bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bimodal single cell RNA sequencing reveals changes in CD4+ T cell transcriptomes with age
Authors: Khan Amir , Oliaeimotlagh Mohammad , Kumar Sunil , Hedrick Catherine , Ley Klaus 
Published: November 2024

Abstract
Aging affects the human immune system, resulting in modified autoimmunity, responses to infection and cancer. Here, we studied changes in CD4 T cells in subjects with and without coronary artery disease (CAD). PBMCs of 61 men and women who underwent cardiac catheterization were interrogated by single cell RNA sequencing combined with 49 protein surface markers via CITE-Seq. After quality, we identified 139,343 PBMCs from these patients, 40,816 were CD4 T cells, identified as CD19- CD3+ CD4+ CD8-. Linear regression was used to assess the impact of age on gene expression in these cells, adjusted for disease severity, sex, statin status, diabetes, and smoking status. As expected, the surface markers CD25 and CD45RO were positively and CD45RA negatively correlated with age. Across all subjects, 24 genes: GLUL, F5, CXCL10, CTSA, IL32, IFITM1, LAT2, TNFRSF8, RPN2, HLA.A, RGS1, TRAT1, TIGIT, STAT1, BAX, MKI67, CLC, LGALS1, F13A1, SPON2, CD163, IL3RA, VSIG4, CD200 were significantly correlated with age. Other genes were correlated in cases, but not controls: IL2RA, THBS1, VPREB3, PIK3AP1, TNFSF8, PAX5, IL2, LIF, CLEC4E, MMRN1, KLRC4, ADGRG3, PTPRC, ZNF683, IL22, TNFRSF25, CAVIN2, SYNE2, CD72, CD300A. Significant transcriptomic changes with age were observed in naïve, Th1, Tregs and exTregs CD4+ T cells. We conclude that age significantly changes the proportions and transcriptomes in CD4 + T cells. Also, sex, diabetes and use of statin confound these changes with age.
Prostaglandin I2 signaling in Treg restrains ST2 expression and associated pathogenicity
Authors: Norlander Allison , Abney Masako , Peebles Jr. R Stokes 
Published: November 2024

Abstract
We reported Prostaglandin I2 (PGI2) signaling within Treg is critical for Treg suppressive function in allergic airway inflammation (AAI). Interestingly, pathogenic Treg that have impaired suppressive capacity and promote AAI have greater ST2 expression. We hypothesized that Treg PGI2 signaling limits ST2 expression via restraint of β-Catenin signaling in AAI to prevent Treg pathogenicity. The percentage of ST2+ Tregs was elevated at baseline in IP deficient (IP KO) Treg, which lack the receptor for PGI2, compared to WT Treg. To further test our hypothesis, we utilized an Alternaria alternata (Alt) extract sensitization and challenge protocol. Alt-challenged mice that lacked IP signaling only on Treg (Foxp3YFPcrexIPflox) had elevated BAL IL-13, BAL eosinophils, lung vascular remodeling, and lung ST2+ Treg percentages compared to Foxp3YFPcre controls. Moreover, there were elevated total lung ST2+IL13+ Treg and ex-Treg in Alt-challenged fate-mapping IP KO mice compared to fate-mapping controls. Interestingly, BAL IL-13, BAL eosinophils, lung ST2+ Treg percentages were significantly decreased in Alt-challenged mice that had Treg specific deficiency for both IP and β-Catenin (Foxp3YFPcrexIPfloxxCtnnb1flox) compared to Foxp3YFPcrexIPflox mice. In summary, we demonstrate an association of Treg ST2 expression with enhanced Treg pathogenicity in a mouse model of AAI in IP deficient Treg mediated by β-Catenin. These data support PGI2 as a therapeutic for asthma.
BLOC1S1 deficiency promotes differentiation of Inflammatory Th2 cells and exacerbates atopic dermatitis and allergic airway inflammation in mice
Authors: Sharma Rahul , Wu Kaiyuan , Han Kim , Sack Michael 
Published: November 2024

Abstract
The levels of biogenesis of lysosome organelles complex 1 subunit 1 (BLOC1S1) control mitochondrial and endolysosome organelle homeostasis and function. Reduced fidelity of these vacuolar organelles is increasingly being recognized as influential in instigating cell-autonomous immune cell activation. We reasoned that exploring the role of BLOC1S1 in CD4+ T cells may further advance our understanding of regulatory events linked to mitochondrial and endolysosomal function in adaptive immunity.
We report that BLOC1S1-/- CD4+ T cells from mice and humans show enhanced Th2 activation. Transcript levels of the canonical transcription factors driving CD4+ T cell showed that the Th2 regulator GATA3 was exclusively induced in BLOC1S1-/- CD4+ cells. In parallel, in response to both T cell receptor activation and to Th2 polarization, the levels of IL-4, IL-5 and IL-13 were markedly induced in the absence of BLOC1S1. At a functional level, BLOC1S1-/- mice displayed increased susceptibility to allergic conditions, including atopic dermatitis and asthma. At the organelle level, mitochondrial DNA leakage is evident with STING accumulation on lysosomes and activation of the cGAS-STING NF-kB pathway to drive Th2 polarization. The genetic knockdown of STING in cultured CD4+ T cells ameliorates this immune regulatory cascade. In conclusion, we provide the first evidence that BLOC1S1 is essential in regulating Th2 cell expansion and developing type 2 allergic responses.
A Novel CD28-Targeting Molecule with Potent Therapeutic Impact on Asthma
Authors: Kuo Chieh-Ying , Chen Li-Chen , Kuo Ming-Ling 
Published: November 2024

Abstract
It has been well established that cytokines produced by T helper 2 (Th2) cells are responsible for asthmatic pathogenesis. Thus, the blockade of co-stimulatory molecules may control Th2-cell activation and attenuate asthmatic responses. We firstly identified Cyn-1324, a small compound, with high binding affinity to CD28 and can disrupt the interaction between CD28/CD80. This study investigated whether Cyn-1324 serves as an immunomodulator via blocking CD28/CD80 signaling, leading to the interference of CD4+ T cell activations and the relief of allergic asthma. Among house dust mite (HDM)-induced asthmatic mice model, the intranasal administration of Cyn-1324 significantly reduced airway resistance, eosinophilia in lung, and Th2-associated cytokines production in antigen-stimulated lymphocytes culture supernatants. Furthermore, we further studied the immunosuppression effect of Cyn-1324 in vitro. Cyn-1324 decreased not only murine but also human T-cell proliferation and IL-2 secretion, through the induction of T-cell anergy. This is the first identified compound that directly binds to CD28 and leads to T-cell anergy, but not the induction of Tregs. In addition, these findings suggest the potential of Cyn-1324 as an immunosuppressive agent capable of attenuating allergic responses through the blockade of the CD28/CD80 interaction. Cyn-1324 emerges as a promising candidate for further exploration in developing immunosuppressive therapies for allergic or autoimmune diseases.
GluK2 agonism suppresses dermal mast cell activation and proliferation
Authors: Zhang Youran , Keshari Swapnil , Das Jishnu , Yang Yufan , Zhang Jiying , Sumpter Tina , Kaplan Daniel 
Published: November 2024

Abstract
It has been recently appreciated that mast cells respond to glutamate in the context of neural transimtter release and tissue injuries. However, the precise subtype of glutamate receptor expressed on dermal mast cells at steady states and its function remain to be elucidated.
Herein, we identified the kainate receptor GluK2/KA2 as the predominant glutamate receptor expressed on dermal MCs at the mRNA and protein level. GluK2 agonists such as glutamic acid and kainic acid suppressed the activation of cultured peritoneal mast cells (PMCs) in response to MrgprB2 ligand compound 48/80, corroborating a previously demonsrated neuroimmune pathway.
The GluK2 selective agonist SYM2081 downregulated MrgprB2 expression and inhibited compound 48/80-mediated PMC activation. SYM2081 suppresed various mast cell-dependent inflammation models in vivo, such croton oil-induced irritant dermatitis, DNFB contact hypersensitivity, and LL-37 induced rosacea. The suppressive effect of SYM2081 on mast cells holds true in a model of human skin explants as well.
Transcriptomic analysis revealed that GluK2 agonism suppresses proliferation pathways in mast cells and downregulates granule content synthesis, such as mast cell chymase 1. Together, this study identified a previously unappreciated glutamate receptor on dermal mast cells and raised the interesting posibility of using selective GluK2 agonists to as a therapeutic agent for inflammatory conditions where MCs play a key role in the pathogenesis.
A model for cross-disciplinary and cross-institutional student collaboration for undergraduate immunologists
Authors: Singh Jastaranpreet 
Published: November 2024

Abstract
Immunology is a cross-disciplinary field, existing at the interface of biology, engineering and medicine. Therefore, a crucial skill for immunologists to develop is their ability to collaborate with others who have vastly different expertise and skillsets, such as biomedical engineers and statisticians. Undergraduate students at the University of Toronto (UofT) have few formal opportunities to engage in these types of collaborations. Most team-based projects allow students to work with fellow immunology peers, or students from other biology disciplines; however, the opportunity to do so with students in other fields is rare. Even fewer opportunities exist to collaborate with students from other academic institutions. To address this gap, two undergraduate courses, IMM360 (Scientific Methods and Research in Immunology, UofT) and BMEG372 (Biomedical Materials and Drug Delivery, University of British Columbia), were knit together in September-December 2022 and 2023. Here, we present our scaffolded approach for promoting collaboration on a cross-disciplinary, cross-institutional project. Furthermore, we will report student attitudes towards cross-disciplinary collaboration, which were assessed via surveys both at the start and end of the collaborative project. We hope that learnings from this work will inform an effort to weave cross-disciplinary collaboration throughout all years of the Immunology undergraduate program at the University of Toronto and other institutions.
Oxidized phospholipids regulate tenocyte function via the induction of amphiregulin in dendritic cells
Authors: Pinnaro' Veronica , Kirchberger Stefanie , Künig Sarojinidevi , Gil Cantero Sara , Della Porta Giovanna , Stöckl Johannes 
Published: November 2024

Abstract
Inflammation is a driving force of tendinopathy. Oxidation of phospholipids by free radicals is a consequence of inflammatory reactions. Here we have studied the impact of oxidized phospholipids (OXPAPC) on the function of human tenocytes. We observed that treatment with OXPAPC did not alter the morphology, growth, and capacity to produce collagen in healthy or diseased tenocytes. Since OXPAPC is a known modulator of the function of immune cells, we analyzed whether OXPAPC-treated immune cells might influence the fate of tenocytes. Treatment of immature, monocyte-derived dendritic cells with OXPAPC (Ox-DCs) was found to enhance the proliferation of tenocytes, in particular tenocytes from diseased tendons.
In contrast, the production of collagen by tenocytes was not altered upon co-culture with Ox-DCs. Since the supernatant of Ox-DCs was also able to stimulate the growth of tenocytes, we searched for a growth factor in the secretome of Ox-DCs and could identify amphiregulin (AREG), a ligand for EGFR. The addition of recombinant AREG to tenocytes was indeed a stimulus of proliferation. Diseased tenocytes were found to express higher levels of EGFR compared to tenocytes isolated from healthy donors and show a stronger proliferative response. In summary, inflammatory reactions in the tendon might lead to the oxidation of phospholipids which can trigger the production of AREG in resident DCs and thereby stimulate the proliferation of tenocytes.
Cx3cr1 deficiency exacerbates glomerulonephritis in MRL/lpr mice through modulating renal infiltration of IL-17 producing double negative T cells
Authors: Estaleen Rana , Oakland David , Montano Hilary , Alajoleen Razan , Lu Ran , Amin Pavly , Shakeri Aida , Reilly Christopher , Luo Xin 
Published: November 2024

Abstract
The CX3CR1 chemokine receptor initiates intracellular signaling cascades responsible for cellular activity, proliferation, and survival. CX3CR1 loss-of-function leads to exacerbation of chronic kidney disease in patients. Renal disease is a severe complication that often occurs in patients with systemic lupus erythematosus (SLE). We had previously reported that Cx3cr1 deficiency exacerbated glomerulonephritis in lupus-prone MRL/lpr mice. In our current studies, we sought to investigate the role of Cx3cr1-deficiency at different stages of SLE disease. We investigated glomerulonephritis development and renal infiltrating immune cells in MRL/lpr mice at 3, 7, 11, and 15 weeks of age. Inflammation in lupus-like disease was initiated at an earlier time-point in the Cx3cr1-deficient (Cx3cr1-/-) mice when compared to Cx3cr1-wildtype (Cx3cr1+/+) mice, where Cx3cr1-/- mice had significantly higher proteinuria at all time points. Double negative (DN) T cells which are pathogenic in lupus were found to be significantly expanded in the kidney of Cx3cr1-/- MRL/lpr mice at 3, 7, and 11 weeks of age with alterations in the production of two IL-17 isoforms, IL-17A and IL-17F. Our data suggest that CX3CR1 plays a role in a balanced production of IL-17A and IL-17F by DN T cells and that Cx3cr1 deficiency may alter disease pathogenesis through modulation of IL-17 isoforms.
Role of type Ⅰ interferon signaling in kainic acid-induced seizure model
Authors: Ma Jeong-Hwa , Hwang Inhwa , Yu Je-Wook 
Published: November 2024

Abstract
Type Ⅰ interferon (IFN) signaling has emerged as a significant factor in brain development and homeostasis. Also, its dysregulation has been associated with various central nervous system (CNS) diseases, including Alzheimer's disease. According to a recent study, microglia in kainic acid-induced seizures show an increase in interferon beta responsiveness. However, the specific role of type Ⅰ IFN signaling in seizure-related processes remains elusive. Therefore, in this study, we aimed to investigate the function of type Ⅰ IFN signaling in seizures. Here, we found the upregulation of interferon beta and interferon-stimulated genes in the hippocampus of mice subjected to kainic acid, which indicates the involvement of type Ⅰ IFN signaling in seizure events. To examine the specific roles of type Ⅰ IFN signaling in seizures, we induced seizures in C57BL/6 wild-type mice and IFNAR1 knockout mice and compared the severity of seizures and subsequent events. Interestingly, IFNAR1 knockout mice showed rapid rises in seizure severity in the early stages, but later exhibited a decrease in severity compared to the wild-type. On the other hand, interferon signaling did not have a significant impact on late-phase gliosis after seizures. These data provide novel insights into the crucial role of the interferon pathway in seizure progression, suggesting its potential as a therapeutic target for the treatment of seizures and epilepsy.
Maternal Infection and altered fetal immune programming.
Authors: Coronado J 
Published: November 2024

Abstract
The maternal-fetal interface involves complex and balanced interactions between mother and fetus, which support the development of the fetal immune system. While we know maternal helminth infection during pregnancy is known to disrupt this relationship and affect neonatal immune development, the fundamental mechanisms that drive fetal immune programming is not completely understood. To further examine how maternal parasitic infection influences offspring immunity, we established a model in which female mice prior to mating are infected with the persistent mouse intestinal helminth, Heligmosomoides polygyrus (HP). One week after infection, female mice are mated, and the progeny are aged to adulthood. The offspring are then challenged with influenza virus. Intriguingly, we found that offspring born from mothers with HP infections were less susceptible to influenza challenge than offspring born from uninfected mothers. This data implies that the effects of maternal helminth infection are long lasting, and potentially involve fetal programming during the early development of the immune system.
Investigating Neutrophil Subpopulations involved in Acute Lung Injury in Pediatric Patients with Congenital Heart Disease using a Single Cell Approach
Authors: Gianoli Stefano 
Published: November 2024

Abstract
Congenital Heart Disease (CHD) is a significant health concern (4-10/1,000 live births). Morbidity in CHD includes a younger age, thrombotic complications, and organ dysfunction. Acute lung injury (ALI) occurs intra/postoperatively in 2–3% of pediatric patients, particularly neonates and infants. Neutrophil recruitment to the lungs during CPB-induced ALI is noted. Recognizing the dual role of neutrophils in both defense and tissue damage, a nuanced strategy is essential.
Our preliminary single-cell RNA sequencing (scRNAseq) analysis of blood from pediatric patients undergoing longer (&gt;=3 hours) versus shorter (&lt;3 hours) CPB surgery reveals distinct neutrophil subpopulations to be enriched post-CPB and associated with ALI. Specifically, in patients with a longer CPB, the IFTIM2 gene, associated with type I interferon responses, is enriched. Pathway analysis confirms associations with interferon responses, chemotaxis, cell migration, reactive oxygen species, and cell death. Preliminary data shows that upregulated β2 integrin levels post-longer CPB suggest a predisposition to ALI.
This insight aims to guide the design of targeted therapies for specific neutrophil subpopulations while preserving their critical functions. This study will improve the treatment of these patients, addressing a crucial and critical gap in pediatric cardiac intensive care.
CD8+ T cells recognize de novo epitopes induced by TDP-43 dysfunction.
Authors: Chizari Shahab , Saigal Vidur , Gu Albert , Malaspina Andrea , Fratta Pietro , Jiang Jenny 
Published: November 2024

Abstract
Cytoplasmic aggregation and dysfunction of the DNA-binding protein, TDP-43, is an underlying pathology in disorders including amyotrophic lateral sclerosis (ALS), Alzheimer’s disease (AD), and inclusion body myositis (IBM). The functional loss of TDP-43 results in aberrant splicing and the inclusion of cryptic exons in hundreds of mRNA transcripts which ultimately lead to the expression of de novo proteins. Whether these de novo proteins can stimulate and activate T cells is unknown but would be critical in understanding the pathogenesis of these disorders. Cryptic peptides are strong candidates for T cell responses as they are likely not presented during T cell selection. Additionally, it has been demonstrated that there are highly differentiated and clonal populations of CD8+ T cells circulating the blood of patients with ALS-4. Therefore, we hypothesize that cryptic peptides induced by TDP-43 aggregation could be recognized by clonally expanded CD8+ T cells that exhibit an activated phenotype. In exploration of our hypothesis, PBMCs from ALS and IBM donors were collected and HLA-genotyped. Cryptic epitopes were bioinformatically predicted using a sliding window approach. From this epitope library, we have generated barcoded and fluorescently tagged peptide-MHC tetramers to capture and single cell sequence cryptic peptide-specific T cells. Preliminary results highlight several populations of circulating CD8+ T cells capable of recognizing cryptic peptides in ALS and IBM.
Structural variants of Bacteroides fragilis-derived alpha-galactosylceramides induce unique natural killer T cell responses.
Authors: Jung Da-Jung , Lee Jesang , Son Sumin , Park Seung Bum , Oh Sungwhan 
Published: November 2024

Abstract
Natural killer T (NKT) cell is a unique subset of thymus-derived T cells that recognizes glycolipids presented by CD1d molecule expressed on antigen-presenting cells. The most studied agonistic antigen of NKT cells is alpha-galactosylceramide (αGC). It has been shown that structural features of lipid antigens determine distinct NKT cell responses. In order to drive context-dependent NKT cell responses, understanding the structural characteristics of lipid antigens is important. In the previous study, we have shown that human gut symbiont Bacteroides fragilis (B.fragilis) uniquely produces αGCs (BfaGC), which can normalize the overproliferation of neonatal colonic NKT cells in germ-free mice, and chemically-synthesized structural isomers of BfaGCs induce structure-specific NKT cell responses. In this study, to further investigate the essential structural moiety of BfaGC for the unique immunomodulatory activity, we synthesized BfaGC analogues by modifying their chain lengths and functional groups. We have examined how the analogues differently stimulate NKT cells by analyzing in vitro cytokine production, NKT cell proliferation and effect on specific NKT cell subpopulations. We found the critical features and functional groups on the BfaGC structure leading to immunomodulatory responses. It is expected that our findings may advance further development of lipid antigens to fine-tune context-specific NKT cell responses in immunological diseases.
IL-7 improves the T cell IFNγ response in sepsis patients
Authors: Kim Caleb , Swanson Whitney , Xu Julie , Kucaba Tamara , Kancans Kristine , Badovinac Vladimir , Gould Robert , Griffith Thomas 
Published: November 2024

Abstract
Sepsis is the life-threatening organ dysfunction stemming from the severe inflammatory response to systemic microbial infection. Immune consequences for post-septic survivors include acute lymphopenia and prolonged susceptibility to infection. Stratifying Patient Immune Endotypes in Sepsis (‘SPIES’) is a prospective observational study testing the utility of ELISpot as a bioassay to identify the immunosuppressed endotype, and test potential immune stimulants for clinical use. Our data show a whole blood IFNγ ELISpot assay can identify: 1) septic patients at increased risk of late mortality, and 2) immunosuppressed sepsis patients. We wanted to determine which cells in the blood were producing IFNγ. Flow cytometry revealed memory CD4 and CD8 T cells were making the majority of IFNγ after ex vivo stimulation with anti-CD3/CD28 mAb. We next defined the breadth of cytokines produced by whole blood samples from sepsis patients after stimulation. Last, we tested the potential for IL-7 to improve the functional activity of T cells from sepsis patients. Using anti-CD3/CD28 mAb-stimulated PBMC from healthy and septic donors, we found adding IL-7 to the stimulation milieu improves both the number of cytokine-producing cells, and magnitude/variety of cytokines produced from T cells. In sum, these data reveal important functional information about the degree of immune suppression experienced by sepsis patients, along with a potential means of restoring T cell function in these patients.