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. Author manuscript; available in PMC: 2024 Sep 1.
Published in final edited form as: Nat Cell Biol. 2023 Aug 17;25(9):1346–1358. doi: 10.1038/s41556-023-01210-z

Fig. 6. NEUROD1 Induction after KDM6A Inactivation is Partially Mediated by KMT2A.

Fig. 6.

(a) Venn diagram of factors binding NEUROD1 (orange), upregulated expression in Kdm6a-Mutant tumors (red), and candidate regulators of accessible peaks at promoters in Kdm6a-Mutant tumors (blue). (b,c) Kmt2a feature plot (b) and violin plot (c) using scRNA-seq data from Fig. 3i of tumor cells from Kdm6a-Mutant and Kdm6a-WT tumors. For c, non-parametric Wilcoxon rank sum test was used to generate a two-tailed p-value adjusted for multiple comparisons by Bonferroni correction. Minimum and maximum values define the range of violin plot. n=35,446 Kdm6a-Mutant and n=6612 Kdm6a-WT tumor cells. (d-f) Immunoblot analysis of 236L (d) and 656 (e) Kdm6a-Mutant tumor derived cells lines or 1014 Kdm6a isogenic cells from Fig. 1f (f) treated with inhibitors that block the function of epigenetic modifiers that normally maintain gene expression including VTP50469 (Menin/MLL1 inhibitor, 500 nM), EPZ-5676 (DOT1L inhibitor, 1 μM), PF-9363 (KAT6A/KAT6B inhibitor, 100 nM), JQAD1 (EP300 degrader, 500 nM) or DMSO for 6 days. (g) Pie charts of Menin ChIP-seq data showing peak distributions throughout the genome of 1014 cells with Kdm6a CRISPR inactivation treated with VTP50469 (500 nM) or DMSO for 5 days. (h, i) Genome wide rank-ordered heat map of Menin ChIP signal at all peaks (h) or across promoters (TSS −3kB/+3kB) (i). A second replicate of the Menin-ChIP experiment in shown in Supplementary Fig. 5. (j-l) Menin ChIP-seq tracks at Neurod1 (j) and two canonical Menin target genes Bahcc1 (k) and Cdkn2c (l). (m) Schematic of the role of KDM6A in SCLC subtype plasticity. When KDM6A is present, KDM6A binds enhancers to increase H3K4 mono-methylation (H3K4me1) and decrease H3K27 tri-methylation (H3K27me3) maintaining a chromatin state most permissive for the ASCL1 subtype. When KDM6A is inactivated, ASCL1 subtype genes lose H3K4me1 and gain H3K27me3 at enhancers and chromatin becomes less permissive for the ASCL1 subtype. Upon KDM6A inactivation, KMT2A (MLL1) expression is upregulated and KMT2A/Menin binds the NEUROD1 promoter to promote NEUROD1 expression resulting in SCLC tumors with heterogenous ASCL1 and NEUROD1 expression. This figure was created with BioRender.com and publication license has been obtained.