bluuebunny/crossref_metadata_2025_split huggingface dataset:
Longitudinal analysis reveals age-dependent immune responses to SARS-CoV-2 infection in a mouse model
Authors: Qian Wei , Wei Xiaoqin , Mann Barbara J , Sun Jie 
Published: August 2023

Abstract
Aging is a prominent risk factor for COVID-19 disease severity and mortality in humans. To gain insight into the age-associated alterations of host responses, we performed flow cytometry and single-cell RNA sequencing (scRNA-seq) on lungs and bronchoalveolar lavage (BAL) from young and aged wildtype C57BL/6 mice at days 0, 3, 10, and 21 after infection with the mouse-adapted SARS-CoV-2 strain MA10. We revealed that disease severity and infection kinetics were age-related, as reported in humans, with increased morbidity and mortality in aged mice. During the acute phase of infection, aged animals had a higher local inflammatory response than young mice, as evidenced by the rapid accumulation of neutrophils and inflammatory monocytes in the lung parenchyma and BAL. During the post-acute phase of disease, these features further divided, with aged mice displaying prolonged proinflammatory responses, as well as deficits in cellular and humoral responses. Using scRNA-seq, we identified 33 clusters in the lung. Differential gene expression revealed several age-dependent and dynamic changes within various immune, epithelial, and endothelial cell types. Cell-cell interactions following infection are also altered in the lung by aging. Taken together, our findings suggest that advanced age is associated with a prolonged inflammatory state, poorly induced adaptive immune responses, and altered cell-cell interactions following SARS-CoV-2 infection.
SARS-CoV-2 Delta requires human ACE2 but not human TMPRSS2 to infect mice and elicits greater lung injury and adaptive immune response than Omicron in human ACE2 knock-in mice
Authors: Verma Shailendra Kumar , Ana-Sosa-Batiz Fernanda , Shafee Norazizah , Timis Julia , Maule Erin , Miller Robyn , Pinto Paolla D A , Valentine Kristen , Conner Chris , Webb Devid , Jarnagin Kurt , Kim Kenneth , Shresta Sujan 
Published: August 2023

Abstract
SARS-CoV-2 pathogenesis remains poorly understood in large part due to lack of knowledge about the mechanisms of entry and behaviors of SARS-CoV-2 variants in vivo. We generated single and double knock-in (KI) mice expressing human ACE2 (hACE2) and/or human TMPRSS2 (hTMPRSS2) under endogenous promoters in place of murine ACE2 (mACE2) and TMPRSS2 on the C57BL/6 and BALAB/c genetic backgrounds to evaluate Delta vs Omicron BA.1 infection, disease, and immune response. Delta replication was observed in lungs of mice expressing hACE2 but not hTMPRSS2 or mACE2 following intranasal inoculation, and similar levels of Delta replication were observed in lungs of hACE2-KI and hACE2xhTMPRSS2-KI mice. Thus, Delta requires hACE2 but not hTMPRSS2 to infect mice. In contrast, BA.1 established similar levels of replication in lungs of single and double KI mice, demonstrating that BA.1 requires neither hACE2 nor hTMPRSS2 to infect mice. Although no significant differences in viral burden were observed in hACE2-KI mice infected with Delta vs BA.1, Delta-infected hACE2-KI mice exhibited increased histopathologic lung injury and higher SARS-CoV-2-specific CD4+ and CD8+ T cell responses (spleen) and anti-SARS-CoV-2 spike IgG titers (serum). Additionally, hACE2-KI mice on the C57BL/6 background showed more severe lung disease and stronger Th1 response than BALB/c. These results associate the severity of lung disease with the magnitude of Th1-dominant immune responses, and set a foundation for dissecting mechanisms of COVID-19 pathogenesis in hACE2-KI mice representing Th1- vs Th2-dominant genetic backgrounds.
Multi-omic spatial profiling in COVID-19 lung revels temporal evolution of the disease and novel collagen VI biomarker for outcome
Authors: Pugh Matthew R , Fennel Éanna , Leahy Ciara , Ross Aisling M , Reynolds Gary , Perry Tracey , Youd Ester , Leopold Gareth , Taylor Graham S , Murray Paul G 
Published: August 2023

Abstract
Whilst the peripheral immune response to COVID-19 infection is well characterised, less is known about the tissue response in the lungs of affected patients. We conducted a multi-omic investigation in post-mortem lung tissue from fatal COVID-19 infection comprising bulk Quantseq RNA sequencing, spatial transcriptomic profiling on the Nanostring GeoMX, multiplex immunohistochemistry on the Lunaphore COMET and in-situ transcriptomcics with RNAscope. We found the SARS-CoV-2 virus was progressively cleared in more temporally advanced disease. Furthermore, collagen VI was found to be transcriptionally up-regulated by bulk sequencing and within the interstitium on spatial transcriptomics. These findings were supported by multiplex immunohistochemistry at a proteomic level which showed fibrillar deposition of collagen VI in the interstitum. To validate these findings clinically, we looked at blood markers for collagen VI synthesis and degradation by ELISA in a cohort of severe and mildly infected COVID-19 patients. Blood markers of collagen VI synthesis (PRO-C6) was significantly predictive for mortality in hospitalised (p = 0.0065) and intensive care (p = 0.028) COVID-19 patients. Overall, blood PRO-C6 levels, based on increase interstitial lung deposition, could help identify high-risk of patients enabling better treatment stratification. The study also demonstrates the power of post-mortem investigation and spatial profiling in elucidating clinically relevant insights into complex disease phenomena.
Anamnestic expansion of Omicron-reactive CD8+ T cells after booster SARS-CoV-2 mRNA vaccination across different immunocompromised states
Authors: Müller Thomas R , Sekine Takuya , Trubach Darya , Niessl Julia , Olofsson Anna , Gao Yu , Cai Curtis , Nowak Piotr , Blennow Ola , Hansson Lotta , Mielke Stephan , Bergman Peter , Ljunggren Hans-Gustaf , Karlsson Annika C , Saini Sunil K , Aleman Soo , Buggert Marcus 
Published: August 2023

Abstract
Restricted immune responses to SARS-CoV-2 mRNA vaccination have been observed frequently in individuals suffering from various immunodeficiencies. With increased antibody evasion properties of rising Omicron subvariants, there is a need to assess if other components of adaptive immunity generate resilient responses against SARS-CoV-2 across immunodeficient states. Here we assessed T cell responses of n=279 individuals covering five different immunodeficiencies and healthy controls before and after booster vaccination and - in a subset of patients - additional Omicron infection. We observed significantly increased Omicron-reactive T cell responses upon booster vaccination, particularly in initial poor responders, across all patient groups. Overall T cell composition shifted towards an increased CD8/CD4-ratio, which was accompanied by a more pronounced cytotoxic profile. Moreover, Omicron-reactive T cell responses showed signs of longevity represented by a novel TEMRA subpopulation with stem-cell-like characteristics and increased proliferative capacity. Regardless of underlying immunodeficiency, booster-vaccinated and Omicron-infected individuals were protected against severe disease and exhibited ameliorated and diversified T cell responses directed explicitly against Omicron, despite a solid immunological imprint of multiple wildtype Wuhan-based vaccine doses.
Supported by grants from SciLifeLab National COVID-19 Research Program and financed by the Knut and Alice Wallenberg Foundation, the Swedish Research Council, Nordstjernan AB, Region Stockholm (Clinical research position-, ALF-, and CIMEDgrants). TRM is funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation, project: 496946670).
Identifying Epitope Sites on the Receptor Binding Domain (RBD) of SARS-CoV-2
Authors: Jiang Jiansheng , Boughter Christopher T , Ahmad Javeed , Byod Lisa F , Natarajan Kannan , Meier-Schellersheim Martin , Margulies David H 
Published: August 2023

Abstract
COVID-19 and SARS-CoV-2 variants continue to threaten human health and life worldwide. Thousands of structures related to SARS-CoV-2 have been rapidly determined, either by X-ray crystallography or CryoEM and deposited in the Protein Data Bank (PDB) since 2020. Here, we systematically investigated the structures of 302 antibodies and 78 nanobodies in complex with spike protein or the receptor binding domain (RBD) of SARS-CoV-2. We identified 23 common epitopic sites (ES) on the RBD surface and revealed the vital role of the complementarity-determining Region (CDR) loops in recognizing epitopes. The 23 ES are characterized according to the secondary structure feature and accessible surface area. About 75% of the total surface of RBD areas could access by the elicited antibodies, while the CDR3 loops occupied 50% of the contact surface. The analysis of paratope-epitope (antibody-antigen) interaction based on these epitope sites revealed the features of potent neutralizing the virus and the unique usage of amino acids of antibody. The clustering analysis of the antibody biophysical properties and surface area availabilities on the RBD found many binding motifs. Remarkably, most variants of concern (VOC) escape mutations, including Omicron occur within these 23 ES. This analysis not only explains the differential ability of antibodies to recognize epitope sites on the RBD surface but also offers predictive guidelines for understanding the role that accumulated SARS mutations might play in escape from antibodies elicited by immunogens. This structural characterization of the epitope-paratope interactions provides insights for structure-based vaccine design and therapeutic strategies and drugs against the future virus.
Inflammatory and immune response signatures associated with COVID-19 severity
Authors: Gibson David S , McLaughlin Joseph , McDaid Darren , Lynch Seodhna , Okane Maurice , Kelly Martin , Bhavsar Manav , McGilligan Victoria , Shukla Priyank , Zhang Shu-Dong , Murray Elaine , Rai Taranjit Singh , Walsh Colum , Bjourson Anthony J 
Published: August 2023

Abstract
Severe COVID-19 is characterised by an overactive pro-inflammatory response of the immune system which is associated with new persistent symptoms. Differences in the persistence of symptoms, plasma inflammatory proteins and antibodies between hospitalised and non-hospitalised cases were investigated in the current study.
n=120 participants were recruited with informed consent, of whom n=60 were hospitalised with severe disease. Blood samples and detailed symptom data were collected 3 months after a positive PCR test for SARS-CoV-2. Plasma samples were analysed by OLINK Explore 384 inflammation panel and ACE2 neutralisation and IgG assays. R software was used to identify statistically significant differences in protein concentration in hospitalised cases, relative to non-hospitalised cases. Differences in anti-SARS-CoV-2 IgG antibody concentration, ACE2 neutralisation and symptoms were also analysed between hospitalisation subgroups.
14 proteins including angiopoietin-like protein 2 and C-X-C motif chemokine 17 were significantly elevated (by greater than +/− 0.20 log2 fold change; p &lt; 0.05) at 3 months in the hospitalised study group, relative to non-hospitalised cases. The concentrations of BA.2 and BA.3 specific anti-SARS-CoV-2 IgG and spike receptor binding domain neutralising antibodies were more frequently detected in non-hospitalised cases. The hospitalised cohort more frequently reported persistence of muscle pain, headache, fatigue and shortness of breath.
Characteristic changes in the plasma proteome and symptom clusters that persist 3 months after infection have been observed in hospitalised COVID-19 cases. This data could help inform clinical care requirements for longer term COVID-19 recovery.
Supported by grants from UKRI, SFI and HSC R&D Office
RORα plays an important role in generation and maintenance of memory B cells
Authors: Xu Yijiang , Moroney Justin , Zhou Yulai , Zan Hong , Casali Paolo 
Published: August 2023

Abstract
Memory B cells (MBCs) are antigen-specific and long-lived. Upon reactivation, they can differentiate into plasma cells to secrete large amounts of high-affinity mostly class-switched antibodies. Prompted by our integrative analysis of the human MBC transcriptome and chromatin landscape which redundantly identified the transcriptional factor RORα as central to the identity of human class-switched (sw)MBCs, we investigated the contribution of RORα to the generation and maintenance of MBCs. We found that RORα is selectively expressed at a high level in both human and mouse swMBCs. We then constructed genetically modified AicdacreRorafl/fl mice, in which RORα is specifically deleted in activated B cells undergoing class switching. Upon immunization with NP-CGG, AicdacreRorafl/fl mice significantly reduced the generation of NP-specific swMBCs as part of a primary response otherwise without perturbation of germinal center formation, class-switch DNA recombination, somatic hypermutation or plasma cell differentiation, but leading to a defective anamnestic anti-NP-antibody response. To define the role of RORα in MBC maintenance, we generated tamoxifen-inducible B cell RORα conditional knockout CD19cre/ERT2Rorafl/fl mice, in which RORα could be ablated in swMBCs already generated in response to immunization with NP-CGG. RORα ablation in swMBCs led to loss of swMBCs and the anamnestic anti-NP-response. Thus, B cell RORα plays an important role in not only the generation but also the maintenance of swMBCs. Further mechanistic insight in swMBC generation and maintenance will be provided by Cut&Tag and RNA-Seq experiments to identify sites of RORα enrichment across the genome and transcriptional targets of RORα in swMBCs.
Supported by NIH grants AI 079705, AI 105813, AI 167416 and LRA grant 641363 to PC.
The Ikaros zinc finger transcription factor Eos promotes TH2 differentiation and function by propagating IL-2/STAT5 signaling
Authors: Tuazon Jasmine , Read Kaitlin , Sreekumar Bharath , Yaeger Michael , Varikuti Sanjay , Jones Devin , Warren Robert , Powell Michael , Rasheed Mustafa , Duncan Elizabeth , Childs Lauren , Gowdy Kymberly , Oestreich Kenneth 
Published: August 2023

Abstract
The Ikaros zinc finger transcription factor Eos has largely been associated with chromatin regulation promoting immunosuppressive regulatory T cells. However, Eos’ role in the differentiation and function of pro-inflammatory T cells has remained unclear. Surprisingly, our work reveals that Eos is a positive regulator of CD4+ T helper 2 (TH2) cells—effector T cells that participate in anti-helminthic immunity but are also implicated in inducing allergic asthma. Using in vitro-generated TH2 cells and an in vivo allergic asthma mouse model, we found that Eos-deficient T cells had reduced gene and protein expression of critical TH2 transcription factors (including the lineage-defining transcription factor Gata3), effector cytokines, and differentiation receptors. Among the various TH2-polarizing pathways, the IL-2/STAT5 axis and its downstream TH2 gene targets emerged as one of the most significantly downregulated networks in Eos deficiency. Using in vitro-generated TH2 cells and overexpression of Eos zinc-finger-domain mutants, we discovered that Eos forms a novel complex with and promotes the tyrosine-phosphorylated activation of STAT5. Additionally, we showed that components of the IL-2/STAT5 pathway participate in a feed-forward loop to promote Eos expression in TH2 cells, further supporting Eos’ regulatory connection with the IL-2/STAT5 axis. Together, these data define a novel mechanism whereby Eos mediates IL-2/STAT5 activity to facilitate TH2 differentiation. This work is significant, as its findings reframe our understanding of Eos’ role in T cell differentiation.
K.J.O. is supported by a grant from The National Institutes of Health (NIH) AI134972, as well as from The Ohio State University College of Medicine and The Ohio State University Comprehensive Cancer Center. J.A.T. is supported by funding through the Susan Huntington Dean’s Distinguished University Fellowship and the NIH T32 “Interdisciplinary Program in Microbe-Host Biology” pre-doctoral fellowship administered through the OSU Infectious Diseases Institute and OSU Department of Microbial Infection and Immunity. K.M.G. is supported by NIH grant 1R01ES028829-01A1. L.M.C. and K.J.O. were supported in part by the Jeffress Trust Awards Program in Interdisciplinary Research. K.A.R. is supported by funding through The Ohio State University College of Medicine Advancing Research in Infection and Immunity Fellowship Program.
Exposure of autoimmune uveitis-prone germ-free mice to commensal microbiota promotes development of ocular inflammation
Authors: Murphy Caitlin Elizabeth , Horai Reiko , Zhang Amy , Jittayasothorn Yingyos , Nagarajan Vijayaraj , Caspi Rachel R 
Published: August 2023

Abstract
Autoimmune uveitis is a group of intraocular inflammatory diseases driven by retina-specific T cells that target the neuroretina and is one of the leading causes of blindness. Using a spontaneous mouse model of autoimmune uveitis (R161H), in which CD4 T cells express a transgenic retina-specific T cell receptor, we have shown that gut commensal microbiota are involved in activating retina-specific T cells and promoting uveitis. To study how a germ-free (GF) host responds to de novo microbiota exposure, R161H TCRa−/− mice, rederived into GF conditions and developing much milder disease than their SPF counterparts, were cohoused with SPF mice for 4 wks (exGF). Fecal samples were collected weekly to examine changes in the gut microbiome by 16S amplicon sequencing. Disease progression was monitored twice weekly by fundus examination. At the endpoint, eyes were collected for histopathology, and T cells from lymph nodes, eyes, and intestinal lamina propria were analyzed by flow cytometry and RNAseq for immunophenotype and gene expression.
Exposure to commensal microbiota strongly promoted disease development. After 2 wks of cohousing, exGF disease scores reached the severity of age-matched SPF mice and were significantly higher than those of control GF mice. Flow cytometry analyses revealed an increased percentage of CD4 T cells expressing the proinflammatory cytokines IL-17A and IFN-g in exGF mice. 16S analyses showed that by 1 wk of cohousing exGF mice had acquired gut microbiota of SPF mice, which we hypothesize to include microbes affecting disease outcomes. RNAseq data will provide insights into phenotypic differences among retina-specific T cells in different tissues and may uncover novel pathways involved in uveitis development.
Gut microbiome-derived isoflavone metabolites may ameliorate experimental autoimmune encephalomyelitis (EAE) through estrogen receptor signaling in CD8 T-cells
Authors: Peterson Stephanie R , Jensen Samantha , Mangalam Ashutosh K 
Published: August 2023

Abstract
Multiple sclerosis (MS) is an autoimmune demyelinating disease of the CNS which may be influenced by diet- and gut bacteria-produced metabolites. We have shown that phytoestrogen-metabolizing bacteria are reduced in MS patients compared to healthy individuals. The importance of phytoestrogen-metabolizing bacteria was validated in EAE, an animal model of MS, where lack of isoflavones (a type of phytoestrogen) in the diet and/or lack of phytoestrogen-metabolizing bacteria lead to increased disease severity. However, the cellular and molecular pathways through which isoflavones/gut microbiota modulate EAE is unknown. Cellular analysis of the gut and periphery showed that isoflavone-fed mice have an increased number of CD8 T-cell in the colon compared to mice on an isoflavone-free diet. Moreover, CD8 T-cell knockout mice lose isoflavone-mediated disease protection, suggesting an important role of CD8 T-cells in this process. Due to the structural similarity between isoflavone metabolites and endogenous estrogen, we hypothesize that isoflavone metabolites may induce regulatory CD8 T-cells via engagement of estrogen receptors (ERs). Flow cytometric analysis of colonic CD8 T-cells showed that isoflavone-fed mice had higher expression of both ERα and ERβ and produced lower levels of IFNγ, perforin, and IL10. We are utilizing conditional KO mice lacking ERα or ERβ exclusively in CD8 cells to determine the importance of ERs in the generation of diet-induced CD8 T-cells. In summary, our data suggest that bacterial metabolism of isoflavones may lead to EAE disease suppression through immunomodulation of CD8 T-cells via estrogen receptor signaling.
Supported by grants from NIH (1R01AI137075-01) and VA (1I01CX002212)
Comparison of the effect of autoclaved and non-autoclaved soil exposure on mouse immune system
Authors: Gonzalez-Rodriguez Martin Ignacio , Kummola Lura , Salomaa Tanja , Nurminen Noora , Hiihtola Lotta , Marnila Pertti , Laitinen Olli , Sinkkonen Aki , Hyöty Heikki , Junttila Ilkka 
Published: August 2023

Abstract
The biodiversity hypothesis suggests that decreased interaction with microbes can lead to an imbalance in the human microbiota (referred to as dysbiosis), which in turn will contribute to the development of immune-mediated diseases including asthma, allergies, and autoimmune diseases such as type 1 diabetes. We have previously utilised a novel approach of bringing humans and mice into contact with microbially rich plant- and soil-based material. In humans, exposure to this material increased commensal microbial diversity in daycare children which also linked to higher levels of anti-inflammatory cytokines TGF-b and IL-10 in plasma. Here, we compared the effects of autoclaved and non-autoclaved, fresh soil powder on the mouse immune system, to understand if soil-derived material contains molecular structures that convey the immunoregulatory signals. These effects were evaluated phenotyping immune populations by flow cytometry, assessing cytokine profiles in serums and microbiome diversity by genetic sequencing. Our results indicate that exposure to non-autoclaved soil did not influence the health of mice but was associated with elevated serum IFN-g expression, and reduction of GATA-3 and Foxp3 expression in mLNs. The observed immunological effects warrant further studies with autoclaved and non-autoclaved soil exposure in immune-related diseases, such as allergy and inflammatory bowel disease models in mice.
Academy of Finland, Tampere Tuberculosis Foundation, State Research Funding (for Fimlab Laboratories), Finnish Medical foundation and Northern Finland Laboratory Centre (NordLab).