bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeting IRF3 to increase the efficacy of oncolytic herpesvirus in mouse cancer cells
Authors: Benencia Fabian , Matocha Grace , Courreges Maria , McCall Kelly 
Published: November 2024

Abstract
Oncolytic viruses (OV) specifically infect and kill tumor cells because these cells harbor a defective IFN response or express proteins that block apoptosis pathways. Oncolytic herpesvirus (HSV) infection activates pathogen recognition receptors as part of the innate immune response. HSV genome contains un-methylated CpG motifs which activate toll-like receptor TLR9, and during infection it generates dsRNA intermediates which can activate TLR3, RIG-I, MDA5, and STING. Signaling pathways downstream of dsRNA recognition activate pro-apoptotic IRF3 leading to the production of type-I IFN, induction of co-stimulatory molecules and caspase cascade activation. We hypothesize that inhibiting IRF3 will diminish the antiviral response, increasing the efficacy of the OV. Here, we inhibited IRF3 expression in murine ovarian cancer cells with phenylmethimazole (C10), which inhibits dsRNA-triggered IRF3 signaling, preventing induction of type-I IFN gene expression, and type-I IFN production and signaling. Cancer cells treated with C10 were more susceptible to oncolytic HSV, as measured by increased cell death. The innate antiviral response in those cells was diminished as shown by lower levels of CXCL10 produced by infected cells. The levels of immunogenic cell death markers, e.g., HGMB1, were not decreased in C10-treated infected cells, indicating that the immunogenicity of the killed tumor cells is preserved. Thus, targeting IRF3 can be a strategy to increase the efficacy of OV.
Effect of extracellular matrix components and tumors factors from breast cancer on the biological properties of myeloid cells in the mouse model
Authors: Benencia Fabian , Matocha Grace , Cunningham Aiden , Courreges Maria 
Published: November 2024

Abstract
The tumor microenvironment (TME) is composed of cells and extracellular matrix (ECM) components that oftentimes help cancer cells to survive and growth. Immune cells, whose role is to protect against infections or malignancies, can be coopted by the TME or reprogrammed by tumor factors rendering them incapable of fighting the tumor inducing a protumor phenotype. Key immune cells affected in this process are antigen presenting cells (APCs) such as dendritic cells (DC) and macrophages (Macs). The effect of soluble factors produced by tumors (i.e., VEGF and TGF beta) on these cells has been broadly studied, but other factors such as extracellular matrix components can also alter their biology. Herewith, we were able to determine that APCs infiltrating the TME of the 4T1 model of breast cancer express angiogenic factors and chemokine receptors. In addition, we observed that tumor factors were able to induce migration of DCs and Macs. Furthermore, we detected markers of proliferation in tumor-infiltrating APCs, indicating that these cells might also be able to proliferate within the TME. We observed that tumor supernatants can activate these APCs invitro, and that this activation is partially mediated via TLR4 signaling. Finally, we observed that tumor cells and mouse tumors produce both fibronectin and fibronectin-extracellular domain (a known DAMP and activator of TLR4). Thus, production of ECM components by tumor cells can help shape the phenotype of tumor-associated APCs.
Gamma-Delta (γδ) CAR-T Cells targeting CD33 and lacking the CD3ζ signaling domain enhance killing of AML cells without toxicity to normal hematopoietic cells
Authors: Lamb Lawrence , Ding Lei , Li Yanjie , Li Jixue , ter Haak Mariska 
Published: November 2024

Abstract
Extending CAR-T therapy to myeloid malignancies has proven challenging due to co-expression of targetable antigens on hematopoietic progenitors. We leveraged the enhanced targeting conferred by CAR-T technology with the broad stress-associated antigen recognition and killing capabilities of γδ T cells by employing a non-signaling CAR (nsCAR) that excludes the CD3ζ domain, thereby facilitating targeted tumor recognition while sparing healthy tissues. Jurkat cells expressing a CD3ζ+ CD33+ CAR showed significant upregulation of CD69 in co-culture with KG1a AML cells but nsCAR-expressing Jurkat cells did not upregulate CD69. A time-dependent reduction (43%) in the CD3ζ+CD33CAR+ Jurkat population was also noted over a 7-day coculture while the nsCAR+ Jurkat population remained stable, suggesting improved durability of the nsCAR modified Jurkat cells. nsCAR-expressing expanded and activated γδ T cells from healthy donors exhibited enhanced killing against AML lines HL-60 (1.3x) and K-562 (1.6x) compared to unmodified γδ T cells (UTD) in a 24-hour cytotoxicity assay. Incorporation of sIL-15 also increased killing (1.8x for HL-60, 2.6x for KG-1a, 2.0x for MOLM-13 2.0x for K-562). Minimal cytotoxicity (&lt;10%) was observed for nsCARs or UTD γδ T cells against CD34+ HPCs. Our findings suggest that combining nsCAR constructs with γδ T cells may widen the therapeutic window to enable of CAR-T therapy for cancers with target antigen expression on healthy tissues.
A viral-specific CD4+ T cell response protects female mice from Coxsackievirus B3 infection
Authors: Pattnaik Aryamav , Dhalech Adeeba , Condotta Stephanie , Corn Caleb , Richer Martin , Snell Laura , Robinson Christopher 
Published: November 2024

Abstract
Biological sex significantly influences the ability of humans to respond to various pathogens. Males are frequently more susceptible to viral, bacterial, and fungal infections, often attributed to weaker immune responses. In contrast, a heightened immune response in females enables better pathogen elimination but leaves females more predisposed to autoimmune diseases. Unfortunately, the underlying basis for sex-specific immune responses remains poorly understood. Here, we show that Coxsackievirus B3 (CVB3) elicits a distinctive CD4+ T cell response in female but not male mice. We found that CVB3 elicits the expansion of CD62Llo CD4+ T cells in the mesenteric lymph node and spleen of female but not male mice five days post-inoculation, signifying early activation. Using a recombinant CVB3 expressing a model CD4+ T cell epitope, we found that this response is due to viral antigen. Further, we found that depleting CD4+ T cells before CVB3 infection increases mortality in females, underscoring their protective role against CVB3. Currently, we are characterizing the differentiation of CD4+ T cells to examine the role of specific subtypes in the sex bias. Overall, our data demonstrate that CVB3 induces a sex -specific early CD4+ T cell response and emphasizes the impact of sex differences on immune-mediated disease outcomes.
Identification of T cell subpopulations exhibiting a high-degree of TCR-independent, IL-15-induced activation in pateints with acute hepatitis A
Authors: Yu Hosun , Lee Hoyoung , Kim So-Young , Moon Bae-Hyeon , Shin Eui-Cheol 
Published: November 2024

Abstract
During acute hepatitis A, pre-existing memory CD8+ T cells specific to hepatitis A virus-unrelated antigens are activated by IL-15 in a T-cell receptor (TCR)-independent manner, which is termed bystander activation, and these T cells contribute to liver injury (Immunity 2018, 48:161). However, it has been remained to be elucidated if other types of T cells are also activated by IL-15 without TCR engagement during acute hepatitis A. Here, we performed CITE-seq analysis in combination with single-cell RNA sequencing (scRNA-seq) using peripheral blood mononuclear cells (PBMCs) from patients with acute hepatitis A at acute and convalescent phases and healthy controls. In the scRNA-seq analysis, we used a gene set that was previously known to be upregulated by IL-15 in the absence of TCR stimulation to identify T-cell clusters that undergo TCR-independent, IL-15-induced activation. Among CD8+ T and γδ T cells, subclusters expressing CD45RO, CD57, and KLRG1 exhibited the highest module score of TCR-independent, IL-15-induced activation. Among MAIT cells, subclusters expressing CD8 and CD226 showed the highest module score of TCR-independent, IL-15-induced activation. Notably, these subclusters with the highest module score were exclusively found at the acute stage compared to the convalescent phase. In summary, T cell subpopulations exhibiting a high-degree of TCR-independent, IL-15-induced activation express distinct cell surface protein markers in patients with acute hepatitis A.
Differential activation of human lung epithelial cell subsets by virus-specific CD8+ T cell derived IFNg
Authors: Mattingly Cameron , Jimenez Ariana , Williams Mark , Kost Kirsten , Michalets Sarah , Thomas Jeronay , Kohlmeier Jacob 
Published: November 2024

Abstract
Lung CD8+ tissue resident memory T cells (TRM) act as sentinels that rapidly respond to respiratory viruses. While mouse models have shown that TRM mediate protection at barrier sites, our understanding in human lungs remains limited. We examined the functionality of virus-specific CD8+ TRM from non-transplantable, healthy human lungs by first quantifying their frequency and phenotype against prevalent viruses. While CD8+ T cells targeting respiratory viruses displayed a heightened tissue residency profile, RNAseq revealed that Flu and CMV specific lung CD8+ T cells are functionally and transcriptionally similar. Next, we investigated how virus-specific CD8s impact cells in the local lung environment. Following antigen stimulation, we noted activation of both innate and epithelial cells, dependent on IFNg. Examination of epithelial subsets showed that basal cells were more activated than ciliated cells. Upon stimulating lung CD8+ TRM with flu peptide +/- anti-IFNg, we conducted scRNAseq on epithelial cells and observed that stimulated CD8+ TRM robustly activated anti-viral genes in basal cells and to a lesser degree in secretory cells. Using Air-Liquid Interface (ALI) cultures, we modeled the effects of IFNg mediated epithelial activation on viral replication. Our findings show how crosstalk between CD8+ TRM and respiratory epithelium activates ISG pathways in epithelial cells and by doing so significantly decreases the frequency of infection and overall viral load.
CD2 costimulation as a method to improve mouse T cell activation by soluble antibody complexes
Authors: Rogers Trevor , Eaves Allen , Louis Sharon , Antignano Frann 
Published: November 2024

Abstract
Immunology research using mouse T cells requires cell activation that is often achieved using anti-CD3/CD28 antibodies immobilized (imm) on beads or cultureware. This immobilization can be tedious, leading us to investigate mouse T cell activation using soluble (sol) antibody complexes. Purified mouse T cells were activated by immCD3/CD28 or solCD3/CD28 complexes for 2 days, resulting in an average of 85% and 68% CD25+ T cells by flow cytometry, respectively (n = 12). However, adding CD2 to the solCD3/CD28 complex increased the %CD25+ T cells to 99% after 2 days (n = 12), suggesting that CD2 enhances activation. Purified T cells activated by solCD3/CD28/CD2 complexes showed improved fold expansion (28-fold) after 7 - 8 days compared to activation by immCD3/CD28 (15-fold) or solCD3/CD28 (18-fold) complexes (n = 17). As well, purified CD4+ T cells activated by solCD3/CD28 complexes exhibited increased fold expansion from 1- to 20-fold after 8 days by adding CD2 to the complexes (n = 3). Lastly, we investigated how activation methods impact a 6-day polarization of naive CD4+ T cells to T helper subsets. Cells activated by solCD3/CD28 complexes resulted in 53% Th1, 29% Th2, or 67% Treg cells, whereas solCD3/CD28/CD2 complexes resulted in 77% Th1, 24% Th2, or 79% Treg cells (n = 6). In summary, these soluble ImmunoCult™ Mouse T Cell Activators effectively activate, expand, and polarize mouse T cell subsets, which is enhanced by CD2 costimulation.
Application of Deep Learning Models on Single-Cell RNA Sequencing Analysis Uncovers Novel Markers of Double Negative T Cells
Authors: Xu Tian , Xu Qin , Lu Ran , Oakland David , Li Song , Luo Xin 
Published: November 2024

Abstract
Double negative T (DNT) cells, a unique subset of CD3+TCRαβ+ T lymphocytes lacking CD4, CD8, or NK1.1 expression, constitute 3-5% of the total T cell population in C57BL/6 mice. Traditional machine learning models such as principal component analysis in single-cell RNA sequencing (scRNA-seq) analysis have been utilized to characterize this subset, but only deep learning models such as Single Cell Variational Inference (SCVI) can capture nonlinear gene expression in the sequencing data. In this study, using the deep learning approach, we have uncovered novel markers of splenic DNT cells in C57BL/6 mice. We classified DNT cells into two subgroups, naïve DNT (nDNT) cells and activated DNT (aDNT) cells, which could be differentiated by the expression of Ly6C and MHC-II, respectively. In addition, our data identified CD153 and CD153 as unique markers for aDNT cells. SCVI analysis suggested, and flow cytometry analysis confirmed, that Ly49G2 and CCR2 are respective markers for two distinct subsets within nDNT and aDNT populations. In addition to cell surface markers, we further discovered that nDNT cells expressed higher Rgs2 that is required for T cell activation and that aDNT cells expressed higher Rbpj involved in Notch signaling. Together, our comprehensive analysis has uncovered and validated novel markers for different subpopulations of DNT cells that can be used in the phenotypic and/or functional characterization of these relatively rare cells in health and disease.
B cell-intrinsic IL-27 and IFNγ receptor signaling drive PD-L1 expression, IgG2a autoantibody production, VEGF-dependent tumor angiogenesis and cancer progression
Authors: Hinton Karli , Cervantes Christian , Viswanadhapalli Suryavathi , Vankamamidi Sai Eashan , Yan Hui , Luo Weiwei , Vadlamudi Ratna , Xu Zhenming 
Published: November 2024

Abstract
B effector cells produce Abs and autoantibodies, while B regulatory cells use cytokines and transmembrane proteins to fine tune immune functions. Our lab recently revealed that tumor-infiltrating B cells produce IL-27 to promote immune evasion, partly by upregulating tumoral PD-L1, including that expressed by B cells per se. To investigate the autocrine activity of IL-27 in tumor progression, we generated μMT:Il27ra–/– bone marrow chimera mice lacking the IL-27 receptor specifically in B cells. These mice displayed substantially reduced tumor growth from orthotopically engrafted ER+ E0771 breast cancer cells, as associated with only moderately decreased PD-L1 levels but, unexpectedly, severely compromised blood vessel integrity. The residual PD-L1 levels and tumor growth were virtually abolished by additional B cell-specific deficiency in IFNγ receptor signaling, as occurring in double KO μMT:Il27ra–/–Ifngr1–/– mice, in which the microvessel permeability was also worsened. Mechanistically, this aligned with our findings that IL-27-producing B cells expressed high levels of VEGFA, whose transcription in activated B cells could be further enhanced by IL-27 and IFNγ. Double KO mice also lacked anti-dsDNA IgG2a autoantibodies, as elicited by tumor engraftment. Thus, B cell-intrinsic IL-27 and IFNγ receptor signaling synergize to promote B-cell PD-L1 expression, IgG2a autoantibody production, and vascular integrity, all of which may contribute to cancer development.
Therapeutic potential of VBY-825 in MSU crystal-induced NLRP3 inflammasome activation
Authors: Orellano Laura , Rock Kennet , Lai Jiann-Jyh 
Published: November 2024

Abstract
In gout patients, MSU crystals formed in the joints cause inflammation, and the activation of the NLRP3 inflammasome is believed to mediate these responses. Cathepsins play an important role in crystal-induced NLRP3 activation that results in subsequent speck formation, caspase-1 activation, IL-1β secretion, and pyroptosis. In this study, we investigated if cathepsins can also influence MSU-induced NLRP3 activation in a gout mouse model. VBY-825 is a reversible pan-cathepsin inhibitor, and we found that VBY-825 significantly suppressed IL-1β secretion and LDH levels from peritoneal naïve macrophages upon MSU stimulation in vito. In a mouse peritonitis model, we found that VBY-825 suppressed MSU-induced inflammation when compared to the control treatment. Interestingly, the inflammation demonstrated by histology and MPO activity in the joints was also reduced by VBY-825 treatment in MSU-induced arthritis. These findings suggest that cathepsins play a critical role in MSU-induced inflammation and could potentially be a target for gout treatment.
Reshaping immune cells and the antigen-specific repertoire by anti-CD3 mAb teplizumab in Type 1 diabetes
Authors: lledo delgado ana , Preston-Hurlburt paula , Currie Sophia , Clark Pamela , Herold Kevan 
Published: November 2024

Abstract
Teplizumab, a FcR non-binding anti-CD3 mAb, is approved to delay progression of type 1 diabetes (T1D) at-risk patients. Previous investigations described the immediate effects of the 14-day treatment, but longer-term effects of the drug remain unknown. We analyzed the phenotypes, transcriptome, and repertoire of peripheral blood and autoreactive CD8+ T cells from individuals at-risk for T1D, before and after teplizumab.
There were changes in CD4+ and CD8+ T cells at 3 months and 18 months after treatment in genes related to immune regulation. The differential gene expression in the T cells increased after drug was cleared. Persistent EOMES expression was a predictor for the time to clinical T1D diagnosis. Our trajectory analysis showed differentiation into cells with gene signatures related to immunoregulation and exhaustion after teplizumab treatment. This analysis aligned with inhibition of expansion of autoreactive CD8+, which was observed with the placebo, but not following teplizumab.
These findings illustrate that a single course of teplizumab can instigate substantial T cell changes at 3 months, with evolution of CD8+ T cell exhaustion up to 18 months. Teplizumab restrains the expansion of autoantigen reactive CD8+ cells, suggesting mechanisms underlying operational tolerance.
Targeting Hippo pathway diminishes disease signaling in scleroderma skin.
Authors: Plazyo Olesya , Wasikowski Rachael , Gharaee-Kermani Mehrnaz , Tsou Eliza Pei-Suen , Tsoi Lam , Billi Allison , Kahlenberg J , Varga John , Khanna Dinesh , Gudjonsson Johann 
Published: November 2024

Abstract
Scleroderma (SSc), a female-biased autoimmune disease that causes inflammation and fibrosis in skin and internal organs, lacks effective treatment options. Our previous work, including single-cell RNA sequencing (scRNA-Seq) of skin from a large cohort of SSc patients, suggested that Hippo pathway regulates a female-specific immune gene network and drives myofibroblast differentiation in SSc skin. Our objective herein was to assess if inhibiting Hippo pathway pharmacologically can suppress disease signaling in SSc. We targeted distinct steps of Hippo pathway using 3 inhibitors (TRULI, Verteporfin, and MGM-CP1) that were applied to SSc skin biopsies ex vivo, followed by in-depth scRNA-Seq analyses to characterize molecular changes in affected cell populations. We found that Verteporfin, which prevents interaction of TEADs with YAP and VGLL3, selectively depleted myofibroblasts and endothelial-mesenchymal transition cells – the stromal cells pathologically activated in SSc. It also reduced expression of inflammatory, pro-fibrotic, and endothelial activation markers. Moreover, cell-cell interactions that sustain disease signaling were markedly hindered by Verteporfin. We saw a striking overlap between the genes downregulated by Verteporfin and those upregulated in SSc vs healthy patients. Thus, targeting Hippo pathway by Verteporfin effectively reverses molecular hallmarks of SSc. Our data further showcase the utility of this novel approach for modeling drug targeting ex vivo.
Unique T cell signatures are associated with reduced Chlamydia trachomatis reinfection in a highly exposed cohort.
Authors: Yount Kacy , Chen Chi-Jane , Kollipara Avinash , Liu Chuwen , Mokashi Neha , Zheng Xiaojing , O'Connell Catherine , Bagwell C , Iannone Marie , Wiesenfeld Harold , Hillier Sharon , Stanley Natalie , Darville Toni 
Published: November 2024

Abstract
Chlamydia trachomatis (CT) is the most common bacterial sexually transmitted infection (STI) in the U.S. despite effective antibiotics. Understanding natural immunity to CT is crucial to inform vaccine design. This study aimed to identify immune cell populations and functional features associated with reduced risk of CT reinfection. PBMCs were collected from 82 CT-exposed women tested for CT and other STIs upon enrollment, and repeatedly over 1 year of follow-up. Immune responses were profiled by mass cytometry. Women with CT at enrollment exhibited higher frequencies of CD4+ effector memory T cells (TEM) than uninfected women. Specifically, Th2, Th17, and Th17 DN CD4 TEM were increased. However, functional features indicated diminished expression of T cell activation and differentiation markers, underscoring weaknesses of natural immunity that could be addressed by vaccine design. Comparing responses in women who remained follow-up negative (FU-) to those who were reinfected (FU+), higher frequencies of Th1, Th17, and Th17 DN CD4 T cells were observed in FU- women. Conversely, Th2 CD4 T cells were increased in FU+ women. Furthermore, markers of T cell differentiation, memory, and cytotoxicity were increased in FU- women. These data indicate that peripheral T cells exhibit distinct features associated with natural immunity to CT. Notably, the highly plastic Th17 lineage appears to contribute to protection. Addressing these immune nuances could promote efficacy of CT vaccines.
Identifying the role of antigen-specific resident memory CD4 T cells in maintaining disease during Experimental Autoimmune Encephalomyelitis a murine model of Multiple Sclerosis.
Authors: Yuzefpolskiy Yevgeniy , Oukka Mohamed , Bettelli Estelle 
Published: November 2024

Abstract
Multiple sclerosis (MS) is an autoimmune disease of the central nervous system (CNS) driven by antigen-specific CD4+ T cell mediated destruction of the myelin sheath. Most T cells circulate between lymphoid organs and peripheral tissues, but a fraction can establish tissue residence and do not recirculate. Growing evidence suggests resident T cells exist in the CNS of MS patients, however, their contribution to disease progression and whether they can cause relapses independently of peripheral T cells is unclear. Current disease modifying therapies for MS patients are not curative and none target CNS resident T cells. Using a murine model of MS, Experimental autoimmune encephalomyelitis (EAE), we investigated whether resident T cells form in the CNS of diseased mice and their contribution to disease pathogenesis. Our data show that antigen-specific CNS resident T cells can be detected during EAE by intravital antibody staining and CD69 expression. Following depletion of circulating CD4+ T cells, CNS resident CD69+ CD4+ T cells maintained their numbers, while the number of CD69- T cells in the CNS was significantly depleted. These CNS resident T cells can drive severe disease in the absence of circulating CD4+ T cells and showed memory-like properties including high proliferative capacity and increased cytokine polyfunctionality compared to early effector T cells. Therefore, disruption of resident T cell function in MS patients could represent a novel target for MS therapies.