/NCI U01 CA224166-01 NIH/NCI T32 CA251007-01
Epigenetic Remodeling by Vitamin C Potentiates the Differentiation of Mouse and Human Plasma Cells
Authors: Lio Chan-Wang Jerry , Chen Heng-Yi , Almonte-Loya Ana , Lay Fang-Yun , Johnson Eric , Gonzalez-Avalos Edahi , Yin Jieyun , Ma Qin , Wozniak Daniel , Harrison Fiona 
Published: January 2023

Abstract
Ascorbate (vitamin C) is an essential micronutrient in humans. The chronic severe deficiency of ascorbate, termed scurvy, has long been associated with increased susceptibility to infections. How ascorbate affects the immune system at the cellular and molecular levels remained unclear. Here, from a micronutrient screen, we identified ascorbate as a potent enhancer for antibody response by facilitating the IL-21/STAT3-dependent plasma cell differentiation in mouse and human B cells. The effect of ascorbate is unique, as other antioxidants failed to promote plasma cell differentiation. Ascorbate is critical during early B cell activation by poising the cells to plasma cell lineage without affecting the proximal IL-21/STAT3 signaling and the overall transcriptome. Consistent with its role as a cofactor for epigenetic enzymes, ascorbate potentiates plasma cell differentiation by remodeling the epigenome via TET (Ten Eleven Translocation), the enzymes responsible for DNA demethylation by oxidizing 5-methylcytosines into 5-hydroxymethylcytosine (5hmC). Genome-wide 5hmC profiling identified ascorbate responsive elements (EAR) at the Prdm1 locus, including a distal element with a STAT3 motif overlapped with a CpG that was methylated and modified by TET in the presence of ascorbate. The results suggest that an adequate level of VC is required for antibody response and highlight how micronutrients regulate the activity of epigenetic enzymes to regulate gene expression. Our findings imply that epigenetic enzymes can function as sensors to gauge the availability of metabolites and influence cell fate decisions.
This research was funded by LJI/KKR young investigator fund; NIH National Cancer Institute K22 (K22CA241290); startup funds from the Department of Microbial Infection and Immunity and from the Pelotonia Institute of Immuno-oncology at the Ohio State University.