Processed pseudogenes acquired somatically during cancer development

Susanna S.l Cooke ,Jack A Taylor,Graham R Bignell,Andrew Menzies,Ultan Mcdermott,Sam M Janes,Michael R Stratton,Helen Davies,Mel Greaves,Sancha Martin,Laura Mudie,Keiran Raine,Jon W Teague,Christodoulos P Pipinikas,Serena Nik-Zainal,Peter J Campbell,P Andrew Futreal,John Marshall,Thomas Santarius,Richard G Grundy,Alex Boussioutas,Adrienne M Flanagan,Manasa Ramakrishna,Sarah O’Meara,Adam Shlien,David Malkin,Sam Behjati,Denis Larsimont,Elli Papaemmanuil,Lucy R Yates ,Adam Butler ,Iñigo Martincorena ,Vítor Hugo Teixeira ,David D.l Bowtell ,Christine C Iacobuzio-Donahue ,José M C Tubío ,Yilong Y Li ,Neil Hayes ,Maryam S Dodoran ,Jorge S Reis‐Filho ,Patrick Tarpey ,Nikhil C Munshi ,Niccolò Bolli

doi:10.1038/ncomms4644

Abstract

Cancer evolves by mutation, with somatic reactivation of retrotransposons being one such mutational process. Germline retrotransposition can cause processed pseudogenes, but whether this occurs somatically has not been evaluated. Here we screen sequencing data from 660 cancer samples for somatically acquired pseudogenes. We find 42 events in 17 samples, especially non-small cell lung cancer (5/27) and colorectal cancer (2/11). Genomic features mirror those of germline LINE element retrotranspositions, with frequent target-site duplications (67%), consensus TTTTAA sites at insertion points, inverted rearrangements (21%), 5′ truncation (74%) and polyA tails (88%). Transcriptional consequences include expression of pseudogenes from UTRs or introns of target genes. In addition, a somatic pseudogene that integrated into the promoter and first exon of the tumour suppressor gene, MGA, abrogated expression from that allele. Thus, formation of processed pseudogenes represents a new class of mutation occurring during cancer development, with potentially diverse functional consequences depending on genomic context.

Highlights

Cancer evolves by mutation, with somatic reactivation of retrotransposons being one such mutational process
Paired-end sequencing reads were aligned to the genome and transcriptome with a view to identifying reads that split exactly across canonical splice sites, were mapped to exons separated by more than the library insert size, or mapped between a pseudogene and its insertion site (Supplementary Fig. 1)
To define a putative pseudogene, we required that at least three exons from a single gene were represented in the tumour DNA, with at least two canonical splice junctions directly observed from either split reads or confirmatory capillary sequencing

Summary

Introduction

With somatic reactivation of retrotransposons being one such mutational process. Results We developed bioinformatic methods to detect somatically acquired processed pseudogenes in massively parallel sequencing data from both targeted exome and genome-wide studies in cancer. We performed PCR on tumour and matched normal DNA for all predicted pseudogenes with mapped insertion sites, and excluded variants with a positive germline PCR band from this analysis (Supplementary Fig. 2).

Results

Conclusion