Biology subjects

Borcherding, N.

Publications and source records attributed to Borcherding, N..

At least 19 recordsLinked to original sources

bioRxiv2026

Large-scale integrated single-cell analysis reveals molecular subtypes and microenvironmental remodeling in cutaneous T cell lymphoma

Cutaneous T cell lymphoma (CTCL) comprises a clinically and molecularly heterogeneous group of skin-homing non-Hodgkin lymphomas for which robust biomarkers remain limited. Prior single-cell RNA sequencing (scRNA-seq) studies have provided important insights into CTCL biology, but many of these prior studies have been limited by small sample sizes and focused on niche questions of interest. Additionally, many studies have suffered from pseudoreplication, resulting in inflated test statistics and reduced external validity. Here, we assembled and integrated scRNA-seq data spanning 244 unique samples and 132 patients across CTCL, healthy control (HC), and benign inflammatory dermatoses (BID) conditions, generating the most diverse atlas of CTCL to date. Following identification of malignant cell populations and heterogeneous, within-sample gene expression alterations, we applied pseudobulk aggregation and robust linear mixed-effects modeling to nominate recurrent changes across this highly heterogeneous patient cohort. Interrogation of the skin microenvironment identified significant compositional and cell type-specific expression changes in CTCL lesions as compared to control lesions and across clinical stages of disease. Finally, we used unbiased clustering to identify stable, molecularly defined subtypes of disease that were predictive of outcome in an independent dataset. Together, this study provides a rigorous analysis of the most diverse scRNA-seq dataset of CTCL ever compiled, nominating specific alterations in cell type composition and gene expression across malignant cell and microenvironmental populations with significant clinical implications.

bioinformatics↗

bioRxiv2026

Refinement of the Pathogenic T Cell Receptor Motif Suggests Type 17 CD8+ T Cells Initiate HLA-B*27-associated Autoimmunity

Human leukocyte antigen B*27 (HLA-B*27) is a major risk factor for autoimmune diseases such as axial spondyloarthritis (axSpA), acute anterior uveitis (AAU), and psoriatic arthritis (PsA). HLA-B*27 presents bacterial and self-antigens to disease-associated CD8+ T cells, however, how this leads to a pathogenic IL-17-mediated disease remains unclear. We performed mutational experiments in an established disease-associated TCR and demonstrated that the pathogenic motif encompasses a wider range of TCR sequences than previously appreciated. We next leveraged computational pairing of alpha/beta TCR sequencing (TCR-seq) to demonstrate that the broadened pathogenic motif distinguishes axSpA and AAU patients from healthy controls. Paired single-cell RNA sequencing and single-cell TCR sequencing datasets demonstrated that the pathogenic cells have a distinct transcriptional signature. We find a coupling of pathogenic TCRs to this transcriptional signature in public datasets from axSpA and PsA joint fluid and AAU ocular fluid. Finally, we detect the pathogenic CD8+ T cells in the gut and demonstrate that they express a Type 17 program. Our findings suggest that HLA-B*27+ axSpA, AAU, and PsA are initiated by HLA-B*27-restricted pathogenic CD8+ T cells that undergo Type 17 differentiation in response to intestinal antigens.

immunology↗

bioRxiv2026

Pre-transplant TCR Network Topology Predicts Kidney Allograft Rejection Independent of HLA Mismatch

Despite extensive pretransplant serological screening and HLA matching, 10-15% of kidney allografts experience acute rejection within the first year. Currently, risk stratification for transplantation relies primarily on antibody reactivity to HLA molecules, with no assessment of the T cell compartment before or after transplantation. In our previously established longitudinal cohort of 54 patients, T cell receptor {beta} (TCR{beta}) sequencing was performed on paired kidney biopsy and peripheral blood samples. Here, we further analyzed the data to construct a comprehensive set of sequence-similarity networks and quantify over 30 network metrics. After adjusting for repertoire size, graft status was the strongest signal for the underlying differences in network metrics. Individuals who rejected the kidney graft generally exhibited more fragmented and less connected networks at baseline, with fewer interconnect T cell clones and more isolated sequences. Notably, pre-transplant peripheral blood mononuclear cell (PBMC) network topology alone predicted non-stable outcomes with an area under the curve (AUC) of 0.81, sensitivity of 76%, and specificity of 76%. The performance of this prediction model was independent of HLA mismatch, while changes in network topology at three months post-transplantation further improved prediction to an AUC of 0.88 (permutation p = 0.009). Collectively, TCR sequencing and network analysis represent a potential novel, non-invasive approach for pre-transplant risk stratification and immune monitoring, capturing functional immunological risk that may not be accessible through HLA genotyping or serology.

immunology↗

bioRxiv2026

Autoimmune-like CD8⁺ T Cell Responses Drive Atherosclerotic Plaque Instability and Predict Cardiovascular Events

Background and aimsAtherosclerotic plaque rupture is a major cause of myocardial infarction and stroke. However, the precise drivers of plaque destabilisation remain elusive. We hypothesised that antigen-driven, autoimmune-like T cell responses are central to the destabilisation and rupture of atherosclerotic plaques. MethodsTo dissect T cell responses specifically in unstable compared to stable plaques, we leveraged near-infrared autofluorescence (NIRAF) imaging-guided dissection of human carotid plaques. We also used our tandem stenosis model reflecting plaque instability as seen in patients to differentiate between unstable and stable plaques in mice. To explore T cell involvement, we studied T cell differentiation states and T cell receptor (TCR) repertoires by single-cell multi-omics. Then, testing if antigen-driven CD8+ T cell responses drive plaque instability in mice, we applied a combination of AAV8-PCSK9-induced atherosclerosis, tandem stenosis and TCR transgenic mice. Finally, we leveraged data from the AtheroExpress Biobank Study to link T cell immunity to histology-defined instability and cardiovascular outcomes. ResultsT cell responses in unstable versus stable atherosclerosis were distinct. Unstable human plaques contained highly expanded, autoimmune-like CD8 T cells with markedly increased cytotoxic signatures, reduced exhaustion and distinct clonal repertoires compared to stable regions. Most plaque CD8 T cells exhibited a pronounced tissue-resident transcriptional program. Moreover, the transcriptional signature of these plaque resident T cells was distinct from multiple other human tissues. Autoimmune-like cytotoxic and tissue-resident CD8+ T cell responses were also evident in murine atherosclerosis, where restricting the activation of antigen-driven CD8+ T cells prevented plaque destabilisation. Importantly, analysis of carotid endarterectomy samples from >1000 patients identified that intraplaque cytotoxic CD8 T cell gene signatures strongly correlated with histological instability and predicted future strokes. ConclusionsIntegrated human, murine and clinical analyses demonstrate that autoimmune-like, cytotoxic CD8 T cell responses are central drivers of plaque instability and major cardiovascular events. Targeting pathogenic CD8 T cell responses may thus offer a compelling immunomodulatory strategy to stabilise plaques and reduce the risks of stroke and myocardial infarction. Graphical AbstractO_ST_ABSKey QuestionC_ST_ABSRupture of unstable atherosclerotic plaques is a typical cause of myocardial infarction and stroke. To understand the underlying cause and to prevent plaque rupture, we addressed the central hypothesis that autoimmune-like T cell responses drive plaque destabilisation and rupture. Key FindingsCD8+ T cells are clonally expanded with increased cytotoxic signatures in unstable versus stable plaques (mice and humans) and require antigen recognition to drive plaque instability. Cytotoxic CD8+ T cell signatures in excised plaques correlate with increased future cardiovascular events. Take Home MessageAutoimmune-like adaptive immune reactions, dominated by CD8+ T cells, are a major driver of plaque instability/rupture. Therefore, targeting pathogenic CD8 T cell responses offers a compelling immunomodulatory strategy to stabilise plaques and reduce the risk of myocardial infarction and stroke. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/720043v1_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@bd83dcorg.highwire.dtl.DTLVardef@1bee3borg.highwire.dtl.DTLVardef@1b56bc0org.highwire.dtl.DTLVardef@1b5176f_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

High-resolution single-cell RNA sequencing using canFam4 reveals novel immune subsets and checkpoint programs in healthy dogs

Single-cell RNA sequencing (scRNA-seq) enables high-resolution profiling of immune heterogeneity. Although previous studies have mapped the single-cell transcriptomic atlases of peripheral leukocytes in healthy dogs, the identification and functional characterization of distinct immune subsets remain incomplete. We constructed a single-cell atlas of peripheral leukocytes from six healthy small-breed dogs using the 10x Genomics platform and the updated canFam4 genome. Analysis of 30,040 high-quality transcriptomes revealed 51 distinct immune subsets, including CD14{square}CD33{square} monocytes, XCR1{square}CD1D{square} dendritic cells, CEACAM1{square}CD24{square} neutrophils, and IL32{square}BATF{square} regulatory T cells, which were underrepresented in canFam3.1-based studies. Interferon-enriched CD14{square} monocytes and CD4{square} T subsets associated with myxomatous mitral valve disease were also identified. Functional analysis revealed that PDCD1 attenuates TCR signaling, LAG3 modulates malate metabolism in CD4{square} T cells, and suppresses TBX21 in CD8{square} T cells associated with viral response. CD274 encoding PD-L1 was linked to IL-10 production in neutrophils, and CTLA4 represented an initial activation of double-negative T subsets. T cell exhaustion scores and proliferative fractions varied across cohorts, reflecting differences in environmental antigenic exposures. Our study represents the first comprehensive, gene-resolved single-cell analysis that reveals immunoregulatory checkpoint mechanisms underlying immune homeostasis in healthy dogs. Our dataset will serve as a valuable resource for future comparative and translational immunology research in dogs.

immunology↗

bioRxiv2025

dandelionR: Single-cell immune repertoire trajectory analysis in R

Integration of single-cell RNA-sequencing (scRNA-seq) and adaptive immune receptor (AIR) sequencing (scVDJ-seq) is extremely powerful in studying lymphocyte development. A python-based package, Dandelion, introduced VDJ-feature space method, which addresses the challenge in integration of single-cell AIR data with gene expression data and enhanced the trajectory analysis results. However, no R-based equivalent or similar methods currently exist. To fill this gap, we present dandelionR, an R implementation of Dandelions trajectory analysis workflow, bringing the VDJ feature space construction and trajectory analysis using diffusion map and absorbing Markov chain to R, offering a new option for scRNA-seq and scVDJ-seq analysis to R language users.

bioinformatics↗

bioRxiv2024

scRepertoire 2: Enhanced and Efficient Toolkit for Single-Cell Immune Profiling

Single-cell adaptive immune receptor repertoire sequencing (scAIRR-seq) and single-cell RNA sequencing (scRNA-seq) provide a transformative approach to profiling immune responses at unprecedented resolution across diverse pathophysiologic contexts. This work presents scRepertoire 2, a substantial update to our R package for analyzing and visualizing single-cell immune receptor data. This new version introduces an array of features designed to enhance both the depth and breadth of immune receptor analysis, including improved workflows for clonotype tracking, repertoire diversity metrics, and novel visualization modules that facilitate longitudinal and comparative studies. Additionally, scRepertoire 2 offers seamless integration with contemporary single-cell analysis frameworks like Seurat and SingleCellExperiment, allowing users to conduct end-to-end immune profiling with transcriptomic data. Performance optimizations in scRepertoire 2 substantially reduce computational time and memory usage, addressing the demands of the ever-increasing size and scale of single-cell studies. This release marks an advancement in single-cell immunogenomics, equipping researchers with a robust toolset to uncover immune dynamics in health and disease.

immunology↗

bioRxiv2024

Epithelial IL-2 is critical for NK cell-mediated cancer immunosurveillance in mammary glands

Interleukin 2 (IL-2) is the first identified cytokine and its interaction with receptors has been known to shape the immune responses in many lymphoid or non-lymphoid tissues for more than four decades. Active T cells are the primary cellular source for IL-2 production and epithelial cells have never been considered the major cellular source of IL-2 under physiological conditions. It is, however, tempting to speculate that epithelial cells could potentially express IL-2 that regulates the intricate interactions between epithelial cells and lymphocytes. Datamining our recently published single-cell RNAseq in the mouse mammary gland identified IL-2 expression in mammary epithelial cells, which is induced by prolactin via the STAT5 signaling pathway. Furthermore, epithelial IL-2 plays a crucial role in maintaining the physiological functions of natural killer (NK) cells within the mammary glands. IL-2 deletion in the mammary epithelial cells leads to a significant reduction in the number and function of NK cells, which in turn results in defective immunosurveillance, expansion of luminal epithelial cells, and tumor development. Interestingly, T cells in the mammary glands are not changed, indicating the specific regulation of NK cells by epithelial IL-2 production. In agreement, we also found that human epithelial cells express IL-2 and NK cells express the highest level of IL2RB among all the immune cells. Here, we provide the first evidence that epithelial cells produce IL-2, which is critical for maintaining the physiological functions of NK cells in immunosurveillance.

immunology↗

bioRxiv2024

Type I interferon drives a cellular state inert to TCR-stimulation and could impede effective T-cell differentiation in cancer

Head and neck squamous cell carcinoma (HNSCC) arises from the mucosal epithelium of the oral cavity, pharynx, or larynx and is linked to exposure to classical carcinogens and human papillomavirus (HPV) infection. Due to molecular, immunological, and clinical disparities between HPV+ and HPV-HNSCC, they are recognized as distinct cancer types. While immune checkpoint inhibition (ICI) has demonstrated efficacy in recurrent/metastatic HNSCC, response variability persists irrespective of HPV status. To gain insights into the CD8+ T-cell landscape of HPV-HNSCC, we performed multimodal sequencing (RNA and TCR) of CD8+ tumor-infiltrating lymphocytes (TILs) from treatment-naive HPV-HNSCC patients. Additionally, we subjected cells to ex vivo TCR-stimulation, facilitating the tracing of clonal transcriptomic responses. Our analysis revealed a subset of CD8+ TILs highly enriched for interferon-stimulated genes (ISG), which were found to be clonally related to a subset of granzyme K (GZMK)-expressing cells. Trajectory inference suggests ISG transition via GZMK cells towards terminal effector states. However, unlike GZMK cells, which rapidly an effector-like phenotype in response to TCR stimulation, ISG cells remain transcriptionally inert. Consequently, ISG cells may impede effective T-cell differentiation within the TME. Although, the functional consequences of ISG cells are poorly understood, we revealed that they possess receptors and ligands enabling cell-cell communication networks with key TME immunomodulators such as dendritic cells. Additionally, ISG cells were found to be a core feature across various tumor entities and were specifically enriched within tumor tissue. Thus, our findings illuminate the complexity of T-cell heterogeneity in HPV-HNSCC and reveal an overlooked population of IFN-stimulated CD8+ TILs. Further exploration of their functional significance may offer insights into therapeutic strategies for HPV-HNSCC and other cancer types.

immunology↗

bioRxiv2023

Contrasting roles of different mismatch repair proteins in basal-like breast cancer

The mismatch repair (MMR) pathway is known as a tumor suppressive pathway and genes involved in MMR are commonly mutated in hereditary colorectal or other cancer types. However, the function of MMR genes/proteins in breast cancer progression and metastasis are largely undefined. We found that MSH2, but not MLH1, is highly enriched in basal-like breast cancer (BLBC) and that its protein expression is inversely correlated with overall survival time (OS). MSH2 expression is frequently elevated due to genomic amplification or gain-of-expression in BLBC, which results in increased MSH2 protein to pair with MSH6 (collectively referred to as MutS). Genetic deletion of MSH2 or MLH1 results in a contrasting phenotype in metastasis, with MSH2-deletion leading to reduced metastasis and MLH1-deletion to enhanced liver or lung metastasis. Mechanistically, MSH2 - but not MLH1 - binds to the promoter region of interferon receptor 1 (IFNAR1) and suppresses its expression in BLBC. Deletion of MSH2 initiates a chain of immune reactions via the upregulation of IFNAR1 expression and the activation of type 1 interferon signaling, which explains a highly immune active tumor microenvironment in tumors with MSH2-deficiency. Our study supports the contrasting functions of MSH2 and MLH1 in BLBC progression and metastasis due to the differential regulation of IFNAR1 expression, which challenges the paradigm of the MMR pathway as a universal tumor suppressive mechanism.

cancer biology↗

bioRxiv2022

Enhanced survival and low proliferation marks multifunctional virus specific memory CD4 T cells

Cytokine production by memory T cells is a key mechanism of T cell mediated protection. However, we have a limited understanding of the survival and secondary responses of memory T cells with cytokine producing capacities. We interrogate antigen-specific CD4 T cells using a mouse influenza A virus infection model. CD4 T cells with the capacity to produce cytokines survive better than non-cytokine+ cells, displaying a low fold contraction and expressing high levels of pro-survival molecules, CD127 and Bcl2. Transcriptomic analysis reveals a heterogenous population of memory CD4 T cells with three clusters of cytokine+ cells. These clusters match flow cytometry data revealing an enhanced survival signature in cells capable of producing multiple cytokines. These multifunctional cells are, however, less likely to proliferate during and following primary and secondary infections. Despite this, multifunctional memory T cells form a substantial fraction of the secondary memory pool, indicating that survival rather than proliferation may dictate which populations survive within the memory pool. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=86 SRC="FIGDIR/small/520219v3_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@93e62forg.highwire.dtl.DTLVardef@1ed2444org.highwire.dtl.DTLVardef@1e7f79borg.highwire.dtl.DTLVardef@30e31d_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG

immunology↗

bioRxiv2022

Ibex: Variational autoencoder for single-cell BCR sequencing.

SummaryB cells are critical for adaptive immunity and are governed by the recognition of an antigen by the B cell receptor (BCR), a process that drives a coordinated series of signaling events and modulation of various transcriptional programs. Single-cell RNA sequencing with paired BCR profiling could offer insights into numerous physiological and pathological processes. However, unlike the plethora of single-cell RNA analysis pipelines, computational tools that utilize single-cell BCR sequences for further analyses are not yet well developed. Here we report Ibex, which vectorizes the amino acid sequence of the complementarity-determining region 3 (cdr3) of the immunoglobulin heavy and light chains, allowing for unbiased dimensional reduction of B cells using their BCR repertoire. Ibex is implemented as an R package with integration into both the Seurat and Single-Cell Experiment framework, enabling the incorporation of this new analytic tool into many single-cell sequencing analytic workflows and multimodal experiments. Availability and ImplementationIbex is available as an R package at https://github.com/ncborcherding/Ibex. Reproducible code and data for the figure appearing in the manuscript are available at https://github.com/ncborcherding/Ibex.manuscript. A companion TCR-based approach is available at https://github.com/ncborcherding/Trex.

bioinformatics↗

bioRxiv2022

Mouse tissue harvest-induced hypoxia rapidly alters the in vivo metabolome, between-genotype metabolite level differences, and 13C-tracing enrichments

Metabolism is potently regulated by oxygen as the terminal acceptor of the electron transport chain. Thus, a challenge for capturing the in vivo metabolome of animal tissues is to achieve rapid freezing after dissection-induced loss of perfusion before the onset of hypoxia-driven metabolomic remodeling. However, the timing of the metabolomic changes elicited by post-dissection freezing delays are not well described. We addressed this problem by carefully and systematically assessing broad, genotype-specific, and 13C isotopologue metabolomic change resulting from post-dissection, ex vivo mouse tissue metabolism. Based on experiments with mouse liver, heart muscle, and skeletal muscle, we show that broad metabolomic change is rapid, that both false negative and false positive between genotype differences are induced, and that 13C-isotopologue abundances and enrichment percentages change with post-dissection hypoxia. These findings provide a previously absent, systematic illustration of the extensive and confounding metabolomic changes occurring within the early minutes of delayed tissue freezing.

biochemistry↗

bioRxiv2022

IL-17A controls CNS autoimmunity by regulating gut microbiota and inducing regulatory T cells

A disrupted equilibrium among gut microbiota, IL-17A-producing CD4 T-cells (Th17), and regulatory CD4 T-cells (Treg) have been linked with the pathobiology of multiple sclerosis (MS). While gut microbiota can regulate both Treg and Th17 cells, the impact of IL-17A on this gut-immune connection remains unclear. Utilizing HLA-DR3 transgenic mouse model of MS, we show that IL-17A deficiency (HLA-DR3.IL17A-/-) resulted in milder disease characterized by increased Tregs and expansion of Treg-promoting gut microbes, including Prevotella. Cohousing HLA-DR3 mice with HLA-DR3.IL17A-/- transferred the milder disease phenotype and associated microbiota changes to DR3 mice, highlighting the dominant role of gut microbiota in Treg induction and disease amelioration. DR3.IL17A-/- mice also showed a higher abundance of functional pathways linked with short-chain fatty acid synthesis and elevated IL-10 in dendritic cells. Enrichment of the Treg-promoting PPAR signaling pathway expression in the colon of HLA-DR3.IL17A-/- mice and following Prevotella administration in HLA-DR3 mice underscores the importance of gut microbiota in IL-17A-mediated immune regulation. Thus, our study uncovers a previously unappreciated role for IL-17A in shaping gut microbiota and immune regulation, with far-reaching implications for MS treatment. One-Sentence SummaryIL-17A modulates Treg and gut microbiota to control EAE

immunology↗

bioRxiv2021

Dissecting the Cellular Landscape and Transcriptome Network in Viral Myocarditis by Single-Cell RNA Sequencing

Myocarditis induced with Coxsackievirus B3 (CVB3) is commonly employed to study viral pathogenesis in mice. Although infectious virus is cleared after the acute phase, affected animals chronically develop the features of dilated cardiomyopathy, which may involve the mediation of immune and non-immune cells. To dissect this complexity, we performed single-cell RNA sequencing on heart cells obtained from healthy and myocarditic mice, leading us to note that myocarditic mice had significantly higher proportions of myeloid cells, CD4 and CD8 T cells, and fibroblasts, whereas NK cells, ILCs and B cells were low. While the transcriptome profiles of myeloid cells revealed detection of monocytes and macrophages of M2 phenotype with pathways important in immune metabolism and inflammation, T cells consisted of Th17 cells, CTLs, and Treg cells with transcriptome signatures critical for cytotoxic functions. Although fibroblasts detected in myocarditic mice were phenotypically heterogeneous, their transcriptomes played roles in fibrosis and regulation of inflammation and immune responses. Additionally, analysis of intercellular communication networks revealed unique interactions and signaling pathways in the cardiac cellulome, whereas myeloid cells and T cells in myocarditic mice revealed uniquely upregulated transcription factors modulating cardiac remodeling functions. Taken together, our data suggest that M2 cells, T cells, and fibroblasts may cooperatively or independently participate in the pathogenesis of viral myocarditis.

immunology↗

bioRxiv2020

TAZ-CAMTA1 and YAP-TFE3 modulate the basal TAZ/YAP transcriptional program by recruiting the ATAC histone acetyltransferase complex

Epithelioid hemangioendothelioma (EHE) is a vascular sarcoma that metastasizes early and lacks an effective medical therapy. The TAZ-CAMTA1 and YAP-TFE3 fusion proteins are chimeric transcription factors and initiating oncogenic drivers of EHE. A combined proteomic/genetic screen identified YEATS2 and ZZZ3, components of the Ada2a-containing histone acetyltransferase (ATAC) complex, as key interactors of both TAZ-CAMTA1 and YAP-TFE3 despite the dissimilarity of the C terminal fusion partners CAMTA1 and TFE3. An integrative next generation sequencing approach showed the fusion proteins drive expression of a unique transcriptome distinct from TAZ and YAP by simultaneously hyperactivating a TEAD-based transcriptional program and modulating the chromatin environment via interaction with the ATAC complex. Interaction of the ATAC complex with both TAZ-CAMTA1 and YAP-TFE3 indicates the histone acetyltransferase complex is an oncogenic driver in EHE and potentially other sarcomas. Furthermore, the ATAC complex is an enzymatic transcriptional cofactor required for both fusion proteins in EHE, representing a unifying therapeutic target for this sarcoma. Gene fusions are the most common genetic alterations activating TAZ and YAP in cancer, and this study serves as a template for identifying epigenetic modifiers recruited by the C terminal fusion partners of other TAZ/YAP gene fusions occurring in gliomas, carcinomas, and other sarcomas. SummaryTAZ-CAMTA1 and YAP-TFE3 alter the TAZ/YAP transcriptional program by recruiting the ATAC complex and modifying the chromatin landscape.

cancer biology↗

bioRxiv2020

Single cell BCR and transcriptome analysis after respiratory virus infection reveals spatiotemporal dynamics of antigen-specific B cell responses.

B cell responses are a critical component of anti-viral immunity. However, a comprehensive picture of antigen-specific B cell responses, differentiation, clonal proliferation and dynamics in different organs after infection is lacking. Here, we combined single-cell RNA sequencing with single-cell B cell receptor (BCR) characterization of antigen-specific cells in the draining lymph nodes, spleen and lungs after influenza infection. We identify several novel B cell subpopulations forming after infection and find organ-specific differences that persist over the course of the response. We discover important transcriptional differences between memory cells in lungs and lymphoid organs and describe organ-restricted clonal expansion. Strikingly, by combining BCR mutational analysis, monoclonal antibody expression and affinity measurements we find no differences between germinal center (GC)-derived memory and plasmacells, at odds with an affinity-based selection model. By linking antigen-recognition with transcriptional programming, clonal-proliferation and differentiation, these finding provide important advances in our understanding of antiviral B cell immunity.

immunology↗

bioRxiv2020

AP-2γ is Required for Maintenance of Pluripotent Mammary Stem Cells

Mammary gland ductal morphogenesis depends on the differentiation of mammary stem cells (MaSCs) into basal and luminal lineages. The AP-2{gamma} transcription factor, encoded by Tfap2c, has a central role in mammary gland development but its effect in mammary lineages and specifically MaSCs is largely unknown. Herein, we utilized an inducible, conditional knockout of Tfap2c to elucidate the role of AP-2{gamma} in maintenance and differentiation of MaSCs. Loss of AP-2{gamma} in the basal epithelium profoundly altered the transcriptomes and decreased the number of cells within several clusters of mammary epithelial cells, including adult MaSCs and luminal progenitors. AP-2{gamma} regulated the expression of genes known to be required for mammary development including C/EBP{beta}, I{kappa}B, and Rspo1. As a result, AP-2{gamma}-deficient mice exhibited repressed mammary gland ductal outgrowth and inhibition of regenerative capacity. The findings demonstrate that AP-2{gamma} is required for maintenance of pluripotent MaSCs and their ability to develop mammary gland structures. HighlightsO_LIAP-2{gamma}-deficient mice exhibited repressed ductal outgrowth and regenerative capacity C_LIO_LILoss of AP-2{gamma} reduced the number of mammary stem and luminal progenitor cells C_LIO_LIAP-2{gamma} target genes, including C/EBP{beta}, I{kappa}B, and Rspo1, regulate mammary development C_LIO_LIAP-2{gamma} is required for maintenance of pluripotent mammary stem cells C_LI eTOC blurbGu, Cho and colleagues utilized a conditional knockout of Tfap2c to examine transcriptional effects of AP-2{gamma} on mammary stem cells. Single cell analysis demonstrated that AP-2{gamma}-deficient mice have decreased numbers of mammary stem cells and alteration of genes required for mammary development including C/EBP{beta}, I{kappa}B, and Rspo1. They demonstrate that AP-2{gamma} is necessary for maintenance of pluripotent mammary stem cells.

developmental biology↗