CSTF2-Induced Shortening of the RAC1 3′UTR Promotes the Pathogenesis of Urothelial Carcinoma of the Bladder

Abstract

Shortening of the 3' untranslated regions (3'UTR) of mRNA is an important mechanism for oncogene activation. However, 3'UTR alteration events, their pathologic functions, and underlying mechanisms in human urothelial carcinoma of the bladder (UCB) are not clear. Here, we combine RNA sequencing, bioinformatics, and clinical studies in two independent cohorts of patients with UCB to identify a novel shorter 3'UTR isoform that is frequently expressed in UCB and is critical in the tumorigenesis and acquisition of a poor prognostic phenotype in patients. Short 3'UTR isoform of substantially upregulated RAC1 expression by escaping from miRNA-targeted repression and played an essential oncogenic role in UCB pathogenesis. An important cleavage/polyadenylation factor, cleavage stimulation factor 2 (CSTF2), induced 3'UTR shortening of in UCB by mediating slow transcriptional elongation at Cotranscriptional recruitment of CSTF2 on the GUAAU motif at proximal polyadenylation site of attenuated the recruitment of two transcription factors AFF1 and AFF4, causing the defects in elongation. CSTF2 regulated the tumorigenic functions of the shorter isoform in UCB cells, enhancing cell proliferation, migration, and invasion. The combination of high expression of CSTF2 and high usage of short-3'UTR isoform may be used as a powerful biomarker to predict poor prognosis in UCB. Our findings also suggest a CSTF2-regulated-3'UTR shortening program as an exploitable therapeutic strategy for patients with UCB. These findings demonstrate that the short isoform of is critical in UCB tumorigenesis and may have implications for developing new therapeutic strategies to treat this disease..

Alternative polyadenylation drives oncogenic gene expression in pancreatic ductal adenocarcinoma

“…We processed the tumor and normal aligned files to generate coverage files that were used as an input for the DaPars (Dynamic Analysis of Alternative Polyadenylation from RNA-Seq) algorithm 41 . DaPars is a regression-based algorithm that performs de-novo identification of APA events between two conditions using standard RNA-seq data 32,33,41 . DaPars generates a mean PDUI score (Percentage Distal Usage Index) for each gene, quantifying the extent of usage of the distal PAS across each group.…”

“…4). CSTF2 has previously been implicated as a promoter of lung and bladder cancer, through the regulation of ERBB2 and RAC1 3’-UTRs, respectively 33,34 . We find frequent 3’-UTR alterations in several notable PDA-relevant genes whose mechanisms of regulation were previously unknown, including PAF1 , ALDOA and FLNA .…”

“…Indeed, APA has important roles in muscle stem cell function, cell proliferation, chromatin signaling, pluripotent cell fate, cellular senescence and other physiological processes 25–29 . Recently, dysregulation of APA has gained recognition as a driver of tumorigenesis 28,30–33 . APA factor expression is altered in a variety of cancer types and promotes tumorigenesis by regulating the expression of oncogenes (via loss of miRNA regulation) and tumor suppressors (via disruption of competing-endogenous RNA crosstalk) 32–36 .…”

“…APA factor expression is altered in a variety of cancer types and promotes tumorigenesis by regulating the expression of oncogenes (via loss of miRNA regulation) and tumor suppressors (via disruption of competing-endogenous RNA crosstalk) 32–36 . The relevance of APA in cancer was established with the discovery of a systemic increase in the usage of a proximal PAS leading to consistently shortened 3’-UTRs of oncogenes such as Insulin-like growth factor 2 mRNA-binding protein 1 ( IMP1 ), Ras-Related C3 Botulinum Toxin Substrate 1 ( RAC1 ) and Cyclin D2 30,33 . Functional studies of the genes comprising the APA machinery have highlighted their relevance to tumor growth; for example, in glioblastoma, overexpression of the APA factor NUDT21 (a repressor of proximal 3’-UTR PAS usage) reduces tumor cell proliferation and inhibits tumor growth in vivo 32 .…”

FNDC3B 3′‐UTR shortening escapes from microRNA‐mediated gene repression and promotes nasopharyngeal carcinoma progression

“…The shortening of mRNA 3′‐UTRs results in the activation of oncogenes and the repression of tumor suppressors 9,10 . It has been reported that 3′‐UTR shortening of certain genes could enhance tumor cell proliferation, migration, and invasion 11‐13 . In addition, shorter 3′‐UTRs of target genes were associated with poor prognosis of certain tumors, such as breast, lung, colorectal, and bladder cancers 13‐15 .…”