Study: JGAS00000000179

Identifier

AccessionJGAS00000000179

Description

TitleIdentification of driver oncogenes in scirrhous-type gastric cancer cell lines
AbstractScirrhous type gastric cancer (SGC) is one of the most intractable cancer subtypes in human, and its therapeutic targets have been rarely identified to date. Exploration of somatic mutations in the SGC genome with the next generation sequencers has been hampered by low tumor contents by the markedly increased fibrous tissues. Thus, SGC cell lines may be useful resources to search for novel oncogenes in. Here we have conducted whole exome sequencing and RNA sequencing on two SGC cell lines, OCUM-8 and OCUM-9. Interestingly, most of the mutations thus identified have not been reported. In OCUM-8 cells, a novel CD44-IGF1R fusion gene is discovered, the protein product of which ligates the amino-terminus of CD44 to the transmembrane and the tyrosine-kinase domains of IGF1R. Further, both of CD44 and IGF1R are markedly amplified in the OCUM-8 genome and abundantly expressed. CD44-IGF1R has a transforming ability, and the suppression of its kinase activity leads to rapid cell death of OCUM-8. On the other hand, OCUM-9 seems to possess multiple oncogenic events in its genome. The MET gene is highly amplified, and the treatment of OCUM-9 with crizotinib, a MET inhibitor, results in cell death. Further, a novel BORCS5-ETV6 fusion gene is identified in the OCUM-9 genome. BORCS5-ETV6 possesses oncogenic activity, and suppression of its message partially inhibits cell growth. Prevalence of these novel fusion genes among SGC awaits further investigation, but we validate the significance of cell lines as appropriate reagents for detailed genomic analyses of SGC.
Study Type 1
Study TypeExome Sequencing
Study Type 2
Study TypeTranscriptome Sequencing

Study Attribute

NBDC Numberhum0188
Registration date2019-05-17
Submitting organizationNational Cancer Center Research Institute
Principal InvestigatorHiroyuki Mano
Molecular Data TypeWhole Exome Sequencing
PlatformHiSeq 2500
VendorIllumina
Comment
Molecular Data TypeRNA Sequencing
PlatformHiSeq 2500
VendorIllumina
Comment
Primary PhenotypeGastric cancer
Dataset
Accession Title Dataset type Data objects Policy
JGAD00000000260 Bam and fastq files of OCUM-8 and OCUM-9 4 JGAP00000000001