LINE-1 expression and retrotransposition in Barrett’s esophagus and esophageal carcinoma

Abstract

Barrett's esophagus (BE) is a common disease in which the lining of the esophagus transitions from stratified squamous epithelium to metaplastic columnar epithelium that predisposes individuals to developing esophageal adenocarcinoma (EAC). We hypothesized that BE provides a unique environment for increased long-interspersed element 1 (LINE-1 or L1) retrotransposition. To this end, we evaluated 5 patients with benign BE, 5 patients with BE and concomitant EAC, and 10 additional patients with EAC to determine L1 activity in this progressive disease. After L1-seq, we confirmed 118 somatic insertions by PCR in 10 of 20 individuals. We observed clonal amplification of several insertions which appeared to originate in normal esophagus (NE) or BE and were later clonally expanded in BE or in EAC. Additionally, we observed evidence of clonality within the EAC cases; specifically, 22 of 25 EAC-only insertions were present identically in distinct regions available from the same tumor, suggesting that these insertions occurred in the founding tumor cell of these lesions. L1 proteins must be expressed for retrotransposition to occur; therefore, we evaluated the expression of open reading frame 1 protein (ORF1p), a protein encoded by L1, in eight of the EAC cases for which formalin-fixed paraffin embedded tissue was available. With immunohistochemistry, we detected ORF1p in all tumors evaluated. Interestingly, we also observed dim ORF1p immunoreactivity in histologically NE of all patients. In summary, our data show that somatic retrotransposition occurs early in many patients with BE and EAC and indicate that early events occurring even in histologically NE cells may be clonally expanded in esophageal adenocarcinogenesis.retrotransposon | LINE-1 | Barrett's esophagus | esophageal adenocarcinoma | retrotransposition

Novel Aberrations Uncovered in Barrett's Esophagus and Esophageal Adenocarcinoma Using Whole Transcriptome Sequencing

“…We observed increased expression of LINE elements, consistent with recent reports describing increased LINE-1 retrotransposition activity in both BE and EAC (21). Interestingly, however, Alu elements, primate-specific short interspersed nuclear elements (SINE), showed almost uniform downregulation in EAC compared with premalignant Barrett's and normal squamous tissues.…”

“…For example, repeat elements, which make up two thirds of the human genome (18), have been associated with cancer (19) and double stranded breaks (20), and long-interspersed nuclear element 1 (LINE-1) retrotransposition is increased in EAC and Barrett's (21).…”

Human transposon insertion profiling: Analysis, visualization and identification of somatic LINE-1 insertions in ovarian cancer

“…This conclusion is even more true for Alu insertion variants (45,46). These studies have also demonstrated that several types of epithelial cancers acquire somatic insertions of LINE-1 as they develop (15,19,24,26). Recent projects mining whole-genome sequencing data have extended our understanding of the scope of heritable LINE-1 insertions (20,21,47) and somatic retrotransposition (22,23,48) greatly.…”

“…Recently, however, strategies for mapping these elements have been developed based on selective PCR amplification (15)(16)(17), hybridizationbased enrichment (18,19), and read selection from wholegenome sequencing data (20)(21)(22). These studies underscore the continued activity of LINE-1 in modern humans, and demonstrated somatic insertions in several types of human malignancy (15,19,(22)(23)(24)(25)(26)(27).…”

A hot L1 retrotransposon evades somatic repression and initiates human colorectal cancer

“…Until recently, L1 elements were thought to be mobilized primarily in the germline and then silenced in somatic cells throughout adulthood. However, several recent reports have shown that L1 elements are active in at least some adult somatic tissues, including the brain (Muotri et al 2005;Coufal et al 2009;Baillie et al 2011;Evrony et al 2012;Upton et al 2015) and epithelial somatic tumors Iskow et al 2010;Lee et al 2012;Solyom et al 2012;Shukla et al 2013;Helman et al 2014;Tubio et al 2014;Doucet-O'Hare et al 2015;Ewing et al 2015;Rodic et al 2015). These observations have led to the suggestion that L1 might play a role in initiating human cancers by mutating specific oncogenes or tumor suppressor genes in somatic cells.…”