Molecular heterogeneity in the novel fusion gene APIP-FGFR2: Diversity of genomic breakpoints in gastric cancer with high-level amplifications at 11p13 and 10q26

Abstract

Several novel fusion transcripts were identified by next-generation sequencing in gastric cancer; however, the breakpoint junctions have yet to be characterized. The present study characterized a plethora of APIP-FGFR2 genomic breakpoints in the SNU-16 gastric cancer cell line, which harbored homogeneously staining regions (hsrs) and double minute chromosomes. Oligonucleotide microarrays revealed high-level amplifications at chromosomes 8q24.1 (0.8 Mb region), 10q26 (1.1 Mb) and 11p13 (1.1 Mb). These amplicons contained MYC and PVT1 at chromosome 8q24.1, BRWD2, FGFR2 and ATE1 at chromosome 10q26, and 24 genes, including APIP, CD44, RAG1 and RAG2, at chromosome 11p13. Based on these findings, reverse transcription-polymerase chain reaction (PCR) was performed using various candidate gene primers to detect possible fusion transcripts, and several products using primer sets for the APIP and FGFR2 genes were detected. Eventually, three in-frame and two out-of-frame fusion transcripts were detected. Notably, PCR analysis of the entire genomic DNA detected three distinct genomic junctions. The breakpoints were within intron 5 of APIP, which contained three distinct breakpoints, and introns 5, 7 and 9 of FGFR2. Fluorescence in situ hybridization showed several fusion signals within hsrs using two short probes (~10-kb segments of a bacterial artificial chromosome clone) containing exons 2–5 of APIP or exons 11–13 of FGFR2. Although, for any given fusion, a multiplicity of transcripts is thought to be created by alternative splicing of one rearranged allele, the results of the present study suggested that genomic fusions of APIP and FGFR2 are generated in hsrs with a diversity of breakpoints that are then faithfully transcribed.

lncRNA ACTA2-AS1 inhibits malignant phenotypes of gastric cancer cells

“…In addition, targeted therapies have become heated due to advancement in microarrays and next generation sequencing [ 7 ]. However, developing targeted drugs for GC still has a long way to go due to molecular complexity [ 8 ]. Therefore, understanding the functions and mechanisms of dysregulated molecules in GC is of great significance.…”

Functional and regulatory impact of chimeric RNAs in human normal and cancer cells

“…A significant association between TMPRSS2‐ERG rearranged tumors through deletions, and a higher tumor stage with metastatic disease can explain the heterogeneity associated with prostate cancer (Perner et al, 2006). Several APIP‐FGFR2 chimeric RNAs with diverse genomic breakpoints were found to be associated with molecular heterogeneity in gastric cancer (Okuda et al, 2017). In a subset of nonsmall cell lung cancers, EML4–ALK fusion is observed (Soda et al, 2007).…”