bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of highly specific peptibody against Porcine epidemic diarrhea virus
Authors: Ryu Jihoon , Shin Hyun-Jin 
Published: January 2023

Abstract
Porcine epidemic diarrhea virus (PEDV) is an etiological agent of porcine epidemic diarrhea (PED), causing dehydration, vomiting, and acute watery diarrhea. Because it has a high mortality rate in neonatal piglets, PEDV is one of the critical pathogens affecting the swine industry. Since PEDV has shown rapid spreading in herds of swine, early diagnosis of this virus is very important to control the disease. Serological diagnosis test is a simple, rapid method for detecting PEDV infected pigs, and the development of PEDV-specific antibodies is essential for an accurate serological diagnostic test. Because conventional methods of development of monoclonal antibodies are time and hand-consuming work, recombinant antibodies are considered as an alternative strategy for the development of target-specific monoclonal antibodies. Peptibody is one of the promising recombinant antibodies that target-specific peptide is fused with the Fc domain of immunoglobulin G. The peptibody which have a specificity of peptides and immune function of Fc region as advantages have developed for therapeutic and diagnostic purpose. Here, we generated a PEDV-specific peptibody (PEDV-PB) that is fused with PEDV-specific peptide and mouse IgG2b Fc region. PEDV-specific peptide sequences were discovered by random phage display library and PEDV-PB was produced from Chinese hamster ovary (CHO) cells. PEDV-PB showed highly specific binding in several serological tests for PEDV, such as western blotting, immunofluorescence assay, and enzyme-linked immunosorbent assay. Our results suggest that PEDV-PB is very useful for the development of a rapid detection kit for PEDV.
Computational fingerprinting of immune-mediated pressure on SARS-CoV-2 viral evolution reveals preliminary evidence for immune-evasion
Authors: Hertz Tomer , Cohen-Lavi Liel , Sachren Sinai , Koren Eilay , Burkovitz Anat 
Published: January 2023

Abstract
The global emergence of SARS-CoV-2 variants and Omicron in particular, has highlighted the risk of novel variants that will evade adaptive immune responses following vaccination and natural infection. Determining which viral mutations escape T-cells and antibodies is crucial for designing therapeutics and vaccines and assessing the implications of newly emerging variants.
We developed an automated immunoinformatic pipeline that considers both data on viral sequences and experimentally identified T-cell and antibody responses, to identify specific viral mutations that may be associated with immune escape. We used an unsupervised clustering method to cluster a set of 108 non-redundant anti-SARS-CoV-2 spike protein antibodies with solved 3D structures from the PDB database, and identified 9 unique antibody clusters. We computed the predicted changes in binding energies (ΔΔG) for each antibody and each specific mutation within its contact footprint. Using these ΔΔG scores, we computed an antibody escape score for each mutation. We also predicted the change in binding between predicted and experimentally verified T-cell epitopes and their presenting MHC molecules. We ranked frequent spike protein mutations based on their predicted effect on immune evasion, as well as individual SARS-CoV-2 variants, with a specific focus on VOCs. Our novel immune escape scores identified several key mutations in the Omicron variant, which were not present in previous VOCs, and may be used to identify key mutations that are likely associated with immune escape, which may appear in novel variants of concern.
Supported by an NIH grant (75N93021C00016)
Identifying distinct T cell subsets in the context of pediatric ARDS
Authors: Clark Brandi L , Flerlage Tim , Schattgen Stefan A , Allen E Kaitlynn , Boyd David F , Crawford Jeremy C , Thomas Paul G 
Published: January 2023

Abstract
Acute respiratory distress syndrome (ARDS) is a condition defined by sudden respiratory failure caused by severe lung injury, with disease etiology that can differ across pediatric and adult patients. While T lymphocytes have been implicated in ARDS, the role of T cell subsets in pediatric ARDS (pARDS) is not fully understood. In this study, we sought to characterize the potential role of T cells in pARDS caused by viral lower respiratory tract infection (LRTI). To do this, we performed single cell RNA-Seq on tracheal aspirate samples from three categories of mechanically ventilated pediatric patients: 1) LRTI patients with pARDS, 2) LRTI patients without pARDS, and 3) ventilated patients without underlying LRTI or pARDS. All LRTI patients were diagnosed with respiratory viral infections, 70 percent of which were respiratory syncytial virus (RSV). Within the T lymphocytes, we identified populations of CD8+ T cells, CD4+ regulatory T cells, and γδ T cells that each expressed unique gene signatures with distinct distribution across disease states. We compared these data to T cell subsets within healthy lung tissue at multiple ages, and within the periphery of healthy adults. These analyses identified age, location, and disease-specific differences within T cell subsets, highlighting the unique role of T cells in pARDS.
Supported by grants from NIH (R01 AI54470, R01 AI121832)
DEC-205-expressing dendritic cells inhibit T cell responses during West Nile Virus encephalitis in the central nervous system
Authors: Mo Chiefe , Durrant Douglas Matthew 
Published: January 2023

Abstract
West Nile Virus (WNV), a neurotropic flavivirus, is the leading cause of mosquito-borne neuroinvasive disease in the U.S. Recent studies show that dysfunctional T cell responses correlate with severe disease in both humans and mice. Dendritic cells (DCs) are critical for reactivating antiviral CD8+ T cell responses in the CNS that are required to mitigate viral encephalitis. Previous reports have shown that CNS-localized DEC-205+ DCs accumulate within the CNS during WNV encephalitis; however, their specific role in programming T cell immunity remains poorly understood. DEC-205, an endocytic receptor expressed by DC subsets can promote either antigen-specific effector T cell activation or immunological T cell tolerance. Using a mouse model of WNV encephalitis, we demonstrate that DEC-205−/− mice exhibit enhanced clinical signs of disease and increased mortality compared to WT controls. The enhanced susceptibility in DEC-205−/− mice arose from an increased viral burden with the CNS; however, this was associated with increased inflammatory myeloid, CD4+, and CD8+ T cell infiltrates. In addition, expression of activation markers CD25 and CD44 increased while CD69 levels decreased within the DEC-205−/− mice compared with their WT counterparts. CD69 expression has been shown to be associated with regulatory T cells. To confirm the immunomodulatory role of DEC-205, we will measure CD4+ regulatory T cell frequencies within the CNS of DEC-205−/− and WT animals following WNV infection. Taken together, these data suggest that DEC-205 critically regulates WNV pathogenesis and neuroinvasive disease by limiting immune-mediated pathology in the CNS following WNV infection.
Supported by grants from NIH (SC3GM130472).
A Unique Cooperativity between Optineurin and CCL5 Triggers Early Cell Death during Herpes Simplex Virus-1 Infection of the Cornea
Authors: Patil Chandrashekhar Devidas , Shukla Deepak 
Published: January 2023

Abstract
Induction of cell death is considered an effective strategy to control viral infections. Rapid killing of infected cells prevents propagation of viruses and thereby, effectively reduces the infection. Herpes Simplex Virus-1 (HSV-1) is known to cause ocular and nervous system infections. While studying an autophagy receptor protein, Optineurin (OPTN), we found evidence of a unique collaboration between OPTN and CCL5 to generate signal for early cell death in HSV-1 infected cells in the cornea. OPTN knockout mice tend to die due to rapid spread of HSV-1 infection to the brain causing encephalitis. Interestingly, the OPTN knockout animals also exhibit a marked reduction in CCL5 induction. Human transcriptomic profile dataset shows a strong positive correlation between CCL5 upregulation and OPTN expression during HSV infection. Our data shows that a well-coordinated activity of both, OPTN and CCL5, is needed to trigger an early cell death signal that mimics pyroptosis to prevent viral spread. Downregulation of CCL5 and/or OPTN causes interference with this signal and a corresponding delay in cell death. Our results provide new information on an anti-HSV1 chemokine signaling pathway that participates in innate immune control of HSV-1 spread and viral transmission.
Influenza A virus-specific maternal antibodies impair vaccine-induced antibody responses and protection in male to a greater extent than female offspring.
Authors: Campbell Ariana Denise , Creisher Patrick S , Perry Jamie Lynn , Roznik Katerina , Sherer Morgan L , Burd Irina , Klein Sabra L 
Published: January 2023

Abstract
Influenza A virus (IAV) is a public health threat to pregnant people and infants. Transfer of antibodies across the placenta to the fetus and during lactation provides key protection from infectious pathogens during the neonatal period. Despite this, pathogen-specific maternal antibodies may interfere with infant vaccination. We hypothesized that transfer of IAV-specific maternal antibody, would negatively affect vaccine-induced immunity and protection in male and female offspring, with males being more impacted. Pregnant CD1 mice were infected on embryonic day 10 with 103 TCID50 of mouse adapted A/California/09 H1N1 (ma2009 H1N1) or mock inoculated. In offspring of IAV-infected dams, maternal anti-ma2009 H1N1 IgG peaked at 3-weeks, declined at 7-weeks, and undetectable at 15-weeks of age. At 3-, 7-, and 15-weeks, male and female offspring were intramuscularly vaccinated with inactivated ma2009 H1N1 vaccine, boosted 21 days later, and had serum collected 14 days post-boost. Following vaccination, 3-week-old offspring of IAV-infected dams displayed significantly lower vaccine-induced anti-ma2009 H1N1 IgG titers compared to offspring born from mock-infected dams. At 7 weeks of age, vaccine-induced IgG titers were significantly inhibited in male but not female offspring. In 15-week-old offspring of IAV-infected dams, vaccine-induced antibody responses were similar to offspring of mock-infected dams, being greater in female than male offspring. These data suggest that IAV-specific maternal antibodies negatively impact the offspring response to IAV-vaccination, with this more pronounced in males than females. This research is important for understanding the factors that impact vaccine-induced immunity in early life.
Supported by funding from the Johns Hopkins Vivien Thomas Scholars Initiative and grants from NIH/NICHD R01 HD097608, JH-CEIRS contract HHSN272201400007C, and NIH/NIA U54AG062333, NIH/NIAD 2T32A1007417-26
B cell-derived acetylcholine controls local inflammation and replication of influenza virus during respiratory tract infections
Authors: Prieto Antonio Cembellin , Murray Kaitlin , Reardon Colin , Baumgarth Nicole 
Published: January 2023

Abstract
Acetylcholine (ACh), a well-known neurotransmitter, is produced by the action of choline acetyltransferase (ChAT). Recently, ChAT expression was shown also in leukocytes, however, its function there remains to be more fully explored. Flow cytometry revealed that most ChAT-expressing cells in spleen, lymph nodes, lung, and pleural cavity of ChAT-GFP reporter mice are B cells, with B-1 cells having the highest frequency of ChAT+ cells among them. B cell-specific mb1-Cre ChATflx/flx knockouts (BChat-KO) had apparent normal bone marrow B cell development. Also, serum IgG and IgM levels and spontaneous IgM secretion in the spleen were comparable to wild-type littermate controls. Nonetheless, their spleen B-1 cell numbers were reduced. Intranasal infection of BChat-KO with influenza A/Puerto Rico/8/34 showed significantly smaller increases in IgM-secreting cells in the spleen and mediastinal lymph nodes (medLN) at 7 days post-infection (dpi) compared to controls. Inflammation-induced emigration of CD5+ B-1 cells from the pleural cavity to the medLN, which we showed previously to occur early during influenza infection, appeared exaggerated in the BChat-KO mice, leading to reductions in pleural cavity B-1 cells. Additional alterations to the macrophage and neutrophil composition suggested enhanced pleural inflammation in BChat-KO. This was correlated with reduced control of lung virus replication at 7 dpi. Overall, the data suggest a non-redundant function for B cell-derived ACh in the regulation of pleural inflammation and the control of virus replication following infection with influenza A.
The study was supported by a grant from the Chan Zuckerberg Initiative to Colin Reardon and Nicole Baumgarth
Impact of B-cell depletion therapy on respiratory viral infection
Authors: Allushi Bujana , Chlebicz Magdalena , Turner Sean , Kovats Susan , Axtell Robert C 
Published: January 2023

Abstract
B cell depletion therapy with anti-CD20 antibodies ameliorates autoimmune diseases such as multiple sclerosis, rheumatoid arthritis as well as haematological malignancies. Anti-CD20 antibodies deplete pre-B cells, mature B cells and malignant B cells but do not reduce plasma cells. Recently, studies have associated anti-CD20 therapy with severe manifestation of SARS-CoV2 infection. However, the mechanism of this adverse effect of anti-CD20 therapy remains unclear.
This study was undertaken to investigate the effect of anti-CD20 therapy on respiratory viral infection. C57BL/6 mice were treated with anti-CD20 antibody to induce B cell depletion and then were infected intratracheally with H1N1 Influenza A mouse-adapted A/Puerto Rico/8/1934 virus (IAV). Our results show that B cell depletion therapy worsens lung infection with more severe and prolonged weight loss. Higher viral titers were found in the lungs of anti-CD20 treated mice, indicating impairment in virus clearance. Flow cytometry analysis showed no difference between groups in CD4+ and CD8+ PR8 antigen specific T cells on day 9 post-infection. However, higher numbers of inflammatory, SiglecF+ neutrophils were found in B cell depleted mice.
In summary, our data show that anti-CD20 therapy exacerbates the viral pathology in respiratory lung infections. We further have identified that B cell depletion therapy affects viral clearance and inflammatory neutrophils but has no effect on T cell numbers in the lung at the peak of infection. Our future studies will identify the mechanisms driving the severe pathology in influenza infection with B cell depletion.
Supported by grants from NIH (R01AI137047 and R01EY027346) A grant awarded to Dr. Kovatz and Dr Axtell from the Presbyterian Health Foundation
Non-classical major histocompatibility factor H2-O counteracts gammaherpesvirus manipulation of the germinal center response
Authors: Stoltz Kyle , Golovkina Tatyana , Tarakanova Vera 
Published: January 2023

Abstract
Gammaherpesviruses, such as Epstein Barr virus, infect 95% of adults and form lifelong infection primarily through manipulation of B cells. During primary infection, gammaherpesviruses establish latent infections within B cells and drive robust, polyclonal germinal center (GC) responses, which atypically include B cells specific to both viral and self antigens. Consequently, this humoral response results in production of both autoantibodies, and interestingly, antibodies reactive to antigens of non-human species. While this non-physiological production of antibodies suggests viral manipulation of immune tolerance, the underlying mechanisms driving these phenomena are poorly understood.
Utilizing murine gammaherpesvirus 68 (MHV68), a rodent pathogen highly similar to EBV which serves as an animal model of EBV infection, we have discovered that the host factor H2-O (HLA-DO in humans) attenuates MHV68 latency establishment and the MHV68 driven GC response. H2-O acts as an inhibitor of H2-M (HLA-DM), the protein which regulates peptide exchange and thus the repertoire of peptides associated with the MHC-II peptide binding groove. We found that mice deficient in H2-O displayed increased MHV68 latent reservoirs, increased GC response, and a selective increase in dsDNA specific IgG, with no change in virus specific IgG at the peak of latent viral infection. These results show a novel role of H2-O in attenuating the non-physiological, self-directed B cell response driven by MHV68. Furthermore, these studies are the first to demonstrate that fine tuning of MHC-II antigen presentation is sufficient to alter the self-directed B cell differentiation usurped by a ubiquitous viral pathogen during establishment of life-long infection.
Modeling chronic gammaherpesvirus infection as a risk factor for MS reveals a profound impact of host genotype on control of viral load and T helper reprogramming
Authors: Holt Emily A , Lahue Karolyn G , Usherwood Edward J , Teuscher Cory , Krementsov Dimitry N 
Published: January 2023

Abstract
Multiple Sclerosis (MS) is an autoimmune disease of the central nervous system (CNS) that impacts approximately 2 million people worldwide. The etiology of the disease is multifactorial, consisting of multiple environmental and genetic risk factors. A major risk factor is chronic infection with the gammaherpesvirus, Epstein Barr Virus (EBV). The mechanisms by which EBV increases MS risk, including the role of host genetics, are still unclear. To examine the role of host genetics on gammaherpesvirus infection outcomes, we infected male and female C57BL/6 (B6) and wild-derived PWD/PhJ (PWD) mice with MHV-68, a gammaherpesvirus homologous to EBV. Given the central role of CD4 T cells in MS, we first determined the effect of latent gammaherpesvirus infection on the CD4 T cell transcriptome. CD4 T helper cells were isolated from chronically infected mice followed by transcriptional profiling. Chronic MHV-68 infection resulted in a dramatic upregulation of genes characteristic of so-called cytotoxic T helper cell (ThCTL) phenotypes, including Gzmb, Cx3cr1, Klrg1, Prdm1, and Tbx21, which was most pronounced in B6 females, and highly muted in PWD mice of either sex. Flow cytometric analyses confirmed the genotype-specific expansion of ThCTL-like cells, beginning within 9 days of infection and continued into latency. Analysis of MHV-68 replication kinetics demonstrated that PWD mice had remarkably superior control of viral load early and late in infection. Because poor control of EBV viral load and enhanced anti-EBV responses are associated with greater MS risk, taken together, our findings suggest that the increased risk of MS due to EBV infection might be due to genetically determined poor control of viral load and augmented ThCTL responses.
Supported by a grant from the NIH (R21 NS095007)
IRF5 risk variants contribute to pre-symptomatic SLE by enhancing the levels of circulating NET antigens
Authors: Matta Bharati , Battaglia Jenna , Thomas Lydia , Barnes Betsy J 
Published: January 2023

Abstract
SLE is a complex multifactorial autoimmune disease characterized by high levels of autoantibodies that impact many organs. Neutrophil extracellular traps (NETs) are a potential source of antigen leading to the production of autoantibodies, as antibodies against NET components are detected in SLE patients. Higher level of NETs and decreased clearance of NETs are associated with SLE and other autoimmune diseases. Neutrophils play an key role in pediatric lupus and NETs from pediatric lupus patients activate plasmacytoid dendritic cells (pDCs) to produce high levels of IFN-α. Polymorphisms within and around the IRF5 gene associate with risk of developing SLE. We previously reported that healthy donor neutrophils from IRF5 homozygous risk carriers underwent increased spontaneous NETosis, as compared to non-risk donors, that resulted in increased IFN-α production, plasma cell differentiation and autoantibody production. Whether the observed increase in neutrophil-mediated ETosis is a systemic signature of IRF5-driven pre-symptomatic SLE is not known, nor is it known whether these IRF5 risk carriers have defects in NET clearance. We thus developed and optimized new assays to detect small quantities of NET remnants in plasma samples using a combined MPO-CitH3 antibody cocktail followed by detection of DNA by ELISA. Further, we designed a novel immunofluorescence technique to visualize and quantify plasma NETs in healthy donor risk and non-risk carriers, as compared to pediatric and adult SLE patients. In addition, plasma DNase 1 and DNase 1L3 levels were measured. This study will report on the mechanisms by which circulating NETs are increased in pediatric and adult SLE, as well as the contribution of IRF5 genetic risk to NET clearance.
Supported by Lupus Research Alliance Department of Defense CDMRP LRP W81XWH-18-1-0674
Androgens can modulate immunoregulation directly through gut cells and indirectly through alteration of microbiota composition/function in a lupus mouse model.
Authors: Ma Jing , Harder James , Alard Pascale , Kosiewicz Michele M 
Published: January 2023

Abstract
Hormones and gut microbiota affect lupus. In female NZBxNZW1(BWF1) mice, androgen treatment abrogates lupus; castration/treatment with androgen receptor blocker (flutamide) induces disease in BWF1 male mice. Gut microbiota alterations have been reported in lupus. Our goal is to understand the androgen/gut microbiota relationship, and its affect on lupus. We found male castration decreases peripheral, not thymic, derived Tregs; this correlates with decreased gut CD103 dendritic cells (CD103DC) function (induce Treg conversion) and RALDH2 [required for retinoic acid (RA) production) expression. CD103DC have very low androgen receptor (AR) expression, thus unlikely to be affected by androgens. We found that lamina propria stromal cells (LPSC), a major source of RA (via RALDH1/2 expression) required for normal gut CD103DC development, express very high AR levels. Castration/flutamide treatment in male mice decreased RALDH1/2 expression in LPSC, suggesting androgens may affect CD103DC function through LPSC. Castration/flutamide treatment also altered gut microbiota composition. Interestingly, intact male microbiota transfer to castrated male mice restored RALDH2 expression and CD103DC function, suggesting male microbiota factors may also alter CD103DC function. Metabolomic analysis of castrated male feces showed reduced phytanic acid (PA) levels. Administration of PA in vitro/in vivo restored castrated CD103DC function. These data strongly suggest that androgens alter (1) immunoregulatory function through gut cells and (2) gut microbiota composition/function that in turn modulate immunoregulatory function, and reveal how androgens may influence lupus and provide the basis for effective therapy development.
Funded by a TIL grant from the Alliance for Lupus Research and the NIH (R01AR067188)