Pan-cancer analysis of whole genomes reveals driver rearrangements promoted by LINE-1 retrotransposition in human tumours

Abstract

About half of all cancers have somatic integrations of retrotransposons. To characterize their role in oncogenesis, we analyzed the patterns and mechanisms of somatic retrotransposition in 2,954 cancer genomes from 37 histological cancer subtypes. We identified 19,166 somatically acquired retrotransposition events, affecting 35% of samples, and spanning a range of event types. L1 insertions emerged as the first most frequent type of somatic structural variation in esophageal adenocarcinoma, and the second most frequent in head-and-neck and colorectal cancers. Aberrant L1 integrations can delete megabase-scale regions of a chromosome, sometimes removing tumour suppressor genes, as well as inducing complex translocations and large-scale duplications. Somatic retrotranspositions can also initiate breakage-fusion-bridge cycles, leading to high-level amplification of oncogenes. These observations illuminate a relevant role of L1 retrotransposition in remodeling the cancer genome, with potential implications in the development of human tumours.Long interspersed nuclear element (LINE)-1 (L1) retrotransposons are widespread repetitive elements in the human genome, representing 17% of the entire DNA content 1,2 . Using a combination of cellular enzymes and self-encoded proteins with endonuclease and reverse transcriptase activity, L1 elements copy and insert themselves at new genomic sites, a process called retrotransposition. Most of the ~500,000 L1 copies in the human reference genome are truncated, inactive elements not able to retrotranspose. A small subset of them, maybe 100-150 L1 loci, remain active in the average human genome, acting as source elements, of which a small number are highly active copies termed hot-L1s 3-5 . These L1 source elements are usually transcriptionally repressed, but epigenetic changes occurring in tumours may promote their expression and allow them to retrotranspose 6,7 . Somatic L1 retrotransposition most often introduces a new copy of the 3' end of the L1 sequence, and can also mobilize unique DNA sequences located immediately downstream of the source element, a process called 3' transduction 7-9 . L1 retrotransposons can also promote the somatic trans-mobilization of Alu, SVA and processed pseudogenes, which are copies of messenger RNAs that have been reverse transcribed into DNA and inserted into the genome using the machinery of active L1 elements 10-12 .6 Approximately 50% of human tumours have somatic retrotransposition of L1 elements 7,13-15 .Previous analyses indicate that although a fraction of somatically acquired L1 insertions in cancer may influence gene function, the majority of retrotransposon integrations in a single tumour represent passenger mutations with little or no effect on cancer development 7,13 .Nonetheless, L1 insertions are capable of promoting other types of genomic structural alterations in the germline and somatically, apart from canonical L1 insertion events [16][17][18] , which remain largely unexplored in human cancer 19,20 .To further understand the roles...

Spontaneous retrotranspositions in normal tissues are rare and associated with cell-type-specific differentiation

“…Across all samples we identified 528 RT events. Consistent with previous studies in tumors [7][8][9] , most of the RTs were L1 insertions (77.5%), with Alu as the second most frequent type (14.2%) ( Fig. 1a, Fig.…”

“…On average, 30.3±8.4x depth of single cells and clones, and 29.4±7.2x depth of bulk DNA were obtained after alignment, covering on average 87.3±9.2% and 91.9±0.3% of the genome of single cells/clones, and bulk DNA separately (Table S2). Somatic RTs were then identified comparing the alignment of single cells and clones to their corresponding bulk DNAs using TraFiC 8,9 . We validated our variant calling by PCR analysis of 10 randomly chosen RTs (Supplementary Information; Table S3).…”

GRIDSS, PURPLE, LINX: Unscrambling the tumor genome via integrated analysis of structural variation and copy number

“…First, we annotate individual breakends with several basic geometric and genomic properties which are important to the clustering and chaining algorithm including whether each breakend is part of a foldback inversion, flanks a region of loss of heterozygosity, or is in a well known fragile site region [19]. LINX also uses a combination of previously known line element source information [21] and identification of both the local breakpoint structure and poly-A sequences to identify suspected mobile LINE source elements Second, LINX performs a clustering routine. The fundamental principle for clustering in LINX is to join breakpoints where it is highly unlikely that they could have occurred independently.…”

Evidence that APP gene copy number changes reflect recombinant vector contamination

“…Considering that far less than one somatic retrogene insertion per sample would be expected for human cells, even for human cancers with a high rate of somatic LINE1 retrotransposition (e.g., lung and colorectal cancer) [9][10][11] , this result strongly suggests that cDNA-supporting reads originated from genome-wide mRNA contamination rather than from true somatic retrogene insertions. We also found some cDNA-supporting reads, including APP cDNA-supporting reads, originating from mouse mRNA, additionally confirming mRNA contamination of the data ( Fig.…”