Comprehensive characterization of alternative polyadenylation in human cancer

Yu Xiang, Youqiong Ye, Yanyan Lou, Yang Yang, Chunyan Cai, Zhao Zhang, Tingting Mills, Ning Yuan Chen, Yoonjin Kim, Fatma Muge Ozguc, Lixia Diao, Harry Karmouty-Quintana, Yang Xia, Rodney E. Kellems, Zheng Chen, Michael R. Blackburn, Seung Hee Yoo, Ann Bin Shyu, Gordon B. Mills, Leng Han

Research output: Contribution to journalArticle

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Abstract

Background: Alternative polyadenylation (APA) is emerging as a major post-transcriptional mechanism for gene regulation, and dysregulation of APA contributes to several human diseases. However, the functional consequences of APA in human cancer are not fully understood. Particularly, there is no large-scale analysis in cancer cell lines. Methods:Wecharacterized the global APA profiles of 6398 patient samples across 17 cancer types fromThe Cancer Genome Atlas and 739 cancer cell lines from the Cancer Cell Line Encyclopedia.Webuilt a linear regressionmodel to explore the correlation between APA factors and APA events across different cancer types.We used Spearman correlation to assess the effects of APA events on drug sensitivity and theWilcoxon rank-sumtest or Cox proportional hazards model to identify clinically relevant APA events. Results: We revealed a striking global 3'UTR shortening in cancer cell lines compared with tumor samples. Our analysis further suggested PABPN1 as the master regulator in regulating APA profile across different cancer types. Furthermore, we showed that APA events could affect drug sensitivity, especially of drugs targeting chromatin modifiers. Finally, we identified 1971 clinically relevant APA events, as well as alterations of APA in clinically actionable genes, suggesting that analysis of the complexity of APA profiles could have clinical utility. Conclusions: Our study highlights important roles for APA in human cancer, including reshaping cellular pathways and regulating specific gene expression, exemplifying the complex interplay between APA and other biological processes and yielding new insights into the action mechanism of cancer drugs.

Original languageEnglish (US)
Pages (from-to)379-389
Number of pages11
JournalJournal of the National Cancer Institute
Volume110
Issue number4
DOIs
StatePublished - Apr 1 2018

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Polyadenylation
Neoplasms
Cell Line
mRNA Cleavage and Polyadenylation Factors
Pharmaceutical Preparations
Encyclopedias
Biological Phenomena
Atlases
3' Untranslated Regions
Drug Delivery Systems
Systems Analysis
Proportional Hazards Models
Genes
Chromatin

ASJC Scopus subject areas

  • Oncology
  • Cancer Research

Cite this

Comprehensive characterization of alternative polyadenylation in human cancer. / Xiang, Yu; Ye, Youqiong; Lou, Yanyan; Yang, Yang; Cai, Chunyan; Zhang, Zhao; Mills, Tingting; Chen, Ning Yuan; Kim, Yoonjin; Ozguc, Fatma Muge; Diao, Lixia; Karmouty-Quintana, Harry; Xia, Yang; Kellems, Rodney E.; Chen, Zheng; Blackburn, Michael R.; Yoo, Seung Hee; Shyu, Ann Bin; Mills, Gordon B.; Han, Leng.

In: Journal of the National Cancer Institute, Vol. 110, No. 4, 01.04.2018, p. 379-389.

Research output: Contribution to journalArticle

Xiang, Y, Ye, Y, Lou, Y, Yang, Y, Cai, C, Zhang, Z, Mills, T, Chen, NY, Kim, Y, Ozguc, FM, Diao, L, Karmouty-Quintana, H, Xia, Y, Kellems, RE, Chen, Z, Blackburn, MR, Yoo, SH, Shyu, AB, Mills, GB & Han, L 2018, 'Comprehensive characterization of alternative polyadenylation in human cancer', Journal of the National Cancer Institute, vol. 110, no. 4, pp. 379-389. https://doi.org/10.1093/jnci/djx223
Xiang, Yu ; Ye, Youqiong ; Lou, Yanyan ; Yang, Yang ; Cai, Chunyan ; Zhang, Zhao ; Mills, Tingting ; Chen, Ning Yuan ; Kim, Yoonjin ; Ozguc, Fatma Muge ; Diao, Lixia ; Karmouty-Quintana, Harry ; Xia, Yang ; Kellems, Rodney E. ; Chen, Zheng ; Blackburn, Michael R. ; Yoo, Seung Hee ; Shyu, Ann Bin ; Mills, Gordon B. ; Han, Leng. / Comprehensive characterization of alternative polyadenylation in human cancer. In: Journal of the National Cancer Institute. 2018 ; Vol. 110, No. 4. pp. 379-389.
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abstract = "Background: Alternative polyadenylation (APA) is emerging as a major post-transcriptional mechanism for gene regulation, and dysregulation of APA contributes to several human diseases. However, the functional consequences of APA in human cancer are not fully understood. Particularly, there is no large-scale analysis in cancer cell lines. Methods:Wecharacterized the global APA profiles of 6398 patient samples across 17 cancer types fromThe Cancer Genome Atlas and 739 cancer cell lines from the Cancer Cell Line Encyclopedia.Webuilt a linear regressionmodel to explore the correlation between APA factors and APA events across different cancer types.We used Spearman correlation to assess the effects of APA events on drug sensitivity and theWilcoxon rank-sumtest or Cox proportional hazards model to identify clinically relevant APA events. Results: We revealed a striking global 3'UTR shortening in cancer cell lines compared with tumor samples. Our analysis further suggested PABPN1 as the master regulator in regulating APA profile across different cancer types. Furthermore, we showed that APA events could affect drug sensitivity, especially of drugs targeting chromatin modifiers. Finally, we identified 1971 clinically relevant APA events, as well as alterations of APA in clinically actionable genes, suggesting that analysis of the complexity of APA profiles could have clinical utility. Conclusions: Our study highlights important roles for APA in human cancer, including reshaping cellular pathways and regulating specific gene expression, exemplifying the complex interplay between APA and other biological processes and yielding new insights into the action mechanism of cancer drugs.",
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AU - Ye, Youqiong

AU - Lou, Yanyan

AU - Yang, Yang

AU - Cai, Chunyan

AU - Zhang, Zhao

AU - Mills, Tingting

AU - Chen, Ning Yuan

AU - Kim, Yoonjin

AU - Ozguc, Fatma Muge

AU - Diao, Lixia

AU - Karmouty-Quintana, Harry

AU - Xia, Yang

AU - Kellems, Rodney E.

AU - Chen, Zheng

AU - Blackburn, Michael R.

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AU - Shyu, Ann Bin

AU - Mills, Gordon B.

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N2 - Background: Alternative polyadenylation (APA) is emerging as a major post-transcriptional mechanism for gene regulation, and dysregulation of APA contributes to several human diseases. However, the functional consequences of APA in human cancer are not fully understood. Particularly, there is no large-scale analysis in cancer cell lines. Methods:Wecharacterized the global APA profiles of 6398 patient samples across 17 cancer types fromThe Cancer Genome Atlas and 739 cancer cell lines from the Cancer Cell Line Encyclopedia.Webuilt a linear regressionmodel to explore the correlation between APA factors and APA events across different cancer types.We used Spearman correlation to assess the effects of APA events on drug sensitivity and theWilcoxon rank-sumtest or Cox proportional hazards model to identify clinically relevant APA events. Results: We revealed a striking global 3'UTR shortening in cancer cell lines compared with tumor samples. Our analysis further suggested PABPN1 as the master regulator in regulating APA profile across different cancer types. Furthermore, we showed that APA events could affect drug sensitivity, especially of drugs targeting chromatin modifiers. Finally, we identified 1971 clinically relevant APA events, as well as alterations of APA in clinically actionable genes, suggesting that analysis of the complexity of APA profiles could have clinical utility. Conclusions: Our study highlights important roles for APA in human cancer, including reshaping cellular pathways and regulating specific gene expression, exemplifying the complex interplay between APA and other biological processes and yielding new insights into the action mechanism of cancer drugs.

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