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

Abstract

LINE-1 retrotransposons are sequences capable of copying themselves to new genomic loci via an RNA intermediate. New studies implicate LINE-1 in a range of diseases, especially in the context of aging, but without an accurate understanding of where and when LINE-1 is expressed, a full accounting of its role in health and disease is not possible. We therefore developed a method—5′ scL1seq—that makes use of a widely available library preparation method (10x Genomics 5′ single cell RNA-seq) to measure LINE-1 expression in tens of thousands of single cells. We recapitulated the known pattern of LINE-1 expression in tumors—present in cancer cells, absent from immune cells—and identified hitherto undescribed LINE-1 expression in human epithelial cells and mouse hippocampal neurons. In both cases, we saw a modest increase with age, supporting recent research connecting LINE-1 to age related diseases.

Steady-state neuron-predominant LINE-1 encoded ORF1p protein and LINE-1 RNA increase with aging in the mouse and human brain

“…While LINE-1 derepression in aging has been extensively explored in peripheral tissues and various pathologies, including cancer, our understanding of LINE-1, particularly ORF1p expression, in the central nervous system within this context remains limited 18,65,66 . A recent search of ORF1p peptides in mass spectrometry data spanning 29 different healthy tissues did not reveal the presence of ORF1p in the brain, suggesting that its presence might lie below detection limits 18 .…”

“…While LINE-1 derepression in aging has been extensively explored in peripheral tissues and various pathologies, including cancer, our understanding of LINE-1, particularly ORF1p expression, in the central nervous system within this context remains limited 18,65,66 . A recent search of ORF1p peptides in mass spectrometry data spanning 29 different healthy tissues did not reveal the presence of ORF1p in the brain, suggesting that its presence might lie below detection limits 18 . Only a few studies explored ORF1p encoded LINE-1 protein expression in the brain, most focusing on a specific region (in mice 16,32 in rats 68 and in human post-mortem brain 17 ), but it remained unclear if ORF1p is expressed throughout the entire brain, exhibits cell-type specificity, and most intriguingly, if its expression is influenced by the aging process.…”

“…It is now, 31 years after the initial proposition of the “transposon theory of aging” by Driver and McKechnie 13 , generally accepted that TE activation can be both, a cause and a consequence of aging 14,15 . Sparse data has shown that the LINE-1 encoded protein ORF1p is expressed at steady-state in the mouse ventral midbrain 16 and in some regions of the human post-mortem brain 17 and recent data informed about the presence of full-length transcripts in various tissues 18 . Repression of LINE-1 might…”

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

“…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 .…”

“…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.…”