Transcriptional effects of copy number alterations in a large set of human cancers

Arkajyoti Bhattacharya, Rico D. Bense, Carlos G. Urzúa-Traslaviña, Elisabeth G. E. Vries, Marcel A. T. M. Vugt and Rudolf S. N. Fehrmann ()
Additional contact information
Arkajyoti Bhattacharya: University of Groningen
Rico D. Bense: University of Groningen
Carlos G. Urzúa-Traslaviña: University of Groningen
Elisabeth G. E. Vries: University of Groningen
Marcel A. T. M. Vugt: University of Groningen
Rudolf S. N. Fehrmann: University of Groningen

Nature Communications, 2020, vol. 11, issue 1, 1-12

Abstract: Abstract Copy number alterations (CNAs) can promote tumor progression by altering gene expression levels. Due to transcriptional adaptive mechanisms, however, CNAs do not always translate proportionally into altered expression levels. By reanalyzing >34,000 gene expression profiles, we reveal the degree of transcriptional adaptation to CNAs in a genome-wide fashion, which strongly associate with distinct biological processes. We then develop a platform-independent method—transcriptional adaptation to CNA profiling (TACNA profiling)—that extracts the transcriptional effects of CNAs from gene expression profiles without requiring paired CNA profiles. By applying TACNA profiling to >28,000 patient-derived tumor samples we define the landscape of transcriptional effects of CNAs. The utility of this landscape is demonstrated by the identification of four genes that are predicted to be involved in tumor immune evasion when transcriptionally affected by CNAs. In conclusion, we provide a novel tool to gain insight into how CNAs drive tumor behavior via altered expression levels.

Date: 2020
References: Add references at CitEc
Citations: View citations in EconPapers (6)

Downloads: (external link)
https://www.nature.com/articles/s41467-020-14605-5 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-14605-5

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-020-14605-5

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().