Extended Data Fig. 4: Mechanisms of NF2/Merlin tumor suppression in meningioma cells.
From: Meningioma DNA methylation groups identify biological drivers and therapeutic vulnerabilities
a, Meningioma NF2 copy-number deletions containing the entire locus and targeted sequencing of somatic short variants (SSV, n = 65) across DNA methylation groups (Chi-squared test, two-sided). b, QPCR for NF2 in M10GdCas9-KRAB cells expressing a non-targeting control single-guide RNA (sgNTC) or a single-guide RNA suppressing NF2 (sgNF2). 3 biological replicates per condition (Student’s t test, one sided). c, Immunoblot for Merlin or GAPDH in M10GdCas9-KRAB cells expressing sgNTC, sgNF2, or sgNF2 with NF2 rescue (sgNF2 + NF2HA). d, Confocal immunofluorescence microscopy and quantification of Ki-67 in M10GdCas9-KRAB cells from b. DNA is marked with Hoechst 33342. Scale bar 10 μM. From left to right, 123 or 145 cells are shown (Student’s t test, one sided). e, QPCR for NF2 in IOMM-Lee cells stably expressing a non-targeting control shRNA (shNTC) or shRNAs suppressing NF2 (shNF2-1 or shNF2-2). From left to right, 3, 3, or 2 biological replicates are shown (ANOVA, one sided). f, MTT cell proliferation of IOMM-Lee cells from e, normalized to shNTC at 120 h. 4 biological replicates per condition per timepoint. *p = 0.0101, **p≤0.01 (ANOVA, one sided). g, Volcano plots of relative gene expression from RNA sequencing of M10GdCas9-KRAB cells in c. Interferon-regulated genes (including IFIT2, validated in j) are marked in red. h, Gene ontology analysis of differentially expressed genes from RNA sequencing of M10GdCas9-KRAB cells in g. i, QPCR for NF2 in MSC1 cells stably expressing shNTC, shNF2-1, or shNF2-2. 3 biological replicates per condition (ANOVA, one sided). j, QPCR for the IRF target gene IFIT2 in MSC1 cells from i. From left to right, 3, 2, or 3 biological replicates are shown (ANOVA, one sided). Lines represent means, and error bars represent standard error of the means.
