bluuebunny/crossref_metadata_2025_split huggingface dataset:
Elucidating Inflammation-induced Cell Fate Decisions in Primary Human Tregs
Authors: Ho Patrick , Bluestone Jeffrey A , Tang Qizhi 
Published: August 2023

Abstract
Adoptive regulatory T-cell (Treg) therapy is an emerging therapeutic paradigm for promoting immune tolerance in transplant and autoimmune disease settings. Prior investigations demonstrate that murine Tregs can undergo epigenetic reprogramming within chronically inflamed tissue environments, resulting in acquisition of proinflammatory functions and the capacity to exacerbate tissue damage. Despite the ramifications of Treg lineage decommitment for cell therapy applications, inflammation-induced human Treg cell fate decisions remain poorly understood. Here, we present a robust in vitro model of IL6, IL1β, and IL23-driven Treg instability characterized by progressive FOXP3 and HELIOS downregulation, FOXP3 conserved non-coding sequence (CNS)2 enhancer re-methylation, diminished in vitro suppressive function, and elevated proinflammatory cytokine expression. To gain insight into the gene regulatory networks enabling the loss of Treg identity, we generated single-cell transcriptomic and chromatin accessibility profiles of primary human Tregs maintained in the presence or absence of IL6, IL1β, and IL23. Unsupervised clustering revealed a dysfunctional Treg population with an epigenetic signature consistent with murine Treg to “exTreg” conversion, including altered chromatin accessibility at the IFNγ, IL17A, and FOXP3 CNS2 loci. Inference of transcription factor (TF)-associated changes in chromatin accessibility indicated a key role for E26 transformation-specific (ETS) family members. Ongoing experiments aim to identify specific TF modules that can be targeted to better safeguard the function and stability of Treg therapeutics.
Characterization and Neutralization of Pathologic Memory CD4+ T Cells in Spondyloarthritis Synovial Fluid
Authors: Song Woogil , Yi Kijong , Jo Sungsin , Jung Seyoung , Lee Eun Young , Kim Tae-Jong , Lee Jeong Seok 
Published: August 2023

Abstract
Spondyloarthritis (SpA), which has increased T helper 17 (Th17) cell activity, and neutralizing antibodies targeting IL-17 are effective in patients with SpA. However, not all Th17 cells are pathologic; most Th17 cells have physiological roles. Here, we characterize the immune landscape of blood and synovial cells in SpA through single cell to demonstrate the molecular characteristics of pathologic memory CD4+ T cells with Th17 characters. We identified pathologic Th17 (pTh17) cells as polyfunctional IL-17A and IFN-γ-producing memory CD4+ T cells, with clinically supporting evidence for their pathogenic roles at the inflammatory site of SpA. Transcriptome and flow cytometric analysis found that the co-expression of TNFRSF4 and TNFRSF18 is increased in pTh17 cells. Suppression of ligand-receptor interactions via TNFRSF4 and TNFRSF18 effectively decreased clinical arthritis and decreased pTh17 cells in the curdlan-injected SKG mouse model. Our results provide understanding pTh17 cells in SpA and suggest potential therapeutic targets.
Modified Immune Cell (MIC) Therapy disrupts Tertiary Lymphoid Structures in Murine Lupus Nephritis
Authors: Ponath Gerald , Speer Claudius , Arnold Iris , Hidmark Asa , Wang Lei , Kleist Christian , Schmitt Anita , Daniel Volker , Opelz Gerhard , Terness Peter , Schmitt Michael , Zeier Martin , Morath Christian , Schaier Matthias 
Published: August 2023

Abstract
Induction of tolerance can be achieved with Modified Immune Cells (MIC) by infusion of mononuclear cells challenged with mitomycin C (MMC). Although MIC treatment has been successful in several animal models for autoimmunity and in clinical studies of solid organ transplantation, the mechanism of immunosuppression is not fully elucidated.
In lupus nephritis, the glomerular deposition of immune complexes is associated with accumulating immune cells in the kidney. The infiltrating immune cells frequently establish tertiary lymphoid structures (TLS) supporting adaptive autoimmune responses toward locally displayed antigens.
Since TLS display a high persistence to peripheral B cell depletion, the destruction of TLS presents an essential treatment goal in lupus nephritis. In this study, we used lupus nephritis prone NZB/W F1 mice to show the destruction of TLS in the kidney after MIC treatment.
Independent of treatment, &gt;86% of animals displayed dense lymphocytic aggregates proximal to the pelvic wall of the medulla and the arcuate arteries within the cortex of kidneys. Cell type composition of TLS changed drastically after MIC treatment leading to diminished B-cells, a decreased B-cell/T-cell ratio, and a T cell dominated phenotype. Furthermore, a loss of organization of the TLS was observed after MIC treatment. The strict separation of B-cell and T-cell areas was abrogated, and germinal centers were disintegrated. However, regulatory T-cells remained unchanged indicative of a B-cell centric treatment mechanism.
Our data provides a putative in vivo mechanism how MIC treatment inhibits progression of active lupus nephritis by the destruction of tertiary lymphoid structures within the kidney.
Commercial Support - TolerogenixX GmbH
Glucocorticoids redirect naive T cells to the bone marrow in malnourished mice
Authors: Pearson Caroline , Saravanan Rithanya , Marczak Marissa , Washington Aja , Foster Takesha R , Dadzie Nana , Hanes Jacob , Moore Lindsay , Mister Abigail , Goulmamine Syreen , Gibson David , Adams Olivia , Gubbels Bupp Melanie R 
Published: August 2023

Abstract
Glucocorticoids contribute to the daily migration patterns of T cells in well-nourished organisms and are elevated in the malnourished. We examined the effect of malnutrition on T cell migration by comparing the migration patterns of adoptively transferred malnourished and control T cells in the lymphoid organs of malnourished and control recipients. We found that malnourished T cells generally entered lymphoid tissues more efficiently than control T cells, regardless of recipient. Strikingly, the bone marrow of malnourished recipients attracted naïve malnourished T cells, but not control T cells, more efficiently than control bone marrow. In contrast, the spleens of malnourished and control mice attracted similar numbers of naïve T cells. Further experiments revealed that T cells residing in the bone marrow of malnourished mice express higher levels of CCR7 and lower levels of CD11a than control T cells. We also examined the effect of T cell-specific deficiency of the glucocorticoid receptor on T cell migration to the bone marrow in malnourished mice. Indeed, similarly low percentages of glucocorticoid receptor deficient T cells were observed in the bone marrow of malnourished and control mice, indicating that T cell expression of the glucocorticoid receptor is required for T cell migration to the bone marrow. Overall, we have determined that malnutrition modifies both the bone marrow and naïve T cells to promote naïve T cell migration to the bone marrow and that at least the T cell-specific effects are mediated via the glucocorticoid receptor.
NSF-MRI [DBI- 1920116] NSF-RUI [IOS-1951881]
Early Generation and Anatomical Commitment of Stem-like CD8 T cells
Authors: McManus Daniel Thomas , Medina Christopher , Sobierajska Ewelina , Cardenas Maria A , Prokhnevska Nataliya , Hashimoto Masao , Nasti Tahseen , Valanparambil Rajesh , Ross James , Gill Amanda , Scharer Christopher D , Kissick Haydn , Ahmed Rafi 
Published: August 2023

Abstract
Stem-like CD8 T cells sustain the CD8 T cell response during chronic viral infection and cancer, and residency in lymphoid tissues is a key aspect of their biology. We used the chronic LCMV strain, clone 13, to determine when these cells first emerge and commit to positioning in lymphoid sites. Phenotypical and transcriptional profiling of virus-specific CD8 T cells indicated that stem-like and effector fates diverge as early as day 5 after infection. PD-1+ stem-like CD8 T cells sorted from the early (day 5) and established phases (&gt;day 45) of clone 13 infection showed substantial transcriptional overlap indicating that the canonical gene signature of these cells manifests early and is maintained throughout infection. Intravascular labeling and imaging showed that the spatial commitment of these cells to the splenic white pulp also began on day 5. These observations were striking as stem-like CD8 T cells are considered an adaptation to prolonged antigen exposure, yet their fate and anatomical commitments are made before the trajectory of infection is clearly acute or chronic. There were important time-related changes to these cells as well. Early stem-like cells were proliferating and expressed genes involved in the cell cycle, mTOR signaling, and anabolic metabolism. As infection progressed, they upregulated multiple inhibitory molecules and eventually became quiescent. Thus, the stem-like transcriptional and anatomical commitment occurs very early after infection. These data indicate that the CD8 T cell response is equipped for chronic antigen exposure before the trajectory of infection is clearly acute or chronic and further highlight the importance of location for stem-like CD8 T cells.
Supported by grants from NIH (5R01AI030048-29)
TCR signaling dynamically regulates TCF1 expression and effector differentiation
Authors: Favret Natalie , Rudloff Michael W , Zumbo Paul , Betel Doron , Philip Mary 
Published: August 2023

Abstract
T Cell Factor 1, or TCF1, is a transcription factor required for thymic T cell development, memory T cell formation, and maintenance of exhausted/dysfunctional T cell stem/progenitors in tumors and chronic infection. However, TCF1 regulation and function during T cell activation is not well-understood. We analyzed the expression kinetics of Tcf7 mRNA, encoding TCF1 (RNA-SEQ) and TCF1 protein (flow cytometry and western immunoblotting) in CD8 T cells during the initial hours and cell divisions following activation in vivo. Naive CD8 T cells robustly express TCF1. Within 6 hours after activation in L. monocytogenes-infected B6 mice, antigen-specific CD8 T cells downregulated Tcf7 mRNA/TCF1 protein, only to re-express both prior to undergoing the first cell division. We observed a similar pattern of TCF1 kinetics in polyclonal CD8 and CD4 T cells activated with anti-CD3/CD28 antibody and PMA/ionomycin, which activates signaling pathways downstream of the T cell receptor (TCR). We further determined that the magnitude of pre-division TCF1 downregulation correlated with cognate peptide concentration and TCR avidity, but also with higher granzyme B expression during later cell divisions. Thus, our data suggests that the pre-division TCF1 drop is regulated by TCR signaling strength and may determine effector fate. By decoding TCF1 regulation during T cell activation, we could gain insights allowing us to target TCF1 to augment or inhibit effector T cell function in different disease contexts, including cancer, chronic infection, and autoimmunity.
Supported by grants from NHI (T32 GM137793-02, R37 CA263614)
Microbiome protection against Coccidioides growth
Authors: Hoyer Katrina K , Tejeda-Garibay Susana , Zhao Lihong , Hum Nicholas , Loots Gabriela 
Published: August 2023

Abstract
During infection, the host utilizes multiple mechanisms to prevent colonization and dissemination. Protection begins at the surface, often via the commensal community found within our respiratory, skin, and intestinal tract. Microbiota disruption reduces the effectiveness of this protective barrier. Coccidioidomycosis, or Valley fever, is often misdiagnosed as community acquired bacterial pneumonia and treated with antibiotics that alter microbiota density and diversity. Commensal bacteria influence host immune responses to infection, and antibiotic treatment alters host immunity. A soil microbial antagonist related to Bacillus subtilis inhibits in vitro growth of Coccidioides through a clear zone of inhibition between fungi and bacteria. Whether host microbiota also inhibits Coccidioides is unknown. To assess if host microbiota has inhibition capabilities against Coccidioides, we performed two inhibition assays and measured Coccidioides growth area. A 50/50 inhibition assay was performed in which host microbiota and Coccidioides were placed in direct competition on agar plates. A spike in inhibition assay was performed where host microbiota was grown to 80% confluency, to mimic an established in vivo microbiome, before spiking in Coccidioides. Our data indicate that intestinal and respiratory host microbiome species inhibit Coccidioides growth. To assess if host microbiota depletion allows greater Coccidioides growth, in vitro antibiotic disc diffusion assays and in vivo treatments were performed. Our data suggests that host respiratory and intestinal commensals inhibit Coccidioides growth. Antibiotic treatment may kill protective host bacteria that creates a niche for Coccidioides invasion.
Supported by grant VFR-19-633952 from University of California Office of the President.
Development and validation of multiplexed non-human primate ELISA assays
Authors: Christensen Preston B , Nelson Andy B , Tyler Abby B , Berg Kyle B 
Published: August 2023

Abstract
Multiplex ELISA assays are widely used in biomedical research for drug development and other therapeutic interventions. Monitoring of the immune responses of subjects receiving candidate therapeutics is crucial for mitigating adverse reactions and is necessary for the validation of new drug candidates. Non-human primates (NHP) serve as a crucial animal model for development of novel therapeutics due to similarities in immune and organ systems to humans. To support this line of research and maximize data generated from potentially limited samples, new multiplex ELISAs capable of concurrently detecting up to 18 NHP-specific analytes were developed.
The objective of this development was to develop and validate assays for 35 NHP biomarkers. Characterization of assay performance included intra- and inter-assay precision, linearity/parallelism, interference, and assay robustness. Validation and verification testing show functionality and reproducibility of multiplexed NHP panels containing analytes related to cytokine, chemokine, and cancer proteins. Comparisons between stimulated and unstimulated peripheral blood mononuclear cells showed increased concentrations of target analytes.
In conclusion, Quansys Biosciences demonstrated that Q-Plex™ technology is a reliable and accurate tool for measuring NHP specific immunological biomarkers, therefore improving drug research and development processes. This technology will aid in the discovery, diagnosis, and treatment of disease by utilizing NHP models in the discovery process.
The pathogenic anti-PLA2R autoantibodies cooperatively elicit the activation of complement in primary membranous nephropathy
Authors: Wu Tsai-Yi , Tu Kun-Hua , Lin Kung-Wei , Peng Jhan-Jie , Shih Han-Po , Ku Cheng-Lung 
Published: August 2023

Abstract
Primary membranous nephropathy (pMN) is an autoimmune disease associated with autoantibody-mediated immune complexes and the deposition of activated complement proteins on the glomerulus. The phospholipase A2 receptor 1 (PLA2R) has been identified as a major antigen for autoantibodies in 80% of pMN patients. Antibodies of IgG1 and IgG3, but not IgG4, can activate complement. Unexpectedly, in pMN patients, the PLA2R autoantibodies are IgG4 predominance, and those of IgG1 and IgG3 are less abundant in the affected tissues, arguing the role of PLA2R autoantibodies in the pathologies of pMN.
To study the molecular basis of individual PLA2R-reactive IgGs mediating complement activation in pMN, we employed a single-cell capture method and generated 16 anti-PLA2R monoclonal antibodies (mAbs). We characterize mAbs properties including epitope, affinity and gene feature. Then we adopted the CDC assay with PLA2R-podocytes to investigate the complement activation of the mAbs. Our data show that the combination of CTLD1 and any other epitope showed a synergistic effect that enhanced CDC activation, which single epitope anti-PLA2R mAb cannot achieve. Surprisingly, IgG1 mAb can still promote the CDC when pair with IgG4 mAb in synergistic effects. Moreover, polyclonal anti-PLA2R IgGs from pMN patients but not healthy volunteers can induce CDC. Next, we found that a group of patients only have CysR-IgG3, neither CTLD1-IgG1 nor IgG3; when we add CTLD1-IgG1 mAb can enhance CDC activation.
Our data identify an essential role of complement-reactive IgGs, presumably IgG1 and IgG3 synergies between epitopes synergistic effects, and highlight the importance of immune complexes in complement activation by PLA2R autoantibodies, which underlies pMN.
Complement C4 gene copy number variations and polymorphisms, autoantibodies, and clinical manifestations of juvenile dermatomyositis– a multi-center study
Authors: Coss Samantha Lynn , Aziz Rabheh Abdul , Zhou Danlei , Zhou Bi , Miller Katherine , Wu Yee Ling , Ardoin Stacy , Oberle Edward , Driest Kyla , Al Ahmed Ohoud , Patwardhan Anjali , Akoghlanian Shoghik , Sivaraman Vidya , Barbar-Smiley Fatima , Drew Joanne , Spencer Charles , Pachman Lauren , Morgan Gabrielle , Mamyrova Gulnara , Curiel Rodolfo , Jones Olcay , O’Hanlon Terry , Rider Lisa , Miller Frederick , Padyukov Leonid , Lundberg Ingrid , Notarnicola Antonella , Vencovský Jiří , Stibůrková Blanka , Kryštůfková Olga , Yu Chack-Yung 
Published: August 2023

Abstract
Juvenile dermatomyositis (JDM) is an autoimmune myopathy characterized by rash and muscle weakness. Complement C4 gene copy number (GCN) variation is a known risk factor for JDM. JDM patients often develop autoantibodies. We investigated the relationship between C4 GCN, clinical features, and antibody development.

METHODS
Subjects were recruited (n=255) from the US, Sweden, and the Czech Republic. C4 GCN was determined by real time PCR. Comparative analyses were performed via student’s t test or Mann Whitney U test. Correlation was assessed via linear regression or Fisher’s exact test. All studies were IRB approved, and informed consent was obtained.

RESULTS
C4 GCN correlated with muscle pathology and extra-muscular disease at diagnosis. Lower C4A and C4L GCN were associated with a higher number of abnormal muscle enzymes (p=0.0062 and p=0.0029), while the opposite was true for C4S (p=0.024). Higher C4S GCN correlated with lower muscle strength scores (p=0.039). Lower C4L correlated with abnormal MRI (p= 0.042). C4B GCN correlated with dysphagia (p=0.035). Higher GCN of C4S was a risk factor for arthritis (p=0.032), systemic symptoms (p=0.020), and dysphagia (p=0.0078). C4 GCN was associated with myositis-specific (MSA) and myositis-associated (MAA) antibodies. Patients with homozygous C4A deficiency were more likely to test positive for anti-NXP2 (OR 20.0, p=0.011), and C4A GCN was lower in anti-NXP2 positive subjects (p=0.030). A higher C4B GCN correlated with positive MAA (p=0.043).

DISCUSSION
Here, we show that low C4A/C4L GCN and high C4B/C4S GCN correlate with worse muscle disease, extra-muscular pathology, and autoantibodies. Our data suggest that complement C4 may play a key role in the ongoing pathogenesis of JDM.

Supported by grants from NIH (R21 AR070509) and the CureJM Foundation
The Probable Role of Tregs in Improved Heat Tolerance in Heat-acclimated Mice
Authors: Li Jintao , Qiu Minyue , Zhao Lixin , Zhou Yuxin 
Published: August 2023

Abstract
Heatstroke is a life-threatening illness related to systematic inflammation-induced multiple organ dysfunction. The severity of systematic inflammatory response may be related to the changes in immune regulation triggered by heat acclimation. However, the mechanisms of heat acclimation and its effect on immune regulation are unclear. Here, we assessed the differences in immunocyte subsets in the spleen and lymph nodes of heat-acclimated mice. Higher frequencies of CD4+ Foxp3+ regulatory T cells (Tregs) were observed in the heat-acclimated mice. Our results indicate that the improvement in heat tolerance during acute heat stress correlates with the increase in the number of Tregs. These Tregs mitigated the recruitment of neutrophils, inhibited their activation, and suppressed the severity of acute inflammation. The increased differentiation and development of Tregs might stem from an enhanced expression of Foxp3 and PD-L1. Our results strongly suggest that the increase of Tregs has a regulatory effect on neutrophils, and that the PD-1/PD-L1 pathway may be involved in this regulation. The anti-inflammatory effects of Tregs have never been studied in the context of heat stress-induced systemic inflammation. Thus, the results of our study are significant for devising a potential treatment for systemic inflammatory response syndrome and heatstroke.
National Natural Science Foundation of China (grant number 81570497)
Thresholding CITE-Seq-based Antibody Expression Data to Improve Cell Type Identification in scRNA-Seq
Authors: Khan Amir , Oliaeimotlagh Mohammad , Suthahar Sujit Silas Armstrong , Iqneibi Shahad , Nettersheim Felix , Ley Klaus 
Published: August 2023

Abstract
scRNA-seq is widely used to assess immune cell heterogeneity by measuring individual cell transcriptomes. Surface markers have been used for decades to type immune cells by flow and more recently mass cytometry. Expression of surface markers is poorly correlated with the mRNA levels of their encoding transcripts. CITE-Seq provides a systematic approach to analyze surface phenotypes along with cell transcriptomes by using oligonucleotide-tagged antibodies. Like flow cytometry, CITE-seq-based assessment of surface markers is complicated by non-specific binding. Here, we introduce and validate a systematic method of thresholding the levels of protein marker expression to address the issue of non-specific antibody binding. To remove the non-specific signal, a threshold value separating noise from expression for each surface marker is obtained by comparing the antibody signal in a cell type known to not express this surface marker. If no negative cell type is available, we use deconvolution of overlapping normal distributions to find the best separator in density plots (Ridgeline plots) by deconvolution (normalmixEM tool) of overlapping normal distributions. In total, 34 of 49 antibodies tested were reliably thresholded, thus effectively removing the noise from the signal. In a validation experiment testing 188 antibodies at 4 different concentrations, 124 were successfully thresholded, including all 34 mentioned above.
Supported by the National Institutes of Health (NIH) P01 HL136275