Project description:Two distinct and anatomically restricted modes of ossification, which are endochondral ossification and intramembranous ossification, govern osteogenesis and joint formation throughout the human skeleton and, to our knowledge, the cellular bases by which they form and mature remain incompletely described in human development at single-cell resolution. To address this, we apply single-nuclei paired RNA and ATAC sequencing to decipher the molecular gene regulatory programmes that mediate maturation of the distinct bone and joint-forming niches in the cranium and appendicular skeleton across space and time from 5-11 PCW.
Project description:Using Multiome and previously published sc/snRNA-seq data, we studied eight anatomical regions of the human heart including left and right ventricular free walls (LV and RV), left and right atria (LA and RA), left ventricular apex (AX), interventricular septum (SP), sino-atrial node (SAN) and atrioventricular node (AVN). For the first time, we profile the cells of the human cardiac conduction system, revealing their distinctive repertoire of ion channels, G-protein coupled receptors and cell-cell interactions. We map the identified cells to spatial transcriptomic data to discover cellular niches within the eight regions of the heart.
Project description:To investigate the role of MYCN in neonatal heart development, we performed Single nucleus multiome (GEX and ATAC) on isolated nuclei from control and Mycn conditional knockout (CKO) P4 mouse ventricles. Clustering analysis assigned cardiomyocytes (CMs) into five previously defined neonatal states (CM1–CM5). CKO hearts showed a marked depletion of proliferative CM2 and CM4 populations and an increase in differentiated CM1 cells. G2/M phase CMs were significantly reduced in the CKO, particularly within CM4. RNA velocity analysis revealed disrupted transitions from immature CM states to mature ones in the CKO. Latent time and metabolic profiling further confirmed a shift toward a mature, non-regenerative phenotype, with upregulation of hypertrophic and fatty acid oxidation pathways and downregulation of glycolysis and cell cycle genes. These results highlight MYCN’s role in maintaining proliferative, regenerative CM states during neonatal heart development. Bulk RNA-seq was performed on P30 mouse ventriclar tissue 28 days after ischemic injury to compare Mycn conditional knockout (CKO) and control groups. The analysis revealed that cell cycle and muscle development pathways were downregulated, while inflammatory pathways were upregulated in the Mycn CKO hearts. These findings suggest that MYCN is essential for maintaining proliferative and regenerative gene programs following cardiac injury, and its deletion impairs regenerative potential at the transcriptomic level.
Project description:Human embryonic bone and joint formation is determined by coordinated differentiation of progenitors in the nascent skeleton. The cell states, epigenetic processes and key regulatory factors that underlie lineage commitment of these cells remain elusive. Here we applied paired transcriptional and epigenetic profiling of approximately 336,000 nucleus droplets and spatial transcriptomics to establish a multi-omic atlas of human embryonic joint and cranium development between 5 and 11 weeks after conception. Using combined modelling of transcriptional and epigenetic data, we characterized regionally distinct limb and cranial osteoprogenitor trajectories across the embryonic skeleton and further described regulatory networks that govern intramembranous and endochondral ossification. Spatial localization of cell clusters in our in situ sequencing data using a new tool, ISS-Patcher, revealed mechanisms of progenitor zonation during bone and joint formation. Through trajectory analysis, we predicted potential non-canonical cellular origins for human chondrocytes from Schwann cells. We also introduce SNP2Cell, a tool to link cell-type-specific regulatory networks to polygenic traits such as osteoarthritis. Using osteolineage trajectories characterized here, we simulated in silico perturbations of genes that cause monogenic craniosynostosis and implicate potential cell states and disease mechanisms. This work forms a detailed and dynamic regulatory atlas of bone and cartilage maturation and advances our fundamental understanding of cell-fate determination in human skeletal development.