Biology subjects

Sanborn, M. A.

Publications and source records attributed to Sanborn, M. A..

11 recordsLinked to original sources

bioRxiv2026

Ionic Regulation of Mechanosurveillance and Metastasis via the MRTFA/KCNMB1 Axis

Cellular stiffness profoundly impacts cancer metastasis at multiple levels, but mechanisms that regulate cancer cells stiffness remain poorly understood. Here, we identified potassium efflux and KCNMB1, an auxiliary subunit of the large conductance potassium efflux (BK) channels, as regulators of cellular stiffness downstream of myocardin related transcription factor A (MRTFA). In primary pericytes, KCNMB1 knockdown increased cellular stiffness, which is consistent with the role of potassium efflux in promoting relaxation during excitation-contraction coupling. In a striking contrast, however, KCNMB1 knockdown decreased cellular stiffness in cancer cells. Softer cancer cells were resistant to NK cell mediated cytotoxicity and the low KCNMB1 expression was associated with worse survival in breast cancer patients. Importantly, pharmacological activation of BK channels reduced metastatic burden in mice and improved lysis of cancer cells by cytotoxic T-lymphocytes. These results highlight the unique ionic regulation of stiffness in cancer cells and point to BK channel agonism as a new therapeutic approach in cancer.

cancer biology↗

bioRxiv2025

Integrative analysis of spatiotemporal transcriptomics delineates dynamic cell states in squamous tumorigenesis

Squamous cell cancers are responsible for 1 in 5 cancer deaths and survival improvements lag behind those seen in adenocarcinomas. This disparity is in large part due to the limited impact of immunotherapy due to therapeutic resistance, where less than ten percent of patients respond in early stage squamous cell carcinomas of the Head and Neck. Mechanisms that govern intrinsic resistance remain poorly understood and likely arise during the premalignant or dysplastic state. Here, we generated a dataset of murine and human oral squamous epithelia spanning the earliest premalignant stages through invasive carcinoma. Integrative analysis of single-cell and spatial transcriptomics data across the dysplasia to carcinoma continuum reveals early and sustained shifts in epithelial transcriptomes. Spatially informed cell-cell interaction analysis reveals dysplasia-specific upregulation of wound healing and immune remodeling programs in severe dysplasia and invasive carcinoma in a human sample of oral dysplasia. The presence of these transcriptomic programs within early dysplasia may account for the aggressive clinical presentations of squamous cancers including intrinsic therapeutic resistance.

cancer biology↗

bioRxiv2025

Persistent Immune Dysregulation during Post-Acute Sequelae of COVID-19 is Manifested in Antibodies Targeting Envelope and Nucleocapsid Proteins

Post-Acute Sequelae of SARS-CoV-2 infection (PASC) syndrome or "Long COVID" represents a widespread health challenge that necessitates the development of novel diagnostic approaches and targeted therapies that can be readily deployed. Immune dysregulation has been reported as one of the hallmarks of PASC, but the extent of PASC immune dysregulation in patients over time remains unclear. We therefore assessed SARS-CoV-2-specific antibody responses, peripheral immune cell profiles, autoantibody profiles and circulating cytokines for up to 6 months in participants with a SARS-CoV-2 infection who either convalesced or developed PASC. Compared to convalescent, PASC participants with a broad range of PASC phenotypes exhibited persistently elevated IgG titers for SARS-CoV-2 Envelope and Nucleocapsid proteins over the 6 months of study duration. In contrast, the IgG responses to Spike protein were significantly lower in the PASC cohort with predominantly IgG1 and IgG3 class-switched bias. Using CyTOF analysis, we show elevated numbers of circulating T follicular helper cells (cTFH) and mucosa-associated invariant T cells (MAIT), which also correlated with high anti-Envelope IgG titers. Persistent immune activation was accompanied by augmented serum cytokine profiles with LIF, IL-11, Eotaxin-3, and HMGB-1 in PASC participants, who also demonstrated significantly higher rates of autoantibodies. These findings highlight the persistence of immune dysregulation in PASC, underscoring the need to explore targeted therapies addressing viral persistence, dysregulated antibody production, and autoimmunity.

immunology↗

bioRxiv2024

Inhibition of β-catenin signaling by Amyloid-β in endothelial cells impairs vascular barrier integrity

Dysfunction of the blood-brain barrier (BBB) is emerging as a critical mediator of Alzheimers Disease (AD) progression and precedes the formation of large Amyloid-{beta} (A{beta}) plaques in AD patients. Maintenance of the blood brain barrier integrity by brain microvascular endothelial cells (BMECs) is essential for brain homeostasis and is in part maintained by WNT/{beta}-catenin signaling. We hypothesized that A{beta} induces blood-brain barrier dysfunction by inhibiting WNT/{beta}- catenin signaling in brain endothelial cells, leading to reduced expression of BBB-related genes and barrier function. In brain endothelial cells, we found that A{beta} directly decreased {beta}-catenin transcriptional activity, but also inhibited activation of {beta}-catenin by the WNT3A peptide. Additionally, A{beta} reduced barrier integrity of ECs, which was in part restored by exposure to exogenous WNT3A. We observed A{beta}-induced inhibition within 3 hours of exposure. A{beta}-induced inhibition of {beta}-catenin signaling was consistent across both immortalized brain ECs and ECs differentiated from human induced pluripotent stem cells(iPSCs). We next investigated human iPSCs with and without the N141I mutation in presenilin-2 (PSEN2), known to increase A{beta} buildup and familial AD risk. We found the AD ECs showed smaller cell size and expressed lower VE-cadherin at the protein level. RNA sequencing revealed that the presence of PSEN2 N141I did not significantly impact gene expression of genes coding for proteins canonically involved in barrier integrity but did show differences in the expression of transposable elements. These results indicate that BBB dysfunction early in AD may be the result of A{beta} in the brain impairing WNT/{beta}-catenin signaling which maintains the barrier integrity of brain endothelial cells.

neuroscience↗

bioRxiv2024

Matrimeres are systemic nanoscale mediators of tissue integrity and function

Tissue barriers must be rapidly restored after injury to promote regeneration. However, the mechanism behind this process is unclear, particularly in cases where the underlying extracellular matrix is still compromised. Here, we report the discovery of matrimeres as constitutive nanoscale mediators of tissue integrity and function. We define matrimeres as non-vesicular nanoparticles secreted by cells, distinguished by a primary composition comprising at least one matrix protein and DNA molecules serving as scaffolds. Mesenchymal stromal cells assemble matrimeres from fibronectin and DNA within acidic intracellular compartments. Drawing inspiration from this biological process, we have achieved the successful reconstitution of matrimeres without cells. This was accomplished by using purified matrix proteins, including fibronectin and vitronectin, and DNA molecules under optimal acidic pH conditions, guided by the heparin-binding domain and phosphate backbone, respectively. Plasma fibronectin matrimeres circulate in the blood at homeostasis but exhibit a 10-fold decrease during systemic inflammatory injury in vivo. Exogenous matrimeres rapidly restore vascular integrity by actively reannealing endothelial cells post-injury and remain persistent in the host tissue matrix. The scalable production of matrimeres holds promise as a biologically inspired platform for regenerative nanomedicine.

bioengineering↗

bioRxiv2023

SenePy: Unveiling the Cell-Type Specific Landscape of Cellular Senescence through Single-Cell Analysis in Living Organisms

Senescent cells accumulate in tissues with organismal age and contribute causally to multiple chronic diseases. In vivo senescent cell phenotypes are heterogeneous because cellular context and stressors vary by cell type and tissue. Due to the variability of senescence programs, there is no universal method to identify senescent cells and even widely used markers, such as CDKN2A, are not ubiquitous. Therefore, we interrogated the Tabula Muris Senis mouse single-cell aging atlas and an array of single-cell datasets from human donors that spanned many ages to find cell-specific signatures of cellular senescence. We derived 75 mouse and 65 human senescence signatures from individual cell populations. CDKN2A and other markers of senescence were overrepresented in these signatures but there were many novel senescence genes present at higher rates. Within individual cell populations, we observed multiple programs of senescence with distinct temporal and transcriptional characteristics. We packaged the signatures along with a single-cell scoring method into an open-source package: SenePy. SenePy signatures better recapitulate cellular senescence than available methods when tested on multiple in vivo RNA-seq datasets and a p16ink4a reporter single-cell dataset. We used SenePy to map the kinetics of senescent cell accumulation across 97 cell types from humans and mice. SenePy also generalizes to disease-associate senescence and we used it to identify an increased burden of senescent cells in COVID-19 and myocardial infarction. This work provides a significant advancement towards our ability to identify and characterize in vivo cellular senescence.

cell biology↗

bioRxiv2022

Impaired Barrier Integrity of the Skeletal Muscle Vascular Endothelium Drives Progression of Cancer Cachexia

Cancer patients experience cachexia, which is characterized by extensive skeletal muscle wasting that worsens the quality of life and increases mortality. Currently, there are no approved treatments that can effectively counteract cancer cachexia. Vascular endothelial cells (ECs) are essential for maintaining tissue perfusion, nutrient supply, and preventing inappropriate transmigration of immune cells into the tissue. However, little is known about the role of the muscle vasculature in cancer cachexia. We hypothesized that endothelial dysfunction in the skeletal muscle mediates cancer cachexia. Using transgenic pancreatic ductal adenocarcinoma (PDAC) mice and a tissue clearing and high-resolution 3D-tissue imaging approach, we found that the loss of skeletal muscle vascular density precedes the loss of muscle mass. Importantly, we show that cancer cachexia patients exhibit significantly decreased muscle vascular density and severe muscle atrophy when compared to non-cancer patients. Unbiased single cell transcriptomic analyses of the muscle endothelium unveiled a unique EC population present in cachexia muscles. Increased circulating Activin-A suppresses the expression of the transcriptional co-activator PGC1 in the muscle endothelium, thus disrupting junctional integrity in the vasculature and increasing vascular leakage. Conversely, restoration of endothelial-specific PGC1 prevented the decreased vascular density and muscle loss observed in tumor-bearing mice. Our study suggests that EC-PGC1 is essential for maintaining the integrity of the skeletal muscle vascular barrier and that restoring muscle endothelial function could be a valuable therapeutic approach to prevent or reverse cancer cachexia.

cancer biology↗

bioRxiv2021

Identification of Japanese Encephalitis Virus Genotype V and Other Mosquito-borne Viruses in Camp Humphreys, Republic of Korea, using Metagenomic Analysis

Recent outbreaks of emerging and re-emerging viruses such as Zika, West Nile and Japanese encephalitis (JEV) viruses have shown that timely detection of novel arboviruses with epidemic potential is essential to mitigate human health risks. There have been rising concerns that an emergent JEV genotype (genotype V, GV) is circulating in Asia, against which the current US-FDA-approved JEV vaccine may not be efficacious. To ascertain if JEV GV and other arboviruses are circulating in East Asia, we conducted next-generation sequencing on 260 pools of Culex tritaeniorhynchus and Culex bitaeniorhynchus mosquitoes (6,540 specimens) collected at Camp Humphreys, Republic of Korea (ROK), from mid-May - October 2018. Metagenomic analysis demonstrated a highly abundant and diverse virome with correlates of health and ecological relevance. Additionally, two complete JEV GV genome sequences were obtained from separate mosquito pools, indicating that JEV GV is circulating in the Pyeongtaek area near Seoul, ROK. Retrospective sample and sequence analyses showed that JEV GV was also present in 2016 mosquito pools collected in Seoul, ROK. Sequence-based analysis of JEV GV indicates a divergent genotype that is the most distant from the GIII derived live attenuated SA14-14-2 vaccine strain. A GV E protein investigation and 3D modeling in context to SA14-14-2 indicated likely regions responsible for reduced antibody affinity, including clusters of significant amino acid changes at externally exposed domains. These data highlight the critical need for continued mosquito surveillance as a means of detecting and identifying emerging and re-emerging arboviruses of public health relevance. Importantly, our results emphasize recent concerns that there may be a possible shift in the circulating JEV genotype in East Asia and highlights the critical need for a vaccine proven to be efficacious against this re-emergent virus.

genomics↗

bioRxiv2021

A comparative recombination analysis of human coronaviruses and implications for the SARS-CoV-2 pandemic

The SARS-CoV-2 pandemic prompts evaluation of recombination in human coronavirus (hCoV) evolution. We undertook recombination analyses of 158,118 public seasonal hCoV, SARS-CoV-1, SARS-CoV-2 and MERS-CoV genome sequences using the RDP4 software. We found moderate evidence for 8 SARS-CoV-2 recombination events, two of which involved the spike gene, and low evidence for one SARS-CoV-1 recombination event. Within MERS-CoV, 229E, OC43, NL63 and HKU1 datasets, we noted 7, 1, 9, 14, and 1 high-confidence recombination events, respectively. There was propensity for recombination breakpoints in structural genes, and recombination severely skewed the temporal structure of these data, especially for NL63 and OC43. Bayesian time-scaled analyses on recombinant-free data indicated the sampled diversity of seasonal CoVs emerged in the last 70 years, with 229E displaying continuous lineage replacements. These findings emphasize the importance of genomic based surveillance to detect recombination in SARS-CoV-2, particularly if recombination may lead to immune evasion.

genomics↗

bioRxiv2020

Rapid High Throughput Whole Genome Sequencing of SARS-CoV-2 by using One-step RT-PCR Amplification with Integrated Microfluidic System and Next-Gen Sequencing

The long-lasting global COVID-19 pandemic demands timely genomic investigation of SARS-CoV-2 viruses. Here we report a simple and efficient workflow for whole genome sequencing utilizing one-step RT-PCR amplification on a microfluidic platform, followed by MiSeq amplicon sequencing. The method uses Fluidigm IFC and instruments to amplify 48 samples with 39 pairs of primers in a single step. Application of this method on RNA samples from both viral isolate and clinical specimens demonstrate robustness and efficiency of this method in obtaining the full genome sequence of SARS-CoV-2.

molecular biology↗

bioRxiv2020

Analysis of cell-associated DENV RNA by oligo(dT) primed 5' capture scRNAseq

Dengue is one of the most widespread vector-borne viral diseases in the world. However, the size, heterogeneity, and temporal dynamics of the cell-associated viral reservoir during acute dengue virus (DENV) infection remains unclear. In this study, we analyzed cells infected in vitro with DENV and PBMC from an individual experiencing a natural DENV infection utilizing 5 capture single cell RNA sequencing (scRNAseq). Both positive- and negative-sense DENV RNA was detected in reactions containing either an oligo(dT) primer alone, or in reactions supplemented with a DENV-specific primer. The addition of a DENV-specific primer did not increase the total amount of DENV RNA captured or the fraction of cells identified as containing DENV RNA. However, inclusion of a DENV-specific cDNA primer did increase the viral genome coverage immediately 5 to the primer binding site. Furthermore, while the majority of intracellular DENV sequence captured in this analysis mapped to the 5 end of the viral genome, distinct patterns of enhanced coverage within the DENV polyprotein coding region were observed. The 5 capture scRNAseq analysis of PBMC not only recapitulated previously published reports by detecting virally infected memory and naive B cells, but also identified cell-associated genomic variants not observed in contemporaneous serum samples. These results demonstrate that oligo(dT) primed 5 capture scRNAseq can detect DENV RNA and quantify virus-infected cells in physiologically relevant conditions, and provides insight into viral sequence variability within infected cells. IMPORTANCEDengue is one of the most widespread vector-borne viral diseases in the world. However, it is still unclear which cells harbor virus during DENV infection, and how viral reservoirs in serum and infected cells are related. These results demonstrate for the first time that intracellular DENV RNA can be identified and infected cells quantified by 5 capture scRNAseq. This strategy provides a significantly greater throughput and higher sensitivity than previously published methods and has the potential to provide additional information on the genomic heterogeneity of intracellular DENV RNA.

microbiology↗