Biology subjects

Marsh, L.

Publications and source records attributed to Marsh, L..

5 recordsLinked to original sources

bioRxiv2026

CAD variants act through ox-LDL-induced enhancer remodelling to alter VSMC gene programmes

BackgroundVascular smooth muscle cells (VSMCs) play a central role in atherosclerotic coronary artery disease (CAD). Oxidised low-density lipoprotein cholesterol (ox-LDL) induces VSMCs dysfunction but the underlying molecular mechanisms are unclear. CAD genome-wide association studies (GWAS) have identified hundreds of disease-associated loci but their biological roles remain poorly defined. We hypothesised that ox-LDL drives pro-atherogenic changes in VSMCs by altering gene regulatory programs involving causal CAD variants. MethodsEx-vivo human coronary VSMCs were exposed to ox-LDL and profiled using RNA-seq, ATAC-seq, and H3K27ac ChIPmentation. Enhancer-gene links were inferred by integrating these data with Hi-C using the Activity-by-Contact (ABC) model. Variant effect predictions were done using AlphaGenome and key target genes functionally tested by CRISPR/Cas9 knockout. ResultsOx-LDL induced widespread transcriptional reprogramming in coronary VSMCs, with 1,487 upregulated and 1,864 downregulated genes (FDR < 0.05). Single-cell RNA-seq meta-analysis demonstrated that ox-LDL-associated programmes enriched in pro-inflammatory and synthetic-inflammatory VSMC clusters in vivo. ATAC-seq identified [~]22k differentially accessible regions following ox-LDL exposure (FDR < 0.05). Integration of ATAC-seq, H3K27ac, and Hi-C using the ABC framework showed that ox-LDL-driven chromatin remodelling was concentrated at distal enhancers, which linked to 2,008 differentially expressed genes via 4,243 peak-gene connections. ABC enhancers were significantly enriched for CAD variants compared with non-vascular disease controls, with stronger enrichment in dynamically accessible enhancers. AlphaGenome predicted larger regulatory effects of prioritised CAD variants in smooth muscle cells than in a non-vascular comparator, and motif analyses indicated allele-dependent transcription factor binding at prioritised enhancer variants. Locus-level prioritisation nominated candidate enhancer-mediated mechanisms at the SPECC1L and MAP1S loci, and CRISPR knockout of the target genes GUCD1 and BACH1 rescued ox-LDL-induced growth arrest/senescence phenotypes in human coronary artery VSMCs. ConclusionsOur unbiased multi-omics framework shows that ox-LDL rewires VSMC regulatory programmes that influence CAD genetic risk. Enhancer-gene mapping refines effector-gene assignment at CAD loci and prioritises regulatory targets in coronary VSMCs.

genomics↗

bioRxiv2025

Development of a universal imaging "phenome" using Shape, Appearance and Motion (SAM) features and the SAM Observation Tool (SPOT)

Cells are plastic, highly heterogeneous and change over time. High-content timelapse imaging promises to reveal dynamic cell behaviors, enabling more accurate identification of cell state and cell fate prediction for biological hypothesis generation and perturbation screens. To empower live-cell imaging based screen, we report the development of 1) a Shape, Appearance, Motion (SAM) "phenome"; a universal set of 2185 image-derived features that act as a image-"transcriptome" to comprehensively quantify an objects instantaneous phenotype; 2) the SAM-Phenotype-Observation-Tool (SPOT), for image-"sequencing" analysis of phenomes. We validated the effectiveness of unbiased SAM-SPOT workflow on publicly available computer vision and 2D single cell imaging datasets. Importantly, we demonstrated that SAM-phenome outperformed features generated by deep learning AI models trained on >1 million fixed single cell and >5000 single cell video frames, respectively. SAM-phenome and SPOT delivers high-throughput, object-treatment-agnostic, comprehensive screening readouts of dynamics, promising to advance novel molecular target discovery and new medicine development.

bioinformatics↗

bioRxiv2025

Identifying phenotype-genotype-function coupling in 3D organoid imaging using Shape, Appearance and Motion Phenotype Observation Tool (SPOT)

Live cells in tissue are plastic, phenotypically dynamic, and modify their function in response to genetic and environmental perturbations. To unleash the power of live-cell imaging to identify phenotype-genotype-function coupling over time, we report the development of a standardized Shape-Appearance-Motion (SAM) "phenome" and SAM-Phenotype-Observation-Tool (SPOT), that act as an image-"transcriptome" and image-"transcriptome analyzer" respectively, and provide unbiased and comprehensive description of morpho-dynamic phenotypes without prior knowledge. We developed and applied SAM-SPOT to our simulated organoids database with known ground-truth and >1.6 million mouse and human organoid instances with defined genetic and chemical perturbations. SAM-SPOT can effectively and robustly characterize 3D morpho-dynamics from 2D projection videos. Combined with single-cell RNA sequencing, SAM-SPOT revealed that altered WNT signaling, but not mutant RAS or p53, predisposes intestinal organoids to irregular morphogenesis. SAM-SPOT advances biomedical discovery by empowering live-cell imaging to identify phenotype-genotype-function relationships through large-scale and cost-effective label-free live-cell imaging.

cancer biology↗

bioRxiv2025

Adjuvants to improve efficacy of miticides in managed honey bee (Apis mellifera) colonies to control Varroa destructor

Beekeepers must manage Varroa destructor mites to maintain colony health. Large-scale beekeepers often use chemical treatments (miticides) to manage this pest. Miticide resistance drives a need for compounds with alternative modes of toxic action that can be used in a rotation as part of a Varroa management plan. This research aimed to determine the efficacy of oxalic acid, clove oil, and fenpyroximate when delivered in glycerin soaked in strips and combined with a range of bee-safe adjuvants. Adjuvants are a group of compounds used in plant pesticide applications to increase the spreading and penetration of a pesticide. Laboratory cage trials tested a miticidal active ingredient (oxalic acid, clove oil, or fenpyroximate) and an adjuvant (Ecostep BC-12(R), Ecostep SE-11(R), Ecostep AE-13(R), Ecostep CE-13(R), or Silwet L-7500(R)) in glycerin-soaked strips; field trials evaluated oxalic acid combined with Ecostep BC-12(R) adjuvant in glycerin-soaked strips. Field trials with oxalic acid and adjuvant in glycerin caused a significant decrease in Varroa in year 1 and a significant reduction in Varroa, relative to the solvent control, in year 2. On the other hand, field trials with oxalic acid alone did not reduce Varroa loads in colonies relative to the solvent control. Additionally, mite drop data indicate increased speed for the miticidal effect when an adjuvant is included with oxalic acid. This research informs formulation chemistries for oxalic acid and other miticides to help beekeepers maintain healthy hives.

zoology↗

bioRxiv2018

Effect of the macroalgae Asparagopsis taxiformis on methane production and the rumen microbiome assemblage

BackgroundRecent studies using batch-fermentation suggest that the red macroalgae Asparagopsis taxiformis might reduce methane (CH4) emission from beef cattle by up to ~99% when added to rhodes grass hay, a common feed in the Australian beef industry. These experiments have shown significant reductions in methane without compromising other fermentation parameters (i.e. volatile fatty acid production) with A. taxiformis organic matter (OM) inclusion rates of up to 5%. In the study presented here, A. taxiformis was evaluated for its ability to reduce methane production from dairy cattle fed a mixed ration widely utilized in California; the largest milk producer in the US.\n\nResultsFermentation in a semi-continuous in-vitro rumen system suggests that A. taxiformis can reduce methane production from enteric fermentation in dairy cattle by 95% when added at a 5% OM inclusion rate without any obvious negative impacts on volatile fatty acid production. High-throughput 16S ribosomal RNA (rRNA) gene amplicon sequencing showed that seaweed amendment effects rumen microbiome communities consistent with the Anna Karenina hypothesis, with increased beta-diversity, over time scales of approximately three days. The relative abundance of methanogens in the fermentation vessels amended with A. taxiformis decreased significantly compared to control vessels, but this reduction in methanogen abundance was only significant when averaged over the course of the experiment. Alternatively, significant reductions of methane in the A. taxiformis amended vessels was measured in the early stages of the experiment. This suggests that A. taxiformis has an immediate effect on the metabolic functionality of rumen methanogens whereas its impact on microbiome assemblage, specifically methanogen abundance, is delayed.\n\nConclusionsThe methane reducing effect of A. taxiformis during rumen fermentation makes this macroalgae a promising candidate as a biotic methane mitigation strategy in the largest milk producing state in the US. But its effect in-vivo (i.e. in dairy cattle) remains to be investigated in animal trials. Furthermore, to obtain a holistic understanding of the biochemistry responsible for the significant reduction of methane, gene expression profiles of the rumen microbiome and the host animal are warranted.

systems biology↗