bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discovery of potently-neutralizing antibodies against SARS-CoV-2 using Barcode Enabled Antigen Mapping (BEAM)
Authors: Stubbington Michael J T , Adams Bruce , Reyes Daniel , Royall Ariel , Song Maengseok , Marrache Sean , Shahi Payam , Tsai FuNien , Finnegan Peter , Vollbrecht Thomas , Khadilkar Tanmayee , Jaffee David , Ramenani Ravi , McDonnell Wyatt 
Published: January 2023

Abstract
Humans who have recovered from infectious disease possess a memory B cell pool that contains highly-potent antibodies against the cleared pathogenic agent. This pool is a valuable source of therapeutic antibodies but identifying these requires a method that can screen a large number of cells rapidly to identify promising candidates.
We used Barcode Enabled Antigen Mapping (BEAM) to screen 100 million peripheral blood mononuclear cells (PBMCs) from a donor who had recovered from COVID-19. This method labels antigens of interest with unique reporter oligonucleotides and uses these labeled antigens to stain lymphocytes according to the binding specificity of their antigen receptors. Individual antigen-bound cells are then captured and analysed using the 10x Genomics Single Cell Immune Profiling Solution. This allows us to identify the antigen-specific cells while also generating transcriptomic profiles and natively paired, heavy and light chain full-length B-cell receptor sequences from each cell.
We used BEAM to identify B cells that bound to the spike protein of SARS-CoV-2 and discovered 222 antibodies with high binding affinity confirmed by SPR. The majority of these antibodies bound to multiple variants of concern with some also recognising endemic coronaviruses. We then investigated the potential for these antibodies to neutralize live SARS-CoV-2 and confirmed that 55 exhibited potent neutralization activity. Finally, we performed epitope binning and discovered that the collection of antibodies bound to multiple different epitopes on the spike protein.
Compared with hybridoma or other approaches, single cell methods have the potential to discover therapeutic antibodies more rapidly and with a higher diversity of leads.
Combination of αPD-1 and extended half-life IL-2 is effective against the GL261 glioma and uniquely reverses GBM-associated immunosuppression
Authors: Tritz Zachariah Peter , Ayasoufi Katayoun , Malo Courtney Sarah , Himes Benjamin , Zastrow Alexi , Wolf Delaney , Goddery Emma , Khadka Roman , Fain Cori , Chen Maggie , Yokanovich Lila T , Jin Fang , Hansen Michael , Wang Chensu , Moynihan Kelly , Irvine Darrell J , Wittrup K Dane , Parney Ian F , Johnson Aaron J 
Published: January 2023

Abstract
Glioblastoma multiforme (GBM) is a deadly CNS malignancy with an average survival of ~12–18 months post diagnosis. The unique immune environment of the brain and the immunosuppressive features of GBM complicate the use of immunotherapies against these tumors. We aimed to promote the efficacy of αPD-1 against the GL261 murine model of GBM by supplementing this therapy with an engineered IL-2 cytokine. IL-2 therapy has been used clinically for metastatic melanoma and renal cancer, but its short half-life in circulation necessitated high doses to keep the drug concentration sufficiently high. Fusing IL-2 to the mouse serum albumin molecule (MSA-IL-2), extends the cytokine’s half-life. Neither αPD-1 nor MSA-IL-2 are effective monotherapies for GL261 tumors, but the combination provides durable tumor clearance and prevents subsequent rechallenge. Most strikingly, this combination therapy cleared established GL261 tumors even in mice incapable of MHC class I restricted antigen presentation. Instead, therapeutic efficacy was abrogated by the depletion of CD4 T cells. Our combination therapy also reversed multiple key features of GBM-associated peripheral immune suppression, including depressed CD4 T cell counts and dampened MHC class II expression. Our combination therapy’s ability to overcome these immune derangements associated with glioma growth and to function independent of MHC class I restricted antigen presentation enhance the appeal of this therapy for future translational adaptation.
This work was supported by the National Institutes of Health (R01 NS103212) and the Mayo Clinic-Koch Institute Cancer Solutions Team Grant
Monoclonal antibodies displaying mutations in Fc region to prolong protection against fentanyl toxicity
Authors: Khaimraj Aaron J , Hicks Dustin , Baehr Carly , Pravetoni Marco 
Published: January 2023

Abstract
Synthetic opioids including fentanyl are the lead cause of opioid-related deaths in the United States. Current treatments for opioid overdose include the opioid receptor antagonist naloxone; however, naloxone is not as effective against highly potent opioids, has a relatively short half-life, and precipitates withdrawal symptoms. Monoclonal antibody (mAb) therapy offers a promising strategy to combat opioid-related overdoses. Opioid-specific mAb bind to target molecules in the bloodstream and inhibit them from crossing the blood-brain barrier. We produced a lead fentanyl-specific mAb that protects against fentanyl toxicity in rats. The efficacy of mAbs is reliant on maintaining a high concentration in the bloodstream to ensure sufficient binding to the target drug. The neonatal Fc receptor (FcRn) is responsible for the recycling of IgG in circulation, thus increasing their effective half-life. Therefore, to increase the duration of efficacy of a lead chimeric fentanyl-specific mAb, we introduced three different mutations to the Fc region of the mAb. Biolayer interferometry paired with recombinant FcRn showed a 10-fold increase in affinity of the recombinant mAb compared to wild-type. Efficacy of the mutated and WT mAb against fentanyl-induced behavior and toxicity was also tested in mice. Both the mutated and WT mAb reduced fentanyl-induced antinociception, respiratory depression, and bradycardia. Finally, the half-life and long-term efficacy of these mutated mAbs was assessed in transgenic mice expressing human FcRn. Extending the half-life of these mAbs will facilitate more successful clinical approaches in preventing opioid-related overdoses.
This work was funded by NIDA under CounterACT grant U01-DA051658
The effects of dietary zinc supplement on intracellular zinc concentration in bovine immune cells
Authors: Franco Carlos Enrique , Diaz Fabian Esteban , Rients Emma , Smerchek Dathan T , Hansen Stephanie L , McGill Jodi L 
Published: January 2023

Abstract
Zinc (Zn) is one of the most abundant metals in our body and is critical for innate and adaptive immune functions. In humans and mice, Zn deficiency may lead to immunodeficiency, reduced reproductive health, and increased disease susceptibility. However, trace mineral requirements and evidence of Zn dysregulation are poorly defined in cattle. This study aimed to evaluate intracellular Zn concentrations in immune cells from young growing steers with different Zn dietary supplements. Eighteen Angus crossbred steers were stratified by body weight and randomly assigned to two dietary treatments groups: 1) control, no supplemental Zn, or 2) high Zn; 150 ppm of Zn delivered in premixes in total mixed rations. To evaluate the intracellular Zn concentration of immune cells, whole blood cells were loaded with FluoZinTM-3, a fluorescent cell-permeant Zn indicator, then stimulated with Zn pyrithione (100 μM) or TPEN [N,N,N′,N′-tetrakis(2-pyridinylmethyl)-1,2-ethanediamine] (50 μM) to measure maximum and minimum mean fluorescent intensity. Cells were stained with surface antibodies to identify immune cell populations and data were collected by flow cytometry. The intracellular Zn concentrations of circulating CD8 T cells and γδ T cells, but not other populations, differed significantly between treatment groups. These results indicate that intracellular Zn concentration can be influenced by dietary Zn intake, and that certain immune populations are differentially affected by Zn status.
This project was supported by Agriculture and Food Research Initiative Competitive Grant no. 2020-06540 from the USDA National Institute of Food and Agriculture.
Characterization of SARS-CoV-2-specific CD8+ T cells in COVID-19 convalescent, vaccinated, and individuals with respect to age
Authors: Choy Cecily , Lu Jian , Li Jiangyuan , Hemani Humza , Chen Joseph , Lustig Ana , McKelvey Julia , Melvin Denise , Ruffolo Jeannie , Zukley Linda , Wallace Tonya , Dunn Christopher , Nguyen Cuong , Fan Jinshui , De Supriyo , Chia Chee , Ferrucci Luigi , Egan Josephine , Weng Nan-ping 
Published: January 2023

Abstract
COVID-19, an infectious disease caused by SARS-CoV-2, has given rise to the current global pandemic. Despite the number of infections nearing 300 million people worldwide, CD8+ T cells against SARS-CoV-2 in COVID-19 convalescent, vaccinated, and healthy adults and their changes with age have not been fully characterized. Here, we report the frequency, phenotype, and in vitro expansion capacity of circulating CD8+ T cells recognizing twenty-two epitopes from five SARS-CoV-2 proteins (S, N, M, ORF1ab, and ORF3a). Through multi-color flow cytometry using antigen-specific tetramers, we found that the frequencies of circulating CD8+ T cells ranged from undetectable to 1% in healthy, convalescent, and vaccinated individuals. Analysis of healthy adults ranging from 17 to 98 years of age revealed that the frequency of CD8+ T cells recognizing the epitope N-LLL (N222–230, LLLDRLNQL) is negatively correlated with age, particularly in the frequency of naive N-LLL-specific CD8+ T cells. Furthermore, the percentage of donors which displayed expansion of N-LLL-specific CD8+ T cells in response to in vitro peptide stimulation was significantly higher in convalescent patients than in healthy donors. These preliminary results suggest that there is an age-associated reduction of N-LLL-specific CD8+ T cells and exposure to SARS-CoV-2 primes these cells for robust expansion in response to stimulation with the N-LLL epitope. This work is still ongoing, and we will present the final results during the meeting.
Sodium Pyruvate Inhalation for COVID-19 Long Hauler Symptoms – An Effective and Inexpensive Treatment
Authors: Nadler Riley A 
Published: January 2023

Abstract
Studies show that 1 in 4 COVID-19 patients are afflicted with chronic, or long hauler, symptoms. This means that approximately 12 million Americans continue to suffer from COVID weeks and months after the active infection subsides. The long hauler symptoms include hypoxemia (low SaO2), fatigue, coughing/sneezing, trouble breathing, body aches and headaches. N115 (EmphyCorp/Cellular Sciences Inc.) is a clinical grade sodium pyruvate nasal spray currently under evaluation by the FDA for the treatment of COPD, Pulmonary Fibrosis and other chronic respiratory diseases. This study examined the effects of N115 treatment on the symptoms associated with COVID-19 long haulers. We have observed significant improvement in SaO2 levels, trouble breathing and fewer headaches indicating that N115 is a potential therapeutic for a major disease with few current options for treatment.
Characterization of pathological IgE-mediated mast cell activation in Lyme disease
Authors: Galloway Sarah D , Shoham Maia , Lee Brandon , Torrez-Dulgeroff Laughing Bear , Irnov Irnov , Lin Athena , Strausz Satu , Hansen Paige , Blacker Grace , Salomon-Shulman Rachel , Potula Hari-Hara Surya Kumar , Markovic Maxim , Nahass George R , Colace Olivia , Raveh Tal , Pollack Beth , Sanders Erin , Ollila Hanna , Wagner Christine Jacobs , Robinson William H , Weissman Irving L , Tal Michal C 
Published: January 2023

Abstract
Lyme disease, caused by the bacteria Borrelia burgdorferi, is the most common and rapidly growing vector-borne infectious disease in the United States and Europe. High variability in disease burden among Lyme patients suggests that individual immune responses may be key drivers of clinical presentation and patient outcomes. Use of high resolution flow-based immunosorbent profiling revealed that a subset of Lyme patients with persistent symptoms were producing high concentrations of IgE specific to B. burgdorferi. Comparing C57B/6 mice, which are tolerant to B. burgdorferi, and C3H/HeJ mice, which are susceptible to disease, we find high levels of IgE specific for B. burgdorferi in C3H/HeJ but not C57B/6 mice. Furthermore, IgE was found to target Borrelia peptidoglycan in both acute and chronic infection models. Histologic analysis of mouse Lyme arthritic ankle tissue showed mast cells, which release highly immunogenic effectors upon activation by bound IgE, degranulating at significantly higher rates compared to uninfected controls. Forced mast cell degranulation exacerbated Lyme arthritis in infected mice. This data suggests that a subset of Lyme patients with persistent symptoms may have developed an allergic response to conserved bacterial antigens from a B. burgdorferi infection, as opposed to an autoimmune type response. Inclusion of IgE reactivity in diagnostic testing and examination of pathological immune responses to bacterial antigens could assist clinicians in patient care and effective treatments.
Research reported in this publication was supported by the Fairbairn family foundation; Bay Area Lyme Foundation; the Younger family foundation; the Robert J. Kleberg, Jr., and Helen C. Kleberg Foundation; the Virginia and D. K. Ludwig Fund for Cancer Research; M.C.T. was supported by Stanford Immunology training grant 5T32AI007290, and the NIH NRSA 1 F32 AI124558-01 award. L.B.T.D. was supported by a Stanford Diversifying Academia Recruiting Excellence fellowship. S.D.G was supported by the California Institute for Regenerative Medicine Bridges 2.0 Training Program grant EDUC2-08397. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Epigenetic immunophenotyping in monitoring of SARS-CoV2 vaccine response and COVID-19 disease course
Authors: Jung Janine Nadine , Hoffmueller Ulrich , Samans Bjoern , Raschke Eva , Chornet Marta Rossello , Schildknecht Konstantin , Lozza Laura , Chornet Araceli Rossello , Zaragoza Lourdes Alos , Laforet Javier Hernandez , Babel Nina , Olek Sven 
Published: January 2023

Abstract
The objective was to explore whether epigenetic immune cell counting can advance efficiency and quality of diagnostic and immune monitoring related to COVID-19. Application areas were monitoring disease course, therapeutic clinical development, and measurements of SARS-CoV2 vaccine responses.
Immune cell type specific epigenetic assays have been developed over the last decade. They are primarily used in therapeutic clinical research in oncology and autoimmune disease. Due to the high sample stability and low amount requirements for epigenetic measurements and available assay portfolio for key immune cell populations relevant in COVID-19, the method promised to be useful and practical in the pandemic setting.
Epigenetic immunophenotyping using whole blood of hospitalized Covid19 patients was applied and CD3, CD4, CD8 and regulatory T cell populations, NK cells, naïve and memory B cells were quantified, and measurement results show to predict mild or severe COVID-19 disease courses. Furthermore, nasopharyngeal swab and saliva samples were applied demonstrating that epigenetic immune monitoring can measure immune cell content in such non-invasive sample types.
Due to the low sample volume and handling requirements and availability of 35 assays for relevant immune cell populations, epigenetic immune monitoring is suitable for therapeutic COVID-19 clinical trials. Another possibility for sample collection is single drops of capillary blood deposited on filter paper (dried blood spots), which have been collected pre and post SARS-CoV2 booster vaccinations in healthy subjects. Such measurements revealed vaccine response for example in changes of cell populations epigenetically active in the markers CCR7 and TIGIT.
Electromyographic characterization and bioinformatic pathway analysis of spinal cord inflammation in a Tat induced HIV-associated sensory neuropathy model
Authors: Cao Ling , Kohsar Ahmad , Wilson-Braun Peter , Harrison Benjamin 
Published: January 2023

Abstract
HIV sensory neuropathy (HIV-SN) is the most prevalent neurological complication of HIV infection. The contribution of Tat in HIV-SN has not been studied extensively. Previously, doxycycline (DOX) inducible HIV-1 Tat transgenic (iTat) mice have been shown to exhibit neuropathy-like behaviors following Tat induction. To further understand Tat-associated HIV-SN, here, we first characterized the model via electromyographic (EMG) evaluation. EMG testing of the hind leg along the sciatic nerve was conducted before DOX (daily i.p. for 14 days at 100 mg/kg) or vehicle (pH-matched phosphate-buffered saline) injection and at days 3, 7, 14, 21, 28 and 35 post the first injection. Initial analysis showed a slightly increased maximal amplitude in DOX mice along with the decreased hind paw grip strength. Further, we performed a NanoString RNA assessment of lumbar spinal cord tissues using a panel of 200+ inflammation-related genes, which was followed by a series of bioinformatic pathway analyses. Short Time-Series Expression Miner (STEM) cluster analysis identified four significant temporal expression patterns of genes. These four profiles were characterized by continuous downregulation, early-, mid-, and late-upregulation. Using PANTHER GO-pathway analysis we found that three signaling pathways were common amongst the four STEM profiles which were the apoptosis signaling, inflammation mediated by chemokine and cytokine signaling, and the Toll-like receptor signaling pathways. Previous studies highlighted selected genes that belong to these pathways and are also targets of Tat. Future work will focus on investigating how these pathways contribute to sensory neuropathy and identifying biomarkers for HIV-SN.
Supported by NIH/NIDA 1R21DA044886 (Cao)
Choline metabolism underpins macrophage IL-4 polarization in vitro and in vivo
Authors: Ghorbani Peyman , Kim Sang Yong , Alecu Irina , Woo Daniel , Ilijevska Maja , Smith Tyler K T , Nunes Julia R C , Minarrieta Lucia , St-Pierre Julie , Bennett Steffany A L , Nair Meera G , Fullerton Morgan D 
Published: January 2023

Abstract
Choline homeostasis in macrophage biology is important for LPS-polarized inflammation. In macrophages, choline mainly supports phosphatidylcholine (PC) synthesis, which is crucial for membrane production and cytokine secretion. Here, we examined choline metabolism in IL-4 polarized macrophages in vitro and in vivo. Like LPS, IL-4 increased choline transporter-like protein 1 (CTL1) expression, choline uptake and the incorporation of choline into PC. Targeted lipidomics analysis revealed increased PC content in IL-4-polarized macrophages, with an enrichment in low-saturated species. Pharmacological inhibition of choline uptake/choline kinase with hemicholinium-3 or RSM-932a showed no effect on certain hallmark IL-4-induced macrophage genes (Chil3, Mrc1, Arg1) but significantly reduced the transcript and protein expression of RELMα. Consistent with the function of RELMα in wound healing, 3T3-L1 cells healed more slowly in a scratch wound assay with conditioned media from IL-4 polarized macrophages in which choline metabolism was inhibited compared to vehicle-treated conditioned media. In addition, inhibiting choline metabolism completely prevented PD-L2 upregulation and increased PD-L1 expression on IL-4-polarized macrophages, together with suppressed cellular respiration and increased glycolysis. Furthermore, in vivo administration of RSM-932a (3 mg/kg i.p.) in C57BL/6J mice lowered RELMα in macrophages, decreased PD-L2 and increased PD-L1, and resulted in a loss of resident peritoneal F4/80hi macrophages. Choline represents an underappreciated regulator of macrophage immunometabolism and strategies to target macrophage choline uptake or choline metabolism may be therapeutically valuable.
Understanding the temporal requirement for T follicular helper cells for germinal center output of long-lived plasma cells and B memory cells.
Authors: Zilch Tiago , Leddon Scott , Fowell Deborah J 
Published: January 2023

Abstract
T follicular helper cells (Tfh) play a critical role in supplying help to B cells for the selection of high-affinity B cells in germinal centers (GC), that give rise to memory B cells (Bmem) and long-lived plasma cells (LLPCs). The products of the GC reaction appear to be temporally distinct, with Bmem cells produced early and LLPCs late.
The temporal requirements for Tfh help are not well understood and we still do not know when and for how long this help is critical. In the total absence of help supplied by Tfh cells, both GCs and LLPCs are greatly diminished. Our previous work (Schrock, Leddon et al 2019, PNAS) suggested that sustained GC Tfh were critical for LLPC generation, but interestingly not for Bmem generation. We hypothesize that a temporal requirement for GC Tfh regulates LLPC versus Bmem GC output. To test this, we have established a number of models that allow for deletion of Tfh at different times post OVA/CFA immunization. To specifically target Tfh cells, CD4 iCRE Bcl6fl/fl mice were used for time-dependent deletion of Bcl6 upon tamoxifen administration at different stages of the GC reaction. Tfh and GC output are determined using multicolor Flow Cytometry panels, BM B cell Elispot for LLPCs and a Bmem Elispot. With these systems in place, we aim to pinpoint the temporal requirement for Tfh for both Bmem and LLPCs, speculating that timing of Tfh help will differ for these two arms of the GC response.
Understanding this temporal requirement of Tfh help within the GC can not only help us to better design future vaccines that promote LLPCs, but also guide the development of drugs to modulate Tfh longevity in autoimmune disorders, where aberrant Tfh development or maintenance contribute to pathology.
Developmental dynamics and genomic programming of GC-derived precursors that give rise to long lived plasma cells
Authors: Vijay Godhev Kumar Manakkat , Thakkar Kairavee , Chetal Kashish , Hay Stuart , Fan Jingyu , Joglekar Alok V , Salomonis Nathan , Singh Harinder 
Published: January 2023

Abstract
Plasma cell (PC) precursors are generated during a germinal center (GC) response and migrate to the bone marrow (BM) where they undergo terminal differentiation into short-lived (SL) or long-lived (LL) antibody secreting cells. The developmental dynamics and genomic states of PC precursors remain to be elucidated1. We utilize a novel experimental system, involving CD138+ splenocytes isolated from NP-KLH immunized C57Bl/6J mice (21–42 dpi) and their adoptive transfer into B cell deficient mMT mice, to analyze developmental dynamics of antigen-specific PC precursors and their progeny at single-cell resolution. We demonstrate that SLPC precursors are generated earlier (d21), whilst LLPC precursors are generated later (d35) during a GC response. scRNA-seq analyses reveals increased frequency of a novel cluster of transitional cells expressing both B-lineage and plasma cell-specific genes. Coupled analyses using BCR-seq shows that NP-specific transitional cells express cell cycle genes and undergo greater clonal expansion on d35 to give rise to proliferating and quiescent PCs. Antigen-specific clonal tracking in the spleen and BM compartments suggests that the transitional cells emanating from the GC, differentiate into proliferating PCs before migrating to the BM. CITE-seq analyses and reconstitution experiments demonstrate that proliferating PCs are contained within the B220− CD138+ CD44+ CD11a+ subset and are enriched for BMPC precursors. These results reveal novel GC-derived transitional cells that generate precursors of both SLPCs and LLPCs with differing developmental and proliferation dynamics in a humoral immune response.