Robust gene expression programs underlie recurrent cell states and phenotype switching in melanoma

Abstract

Melanoma cells can switch between a melanocytic and mesenchymal-like state. Scattered evidence indicates that additional, intermediate state(s) may exist. To search for such states and decipher their underlying gene regulatory network (GRN), we studied ten melanoma cultures by single-cell RNA-seq, and 26 additional cultures by bulk RNA-seq. Although each culture exhibited a unique transcriptome, we identified shared GRNs that underlie the extreme melanocytic and mesenchymal states, and the intermediate state. This intermediate state is corroborated by a distinct chromatin landscape and governed by the transcription factors SOX6, NFATC2, EGR3, ELF1 and ETV4. Single-cell migration assays confirmed its intermediate migratory phenotype. By time-series sampling of single cells after knockdown of SOX10, we unravelled the sequential and recurrent arrangement of GRNs during phenotype switching. Jointly, these analyses indicate that an intermediate state exists and is driven by a distinct and stable "mixed" GRN rather than being a symbiotic, heterogeneous mix of cells.

Spatially resolved transcriptomics reveals the architecture of the tumor/microenvironment interface

“…5a ). Although ETS-family transcription factors have not been widely studied in melanoma, they have been reported to function in melanoma invasion (Rothhammer et al, 2004) and phenotype switching (Wouters et al, 2020), and are aberrantly upregulated in many types of solid tumors (Sizemore et al, 2017). Interestingly, zebrafish ETS-family transcription factors were downregulated in the interface in both our scRNA-seq and ST datasets ( Fig.…”

“…Pearson’s correlation coefficient ( R ) is indicated. g-h. UMAP projection of human melanoma scRNA-seq data from Wouters et al (2020). Cell lines (g) and interface marker gene expression score (h) are indicated.…”

“…Finally, we investigated whether “interface” cells, distinguished by upregulation of cilia genes and downregulation of ETS transcription factors, are also found in human melanoma. We analyzed a recently published human melanoma scRNA-seq dataset, composed of 4,323 cells from nine patient-derived cultures (MM lines) and a well-characterized human melanoma cell line (A375) (Wouters et al, 2020) ( Fig. 5g ).…”

The CoREST Repressor Complex Mediates Phenotype Switching and Therapy Resistance in Melanoma

“…This process is quite malleable, as such plasticity lends itself to rapid reorganization under conditions of stress and serves as a cellular survival mechanism. Additionally, the rapid transitions afforded by epigenetic controls of gene expression serve as important mechanisms to evade therapeutic interventions 39 . Remarkably, we find that inhibition of CoREST activity in human melanoma specifically inhibits both distinctive proliferative and invasive cellular phenotypes and that such inhibition promotes resensitization of treatment-resistant melanoma cells to targeted BRAF inhibition.…”

A bridge between melanoma cell states

“…The same study also validated the existence of Hoek's cohorts A (C4) and B (C3), but it was not possible to determine from bulk RNA-sequencing analysis whether the intermediate phenotype of C3 was due to a mixed population of C4 and C1/2 cells or if it represented a distinct, stable cell state 5 . In this issue of Nature Cell Biology, Wouters et al set out to distinguish between these two potential models of the intermediate cell state and define the gene regulatory networks that maintain phenotypic diversity in melanoma 6 (Fig. 1).…”