Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis
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. Her...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Springer Science and Business Media LLC
2021
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| Online Access: | https://hdl.handle.net/1721.1/129450 |
| _version_ | 1826205722183991296 |
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| author | Carlevaro-Fita, Joana Lanzós, Andrés Feuerbach, Lars Hong, Chen Mas-Ponte, David Pedersen, Jakob Skou Johnson, Rory Kellis, Manolis PCAWG Drivers and Functional Interpretation Group |
| author2 | Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science |
| author_facet | Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science Carlevaro-Fita, Joana Lanzós, Andrés Feuerbach, Lars Hong, Chen Mas-Ponte, David Pedersen, Jakob Skou Johnson, Rory Kellis, Manolis PCAWG Drivers and Functional Interpretation Group |
| author_sort | Carlevaro-Fita, Joana |
| collection | MIT |
| description | 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. |
| first_indexed | 2024-09-23T13:17:34Z |
| format | Article |
| id | mit-1721.1/129450 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T13:17:34Z |
| publishDate | 2021 |
| publisher | Springer Science and Business Media LLC |
| record_format | dspace |
| spelling | mit-1721.1/1294502022-09-28T13:13:35Z Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis Carlevaro-Fita, Joana Lanzós, Andrés Feuerbach, Lars Hong, Chen Mas-Ponte, David Pedersen, Jakob Skou Johnson, Rory Kellis, Manolis PCAWG Drivers and Functional Interpretation Group Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory 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. 2021-01-19T20:25:17Z 2021-01-19T20:25:17Z 2020-02 2018-03 2021-01-06T19:13:48Z Article http://purl.org/eprint/type/JournalArticle 2399-3642 https://hdl.handle.net/1721.1/129450 Carlevaro-Fita, Joana et al. "Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis." Communications Biology 3, 1 (February 2020): 56 © 2020 The Author(s) en http://dx.doi.org/10.1038/s42003-019-0741-7 Communications Biology Creative Commons Attribution 4.0 International license https://creativecommons.org/licenses/by/4.0/ application/pdf Springer Science and Business Media LLC Nature |
| spellingShingle | Carlevaro-Fita, Joana Lanzós, Andrés Feuerbach, Lars Hong, Chen Mas-Ponte, David Pedersen, Jakob Skou Johnson, Rory Kellis, Manolis PCAWG Drivers and Functional Interpretation Group Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis |
| title | Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis |
| title_full | Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis |
| title_fullStr | Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis |
| title_full_unstemmed | Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis |
| title_short | Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis |
| title_sort | cancer lncrna census reveals evidence for deep functional conservation of long noncoding rnas in tumorigenesis |
| url | https://hdl.handle.net/1721.1/129450 |
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