VINIF.2022.DA00036 – Evaluating DNA methylation of transposable elements LINE-1 and Alu in cancers for developing blood based epigenetic diagnosis biomarkers

Principle Investigator
Assoc.Prof. Vo Thi Thuong Lan
Host Organization
University of Science, Vietnam National Universty

Urgency:

Alteration of DNA methylation on cytosine in the CpG dinucleotide occurs very early in carcinogenesis. In particular, unlike mutations in nucleotide sequences, alteration in DNA methylation are specific to the origin of cancer cells and tissues. Therefore, in recent years, DNA methylation levels have been researched extensively to develop benchmark markers for screening, diagnosis, prognosis and targeted treatment of cancer. The technique of DNA bisulfite treatment to convert unmethylated cytosine to uracil but leaving methylated cytosine intact is applied in all kits licensed by the US Food and Drug Administration (FDA) for use as a benchmark for early detection or prognostic screening of lung, colon and breast cancers. However, the requirement for large amounts of blood samples for each test is the main barrier limiting the routine use of these markers. Therefore, the repetitive DNA sequences LINE-1 and Alu, which account for up to 40% of the DNA in the genome and contain more than 90% of the genome’s methylated CpG sites, are of particular interest in the strategy of developing new generation markers (epi-biomarkers) because a small amount of blood sample was adequate in terms of free DNA and number of CpG sites for methylation ratio analysis.

Novelty:

The mobility of LINE-1 and Alu elements are repetitive DNA with up to 106 copies/genome (whereas single-copy genes have only 2 copies/genome). Their movement through transcription and integration of cDNA into any location leads to genome instability, gene mutations, changes in transcription control, gene translation, and impacts on cell differentiation, immune response, aging and cancer. The mobility of LINE-1 and Alu is controlled by CpG methylation in the sequences of these two factors. The methylation ratio of LINE-1 and Alu clearly changes between healthy people and cancer patients, and meets all the strict requirements of DNA methylation benchmarks in screening, diagnosis, prognosis and targeted cancer therapy when using non-invasive samples (blood, fluid, urine). However, in the world, there is currently no standard procedure to determine the methylation ratio of LINE-1 and Alu. The meta analysis have had controversial results, causing the methylation standards LINE-1 and Alu to not be licensed for use. We were the first to determine the amount of DNA required for bisulfite treatment when analyzing methylation rates in repetitive DNA sequences and demonstrated the accuracy of the LINE-1 methylation ratio depends on the amount of DNA in the sample. This result sheds light on the cause of controversy and confirms the value of LINE-1 methylation as a standard marker for cancer diagnosis. The results published in the journal PloS One in 2021 are the scientific basis for us to continue research to build and perfect the process of using LINE-1 and Alu methylation standards in peripheral blood samples serving paraclinical, supporting diagnosis and prognosis of some common types of cancer (breast, lung, colon cancer) in Vietnamese people.

Impact:

Developing and testing epigenetic molecular markers (epi-biomarkers) using blood samples in screening, diagnosis, prognosis and supporting targeted treatment of cancer have important value in approaching epigenetics research in modern biomedicine and developing new molecular markers to serve health care, improve the quality of life of Vietnamese people.

Principle Investigator
Assoc.Prof. Vo Thi Thuong Lan
Host Organization
University of Science, Vietnam National Universty

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Expect Progress
01/12/2022
30/07/2023
Giai đoạn 1

– Biological samples: breast cancer/breast disease (200 samples), lung cancer/lung disease (200 samples), colorectal cancer (200 samples).
– DNA extracted from 600 tissue samples + Concentration and copy number determined from bisulfite-treated samples for 300 samples, ensuring optimal processing and recovery.
– Design and determination of the specificity of MSP, MIP primer pairs for methylated and unmethylated sequences of LINE-1 and Alu.
– Standard samples: positive control, negative control, reference sample, calibrated standard samples separated into plasmids (100 ng/sample).
– Quantification process of LINE-1 and Alu methylation ratio ensuring sensitivity, specificity, and stability with parameters including DNA concentration; copy number; MSP, MIP primer sequences and qPCR conditions; LINE-1 and Alu sequence regions subjected to methylation analysis.

30/04/2024
Giai đoạn 2

– Intellectual property registration application submitted to the Intellectual Property Office accepted as valid and evaluated as competent by the Scientific Council of the Fund;
– A draft submitted to a Q1 journal.

30/11/2024
Giai đoạn 3

– 2 articles accepted for publication in Q1 journals;
– 2 master’s students (who have defended their theses on the research topic);
– 1 PhD student (who has completed or is completing their dissertation on the project’s research topic);
– 1 project summary report.

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