Publications

@article{Chen2017,

title = {APOBEC3A is an oral cancer prognostic biomarker in Taiwanese carriers of an APOBEC deletion polymorphism},

author = {T. -W. Chen and C. -C. Lee and H. Liu and C. -S. Wu and C. R. Pickering and P. -J. Huang and J. Wang and I. Y. -F. Chang and Y. -M. Yeh and C. -D. Chen and H. -P. Li and J. -D. Luo and B. C. -M. Tan and T. E. H. Chan and C. Hsueh and L. J. Chu and Y. -T. Chen and B. Zhang and C. -Y. Yang and C. -C. Wu and C. -W. Hsu and L. -C. See and P. Tang and J. -S. Yu and W. -C. Liao and W. -F. Chiang and H. Rodriguez and J. N. Myers and K. -P. Chang and Y. -S. Chang},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85028934689&doi=10.1038%2fs41467-017-00493-9&partnerID=40&md5=2c10395e48de87bc22d79acdf9d8c6d6},

doi = {10.1038/s41467-017-00493-9},

issn = {20411723},

year  = {2017},

date = {2017-01-01},

journal = {Nature Communications},

volume = {8},

number = {1},

publisher = {Nature Publishing Group},

abstract = {Oral squamous cell carcinoma is a prominent cancer worldwide, particularly in Taiwan. By integrating omics analyses in 50 matched samples, we uncover in Taiwanese patients a predominant mutation signature associated with cytidine deaminase APOBEC, which correlates with the upregulation of APOBEC3A expression in the APOBEC3 gene cluster at 22q13. APOBEC3A expression is significantly higher in tumors carrying APOBEC3B-deletion allele(s). High-level APOBEC3A expression is associated with better overall survival, especially among patients carrying APOBEC3B-deletion alleles, as examined in a second cohort (n = 188; p = 0.004). The frequency of APOBEC3B-deletion alleles is ~50% in 143 genotyped oral squamous cell carcinoma -Taiwan samples (27A3B -/-:89A3B +/-:27A3B +/+), compared to the 5.8% found in 314 OSCC-TCGA samples. We thus report a frequent APOBEC mutational profile, which relates to a APOBEC3B-deletion germline polymorphism in Taiwanese oral squamous cell carcinoma that impacts expression of APOBEC3A, and is shown to be of clinical prognostic relevance. Our finding might be recapitulated by genomic studies in other cancer types. © 2017 The Author(s).},

note = {cited By 52},

keywords = {Adult; Asian Continental Ancestry Group; Biomarkers, allele; biomarker; cancer; gene; gene expression; mutation; organic nitrogen compound; polymorphism; protein; survival, Genetic; Proteins; Sequence Deletion; Taiwan, human; cytidine deaminase; protein; tumor marker, Neoplastic; Germ-Line Mutation; Humans; Kaplan-Meier Estimate; Male; Middle Aged; Mouth Neoplasms; Polymorphism, Squamous Cell; Cohort Studies; Cytidine Deaminase; Female; Gene Expression Regulation, Taiwan, Tumor; Carcinoma},

pubstate = {published},

tppubtype = {article}

}

@article{Chen201518066,

title = {Ultra-deep targeted sequencing of advanced oral squamous cell carcinoma identifies a mutation-based prognostic gene signature},

author = {S. -J. Chen and H. Liu and C. -T. Liao and P. -J. Huang and Y. Huang and A. Hsu and P. Tang and Y. -S. Chang and H. -C. Chenx and T. -C. Yen},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84938613758&doi=10.18632%2foncotarget.3768&partnerID=40&md5=e401b9db26d05a7c7dea4e6761bcb03b},

doi = {10.18632/oncotarget.3768},

issn = {19492553},

year  = {2015},

date = {2015-01-01},

journal = {Oncotarget},

volume = {6},

number = {20},

pages = {18066-18080},

publisher = {Impact Journals LLC},

abstract = {Background: Patients with advanced oral squamous cell carcinoma (OSCC) have heterogeneous outcomes that limit the implementation of tailored treatment options. Genetic markers for improved prognostic stratification are eagerly awaited. Methods: Herein, next-generation sequencing (NGS) was performed in 345 formalin-fixed paraffin-embedded (FFPE) samples obtained from advanced OSCC patients. Genetic mutations on the hotspot regions of 45 cancer-related genes were detected using an ultra-deep (>1000×) sequencing approach. Kaplan-Meier plots and Cox regression analyses were used to investigate the associations between the mutation status and disease-free survival (DFS). Results: We identified 1269 non-synonymous mutations in 276 OSCC samples. TP53, PIK3CA, CDKN2A, HRAS and BRAF were the most frequently mutated genes. Mutations in 14 genes were found to predict DFS. A mutation-based signature affecting ten genes (HRAS, BRAF, FGFR3, SMAD4, KIT, PTEN, NOTCH1, AKT1, CTNNB1, and PTPN11) was devised to predict DFS. Two different resampling methods were used to validate the prognostic value of the identified gene signature. Multivariate analysis demonstrated that presence of a mutated gene signature was an independent predictor of poorer DFS (P = 0.005). Conclusions: Genetic variants identified by NGS technology in FFPE samples are clinically useful to predict prognosis in advanced OSCC patients.},

note = {cited By 37},

keywords = {4, 5 trisphosphate 3 phosphatase; protein p53; protein tyrosine phosphatase SHP 2; Smad4 protein; tumor marker, Adult; Aged; Biomarkers, B Raf kinase; cyclin dependent kinase inhibitor 2A; fibroblast growth factor receptor 3; Notch1 receptor; phosphatidylinositol 3, Tumor; Carcinoma},

pubstate = {published},

tppubtype = {article}

}