Mutation Analysis of TGFβ Pathway in Pancreatic Ductal Adenocarcinoma among Pakistani Population through Whole Exome Sequencing

Abstract

Pancreatic cancer is a lethal malignancy with its number increasing substantially, and a survival rate of less than 5 years. It is reported to be the 4th leading cause of death worldwide. The most common type of PC is the PDAC constituting about 90% of cases. It originates when multiple mutations occur in the DNA of pancreatic cells, causing the cells to grow uncontrollably with limitless proliferative potential. It begins in pancreatic ducts and later metastasizes to the nearby tissues. The four genes i.e. KRAS, CDKN2A, p53, and SMAD4 are frequently mutated in PDAC and are considered driver genes of PDAC. This study aimed at molecular characterization of PDAC samples to identify the role of TGFβ signaling in causing PDAC. For this purpose, the tumor and its matched control were profiled at molecular level through whole exome sequencing to look for variants in TGFβ pathway components, including TβRs, and SMADs. Later in silico analysis was done to identify the pathogenic variants. Deletions were found in the signal peptide and kinase domain of TβRⅠ. A non-synonymous variation was found in the extracellular domain of TβRⅡ. Non-synonymous variations were found in the MH2 domain and linker region of SMAD2 and SMAD4 respectively. A stop loss variation was found in SMAD3. For variations in TβR1 and TβR2, no data was provided by the in silico tools; but homology modeling confirmed that these variations altered the normal secondary structure of the functional proteins. The data from all the tools applied showed that the variation in SMAD2 and SMAD4 was found to be highly deleterious and disease causing with the highest damage prediction score. SMAD3 variant was also found to be disease-causing. All in all, these variations might have a role in the dysregulation of normal tumor suppressor role of TGFβ signaling, thereby causing PDAC. Further transcriptome analysis and molecular docking can provide deep insights that can expedite the development of efficient prognostic/diagnostic markers, and can also help in devising potential treatments against PDAC. Keywords: Pancreatic cancer (PC), Pancreatic Ductal Adenocarcinoma (PDAC), Transforming Growth Factor β (TGFβ), Mothers against decapentaplegia homolog 4 (SMAD4), Whole Exome Sequencing (WES).