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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 ; Hong, Chen ; Mas-Ponte, David ; Pedersen, Jakob Skou ; Johnson, Rory ; Abascal, Federico and von Mering, Christian (2020) In Communications Biology 3.
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... (More)

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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LU ; LU orcid and LU orcid
author collaboration
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Animals, Biomarkers, Tumor, CRISPR-Cas Systems, Cell Transformation, Neoplastic/genetics, Databases, Genetic, Disease Susceptibility, Evolution, Molecular, Genome, Human, Genomics/methods, Humans, Neoplasms/genetics, Polymorphism, Single Nucleotide, RNA, Long Noncoding
in
Communications Biology
volume
3
article number
56
pages
16 pages
publisher
Nature Publishing Group
external identifiers
  • scopus:85079071080
  • pmid:32024996
ISSN
2399-3642
DOI
10.1038/s42003-019-0741-7
language
English
LU publication?
yes
id
9994cf41-e86b-40f1-860c-5b5fcabd1522
date added to LUP
2023-01-05 14:54:38
date last changed
2024-04-18 17:43:11
@article{9994cf41-e86b-40f1-860c-5b5fcabd1522,
  abstract     = {{<p>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.</p>}},
  author       = {{Carlevaro-Fita, Joana and Lanzós, Andrés and Feuerbach, Lars and Hong, Chen and Mas-Ponte, David and Pedersen, Jakob Skou and Johnson, Rory and Abascal, Federico and von Mering, Christian}},
  issn         = {{2399-3642}},
  keywords     = {{Animals; Biomarkers, Tumor; CRISPR-Cas Systems; Cell Transformation, Neoplastic/genetics; Databases, Genetic; Disease Susceptibility; Evolution, Molecular; Genome, Human; Genomics/methods; Humans; Neoplasms/genetics; Polymorphism, Single Nucleotide; RNA, Long Noncoding}},
  language     = {{eng}},
  month        = {{02}},
  publisher    = {{Nature Publishing Group}},
  series       = {{Communications Biology}},
  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}},
  doi          = {{10.1038/s42003-019-0741-7}},
  volume       = {{3}},
  year         = {{2020}},
}