bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selective depletion of anti-dsDNA long-lived plasma cells in SLE
Authors: Deokar Aditi , Huang Yina 
Published: November 2024

Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease driven by secretion of autoantibodies including those specific for double stranded-DNA (dsDNA) by short- or long-lived plasma cells (PCs). Most SLE treatments are generally immunosuppressive and indirectly decrease short-lived PCs. New therapies are needed to selectively eliminate SLE-causing long-lived PCs while preserving immunity and avoiding side effects. Prior research fusing the model antigen ovalbumin (OVA) with an antibody specific for a PC-specific protein, CD138, showed selective depletion of anti-OVA long-lived PCs. We hypothesize that a similar fusion protein comprising anti-CD138 antibody and a dsDNA peptide mimic can selectively deplete long-lived dsDNA-specific PCs. We tested the ability of two previously reported peptide mimics, ALW and DWEYS, to competitively inhibit detection of anti-dsDNA autoantibodies from NZB/NZW mice. We found DWEYS but not ALW inhibited detection. We also validated a method to indirectly measure anti-dsDNA PCs by measuring levels of secreted antibody by ELISA. We then confirmed efficient in vivo CD138 depletion. The next step is to fuse DWEYS with anti-CD138 antibody and test for selective depletion in vitro and in vivo. Successful selective depletion of anti-dsDNA PCs using a DWEYS/anti-CD138 fusion protein may support its future development as an improved treatment for SLE patients not benefited by current treatments.
Protective Effects of Delta-8-THC Against EAE-Induced Enteric Neuropathy and Neuroinflammation through Regulation of miRNA-Mediated Signaling Networks
Authors: kakar khadija , Halder urmi , nagarkatti Mitzi , nagarkatti Prakash 
Published: November 2024

Abstract
Multiple sclerosis has long been associated with neurological symptoms, yet the connection between neuroinflammation and enteric neuropathy remains understudied. To test the complex brain-gut connection, we administered Δ8-THC (10mg/kg) i.p to mice with Experimental autoimmune encephalomyelitis (EAE), animal model of MS. We observed that treatment significantly reduced the clinical score and reversed the weight loss in treated group by suppression of proinflammatory Th1 phenotypes such as Tbet and IFN-g and increase anti-inflammatory phenotype such as Tregs and IL-10.miRNAseq analysis of brain infiltrating CD4+ cells revealed that decrease in neuroinflammation following treatment was associated with downregulation of miRNAs, involved in Pyroptosis, Th1 and Th2 pathway regulation. The EAE mice exhibit persistent gastrointestinal symptoms. To investigate bowel dysfunction miRNAseq analysis was performed for colonic and ileal tissues and contents. A highly dysregulated miRNA6538 found in all four miRNAseq analyses. miRNA6538 downregulation in colonic and ileal tissues, along with ileal content in treated EAE mice, suggests a protective role against EAE-induced bowel symptoms while its upregulation in colonic content could be due to the shedding of cells as a part of homeostasis during cellular turnover.In summary, Δ8-THC's suppression of EAE involves a dual impact on the brain and gut, showing its potential as a therapeutic strategy for mitigating neurodegenerative disorders.
Multi-omic studies in Cutaneous T Cell Lymphoma (CTCL) reveal progression-associated alterations in epigenetic and lymphocyte signaling pathways
Authors: Payton Jacqueline , Dorando Hannah , Andrews Jared , Borcherding Nicholas , Quinn Chaz , Schmidt Jennifer , Aluri Jahnavi , Cooper Megan , Musiek Amy , Mehta-Shah Neha 
Published: November 2024

Abstract
Patients with advanced stage CTCL have a 20% 5-year survival rate and molecular factors that drive disease progression are undefined. To address this, we collected 52 longitudinal tumor and normal samples from 10 CTCL patients and subjected them to exome + whole genome (eWGS), single-cell (sc)RNA and TCR sequencing. Clustering and cell-type inference of scRNAseq (UMAP/Seurat/singleR) from 92496 total cells showed canonical CTCL marker genes and high proportions of patient-specific TCR clonotypes. Somatic genome copy number alterations (CNA) and deleterious/damaging single nucleotide variants (SNV) (cnvkit, GATK/Mutect2, copykat, cb_sniffer) were identified. We defined molecular changes associated with progression and/or resistance to therapy (APR) as CNA and SNV detected in samples collected at later timepoints with progression and/or lack of therapy response in &gt;30% of patients. This novel approach identified pathways in chromatin modification, particularly DNA and histone methylation, lymphocyte signaling and transcriptional regulation. A novel-to-CTCL SNV in STAT3 had gain-of-function activity and aberrant genomic binding (CUT&RUNseq). CNA and mutant allele levels correlate with disease progression and therapy response in scRNAseq. Our findings represent new insights into CTCL progression, reveal new markers for response assessment, and identify new targets for therapeutic development. Based on these results, we have initiated two clinical trials at WUSM.
Molecular Mimicry in Pathogen Immune Evasion
Authors: Santambrogio Laura , Clement Cristina , Osan Jaspreet , Becerra Aniuska , Mota Ines , Nanaware Padma , Franco Alessandra , Stern Lawrence 
Published: November 2024

Abstract
Molecular mimicry is the immunological mechanism by which pathogen-derived peptides can modulate immune responses due to sequence similarity with self-peptides. Herein, we report molecular mimicry associated with pathogen immune evasion. A quantitative analysis of the immunopeptidome presented by in vivo mycobacteria tuberculosis (MTB)-matured dendritic cells in HLA-DR0101 (DR1) transgenic mice identified an MTB-processed peptide which presented immunosuppressive capability and shared a DR1 core sequence with a human and mouse self-protein. The TB peptide could expand nTreg with generation of immunosuppressive cytokines in DR1 mice and DR1 subjects diagnosed with active or latent TB. In TB-infected patients the tolerogenic TB peptide reduced the inflammatory response generated to a series of immunogenic TB peptides as quantified by the QuantiFERON test. Additionally, the tolerogenic TB peptide presented an MHC-binding core sequence shared by a multitude of pathogens. Our analysis characterizes a pathogen-derived peptide which, through molecular mimicry facilitate immune evasion by activating/inducing nTreg.
Detection of lipid nanoparticles phagocytosed by antigen presenting cells using imaging flow cytometry
Authors: D'Cruz Louise , Phan Anthony , Shi Xiaoshan , Widmann Stephanie , Alameh Mohamad-Gabriel , Hunter Christopher , Tyznik Aaron 
Published: November 2024

Abstract
mRNA vaccines were critical for the prevention of severe disease during the COVID-19 pandemic and efficacy of their delivery was achieved through nucleic acid-encapsulated lipid nanoparticles (LNPs). Despite the effectivness of mRNA vaccines, the mechanisms by which antigen-presenting cells (APCs) recognize and phagocytose the LNP cargo are not fully understood. Here, we used the BD CellView™ Image Technology on the BD FACSDiscover™ S8 Cell Sorter to visualize LNPs phagocytosed by host cells. LNPs formulated with green fluorescent (DiO)-labeled lipids were injected intramuscularly into mice. With the imaging capabilities of the BD FACSDiscover™ S8 Cell Sorter, we visualized LNPs in different APCs and observed different morphology of LNPs in dendritic cell subsets and monocytes. A time course experiment uncovered the kinetics of antigen recognition upon LNP-mediated cargo delivery. Analysis using the instrument imaging parameters revealed unique cell clusters associated with distinct morphology of LNP phagocytosis. We then sorted the LNP+ cells and evaluated their transcriptomic signature by real-time PCR. This work provides a workflow to visualize LNP phagocytosis followed by image-based cell sorting for downstream characterization enabled by the BD FACSDiscover™ S8 Cell Sorter. With increased adoption of LNP-mediated nucleic acid vaccines, the image-based cell sorter provides a powerful tool to understand the host immune response upon vaccination.
Reversal of dysfunction of dendritic cells induced by Treg cells for enhancing cancer immunotherapy
Authors: Liu Xia , Zhang Yuanqin , Tao Yan , Zhao Lei , Peng Guangyong 
Published: November 2024

Abstract
Different types of Regulatory T (Treg) cells create immunosuppressive microenvironments in cancer patients, which are a major obstacle to effective antitumor immunity. A precise understanding of the molecular mechanisms utilized by Treg cells for immune suppression on different types of immune cells is critical for the development of effective strategies for cancer immunotherapy. We investigated the interaction between breast cancer tumor-derived gamma-delta Treg cells with dendritic cells (DCs) and determined the phenotypic and functional changes of DCs. We showed that tumor-derived gamma-delta Treg cells promote the development of senescent DCs with tolerogenic functions in breast cancer. In addition, we demonstrated that PD-L1 and STAT3 signaling pathways are involved in senescence induction in DCs mediated by gamma-delta Treg cells. Importantly, our complementary in vivo studies further demonstrated that blockages of PD-L1 and STAT3 signaling can prevent gamma-delta Treg-induced senescence and reverse tolerogenic functions in DCs, as well as enhance anti-tumor immunotherapy in the human breast cancer models. These studies not only dissect the suppressive mechanism mediated by tumor-derived gamma-delta Treg cells but also provide novel strategies to enhance anti-tumor efficacy mediated by tumor-specific T cells for cancer immunotherapy.
CD91 and its ligand heat shock proteins regulate dendritic cell functions during immunosurveillance of emerging tumors
Authors: Nayak Devanshi , Sedlacek Abigail , Cillo Anthony , Watkins Simon , Binder Robert 
Published: November 2024

Abstract
Dendritic cells (DCs) play a pivotal role in initiating and modulating responses against nascent tumors. This study investigates how immunogenic heat shock proteins (HSPs), particularly glycoprotein 96 (gp96), efficiently chaperone minute amounts of peptides during early tumor development to evoke antigen-specific immunity. Tumor-derived gp96 is endocytosed by CD91, a receptor on DCs that is crucial for cross-priming T cells. Here we generated mouse models with DC-specific CD91 deficiency (CD11cCre, XCR1Cre, Mgl2Cre) and a system to track dispersal of tumor-derived gp96. Our data suggests that CD91 expression on type 1 conventional DCs (cDC1) is essential for uptake of gp96 during cancer immunosurveillance. While gp96+ cDC1s contribute to early tumor control, sustained and long-term tumor control is facilitated by other gp96+ cross-priming DCs (CD11b+ cDCs) through intercellular transfer of gp96. Single cell analysis of antigen-presenting cells (APCs) in tumor-draining lymph nodes illustrates that CD91 promotes T cell priming, while downregulating immune regulatory pathways. Engagement of CD91 initiates co-stimulation, cytokine production and cross-presentation of HSP-chaperoned peptides establishing it as a primary mechanism immunosurveillance. Understanding the role of CD91+ DCs in cancer immunosurveillance holds significant implications for cancer prognosis and therapy, revealing the division of labor among APCs in the successful elimination of cancer cells.
Quantifying how TCR sequence influences cell fate commitment in chronic LCMV infection
Authors: Brown Ryan , Cui Weiguo 
Published: November 2024

Abstract
Repetitive T cell receptor (TCR) engagement on CD8 T cells during chronic infection is a critical driver of the dysfunctional state termed exhaustion. These exhausted cells are characterized by additional heterogeneity including a memory-like progenitor cell (Tpro) that continuously gives rise to either non-cytolytic exhausted cells (Texh) or cytotoxic effector cells (Teff). While we and others have shown that TCR avidity influence cell fate commitment to Texh or Teff, it is not certain if TCR sequence features influence this fate choice. In this study, we identify how TCR V(D)J gene recombination influences T cell differentiation at the single-cell resolution. To investigate this, we performed single-cell resolution TCR sequencing (scTCR-seq) on GP33+ tetramer sorted cells within lymphocytic choriomeningitis virus (LCMV) Clone 13 model of chronic infection across 7 different mice. Utilizing TCRdist and Clonotype Neighbor Graph Analysis (CoNGA), we construct correlations between gene expression and TCR features. We find that both chain usage and cdr3 motifs correlate to effector or exhausted cell fate commitment across these different mice. Overall, our results suggest that TCR gene rearrangement is critical not only for antigen specificity, but also determining CD8 T cell phenotypic outcomes during chronic viral infection.
Molecular characterization of post-translational modifications of DUSP12 in T cells
Authors: Yang Chia-Yu 
Published: November 2024

Abstract
Dual-specificity phosphatase 12 (DUSP12) belongs to a family of DUSP protein phosphatases (DUSPs) that are associated with cell cycle regulation, insulin sensitivity, and Toll-like receptor signaling. It has been reported that protein expression and phosphatase activity of DUSPs are regulated by post-translational modifications that may be mediated through phosphorylation, ubiquitination, or methylation. However, the functional roles of post-translational modifications on DUSP12 in T cells remain unclear. Our results showed that DUSP12 expression was increased upon T cell receptor (TCR) signaling. The number of T cells was decreased in DUSP12-deficient mice. To study the upstream regulators of DUSP12 in T cells, we used a proteomics approach to identify the potential post-translational modifications on DUSP12 protein. Our result showed that DUSP12 may be ubiquitinated, and we also identified multiple ubiquitination sites on DUSP12. Using DUSP12 co-immunoprecipitation and liquid chromatography-mass spectrometry experiment, we have identified a novel E3 ligase as a DUSP12-binding protein, which may regulate T-cell activation. Furthermore, the effects of ubiquitination in regulating the activity and expression of DUSP12 in T cells upon T cell receptor signaling were explored. Our study reveals the molecular regulation of DUSP12 in T-cell activation and immune responses.
Understanding the role of TNFR2 signaling in CD8 T cell exhaustion.
Authors: Hoyt-Miggelbrink Alexandra , Waibl Polania Jessica , Wachsmuth Luke , Lorrey Selena , Wilkinson Daniel , Hotchkiss Kelly , Lerner Emily , Cook Quackenbush Sarah , Hemmers Saskia , Ayasoufi Kathy , Fecci Peter 
Published: November 2024

Abstract
Glioblastoma (GBM) is the most common primary brain cancer in adults with a median survival less than 15 months. Approaches harnessing the immune response are hindered by multiple factors, including T cell exhaustion. Exhausted T cells are less capable of limiting tumor progression. As cells progress along the exhaustion pathway, SLAM Family Member 6 (SLAMF6) gets downregulated and T cell immunoglobulin and mucin domain-containing protein 3 (TIM3) and TOX are upregulated. TOX is both necessary and sufficient to initiate the terminal exhaustion program. However, our understanding of the pathways that lead to the upregulation of TOX remains incomplete.
We hypothesized that tumor necrosis factor (TNF) could be involved in the upregulation of TOX, as TNF has been shown to induce exhaustion. We observed upregulation of the TNF receptor type II (TNFR2) in tumor-infiltrating T cells, but not in lymphoid organs. Furthermore, TNFR2 expression is correlated with canonical exhaustion markers. Interestingly, TNFR2 knock out (KO) CD8 T cells express TIM3 but exhibit significantly less TOX. These data suggest that TIM3 and TOX are regulated independently. Finally, TNFR2 KO mice have significantly better CD8-mediated tumor control against subcutaneous GBM tumors. Further studies will need to be performed to determine whether TNFR2 expression on CD8 T cells is sufficient to mediate this anti-tumor effect and whether TNFR2 blockade could improve the efficacy of current treatments.
StarBright Dyes — Simplifying Flow Cytometry with 8-color No Compensation Panels
Authors: Sanderson Sharon , Santos Magda , Perike Srikanth , Dreskin Elizabeth , Blundell Michael , Long Tracey 
Published: November 2024

Abstract
Flow cytometry is a powerful technique, allowing a vast amount of information to be obtained from a single sample. A well-designed panel is vital for good quality data. One aspect of panel design is to use fluorophore combinations that avoid close or overlapping spectra. If not, the panel will risk having high spillover, spreading, and reduced population resolution.
We have designed 8-color, no compensation panels for conventional flow cytometry where the fluorophores used have distinct spectra, therefore they have minimal signal into detection filters other than their own. This removes the need for post-acquisition compensation, saving time, as well as ensuring high resolution of cells due to the lack of spread. We show 8-color immunophenotyping panels, acquired on a 5-laser ZE5 Cell Analyzer, for human peripheral blood and mouse splenocytes which require no compensation. B cell, cytotoxic and memory T cell, natural killer cell, and monocyte populations were easily identified. These panels can also be used as a backbone for building larger panels by adding additional markers to detect other cells of interest.
Many antibodies incorporated into these panels, have been conjugated to StarBrightTM Dyes which have narrow excitation and emission profiles, making them ideal for inclusion in no compensation panels. StarBright Dyes also simplify panel design as they work with all buffers and most fixatives making them suitable for use in a wide range of protocols.
Detecting immune activity in human tumors with novel high-throughput whole slide imaging approaches using Imaging Mass Cytometry.
Authors: Motta Vinicius , Raza Qanber , Pfister Thomas , Lim Liang , Howell David , Parsotam Nikesh , King David , Loh Christina 
Published: November 2024

Abstract
Deciphering the spatial biology of the tumor immune microenvironment (TIME) has potential to inform clinical and translational researchers about the likelihood of immunotherapy success. Imaging Mass Cytometry™ (IMC™) is a spatial biology imaging technique that enables deep characterization of the TIME while fully retaining spatial features of tissues using 40-plus markers simultaneously.
We developed two new whole slide imaging methods for IMC. Tissue mode (TM) rapidly acquires an image of the whole tissue that can be used for quantitative analysis of spatial biology. Preview mode (PM) samples the entire tissue at predefined spacing to rapidly capture a low-resolution image of all expressed markers, improving informed identification of areas for high-resolution cell mode (CM) imaging on the same slide.
Tumor tissues were stained using a 40-marker panel comprised of the Maxpar™ Human Immuno-Oncology IMC Panel Kit, designed for tumor and immune cell profiling. TM imaging in combination with pixel-based analysis quantified tissue areas containing high or low abundance of myeloid and lymphoid immune, tumor and stromal cell compartments. PM in combination with CM imaging followed by single-cell analysis on selected tumor regions identified cell populations with varying activation states and expression profiles.
Overall, we highlight the power of IMC to provide quantitative insights into the spatial biology of the TIME.
For Research Use Only. Not for use in diagnostic procedures.
The use of DNAPK inhibitors increases the efficacy of Lentiviral vectors and decreases off-target effects.
Authors: Corbin Seana , Johnson Lauren , Azevedo-Pouly Ana , Burdine Marie , Burdine Lyle 
Published: November 2024

Abstract
Lentiviral vectors are a powerful tool in many models to deliver genetic material to target cells. Many methods of developing gene therapy treatment for multiple human diseases rely on using viral vectors to deliver genetic material into target cells. While viral vectors are a powerful tool, their use is not without its limitations and hurdles. Work must be done to overcome these hurdles to improve the delivery and reliability of vector-based gene therapy mechanisms in a clinically relevant and affordable manner.
The primary objective of this study was to enhance the precision and efficacy of lymphocyte modification while minimizing the systemic spread of the vectors. This was achieved through the strategic inhibition of DNA-PK, a key enzyme in DNA repair, to facilitate effective gene integration into lymphocyte genomes. These vectors were administered through trans-splenic injection, a novel approach aimed at directly targeting the lymphocyte-rich environment of the spleen with concurrent DNA-PK inhibition.
The results were significant. We observed a markedly high level of gene transduction in splenocytes 30% of T lymphocytes with minimal off-target effects. Notably, there was a substantial reduction in the systemic spread of the vectors, which is a critical factor in mitigating potential side effects. The transduced lymphocytes demonstrated stable gene expression, indicating the success of this method in achieving persistent genetic modification.
Development of NULISAseq™ 250-Plex Inflammation Panel for Immune Profiling of Autoimmune Diseases
Authors: Ma Xiao-Jun , Hao Qinyu , Sun Helena , Murlidhar Vasudha , Lee Anna , Yu Ming , Ariyapala Ishara , Kim Sean , Beer Joanne , Kuo Dwight , Fang Lei , Luo Yuling 
Published: November 2024

Abstract
Comprehensive profiling of cytokines and chemokines in blood can provide deeper insights into the mechanisms underlying this highly complex and heterogeneous group of diseases. However, many of these proteins are present at very low concentrations in plasma, below the limit of detection of current immunoassays. We recently developed a novel automated multiplex immunoassay technology, NULISA™, capable of attomolar-level sensitivity and high levels of multiplexing. Here we report the development of a 250-plex inflammation-focused panel targeting a broad range of cytokines/chemokines and other important inflammation and immune response-related proteins. We conducted a pilot study to assess the utility of this panel for autoimmune disease research. We analyzed plasma samples from patients with rheumatoid arthritis (RA), Sjögren's syndrome (SjS), systemic lupus erythematosus (SLE), and ulcerative colitis (UC), and compared to healthy donors. Linear model analysis identified differentially abundant proteins associated with diseases including many low-abundance targets with important roles in autoimmune diseases, such as IL4, IL5, IL20, IL17A, IL17F, IL33, and IL2RB. In summary, with the ultrahigh sensitivity and the most comprehensive inflammatory cytokine/chemokine panel, the NULISA™ Platform promises to be a powerful discovery tool for autoimmune disease research, which may lead to new diagnostic biomarkers and therapeutic targets.