Aberrant transcriptional events caused by complicated local structural aberrations. (A) Structures of STK11 transcripts in RERF-LC-KJ. Sequencing tags of whole-genome sequencing (PromethION) and full-length RNA-seq (MinION) were visualized by IGV. PC-14 RNA-seq was also shown as a wild-type control. (B) Multilayered statuses in the STK11 region. Patterns of whole-genome sequencing, ChIP-seq, and RNA-seq tags of short-read data were visualized by IGV. The status of RERF-LC-KJ and PC-9 (control) is shown. (C) Structures of PTEN transcripts in PC-14. Sequencing tags of whole-genome sequencing (PromethION) and full-length RNA-seq (MinION) were visualized by IGV. The transcripts indicated that exon 6 was skipped (black arrow). (D) Expression levels of STK11, NF1, SMARCA4, and PTEN in 26 lung cancer cell lines. Cell lines with deleterious mutations, such as large deletions, frameshift indels, and nonsense SNVs, are shown in black. Cell lines with complicated SVs are also shown in black with a diagonal line. (E) Western blotting of genes affected by complicated SVs and their downstream targets. (MW) Molecular weight; (WT) wild type; (DEL) large deletion; (CLCL) complicated local SV focused on in this study. Bar charts indicate the normalized ratio of density of phosphorylated proteins and total proteins. Each protein is downstream from proteins encoded by the genes.
