bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional Interrogation and Mining of Natively-Paired Human VH:VL Antibody Repertoires
Authors: DeKosky Brandon J. , Wang Bo , Timm Morgan , Lee Jiwon , Normandin Erica , Misasi John , Kong Rui , McDaniel Jonathan R. , Delidakis George , Leigh Kendra E. , Niezold Thomas , Ploquin Aurélie , Viox Elise G. , Fahad Ahmed , Cagigi Alberto , Leung Kwanyee , Yang Eun Sung , Kong Wing-Pui , Voss William , Schmidt Aaron G. , Moody M. Anthony , Ambrozak David , Henry Amy R. , Laboune Farida , Ledgerwood Julie E. , Graham Barney S. , Connors Mark , Douek Daniel C. , Sullivan Nancy , Ellington Andrew D. , Georgiou George 
Published: January 2023

Abstract
Next-Generation sequencing has become an essential tool in the analysis of antibody responses in the settings of health, vaccination, and disease. However, immune receptors comprise two chains encoded by separate mRNA strands, and conventional NextGen sequencing fails to identify the native pairings encoded by individual lymphocytes. To overcome this limitation we have applied recent technical advances in high-throughput sequencing and functional analysis of complete antibodies (i.e., paired heavy and light chain sequencing) to generate a comprehensive understanding of the antibody response to vaccination and natural infection. Here we present a new technology to screen natively-paired human antibody repertoires from millions of B cells. Libraries of natively-paired variable region heavy and light (VH:VL) amplicons were expressed in a yeast display platform that was optimized for human Fab surface expression, and the resulting libraries were interrogated for binding to viral vaccine antigens via FACS paired with next generation sequencing. Using our method we identified HIV-1 broadly neutralizing antibodies (bNAbs) from an HIV-1 slow progressor and high-affinity neutralizing antibodies responding to an Ebola virus glycoprotein vaccination. These next-generation approaches are providing detailed molecular feedback on immune receptor responses and are informing the design and discovery of new vaccines and therapeutics.
A high-resolution, genome-scale promoter interactome in human T follicular helper cells implicates novel causal genes at SLE GWAS loci
Authors: Wells Andrew D. , Johnson Matthew , Manduchi Elisabetta , Le Coz Carole , Leonard Michelle , Lu Sumei , Hodge Kenyaita , Romberg Neil , Chesi Alessandra , Grant Struan 
Published: January 2023

Abstract
Genome-Wide Association Studies (GWAS) have implicated &gt;60 loci in the susceptibility to systemic lupus erythematosus (SLE). However, GWAS reports signals in non-coding genomic regions, not the precise location of culprit genes. Chromatin conformation capture (3C) technologies that detect physical contacts between regions of the genome offer a powerful opportunity to map disease variants to target genes. We developed a massively parallel, high-resolution method to characterize the genome-wide interactomes of 36,691 promoters of protein-coding, noncoding, antisense, snRNA, miRNA, snoRNA and lincRNA genes in any cell type. Using this method, we generated promoter interactomes of primary human T follicular helper (TFH) cells from healthy tonsil, a cell type relevant to SLE as TFH operate upstream of pathogenic autoantibody-producing B cells. These sub-1kb TFH promoter interactome datasets were intersected with maps of TFH open chromatin generated by ATAC-seq and SLE SNPs from the 63 candidate loci, resulting in detection of consistent interactions between genes and accessible SNPs at 48 loci. We find that ~25% of accessible SLE SNPs interact with the nearest gene, e.g. STAT4 and IKZF3, while ~75% of accessible SNPs ‘skip’ the nearest gene to interact with distant genes, e.g. LCLAT1 at the ‘LBH’ locus, and the master TFH transcription factor BCL6 at the ‘LPP-TPRG1’ locus. Gene ontology analysis confirms that genes directly implicated by SNP interactions reside in SLE-relevant networks while ‘nearest to SNP’ genes do not. In conclusion, high-resolution, 3-dimensional promoter interactions with accessible, disease-associated SNPs in disease-relevant tissue connect variants to relevant genes with high apparent accuracy.
Robust prediction of clinical outcomes using cytometry data
Authors: Hu Zicheng , Glicksberg Benjamin , Butte Atul 
Published: January 2023

Abstract
Flow cytometry and mass cytometry are used to diagnose diseases and to predict clinical outcomes. Here, we propose a novel strategy to predict clinical outcomes using cytometry data without cell gating (CytoDx; accessible at github.com/hzc363/CytoDx). CytoDx is able to predict the response to influenza vaccine using heterogeneous datasets, demonstrating that it is not only accurate but also robust to batch effects and cytometry platforms.
Sensitive detection of human drug-induced liver injury by measurement of microRNA-122 using single molecule arrays
Authors: Lambert Jeremy , Rissin David , Duffy David 
Published: January 2023

Abstract
Drug-induced liver injury (DILI) is a major challenge in clinical medicine and drug development. MicroRNA-122 (miR-122) is a sensitive and specific biomarker for hepatocyte injury that has received formal regulatory support. A major roadblock to its widespread adoption is a lack of a fit-for-purpose, scalable assay that can provide quantification of circulating miR-122 with appropriate accuracy and time-to-result. We have developed a PCR-free, sensitive and highly specific assay for measuring miR-122. The assay is based on the hybridization of miR-122 to a peptide nucleic acid (PNA) probe attached to superparamagnetic beads, followed by the specific incorporation of a biotinylated nucleobase. The biotin labels are then labeled with an enzyme, and single enzymes are detected using single molecule arrays (Simoa).
The miR-122 single molecule assay had a limit of detection (LOD) of 500 fM, approximately 500 times more sensitive than a corresponding analog bead-based assay. The specificity of the assay to a single base mismatch in the microRNA sequence was &gt;107-fold ((highest concentration of mismatched target with signal below LOD)/(LOD)). As measured by our single molecule assay, all patients with DILI had higher concentrations of miR-122 in their serum compared to healthy controls, and the concentrations of miR-122 measured correlated closely with those determined using the gold standard PCR (r2 = 0.93; slope = 0.64).
This novel single molecule assay enabled the accurate measurement of miR-122 in the serum of patients with DILI. This assay could have utility in clinical practice as it has the potential to deliver the user-independent sensitivity and time-to-result that are needed to inform pre-clinical and clinical decision making.
Dynamic live cell imaging of immune cell interactions using microfluidics cell trap
Authors: Park Jun , Chen Cindy , Yeh Victor , Booth Ross 
Published: January 2023

Abstract
While providing indispensable insight into immune processes, the live cell imaging of immune cells poses unique challenges due to their non-adherent nature. Suspension cells such as immune cells can easily move away from the FOV (field of view) during imaging by any physical perturbations such as introduction of agonist or even simple media change, often necessitating the use of surface coating to artificially immobilize cells. In addition, unlike adherent cells, interacting suspension cells form aggregates, making it very difficult to track and analyze individual cells during imaging. Previously, we have described the novel microfluidic-based dynamic live cell imaging platform CellASIC ONIX2, where microenvironmental parameters such as the perfusion of media/reagent, temperature, and gas compositions can be precisely controlled on demand via software during the entire imaging experiment. We now report further utility of the system with a new non-adherent cell trap culture plate comprising an array of walled ~100μm square pads with a 12μm height restriction and 3μm wall gap, allowing physical trapping of immune cells within FOV while enabling their natural movement, and preventing vertical cell stacking of aggregated cells while preserving cell-cell interactions. Using Jurkat T cells and super antigen loaded Raji B cells, we demonstrate dynamic live cell imaging of immune cell interactions. Unlike systems where cells are artificially immobilized, we show that these cells are extremely motile and behave in much more complex and dynamic fashion during their interactions. The technology should benefit live cell imaging of any suspension cells and is amendable for wider applications in addition to immune cell imaging.
Ultrasensitive Quantification of Inflammatory Biomarkers in Breast Cancer Survivors
Authors: Osier Nicole D. , Slote Claire , McGreevy Emily , Henneghan Ashley 
Published: January 2023

Abstract

Background
Inflammatory changes in breast cancer survivors, have been linked to symptoms including sleep disturbance and fatigue. While inflammation is well-studied, limitations in detection of inflammatory proteins in human serum may obscure scientific understanding; traditional methodologies (e.g. enzyme-linked immunosorbent assay (ELISA)) often cannot detect beyond the picomolar level).

Purpose
This study describes new methodologies for evaluating biomarkers by comparing IL-6- levels in the serum of breast cancer survivors previously obtained in the parent study using the BioPlex200 System (Luminex®) to those obtained in this study using the SMCxPRO (MilliporeSigma).

Methods
The principles outlined in the Declaration of Helsinki and U.S. Government regulations (45 CFR Part 46; 56 FR 28003) were followed. Following Institutional Review Board (IRB) approval and informed consent, survivors of treated Stage I–III breast cancer (6 to 10 years prior) were recruited into the parent study. Serum and self-reported measurements of sleep and fatigue (e.g. Pittsburgh Sleep Quality Index, Epworth Sleepiness Scale, Patient-Reported Outcomes Measurement Information System Fatigue scale) were collected at a single time point. A bead-based assay system was then used to perform single molecule counting and these results were compared to those previously obtained using conventional methods.

Results
Inflammatory changes are detectable using both systems, but the SMCxPRO assay has a lower limit of quantification. Femtomolar-level sensitivity may result in identification of meaningful associations that could not be determined otherwise. Future research efforts to replicate and expand upon these findings are needed.
REAlease™ Immunomagnetic Separation Technology with reversible labeling for positive selection of leukocytes
Authors: Evaristo Cesar , Steinbrück Philipp , Pankratz Jennifer , Yu Zhong , Dose Christian 
Published: January 2023

Abstract
Immunomagnetic enrichment of leukocytes is an important technique in both research and clinical applications. Accordingly, there is a continuous need for improved, reliable cell separation methods. Current enrichment strategies using magnetic labeling of the target cells allow for highly efficient isolation, but in some instances removal of residual cell surface labeling after isolation is of high interest. To this end, we have combined the benefits of positive selection by MACS® Technology, the proven state-of-the-art method for the isolation of functional, viable cells, with a novel technology enabling the removal of both superparamagnetic beads and antibody fragments. REAlease™ Technology provides an easy and fast solution for the highly specific isolation of unlabeled leukocytes directly from PBMCs. We present our latest results on cell separation with REAlease Technology based on key human immune cell markers, i.e., CD3, CD4, CD8, CD19, and CD56. The benefits of these releasable labels are demonstrated for the isolation of important subsets such as CD3−CD56+ NK cells, and CD4+ and CD8+ cell populations from a single sample. Using various assays, we show that functionality and viability of the target cells are preserved without cell activation.
Isolation of functionally unaffected cells Straight From buffy coat, LRSC or Leukopak
Authors: Winkels Gregor , Schlemminger Maike , Weber-Lohmann Silke , Kolnik Martin , Yu Zhong , Höher-Peters Susanne 
Published: January 2023

Abstract
Enrichment of leukocytes from blood products like buffy coat, leukocyte reduction chambers (LRSC) or leukapheresis material can be time consuming and could influence the physiology of the target cells.
Our new StraightFrom cell separation reagents were specifically developed to minimize time and handling steps, omitting the need to perform density gradient centrifugation methods or erythrocyte lysis prior to isolation thereby preserving cell intergrity.
Based on positive isolation, Th cells (CD4), cytotoxic T cells (CD8), Monocytes (CD14), B cells (CD19) or NK cells (CD56) can be isolated from complete buffy coats, LRSC or half pack LPs within less than 30 minutes with purities above 95%. The positive enrichment process enables thereby the consecutive enrichment of more than one cell population from a sample and is automatable.
Using various assays, we show that functionality (e.g activation and expansion, cytokine secretion, ROS production) and viability of the target cells are preserved without cell activation. Ultimately, this optimized magnetic cell separation technology allows the isolation of physiologically relevant cells in a quick and easy manner.
Development of a murine model resembling human lupus in mice parasitized with Trichinella spiralis
Authors: Nevárez-Lechuga Christian Irene , Sánchez-Barbosa Sandra , Landa-Saldívar Carla , Wong Carlos , Wong-Baeza Carlos , Escobar-Gutiérrez Alejandro , de-la-Rosa-Arana Jorge-Luis , Baeza Isabel 
Published: January 2023

Abstract
Deregulation of Th1 and Th17 immune responses is fundamental in the development of autoimmune diseases, like Systemic Lupus Erythematosus that is a chronic inflammatory autoimmune disease characterized by the production of autoantibodies that cause inflammation and damage to different organs. New therapeutic approaches for autoimmune diseases have been based on the fact that nematodes such as Trichinella spiralis decrease the inflammatory response by inducing the production of anti-inflammatory cytokines, which are potent modulators of T cell function. Recent studies have shown that the proteins secreted by T. spiralis, or the infection itself, induce a polarized Th2/Treg response and the production of regulatory cytokines, which are associated with the amelioration of autoimmune diseases such as colitis, respiratory tract inflammation, type 1 diabetes and experimental autoimmune encephalomyelitis. In this work, mice were infected and, after the life cycle was completed, a procedure to develop lupus was performed. The level of autoantibodies and antibodies anti-Trichinella were detected as well as the levels of Th1 and Th2 cytokines. Here, we show the relevance of studying the immune response in a murine model resembling the human lupus in the presence of T. spiralis muscular larvae, because it provides new information on the immunoregulation of lupus and reveals the effect on its progression.
Single-walled carbon nanotubes target neutrophils and Ly-6Chi monocytes and localize to joints in murine models of arthritis
Authors: Hung Shu-Chen , Rajasekaran Narendiran , Zhu Shoujun , Ma Zhuoran , Ghosn Eliver , Mellins Elizabeth D. 
Published: January 2023

Abstract
Rheumatoid arthritis (RA) is a chronic autoimmune disease that often leads to joint damage. The etiology of RA remains unclear, but new insights and therapeutic strategies have been facilitated by murine models. In the K/BxN serum transfer (STA) model, arthritis is triggered by autoantibodies against glucose-6-phosphate isomerase. The SKG model has a ZAP70 point mutation that reduces TCR signaling. After zymosan exposure, SKG mice develop arthritis, mediated by autoreactive Th17 cells. Joint inflammation in these models shares many features with RA, including leukocyte invasion, synovitis, and bone resorption. Neutrophils and Ly-6Chi monocytes are known to play critical roles in these models.1–4 Here, we investigated single-walled carbon nanotubes (SWNT) as candidate drug carriers to specifically target pathogenic cells in arthritic joints. Using FACS analysis, we found that, 2h and 4h after IV administration of SWNT, nearly 80% Ly-6Chi monocytes in blood had taken up SWNT in STA and SKG model, respectively. Near-infrared (NIR) photoluminescence whole-animal imaging of the STA model showed that SWNT were first detected in arthritic joints 3h post injection (p.i.) and reached a maximal level 24h p.i., In contrast, in non-arthritic mice, SWNT detected in joints remained low 24h p.i., suggesting SWNT can specifically target cells homing to or present in arthritic joints. In SKG mice, 2d p.i., SWNT were found in Ly-6Chi monocyte and in neutrophils in bone marrow and liver, but not in blood and spleen. FACS analysis indicated specific uptake of SWNT labelled with Cy5.5 in monocytes and neutrophils in human blood. We conclude that SWNT is a potential carrier to target drugs to pathogenic neutrophils and monocytes in arthritic joints.
T cells directed against different myelin antigen epitopes cooperate to induce autoimmune encephalomyelitis in mice
Authors: Rojano Elba Mirelle , Robinson Rachel R. , Forsthuber Thomas 
Published: January 2023

Abstract
Multiple Sclerosis (MS) is the most common demyelinating autoimmune disease of the central nervous system (CNS). Important insights have emerged into the pathogenic mechanisms that drive the inflammatory events and demyelination in MS, however, much less is known about the events initiating this disease. The murine model of MS, experimental autoimmune encephalomyelitis (EAE), is usually induced through injection with a high dose of single immunodominant peptides found on the myelin sheath of the CNS. Low doses of single peptide do not induce EAE or result in very low disease incidence. In individual MS patients, autoimmune T cell-reactivity is usually directed against multiple myelin antigen epitopes and fluctuates significantly over the course of disease. Thus, we hypothesize that MS is triggered by the emergence of autoreactive T cells directed against multiple myelin epitopes, which together synergize to induce the disease. To test this concept in an animal model of EAE, we explored the effect of induction of EAE using combinations of low dose peptides akin to a “multiple hit” mechanism implicated in other disease conditions. We found that EAE can be induced through the immunization of mice with a combination of low dose myelin peptides from different myelin proteins, which individually are suboptimal to induce disease. The disease observed after multi-peptide immunization is comparable or more severe than with optimal doses of peptide traditionally used to induce EAE. This research provides new insights into the potential mechanisms underlying the induction of MS and could lead to novel approaches for immunotherapy.
Immune Modulation and Vascular Repair Sustain Pancreatic Beta Cell Regeneration To Reverse Late Stage Type 1 Diabetes
Authors: Ukah Tobechukwu Kenneth , Cattin-Roy Alexis N. , Miller Mindy M. , Zaghouani Habib 
Published: January 2023

Abstract
Type 1 diabetes (T1D) is a chronic inflammatory disease which manifests when the pancreatic β-cells are destroyed by cells of the immune system. We have previously shown that antigen-specific therapy with Ig-GAD2, an Ig chimera carrying glutamic acid decarboxylase 206–220 sequence (GAD2), induces regeneration of β-cells and reverses T1D when intervention is made at the pre-diabetic stage. However, Ig-GAD2 could not reverse T1D when the treatment is made at the onset of disease (diabetic stage). Surprisingly, endothelial precursor cells (EPCs), alongside Ig-GAD2, sustain reversal of the disease at the diabetic stage. This combination therapy proved effective in driving immune modulation and repair of the islet vasculature leading to formation of new endogenous β-cells that were able to thrive and restore long-lasting normoglycemia. We now have evidence that combination therapy leads to formation of healthy islets by inducing division of residual β-cells and differentiation of precursor cells. Furthermore, while the pancreas is cleared of immune infiltration during recovery from disease, both the lymph nodes and spleen displayed a significant reduction in Th17 cells and the disease did not rebound. These findings suggest that combination therapy is able to drive long lasting immune modulation and islet vascular repair which provides a micro-environment suitable for regeneration of β-cells at late stages of the disease. These circumstances are relevant to humans as intervention could be made at early as well as late stages after diagnosis.
Contribution of Protein Arginine Methyltransferase (PRMT)5 to House Dust Mite Asthma
Authors: Guerau-De-Arellano Mireia , Sengupta Shouvonik , Amici Stephanie , Webb Lindsay , Weiss Kelly , Asosingh Kewal 
Published: January 2023

Abstract
Severe asthma affects 2.4 million Americans and 23.8 million people worldwide and accounts for the majority of total asthma hospital costs. Most severe asthma is mediated by Th17/neutrophilic responses, alone or combined with Th2 and/or Th1 responses. In contrast, Treg responses are deficient. Protein Arginine Methyl Transferase (PRMT) 5 catalyzes symmetric dimethylation (SDM) of arginine on histones and other proteins, thereby regulating gene expression. PRMT5 promotes murine Th1/Th17 responses in central nervous system autoimmunity. However, its impact on asthma has not been established. We evaluated the role of PRMT5 on mouse models of house dust mite (HDM) asthma. PRMT5 and its symmetric demethylation activity were increased in lung infiltrating cells during Th2/Th17-mediated HDM severe asthma, suggesting a role for PRMT5 in asthma pathogenesis. To determine the contribution of PRMT5 to HDM asthma pathogenesis, we used first-in-class PRMT5-specific inhibitors developed at The Ohio State University. PRMT5 inhibitor HLCL65 modulated Th1, Th2 and Th17 differentiation and suppressed airway hyperreactivity in Th2/Th17 models of house dust mite (HDM)-induced asthma. Overall, these results support a role for PRMT5 in severe asthma pathogenesis.
Rifampicin ameliorates inflammatory responses in asthma experimental animal model
Authors: Kang Tae Jin , Park Jun Woo , Prakash Annamneedi Venkata , Boo Kyung-Jun , Kim Yu Ri , Seong Ju-won 
Published: January 2023

Abstract
Drug repositioning is the application of known drugs and compounds to treat new diseases and is the process of identifying new uses for drugs outside the scope of their original medical indication. Our study previously revealed anti-atopic dermatitis activity of rifampicin, which is used for the treatment of tuberculosis. We herein investigated the effect of rifampicin on asthma. Asthma was induced in BALB/C mice and the mice were treated with rifampicin by oral administration. The inflammatory responses were alleviated in the rifampicin-treated group. Serum The level of inflammatory cytokines was ameliorated in bronchoalveolar lavage fluid (BALF) from mice treated with rifampicin. We next examined whether rifampicin has anti-atopic activity via suppression of mast cell activation. Rifampicin suppressed the release of β-hexosaminidase and histamine from human mast cell (HMC)-1 stimulated with compound 48/80. Treatment with rifampicin inhibited secretion of TNF-α and PGD2 in mast cells activated by compound 48/80. The mRNA expression of COX-2 was reduced in the cells treated with rifampicin. Our findings suggest that rifampicin has efficacy and could be applicable to develop potent therapeutic reagent for the treatment of asthma.