Extended Data Fig. 5: Dysregulated expression of canonical splicing-related genes is associated with disease subtype-specific expression of NJs.
From: Tumour-wide RNA splicing aberrations generate actionable public neoantigens
A. qPCR validation of target gene knockdown by CRISPRi was performed on glioma cell lines (n = 3). B-C. RNA-seq-derived (B) and qPCR (C) TPM expression of CELF2, SNRPD2, and SF3A3 following siRNA knockdown (n = 3). D. (Left) Expression of NJACAP2 in LGG (SF10417 and SF10602) cell line treated with control siRNA or siCELF2 (n = 3). (Right) Expression of NJACAP2 or NJPEA15 in GBM (GBM115) cell line treated with control siRNA or siSNRPD2 or siSF3A3, respectively (n = 3). E. Detection of glioma-derived IDHmut NJs in IDHmut TCGA LIHC (n = 4) and PRAD (n = 3) samples. F. Slope plots demonstrating a decrease in the frequency of IDHmut-specific NJs in CELF2 siRNA-treated SF10417 (left) and SF10602 cells (right). G. Correlation of IDHmut-specific splicing-related genes (right, n = 26) and chromosome 1p and 19q splicing-related genes (left, n = 25) with NJGNAS and NJRPL22. H. RNA-seq-derived read frequency of NJPEA15 and NJACAP2 in GBM115 cells (n = 3) treated with control siRNA and siSF3A3 (left) or control siRNA and siSNRPD2 (right), respectively. I. Slope plots demonstrating an increase in the frequency of IDHmut-O-specific NJs in SF3A3 siRNA- (left) and SNRPD2 siRNA-treated (right) GBM115 cells. J-M. Bar plot (left) showing the total NJs expressed per case across all disease subtypes and heatmap (right) displaying the Wilcoxon rank-sum test of NJ expression between each subtype within TCGA SKCM (BRAF, n = 150; RAS, n = 91; NF1, n = 26; Triple WT, n = 46) (J), KIRP (C1, n = 89; C2a, n = 34, C2b, n = 17; C2cCIMP, n = 9) (K), PRAD (ERG, n = 145; ETV1, n = 24; ETV4, n = 14; FLI1, n = 4; SPOP, n = 33; FOXA1, n = 8; IDH1, n = 2; other, n = 80) (L), KICH (Eosinophilic, n = 19; Classic, n = 43) (M). Further statistical details are found in Supplementary Table 3.
