Biology subjects

Hsu, I.

Publications and source records attributed to Hsu, I..

11 recordsLinked to original sources

bioRxiv2026

Longitudinal in vivo human wound healing model defines key role for smooth muscle cells in ECM remodeling

BackgroundEffective skin wound healing is essential for restoring tissue integrity following injury. Repair proceeds through phases of hemostasis, inflammation, proliferation, and remodeling, but molecular mechanisms governing these stages remain poorly defined. Vascular niche cells (VNCs)-including endothelial cells, vascular smooth muscle cells (SMCs), and fibroblasts-are central regulators of healing, but the lack of longitudinal in vivo human data has limited identification of VNC-derived signals that distinguish effective repair from pathological healing such as ulcers. Thus, defining the regulation of VNCs in wound healing addresses a critical knowledge gap. MethodsWe developed a protocol for wound healing using dermal forearm punch biopsies to track longitudinal repair in healthy volunteers. Single-cell and spatial transcriptomics were performed to identify and validate signaling activities within VNCs. ResultsWe spatiotemporally defined the inflammation, proliferation, and remodeling phases of human skin wound healing with a focus on VNCs. Spatial analysis localized this activity for VNCs and immune cells within a heterogenous granulation zone that later led to re-epithelializion. Angiogenesis was dominated by Vegf, Egf and Hif1 signaling. Extracellular matrix (ECM) remodeling occurred through Collagen, Laminin, Thrombospondin, and Fibronectin. SMCs emerged as dominant drivers of injury-induced remodeling including basement membrane and interstitial ECM components compared to fibroblasts. This SMC-led program was further defined by robust induction of TIMP1, an inhibitor of matrix degradation, which localized to granulation tissue and correlated with re-epithelialization and wound resolution. Lastly, we compared remodeling factors between healing and non-healing human diabetic foot ulcers (DFUs). SMCs in non-healing DFUs had deficient expression for core remodeling factors, including TIMP1, indicating SMC activity is needed for effective healing. ConclusionWe identified an SMC-driven model of wound repair in which TIMP1-dependent activity underpins granulation zone formation. Failure of this program defined a mechanistic basis for impaired healing in ulcers, identifying SMCs and TIMP1 as therapeutic targets.

molecular biology↗

bioRxiv2025

High-resolution transcriptomic profiling of the aortic cellular landscape during hypertension reveals novel drivers of vascular fibrosis

BackgroundAortic stiffening is a consequence of hypertension and a major contributor to end organ damage. A key driver of aortic stiffening is fibrosis involving the excess production of extracellular matrix (ECM) proteins such as collagen, fibronectin and laminin. The present study aimed to identify the cell types and signalling mechanisms that contribute to aortic fibrosis in hypertension. Methods and ResultsMale C57BL/6 mice (10-12-week-old) were randomly assigned to a 28-day angiotensin II (0.7 mg/kg/day) or vehicle (saline) infusion via osmotic minipump (s.c.). At endpoint, scRNA-seq analysis of 26,196 cells recovered all major aortic cell populations. Among these, fibroblasts exhibited the greatest heterogeneity and shift in gene expression after angiotensin II compared to all other cell types. Gene ontology analyses revealed that after angiotensin II treatment, a particular subcluster of fibroblasts (Fibro-Cthrc1) - characterised by its high expression of Cthrc1 - was especially fibrogenic. Fibro-Cthrc1 cells were nearly undetectable in aortas from vehicle-infused mice. Transcripts relating to ECM remodelling (Thbs2, Cdh11 and Postn) and collagen production (specifically collagen type I, III and V) were more highly enriched in Fibro-Cthrc1 compared to other fibroblasts within hypertensive aortas. Moreover, GO terms corresponding to profibrotic signalling pathways (i.e., cell adhesion, extracellular matrix organisation and collagen fibril organisation) were significantly enriched in Fibro-Cthrc1. Spatial transcriptomics and immunohistochemistry confirmed the presence of Fibro-Cthrc1 in the adventitial layer of angiotensin II-infused but not vehicle-infused mice. Finally, analysis of plasma analytes in approximately 24,000 participants of the UK Biobank collection revealed CTHRC1 to be strongly associated with raised systolic blood pressure and pulse pressure, and a strong predictor of the risk of developing hypertension over a 15-year follow-up. ConclusionOur study identifies a novel fibroblast subcluster, Fibro-Cthrc1, as a potential driver of aortic fibrosis and stiffening in hypertension. This cluster is absent in normotensive aortas, suggesting that targeting Fibro-Cthrc1 therapeutically could prevent aortic fibrosis and its associated hypertensive end-organ damage. Notably, such an approach may avoid compromising physiological extracellular matrix production and vessel integrity. Translational perspectiveAortic stiffening is a hallmark of hypertension resulting from functional (vasoconstriction) and structural (extracellular matrix remodelling) alterations of the vessel wall. While several antihypertensive medications address functional changes, no therapies directly target the causes of the structural remodelling. The therapeutic challenge is to distinguish between physiological and pathological extracellular matrix remodelling. This study identifies a novel highly profibrotic fibroblast cell population (Fibro-Cthrc1) present in aortas from hypertensive, but not normotensive mice. This raises the possibility that Fibro-Cthrc1 may be a key driver of aortic stiffening and a promising future therapeutic target.

physiology↗

bioRxiv2024

Reducing oxidative stress improves ex vivo polymer-based human haematopoietic stem and progenitor cell culture and gene editing

Self-renewing multipotent haematopoietic stem cells (HSCs) have the unique capacity to stably regenerate the entire blood and immune systems following transplantation. HSCs are used clinically to reconstitute a healthy blood system in patients suffering from a range of haematological diseases. However, HSCs are very rare and have been challenging to grow ex vivo, which has hampered efforts to collect large numbers of HSCs for both basic research and clinical therapies. Polymer-based culture conditions have recently been developed to support expansion of mouse and human haematopoietic stem and progenitor cells (HSPCs). While mouse HSPCs expanded rapidly in polymer-based cultures, growth speeds for human HSPCs in polymer-based cultures was limited to [~]70-fold over 4-weeks. Here we have found that reducing oxidative stress improves human HSPC growth in these conditions. We describe an optimised culture condition that improves growth to 250-1400-fold over 4-weeks through reducing oxygen tension and the addition of antioxidants. These conditions also enable efficient gene editing in these polymer-based cultures. We envision these improved culture conditions will support a range of research into human HSPC biology and provide a platform for clinical-scale HSPC expansion and gene editing.

cell biology↗

bioRxiv2024

Single-nucleus RNA sequencing reveals cellular and molecular dynamics of white and brown adipose tissue in a mouse model of type-2 diabetes

Excessive adipose tissue expansion is often linked with type-2 diabetes. Despite recent efforts mapping adipose tissue changes in obesity using single-cell omics, an understanding of cellular and gene expression changes in a model of type 2 diabetes, and the transcriptional circuitry controlling it, is still lacking. Here, we use single-nucleus RNA sequencing to analyze the remodeling of gonadal white and interscapular brown adipose tissue from female and male mice with or without diabetes. Analysis of 51,877 nuclei revealed altered phenotypes in every cell population in type 2 diabetes. This included an immunoregulatory response, and changes in extracellular matrix, energy generation, and hormone responses. Key transcription factors were inferred as cell-specific and non-specific nodes controlling diabetes-linked phenotypes. Finally, female-to-male population heterogeneity and gene expression differences were observed. Here we provide a resource detailing how adipose tissue remodeling, and the molecular mechanisms governing it, may contribute to cardiometabolic disease.

cell biology↗

bioRxiv2023

Engineering heterothallic strains in fission yeast

In poor nitrogen conditions, fission yeast cells mate, undergo meiosis and form spores that are resistant to deleterious environments. Natural isolates of Schizosaccharomyces pombe are homothallic. This allows them to naturally switch between the two h- and h+ mating types with a high frequency, thereby ensuring the presence of both mating partners in a population of cells. However, alteration of the mating type locus can abolish mating type switching or reduce it to a very low frequency. Such heterothallic strains have been isolated and are common in research laboratories due to the simplicity of their use for Mendelian genetics. In addition to the standard laboratory strains, a large collection of natural S. pombe isolates is now available, representing a powerful resource for investigating the genetic diversity and biology of fission yeast. However, most of these strains are homothallic, and only tedious or mutagenic strategies have been described to obtain heterothallic cells from a homothallic parent. Here, we describe a simple approach to generate heterothallic strains. It takes advantage of an alteration of the mating type locus that was previously identified in a mating type switching-deficient strain and the CRISPR-Cas9 editing tool, allowing for a one-step engineering of heterothallic cells with high efficiency. Take away points- Conventional methods for obtaining heterothallic fission yeast strains are inefficient - We implemented a streamlined genetic editing approach to engineer heterothallism - All fission yeast isolates reported in Jeffares et al. 2015 can be engineered - This method enhances the exploration of genetic diversity in wild fission yeast

genetics↗

bioRxiv2022

Large-scale in vivo CRISPR screens identify SAGA complex members as a key regulators of HSC lineage commitment and aging

The biological mechanisms that sustain the vast blood production required for healthy life remain incompletely understood. To search for novel regulators of hematopoiesis, we performed genome-wide in vivo hematopoietic stem cell (HSC)-based CRISPR knockout screens for regulators of hematopoiesis. We discovered SAGA complex members, including Tada2b and Taf5l, as key regulators of hematopoiesis. Loss of Tada2b or Taf5l strongly inhibited hematopoiesis in vivo, led to a buildup of immature hematopoietic cells in the bone marrow, and was associated with upregulation of interferon pathway genes. Loss of these factors also enhanced the cell outgrowth and the interferon pathway in an in vivo human myelodysplastic syndrome model, suggesting that loss of SAGA complex activity could contribute to hematological disease progression. In summary, this study has identified the SAGA complex as an important regulator of hematopoiesis.

genetics↗

bioRxiv2022

Multi-omic analysis of the cardiac cellulome defines a vascular contribution to cardiac diastolic dysfunction in obese female mice

Coronary microvascular dysfunction (CMD) is associated with cardiac dysfunction and predictive of cardiac mortality in obesity, especially in females. Emerging evidence suggests development of heart failure with preserved ejection fraction in females with CMD and that mineralocorticoid receptor (MR) antagonism may be more efficacious in obese female, versus male, HFpEF patients. Accordingly, we examined the hypothesis that smooth muscle cell (SMC)-specific MR deletion prevents obesity-associated coronary and cardiac diastolic dysfunction in females. Obesity was induced in female mice via western diet (WD) feeding alongside littermates fed standard diet. Initial studies revealed that global MR blockade with spironolactone prevented impaired coronary vasodilation and diastolic dysfunction in obese females. Importantly, specific deletion of SMC-MR similarly prevented obesity-associated coronary and cardiac dysfunction. Cardiac gene expression profiling suggested reduced cardiac inflammation in WD-fed mice with SMC-MR deletion independent of blood pressure, aortic stiffening, and cardiac hypertrophy. Further mechanistic studies utilizing single-cell RNA sequencing of non-cardiomyocyte cell populations revealed novel impacts of SMC-MR deletion on the cardiac cellulome in obese mice. Specifically, WD feeding induced inflammatory gene signatures in multiple non-myocyte populations (B/T cells, macrophages, and endothelium), independent of cardiac fibrosis, that was prevented by SMC-MR deletion. Further, SMC-MR deletion induced a basal reduction in cardiac mast cells and prevented WD-induced cardiac pro-inflammatory chemokine expression and leukocyte recruitment. These data reveal a central role for SMC-MR signaling in obesity-associated coronary and cardiac dysfunction thus supporting the emerging paradigm of a vascular origin of cardiac dysfunction in obesity.

physiology↗

bioRxiv2022

Circuit-seq: Circular reconstruction of cut in vitro transposed plasmids using Nanopore sequencing

Recombinant DNA is a fundamental tool in biotechnology and medicine. Validation of the resulting plasmid sequence is a critical and time-consuming step, which has been dominated for the last 35 years by Sanger sequencing. As plasmid sequences grow more complex with new DNA synthesis and cloning techniques, we need new approaches that address the corresponding validation challenges at scale. Here we prototype a high-throughput plasmid sequencing approach using DNA transposition and Oxford Nanopore sequencing. Our method, Circuit-seq, creates robust, full-length, and accurate plasmid assemblies without prior knowledge of the underlying sequence for approximately $1.50 per plasmid. We demonstrate the power of Circuit-seq across a wide range of plasmid sizes and complexities, generating accurate and contiguous plasmid maps. We then leverage our long read-data to characterize epigenetic marks and estimate plasmid contamination levels. Circuit-seq scales to large numbers of samples at a lower cost than commercial Sanger sequencing, accelerating a key step in synthetic biology, with low startup costs make it practical for individual laboratories.

molecular biology↗

bioRxiv2021

CLARA: A web portal for interactive exploration of the cardiovascular cellular landscape in health and disease

Mammalian cardiovascular tissues are comprised of complex and diverse collections of cells. Recent advances in single-cell profiling technologies have accelerated our understanding of tissue cellularity and the molecular networks that orchestrate cardiovascular development, maintain homeostasis, and are disrupted in pathological states. Despite the rapid development and application of these technologies, many cardiac single-cell functional genomics datasets remain inaccessible for most cardiovascular biologists. Access to custom visual representations of the data, including querying changes in cellular phenotypes and interactions in diverse contexts, remains unavailable in publicly accessible data portals. Visualizing data is also challenging for scientists without expertise in processing single-cell genomic data. Here we present CLARA--CardiovascuLAR Atlas--a web portal facilitating exploration of the cardiovascular cellular landscape. Using mouse and human single-cell transcriptomic datasets, CLARA enables scientists unfamiliar with single-cell-omic data analysis approaches to examine gene expression patterns and the cell population dynamics of cardiac cells in a range of contexts. The web-application also enables investigation of intercellular interactions that form the cardiac cellular niche. CLARA is designed for ease-of-use and we anticipate that the portal will aid deeper exploration of cardiovascular cellular landscapes in the context of development, homeostasis and disease. CLARA is freely available at https://clara.baker.edu.au.

cell biology↗

bioRxiv2020

Cas9-AAV6 Gene Correction of Beta-Globin in Autologous HSCs Improves Sickle Cell Disease Erythropoiesis in Mice

CRISPR/Cas9-mediated beta-globin (HBB) gene correction of Sickle Cell Disease (SCD) patient-derived hematopoietic stem cells (HSCs) in combination with autologous transplantation represents a novel paradigm in gene therapy. Although several Cas9-based HBB-correction approaches have been proposed, functional correction of in vivo erythropoiesis has not been investigated. Here, we used a humanized globin-cluster SCD mouse model to study Cas9-AAV6-mediated HBB-correction in functional HSCs within the context of autologous transplantation. We discover that long-term multipotent HSCs can be gene corrected ex vivo and stable hemoglobin-A production can be achieved in vivo from HBB-corrected HSCs following autologous transplantation. We observed a direct correlation between increased HBB-corrected myeloid chimerism and normalized in vivo RBC features, but even low levels of chimerism resulted in robust hemoglobin-A levels. Moreover, this study offers a platform for gene editing of mouse HSCs for both basic and translational research.

developmental biology↗

bioRxiv2017

Predicting Transcriptional Regulatory Activities with Deep Convolutional Networks

Massively parallel reporter assays (MPRAs) are a method to probe the effects of short sequences on transcriptional regulation activity. In a MPRA, short sequences are extracted from suspected regulatory regions, inserted into reporter plasmids, transfected into cell-types of interest, and the transcriptional activity of each reporter is assayed. Recently, Ernst et al. presented MPRA data covering 15750 putative regulatory regions. We trained a multitask convolutional neural network architecture using these sequence expression readouts which predicts as output the expression level outputs across four combinations of cell types and promoters. The model allows for the assigning of importance scores to each base through in silico mutagenesis, and the resulting importance scores correlated well with regions enriched for conservation and transcription factor binding.

genomics↗