Correlating tissue and plasma‑specific piRNA changes to predict their possible role in pancreatic malignancy and chronic inflammation

Abstract

The aggressiveness of pancreatic ductal adenocarcinoma is primarily due to lack of effective early detection biomarkers. Circulating non-coding RNAs serve as diagnostic or prognostic biomarkers in multiple types of cancer. Comparison of their expression between diseased tissue and relevant body fluids such as saliva, urine, bile, pancreatic juice, blood etc. may reveal mechanistic involvement of common non-coding RNAs. piwi-interacting RNAs (piRNAs) are a class of non-coding RNAs. The aim of the present study was to investigate plasma and tumour tissue piRNA changes in patients with pancreatic cancer (PC) and explore the possible role in tumorigenesis and pancreatic inflammation. Sequencing of circulating plasma small RNAs from patients with PC and chronic pancreatitis (CP) was performed and differentially expressed piRNAs were compared with those in tissues. Subsequent search for target genes for those piRNAs was performed followed by pathway and cluster analysis. A total of 36 piRNAs were shown to be deregulated in pancreatic tumour tissue and alteration of 11 piRNAs was detected in plasma of patients with PC. piRNAs hsa-piR-23246, hsa-piR-32858 and hsa-piR-9137 may serve a key role in PC development as their expression was correlated in both plasma and tumour tissue. Key piRNA-target interactions interfering with key biological pathways were also characterized. A total of 19 deregulated piRNAs in plasma samples of patients with CP was identified; these targeted genes responsible for chronic inflammation. Therefore, the present study provides a comprehensive description of piRNA alteration in pancreatic malignancy and inflammation; these may be explored for biomarker potential in future.

Keywords: chronic pancreatitis; pancreatic ductal adenocarcinoma; piRNA; plasma; tissue.

Figure 1

Expression of tissue- and plasma-specific piRNAs in patients with PDAC and healthy individuals. (A) Heatmap of expression of piRNAs across all adjacent normal (n=5) and tumour tissue (n=5). (B) Heatmap of the expression patterns of piRNAs across all plasma samples from healthy individuals (n=16) and patients with PDAC (n=15). Higher expression is shown in dark blue and the lower expression is shown in red colour. (C) Volcano plot shows DE piRNAs in tissue from tumour and adjacent normal samples. (D) Volcano plot showing the DE piRNAs in plasma of healthy individuals and PDAC samples. piRNA, piwi-interacting RNA; DE, differentially expressed; PDAC, pancreatic ductal adenocarcinoma.

Figure 2

GO analysis with the targets of differentially expressed piRNAs in tissue samples. Top 10 pathways derived from GO analysis with the targets of (A) up- and (B) downregulated piRNAs. GO, Gene Ontology; pi, piwi-interacting.

Figure 3

KEGG annotation and enrichment analysis with targets of differentially expressed piRNAs in tissue samples. Top 20 pathways derived from KEGG analysis with the targets of (A) up- and (B) downregulated piRNAs. pi, piwi-interacting; KEGG, Kyoto Encyclopedia of Genes and Genomes.

Figure 4

Distribution of piRNA clusters derived from tumour and adjacent normal samples. (A) piRNA clusters across the chromosome. (B) piRNA clusters from both groups show a bias of 1U and 10A. pi, piwi-interacting.

Figure 5

Distribution of the origin of the piRNA clusters among repeats and retro-repeats. pi, piwi-interacting; LTR, long terminal repeat; LINE, Long Interspersed Nuclear Elements; SINE, Short Interspersed Nuclear Elements).