Clarisse Ganiera,1 , Pavel Mazinb , Gabriel Herrera-Oropezac , Xinyi Du-Harpura,d, Matthew Blakeleya , Jeyrroy Gabriela , Alexander V. Predeusb ,

Batuhan Cakirb , Martin Preteb , Nasrat Haruna , Jean-Francois Darrigranda , Alexander Haisera , Saranya Wylese , Tanya Shawf , Sarah A. Teichmannb,g,

Muzlifah Haniffab,h,i, Fiona M. Watta,j,1,2 , and Magnus D. Lyncha,k,1,2

Contributed by Fiona M. Watt; received August 6, 2023; accepted November 13, 2023; reviewed by Vladimir Botchkarev and Valerie Horsley

Our understanding of how human skin cells differ according to anatomical site and tumour formation is limited. To address this, we have created a multiscale spatial atlas of healthy skin and basal cell carcinoma (BCC), incorporating in vivo optical coherence tomography, single-cell RNA sequencing, spatial global transcriptional profiling, and in situ sequencing. Computational spatial deconvolution and projection revealed the localisation of distinct cell populations to specific tissue contexts. Although cell populations were conserved between healthy anatomical sites and in BCC, mesenchymal cell populations including fibroblasts and pericytes retained signatures of developmental origin. Spatial profiling and in silico lineage tracing support a hair follicle origin for BCC and demonstrate that cancer-associated fibroblasts are an expansion of a POSTN+ subpopulation associated with hair follicles in healthy skin. RGS5+ pericytes are also expanded in BCC suggesting a role in vascular remodelling. We propose that the identity of mesenchymal cell populations is regulated by signals emanating from adjacent structures and that these signals are repurposed to promote the expansion of skin cancer stroma. The resource we have created is publicly available in an interactive format for the research community.

human cell atlas | skin | basal cell carcinoma | single cell RNA sequencing | fibroblasts

Significance

Single-cell RNA sequencing (scRNAseq) has revolutionised cell biology, enabling highresolution analysis of cell types and states within human tissues. Here, we report a comprehensive spatial atlas of adult human skin across different anatomical sites and basal cell carcinoma (BCC)— the most common form of skin cancer—encompassing in vivo optical coherence tomography, scRNAseq, global spatial transcriptomic profiling, and in situ sequencing. In combination, these modalities have allowed us to assemble a comprehensive nuclearresolution atlas of cellular identity in health and disease.

Author contributions: C.G., F.M.W., and M.D.L. designed research; C.G., X.D.-H., M.B., J.G., and N.H. performed research; C.G., G.H.-O., X.D.-H., A.V.P., B.C., M.P., J.-F.D., A.H., T.S., S.A.T., and M.H. contributed new reagents/ analytic tools; C.G., P.M., G.H.-O., A.V.P., B.C., M.P., A.H., S.W., and M.D.L. analyzed data; and C.G., F.M.W., and M.D.L. wrote the paper.

Reviewers: V.B., Boston University School of Medicine; and V.H., Yale University.

Competing interest statement: In the last 3 y, S.A.T. has been a remunerated Scientific Advisory Board member for GlaxoSmithKline, Qiagen, Foresite Labs, and is a cofounder and equity holder of TransitionBio. F.M.W. and M.D.L. are co-founders of Fibrodyne. F.M.W. and M.D.L. have filed two patents related to skin fibroblasts. Copyright © 2024 the Author(s). Published by PNAS.

This open access article is distributed under Creative Commons Attribution License 4.0 (CC BY).

1 To whom correspondence may be addressed. Email: 该Email地址已收到反垃圾邮件插件保护。要显示它您需要在浏览器中启用JavaScript。, 该Email地址已收到反垃圾邮件插件保护。要显示它您需要在浏览器中启用JavaScript。, or magnus. 该Email地址已收到反垃圾邮件插件保护。要显示它您需要在浏览器中启用JavaScript。.

2 F.M.W. and M.D.L. contributed equally to this work. This article contains supporting information online at https://www.pnas.org/lookup/suppl/doi:10.1073/pnas. 2313326120/-/DCSupplemental.

Published January 2, 2024.