Exome sequencing and digital PCR analyses reveal novel mutated genes related to the metastasis of pancreatic ductal adenocarcinoma

• Published in: Cancer biology & therapy 2012-08, Vol.13 (10), p.871-879
• Main Authors: Zhou, Bin, Irwanto, Astrid, Guo, Yun-Miao, Bei, Jin-Xin, Wu, Qiao, Chen, Ge, Zhang, Tai-Ping, Lei, Jin-Jv, Feng, Qi-Sheng, Chen, Li-Zhen, Liu, Jianjun, Zhao, Yu-Pei
• Format: Article
• Language: English
• Subjects: Alleles; Binding; Biology; Bioscience; Calcium; Cancer; Carcinoma, Pancreatic Ductal - genetics; Carcinoma, Pancreatic Ductal - pathology; Cell; Cell Line, Tumor; clonal expansion; Cycle; digital PCR; DNA Mutational Analysis; Exome; exome capture-sequencing; Gene Expression Regulation, Neoplastic; Gene Frequency; Gene Regulatory Networks; Genotype; Humans; KRAS; Landes; Male; metastases; Middle Aged; migration; Molecular Sequence Annotation; Mutation; Neoplasm Metastasis - genetics; Organogenesis; pancreatic cancer; Pancreatic Neoplasms - genetics; Pancreatic Neoplasms - pathology; Polymerase Chain Reaction - methods; proliferation; Proteins; Reproducibility of Results; TP53
• ISSN: 1538-4047; 1555-8576
• DOI: 10.4161/cbt.20839

Pancreatic ductal adenocarcinoma (PDAC) is one of the most malignant cancers with more than 94% mortality rate mainly due to the widespread metastases. To find out the somatically mutated genes related to the metastasis of PDAC, we analyzed the matched tumor and normal tissue samples from a patient diagnosed with liver metastatic PDAC using intensive exome capture-sequencing analysis (> 170× coverage). Searching for the somatic mutations that drive the clonal expansion of metastasis, we identified 12 genes with higher allele frequencies (AFs) of functional mutations in the metastatic tumor, including known genes KRAS and TP53 for metastasis. Of the 10 candidate genes, 6 (ADRB1, DCLK1, KCNH2, NOP14, SIGLEC1, and ZC3H7A), together with KRAS and TP53, were clustered into a single network (p value = 1 × 10 −22 ) that is related to cancer development. Moreover, these candidate genes showed abnormal expression in PDAC tissues and functional impacts on the migration, proliferation, and colony formation abilities of pancreatic cancer cell lines. Furthermore, through digital PCR analysis, we revealed potential genomic mechanisms for the KRAS and TP53 mutations in the metastatic tumor. Taken together, our study shows the possibility for such personalized genomic profiling to provide new biological insight into the metastasis of PDAC.