Biology subjects

Davaapil, H.

Publications and source records attributed to Davaapil, H..

5 recordsLinked to original sources

bioRxiv2024

Multiomic analysis reveals developmental dynamics of the human heart in health and disease

Developmental dynamics involve the specification of diverse cell types and their spatial organization into multicellular niches. Here, we combine single-cell and spatial multiomics to define 19 distinct tissue niches in the developing heart, leading to the development of a context-aware, resolution-agnostic niche classification tool (TissueTypist). Applying high-resolution spatial profiling to the developing sinoatrial node, we resolve three pacemaker cell subtypes arrayed along a linear axis. First trimester subpopulations, such as the pacemaker cells in the sinus horn and sinoatrial node head region, display neuro-attractant programmes and interact with parasympathetic neurons via interactions including Semaphorin-Plexin signalling. Temporal trajectories map maturation of atrial and ventricular cardiomyocytes, uncovering a lipid-metabolic switch and potential key regulators of cell type identity. In the ventricle, we identify cellular and transcriptional gradients along both pseudotime and transmural axes, offering new molecular insights into myocardial compaction and maturation. Comparative profiling of euploid and trisomy 21 hearts shows a depletion of compact cardiomyocytes and heightened apoptosis, validated in isogenic-matched trisomy 21 and euploid iPSC-derived cardiomyocytes. This implicates disrupted myocardial growth may be a mechanism for Downs syndrome-associated congenital heart disease. Overall, we deliver a spatially resolved framework of human cardiac development, enabling systematic exploration of developmental niches in health and disease.

developmental biology↗

bioRxiv2024

High-resolution atlas of the developing human heart and the great vessels

The human heart and adjoining great vessels consist of multiple cell types essential for life, yet many remain uncharacterised molecularly during development. Here, we performed a high-resolution profiling of the developing heart and great vessels between 4 and 20 post-conception weeks using single-cell and spatial transcriptomics defining 63 cell types with distinct identity and location-specific signatures. We reveal previously unreported molecular identities in cell types, including the pericardium and the ductus arteriosus. In the cardiomyocytes, we identify signatures of the trabeculated-compact, and right-left axes of ventricular cardiomyocytes. In vessels, we distinguish the constituents belonging to either coronary or great vessels. We confirm our transcriptional findings spatially, revealing nuanced signatures with specific zonation patterns and validating this atlas as a curated transcriptional reference for future studies. We leverage the temporal scope of the presented atlas to build CMageR, a predictive pipeline for scRNA-seq combining cardiac cell annotation with a transcriptional cardiac clock of single-cell developmental age for each cell type. Our cardiomyocyte clock captures dynamic biology, revealing core functional changes and novel markers of maturity during the first and second trimester. Finally, we benchmark in vitro models, suggesting a transcriptional right-chamber bias in stem cell derived cardiomyocytes with the oldest model age-matched to 12 post-conception weeks. Collectively, our work provides a high-resolution atlas of human cardiac development to enhance our understanding of function in development, health, and disease, and a foundation for building a rich reference to benchmark and improve in vitro models.

developmental biology↗

bioRxiv2023

Differentiation and quality control of smooth muscle cells from human pluripotent stem cells via the neural crest lineage

The Sinha laboratory has developed protocols for differentiating human pluripotent stem cells (hPSCs) into vascular smooth muscle cells along developmental lineage-specific pathways. In development, paraxial mesoderm (PM), lateral plate mesoderm (LM) and neural crest (NC) linages each give rise to smooth muscle cells significant in a location-specific manner. Induced PSCs derived from patients enduring disease provide a platform from which disease-relevant cell models can be established in the laboratory. Here we describe a robust protocol for differentiating hPSCs into vascular smooth muscle cells via a neural crest lineage and the control steps required to ensure consistently high-quality differentiated cells.

cell biology↗

bioRxiv2022

A phenotypic screen of Marfan syndrome iPSC-derived vascular smooth muscle cells uncovers GSK3β as a new target

Marfan syndrome (MFS) is a rare connective tissue disorder caused by mutations in FBN1. Patients with MFS notably suffer from aortic aneurysm and dissection. Despite considerable effort, animal models have proven to be poorly predictive for therapeutic intervention in human aortic disease. Using a "humanised" model system may be more appropriate in identifying new therapeutic targets. Patient-derived induced pluripotent stem cells can be differentiated into vascular smooth muscle cells (VSMCs) and recapitulate major features of MFS. We have screened 1,022 small molecules in our in vitro model, exploiting the highly-proteolytic nature of MFS-VSMCs, and identified 36 effective compounds. Further analysis identified GSK3{beta} as a recurring target in the compound screen. GSK3{beta} inhibition/knockdown did not ameliorate the proliferation defect in MFS-VSMCs but improved MFS-VSMC apoptosis and proteolysis. To conclude, we have identified GSK3{beta} as a novel target for MFS, forming the foundation for future work in MFS and other aortic diseases.

cell biology↗

bioRxiv2021

Regenerative and non-regenerative transcriptional states of the human epicardium: from foetus to adult and backagain

Epicardial activation appears to be required for cardiac regeneration. Although reverting quiescent adult epicardium to an active neonatal or foetal state will likely represent a key therapeutic approach for human cardiac regeneration, the exact molecular differences between human adult and foetal epicardium are not understood. We used single-cell RNA sequencing to compare epicardial cells from both foetal and adult hearts. We found two foetal epicardial cell types, mesothelial and fibroblast-like, with only the mesothelial population present in adults. We also identified foetal-specific epicardial genes associated with regeneration and angiogenesis, and found that adult epicardium may be primed for immune and inflammatory responses. We predict that restoring the foetal epicardial state in human hearts would increase adult angiogenic potential. Finally, we demonstrated that human embryonic stem-cell derived epicardium is a valid model for the foetal epicardium and for investigating epicardial-mediated cardiac regeneration in humans. Our study defines regenerative programs in human foetal epicardium that are absent in the adult, brings human context to animal studies, and provides a roadmap for directing the epicardium in human heart regeneration.

cell biology↗