Identification of Critical Biomarkers Responsive to Anti-Autophagy Therapies for Pancreatic Ductal Adenocarcinoma through a Performance Analysis of miRNA Platforms

Abstract

Background: Autophagy is a fundamental catabolic pathway that involves the degradation of unnecessary or dysfunctional cellular components through the lysosomal machinery. The role of autophagy in cancer is complex, exhibiting tumor suppressive or tumor proliferative effects depending on the cancer type. Pancreatic ductal adenocarcinoma has constitutively activated autophagy that results in the selective proliferation of its tumor cells. Understanding the mechanisms by which the inhibition of autophagy occurs could shape our current therapeutic strategies for pancreatic cancer. Recent research has implicated microRNAs as important regulators of autophagy, but how miRNAs influence this inhibition is largely unexplored. Results: It is known that there exists inter-platform variability across miRNA platforms and therefore in order to identify bona fide miRNAs that are involved with the inhibition of autophagy we carried out a performance analysis of miRNA arrays from three vendors. In this paper we report our findings from this cross-platform analysis of miRNA arrays and the identity of several critical biomarkers of response to anti-autophagy therapies in the immortalized human pancreatic ductal adenocarcinoma cells 8988T as compared to normal human pancreatic ductal epithelial cells. Our cross-platform analysis of three different miRNA arrays revealed that RT-PCR-based technologies provide higher inter-platform reproducibility than hybridization-based technologies, a greater sensitivity indicated by larger dynamic ranges and reduced processing time. We also discovered two miRNAs, miRNA 720 and miRNA 29b to play a role in the inhibition of autophagy in 8988T cells and found miRNA 30a to be involved with the inhibition of autophagy in normal human pancreatic ductal epithelial cells. Conclusion: This cross-platform analysis of miRNA arrays contributed significant information about miRNA expression systems and led to the first report of miRNAs implicated in the inhibition of autophagy in pancreatic ductal adenocarcinoma. Our findings should provide new insights for developing therapeutic solutions for this extremely intractable disease.