Background: Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease. Although the surgical resection is still the first clinical procedure for localized PDAC patients, only few patients (?20%) have opportunity to perform resection at diagnosis. And even after successful resection, majority of the patients develop metastatic recurrence. However, the mechanism underlying the recurrence of PDAC remains unclear. We hypothesized that genetic differences play significant role in various outcomes in patients with early- or late recurrence after resection. This study was designed to apply transcriptome analysis to elucidate the molecular mechanism of PDAC dissemination after resection. Materials and Methods: Four paired snap-frozen PDAC specimens were collected from NCKU tissue bank. To solve the problem of heterogeneity, tumor or adjacent normal cells from clinical samples were collected through laser-capture microdissection (LCM). RNA was extracted by modified protocol to construct library from highly degraded low-input RNA for RNA-deep sequencing. Several computational tools were used to analyze data from RNA sequencing and further analyzed the expression profiles of early (ER group) or late (LR group) recurrence PDACs by two-way ANOVA. Then the expression level of differentially expressed genes (DEGs), long ncRNAs and splicing events were validated by qRT-PCR. Finally, the functional enrichment of DEGs will be analyzed using MetaCore pathway analysis tool. Results: We obtained a total of 424.4 million reads and the average proportion of mapped reads is ?87%. Between ER and LR groups, we identified 525 up- and 442 down-regulated genes that showed significantly differential expression (p-value <0.05). In the meanwhile, we also identified 18 long ncRNAs that were differentially expressed between these 2 groups (p-value <0.05). In addition, 20 putative and novel somatic splicing isoforms which specific in the ER group were found. We will further validate these differentially expressed events by experimental and computational approaches. Discussion: The expression signatures obtained from this study possess the potential to be used as biomarkers for the prediction of early recurrent risk after PDAC resection. Moreover, the approved drugs or small-molecules which specifically target the early recurrence-related signatures may inhibit recurrence after surgical resection thus it provides an alternative therapy for PDAC treatment.
Date:
2014-12
Relation:
Biomarkers and Genomic Medicine. 2014 Dec;6(4):196.
