Splicing-dependent expression of microRNAs of mirtron origin in human digestive and excretory system cancer cells

Abstract

BackgroundAn abundant class of intronic microRNAs (miRNAs) undergoes atypical Drosha-independent biogenesis in which the spliceosome governs the excision of hairpin miRNA precursors, called mirtrons. Although nearly 500 splicing-dependent miRNA candidates have been recently predicted via bioinformatic analysis of human RNA-Seq datasets, only a few of them have been experimentally validated. The detailed mechanism of miRNA processing by the splicing machinery and the roles of mirtronic miRNAs in cancer are yet to be uncovered.MethodsWe experimentally examined whether biogenesis of certain miRNAs is under a splicing control by analyzing their expression levels in response to alterations in the 5′- and 3′-splice sites of a series of intron-containing minigenes carrying appropriate miRNAs. The expression levels of the miRNAs processed from mirtrons were determined by quantitative real-time PCR in five digestive tract (pancreas PANC-1, SU.86.86, T3M4, stomach KATOIII, colon HCT116) and two excretory system (kidney CaKi-1, 786-O) carcinoma cell lines as well as in pancreatic, stomach, and colorectal tumors. Transiently expressed SRSF1 and SRSF2 splicing factors were quantified by western blotting in the nuclear fractions of HCT116 cells.ResultsWe found that biogenesis of the human hsa-miR-1227-3p, hsa-miR-1229-3p, and hsa-miR-1236-3p is splicing-dependent; therefore, these miRNAs can be assigned to the class of miRNAs processed by a non-canonical mirtron pathway. The expression analysis revealed a differential regulation of human mirtronic miRNAs in various cancer cell lines and tumors. In particular, hsa-miR-1229-3p is selectively upregulated in the pancreatic and stomach cancer cell lines derived from metastatic sites. Compared with the healthy controls, the expression of hsa-miR-1226-3p was significantly higher in stomach tumors but extensively downregulated in colorectal tumors. Furthermore, we provided evidence that overexpression of SRSF1 or SRSF2 can upregulate the processing of individual mirtronic miRNAs in HCT116 cells.ConclusionsAn interplay of different splicing factors, such as SRSF1 or SRSF2, may alter the levels of miRNAs of mirtron origin in a cell. Our findings underline the specific expression profiles of mirtronic miRNAs in colorectal, stomach, and pancreatic cancer.Electronic supplementary materialThe online version of this article (doi:10.1186/s13148-016-0200-y) contains supplementary material, which is available to authorized users.

Decreased Expression of SRSF2 Splicing Factor Inhibits Apoptotic Pathways in Renal Cancer

“…These short, non-coding RNAs are powerful regulators of programmed cell death and target multiple genes involved in extrinsic and intrinsic apoptotic pathway [27]. Remarkably, SRSF2 can modulate the expression of microRNAs [28] of which at least one contributes to the regulation of apoptosis [29]. Finally, we cannot exclude also a possibility that some of the apoptotic genes are directly regulated by SRSF2.…”

Features of alternative splicing in stomach adenocarcinoma and their clinical implication: a research based on massive sequencing data

“…The altered profile of AS events in multiple tumor types emphasizes the important mechanism of splicing factors in cancer, which is disordered splicing [40]. It is increasingly believed that changes of SFs in STAD can be involved in tumorigenesis and progression through various mechanisms [41][42][43]. The splicing correlation network analysis has also found out the larger regulated nodes, indicating that they occupy a significant position in the SF-AS network.…”

Features of alternative splicing in stomach adenocarcinoma and their clinical implication: A research based on massive sequencing data

“…The altered pro le of AS events in multiple tumor types emphasizes the important mechanism of splicing factors in cancer, which is disordered splicing [40]. It is increasingly believed that changes of SFs in STAD can be involved in tumorigenesis and progression through various mechanisms [41][42][43]. The splicing correlation network analysis has also found out the larger regulated nodes, indicating that they occupy a signi cant position in the SF-AS network.…”