LINE-1 Retrotransposon expression in cancerous, epithelial and neuronal cells revealed by 5’ single-cell RNA-Seq

Abstract

LINE-1 retrotransposons are known to be expressed in early development, in tumors and in the germline. Less is known about LINE-1 expression at the single cell level, especially outside the context of cancer. Because LINE-1 elements are present at a high copy number, many transcripts that are not driven by the LINE-1 promoter nevertheless terminate at the LINE-1 3’ UTR. Thus, 3’ targeted single cell RNA-seq datasets are not appropriate for studying LINE-1. However, 5’ targeted single cell datasets provide an opportunity to analyze LINE-1 expression at the single cell level. Most LINE-1 copies are 5’ truncated, and a transcript that contains the LINE-1 5’ UTR as its 5’ end is likely to have been transcribed from its promoter. We developed a method, L1-sc (LINE-1 expression for single cells), to quantify LINE-1 expression in 5’ targeted 10x genomics single cell RNA-seq datasets. Our method confirms that LINE-1 expression is high in cancer cells, but low or absent from immune cells. We also find that LINE-1 expression is elevated in epithelial compared to immune cells outside of the context of cancer and that it is also elevated in neurons compared to glia in the mouse hippocampus.

ASSESSMENT OF POTENTIAL SARS-CoV-2 VIRUS N GENE INTEGRATION INTO HUMAN GENOME REVEALS NO SIGNIFICANT IMPACT ON RT-qPCR COVID-19 DIAGNOSTIC TESTING

“…Activity of LINE-1 has been recorded during early stages of development, in some specific cellular contexts such as oocyte attrition or neurogenesis, and under stress conditions such as aging and pathological conditions including cancer [11][12][13][14][15]. Recent experiments suggest activity of LINE-1 elements in epithelial cells [16]. In vitro experiments have shown that, in conditions of high LINE-1 derepression and expression, the machinery that mediates LINE-1 retrotransposition, can mobilize other sequences such as Alu and SVA elements, and can even lead to integration of certain cellular mRNAs, leading to the formation of processed pseudogenes [17][18][19][20].…”

Ultrasensitive detection of circulating LINE-1 ORF1p as a specific multi-cancer biomarker

“…We demonstrate that ORF1p is an early indicator of chemotherapeutic response in gastric and esophageal cancers at timepoints where other parameters are often ambiguous, opening possibilities for monitoring minimal residual disease or relapse. Importantly, ORF1p appears to provide a level of specificity for cancers not achieved by other protein biomarkers, likely due to the unique biology of the retrotransposon, with repression of L1 in normal somatic tissue(9,13,14). ORF1p is therefore attractive as a putative “binary” cancer biomarker, in which a positive signal is highly specific for disease, with diagnostic utility both in tissue and plasma.…”

“…We each inherit, dispersed throughout our genomes, a complement of active L1 loci encoding two proteins: ORF1p, the highly expressed RNA binding protein(8), and ORF2p, an endonuclease and reverse transcriptase with limited expression(9) that generates L1 insertions in cancer genomes(10–13). L1 expression is repressed in normal somatic tissues, resulting in either very low or undetectable levels of L1 RNA and protein that appear to originate from epithelium(9,14). Epigenetic dysregulation of L1 and L1 ORF1p overexpression begin early in carcinogenesis, and histologic precursors of ovarian, esophageal, colorectal, and pancreatic cancers studied all express ORF1p at varying levels(8,15).…”

“…L1 expression is repressed in normal somatic tissues, resulting in either very low or undetectable levels of L1 RNA and protein that appear to originate from epithelium (9,14). Epigenetic dysregulation of L1 and L1 ORF1p overexpression begin early in carcinogenesis, and histologic precursors of ovarian, esophageal, colorectal, and pancreatic cancers studied all express ORF1p at varying levels (8,15).…”