Identification of somatic mutations in EGFR/KRAS/ALK-negative lung adenocarcinoma in never-smokers

Jin W. Ahn, Han S. Kim, Jung Ki Yoon, Hoon Jang, Soo M. Han, Sungho Eun, Hyo S. Shim, Hyun Jung Kim, Dae J. Kim, Jin G. Lee, Chang Y. Lee, Mi K. Bae, Kyung Y. Chung, Ji Y. Jung, Eun Y. Kim, Se K. Kim, Joon Chang, Hye R. Kim, Joo H. Kim, Min G. LeeByoung C. Cho, Ji H. Lee, Duhee Bang

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Abstract

Background: Lung adenocarcinoma is a highly heterogeneous disease with various etiologies, prognoses, and responses to therapy. Although genome-scale characterization of lung adenocarcinoma has been performed, a comprehensive somatic mutation analysis of EGFR/KRAS/ALK-negative lung adenocarcinoma in never-smokers has not been conducted.Methods: We analyzed whole exome sequencing data from 16 EGFR/KRAS/ALK-negative lung adenocarcinomas and additional 54 tumors in two expansion cohort sets. Candidate loci were validated by target capture and Sanger sequencing. Gene set analysis was performed using Ingenuity Pathway Analysis.Results: We identified 27 genes potentially implicated in the pathogenesis of lung adenocarcinoma. These included targetable genes involved in PI3K/mTOR signaling (TSC1, PIK3CA, AKT2) and receptor tyrosine kinase signaling (ERBB4) and genes not previously highlighted in lung adenocarcinomas, such as SETD2 and PBRM1 (chromatin remodeling), CHEK2 and CDC27 (cell cycle), CUL3 and SOD2 (oxidative stress), and CSMD3 and TFG (immune response). In the expansion cohort (N = 70), TP53 was the most frequently altered gene (11%), followed by SETD2 (6%), CSMD3 (6%), ERBB2 (6%), and CDH10 (4%). In pathway analysis, the majority of altered genes were involved in cell cycle/DNA repair (P <0.001) and cAMP-dependent protein kinase signaling (P <0.001).Conclusions: The genomic makeup of EGFR/KRAS/ALK-negative lung adenocarcinomas in never-smokers is remarkably diverse. Genes involved in cell cycle regulation/DNA repair are implicated in tumorigenesis and represent potential therapeutic targets.

Original languageEnglish
Article number18
JournalGenome Medicine
Volume6
Issue number2
DOIs
Publication statusPublished - 2014 Feb 27

All Science Journal Classification (ASJC) codes

  • Molecular Medicine
  • Molecular Biology
  • Genetics
  • Genetics(clinical)

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    Ahn, J. W., Kim, H. S., Yoon, J. K., Jang, H., Han, S. M., Eun, S., Shim, H. S., Kim, H. J., Kim, D. J., Lee, J. G., Lee, C. Y., Bae, M. K., Chung, K. Y., Jung, J. Y., Kim, E. Y., Kim, S. K., Chang, J., Kim, H. R., Kim, J. H., ... Bang, D. (2014). Identification of somatic mutations in EGFR/KRAS/ALK-negative lung adenocarcinoma in never-smokers. Genome Medicine, 6(2), [18]. https://doi.org/10.1186/gm535