Landscape of somatic retrotransposition in human cancers pdf

We applied Tea to whole-genome sequencing data from tumor and matched normal blood samples from a total of 43 colorectal, prostate, ovarian, multiple myeloma, and glioblastoma cancer patients table S1. All of the somatic L1 and Alu insertions were observed in the cancers of epithelial cell origin colorectal, prostate, and ovarian , with colorectal tumors showing the highest frequency of somatic L1 insertions, but not in the blood or brain cancers.

Some of the TE insertions detected by our method may be generated by mechanisms other than classical retrotransposition. S1 and tables S3 and S4. Given the small insertion size [ base pairs bp ] and 2-bp microhomology at both breakpoint junctions, the ERV1 insertion was likely generated via the microhomology-mediated break-induced repair mechanism A Frequency of high-confidence somatic L1 insertions varies across 5 colorectal, 7 prostate, 8 ovarian, 7 multiple myeloma, and 16 glioblastoma tumors.

Three epithelial cancers colorectal, prostate, and ovarian show frequent somatic L1 insertions, whereas no insertions are observed in the blood and brain cancers. One colorectal tumor CR contains L1 insertions, increasing the average somatic event frequency for colorectal tumors from 9 to 28 when this sample is included. The mutation frequency of each gene was adjusted for its total exon size.

Inset The top 15 genes with nonsilent mutations. C The transcript levels of 45 genes with somatic TE insertions in colorectal tumors were compared with those from 28 normal colorectal tissues, and the expression fold changes are shown. KCNIP1 appears twice because of two somatic insertions in two different samples. In contrast, the other colorectal tumors 13 were microsatellite-stable, had a low simple mutation rate 45 to 60 mutations , lacked detectable aberrations among the DNA mismatch repair genes tested, and belonged to CIMP-low or non-CIMP methylation subgroups table S5.

Taken together, this suggests the presence of tumor subtypes with respect to TE activity. A representative set of predicted insertions was selected for PCR-based validation supplementary text S1. Six junctions and two entire L1 insertions were further examined by using Sanger sequencing, confirming the presence of the L1 sequences, insertion breakpoints, target-site duplication TSD sequences, and poly-A tails table S4.

The sensitivity of detection depends on the purity of the tumor samples and clonality of the events. Events present at lower frequency, such as insertions accumulated at later stages of tumorigenesis, were likely missed.

Our approach cannot detect insertions landing in highly repetitive regions, so the true number of events is likely to be higher. We examined nucleotide mutation frequencies single nucleotide or small indel across additional colorectal tumors and found that the TE target genes are significantly enriched for frequently mutated genes Fig.

Because recurrently mutated genes are likely to be important drivers of tumorigenesis, our results suggest potential contribution of TE insertions to cancer development 19 , Although none of the somatic events hit coding regions, insertions of TE sequence in untranslated regions UTRs or intronic regions can disrupt gene expression Indeed, over a quarter of the identified disease-causing TE insertions are located in introns or UTRs 9.

We thus compared the mRNA levels of the 45 genes hit by somatic TEs in colorectal cancer between the affected tumor and normal samples. The impact of L1 insertions may depend on the orientation of the L1 insertion relative to the target gene, with antisense insertions being less disruptive Because the majority of such polymorphic events are passed down through gametes or generated during early embryonic development, we refer to them as germline insertions.

The parts of the L1 sequence found within the identified somatic and germline insertions are illustrated as a coverage plot. B A positive distance between the clipping positions of clipped reads with negative-and positive-strand mapping Fig.

The insertions belonging to the minor TSD peak 0 to 2 bp did not show a significant sequence motif. The distribution of TSD lengths showed a peak around 15 bp, characteristic of endonuclease-mediated retrotransposition, for both somatic and germline insertions Fig.

However, somatic insertions exhibited an additional peak at 0 bp, indicating that some may have been generated by an alternative mechanism such as the one mediated by DNA breaks that does not result in TSDs 29, Consistent with this, somatic L1 insertions with TSDs show sequence motifs at the breakpoints that correspond to the canonical L1-endonuclease recognition sequence 31 , whereas the insertions lacking TSDs do not show such a clear recognition sequence Fig. Somatic and germline L1 insertion sites differ in their genomic distribution and epigenetic characteristics.

S7 to S9. The L1 insertion bias toward common hypomethylation domains suggests that loss of DNA methylation promotes integration of L1 instances. A Somatic L1 insertions are biased toward hypomethylated regions in cancer cells. Colon cancer regions were assessed in independent samples.

B A model of TE insertion preferences and subsequent selection process that bias genomic distribution of TE insertions is illustrated. Somatic insertions are strongly biased toward cancer-specific DNA hypomethylation regions red box and encounter selection that depletes them from transcriptionally active genes unless such insertions promote tumorigenesis.

By contrast, germline insertions are biased toward germline-specific DNA hypomethylation domains blue box and are depleted from all genes. Our analysis suggests that some TE insertions provide a selective advantage during tumorigenesis, rather than being merely passenger events that precede clonal expansion.

We observed differential deregulation of TE activity across and within different cancer types. We also found that such insertions preferentially occur at genes commonly mutated in cancer, including tumor suppressors, substantially disrupting their expression. Although a more extensive panel of matched genomic and epigenetic data is needed to investigate the functional impact of retrotransposition events and the pathways involved, our analysis reveals the extent of TE insertions in human tumors and lays the foundation for determining the role of these events in human neoplasia.

We thank A. Langdon and U. Samarakoon for technical assistance and T. The sequencing data are available at dbGaP www. Supplementary Materials. Supplementary Text. Tables S1 to S8. National Center for Biotechnology Information , U. Author manuscript; available in PMC May Lohr , 4, 5 Christopher C.

Harris , 6 Li Ding , 6 Richard K. Wilson , 6 David A. Wheeler , 7 Richard A. Lovelace J. Luquette, III.

Jens G. Christopher C. Richard K. David A. Richard A. Peter V. Peter J. Skip to main content. Main Menu Utility Menu Search. Landscape of somatic retrotransposition in human cancers.

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