Targeted Genomic Screen Reveals Focal Long Non-Coding RNA Copy Number Alterations in Cancer Cell Lines

Non-coding RNA
Pieter-Jan VoldersJo Vandesompele

Abstract

The landscape of somatic copy-number alterations (SCNAs) affecting long non-coding RNAs (lncRNAs) in human cancers remains largely unexplored. While the majority of lncRNAs remain to be functionally characterized, several have been implicated in cancer development and metastasis. Considering the plethora of lncRNAs genes that have been currently reported, it is conceivable that many more lncRNAs might function as oncogenes or tumor suppressor genes. We devised a strategy to detect focal lncRNA SCNAs using a custom DNA microarray platform probing 10,519 lncRNA genes. By screening a panel of 80 cancer cell lines, we detected numerous focal aberrations targeting one or multiple lncRNAs without affecting neighboring protein-coding genes. These focal aberrations are highly suggestive for a tumor suppressive or oncogenic role of the targeted lncRNA gene. Although functional validation remains an essential step in the further characterization of the involved candidate cancer lncRNAs, our results provide a direct way of prioritizing candidate lncRNAs that are involved in cancer pathogenesis.

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Citations

May 29, 2020·Cellular and Molecular Life Sciences : CMLS·Minna PiipponenVeli-Matti Kähäri
Dec 18, 2020·Frontiers in Genetics·Marina AznaourovaLeon N Schulte
Dec 22, 2021·DNA and Cell Biology·Hossein Ghahramani AlmanghadimSaman Sargazi

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Datasets Mentioned

BETA
GPL22307
GSE85444

Methods Mentioned

BETA
exome sequencing
feature extraction
PCR

Software Mentioned

qbase
Ensembl
tm
perl script
plyr
stringi
mongo shell scripts
word cloud
Browser Extensible Data ( BED
tidyverse

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Cancer Genomics (Keystone)

Cancer genomics approaches employ high-throughput technologies to identify the complete catalog of somatic alterations that characterize the genome, transcriptome and epigenome of cohorts of tumor samples. Discover the latest research using such technologies in this feed.