title: Alternative Polyadenylation in Triple-Negative Breast Tumors Allows NRAS and c-JUN to Bypass PUMILIO Posttranscriptional Regulation.
abstract: Alternative polyadenylation (APA) is a process that changes the posttranscriptional regulation and translation potential of mRNAs via addition or deletion of 3' untranslated region (3' UTR) sequences. To identify posttranscriptional-regulatory events affected by APA in breast tumors, tumor datasets were analyzed for recurrent APA events. Motif mapping of the changed 3' UTR regions found that APA-mediated removal of Pumilio regulatory elements (PRE) was unusually common. Breast tumor subtype-specific APA profiling identified triple-negative breast tumors as having the highest levels of APA. To determine the frequency of these events, an independent cohort of triple-negative breast tumors and normal breast tissue was analyzed for APA. APA-mediated shortening of NRAS and c-JUN was seen frequently, and this correlated with changes in the expression of downstream targets. mRNA stability and luciferase assays demonstrated APA-dependent alterations in RNA and protein levels of affected candidate genes. Examination of clinical parameters of these tumors found those with APA of NRAS and c-JUN to be smaller and less proliferative, but more invasive than non-APA tumors. RT-PCR profiling identified elevated levels of polyadenylation factor CSTF3 in tumors with APA. Overexpression of CSTF3 was common in triple-negative breast cancer cell lines, and elevated CSTF3 levels were sufficient to induce APA of NRAS and c-JUN. Our results support the hypothesis that PRE-containing mRNAs are disproportionately affected by APA, primarily due to high sequence similarity in the motifs utilized by polyadenylation machinery and the PUM complex. Cancer Res; 76(24); 7231-41. ©2016 AACR.
authors.affiliation: Department of Molecular Oncology, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts. dyson@helix.mgh.harvard.edu wayne.miles@osumc.edu.|Department of Molecular Genetics, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio.
authors.forename: Wayne O
authors.initials: WO
authors.lastname: Miles
authors.affiliation: Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy.|Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Milan, Italy.
authors.forename: Antonio
authors.initials: A
authors.lastname: Lembo
authors.affiliation: Department of Pathology, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts.
authors.forename: Angela
authors.initials: A
authors.lastname: Volorio
authors.affiliation: Department of Pathology, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts.
authors.forename: Elena
authors.initials: E
authors.lastname: Brachtel
authors.affiliation: Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey.
authors.forename: Bin
authors.initials: B
authors.lastname: Tian
authors.affiliation: Department of Pathology, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts.
authors.forename: Dennis
authors.initials: D
authors.lastname: Sgroi
authors.affiliation: Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy.|Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Milan, Italy.
authors.forename: Paolo
authors.initials: P
authors.lastname: Provero
authors.affiliation: Department of Molecular Oncology, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts. dyson@helix.mgh.harvard.edu wayne.miles@osumc.edu.
authors.forename: Nicholas
authors.initials: N
authors.lastname: Dyson
mesh_terms: D015153:Blotting, Western; D005260:Female; D020558:GTP Phosphohydrolases / Q000378:metabolism*; D015972:Gene Expression Regulation, Neoplastic / Q000502:physiology*; D006801:Humans; D008565:Membrane Proteins / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis; D026723:Polyadenylation; D016755:Proto-Oncogene Proteins c-jun / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000378:metabolism*; D050436:Regulatory Elements, Transcriptional / Q000502:physiology; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014157:Transcription Factors / Q000378:metabolism*; D059467:Transcriptome; D014162:Transfection; D064726:Triple Negative Breast Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000473:pathology
chemical_list: D008565:Membrane Proteins; D016755:Proto-Oncogene Proteins c-jun; D016601:RNA-Binding Proteins; D014157:Transcription Factors; C465505:pumilio protein, human; D020558:GTP Phosphohydrolases; C579846:NRAS protein, human