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

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.

L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis

“…Repeated attempts to robustly measure KHDRBS2 expression at an exon-exon junction downstream from the L1 insertion were unsuccessful, and the gene was not detected by a previously published genome-wide survey of promoter usage (Hashimoto et al 2015). Thus, consistent with previous reports, we find that a tumor-specific intronic L1 insertion can coincide with down-regulation of host gene expression Shukla et al 2013;Helman et al 2014;Tubio et al 2014;Carreira et al 2016), but the mechanism for this potential dysregulation remains unresolved.…”

“…Although these studies have elucidated driver L1 mutations exonic to APC and PTEN, most of the cataloged tumor-specific L1 insertions represent likely passenger events (Helman et al 2014;Scott et al 2016). Evidence for L1 mobilization in cancers is largely restricted to tumors of epithelial origin, with somatic L1 insertions conspicuously infrequent in brain and blood cancers (Iskow et al 2010;Lee et al 2012;Achanta et al 2016;Carreira et al 2016). Thus, some cancer cell types may be intrinsically susceptible to L1 retrotransposition (Carreira et al 2014;Scott and Devine 2017).…”

Selective silencing of euchromatic L1s revealed by genome-wide screens for L1 regulators

“…1f and 4d,e). The sequences of PCR primers, including the one targeting the 5′UTR of L1Hs 35,36,37 , are summarized in Table S4.…”

Cellular labeling of endogenous virus replication (CLEVR) reveals de novo insertions of the gypsy endogenous retrovirus in cell culture and in both neurons and glial cells of aging fruit flies

“…The discovery that LINE like RTEs are able to replicate during neural development in rodents [5][6][7]14], as well as somatic cells during Drosophila embryonic development [15], however, provided the impetus to more closely examine TE replication in soma. It is increasingly clear that TEs also can be actively expressed and even mobile in somatic tissues such as brain during normal development [5-7, 9-14, 22-25], during aging in a variety of cell types and species [4,[26][27][28][29][30][31], in a variety of neurodegenerative diseases and in animal models of human neurodegeneration [32][33][34][35][36][37][38][39][40][41], and in cancer [17,[42][43][44][45][46][47][48][49][50][51].…”