bluuebunny/crossref_metadata_2025_split huggingface dataset:
Batf3 is a critical transcription factor in IL-2 mediated programming of CD8+ T cell memory.
Authors: Nagaraja Shashank , Pipkin Matthew 
Published: November 2024

Abstract
CD8+ T cell activation triggers chromatin remodeling and transcription factor (TF) binding, leading to differentiation into effector (TEFF) and a spectrum of memory (TMEM) phenotypes. Previous studies have found modified chromatin accessibility at loci encoding Basic Leucine Zipper (bZIP) family motifs; however, specific mechanisms of transcriptional regulation by these TFs to program TMEM are not fully understood. During TCR stimulation, transient upregulation of bZIP TF Batf3 is accompanied by binding of genomic loci encoding its motif. Nascent RNA sequencing of IL-2Rα-/- CD8+T cells shows that Batf3 upregulation upon TCR stimulation is highly dependent on IL-2R signaling. Constitutive loss of either IL-2Rα or Batf3 results in decreased survival of CD8+ T cells during the transition from effector to memory phase of acute LCMVArm infection, and reduced immunological memory towards infection re-challenge. We find that enforced overexpression of Batf3 cDNA using a retroviral vector in virus-specific IL-2Rα-/- CD8+ T cells greatly enhanced their capacity for survival into the contraction phase of primary infection. Upon secondary infection, ectopic Batf3 expression rescued the proliferation defect seen in IL-2Rα-/- CD8+ T cells. These results suggest that Batf3 plays a crucial role within the IL-2R signal transduction cascade during CD8+ T cell activation to promote enhanced cell survival into the memory phase of infection response.
Maternal hypertension alters offspring’s glial cell proportions and behavior
Authors: Johnson Morgan , Liu Yu , Brummond Daniel , Mikkelsen Emma , Bunton Olivia , Scroggins Douglas , Heck Detlef , Scroggins Sabrina 
Published: November 2024

Abstract
Preeclampsia (PreE), a hypertensive disorder during pregnancy, is a primary contributor to global obstetric morbidity and mortality. Its effects encompass heightened risks of cognitive impairment and behavior disorders in children born to mothers with PreE. The objective of our study was to determine whether PreE leads to early modifications in the brain's glial cell populations and/or behavioral changes in offspring. To induce PreE, C57BL/6J dams received vasopressin or saline through subcutaneous infusion throughout gestation. Following natural parturition, offspring were euthanized at various postnatal timepoints for glial cell analysis and behavioral evaluation. Flow cytometry was utilized to assess microglia and astrocyte populations. Offspring of PreE pregnancies exhibited decreased total microglia and astrocytes in the brain. Additionally, when compared to offspring from normotensive pregnancies, those born to mothers with PreE displayed impaired performance in the spontaneous alternation Plus-maze task, signifying altered spatial working memory. Our findings substantiate that PreE leads to diminished glial cell populations in offspring postnatally, and these mice exhibit changes in spatial working memory. Continuing research aims to elucidate the influence of PreE on the numbers and functioning of glial cells, along with examining how the compromised numbers and/or functionality of these cells affects the behavior and cognition of offspring born to mothers with PreE.
Evaluating the impact of influenza infection on pig lungs by single-cell RNA sequencing (scRNA-seq)
Authors: Madrid Darling Melany , Gu Weihong , May Alyssa , Touchard Laurie , Wen Yuhan , Driver John 
Published: November 2024

Abstract
Despite being the most widely consumed meat worldwide, the pig industry faces economic challenges from respiratory viruses including influenza. Pigs are also used as a reliable translational model for human respiratory disorders due to their similar respiratory tracts. However, limited pig-specific reagents have hindered understanding the pig’s immune system. Hence, here we used single cell RNA sequencing (scRNAseq) for unbiased transcriptional profiling of pig immune responses during influenza infection and oseltamivir antiviral therapy. Fourteen six-week-old mixed-breed pigs were intratracheally infected with pandemic 2009 H1N1 influenza virus. Seven of these pigs were treated for 5 days with oseltamivir. A control group was mock-infected. Lung samples were taken 5 days post-infection for scRNAseq, histopathology, and virus titers. We identified 24 pig leukocytes populations which were integrated with previously published human and mouse lung cells. Influenza virus infection/oseltamivir treatment altered the cellular composition, transcriptional networks, and cell-cell interactions in the lung. γδ T cells that are unique to pigs and abundant in the lung responded strongly to infection. Oseltamivir reduced antiviral and inflammatory responses. Our data provide a resource to better understand the pulmonary immune responses of pigs and advances using swine as a model for studying human pulmonary immune responses.
Simultaneous spatial profiling of mRNAs, cell surface proteins and cell surface protein protein interactions in human tonsil.
Authors: wang huili , Xia Junjie , Clark Marcus , Tay Savas 
Published: November 2024

Abstract
Protein-protein interactions are critical for the functionality of proteins and, consequently, for signaling events in numerous biological processes. High-throughput technologies capable of profiling these interactions at a spatial level are essential for deeper insights. In this study, we introduce Spatial Proximity-Sequencing (Sprox-seq), a novel technology that leverages proximity-sequencing with the 10x Visium platform for the concurrent detection of mRNAs, cell surface proteins, and protein-protein interactions. We utilized Sprox-seq to profile 20 proteins and their interactions along with whole transcriptomics in human tonsils. Our analysis revealed that protein-protein interaction-based clustering correlates well with RNA-based clustering and reflects the tissue's anatomical structure. Furthermore, we could distinguish the dark and light zones of germinal centers using differential protein expression and interaction patterns. Detailed examination of four distinct germinal centers revealed that protein and interaction data could identify one germinal center, which mRNA data could not achieve. Moreover, our study identified numerous differentially expressed protein interactions, including a range of previously uncharacterized interactions, indicating an important role in the development of germinal centers. Overall, our findings demonstrate that Sprox-seq can provide a multifaceted view of spatial molecular dynamics and discover new protein protein interactions.
Generating reliable custom MHC tetramers with the QuickSwitchTM tetramer platform.
Authors: Poluektov Yuri , Delcommenne Marc 
Published: November 2024

Abstract
Progress in immunology research depends on the continuous development of novel, more adapted and more user-friendly research tools. In 1996 Altman and Davis invented MHC class I tetramers for directly monitoring MHC/peptide specific CD8+ T cells by flow cytometry. Production of MHC tetramers is long and labor intensive and requires advance knowledge of the peptide sequences to be incorporated in these complexes. The recent Covid-19 pandemic has led to new vaccination strategies, which rely on selecting a collection of immunogenic peptides and generating mRNA constructs that contain these sequences. Peptide selection is primarily based on in silico MHC binding tools, which do not always give reliable results. After this first selection step it is necessary to validate MHC peptide binding. For this purpose, a dual use platform was devised, for both assessing MHC peptide binding in a semi-quantitative manner and for T cell staining. The assay is based on a placeholder peptide (or exiting peptide) that can be exchanged for higher affinity binding peptides. Kits with most frequent MHC class I or II alleles are available. Multiple MHC class I and II tetramers can quickly be generated and used for staining within a couple of days.
Development of a novel long-acting injectable, IVL4002 for modulation of multiple sclerosis: Pharmacokinetics and efficacy studies in an experimental autoimmune encephalomyelitis mouse model
Authors: Kim Ju Hee , Youm Soyoung , Lee Slgirim , Lee Mase 
Published: November 2024

Abstract
Multiple sclerosis (MS), a prevalent autoimmune disease and lacking a well-defined etiology and cures, drove the development of diverse disease-modifying therapies (DMTs). Despite the efficacy of DMTs and immunosuppressants, challenges persist, including adverse effects and varying response rates. A promising approach involves the utilization of a novel drug delivery system (DDS) for controlled drug release. Herein, we introduce a novel long-acting injectable (LAI) designed for MS modulation, IVL4002, developed using IVL-DrugFluidics™ manufacturing platform. IVL4002 comprises monodisperse microspheres encapsulating an FDA-approved drug which was discovered by drug repurposing. The selected drug has been utilized in the clinic for a non-MS CNS indication with a favorable safety profile and has also been used in autoimmune diseases off-label for decades. As shown in the preclinical pharmacokinetics studies, IVL4002 maintains drug levels within the target range over 4 weeks without a burst release. Combined with the advanced DDS, the drug was repurposed for MS management, of which the efficacy was shown in experimental autoimmune encephalomyelitis mice by reducing the pro-inflammatory cytokine release. In conclusion, our physicochemical and pharmacological studies underscored the potential of IVL4002 to be used as a 1-month LAI for MS management. Positive results have led to the approval of a Phase 1 clinical trial and it is expected to begin in the second-half of 2024.
TLR7-agonist nanoparticle adjuvant modulates germinal center responses and promotes broad antibody responses against heterologous viral strains of influenza and SARS-CoV-2
Authors: Yin Qian , Luo Wei , Pulendran Bali , Davis Mark 
Published: November 2024

Abstract
The ideal vaccine against viruses such as influenza and SARS-CoV-2 must provide robust, durable, and broad immune protection against multiple viral variants. However, antibody responses to current vaccines often lack robust cross-reactivity. To tackle this challenge, we develop a polymeric Toll-like receptor 7 agonist nanoparticle (TLR7-NP) adjuvant, which enhances lymph node targeting, promotes persistent immune cell activation, and leads to early germinal center responses. When mixed with alum-adsorbed antigens, this TLR7-NP adjuvant elicits cross-reactive antibodies for both dominant and subdominant epitopes in mice. This TLR7-NP-adjuvanted influenza subunit vaccine successfully protects mice against the viral challenge of a different strain. This strategy also enhances the antibody response to a SARS-CoV-2 subunit vaccine against multiple viral variants that have emerged. Moreover, this TLR7-NP augments antigen-specific immune responses in human tonsil organoids. Overall, we describe a nanoparticle adjuvant to improve immune responses to viral antigens, with promising implications for developing broadly protective vaccines.
Antibody profiling of COVID-19 patients reveals antibodies and autoantibodies that may be associated with faster recovery from COVID-19
Authors: Onabajo Olusegun , Budde Petra , Kuebler Peter , Bräutigam Manuel , Haridha Shivram , Stubbings William , Tsai Larry , Zucht Hans-Dieter , Chandler G Scott , McBride Jacqueline , Bauer Rebecca 
Published: November 2024

Abstract
COVID-19 infection exhibits a broad spectrum of clinical outcomes and a combination of host and viral factors interact to drive variability in COVID-19 outcomes. While some studies showed severe COVID-19 patients were more likely to have neutralizing autoantibodies to type-I IFNs relative to the general population, other studies showed preexisting immunity to endemic coronaviruses could be beneficial. This suggests comprehensive evaluation of antibodies and autoantibodies associated with COVID-19 outcomes could reveal important host factors contributing to disease outcomes. Here we profiled antibodies to 87 bacterial and viral proteins, including SARS-CoV-2, and autoantibodies to 383 immune- and autoimmune-associated antigens using the Oncimmune serological profiling technology. A total of 460 patients from two COVID-19 clinical trials (COVACTA, NCT04320615, and MARIPOSA, NCT04363736) were used in this study, and baseline levels of antibodies and autoantibodies in serum samples were associated with COVID-19 outcomes. We observed higher autoantibodies to type-I IFNs and some chemokines were associated with longer time to hospital discharge (TTHD), while higher autoantibodies to IL-6 and IL-36A led to faster TTHD. High levels of antibodies to endemic coronaviruses and seasonal influenza were also associated with faster TTHD. These findings suggest preexisting host antibody and autoantibody repertoire could provide some protection from the more severe consequences of COVID-19.
Fate mapping LAG3+ exhausted CD8+ T cells.
Authors: Aggarwal Vaishali , Liu Chang , Jian Cui , Wang Haiguang , Manne Sasikanth , Vignali Kate M , Wherry Edward , Workman Creg , Vignali Dario 
Published: November 2024

Abstract
T cell exhaustion, a state of T cell dysfunctionality is well defined in chronic viral infections, however, not completely understood in tumor setting. The exhausted T cells (TEX) express high levels of LAG3, an inhibitory receptor regulating T cell exhaustion. We hypothesize defining lineage heterogeneity and plasticity of LAG3+ T cells, would be insightful in determining fate and functionality of these cells. We generated a novel lineage tracing Lag3iCreERT2Rosa26LSL-tdTomato mouse strain facilitating temporal assessment of LAG3+ cells using tamoxifen induced pulse/chase scheme. This enables fate-mapping of ‘bona fide’ tumor-reactive LAG3+ cells and understanding their transcriptional and epigenetic profiles. We identified two distinct LAG3- tdT+ and LAG3+ tdT+ exhausted T cell populations characterized with tdT+ expression. These two distinct tdT+ subsets are transcriptionally, and epigenetically distinct. The LAG3- tdT+ cells are derived from cleavage of surfaceLAG3 and are ‘stem-like’ exhausted CD8+ T cells with intermediate PD-1 expression. These ‘stem-like’ exhausted CD8+ T cells persist in vivo, have differentiation plasticity and contribute to peripheral tumor-specific memory. The other subset, LAG3+ tdT+ T cells are ‘terminally exhausted’, restricted to tumor microenvironment and express high levels of PD-1, TIM-3 and TIGIT. Overall, this model provides a unique advantage of characterizing LAG3- tdT+ ‘stem-like’ exhausted CD8+ T cells.
Twenty-Color Immuno-Analysis of Tumor-Infiltrating Lymphocytes in Lung Cancer
Authors: Ma Weide , Ma Yanhong , Yue Danqi , Anderson Keon , Chu Dongdong , Zhang Yaxuan , Zhang Long , Deng Jun , Edinger Mark , Wang Xiaoyang (Alice) 
Published: November 2024

Abstract
Tumor-infiltrating lymphocytes (TILs) are naturally occurring immune cells residing in the solid tumor microenvironment. Some of these TILs are tumor specific and may possess cytotoxic anti-tumor activity. The harvesting, selection, expansion, and reinfusion of these cells represent a current therapeutic approach that may prove to be safe and effective.
We developed an immunophenotyping panel to study the tumor microenvironment in human lung cancer specimens. This is a broad panel that includes blood and epithelial cell markers. Twenty lung cancer samples were collected following institutional protocol and dissociated into single cells within 24 hours of resection. Cells were then stained and data was acquired on a 3 laser Cytek™ Aurora™ spectral flow cytometer.
The frequencies of cell populations were measured. Increased percentages of intermediate and non-classical monocyte subsets were observed. PD-L1 was detected on neoplastic epithelial cells and EMT (epithelial-mesenchymal transition) cells. Interestingly, a population of CD45 and EpCAM double positive cells was detected in some samples. These cells expressed both epithelial and macrophage markers, suggesting a macrophage lineage origin with abnormal expression.
This streamlined single cell sample preparation and multiparametric panel provide an efficient method for the analysis of the tumor microenvironment. Expansion of the sorted cytotoxic TILs could potentially be reinfused into a patient for cancer treatment.
Silicosis and silica-induced autoimmunity in multiple Collaborative Cross strains.
Authors: de Ocampo Caroline , Mayeux Jessica , Kono Dwight , Pollard Michael , Janssen Lisa 
Published: November 2024

Abstract
Background: The connection between pulmonary silica dust exposure and the development of systemic autoimmunity is well established. However, the extent to which genetic differences influence the severity of silica-induced autoimmunity remains unclear.
Objective: Investigate the role of silica exposure on disease biomarkers (cytokines/chemokines and antinuclear antibodies (ANA)) and systemic autoimmune disease in genetically diverse Collaborative Cross recombinant inbred (CC RI) mice.
Methods: Baseline serum ANA and chemokines/cytokines were assessed from 61 CC RI strains. Six CC RI strains, chosen to represent different baseline immune phenotypes, were exposed to 5 mg crystalline silica or PBS and examined 12 weeks later for serum ANA, bronchoalveolar lavage fluid cell counts, tracheobronchial lymph node and spleen weights, and histological assessment of silicosis and lupus nephritis.
Results: All strains developed silicosis; however, two strains with low baseline immune activity did not develop silica-induced autoimmunity. In contrast, strains with higher baseline immune activity developed elevated ANA levels with strain variation in ANA types. One strain developed lupus nephritis, with significantly greater severity compared to controls.
Conclusion: Baseline immune activity significantly influences the development of silica-induced autoimmunity and lung inflammation; however, genetics may be mediating silicosis and systemic autoimmunity independently.
Arid5a-dependent RNA translation underlies pathology in IL-17-driven autoantibody-induced glomerulonephritis
Authors: Li Yang , Vyas Shachi , Mehta Isha , Asada Nariaki , Dey Ipsita , Taylor Tiffany , Bechara Rami , Amatya Nilesh , Aggor Felix , Coleman Bianca , Li De-Dong , Yamamoto Kenta , Ezenwa Ogechukwu , Sun Yeque , Sterneck Esta , McManus C Joel , Panzer Ulf 
Published: November 2024

Abstract
Autoantibody-mediated glomerulonephritis (AGN) results from kidney-damaging autoimmune responses, and there is urgent need for better treatment. Emerging studies implicate Th17 cells in AGN. IL-17 signals in part through the noncanonical RNA binding protein Arid5a, which we show is induced in renal epithelial cells (RTECs) in an IL-17-dependent manner during experimental AGN. Arid5a is undetectable in healthy kidney but elevated in human glomerulonephritis biopsies. Arid5a-/- mice were refractory to AGN. Mice lacking C/EBPd but not IkBz were protected from AGN. Although Arid5a bound to Cebpd mRNA, Arid5a-deficiency did not alter cellular Cebpd mRNA concentrations, whereas C/EBPd protein levels were substantially suppressed. In line with this, global protein synthesis was suppressed in RTECs lacking Arid5a. Transcriptome-wide RIP-Seq analysis in RTECs and stromal cells showed that IL-17 prompts Arid5a to bind to inflammatory mRNAs. Additionally and unexpectedly, Arid5a interacted with ribosomal RNAs (rRNAs) and other transcripts involved in protein translation. After IL-17 treatment, Arid5a was enriched in the cytoplasm and associated with the ribosome through interactions with 40S and 60S rRNAs. Accordingly, Arid5a drives IL-17-induced renal autoimmunity through post-transcriptional control of RNA at the level of translation and ribosome interactions, providing mechanistic insight into how cytokines mediate inflammation.
TGFb-JMJD3 pathway regulates fibroblast to myofibroblast transition in wound repair
Authors: Bauer Tyler , Mangum Kevin , Barrett Emily , Shadiow James , Joshi Amrita , Buckley Samuel , Wasilowski Rachel , Moore Bethany , Gudjonnson Johann , Davis Frank , Gallagher Katherine 
Published: November 2024

Abstract
In normal wound healing, resident fibroblasts transition to myofibroblasts, which function to contract and close wounds. In pathologic conditions where wounds fail to heal (such as diabetes), fibroblasts do not increase myofibroblast gene expression; this mechanism is poorly understood. Using human wound scSeq and murine transgenic models, we examined the epigenetic mechanisms that may regulate this transition in the setting of injury. First, we identify that the cytokine TGFb increases myofibroblast genes in vitro. We performed an epigenetic superarray on TGFb-stimulated dermal fibroblasts, where JMJD3, an H3K27 demethylase, was significantly upregulated and was also confirmed by qPCR. ScSeq of human wounds identified JMJD3 as strongly upregulated in myofibroblasts. ChIP identified decreased H3K27me3, the activating mark of JMJD3 at myofibroblast genes further confirming its role in regulating myofibroblast genes. SiRNA knockdown of JMJD3 led to reduced myofibroblast gene expression. These findings were confirmed in a novel, tamoxifen induced, fibroblast specific knockout of JMJD3 unique to our lab. An unbaised superarray focused on remodelling and cell adhesion pathways identified that these mice have deficient levels of many structural and remodelling genes. Murine wounds were found to upregulate JMJD3 compared to distant skin, which was less pronounced in diabetic wounds. This work identifies JMJD3 as a TGFb-mediated regulator of fibroblast to myofibroblast transition.
Lanthionine synthetase C-like receptors reduce eosinophilia, type 2 immune responses and lung inflammatory pathology in mouse models of asthma
Authors: Leber Andrew , Hontecillas Raquel , Tubau-Juni Nuria , Bassaganya-Riera Josep 
Published: November 2024

Abstract
Airway hyperresponsiveness and asthma are associated with altered glucose metabolism with inhibition of anaerobic glycolysis reducing inflammation and lung eosinophilia. LANCL receptors are key focal points for metabolism in immune cells, controlling mitochondrial mass and oxidative pathways all while promoting immunoregulatory differentiation. Knockout of LANCL receptors leads to diminished Treg differentiation, altered epithelial cell metabolism and impaired phagocytic clearance, all of which can contribute to the chronicity of asthma. We developed an oral agonist for LANCL receptors and tested it within ovalbumin and house dust mite induced models of asthma in mice. Treatment in vitro with the agonist resulted in reduced differentiation of inflammatory and allergic CD4+ T cells and reduced production of inflammatory cytokines in macrophages. In the OVA model, oral treatment with an LANCL therapeutic, beginning on the second day of aerosol challenge significantly reduced neutrophilia and eosinophilia in the lung by flow cytometry and histology. LANCL treatment significantly reduced anti-OVA IgE titers and type 2 cytokines, IL-5 and IL-13. Reduction of eosinophilia and type 2 immune responses were validated in the house dust mite model. In both models, lung gene expression trends were consistent with improved pulmonary function and mitochondrial metabolism. Thus, activation of LANCL receptors is a feasible strategy for the treatment of asthma and pulmonary inflammation.