The long non-coding RNA DKFZp434J0226 regulates the alternative splicing process through phosphorylation of SF3B6 in PDAC

Abstract

Background Long noncoding RNAs (lncRNAs), a type of pervasive genes that regulates various biological processes, are differentially expressed in different types of malignant tumors. The role of lncRNAs in the carcinogenesis of pancreatic ductal adenocarcinoma (PDAC) remains unclear. Here, we investigated the role of the lncRNA DKFZp434J0226 in PDAC. Methods Aberrantly expressed mRNAs and lncRNAs among six PDAC and paired non-tumorous tissues were profiled using microarray analysis. Quantitative real-time polymerase chain reaction was used to evaluate DKFZp434J0226 expression in PDAC tissues. CCK-8 assay, wound-healing assay, soft agar colony formation assay, and transwell assay were performed to assess the invasiveness and proliferation of PDAC cells. Furthermore, RNA pull-down, immunofluorescence, RNA immunoprecipitation, and western blotting assays were performed to investigate the association between DKFZp434J0226 and SF3B6. Tumor xenografts in mice were used to test for tumor formation in vivo. Results In our study, 222 mRNAs and 128 lncRNAs were aberrantly expressed (≥ twofold change). Of these, 66 mRNAs and 53 lncRNAs were upregulated, while 75 lncRNAs and 156 mRNAs were downregulated. KEGG pathway analysis and the Gene ontology category indicated that these genes were associated with the regulation of mRNA alternative splicing and metabolic balance. Clinical analyses revealed that overexpression of DKFZp434J0226 was associated with worse tumor grading, frequent perineural invasion, advanced tumor-node-metastasis stage, and decreased overall survival and time to progression. Functional assays demonstrated that DKFZp434J0226 promoted PDAC cell migration, invasion, and growth in vitro and accelerated tumor proliferation in vivo. Mechanistically, DKFZp434J0226 interacted with the splicing factor SF3B6 and promoted its phosphorylation, which further regulated the alternative splicing of pre-mRNA. Conclusions This study indicates that DKFZp434J0226 regulates alternative splicing through phosphorylation of SF3B6 in PDAC and leads to an oncogenic phenotype in PDAC.

Non-coding RNA as future target for diagnose and treatment of perineural invasion in cancers

“…Numerous lncRNAs have been identified with elevated expression levels in cancerous tissues and are significantly associated with PNI (Table 2). For instance, lncRNAs such as DKFZp434J0226, FEZ family zinc finger 1 antisense RNA 1 (FEZF1-AS1), and actin filament-associated protein1-antisense RNA1 (AFAP1-AS1) in PDAC [78][79][80]; opioid growth factor receptor pseudogene 1 (OGFRP1) and HOXA transcript at the distal tip (HOTTIP) in Pca [56,81]; pseudogene 3 of ubiquitin-conjugating enzyme 2C (UBE2CP3), ATMIN-4:2, and gastric cancer associated transcript 2 (GACAT2) in GC [59,82,83]; and translation regulatory long non-coding RNA 1 (TRERNA1), activated by transforming growth factor-β (ATB), and cytoskeleton regulator RNA (CYTOR) in CRC [58,84,85] not only demonstrate high expression in tumor tissues but also exhibit a strong correlation with negative clinical prognostic indicators, such as PNI, OS, lymphovascular invasion, and metastasis. Conversely, the lncRNA AA174084 represents an exception to this trend.…”

Predictive and Prognostic Value of Non-Coding RNA in Breast Cancer

“…In fact, one study indicated that lncRNAs are sometimes not properly spliced and 3′ end processed due to splicing inefficiency, which contrasts with mRNA splicing efficiency [ 24 ]. Some lncRNAs may regulate splicing, recently, Li et al discovered that lncRNA DKFZp434J0226 promotes phosphorylation of splicing factor SF3B6, which regulates pre-mRNA alternative splicing and promotes pancreatic ductal adenocarcinoma (PDAC) carcinogenesis [ 30 ]. Non-coding RNAs are also known to alter gene expression and disease progression by binding protein complexes.…”

Predictive and Prognostic Value of Non-coding RNA in Breast Cancer

“…In fact, one study indicated that lncRNAs are sometimes not properly spliced and 3' end processed due to splicing inefficiency, which contrasts with mRNA splicing efficiency [22]. Some lncRNAs may regulate splicing, recently, Li et al discovered that lncRNA DKFZp434J0226 promotes phosphorylation of splicing factor SF3B6, which regulates pre-mRNA alternative splicing and promotes pancreatic ductal adenocarcinoma (PDAC) carcinogenesis [28]. Non-coding RNAs are also known to alter gene expression and disease progression by binding protein complexes.…”