A5000570545- Single-cell and spatial transcriptomics
- Ion Transport and Channel Regulation
- Congenital heart defects research
- Cell Image Analysis Techniques
- Heart Failure Treatment and Management
- RNA modifications and cancer
- Cancer-related molecular mechanisms research
- Genomics and Chromatin Dynamics
- Cardiac electrophysiology and arrhythmias
- RNA Research and Splicing
- Gene expression and cancer classification
- Pluripotent Stem Cells Research
- Congenital Heart Disease Studies
- Renal and related cancers
- CRISPR and Genetic Engineering
- Genetics and Neurodevelopmental Disorders
- Cardiac Fibrosis and Remodeling
- Cardiovascular Function and Risk Factors
- CAR-T cell therapy research
- Ion channel regulation and function
- Cardiomyopathy and Myosin Studies
- Telomeres, Telomerase, and Senescence
- Advanced Biosensing Techniques and Applications
- Cardiac Structural Anomalies and Repair
- Cancer Genomics and Diagnostics
The University of Queensland
2019-2025
Background: Ischemia–reperfusion injury (IRI) is one of the major risk factors implicated in morbidity and mortality associated with cardiovascular disease. During cardiac ischemia, buildup acidic metabolites results decreased intracellular extracellular pH, which can reach as low 6.0 to 6.5. The resulting tissue acidosis exacerbates ischemic significantly affects function. Methods: We used genetic pharmacologic methods investigate role acid-sensing ion channel 1a (ASIC1a) IRI at cellular...
Abstract Pluripotent stem cells provide a scalable approach to analyse molecular regulation of cell differentiation across developmental lineages. Here, we engineer barcoded induced pluripotent generate an atlas multilineage from pluripotency, encompassing eight-day time course with modulation WNT, BMP, and VEGF signalling pathways. Annotation in vitro types reference vivo development reveals diverse mesendoderm lineage including lateral plate paraxial mesoderm, neural crest, primitive gut....
Granular detail about the location and nature of liver cell interactions metabolic, inflammatory fibrogenic pathways driving progressive fibrosis in metabolic dysfunction-associated steatotic disease (MASLD) is needed to deliver novel therapeutic targets. Here we used spatial transcriptomic data from human MASLD biopsies identify major types their potential interconnected activities within specific tissue regions across spectrum MASLD. Gene expression were generated using 10X Genomics Visium...
Abstract Aims The major cardiac cell types composing the adult heart arise from common multipotent precursor cells. Cardiac lineage decisions are guided by extrinsic and cell-autonomous factors, including recently discovered long noncoding RNAs (lncRNAs). human lncRNA CARMEN, which is known to dictate specification toward cardiomyocyte (CM) smooth muscle (SMC) fates, generates a diversity of alternatively spliced isoforms. Methods results CARMEN locus can be manipulated direct primary cells...
Methods for cell clustering and gene expression from single-cell RNA sequencing (scRNA-seq) data are essential biological interpretation of processes. Here, we present TRIAGE-Cluster which uses genome-wide epigenetic diverse bio-samples to identify genes demarcating diversity in scRNA-seq data. By integrating patterns repressive chromatin deposited across types with weighted density estimation, determines type clusters a 2D UMAP space. We then TRIAGE-ParseR, machine learning method evaluates...
SUMMARY Determining genes orchestrating cell differentiation in development and disease remains a fundamental goal of biology. This study establishes genome-wide metric based on the gene-repressive tri-methylation histone 3 lysine 27 (H3K27me3) across hundreds diverse types to identify genetic regulators differentiation. We introduce computational method, TRIAGE, that uses discordance between tendency expression drivers identity. apply TRIAGE millions single-cell transcriptomes, omics...
SUMMARY Pluripotent stem cells provide a scalable approach to analyse molecular regulation of cell differentiation across multiple developmental lineage trajectories. In this study, we engineered barcoded iPSCs generate an atlas multilineage from pluripotency, encompassing time-course WNT-induced perturbed using modulators WNT, BMP, and VEGF signalling. Computational mapping in vitro types vivo lineages revealed diversity iPSC-derived comprising mesendoderm including lateral plate paraxial...
Regulatory genes are critical determinants of cellular responses in development and disease, but standard RNA sequencing (RNA-seq) analysis workflows, such as differential expression analysis, have significant limitations revealing the regulatory basis cell identity function. To address this challenge, we present TRIAGE R package, a toolkit specifically designed to analyze elements both bulk single-cell RNA-seq datasets. The package is built upon methods, which leverage consortium-level...
Abstract The proton-gated acid-sensing ion channel 1a (ASIC1a) is implicated in the injury response to cerebral ischemia but little known about its role cardiac ischemia. We provide genetic evidence that ASIC1a involved myocardial ischemia-reperfusion (IRI) and show pharmacological inhibition of yields robust cardioprotection rodent human models ischemia, resulting improved post-IRI viability function. Consistent with a key for we polymorphisms ASIC1 locus are strongly associated infarction....
SUMMARY This study establishes the homeodomain only protein, HOPX, as a determinant controlling molecular switch between cardiomyocyte progenitor and maturation gene programs. Time-course single-cell expression with genome-wide footprinting reveal that HOPX interacts controls core cardiac networks by regulating activity of mutually exclusive developmental Upstream hypertrophy proliferation pathways compete to regulate transcription. Mitogenic signals override hypertrophic growth suppress...
Abstract Methods for cell clustering and gene expression from single-cell RNA sequencing (scRNA-seq) data are essential biological interpretation of processes. Here we present TRIAGE-Cluster which uses genome-wide epigenetic diverse bio-samples to identify genes demarcating diversity in scRNA-seq data. integrates patterns repressive chromatin deposited across types with weighted density estimation determine type clusters a 2D UMAP space. We then TRIAGE-ParseR, machine learning method that...
The major cardiac cell types composing the adult heart arise from common multipotent precursor cells. Cardiac lineage decisions are guided by extrinsic and cell-autonomous factors, including recently discovered long noncoding RNAs (lncRNAs). CARMEN locus, which is known to dictate specification towards cardiomyocyte (CM) smooth muscle (SMC) fates, generates a diversity of alternatively spliced lncRNAs. Here, we identify one these isoforms, CARMEN-201, be crucial for SMC commitment....