Promoter methylation, transcription, and retrotransposition of LINE-1 in colorectal adenomas and adenocarcinomas

Abstract

Background: The methylation of the CpG islands of the LINE-1 promoter is a tight control mechanism on the function of mobile elements. However, simultaneous quantification of promoter methylation and transcription of LINE-1 has not been performed in progressive stages of colorectal cancer. In addition, the insertion of mobile elements in the genome of advanced adenoma stage, a precancerous stage before colorectal carcinoma has not been emphasized. In this study, we quantify promoter methylation and transcripts of LINE-1 in three stages of colorectal non-advanced adenoma, advanced adenoma, and adenocarcinoma. In addition, we analyze the insertion of LINE-1, Alu, and SVA elements in the genome of patient tumors with colorectal advanced adenomas. Methods: LINE-1 hypomethylation status was evaluated by absolute quantitative analysis of methylated alleles (AQAMA) assay. To quantify the level of transcripts for LINE-1, quantitative RT-PCR was performed. To find mobile element insertions, the advanced adenoma tissue samples were subjected to whole genome sequencing and MELT analysis. Results: We found that the LINE-1 promoter methylation in advanced adenoma and adenocarcinoma was significantly lower than that in non-advanced adenomas. Accordingly, the copy number of LINE-1 transcripts in advanced adenoma was significantly higher than that in non-advanced adenomas, and in adenocarcinomas was significantly higher than that in the advanced adenomas. Whole-genome sequencing analysis of colorectal advanced adenomas revealed that at this stage polymorphic insertions of LINE-1, Alu, and SVA comprise approximately 16%, 51%, and 74% of total insertions, respectively. Conclusions: Our correlative analysis showing a decreased methylation of LINE-1 promoter accompanied by the higher level of LINE-1 transcription, and polymorphic genomic insertions in advanced adenoma, suggests that the early and advanced polyp stages may host very important pathogenic processes concluding to cancer.

Evaluation of global and intragenic hypomethylation in colorectal adenomas improves patient stratification and colorectal cancer risk prediction

“…Global DNA hypomethylation, measured by LINE-1, was previously recognized as a molecular feature able to confer a higher predisposition to the development of colorectal adenomas and cancers [ 9 , 20 ]. Jiang and colleagues reported that LINE-1 hypomethylation increased in the transition from normal mucosa to CRC and could be used to predict the onset of synchronous CRCs [ 18 ].…”

“…In addition, the specific role of LINE-1 methylation in the transition from normal mucosa to adenoma was proved by a genome-wide expression analysis based on the comparison of normal adjacent, adenomatous and CRC tissues [ 17 ]. Overall, the number of studies testing the involvement of epigenetic regulatory mechanisms in colorectal adenoma–carcinoma transition is rapidly growing [ 20 , 28 , 29 ].…”

“…Moreover, Shademan et al . [ 20 ] showed that LINE-1 promoter methylation in advanced adenomas was significantly lower than that in non-advanced adenomas.…”

Promising Epigenetic Biomarkers for the Early Detection of Colorectal Cancer: A Systematic Review

“…Therefore, the assessment of methylated LINE-1 may serve as a valuable tool for cancer screening. Two studies also evaluated hypomethylation of long interspersed nuclear element-1 (LINE-1) as a potent early detection biomarker in CRC [ 76 , 77 ]. Measurement of cell-free DNA long interspersed nuclear element-1 hypomethylation index (cfDNA LHI) was achieved with 63.2% sensitivity and 90% specificity for early-stage I/II CRC [ 76 ].…”

Invasive and Noninvasive Nonfunctioning Gonadotroph Pituitary Tumors Differ in DNA Methylation Level of LINE-1 Repetitive Elements

“…The assessment of LINE-1 transcripts with qRT-PCR is technically feasible for the screening of a large number of samples as used previously [26,42] but is probably biased by the fact that LINE-1 sequences are incorporated in intronic regions of various genes and can undergo "pass through" transcription not related to the L1 promoter. The precise evaluation of the expression of repetitive elements is very challenging and requires sophisticated methods based on whole transcriptome analysis [43].…”