Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme.

Bo Li,Santiago Morell,Stephanie N. Schauer,Geoffrey J. Faulkner,Adam D. Ewing,Daniel J. Gerhardt,Patricia E. Carreira,Michaela Kindlova,Allister C. Fagg,Patricia Gerdes,Sandra R. Richardson,Paul M. Brennan,Kyle R. Upton,Jun Wang,Guibo Li

doi:10.1186/s13100-016-0076-6

Abstract

BackgroundLINE-1 (L1) retrotransposons are a notable endogenous source of mutagenesis in mammals. Notably, cancer cells can support unusual L1 retrotransposition and L1-associated sequence rearrangement mechanisms following DNA damage. Recent reports suggest that L1 is mobile in epithelial tumours and neural cells but, paradoxically, not in brain cancers.ResultsHere, using retrotransposon capture sequencing (RC-seq), we surveyed L1 mutations in 14 tumours classified as glioblastoma multiforme (GBM) or as a lower grade glioma. In four GBM tumours, we characterised one probable endonuclease-independent L1 insertion, two L1-associated rearrangements and one likely Alu-Alu recombination event adjacent to an L1. These mutations included PCR validated intronic events in MeCP2 and EGFR. Despite sequencing L1 integration sites at up to 250× depth by RC-seq, we found no tumour-specific, endonuclease-dependent L1 insertions. Whole genome sequencing analysis of the tumours carrying the MeCP2 and EGFR L1 mutations also revealed no endonuclease-dependent L1 insertions. In a complementary in vitro assay, wild-type and endonuclease mutant L1 reporter constructs each mobilised very inefficiently in four cultured GBM cell lines.ConclusionsThese experiments altogether highlight the consistent absence of canonical L1 retrotransposition in GBM tumours and cultured cell lines, as well as atypical L1-associated sequence rearrangements following DNA damage in vivo.Electronic supplementary materialThe online version of this article (doi:10.1186/s13100-016-0076-6) contains supplementary material, which is available to authorized users.

Highlights

LINE-1 (L1) retrotransposons are a notable endogenous source of mutagenesis in mammals
targetprimed reverse transcription (TPRT)-mediated L1 mobilisation occurs in many cancers [30,31,32,33,34,35,36,37,38] and neural cells [39,40,41,42], several recent studies employing high-throughput sequencing have reported a surprising absence of somatic L1 insertions in brain tumours [6, 30,31,32, 35]
L1 mutations identified in 4 Glioblastoma multiforme (GBM) tumours We applied retrotransposon capture sequencing (RC-seq) to 9 GBM and 5 lower grade glioma sample sets, including tumour and matched adjacent brain or blood (Additional file 2: Figure S1A, Additional file 1: Table S1)

Summary

Introduction

LINE-1 (L1) retrotransposons are a notable endogenous source of mutagenesis in mammals. Recent reports suggest that L1 is mobile in epithelial tumours and neural cells but, paradoxically, not in brain cancers. Once the RNP enters the nucleus, the L1-encoded EN can cleave genomic DNA [15] and, typically, generate a new L1 insertion via targetprimed reverse transcription (TPRT) [19]. TPRT-mediated L1 mobilisation occurs in many cancers [30,31,32,33,34,35,36,37,38] and neural cells [39,40,41,42], several recent studies employing high-throughput sequencing have reported a surprising absence of somatic L1 insertions in brain tumours [6, 30,31,32, 35]

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Results

Conclusion