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Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis

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Abstract
Joana Carlevaro-Fita, Andres Lanzos et al. present the Cancer LncRNA Census (CLC), a manually curated dataset of 122 long noncoding RNAs (lncRNAs) with experimentally-validated functions in cancer based on data from the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. CLC lncRNAs have unique gene features, and a number display evidence for cancer-driving functions that are conserved from humans to mice. Long non-coding RNAs (lncRNAs) are a growing focus of cancer genomics studies, creating the need for a resource of lncRNAs with validated cancer roles. Furthermore, it remains debated whether mutated lncRNAs can drive tumorigenesis, and whether such functions could be conserved during evolution. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we introduce the Cancer LncRNA Census (CLC), a compilation of 122 GENCODE lncRNAs with causal roles in cancer phenotypes. In contrast to existing databases, CLC requires strong functional or genetic evidence. CLC genes are enriched amongst driver genes predicted from somatic mutations, and display characteristic genomic features. Strikingly, CLC genes are enriched for driver mutations from unbiased, genome-wide transposon-mutagenesis screens in mice. We identified 10 tumour-causing mutations in orthologues of 8 lncRNAs, including LINC-PINT and NEAT1, but not MALAT1. Thus CLC represents a dataset of high-confidence cancer lncRNAs. Mutagenesis maps are a novel means for identifying deeply-conserved roles of lncRNAs in tumorigenesis.
Keywords
GENOME BROWSER, EVOLUTION, DATABASE, ANNOTATION, MALAT1, GENES, TRANSCRIPTION, PRINCIPLES, LANDSCAPE, REGULATOR

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MLA
Carlevaro-Fita, Joana, et al. “Cancer LncRNA Census Reveals Evidence for Deep Functional Conservation of Long Noncoding RNAs in Tumorigenesis.” COMMUNICATIONS BIOLOGY, vol. 3, no. 1, 2020.
APA
Carlevaro-Fita, J., Lanzos, A., Feuerbach, L., Hong, C., Mas-Ponte, D., Pedersen, J. S., … von Mering, C. (2020). Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis. COMMUNICATIONS BIOLOGY, 3(1).
Chicago author-date
Carlevaro-Fita, Joana, Andres Lanzos, Lars Feuerbach, Chen Hong, David Mas-Ponte, Jakob Skou Pedersen, Rory Johnson, et al. 2020. “Cancer LncRNA Census Reveals Evidence for Deep Functional Conservation of Long Noncoding RNAs in Tumorigenesis.” COMMUNICATIONS BIOLOGY 3 (1).
Chicago author-date (all authors)
Carlevaro-Fita, Joana, Andres Lanzos, Lars Feuerbach, Chen Hong, David Mas-Ponte, Jakob Skou Pedersen, Rory Johnson, Federico Abascal, Samirkumar B. Amin, Gary D. Bader, Jonathan Barenboim, Rameen Beroukhim, Johanna Bertl, Keith A. Boroevich, Soren Brunak, Peter J. Campbell, Joana Carlevaro-Fita, Dimple Chakravarty, Calvin Wing Yiu Chan, Ken Chen, Jung Kyoon Choi, Jordi Deu-Pons, Priyanka Dhingra, Klev Diamanti, Lars Feuerbach, J. Lynn Fink, Nuno A. Fonseca, Joan Frigola, Carlo Gambacorti-Passerini, Dale W. Garsed, Mark Gerstein, Gad Getz, Abel Gonzalez-Perez, Qianyun Guo, Ivo G. Gut, David Haan, Mark P. Hamilton, Nicholas J. Haradhvala, Arif O. Harmanci, Mohamed Helmy, Carl Herrmann, Julian M. Hess, Asger Hobolth, Ermin Hodzic, Chen Hong, Henrik Hornshoj, Keren Isaev, Jose M. G. Izarzugaza, Todd A. Johnson, Malene Juul, Randi Istrup Juul, Andre Kahles, Abdullah Kahraman, Manolis Kellis, Ekta Khurana, Jaegil Kim, Jong K. Kim, Youngwook Kim, Jan Komorowski, Jan O. Korbel, Sushant Kumar, Andres Lanzos, Erik Larsson, Michael S. Lawrence, Donghoon Lee, Kjong-Van Lehmann, Shantao Li, Xiaotong Li, Ziao Lin, Eric Minwei Liu, Lucas Lochovsky, Shaoke Lou, Tobias Madsen, Kathleen Marchal, Inigo Martincorena, Alexander Martinez-Fundichely, Yosef E. Maruvka, Patrick D. McGillivray, William Meyerson, Ferran Muinos, Loris Mularoni, Hidewaki Nakagawa, Morten Muhlig Nielsen, Marta Paczkowska, Keunchil Park, Kiejung Park, Jakob Skou Pedersen, Oriol Pich, Tirso Pons, Sergio Pulido-Tamayo, Benjamin J. Raphael, Juri Reimand, Iker Reyes-Salazar, Matthew A. Reyna, Esther Rheinbay, Mark A. Rubin, Carlota Rubio-Perez, Radhakrishnan Sabarinathan, S. Cenk Sahinalp, Gordon Saksena, Leonidas Salichos, Chris Sander, Steven E. Schumacher, Mark Shackleton, Ofer Shapira, Ciyue Shen, Raunak Shrestha, Shimin Shuai, Nikos Sidiropoulos, Lina Sieverling, Nasa Sinnott-Armstrong, Lincoln D. Stein, Joshua M. Stuart, David Tamborero, Grace Tiao, Tatsuhiko Tsunoda, Husen M. Umer, Liis Uuskula-Reimand, Alfonso Valencia, Miguel Vazquez, Lieven P. C. Verbeke, Claes Wadelius, Lina Wadi, Jiayin Wang, Jonathan Warrell, Sebastian M. Waszak, Joachim Weischenfeldt, David A. Wheeler, Guanming Wu, Jun Yu, Jing Zhang, Xuanping Zhang, Yan Zhang, Zhongming Zhao, Lihua Zou, and Christian von Mering. 2020. “Cancer LncRNA Census Reveals Evidence for Deep Functional Conservation of Long Noncoding RNAs in Tumorigenesis.” COMMUNICATIONS BIOLOGY 3 (1).
Vancouver
1.
Carlevaro-Fita J, Lanzos A, Feuerbach L, Hong C, Mas-Ponte D, Pedersen JS, et al. Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis. COMMUNICATIONS BIOLOGY. 2020;3(1).
IEEE
[1]
J. Carlevaro-Fita et al., “Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis,” COMMUNICATIONS BIOLOGY, vol. 3, no. 1, 2020.
@article{8658728,
  abstract     = {Joana Carlevaro-Fita, Andres Lanzos et al. present the Cancer LncRNA Census (CLC), a manually curated dataset of 122 long noncoding RNAs (lncRNAs) with experimentally-validated functions in cancer based on data from the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. CLC lncRNAs have unique gene features, and a number display evidence for cancer-driving functions that are conserved from humans to mice.

Long non-coding RNAs (lncRNAs) are a growing focus of cancer genomics studies, creating the need for a resource of lncRNAs with validated cancer roles. Furthermore, it remains debated whether mutated lncRNAs can drive tumorigenesis, and whether such functions could be conserved during evolution. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we introduce the Cancer LncRNA Census (CLC), a compilation of 122 GENCODE lncRNAs with causal roles in cancer phenotypes. In contrast to existing databases, CLC requires strong functional or genetic evidence. CLC genes are enriched amongst driver genes predicted from somatic mutations, and display characteristic genomic features. Strikingly, CLC genes are enriched for driver mutations from unbiased, genome-wide transposon-mutagenesis screens in mice. We identified 10 tumour-causing mutations in orthologues of 8 lncRNAs, including LINC-PINT and NEAT1, but not MALAT1. Thus CLC represents a dataset of high-confidence cancer lncRNAs. Mutagenesis maps are a novel means for identifying deeply-conserved roles of lncRNAs in tumorigenesis.},
  articleno    = {56},
  author       = {Carlevaro-Fita, Joana and Lanzos, Andres and Feuerbach, Lars and Hong, Chen and Mas-Ponte, David and Pedersen, Jakob Skou and Johnson, Rory and Abascal, Federico and Amin, Samirkumar B. and Bader, Gary D. and Barenboim, Jonathan and Beroukhim, Rameen and Bertl, Johanna and Boroevich, Keith A. and Brunak, Soren and Campbell, Peter J. and Carlevaro-Fita, Joana and Chakravarty, Dimple and Chan, Calvin Wing Yiu and Chen, Ken and Choi, Jung Kyoon and Deu-Pons, Jordi and Dhingra, Priyanka and Diamanti, Klev and Feuerbach, Lars and Fink, J. Lynn and Fonseca, Nuno A. and Frigola, Joan and Gambacorti-Passerini, Carlo and Garsed, Dale W. and Gerstein, Mark and Getz, Gad and Gonzalez-Perez, Abel and Guo, Qianyun and Gut, Ivo G. and Haan, David and Hamilton, Mark P. and Haradhvala, Nicholas J. and Harmanci, Arif O. and Helmy, Mohamed and Herrmann, Carl and Hess, Julian M. and Hobolth, Asger and Hodzic, Ermin and Hong, Chen and Hornshoj, Henrik and Isaev, Keren and Izarzugaza, Jose M. G. and Johnson, Todd A. and Juul, Malene and Juul, Randi Istrup and Kahles, Andre and Kahraman, Abdullah and Kellis, Manolis and Khurana, Ekta and Kim, Jaegil and Kim, Jong K. and Kim, Youngwook and Komorowski, Jan and Korbel, Jan O. and Kumar, Sushant and Lanzos, Andres and Larsson, Erik and Lawrence, Michael S. and Lee, Donghoon and Lehmann, Kjong-Van and Li, Shantao and Li, Xiaotong and Lin, Ziao and Liu, Eric Minwei and Lochovsky, Lucas and Lou, Shaoke and Madsen, Tobias and Marchal, Kathleen and Martincorena, Inigo and Martinez-Fundichely, Alexander and Maruvka, Yosef E. and McGillivray, Patrick D. and Meyerson, William and Muinos, Ferran and Mularoni, Loris and Nakagawa, Hidewaki and Nielsen, Morten Muhlig and Paczkowska, Marta and Park, Keunchil and Park, Kiejung and Pedersen, Jakob Skou and Pich, Oriol and Pons, Tirso and Pulido-Tamayo, Sergio and Raphael, Benjamin J. and Reimand, Juri and Reyes-Salazar, Iker and Reyna, Matthew A. and Rheinbay, Esther and Rubin, Mark A. and Rubio-Perez, Carlota and Sabarinathan, Radhakrishnan and Sahinalp, S. Cenk and Saksena, Gordon and Salichos, Leonidas and Sander, Chris and Schumacher, Steven E. and Shackleton, Mark and Shapira, Ofer and Shen, Ciyue and Shrestha, Raunak and Shuai, Shimin and Sidiropoulos, Nikos and Sieverling, Lina and Sinnott-Armstrong, Nasa and Stein, Lincoln D. and Stuart, Joshua M. and Tamborero, David and Tiao, Grace and Tsunoda, Tatsuhiko and Umer, Husen M. and Uuskula-Reimand, Liis and Valencia, Alfonso and Vazquez, Miguel and Verbeke, Lieven P. C. and Wadelius, Claes and Wadi, Lina and Wang, Jiayin and Warrell, Jonathan and Waszak, Sebastian M. and Weischenfeldt, Joachim and Wheeler, David A. and Wu, Guanming and Yu, Jun and Zhang, Jing and Zhang, Xuanping and Zhang, Yan and Zhao, Zhongming and Zou, Lihua and von Mering, Christian},
  issn         = {2399-3642},
  journal      = {COMMUNICATIONS BIOLOGY},
  keywords     = {GENOME BROWSER,EVOLUTION,DATABASE,ANNOTATION,MALAT1,GENES,TRANSCRIPTION,PRINCIPLES,LANDSCAPE,REGULATOR},
  language     = {eng},
  number       = {1},
  pages        = {16},
  title        = {Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis},
  url          = {http://dx.doi.org/10.1038/s42003-019-0741-7},
  volume       = {3},
  year         = {2020},
}

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