Extended Data Fig. 2: Genome-wide CRISPR–Cas9 screen identifies regulators of MHC-I expression.
From: Targeting Menin disrupts the KMT2A/B and polycomb balance to paradoxically activate bivalent genes
a, Cell surface MHC-I, pan-HLA-A,B,C (top)- and HLA-B (bottom)-specific antibodies in K-562 Cas9 cells treated with the indicated IFN-γ doses for 24 h. b, K-562 cells stably expressing Cas9 were mutagenized by infection with a pooled lentiviral sgRNA library and treated with 1 ng ml−1 IFN-γ for 24 h prior to FACS sorting. Rare MHC-I high cells were enriched by two successive rounds of FACS sorting for mCherry+ (containing sgRNA vector) MHC-I+ cells. FACS dot plots and histograms show MHC-I expression in unsorted, post sort 1 and post sort 2 in K-562 Cas9 cells transduced with the CRIPSR sgRNA library and sorted with either pan-HLA-A,B,C (top)- or HLA-B (bottom)-specific antibodies. c, Table depicting correlation between CRISPR gene-effect scores (Fig. 1e) for top-20 shared EZH2 and EED co-dependent genes calculated from combined CRISPR survival screens in 990 cancer cell lines in Cancer Dependency Map (https://depmap.org/portal/)31,32. Table indicates Pearson’s correlation coefficients. d,e, Immunoblots of K-562 Cas9 cells transduced with control and MTF2 (d) or AEBP2 (e) sgRNA. f, H3K4me3 and H3K27me3 CUT&Tag. Genomic snapshots of bivalent MHC-I genes in K-562 cells transduced with control, MTF2 and AEBP2 sgRNA. The H3K4me3 control tracks are the same control tracks in Fig. 7c. g, Cell surface MHC-I in K-562 Cas9 cells transduced with control or BAHD1-specific sgRNAs and treated with 10 ng ml−1 IFN-γ for 48 h. Representative plots from three experiments (Supplementary Fig. 3). h, Knockout scores of individual sgRNA targeting BAHD1 measured using Synthego Performance Analysis, Interference of CRISPR editing (ICE) Analysis.
