Single-cell transcriptomics of human-skin-equivalent organoids

Adam R Stabell; Grace E Lee; Yunlong Jia; Kirsten N Wong; Shuxiong Wang; Ji Ling; Sandrine D Nguyen; George L Sen; Qing Nie; Scott X Atwood

doi:10.1016/j.celrep.2023.112511

Single-cell transcriptomics of human-skin-equivalent organoids

Cell Rep. 2023 May 30;42(5):112511. doi: 10.1016/j.celrep.2023.112511. Epub 2023 May 16.

Authors

Affiliations

¹ Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA; NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA 92697, USA.
² Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA.
³ Department of Mathematics, University of California, Irvine, Irvine, CA 92697, USA.
⁴ Department of Dermatology, University of California, San Diego, La Jolla, CA 92093, USA.
⁵ Department of Dermatology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA.
⁶ Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA; NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA 92697, USA; Department of Mathematics, University of California, Irvine, Irvine, CA 92697, USA; Center for Complex Biological Systems, Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92697, USA.
⁷ Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA; NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA 92697, USA; Center for Complex Biological Systems, Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92697, USA; Department of Dermatology, University of California, Irvine, Irvine, CA 92697, USA. Electronic address: satwood@uci.edu.

Abstract

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.

Keywords: CP: Stem cell research; differentiation; human epidermis; hypoxia; organoid; single-cell RNA sequencing.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Cell Differentiation
Epidermis / metabolism
Humans
Keratinocytes / metabolism
Organoids
Skin* / metabolism
Transcriptome* / genetics

Abstract

Publication types

MeSH terms

Grants and funding