bluuebunny/crossref_metadata_2025_split huggingface dataset:
In vitro infection of human lung tissue with SARS-CoV-2: Heterogeneity in host defense and therapeutic response
Authors: Schaller Matthew , Sharma Yamini , Dupee Zadia , Nguyen Duy , Uruena Juan , Smolchek Ryan , Machuca Tiago , Sawyer W. Gregory , Mehrad Borna 
Published: February 2023

Abstract
Cell lines are the mainstay in understanding the biology of COVID-19 infection, but do not recapitulate many of the complexities of human infection. The use of human lung tissue is one solution for the study of such novel respiratory pathogens. We hypothesized that a cryopreserved bank of human lung tissue allows for the in vitro study of the inter-individual heterogeneity of host response to SARS-CoV-2 infection, thus providing a bridge between studies with cell lines and studies in animal models. We generated a cryobank of tissues from 16 donors, most of whom had risk factors for severe illness from COVID-19. Cryopreserved tissues preserved 90% of cell viability and contained heterogeneous populations of metabolically active epithelial, endothelial, and immune cell subsets of the human lung. Samples were readily infectible with HCoV-OC43 and SARS-CoV-2 coronavirus strains, and demonstrated comparable susceptibility to infection. In contrast, we observed a marked donor-dependent heterogeneity in the expression of IL-6, CXCL8 and IFNβ in response to SARS-CoV-2 infection. Treatment of tissues with dexamethasone and the experimental drug, N-hydroxycytidine, suppressed viral growth in all samples, whereas chloroquine and remdesivir had no detectable effect. Metformin and sirolimus, molecules with predicted antiviral activity, suppressed viral replication in tissues from a subset of donors. In summary, we developed a novel system for the in vitro study of human SARS-CoV-2 infection using primary human lung tissue from a library of donor tissues. This model may be useful for drug screening and for understanding basic mechanisms of COVID-19 pathogenesis.
SARS-CoV-2 infection drives endothelial dysfunction indirectly through hypoxia and increased pro-inflammatory cytokine production
Authors: Won Taejoon , Wood Megan K , Hughes David M , Talor Monica V , Johns Roger A , Gilotra Nisha A , Pekosz Andrew S , Hooper Jody E , Cihakova Daniela 
Published: February 2023

Abstract
In the Covid-19 patients, vascular thrombosis is observed in the heart, lung, and other organs, leading to multiorgan morbidity and mortality. We obtained heart and lung tissues from autopsies of the patients who died from Covid-19 or unrelated causes as a control. We found that endothelial cells of the hearts and lungs were in dysfunctional state during Covid-19. Cardiac and pulmonary endothelial cells in the Covid-19 group showed decreased level of thrombomodulin, an anticoagulant, and increased level of von Willebrand factor, a procoagulant, compared to non-Covid-19 control. Endothelial cells in the Covid-19 autopsy hearts and lungs also exhibited reduced ICAM-1, VCAM-1, and E-selectin expression. Most of the hearts from the Covid-19 autopsies tested negative for SARS-CoV-2 genome, while all the lungs tested positive. Human coronary artery endothelial cell (HCAEC) in vitro culture was not infected by SARS-CoV-2, showing no dysfunctional phenotype. In the HCAEC culture and in vivo mouse experiments, hypoxia and pro-inflammatory cytokine treatment caused endothelial cell dysfunction including thrombomodulin downregulation similar to what we observed in Covid-19 autopsy tissues. Collectively, endothelial cell dysfunction associated with thrombus formation in Covid-19 is not caused by direct infection with SARS-CoV-2, but it can be induced by pathogenic microenvironments such as hypoxia and increased pro-inflammatory cytokine milieu.
SARS-CoV-2 plasma viral load polarizes the systemic myeloid cell compartment towards an immunosuppressive/regulatory phenotype in severe COVID-19 patients
Authors: Trombetta Amelia Chiara , de Carvalho Farias Guilherme Borlido , Godinho-Santos Ana , Gomes André MC , Rosmaninho Pedro , Conceição Carolina M. , Laia Joel , Santos Diana F. , Neiva Maria Inês Tostão , Almeida Afonso , Sousa Ana E , Fernandes Susana M. 
Published: February 2023

Abstract
Severe COVID-19 determines high death rates and health resources overwhelming. Aim of the present study was to shed light on the immune-pathogenesis of severe COVID-19, evaluating the effects of detectable plasma viral load on circulating myeloid cell phenotype and activation. Adult COVID-19 patients with pneumonia stratified according to the degree of respiratory insufficiency were longitudinally followed. Flow cytometry data of monocytes (Mo) and dendritic cells (DCs) subsets were analysed by supervised and unsupervised approaches, in parallel with SARS-CoV-2 plasma viral load by digital droplet PCR and serum cytokines and chemokines. All patients featured systemic immune-suppressive myeloid cell responses, characterized by a reduction of CD14lowCD16+ Mo and reduced expression of CD80, CD86, and SLAN. All DC subset were significantly reduced and both Mo and DC showed increased expression of CD163, CD204, CD206 and PD-L1 immune-regulatory markers. These changes correlated with an unbalanced cytokine/chemokine response, in which G-CSF, M-CSF, IL-6 increased similarly in all patient groups, while low levels of IFN-alpha, beta, IL-1a and IL-1b persisted, associated with increased concentrations of immune-regulatory cytokines as IL-1RA and IL-10. A significantly greater expansion of a PD-L1 positive M2-like population was seen in classical monocytes from viremic patients. Our data favour the conclusion that massive replication of SARS-CoV-2, leading to release in blood, polarize the systemic myeloid cell compartment response towards a more differentiated immunosuppressive/regulatory phenotype.
Susceptibility to Low Dose Influenza in Mice is Increased by Administration of Ketamine/Xylazine
Authors: Nash Paul B 
Published: February 2023

Abstract
Ketamine/xylazine is an anesthetic commonly used in both research and practice. This study demonstrates a side effect that may have important ramifications. Mice where ketamine/xylazine was used compared to mice not administered the anesthetic were more susceptible to illness caused by administration of low pathogenic preparations of influenza strain A/Puerto Rico/8/34 (PR8). When using one lot of virus, severity of illness as measured by weight loss was increased dramatically by the use of the anesthetic. A slightly more pathogenic lot of virus in other experiments showed that mice with no anesthetic had very mild if any signs of disease, while those with anesthetic succumbed to the illness. In weight loss experiments, mice were affected by the anesthetic even if they were allowed to wake up before inoculation with virus, showing that it was exposure to the drugs that caused the effect, not simply them being asleep. The asleep mice however did recover more slowly from the infection. These results suggest that anesthesia with ketamine/xylazine for treatments may increase the likelihood of post-treatment illness. Likewise experimental results could be affected by using this drug combination such that the immune responses analyzed could be suppressed or the diseases investigated could be more severe.
Rapid activation and expansion of peripheral gammadelta (γδ) T cells in SARS-CoV-2-infected nonhuman primates following aerosol exposure
Authors: Fears Alyssa , Walker Edith , Chirichella Nicole , Slisarenko Nadia , Beddingfield Brandon , Maness Nicholas J , Roy Chad , Rout Namita 
Published: February 2023

Abstract
Infection with SARS-CoV-2, the novel coronavirus responsible for the current COVID-19 pandemic, results in a wide range of pathologies from asymptomatic/mild outcome to fulminant pneumonia and progression to acute respiratory distress syndrome (ARDS). The cellular mechanisms underlying this spectrum of disease remain unknown. We investigated the dynamic changes in frequency and activation status of peripheral innate lymphocyte subsets in two different species of nonhuman primates. Cohorts of Rhesus macaques (n=8) and African Green monkeys (n=8) were infected with SARS-CoV-2 either by small particle or mucosal (IN/IT) route. Flow cytometric analysis of PBMCs revealed a rapid and significant increase in circulating γδ T cell frequencies and activation at d1 postexposure across all animals inoculated by aerosol, which was correlative with peak viral loads in lung lavage and Vδ2 T cell frequencies. Further, elevated GranzymeB expression in both Vδ1 and Vδ2 subsets of γδ T cells was suggestive of increased cytotoxic function in early infection. In contrast, mucosally-infected animals showed little change in circulating γδ T cell frequencies from d1 through d7 post-infection, nor were there remarkable differences in early MAIT and NK cell frequencies. Collectively, these data suggest γδ T cells may be early responders to deep lung SARS-CoV-2 infection and the kinetics and quality of immune response are dependent upon route of exposure despite resulting in similar peak viral loads from infection. Further understanding of γδ T cell functions within the pulmonary compartment during SARS-CoV-2-driven acute inflammation may reveal tractable therapeutic approaches to further mitigate ARDS-like responses in COVID-19 patients.
Phosphatidylserine Receptor Enhancement of SARS-CoV-2 Entry: AXL as a Therapeutic Target for COVID-19
Authors: Bohan Dana , Van Ert Hanora , Rogers Kai , Ruggio Natalie , Chávez Roberth Anthony Rojas , Stokowy Tomasz , Haim Hillel , Gao Boning , Minna John , Micklem David , Lorens James , Maury Wendy 
Published: February 2023

Abstract
Phosphatidylserine (PS) receptors enhance infection of a wide range of enveloped RNA viruses through virion-associated PS binding that is termed apoptotic mimicry. Here we show that this broadly shared uptake mechanism is utilized by SARS-CoV-2. Under ACE2lo conditions, expression of members of the TIM and TAM families of PS receptors synergized with ACE2 to enhance SARS-CoV-2 infection; however, PS receptors alone did not mediate infection. PS receptors enhanced SARS-CoV-2 binding to the surface of cells. While PS receptors did not interact directly with purified SARS-CoV-2 spike, addition of PS liposomes reduced entry of VSV-SARS-CoV-2 spike pseudovirions, providing evidence that PS/PS receptor interactions are mediating the effect. AXL being abundant on airway cell lines, we evaluated small molecule inhibitors of AXL signaling such as bemcentinib for their ability to inhibit SARS-CoV-2 infection. Bemcentinib robustly inhibited virus infection of some lung cell lines that expressed AXL. This inhibition correlated well with inhibitors that block cathepsin activity, consistent with AXL-mediated uptake of SARS-CoV-2 into the endosomal compartment. RNAseq studies in Vero E6 and A549-hACE2 cells demonstrated that bemcentinib reduced SARS-CoV-2 transcripts dramatically. The ability of bemcentinib to decrease coronavirus infection in vivo was assessed using the betacoronavirus mouse hepatitis virus (MHV). Liver titers and virus load of MHV were significantly inhibited by bemcentinib at day 5 of infection. In total, our findings provide evidence that PS receptors facilitate infection of the pandemic coronavirus SARS-CoV-2 and that inhibition of signaling of the PS receptor AXL has therapeutic potential against SARS-CoV-2.
Endogenous retroviruses mediate IFN-independent protection against vaginal HSV-2 infection
Authors: Tokuyama Maria , Jayewickreme Radeesha , Mao Tianyang , Philbrick William , Kong Yong , Dong Huiping , Treger Rebecca S. , Rakib Tasfia , Iwasaki Akiko 
Published: February 2023

Abstract
Endogenous retroviruses (ERVs) are genomic sequences that originated from retroviruses and are present in most eukaryotic genomes. Both beneficial and detrimental functions are attributed to ERVs, but whether ERVs contribute to antiviral immunity is not known. Here we used herpes simplex virus type 2 (HSV-2) infection and found that mice deficient in Toll-like receptor 7 (Tlr7−/−) that have high systemic levels of infectious ERVs are resistant to intravaginal HSV-2 infection compared with wildtype C57BL/6 (B6) mice. We deleted the endogenous ecotropic murine leukemia virus (Emv2) locus on the Tlr7−/− background (Emv2−/−Tlr7−/−) and found that Emv2−/−Tlr7−/− mice are no longer protected against HSV-2. Intravaginal application of purified ERVs prior to HSV-2 infection in both B6 and highly susceptible interferon-alpha receptor-deficient (Ifnar1−/−) mice delayed disease course. We did not observe enhanced type I interferon (IFN-I) signaling in the vaginal tissues from Tlr7−/− mice or B6 mice treated with purified ERVs. Instead, we observed enhanced expression of epithelial tight junction protein, E-cadherin, in the vaginal epithelium of ERV-treated B6 mice. Similar increase in tight junction proteins was observed in Tlr7−/− but not in the Emv2−/−Tlr7−/− mice. Together, our results showed that IFN-independent modulation of the vaginal epithelium by ERVs protects mice against vaginal HSV-2 infection and lowers disease burden.
Using standardized dry antibody panels for flow cytometry in the assessment of altered immune profiles in response to SARS-CoV2 infection
Authors: Lacaille Vashti , Bowers Rita 
Published: February 2023

Abstract
The SARS-CoV-2 virus continues to be a global hazard, further aggravated by the continuous emergence of viral variants. Beside the development of vaccines, the search for immune modulation targets and indicators of disease severity are important objectives of research. A promising approach in order to identify potential crossroads in SARS-CoV2-infection could be to assess proportions, differentiation and functional status of known immune populations. Stimulated by the standardization needs in multi-site research studies, Beckman Coulter has developed several antibody panels for comprehensive profiling of principal human immune populations and commercialized these antibody panels as DURAClone (RUO) kits which are provided off-the-shelf in a dry unitized format, eliminating antibody pipetting and reducing reagent aging. In this technical evaluation, extended versions of these panels with further antibodies of interest added in liquid format have been used to characterize lymphoid and myeloid immune cells in a small number of samples from normal donors and SARS-CoV2-positive donors with either asymptomatic, mild or severe symptoms. Confirming findings in current research of SARS-CoV2, pronounced differences in cellular proportions, differentiation and activation status could be observed in lymphoid and myeloid compartments (not significant in the small number of samples), demonstrating the versatility and usefulness of standardized DURAClone (RUO) antibody panels in hypothesis building and early steps of biomarker discovery.
Malaria infection protects from lupus nephritis at a stage beyond immune complex-induced glomerular inflammation
Authors: Bolland Silvia , Kole Hemanta , Scott Bethany , Qi Chen-Feng , Crompton Peter , Wu Juan , Amo Laura 
Published: February 2023

Abstract
A protective role of malaria infection in SLE was proposed to explain the relatively low prevalence of SLE in West Africa compared to populations of similar genetic background living in the West. Various reports showed an increase of autoantibodies in plasma of West African populations, suggesting that parasite infections were inducing systemic autoreactivity while protecting from tissue pathology. Our own studies from a large longitudinal study in a malaria endemic region confirm the high penetrance of elevated titers of anti-nuclear antibodies in plasma of Plasmodium PCR-positive individuals. In mouse models of malaria, murine Plasmodium infection increases systemic autoreactivity but does not trigger any type of immune-complex induced inflammatory disease. To further investigate the mechanism of kidney protection by Plasmodium, we set up experiments using a malaria parasite in the well characterized SLE mouse model FcγRIIb[KO]. This model system allowed for evaluation of the effect of malaria on autoantibodies, systemic vasculitis and kidney specific pathology, while also assessing the role of parasite-mediated bone marrow alterations, or parasite-produced hemozoin. We found that infection with Plasmodium protects SLE by modifying bone marrow cells and impairing leukocyte infiltration in the kidney, without altering systemic autoimmunity, vasculitis, all independent of the expression of hemozoin. Our results point to a protection of late-stage kidney disease by malaria that targets a step beyond immune complex deposition, hypoxia or innate responses and release of cytokines (IFN, TNF, IL1).
Deficiency of maternal antibodies modulates the development of lupus-like disease in BXSB offspring.
Authors: Zhu Jing , Bowman Nina , Naughton Samantha , Luo Xin M , Leeth Caroline McPhee 
Published: February 2023

Abstract
Maternal factors play an essential role in shaping the immune system of the newborn, yet it is unknown whether maternal factors could modulate the development of systemic lupus erythematosus (SLE) in the offspring. Activation-induced cytidine deaminase (AID) is an enzyme required for somatic hypermutation and class switch recombination. Given that IgG and IgA isotypes account for the vast majority of passive immunity in rodents, our previously established AID-deficient BXSB mice provide a model in which no IgG or IgA antibodies are transferred to the offspring. In this study, we compared genotypically identical mice born to either AID-sufficient dams or AID-deficient dams and evaluated the effects of maternal antibodies in disease progression. Offspring from knockout dams developed disease at a faster rate, as shown by more severe nephritis and elevated pathogenic autoantibodies compared to their counterparts born to wild type dams. In addition, the splenic structure was intensively disrupted with disorganized follicles and fewer discernible germinal centers. A more activated T cell phenotype was also characterized in maternal antibody-deficient mice. When immune competent pups were cross-fostered onto AID deficient dams, these mice exhibited more severe disease phenotypes, indicating the protective antibody effect contributes to the modulation of SLE progression in post-natal period. Overall, these findings highlight the importance of maternal antibodies in programming the immune system and altering the SLE development in the offspring.
Soluble syndecan I (CD138) released by MRL/Lpr T cells enhances APRIL-mediated lupus B cell survival and differentiation
Authors: Liu Lunhua , Akkoyunlu Mustafa 
Published: February 2023

Abstract
High level of soluble serum syndecan-1 (CD138), a heparan sulfate–bearing proteoglycan, in systemic lupus erythematosus (SLE) patients correlates with disease activity and lupus nephritis. Mechanisms responsible for the increase in serum CD138 and the immunopathological function of serum CD138 in lupus development remain poorly understood. In this study, recapitulating the findings in SLE patients, we found a sharp increase in serum CD138 levels parallel to the progression of disease in MRL/Lpr (lupus prone) mice. Although TCRβ+CD138+ T cells expand with age in MRL/Lpr mice, TCRβ+CD138− cells are the likely source of circulating CD138 as the transfer of TCRβ+CD138− cells, but not TCRβ+CD138+ cells, led to an increase in serum CD138 in the recipient mice. We found that CD138 expressed on lupus T cells was resistant to cleavage by MMP9 and collagenase, but it was very sensitive to trypsin. We also found high levels of trypsin production by TCRβ+CD138− cells. Suggesting a role for trypsin expressed by these cells in the elevated serum CD138 in lupus mice, trypsin produced by TCRβ+CD138− cells effectively cleaved CD138 from T cells. Interestingly, soluble CD138 was able to bind APRIL and enhance APRIL-mediated ERK activation and B cell differentiation. The ability of CD138 to potentiate APRIL-induced B cell differentiation was dependent on TACI expression, as the synergistic effect of APRIL and CD138 on plasma cell formation was strongly ablated on TACI deficient B cells. These findings reveal a role for soluble CD138 in B cell differentiation and autoreactive antibody production in MRL/Lpr mice. Understanding the mechanisms by which soluble CD138 is produced and how it functions may reveal novel druggable targets for lupus disease.
CD4 T cell-mediated induction of alopecia areata is dose dependent and requires CD8 T cells
Authors: Connell Samuel J , Crotts Sydney , Christy Payton , Ortolan Luana , Henderson Nicholas , Jabbari Ali 
Published: February 2023

Abstract
Alopecia Areata (AA) is a common autoimmune disease characterized by infiltration of the hair follicle by T cells, resulting in nonscarring hair loss. Our previous work suggested an increased representation of IFN-γ-producing, activated CD4 T cells in the skin-draining lymph nodes of AA mice when compared to unaffected (UA) controls. Our objective was to determine the contribution of CD4 T cells to AA pathogenesis. We adapted a recently described model of mouse AA induction whereby adoptive transfer of in vitro expanded bulk lymph node (LN) cells from previously affected AA mice induced disease in previously unaffected mice. To address the role CD4 T cells play in AA pathogenesis, we first sorted CD4 T cells and assessed their ability to induce AA. Mouse recipients of in vitro expanded CD4 T cells isolated from the LNs of AA mice developed AA at a substantially increased rate compared to mouse recipients of in vitro-expanded CD4 T cells from LNs of UA mice. CD4-mediated AA induction was found to be dose-dependent, with larger numbers of CD4 T cells inducing disease in recipient mice at a higher rate. Using congenic markers, we found that the transferred CD4 T cells were present in the skin draining LNs of recipient mice at three weeks following transfer but largely absent at 16 weeks, suggesting these cells may be conferring their effect early during disease development. Additionally, we found that the CD4 T cell population is critically dependent on the presence of endogenous CD8 T cells in order to transfer disease. Our data suggests that CD4 T cells are working upstream of CD8 T cells in the pathomechanism of AA. Further studies are needed to dissect how CD4 T cells are enabling CD8 T cell-mediated autoimmune attack on the hair follicle.