Fig. 3: Loss of REST prevents the repression of its neuroendocrine targets in SCLC cells.

a–c Representative images of lung sections from TKO and TKO;Rest^fl/fl mice 5 months after Ad-CMV-Cre (TKO;Rest, quadruple mutant), stained with hematoxylin and eosin (H&E). Scale bar, 5 mm. Quantification of tumor numbers (b) and tumor area (c) (n = 9 mice for TKO and 10 mice for TKO;Rest^fl/fl). Error bar, mean ± s.d. d and e Schematic representation (d) and representative brightfield images (e) of neuroendocrine (NE) and non-NE cells sorted from TKO and TKO;Rest mutant tumors based on NCAM1 and ICAM1 expression. Scale bar, 200 μm. f Principal component analysis (PCA) of RNA-seq data comparing non-NE cell lines generated from TKO and TKO;Rest mutant tumors (n = 6 per genotype). WT wild-type for Rest; “Rest”, knockout for Rest. g Volcano plot of differentially expressed genes from RNA-seq data of TKO and TKO;Rest mutant non-NE cell lines. Rest and the classical neuroendocrine markers Syp/Chgb are highlighted (significant genes with more than 2-fold change and p-adj value < 0.05 are in red). Wald test with Benjamini–Hochberg correction. h Gene Ontology (GO) analysis of the upregulated genes in the TKO;Rest mutant non-NE cell lines. i Venn diagram showing the amount of overlap between derepressed genes of TKO;Rest mutant non-NE cell lines with REST and ASCL1 targets identified in Fig. 2. Bar graph showing top 5 candidate transcription factors from Enrichr analysis (ENCODE and ChEA Consensus TFs from ChIP-X) on the 141 derepressed genes that did not overlap with our REST targets. See also Supplementary Figs. 5 and 6 and Supplementary Data 10 and 11. Source data are provided as a Source Data file.