Project description:Several methods for generating human-skin-equivalent (HSE) organoid cultures are in use to study skin biology; however, few studies thoroughly characterize these systems. To fill this gap, we use single-cell transcriptomics to compare in vitro HSEs, xenograft HSEs, and in vivo epidermis. By combining differential gene expression, pseudotime analyses, and spatial localization, we reconstruct HSE keratinocyte differentiation trajectories that recapitulate known in vivo epidermal differentiation pathways and show that HSEs contain major in vivo cellular states. However, HSEs also develop unique keratinocyte states, an expanded basal stem cell program, and disrupted terminal differentiation. Cell-cell communication modeling shows aberrant epithelial-to-mesenchymal transition (EMT)-associated signaling pathways that alter upon epidermal growth factor (EGF) supplementation. Last, xenograft HSEs at early time points post transplantation significantly rescue many in vitro deficits while undergoing a hypoxic response that drives an alternative differentiation lineage. This study highlights the strengths and limitations of organoid cultures and identifies areas for potential innovation.
Project description:In this study, we defined a differentiation approach for guiding human pluripotent stem cells in to complex hair-bearing skin tissue, known as skin organoids. The primary goal of this single-cell RNA-sequencing analysis was to define the cellular composition of skin organoids before, during, and after the process of hair folliculogenesis. The secondary goal was to determine whether skin organoids generated using different cell lines (WA25 hESCs and DSP-GFP hiPSCs) contain similar cell types and accurately reflect features of developing fetal skin tissue.
Project description:We report the first use of genome-edited human kidney organoids, combined with single-cell transcriptomics, to study APOL1 risk variants at the native genomic locus in different nephron cell types. This approach captures interferon-mediated induction of APOL1 gene expression and cellular dedifferentiation with a secondary insult“second hit” of endoplasmic reticulum stress.
Project description:Use of single-cell transcriptomics to test early HD selective vulnerability by comparing CTRL and HD telencephalic organoids at day 45 and 120 of differentiation. To test the influence and the interactions between healthy and HD cells, chimeric organoids composed of CTRL and HD cells juxtaposed within the same organoid were grown and analyzed by scRNAseq at day 120.
Project description:Single cell RNA-seq was performed on healthy mouse skin fibroblasts. This data along with single cell transcriptomics datasets of fibroblasts from other healthy tissues was used to construct a steady state mouse fibroblast atlas.
Project description:Spatial organization of different cell types within prenatal skin across various anatomical sites is not well understood. To address this, here we have generated spatial transcriptomics data from prenatal facial and abdominal skin obtained from a donor at 10 post conception weeks. This in combination with our prenatal skin scRNA-seq dataset has helped us map the location of various identified cell types.
Project description:The formation of tissue patterns is critical for organ functions in development and regeneration. To advance the use of organoids for organ regeneration, we learn principles that govern the skin organoids to regenerate hairs. We show the formation of epidermal-dermal coupled cysts function as competent morphogenetic units (CMU) which harbor the ability of skin organoids to regenerate. ScRNA-sequencing shows the emergence of cell types and new cell interactions during CMU formation. In newborn skin organoids, epidermal cells undergo apical-basal polarization via the IFNr-PKR-PKC signaling module. Dermal-Tgfb regulates Gsk3 to establish basement membranes between the epidermal cyst and dermal cells. Meanwhile, VEGF signaling mediates dermal cell attachment to the cyst. Adult cells cannot form organoids but can be induced to generate CMUs and regenerate hairs by adding IFNr or VEGF. We compare the similar principles and different paths used to establish morphogenetic competency in developing skin, wound-induced hair neogenesis, and organoids.