Widespread and Functional RNA Circularization in Localized Prostate Cancer

被引：350

作者：

Chen, Sujun ^{[1
,2
,3
]}

Huang, Vincent ^{[3
]}

Xu, Xin ^{[2
]}

Livingstone, Julie ^{[3
]}

Soares, Fraser ^{[2
]}

Jeon, Jouhyun ^{[3
]}

Zeng, Yong ^{[2
]}

Hua, Junjie Tony ^{[1
,2
]}

Petricca, Jessica ^{[1
,2
]}

Guo, Haiyang ^{[2
]}

Wang, Miranda ^{[2
]}

Yousif, Fouad ^{[3
]}

Zhang, Yuzhe ^{[2
,4
,5
]}

Donmez, Nilgun ^{[6
]}

Ahmed, Musaddeque ^{[2
]}

Volik, Stas ^{[6
]}

Lapuk, Anna ^{[6
,33
]}

Chua, Melvin L. K. ^{[3
]}

Heisler, Lawrence E. ^{[3
]}

Foucal, Adrien ^{[3
]}

Fox, Natalie S. ^{[1
,3
]}

Fraser, Michael ^{[2
,3
]}

Bhandari, Vinayak ^{[1
,3
]}

Shiah, Yu-Jia ^{[3
]}

Guan, Jiansheng ^{[2
,7
]}

Li, Jixi ^{[8
,9
]}

Orain, Michele ^{[10
]}

Picard, Valerie ^{[10
]}

Hovington, Helene ^{[10
]}

Bergeron, Alain ^{[10
]}

Lacombe, Louis ^{[10
]}

Fradet, Yves ^{[10
]}

Tetu, Bernard ^{[11
]}

Liu, Stanley ^{[1
,11
,12
]}

Feng, Felix ^{[13
,14
,15
,16
]}

Wu, Xue ^{[17
]}

Shao, Yang W. ^{[17
,18
]}

Komor, Malgorzata A. ^{[19
,20
]}

Sahinalp, Cenk ^{[6
]}

Collins, Colin ^{[6
,21
]}

Hoogstrate, Youri ^{[22
]}

de Jong, Mark ^{[23
]}

Fijneman, Remond J. A. ^{[19
]}

Fei, Teng ^{[24
]}

Jenster, Guido ^{[22
]}

van der Kwast, Theodorus ^{[2
,25
]}

Bristow, Robert G. ^{[2
,26
,27
,28
]}

Boutros, Paul C. ^{[1
,3
,25
,29
,30
,31
,32
]}

He, Housheng Hansen ^{[1
,2
]}

机构：

[1] Univ Toronto, Dept Med Biophys, Toronto, ON, Canada

[2] Univ Hlth Network, Princess Margaret Canc Ctr, Toronto, ON, Canada

[3] Ontario Inst Canc Res, Toronto, ON, Canada

[4] Cent China Normal Univ, Coll Life Sci, Wuhan, Hubei, Peoples R China

[5] Dali Univ, Coll Basic Med Sci, Dali, Yunnan, Peoples R China

[6] Vancouver Prostate Ctr, Vancouver, BC, Canada

[7] Xiamen Univ Technol, Coll Elect Engn & Automat, Xiamen, Peoples R China

[8] Fudan Univ, Sch Life Sci, Dept Neurol, State Key Lab Genet Engn, Shanghai, Peoples R China

[9] Fudan Univ, Huashan Hosp, Shanghai, Peoples R China

[10] Univ Laval, CHU Quebec, Res Ctr, Quebec City, PQ, Canada

[11] Sunnybrook Hlth Sci Ctr, Sunnybrook Res Inst, Toronto, ON, Canada

[12] Sunnybrook Odette Canc Ctr, Dept Radiat Oncol, Toronto, ON, Canada

[13] Univ Calif San Francisco, Dept Radiat Oncol, San Francisco, CA 94143 USA

[14] Univ Calif San Francisco, Dept Urol, San Francisco, CA 94143 USA

[15] Univ Calif San Francisco, Dept Med, San Francisco, CA USA

[16] Univ Calif San Francisco, Helen Diller Family Comprehens Canc Ctr, San Francisco, CA 94143 USA

[17] Geneseeq Technol, Translat Med Res Inst, Toronto, ON, Canada

[18] Nanjing Med Univ, Sch Publ Hlth, Nanjing, Jiangsu, Peoples R China

[19] Netherlands Canc Inst, Dept Pathol, Translat Gastrointestinal Oncol, Amsterdam, Netherlands

[20] Vrije Univ Amsterdam, Dept Med Oncol, Med Ctr, Oncoprote Lab, Amsterdam, Netherlands

[21] Univ British Columbia, Dept Urol Sci, Vancouver, BC, Canada

[22] Erasmus MC, Dept Urol, Rotterdam, Netherlands

[23] GenomeScan, Leiden, Netherlands

[24] Northeastern Univ, Coll Life & Hlth Sci, Shenyang, Liaoning, Peoples R China

[25] Univ Toronto, Dept Pharmacol & Toxicol, Toronto, ON, Canada

[26] Univ Manchester, Div Canc Sci, Manchester, Lancs, England

[27] Christie NHS Fdn Trust, Manchester, Lancs, England

[28] Manchester Canc Res Ctr, Manchester, Lancs, England

[29] Univ Calif Los Angeles, Dept Human Genet, Los Angeles, CA USA

[30] Univ Calif Los Angeles, Dept Urol, Los Angeles, CA USA

[31] Univ Calif Los Angeles, Jonsson Comprehens Canc Ctr, Los Angeles, CA 90024 USA

[32] Univ Calif Los Angeles, Inst Precis Hlth, Los Angeles, CA USA

[33] Contextual Genom, Vancouver, BC, Canada

来源：

CELL | 2019年 / 176卷 / 04期

基金：

加拿大创新基金会; 加拿大自然科学与工程研究理事会;

关键词：

R PACKAGE; EXPRESSION; IDENTIFICATION; PROGRESSION; METASTASIS; BIOMARKERS; ALIGNMENT; TARGET;

D O I：

10.1016/j.cell.2019.01.025

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The cancer transcriptome is remarkably complex, including low-abundance transcripts, many not polyadenylated. To fully characterize the transcriptome of localized prostate cancer, we performed ultra deep total RNA-seq on 144 tumors with rich clinical annotation. This revealed a linear transcriptomic subtype associated with the aggressive intraductal carcinoma sub-histology and a fusion profile that differentiates localized from metastatic disease. Analysis of back-splicing events showed widespread RNA circularization, with the average tumor expressing 7,232 circular RNAs (circRNAs). The degree of circRNA production was correlated to disease progression in multiple patient cohorts. Loss-of function screening identified 11.3% of highly abundant circRNAs as essential for cell proliferation; for similar to 90% of these, their parental linear transcripts were not essential. Individual circRNAs can have distinct functions, with circCSNK1G3 promoting cell growth by interacting with miR-181. These data advocate for adoption of ultra-deep RNA-seq without poly-A selection to interrogate both linear and circular transcriptomes.

引用

页码：831 / +

页数：35

共 83 条

[1] Identification of HuR target circular RNAs uncovers suppression of PABPN1 translation by CircPABPN1 [J].

Abdelmohsen, Kotb ;

Panda, Amaresh C. ;

Munk, Rachel ;

Grammatikakis, Ioannis ;

Dudekula, Dawood B. ;

De, Supriyo ;

Kim, Jiyoung ;

Noh, Ji Heon ;

Kim, Kyoung Mi ;

Martindale, Jennifer L. ;

Gorospe, Myriam .

RNA BIOLOGY, 2017, 14 (03) :361-369

[2] Genomic Copy Number Dictates a Gene-Independent Cell Response to CRISPR/Cas9 Targeting [J].

Aguirre, Andrew J. ;

Meyers, Robin M. ;

Weir, Barbara A. ;

Vazquez, Francisca ;

Zhang, Cheng-Zhong ;

Ben-David, Uri ;

Cook, April ;

Ha, Gavin ;

Harrington, William F. ;

Doshi, Mihir B. ;

Kost-Alimova, Maria ;

Gill, Stanley ;

Xu, Han ;

Ali, Levi D. ;

Jiang, Guozhi ;

Pantel, Sasha ;

Lee, Yenarae ;

Goodale, Amy ;

Cherniack, Andrew D. ;

Oh, Coyin ;

Kryukov, Gregory ;

Cowley, Glenn S. ;

Garraway, Levi A. ;

Stegmaier, Kimberly ;

Roberts, Charles W. ;

Golub, Todd R. ;

Meyerson, Matthew ;

Root, David E. ;

Tsherniak, Aviad ;

Hahn, William C. .

CANCER DISCOVERY, 2016, 6 (08) :914-929

[3] The genomic complexity of primary human prostate cancer [J].

Berger, Michael F. ;

Lawrence, Michael S. ;

Demichelis, Francesca ;

Drier, Yotam ;

Cibulskis, Kristian ;

Sivachenko, Andrey Y. ;

Sboner, Andrea ;

Esgueva, Raquel ;

Pflueger, Dorothee ;

Sougnez, Carrie ;

Onofrio, Robert ;

Carter, Scott L. ;

Park, Kyung ;

Habegger, Lukas ;

Ambrogio, Lauren ;

Fennell, Timothy ;

Parkin, Melissa ;

Saksena, Gordon ;

Voet, Douglas ;

Ramos, Alex H. ;

Pugh, Trevor J. ;

Wilkinson, Jane ;

Fisher, Sheila ;

Winckler, Wendy ;

Mahan, Scott ;

Ardlie, Kristin ;

Baldwin, Jennifer ;

Simons, Jonathan W. ;

Kitabayashi, Naoki ;

MacDonald, Theresa Y. ;

Kantoff, Philip W. ;

Chin, Lynda ;

Gabriel, Stacey B. ;

Gerstein, Mark B. ;

Golub, Todd R. ;

Meyerson, Matthew ;

Tewari, Ashutosh ;

Lander, Eric S. ;

Getz, Gad ;

Rubin, Mark A. ;

Garraway, Levi A. .

NATURE, 2011, 470 (7333) :214-220

[4] Molecular landmarks of tumor hypoxia across cancer types [J].

Bhandari, Vinayak ;

Hoey, Christianne ;

Liu, Lydia Y. ;

Lalonde, Emilie ;

Ray, Jessica ;

Livingstone, Julie ;

Lesurf, Robert ;

Shiah, Yu-Jia ;

Vujcic, Tina ;

Huang, Xiaoyong ;

Espiritu, Shadrielle M. G. ;

Heisler, Lawrence E. ;

Yousif, Fouad ;

Huang, Vincent ;

Yamaguchi, Takafumi N. ;

Yao, Cindy Q. ;

Sabelnykova, Veronica Y. ;

Fraser, Michael ;

Chua, Melvin L. K. ;

van der Kwast, Theodorus ;

Liu, Stanley K. ;

Boutros, Paul C. ;

Bristow, Robert G. .

NATURE GENETICS, 2019, 51 (02) :308-+

[5] The Master Neural Transcription Factor BRN2 Is an Androgen Receptor-Suppressed Driver of Neuroendocrine Differentiation in Prostate Cancer [J].

Bishop, Jennifer L. ;

Thaper, Daksh ;

Vahid, Sepideh ;

Davies, Alastair ;

Ketola, Kirsi ;

Kuruma, Hidetoshi ;

Jama, Randy ;

Nip, Ka Mun ;

Angeles, Arkhjamil ;

Johnson, Fraser ;

Wyatt, Alexander W. ;

Fazli, Ladan ;

Gleave, Martin E. ;

Lin, Dong ;

Rubin, Mark A. ;

Collins, Colin C. ;

Wang, Yuzhuo ;

Beltran, Himisha ;

Zoubeidi, Amina .

CANCER DISCOVERY, 2017, 7 (01) :54-71

[6] SPOP Mutation Drives Prostate Tumorigenesis In Vivo through Coordinate Regulation of PI3K/mTOR and AR Signaling [J].

Blattner, Mirjam ;

Liu, Deli ;

Robinson, Brian D. ;

Huang, Dennis ;

Poliakov, Anton ;

Gao, Dong ;

Nataraj, Srilakshmi ;

Deonarine, Lesa D. ;

Augello, Michael A. ;

Sailer, Verena ;

Ponnala, Lalit ;

Ittmann, Michael ;

Chinnaiyan, Arul M. ;

Sboner, Andrea ;

Chen, Yu ;

Rubin, Mark A. ;

Barbieri, Christopher E. .

CANCER CELL, 2017, 31 (03) :436-451

[7]

Borgan O, 2000, Modeling survival data: extending the Cox model

[8] Cribriform and intraductal prostate cancer are associated with increased genomic instability and distinct genomic alterations [J].

Bottcher, Rene ;

Kweldam, Charlotte F. ;

Livingstone, Julie ;

Lalonde, Emilie ;

Yamaguchi, Takafumi N. ;

Huang, Vincent ;

Yousif, Fouad ;

Fraser, Michael ;

Bristow, Robert G. ;

van der Kwast, Theodorus ;

Boutros, Paul C. ;

Jenster, Guido ;

van Leenders, Geert J. L. H. .

BMC CANCER, 2018, 18

[9] The Molecular Taxonomy of Primary Prostate Cancer [J].

Abeshouse, Adam ;

Ahn, Jaeil ;

Akbani, Rehan ;

Ally, Adrian ;

Amin, Samirkumar ;

Andry, Christopher D. ;

Annala, Matti ;

Aprikian, Armen ;

Armenia, Joshua ;

Arora, Arshi ;

Auman, J. Todd ;

Balasundaram, Miruna ;

Balu, Saianand ;

Barbieri, Christopher E. ;

Bauer, Thomas ;

Benz, Christopher C. ;

Bergeron, Alain ;

Beroukhim, Rameen ;

Berrios, Mario ;

Bivol, Adrian ;

Bodenheimer, Tom ;

Boice, Lori ;

Bootwalla, Moiz S. ;

dos Reis, Rodolfo Borges ;

Boutros, Paul C. ;

Bowen, Jay ;

Bowlby, Reanne ;

Boyd, Jeffrey ;

Bradley, Robert K. ;

Breggia, Anne ;

Brimo, Fadi ;

Bristow, Christopher A. ;

Brooks, Denise ;

Broom, Bradley M. ;

Bryce, Alan H. ;

Bubley, Glenn ;

Burks, Eric ;

Butterfield, Yaron S. N. ;

Button, Michael ;

Canes, David ;

Carlotti, Carlos G. ;

Carlsen, Rebecca ;

Carmel, Michel ;

Carroll, Peter R. ;

Carter, Scott L. ;

Cartun, Richard ;

Carver, Brett S. ;

Chan, June M. ;

Chang, Matthew T. ;

Chen, Yu .

CELL, 2015, 163 (04) :1011-1025

[10] The biogenesis and emerging roles of circular RNAs [J].

Chen, Ling-Ling .

NATURE REVIEWS MOLECULAR CELL BIOLOGY, 2016, 17 (04) :205-211

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