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

Joana Carlevaro-Fita; Andrés Lanzós; Lars Feuerbach; Chen Hong; David Mas-Ponte; Jakob Skou Pedersen; PCAWG Drivers and Functional Interpretation Group; Rory Johnson; PCAWG Consortium

doi:10.1038/s42003-019-0741-7

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

Joana Carlevaro-Fita, Andrés Lanzós, Lars Feuerbach, Chen Hong, David Mas-Ponte, Jakob Skou Pedersen, PCAWG Drivers and Functional Interpretation Group, Rory Johnson, PCAWG Consortium

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

151 Citations (Scopus)

Abstract

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.

Original language	English
Article number	56
Journal	Communications Biology
Volume	3
Issue	1
Number of pages	16
DOIs	https://doi.org/10.1038/s42003-019-0741-7
Publication status	Published - 1 Dec 2020

Keywords

ANNOTATION
DATABASE
EVOLUTION
GENES
GENOME BROWSER
LANDSCAPE
MALAT1
PRINCIPLES
REGULATOR
TRANSCRIPTION

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Carlevaro-Fita, J., Lanzós, A., Feuerbach, L., Hong, C., Mas-Ponte, D., Pedersen, J. S., PCAWG Drivers and Functional Interpretation Group, Johnson, R., & PCAWG Consortium (2020). Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis. Communications Biology, 3(1), Article 56. https://doi.org/10.1038/s42003-019-0741-7

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abstract = "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.",

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Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis. / Carlevaro-Fita, Joana; Lanzós, Andrés; Feuerbach, Lars et al.
In: Communications Biology, Vol. 3, No. 1, 56, 01.12.2020.

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

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AU - Carlevaro-Fita, Joana

AU - Lanzós, Andrés

AU - Feuerbach, Lars

AU - Hong, Chen

AU - Mas-Ponte, David

AU - Pedersen, Jakob Skou

AU - PCAWG Drivers and Functional Interpretation Group

AU - Bertl, Johanna

AU - Guo, Qianyun

AU - Hobolth, Asger

AU - Hornshøj, Henrik

AU - Juul, Randi Istrup

AU - Madsen, Tobias

AU - Nielsen, Morten Muhlig

AU - Pedersen, Jakob Skou

AU - Zhang, Yan

AU - Johnson, Rory

AU - PCAWG Consortium

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KW - ANNOTATION

KW - DATABASE

KW - EVOLUTION

KW - GENES

KW - GENOME BROWSER

KW - LANDSCAPE

KW - MALAT1

KW - PRINCIPLES

KW - REGULATOR

KW - TRANSCRIPTION

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SN - 2399-3642

VL - 3

JO - Communications Biology

JF - Communications Biology

IS - 1

M1 - 56

ER -

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

Abstract

Keywords

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