Fig. 2

Aberrant RNA editing re-codes GLI1 transcripts. a Schematic representation of the GLI1 editing site in a putative SUFU binding domain. b Vienna RNA predicted secondary structure changes of GLI1 induced by A-to-I editing in exon 12. c RESSq-PCR analysis of GLI1 editing in primary MM total MNCs. Dots represent ratio of edit (G)/WT (A) GLI1 transcripts (mean values for individual patients ± S.E.M.; ctrl n = 3, smoldering MM n = 4, newly diagnosed MM n = 4, relapsed MM n = 7, PCL n = 4). *p < 0.05, **p < 0.01, by unpaired, two-tailed Student’s t-test. d Representative Sanger sequencing chromatograms for GLI1; the yellow box highlights the double peak A/G, labeled with the percentage of edited transcripts assessed as edit allele burden (%G/(G + A)). e Regression analysis of total ADAR1 mRNA expression and GLI1 editing levels in primary samples (n = 19). f Top 5 gene sets enriched in 1q amp (n = 40) from CoMMpass RNA-seq (IA7 data release) ranked by gene set size. g Venn diagram showing number of core enriched genes between KEGG_Pathways in Cancer and KEGG_Signaling Pathways Regulating Pluripotency of Stem Cells. h Enrichment of Hedgehog signaling in high versus low ADAR1 patients. i GLI1 editing after ADAR1 silencing in 1q-amplified cells (H929). Left: ADAR1 knockdown levels by qPCR (mean ± S.E.M. of three independent experiments). Right: GLI1 editing by RESSq-PCR. *p < 0.05, **p < 0.01 compared to Lenti-shCtrl by unpaired, two-tailed Student’s t-test. j GLI1 editing by RESSq-PCR in normal primary CD34⁺ cells (n = 3) transduced with lentiviral pCDH ADAR1-WT/ADAR1 Mutant, or pCDH backbone control. Histograms represent relative ratios of edit (G)/WT (A) GLI1 transcripts (mean ± S.E.M. of three independent experiments). **p < 0.01, by unpaired, two-tailed Student’s t-test. k GLI1 editing by RESSq-PCR after transient overexpression of GLI1 and WT or editase-deficient ADAR1 in HEK293T. Histograms represent mean ± S.E.M. of three independent experiments. **p < 0.01, by unpaired, two-tailed Student’s t-test. l Relative GLI1-Luciferase/Renilla reporter activity (mean ± S.E.M.). HEK293T cells were co-transfected with a dual reporter plasmid and GLI1 WT, GLI1 Edit or vector control (backbone) pCDH plasmids (n = 4). *p < 0.05, ***p < 0.001, by one way ANOVA plus Bonferroni post-test. Statistical significance was indicated when p < 0.05. See also Supplementary Fig. 2