Intronic polyadenylation(IPA)is an RNA 3'end processing event which has been reported to play important roles in cancer development.However,the comprehensive landscape of IPA events across various cancer types is ...Intronic polyadenylation(IPA)is an RNA 3'end processing event which has been reported to play important roles in cancer development.However,the comprehensive landscape of IPA events across various cancer types is lacking.Here,we apply IPAFinder to identify and quantify IPA events in 10,383 samples covering all 33 cancer types from The Cancer Genome Atlas(TCGA)project.We identify a total of 21,835 IPA events,almost half of which are ubiquitously expressed.We identify 2761 unique dynamically changed IPA events across cancer types.Furthermore,we observe 8855 non-redundant clinically relevant IPA events,which could potentially be used as prognostic indicators.Our analysis also reveals that dynamic IPA usage within cancer signaling pathways may affect drug response.Finally,we develop a user-friendly data portal,IPACancer Atlas(http://www.tingni-lab.com/Pancan_IPA),to search and explore IPAs in cancer.展开更多
Objective:To review alternative polyadenylation(APA)as a mechanism of gene regulation and consider potential roles for APA in prostate cancer(PCa)biology and treatment.Methods:An extensive review of mRNA polyadenylati...Objective:To review alternative polyadenylation(APA)as a mechanism of gene regulation and consider potential roles for APA in prostate cancer(PCa)biology and treatment.Methods:An extensive review of mRNA polyadenylation,APA,and PCa literature was performed.This review article introduces APA and its association with human disease,outlines the mechanisms and components of APA,reviews APA in cancer biology,and considers whether APA may contribute to PCa progression and/or produce novel biomarkers and therapeutic targets for PCa.Results:Eukaryotic mRNA 30-end cleavage and polyadenylation play a critical role in gene expression.Most human genes encode more than one polyadenylation signal,and produce more than one transcript isoform,through APA.Polyadenylation can occur throughout the gene body to generate transcripts with differing 30-termini and coding sequence.Differences in 30-untranslated regions length can modify post-transcriptional gene regulation by microRNAs and RNA binding proteins,and alter mRNA stability,translation efficiency,and subcellular localization.Distinctive APA patterns are associated with human diseases,tissue origins,and changes in cellular proliferation rate and differentiation state.APA events may therefore generate unique mRNA biomarkers or therapeutic targets in certain cancer types or phenotypic states.Conclusions:The full extent of cancer-associated and tissue-specific APA events have yet to be defined,and the mechanisms and functional consequences of APA in cancer remain incompletely understood.There is evidence that APA is active in PCa,and that it may be an untapped resource for PCa biomarkers or therapeutic targets.展开更多
基金This work was financially supported by the National Natural Science Foundation of China(92249302,32370592)the National Key Research and Development Program of China(2023YFC3603300,2021YFA0909300).
文摘Intronic polyadenylation(IPA)is an RNA 3'end processing event which has been reported to play important roles in cancer development.However,the comprehensive landscape of IPA events across various cancer types is lacking.Here,we apply IPAFinder to identify and quantify IPA events in 10,383 samples covering all 33 cancer types from The Cancer Genome Atlas(TCGA)project.We identify a total of 21,835 IPA events,almost half of which are ubiquitously expressed.We identify 2761 unique dynamically changed IPA events across cancer types.Furthermore,we observe 8855 non-redundant clinically relevant IPA events,which could potentially be used as prognostic indicators.Our analysis also reveals that dynamic IPA usage within cancer signaling pathways may affect drug response.Finally,we develop a user-friendly data portal,IPACancer Atlas(http://www.tingni-lab.com/Pancan_IPA),to search and explore IPAs in cancer.
基金The authors would like to acknowledge funding from the Department of Defense Prostate Cancer Research Program W81XWH-17-1-0581 and W81XWH-19-1-0450Shawn EL,the National Cancer Institute P30CA006973William G.Nelson,and The Patrick C.Walsh Cancer Research Fund to Shawn EL,for support of this work.
文摘Objective:To review alternative polyadenylation(APA)as a mechanism of gene regulation and consider potential roles for APA in prostate cancer(PCa)biology and treatment.Methods:An extensive review of mRNA polyadenylation,APA,and PCa literature was performed.This review article introduces APA and its association with human disease,outlines the mechanisms and components of APA,reviews APA in cancer biology,and considers whether APA may contribute to PCa progression and/or produce novel biomarkers and therapeutic targets for PCa.Results:Eukaryotic mRNA 30-end cleavage and polyadenylation play a critical role in gene expression.Most human genes encode more than one polyadenylation signal,and produce more than one transcript isoform,through APA.Polyadenylation can occur throughout the gene body to generate transcripts with differing 30-termini and coding sequence.Differences in 30-untranslated regions length can modify post-transcriptional gene regulation by microRNAs and RNA binding proteins,and alter mRNA stability,translation efficiency,and subcellular localization.Distinctive APA patterns are associated with human diseases,tissue origins,and changes in cellular proliferation rate and differentiation state.APA events may therefore generate unique mRNA biomarkers or therapeutic targets in certain cancer types or phenotypic states.Conclusions:The full extent of cancer-associated and tissue-specific APA events have yet to be defined,and the mechanisms and functional consequences of APA in cancer remain incompletely understood.There is evidence that APA is active in PCa,and that it may be an untapped resource for PCa biomarkers or therapeutic targets.
