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

Okuda,Takashi; Taki,Tomohiko; Nishida,Kazuhiro; Chinen,Yoshiaki; Nagoshi,Hisao; Sakakura,Chouhei; Taniwaki,Masafumi

doi:10.3892/ol.2016.5386

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

Authors:
- Takashi Okuda
- Tomohiko Taki
- Kazuhiro Nishida
- Yoshiaki Chinen
- Hisao Nagoshi
- Chouhei Sakakura
- Masafumi Taniwaki
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Affiliations: Department of Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto 602‑8566, Japan, Department of Molecular Diagnostics and Therapeutics, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto 602‑8566, Japan, Department of Hematology and Oncology, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto 602‑8566, Japan, Department of Digestive Surgery, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto 602‑8566, Japan
Published online on: November 15, 2016 https://doi.org/10.3892/ol.2016.5386
Pages: 215-221
Copyright: © Okuda et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

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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.

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