Single-cell transcriptomics reveals spatial and temporal turnover of keratinocyte differentiation regulators

Abstract

Background: Keratinocyte differentiation requires intricately coordinated spatiotemporal expression changes that specify epidermis structure and function. Results: This paper utilizes single-cell RNA-seq data from 22,338 human foreskin keratinocytes to reconstruct the transcriptional regulation of skin development and homeostasis genes, organizing them by differentiation stage and also into transcription factor (TF)-associated modules. We identify groups of TFs characterized by coordinate expression changes during progression from the undifferentiated basal to the differentiated state and show that these TFs also have concordant differential predicted binding enrichment in the super-enhancers previously reported to turn over between the two states. The identified TFs form a core subset of the regulators controlling gene modules essential for basal and differentiated keratinocyte functions, supporting their nomination as master coordinators of keratinocyte differentiation. Experimental depletion of the TFs ZBED2 and ETV4, both predicted to promote the basal state, induces differentiation. Furthermore, our single-cell RNA expression analysis reveals preferential expression of antioxidant genes in the basal state, suggesting keratinocytes actively suppress reactive oxygen species to maintain the undifferentiated state. Finally, we perform in-silico lineage tracing demonstrating transcriptomic correspondence of basal cell carcinoma (BCC) to a basal keratinocyte subpopulation and squamous cell carcinoma (SCC) to a rapidly proliferating stage that is intermediate between the basal and differentiated cell states, implicating distinct candidate cells of origin for these cancers. Conclusion: Our work demonstrates diverse computational methods integrating single-cell and bulk RNA expression data to advance our understanding of dynamic gene regulation in normal development and in disease.

Stagewise keratinocyte differentiation from human embryonic stem cells by defined signal transduction modulators

“…Our results suggest that basal and suprabasal genes could be expressed in the same progenitor cells. It is supported by recent reports that basal and suprabasal genes can be co-expressed during specific stages of keratinocyte differentiation [44,45]. Fourth, we also revealed that calcium level is important for keratinocyte differentiation.…”

3D Oral and Cervical Tissue Models for Studying Papillomavirus Host‐Pathogen Interactions

“…the stratum level, expression patterns of many of the cellular genes are known, but the regulation of spatiotemporal gene expression is a topic of intense investigation (Cavazza et al, 2016;Finnegan et al, 2019;Joost et al, 2016;Klein et al, 2017;Lopez-Pajares et al, 2015;Rubin et al, 2019). Modeling the physiologically relevant tissues will be critical to further our understanding of the viral life cycle.…”

ZBED2 is an antagonist of interferon regulatory factor 1 and modifies cell identity in pancreatic cancer

“…A prior genomewideassociation study identified ZBED2 as a candidate locus influencing risk of smoking-induced pancreatic cancer (32). More recently, ZBED2 was found to be highly expressed in the basal layer of the epidermis, where it plays a role in regulating keratinocyte differentiation (33). Another study identified ZBED2 as a marker of T cell exhaustion in human CD8 T cells, although the function of ZBED2 was not investigated in this context (34).…”

“…Notably, we also observe high ZBED2 expression in normal squamous epithelial tissues, such as the skin, lung, and esophageal mucosa, suggesting a normal function for ZBED2 in the regulation of squamous epithelial cells. Interestingly, single-cell RNA-seq analysis recently identified ZBED2 as a key TF in the regulation of human keratinocyte differentiation (33). ZBED2 was predicted to promote the basal state and experimental depletion of ZBED2 was shown to induce keratinocyte differentiation, demonstrated by the up-regulation of KRT10 (33).…”

“…Interestingly, single-cell RNA-seq analysis recently identified ZBED2 as a key TF in the regulation of human keratinocyte differentiation (33). ZBED2 was predicted to promote the basal state and experimental depletion of ZBED2 was shown to induce keratinocyte differentiation, demonstrated by the up-regulation of KRT10 (33). It is noteworthy that IRF family members have also been ascribed functional roles in regulation of the skin epidermis.…”