Extended Data Fig. 1: NRF2 activation is prevalent across cancer cell lines and not exclusive to those with canonical activating mutations.
From: Excess cysteine drives conjugate formation and impairs proliferation of NRF2-activated cancer cells
(A) Scatterplot for the relationship between NRF2 dependence, defined by a negative Chronos Score for NFE2L2, and NRF2 activation, calculated based on the variance of mRNA expression of 9 canonical NRF2 target genes, across 973 cancer cell lines from the Cancer Dependency Map. NRF2on cells are depicted in the upper left quadrant formed by the dotted lines, which are those in the highest quintile for both NRF2 dependency and NRF2 activation. Outside of this group are referred to as NRF2off cells. (B) Average NRF2 activation score and NFE2L2 dependency depicted for NRF2off cell lines (n = 871) and NRF2on cell lines (n = 102, total), splitting NRF2on cells (n = 102, total) into those with (n = 46) or without (n = 56) an annotated, potentially NRF2-activating mutation in NFE2L2, KEAP1, or CUL3. (C) Histogram of cell lines ranked by NRF2 activation score (upper) or NRF2 dependency (NFE2L2 Chronos score) (lower), with the presence or absence of potential NRF2-activating mutations depicted by colour. (D) Relative abundance of three metabolites that have been reported to be enriched in cell lines with NRF2 activation (NADP+, glutathione disulfide (GSSG) and glutathione (GSH)), across cell lines that were assigned a NRF2on status (with or without potential NRF2-activating mutations) or NRF2off status, that have available metabolomics measurements. n = 626 (NADP+) or n = 617 (GSSG and GSH). NADP: NRF2on, mutation P < 0.0001, NRF2on, no mutation P = 0.0039. GSSG: NRF2on, mutation P < 0.0001, NRF2on, no mutation P = 0.0002. GSH: NRF2on, mutation P < 0.0001, NRF2on, no mutation P = 0.0047. (E) Average Chronos dependency score for three genes that have been reported to be coessential in NRF2-activated cell lines (SLC33A1, TAPT1, and SUCO), for each cell line group. n = 973 total cell lines, with n = 871 NRF2off cell lines, n = 46 NRF2on, mutation, and n = 56 NRF2on, no mutation. All comparisons P < 0.0001. (F) Fraction of cell lines for each annotated tissue lineage with NRF2on status, with the presence or absence of potential NRF2-activating mutations depicted by colour. Numbers in x-axis labels (n) refer to the total number of cell lines analysed from that lineage, with a minimum of seven cell lines from a lineage being required for graphing. (G) NRF2 activation scores and NFE2L2 Chronos scores for the eight bile duct cancer cell lines used in this study, with 5 assigned NRF2on status (KKU100, SNU308, SSP25, TFK1, OCUG1) and 3 assigned NRF2off status (YSCCC, CCLP1, RBE). For violin plots (B), solid black line is the median and broken grey lines are quartiles. For bar charts (D, E) error bars are S.E.M. Statistical significance was assessed using one-way ANOVA with Dunnett’s correction for multiple comparisons (D, E). ***P < 0.001, ****P < 0.0001.
