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Exome Analysis Links Three Variants to Pancreatic Cancer in Chinese Population

NEW YORK (GenomeWeb) – Researchers have uncovered three low-frequency variants that contribute to pancreatic cancer risk among individuals of Chinese ancestry.

Pancreatic ductal adenocarcinoma (PDAC) affects some 44,000 people each year in the US, according to the National Cancer Institute. It has a low five-year overall survival rate of 5 percent, and, the authors of the new study said, its incidence is on the rise.

A team led by Huazhong University of Sciences and Technology researchers conducted exome-wide association analyses of pancreatic ductal adenocarcinoma in more than 3,000 cases and 8,600 controls. As they reported this week in Nature Communications, the researchers identified three low-frequency coding mutations linked to an increased risk of pancreatic ductal adenocarcinoma. One variant in particular, affecting the PKN1 gene, increased phosphorylation levels and cell proliferation in functional studies, suggesting how it might influence cancer risk.

"These findings highlight the significance of rare coding variants in the development of PDAC and may be useful for the prevention and treatment of this disease in future," Huazhong's Xiaoping Miao and his colleagues wrote in their paper.

In the discovery stage of their three-stage analysis, the researchers conducted an exome-wide association study of 943 people with PDAC and 3,908 controls. For this, they analyzed the research participants' exomes using Illumina's HumanExome Beadchip.

The researchers noted that the chip was designed using exome sequencing data from about 12,000 individuals of African, Chinese, European, and Hispanic ancestry and that it contains more than 240,000 markers thought to encompass some 97 percent to 98 percent of nonsynonymous variants that would be detected through exome sequencing. This, they added, allowed them to focus on low-frequency variants.

In that first stage, the researchers identified 25 variants linked to disease risk. Upon replication in a further 1,048 cases and 2,094 controls, they verified four disease-linked variants, which they then replicated in another set of 1,094 cases and 2,603 controls. In a combined analysis of the discovery and replication stages, the researchers identified three variants associated with PDAC risk.

The variant with the most significant signal was a cytosine-to-adenine change in exon 11 of PKN1, which is a member of the protein kinase C superfamily. The variant leads to a leucine-to-isoleucine amino acid change. This, the researchers noted, is predicted by the PolyPhen2 tool to be probably damaging.

When the researchers conducted a comparative proteomics screen of cells transfected with a plasmid containing the PKN1 C variant, the A variant, or a control plasmid, they found that cells transfected with the A variant had higher PKN1 phosphorylation levels at Ser561 and Ser562, as compared to cells with the C variant or control plasmid.

At the same time, the researchers noted increased phosphorylation of members of the PKN1/FAK/PI3K/AKT pathway. The researchers also overexpressed the different PKN1 variants in PDAC cells to find that cells overexpressing the A variant proliferated more rapidly than the others.

This indicated to the researchers that the variant leads to increased PKN1 phosphorylation, which, in turn, leads to the activation of the FAK/PI3K/AKT signaling pathway to increase PDAC cell proliferation. Additionally, when they treated cells with the PKN1 inhibitors lestaurtinib and Ro318220, the cells' proliferation was reduced.

"[T]hese two PKN1 inhibitors may serve as potential drugs for the treatment of PDAC," the researchers wrote.

The researchers also linked variants in DOK2 and APOB to PDAC risk. DOK2 is often lost in human cancers and it and other DOK family members are substrates for key protein tyrosine kinases. APOB, meanwhile, encodes an apolipoprotein, and as abnormal lipid metabolism has been linked to the development of pancreatic tumors, the researchers said the variant could influence disease risk by altering the lipid metabolic function of APOB.