Biology subjects

Best, K.

Publications and source records attributed to Best, K..

4 recordsLinked to original sources

bioRxiv2026

EndoMT: An R Package Resource for Endothelial-Mesenchymal Transition Gene Set Enrichment Analysis

Introduction: Endothelial-mesenchymal transition (EndoMT) is a dynamic endothelial cell-state transition increasingly implicated in fibrosis, vascular dysfunction, inflammation and cancer. Despite expansion of EndoMT-focused transcriptomic research, EndoMT representation remains limited to broader epithelial-mesenchymal transition (EMT) frameworks in standard gene set repositories. Methods: To address the absence of a general-purpose EndoMT gene set for transcriptomic enrichment analysis, we developed an open EndoMT gene set resource and accompanying R package. A literature-informed EndoMT gene set was curated and directionally assigned to EndoMT UP and EndoMT DOWN signatures according to reported or hypothesised expression during partial EndoMT, defined here as an active transitional state rather than a complete mesenchymal endpoint, to improve capture of EndoMT-associated transcriptional changes across different stages of the process. Genes were annotated by marker subtype and implemented as Gene Matrix Transposed files distributed through the R package, together with exported R objects and gene-level metadata. Benchmarking was performed using bulk RNA-seq data sets GSE118446, comprising seven-day IL-1l{beta}/TGF-{beta}2-treated human umbilical vein endothelial cells (HUVECs) and human pulmonary arterial endothelial cells, and GSE342578, comprising three-day TGF-{beta}1/2/3-treated HUVECs; single-cell RNA-seq data set GSE237895, comprising seven-day TGF-{beta}1-treated and SNAI1-overexpressing HUVECs; and endothelial cell and cancer-associated fibroblast populations from human metastatic melanoma single-cell RNA-seq data set GSE72056. Results: In GSE118446, EndoMT UP was positively enriched and EndoMT DOWN negatively enriched in chronically IL-1{beta}/TGF-{beta}2-treated endothelial cells, concordant with experimentally validated EndoMT induction, while partial EndoMT-associated enrichment was detected in single ligand-treatment. In contrast, EndoMT UP was negatively enriched following acute TGF-{beta}1/2/3 treatment, suggesting temporal differences between acute TGF-{beta} stimulation and chronic EndoMT induction. In GSE237895 mesenchymal-like endothelial cells, EndoMT UP was positively enriched and EndoMT DOWN negatively enriched in both TGF-{beta}1-treated and SNAI1-overexpressing models. EndoMT gene sets also discriminated endothelial and mesenchymal/stromal transcriptional states in GSE72056 metastatic melanoma. Marker subtype and Gene Ontology Biological Process analyses provided additional exploratory resolution of EndoMT-associated components beyond MSigDB Hallmark EMT. Discussion: The EndoMT R package provides a dedicated, accessible and interoperable resource for EndoMT-focused transcriptomic enrichment analysis. Benchmarking demonstrates utility for detecting established, partial and divergent EndoMT-associated states, supporting broad applicability across EndoMT biology research.

bioinformatics↗

bioRxiv2026

Endothelial AMBRA1 loss contributes to vascular dysregulation facilitating metastatic progression in early-stage melanoma

Validated biomarkers for identifying patients with early-stage melanomas at high risk of metastasis are limited. We have previously shown that loss of Activating Molecule in Beclin-1-Regulated Autophagy (AMBRA1) and loricrin in the epidermal microenvironment is associated with tumour recurrence. Here we show that endothelial AMBRA1 deficiency contributes to vascular dysfunction and melanoma progression. Melanoma-conditioned media or exposure to TGF{beta}1-3 ligands induced post-transcriptional loss of AMBRA1 in endothelial cells. Transcriptomic profiling in both in vitro and human melanoma single-cell RNA sequencing datasets showed activation of cell-cycle and metabolic programmes alongside suppression of endothelial junction, adhesion and immune-supportive pathways in AMBRA1-deficient endothelial cells. Functionally, AMBRA1 loss increased endothelial cell proliferation, accelerated early tubulogenesis, impaired three-dimensional spheroid adhesion, stabilised endothelial-to-mesenchymal transition-associated transcription factors Slug and Snail, and reduced Claudin-5, VE-cadherin and N-cadherin, indicative of endothelial plasticity and dysfunction. Furthermore, loss of AMBRA1 in a subset of intratumoural and peritumoural blood and lymphatic vessels correlated significantly with metastatic progression in a cohort of 121 non-ulcerated primary AJCC stage I/II melanomas classified as AMBLor at-risk. Collectively, these findings position endothelial AMBRA1 as a regulator of vascular plasticity, dysfunction, and immune-supportive endothelial function in early-stage melanomas, and a marker of a permissive microenvironment associated with metastasis.

cancer biology↗

bioRxiv2020

Structure and function of yeast Lso2 and human CCDC124 bound to hibernating ribosomes.

Cells adjust to nutrient deprivation by reversible translational shut down. This is accompanied by maintaining inactive ribosomes in a hibernation state, where they are bound by proteins with inhibitory and protective functions. In eukaryotes, such a function was attributed to Stm1 (SERBP1 in mammals), and recently Lso2 (CCDC124 in mammals) was found to be involved in translational recovery after starvation from stationary phase. Here, we present cryo-electron microscopy (cryo-EM) structures of translationally inactive yeast and human ribosomes. We found Lso2/CCDC124 accumulating on idle ribosomes in the non-unrotated state, in contrast to Stm1/SERBP1-bound ribosomes, which display a rotated state. Lso2/CCDC124 bridges the decoding sites of the small with the GTPase-activating center of the large subunit. This position allows accommodation of the Dom34-dependent ribosome recycling system, which splits Lso2-containing but not Stm1-containing ribosomes. We propose a model in which Lso2 facilitates rapid translation reactivation by stabilizing the recycling-competent state of inactive ribosomes.

molecular biology↗

bioRxiv2019

Cell non-autonomous functions of S100a4 drive fibrotic tendon healing

Identification of pro-regenerative approaches to improve tendon healing is of critical importance given the diminished quality of life and physical function that accompanies the typical fibrotic response to tendon injury. S100a4 modulates fibrosis through tissue-type dependent mechanisms, and the role of S100a4 in fibrotic, scar-mediated tendon healing has not been established. In the present study we tested the hypothesis that inhibition of S100a4 improves tendon function following acute injury and surgical repair. We demonstrate cell non-autonomous functions of S100a4 as S100a4 haploinsufficiency promotes regenerative tendon healing, including decreased scar formation and improved mechanical properties. Moreover, inhibition of S100a4 via antagonism of its putative receptor, the Receptor for Advanced Glycation Endproducts (RAGE), also decreases scar formation. Mechanistically, knock-down of S100a4 decreases myofibroblast and macrophage content at the site of injury, with both cell populations being key drivers of fibrotic progression. In contrast, S100a4+ cell depletion displays time-dependent effects on scar formation, and consistent impairments in restoration of mechanical properties, indicating a critical role for these cells in re-establishing tendon strength after injury. Finally, we demonstrate, that S100a4-lineage cells become -SMA+ myofibroblasts, via loss of S100a4 expression. Using a combination of genetic mouse models, small molecule inhibitors and in vitro studies we have defined S100a4 as a novel, promising therapeutic candidate to improve tendon function after acute injury.

cell biology↗