Transposon insertion profiling by sequencing (TIPseq) for mapping LINE-1 insertions in the human genome

Background

Transposable elements make up a significant portion of the human genome. Accurately locating these mobile DNAs is vital to understand their role as a source of structural variation and somatic mutation. To this end, laboratories have developed strategies to selectively amplify or otherwise enrich transposable element insertion sites in genomic DNA.

Results

Here we describe a technique, Transposon Insertion Profiling by sequencing (TIPseq), to map Long INterspersed Element 1 (LINE-1, L1) retrotransposon insertions in the human genome. This method uses vectorette PCR to amplify species-specific L1 (L1PA1) insertion sites followed by paired-end Illumina sequencing. In addition to providing a step-by-step molecular biology protocol, we offer users a guide to our pipeline for data analysis, TIPseqHunter. Our recent studies in pancreatic and ovarian cancer demonstrate the ability of TIPseq to identify invariant (fixed), polymorphic (inherited variants), as well as somatically-acquired L1 insertions that distinguish cancer genomes from a patient’s constitutional make-up.

Conclusions

TIPseq provides an approach for amplifying evolutionarily young, active transposable element insertion sites from genomic DNA. Our rationale and variations on this protocol may be useful to those mapping L1 and other mobile elements in complex genomes.

Electronic supplementary material

The online version of this article (10.1186/s13100-019-0148-5) contains supplementary material, which is available to authorized users.

Somatic retrotransposition is infrequent in glioblastomas

Background

Gliomas are the most common primary brain tumors in adults. We sought to understand the roles of endogenous transposable elements in these malignancies by identifying evidence of somatic retrotransposition in glioblastomas (GBM). We performed transposon insertion profiling of the active subfamily of Long INterspersed Element-1 (LINE-1) elements by deep sequencing (TIPseq) on genomic DNA of low passage oncosphere cell lines derived from 7 primary GBM biopsies, 3 secondary GBM tissue samples, and matched normal intravenous blood samples from the same individuals.

Results

We found and PCR validated one somatically acquired tumor-specific insertion in a case of secondary GBM. No LINE-1 insertions present in primary GBM oncosphere cultures were missing from corresponding blood samples. However, several copies of the element (11) were found in genomic DNA from blood and not in the oncosphere cultures. SNP 6.0 microarray analysis revealed deletions or loss of heterozygosity in the tumor genomes over the intervals corresponding to these LINE-1 insertions.

Conclusions

These findings indicate that LINE-1 retrotransposon can act as an infrequent insertional mutagen in secondary GBM, but that retrotransposition is uncommon in these central nervous system tumors as compared to other neoplasias.

Electronic supplementary material

The online version of this article (doi:10.1186/s13100-016-0077-5) contains supplementary material, which is available to authorized users.

A map of mobile DNA insertions in the NCI-60 human cancer cell panel

Background

The National Cancer Institute-60 (NCI-60) cell lines are among the most widely used models of human cancer. They provide a platform to integrate DNA sequence information, epigenetic data, RNA and protein expression, and pharmacologic susceptibilities in studies of cancer cell biology. Genome-wide studies of the complete panel have included exome sequencing, karyotyping, and copy number analyses but have not targeted repetitive sequences. Interspersed repeats derived from mobile DNAs are a significant source of heritable genetic variation, and insertions of active elements can occur somatically in malignancy.

Method

We used Transposon Insertion Profiling by microarray (TIP-chip) to map Long INterspersed Element-1 (LINE-1, L1) and Alu Short INterspersed Element (SINE) insertions in cancer genes in NCI-60 cells. We focused this discovery effort on annotated Cancer Gene Index loci.

Results

We catalogued a total of 749 and 2,100 loci corresponding to candidate LINE-1 and Alu insertion sites, respectively. As expected, these numbers encompass previously known insertions, polymorphisms shared in unrelated tumor cell lines, as well as unique, potentially tumor-specific insertions. We also conducted association analyses relating individual insertions to a variety of cellular phenotypes.

Conclusions

These data provide a resource for investigators with interests in specific cancer gene loci or mobile element insertion effects more broadly. Our data underscore that significant genetic variation in cancer genomes is owed to LINE-1 and Alu retrotransposons. Our findings also indicate that as large numbers of cancer genomes become available, it will be possible to associate individual transposable element insertion variants with molecular and phenotypic features of these malignancies.

Electronic supplementary material

The online version of this article (doi:10.1186/s13100-016-0078-4) contains supplementary material, which is available to authorized users.

Architectural organization of the metabolic regulatory enzyme ghrelin O-acyltransferase

Ghrelin O-acyltransferase (GOAT) is a polytopic integral membrane protein required for activation of ghrelin, a secreted metabolism-regulating peptide hormone. Although GOAT is a potential therapeutic target for the treatment of obesity and diabetes and plays a key role in other physiologic processes, little is known about its structure or mechanism. GOAT is a member of the membrane-bound O-acyltransferase (MBOAT) family, a group of polytopic integral membrane proteins involved in lipid-biosynthetic and lipid-signaling reactions from prokaryotes to humans. Here we use phylogeny and a variety of bioinformatic tools to predict the topology of GOAT. Using selective permeabilization indirect immunofluorescence microscopy in combination with glycosylation shift immunoblotting, we demonstrate that GOAT contains 11 transmembrane helices and one reentrant loop. Development of the V5Glyc tag, a novel, small, and sensitive dual topology reporter, facilitated these experiments. The MBOAT family invariant residue His-338 is in the ER lumen, consistent with other family members, but conserved Asn-307 is cytosolic, making it unlikely that both are involved in catalysis. Photocross-linking of synthetic ghrelin analogs and inhibitors demonstrates binding to the C-terminal region of GOAT, consistent with a role of His-338 in the active site. This knowledge of GOAT architecture is important for a deeper understanding of the mechanism of GOAT and other MBOATs and could ultimately advance the discovery of selective inhibitors for these enzymes.

Abstract 3148: Mapping mobile DNAs in human cancer cell lines

Genomic instability represented by genetic and epigenetic changes is a hallmark of oncogenesis and tumor progression. The study of genomic instability using conventional methods has necessarily been restricted to regions of unique DNA and excludes repetitive DNA sequences. Repeat elements derived from mobile DNAs comprise a large portion of the human genome and are known sources of genetic variation in humans. Active transposable elements (TE) have recently been shown to cause genetic heterogeneity in tumors through somatic insertions. The functional impact of inherited and somatically acquired TE in cancer development and progression remains unproven. To begin to understand the roles of these mobile DNA elements in transformed cells, we used a novel genomic method to map TEs in a panel of well-characterized human cancer cell lines. Using transposon insertion profiling (TIP)-chip we discover transposition competent families of L1 and Alu TEs. This technique recovered many known reference and polymorphic insertions, novel polymorphisms shared by unrelated tumor cell lines, as well as unique, potentially tumor-specific insertions. Insertions were discovered in several important oncogenes such as KRAS, ALK and BRAF. Most insertions discovered were intronic or intergenic, however 16 TEs were putative exonic. Analysis of the novel and polymorphic insertions revealed a relative enrichment of L1 and Alu insertions in cancer gene loci that are mutated in human cancers or implicated in tumor development in forward genetic screens (p=7.74e-10). We also report associations of individual insertion sites with cellular phenotypes, including DNA methylation status, RNA and protein expression, and drug sensitivities. Epigenetic, gene expression and gene pathway associations were evaluated to delineate local (cis) from pathway (trans) effects. We identified several examples of cis effects of TEs on gene structure as well as nearly 250 curated proliferation pathways affected by a TE insertion. These data suggest that TE insertions may function locally to alter genomic structure or act more globally in concert with other genetic mechanisms to promote the development and progression of several common tumor types.

Citation Format: John G. Zampella, Wan Rho Yang, Nemanja Rodric, Cheng Ran Lisa Huang, Jane Welch, Veena P. Gnanakkan, Toby C. Cornish, Jef D. Boeke, Kathleen H. Burns. Mapping mobile DNAs in human cancer cell lines. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3148. doi:10.1158/1538-7445.AM2013-3148

Active transposition in genomes

Transposons are DNA sequences capable of moving in genomes. Early evidence showed their accumulation in many species and suggested their continued activity in at least isolated organisms. In the past decade, with the development of various genomic technologies, it has become abundantly clear that ongoing activity is the rule rather than the exception. Active transposons of various classes are observed throughout plants and animals, including humans. They continue to create new insertions, have an enormous variety of structural and functional impact on genes and genomes, and play important roles in genome evolution. Transposon activities have been identified and measured by employing various strategies. Here, we summarize evidence of current transposon activity in various plant and animal genomes.