bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antigen-Specific CD4 T cells Protect Against Reproductive Pathology by Subverting Chlamydia-specific CD8 T cell Response
Authors: Li Weidang , Warda Katerina , Moy Lindsay N , Musunuri Tarakarama , Bui Nhi , Wright-McAfee Erika , Murthy Ashlesh K. 
Published: January 2023

Abstract
We have demonstrated previously that CD4 T cells are protective whereas CD8 T cells cause reproductive pathology following genital chlamydial infection. In this study, we explored the interactions of these cell types in context of vaccine-mediated protection. We evaluated three immunization regimens: live-chlamydial elementary body intranasal (EB-i.n.), live-EB i.m. (EB-i.m.), and irrelevant antigen bovine serum albumin i.n. (BSA-i.n.) that induced near-total (90%), partial (50%), and no (0%) protection, respectively against oviduct pathology following i.vag. C. muridarum challenge in C57BL6/J animals. We found no differences in Chlamydia-specific IFN-g, TNF-α, or IL-17 response from purified splenic CD8 T cells on days 7, 14, and 21 after immunization. We further evaluated Chlamydia-specific splenic CD8 T cell responses on days 3, 6, 9, and 12 following i.vag. chlamydial challenge. All groups of challenged animals displayed comparable induction of Ag-specific CD8 T cell cytokine responses on day 6 after challenge. As early as day 9 after challenge, Ag-specific IFN-g and TNF-α production from CD8 T cells was significantly reduced in EB-i.n.-immunized mice, and on day 12, both EB-i.n.- and EB-i.m.-immunized animals displayed minimal Ag-specific TNF-a production, compared to enhanced TNF-a production from CD8 T cells in BSA-i.n. immunized animals. Furthermore, adoptive transfer of Chlamydia-specific CD4 T cells at the time of genital infection induced significant reduction in Chlamydia-specific splenic CD8 T cell response on day 12 after challenge. In summary, these results suggest that Ag-specific CD4 T cells subvert a pathogenic Chlamydia-specific CD8 T cell response to protect against reproductive pathology.
Human liver CD69+CD103−CD8+ memory T cells are regulated by HIF-2α
Authors: Kim Jong Hoon , Han Ji Won , Choi Young Joon , Rha Min-Seok , Koh June-Young , Park Jun Yong , Park Su-Hyung , Joo Dong Jin , Shin Eui-Cheol 
Published: January 2023

Abstract
Human liver CD69+CD8+ T cells are ~95% CD103− and ~5% CD103+. Although CD69+CD103+CD8+ T cells show tissue residency and robustly respond to antigens, CD69+CD103−CD8+ T cells are not yet well understood. Here, we report that human liver CD69+CD103−CD8+ T cells exhibit a phenotype of tissue residency and terminal differentiation with hypoxia-inducible factor (HIF)-2α upregulation. CD103− T cells included both hepatotropic and non-hepatotropic viruses-specific cells whereas CD103+ T cells did only hepatotropic virus-specific cells. Although CD103− cells were weaker effectors on a per cell basis than CD103+ cells following T-cell receptor or interleukin-15 stimulation, they remained the major CD69+CD8+ effector population in the liver, surviving with less cell death. HIF-2α inhibitor or knockdown suppressed the effector functions and survival of CD69+CD103−CD8+ T cells. In addition, HIF-2α expression in liver CD69+CD103−CD8+ T cells was significantly increased in patients with acute hepatitis A or liver cirrhosis (LC). In patients with LC, the activation and increased function of liver CD69+CD103− CD8+ T cells were associated with their HIF-2α expression, which could be controlled by HIF-2α inhibition. In summary, we show that human liver CD69+CD103−CD8+ T cells showed terminally differentiated tissue resident phenotype regulated by HIF-2α.
Specific Subset of Dendritic Cells Control the Priming of Mucosal Th17 Cells
Authors: Ngoi Soo , Yang Yi , Iwanowycz Stephen , Liu Bei 
Published: January 2023

Abstract
Phagocytic mononuclear cells play an essential role in regulating gut immune homeostasis by sensing, internalizing microbial parts, and subsequently driving adaptive response in an antigen- and cytokine-dependent context. In a healthy host, physiological Th17 cells are predominantly generated in the gut, induced by local commensal microbiota. However, the precise subpopulation of antigen-presenting cells responsible for imprinting Th17 program in naïve CD4 T cells have not yet been definitively identified.

Objective
Mapping the functional subset of Th17-inducing dendritic cells (DCs) will uncover new targets for mucosal vaccine design.

Methods & Results
Using transgenic CD4 T cells specifically recognizing a gut-colonizing commensal bacterial antigen, we found that migratory DCs (CD11chiMHCIIhiZbtb46+) in the mesenteric lymph nodes are indispensable for the initial Th17 cell priming. Whereas the absence of CD103+ or CX3CR1+ DCs did not impact Th17 cell differentiation. Single cell RNA sequencing revealed that the migratory DCs are highly heterogeneous and consist of 8 clusters of transcriptionally specialized subsets. Interleukin-6, the Th17-polarizing cytokine, is expressed by a minor population of DCs with a type I interferon signature. Our results indicate that during homeostasis, Th17 cells activation in the mesenteric lymph nodes and later persistence in the small intestine may be controlled and sustained by different groups of antigen-presenting cells. The complexity and heterogeneity of mucosal DCs imply that other effector and regulatory T cell responses may be regulated by different DC subsets at this unique tissue environment.
Immune phenotypic analysis using pre-designed BD® AbSeq pan immune-response panel
Authors: Song Hye-Won , Narayan Punya , Tyznik Aaron J , Martin Jody , Lazaruk Katherine , Mortimer Stefanie 
Published: January 2023

Abstract
High-throughput single cell RNA sequencing (scRNA-seq) has recently emerged as a powerful tool for profiling complex cell populations. While traditional scRNA-seq captures information at transcript level, recent technology using DNA-barcoded antibodies enable multiomic analysis, examining protein alongside mRNA. Although this approach allows high parameter antibody panels, the sequencing cost can escalate quickly for high plexy panel with high antigen density markers. Therefore, thought should be put on panel design in order to gain meaningful results efficiently. Here, we have designed a panel for analyzing multiple immune responses, BD® AbSeq pan immune-response panel. Our immune response panel excludes abundant cell lineage markers which take up a huge amount of reads but provide only cell lineage information that can be easily resolved by RNA profiles only. This panel is focused on analyzing the various immune responses in multiple cell lineages. Therefore, it has a potential to be used to uncover phenotypic changes upon disease status with various immune stimuli. To test the capability of this AbSeq panel in discovery of phenotypic changes in multiple immune response, we have tested it in the various scenarios. We propose that the BD® AbSeq pan immune-response panel can be used to evaluate unpredictable disease phenotypes to identify the cell types affected from the disease as well as the responsible molecular pathways of the disease at a single cell level.
For Research Use Only. Not for use in diagnostic or therapeutic procedures.
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A Novel IL2-based Immunotherapeutic Protein Prevents the Development of Atherosclerosis in ApoE−/− mice and LDLR−/− mice
Authors: li Qiongzhen , Zhu Xiaoyun , Spanoudis Catherine , Ravelo Kristine , Dee Mike , Liu Bai , Prendes Caitlin , You Lijing , Wong Hing 
Published: January 2023

Abstract
Atherosclerosis is the leading cause of coronary heart disease and stroke. Sterile Inflammation, resulting from activation of the inflammasome NLRP3, plays a key role in the pathophysiology of atherosclerosis. Studies suggested that low-dose rIL-2 may be effective in treating autoimmune and inflammatory diseases by inducing Treg cells. Since rIL-2 has unfavorable pharmacokinetic profile in humans, we constructed a fusion protein, designated HCW9302, containing two IL-2 domains linked by an extracellular tissue factor domain, to extend the half-live of IL-2 for Treg expansion. In vitro treatment of human PBMCs with HCW9302 significantly expanded CD4+/CD25+/FoxP3+ Treg cells without activating CD4+ and CD8+ T cells over a broader concentration range than rIL2. Subcutaneous injection of HCW9302 (3 mg/kg every 2 – 3 weeks) into atherosclerosis-prone mice (ApoE−/− mice and LDLR−/− mice fed the Western Diet (WD) for 6 weeks) significantly increased the percentage of Treg cells, NK cells and CD8+ T cells in blood compared to the PBS-treated control group (p&lt;0.001). Cytokines associated with atherosclerosis, including IL-1β and MCP-1, were also significantly decreased in the HCW9302-treated group, suggesting HCW9302 can moderate inflammasome NLRP3 activities. Remarkably, HCW9302 lowered the fasting blood glucose and insulin resistance. In aortas evaluated by the en face method at week 13 of WD, the ratio of plaque size to aortic surface was also significantly lower in HCW9302-treated mice compared to controls. HCW9302 treatment was well tolerated in both models. In summary, HCW9302 can effectively prevent the development of atherosclerosis in ApoE−/− mice and LDLR−/− mice, potentially through expansion of Treg cells.
Infinity Flow: comprehensive single-cell protein profiling via massively parallel flow cytometry and machine learning
Authors: Becht Etienne , Headley Mark , Newell Evan , Gottardo Raphael 
Published: January 2023

Abstract
Modern flow cytometers can quantify around 20 proteins at the single-cell level. Higher-dimensional alternatives exist, such as mass cytometry, or oligonucleotides-tagged antibodies - but they feature lower cellular throughput, higher cost and are not as widely available. To overcome these limitations, we propose a pipeline which allows the quantification of hundreds of proteins across millions of single cells.
Experimentally, cells are stained with a customizable 10–20 “backbone” antibody panel which defines the cellular population structure of the sample. This is followed by aliquoting into hundreds (200–300) of individual wells, each containing a unique “exploratory” antibody. Data acquisition is performed using conventional flow cytometry.
Computationally, multivariate non-linear regression models are trained, one for each well. These models learn how to impute an exploratory antibody signal from backbone measurements. The models are each applied to the backbone data to obtain hundreds of imputed measurements across millions of single cells.
We applied this workflow cell suspensions from the lungs of C57/B6 mice, resulting in 2,660,000 events with imputed expression levels for 266 proteins. Imputed expression and co-expression patterns are accurate and consensual across regression models, allowing near-exhaustive annotation of both immune and non-immune cells, and finer granularity than dimensionality reduction or clustering.
By enabling broad characterization of cellular networks at the protein level, this pipeline is well-suited for systems immunology approaches. Given the wealth of data generated by this pipeline and its accessibility, we anticipate it will be widely adopted.
Cyto-feature engineering: a pipeline for flow cytometry analysis to uncover immune populations and association with disease
Authors: Fox Amy , Dutt Taru S. , Karger Burton , López Mauricio Rojas , Obregón-Henao Andrés , Anderson G. Brooke , Henao-Tamayo Marcela I 
Published: January 2023

Abstract
Flow cytometers can now analyze up to 50 parameters per cell and millions of cells per sample; however, conventional methods to analyze data are subjective and time-consuming. To address these issues, we have developed a novel analysis pipeline to identify a plethora of cell populations efficiently. Coupled with feature engineering and immunological context, researchers can immediately extrapolate novel discoveries through easy-to-understand plots. The R-based pipeline uses Fluorescence Minus One (FMO) controls or distinct population differences to develop thresholds for positive/negative marker expression. The continuous data is transformed into binary data, capturing a positive/negative biological dichotomy often of interest in characterizing cells. Next, a filtering step refines the data, from all identified cell phenotypes to populations of interest. The data can be partitioned by immune lineages and statistically correlated to other experimental measurements. The pipeline’s modular nature allows customization of statistical testing, adoption of alternative initial gating steps, and incorporation of other datasets. Validation of this pipeline through manual gating of two datasets (murine splenocytes and human whole blood) confirmed its accuracy in identifying even rare subsets. Lastly, this pipeline can be applied in all disciplines utilizing flow cytometry regardless of cytometer or panel design. The code is available at https://github.com/aef1004/cyto-feature_engineering.
Detection and Quantification of Extracellular Vesicles with Cargo Protein and RNA Using the Amnis® CellStream® Flow Cytometer
Authors: Kong Raymond K , Pugsley Haley Renee 
Published: January 2023

Abstract
Extracellular vesicles (EVs) are membrane-derived structures that include exosomes, microvesicles, and apoptotic bodies. These EVs—released under normal physiological conditions as well as in the pathogenesis of neurological, vascular, hematological, and autoimmune diseases—have been shown to transfer biological molecules such as protein and RNA between cells, potentially transmitting signals. To understand more about these signaling mechanisms, there is a need for detecting and quantifying EVs with cargo protein and RNA in a reproducible and reliable manner. However, this has been challenging due to the small size of EVs (ranging from 30 to 100 nm in diameter), and the lack of specific staining reagents. Here, we showcase the Amnis® CellStream® Flow Cytometer, which enables high-throughput flow cytometry with increased sensitivity for detecting small particles. We demonstrate that a charge-coupled device (CCD)-based, time-delay-integration image capturing system can be used to detect and quantify EVs and their cargo labeled with ExoGlow™-Protein or ExoGlow™-RNA.
A cloud-based bioinformatic and analytic infrastructure for the Expanded Program on Immunization Consortium
Authors: Vignolo Sofia , Diray-Arce Joann , McEnaney Kerry , Rao Shun , Consortium EPIC-HIPC , Ozonoff Al 
Published: January 2023

Abstract
The overarching goal of the Expanded Program for Immunization Consortium - Human Immunology Project Consortium (EPIC-HIPC) is to identify and characterize vaccine-induced neonatal responses and define biomarkers that may predict immunogenicity. Key to this effort is the establishment of the Data Management Core (DMC) to provide reliable clinical data and bioinformatic infrastructure for centralized curation, storage, and analysis of multiple deidentified ‘omics datasets. The DMC established a cloud-based platform to track, store, and share data according to set standards using Amazon Web Services (AWS). In our clinical core sites, biosamples collected and shipped across sites are tracked using ItemTracker via AWS Elastic Compute Cloud while their associated clinical data are captured using Research Electronic Data Capture software. Multi-omic datasets are stored in access-regulated Amazon Simple Storage Service (S3) for file version control. All data must complete quality control (QC) processes by the site generating said data, which is then exported to the DMC for quality assurance (QA). Data integration is performed using RStudio Server Pro which directly imports the data files from Amazon S3 via a controlled computing environment. The DMC deposits finalized datasets onto public repositories to be shared openly upon publication. Completion of our goal will provide the resources, planning, and scientific expertise to make this discovery platform possible. Robust DMC operations will allow rapid sharing of integrative results across the entire team. Maintenance of standards and public deposition of high quality ‘omics data will further advance scientific progress for the benefit of vaccine development and public health.
A single-marker method of renal cDC2 isolation
Authors: Bates Briana L , Mikulin Joseph A , Wilson Timothy J 
Published: January 2023

Abstract
Because of their ability to present antigens, respond to inflammatory signals, and produce critical acute-phase cytokines, renal dendritic cells are of particular interest to those studying various disease states of the kidney. Markers such as CD11c, MHC-II, CX3CR1, and CD11b have historically been used in the murine system to isolate renal dendritic cells from the various parenchymal cells among which they’re embedded. In this study, we have determined that signaling lymphocyte activation molecule family member 9 (SLAMF9) is sufficient to mark the population of CD11b+ MHCIIhi CX3CR1+ CD11c+ F4/80+ cells in the murine kidney under homeostatic conditions. Using SLAMF9, we have devised a single-marker method of renal cDC2 isolation via fluorescence-activated cell sorting (FACS). This method will allow isolation of mouse CD11b+ dendritic cells with minimal surface receptor interference.
Regulation of body temperature in Canadian beef cattle of various immune response phenotypes when the temperature humidity index is above normal
Authors: Husseini Nasrin , Altvater-Hughes Tess , Beard Shannon , Hodgins Douglas , Mallard Bonnie A 
Published: January 2023

Abstract
Climate change with increases in ambient temperature and humidity, affect animal life dramatically decreasing their production and reproduction potential, as well as making them more susceptible to different diseases. This leads to an increase in their core body temperature and respiration rate which in turn decreases their production, reproduction, and immune function. The High Immune Response (HIR™) technology which has been developed at the University of Guelph ranks animals using two arms of adaptive immune system to high (H), average (A), and low (L) immune responders. (H) immune responders have been reported to have fewer incidents of disease and robust immune response. (H) immune responders have been also reported to have better colostrum and milk quality making them an ideal model to examine the effects of climate change on health traits. The objective of this study was to check if (H) immune responder beef cattle are able to regulate their rectal temperature better. In this study, rectal temperatures of 36 beef cows were recorded during normal Temperature-Humidity Index (THI&lt;74) and above normal THI (THI ≥ 74) once in the morning and once in the afternoon. Results indicated that 62.5% of cows showed increases in rectal temperature in THI ≥ 74. However, mean rectal temperatures of (H) antibody-mediated immune responders did not differ significantly during THI &lt; 74 and THI ≥ 74; indicating that these high antibody responder beef cows were better able to regulate their body temperatures.
This is the first time that genetic regulation of an immune response trait has been shown to influence the response to in vivo heat stress indicating that it may be possible to select cattle with both improved health and heat tolerance.
Development of a competition ELISA (cELISA) for specific detection of Zika virus antibodies in human sera
Authors: Katz David , He Dan , Patrusheva Irina , Maria Clara Echevery G , Ortiz Carolina , Hughes Holly R , Moreno Alberto , Walia Vishakh , Hilliard Julia 
Published: January 2023

Abstract
Infections by Zika virus (ZIKV), a member of the Flavivirus genus, can be diagnosed by virus isolation, detection of virus RNA or by serological methods for detecting ZIKV immunoglobulin M antibodies (IgM), a marker of recent infections, and immunoglobulin G antibodies (IgG), a marker of past infections. In some cases, where IgM antibodies may last for longer periods, accurate diagnosis of recent infections is not always possible. Because commercial and non-commercial serological tests are often confounded by cross-reactivity with other Flaviviruses there is a need for simple, ZIKV-specific serological tests. Here, we present the development of a ZIKV-specific ELISA in which cross-reacting antibodies in serum samples are competed and blocked by Dengue virus antigens (DENV). The competed sera are then tested by ELISA on ZIKV and DENV coated wells to enable a calculation of a ZIKV/DENV (Z/D) cutoff ratio. For the development and validation of the ZIKV specific cELISA we have used three groups of sera from Colombia. 49 sera were obtained in 2018 from individuals that have been infected with ZIKV during a 2016 outbreak. The outbreak was in a DENV endemic area. Another group of 19 sera were obtained from a known DENV endemic area with no evidence of any ZIKV infections. The third group of 12 sera were obtained from patients from an area with no known Flavivirus infections and therefore considered as negative for both ZIKV and DENV. A Z/D ratio of 1.5 was determined as the cutoff value for the specific determination of ZIKV positive or negative sera. Our analysis indicated a 85% agreement with the BOB assay, and a 78% agreement with the commercial IgG ELISA test. The estimated specificity and sensitivity for the cELISA were 70% and 82%, respectively.
The EPIC data analytics platform for clinical mass cytometry
Authors: Wasser Martin , Yeo Joo Guan , Kumar Pavanish , Chew Valerie , Lim Chun Jye , Arkachaisri Thaschawee , Poh Su Li , Leong Jing Yao , Yeo Kee Thai , Albani Salvatore 
Published: January 2023

Abstract
Single cell technologies, such as high-dimensional cytometry, promise to enable the discovery of immune cell populations that will serve as clinical biomarkers. Recently, we reported the creation of a reference database of the healthy immune system from birth to old age and the development of the EPIC (Extended Poly-dimensional Immunome characterisation) data mining platform (Nature Biotech, accepted). Here we extend the analytics pipeline to facilitate detection of clinically stratifying cell populations in mass cytometry (CyTOF or cytometry by time-of-flight) data. Data structures called immune maps are used to integrate single cell protein expression data (over 40) of multiple samples with clinical metadata and phenotypic information inferred from automated clustering and assisted cell type annotation. Clustering is combined with batch effect correction to reduce technical while preserving biological variations. Subsequent single cell exploratory data analysis and statistical tests help to identify cell populations whose frequencies differ significantly between groups of patients. To gain further insights, users can compare their cytometry data with the healthy reference immunome by performing two types of analysis; (1) mapping to existing clusters helps obtain abundance estimates of immune cell types, (2) reclustering of uploaded data merged with reference immunomes uncovers differences to healthy immune profiles of different ages. We implemented the EPIC pipeline using R Shiny to provide interactive visualisation and an intuitive user interface. We will show examples on how the EPIC platform can characterise cellular diversity in the context of disease and the morphogenesis of the healthy immune system.