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Abstract
Cancer is a complex disease, driven by a combination of genetic and epigenetic alterations. DNA and RNA methylation modifications are the most common epigenetic events that play critical roles in cancer development and progression. Bisulfite converted sequencing is a widely used technique to detect base modifications in DNA methylation, but its main drawbacks lie in DNA degradation, lack of specificity, or short reads with low sequence diversity. The nanopore sequencing technology can directly detect base modifications in native DNA as well as RNA without harsh chemical treatment, compared to bisulfite sequencing. Furthermore, CRISPR/Cas9-targeted enrichment nanopore sequencing techniques are straightforward and cost-effective when targeting genomic regions are of interest. In this review, we mainly focus on DNA and RNA methylation modification detection in cancer with the current nanopore sequencing approaches. We also present the respective strengths, weaknesses of nanopore sequencing techniques, and their future translational applications in identification of epigenetic biomarkers for cancer detection and prognosis.
Highlights
Epigenetic alternations are important to different types of human cancers and are known to link genetic changes to drive the initiation and progress of cancers
We summarize the advantages and disadvantages of nanopore sequencing and their future translational applications into the discovery of putative epigenetic biomarkers for diagnosis and prognosis prediction of human cancers
In order to solve the problems caused by bisulfite treatment, some bisulfite-free methods have emerged in recent years, such as teneleven translocation (TET)-assisted pyridine borane sequencing (Liu Y. et al, 2019) and Enzymatic Methyl-Seq (Vaisvila et al, 2019), which are based on the catalysis of specific enzymes
Summary
Epigenetic alternations are important to different types of human cancers and are known to link genetic changes to drive the initiation and progress of cancers. These changes can be observed as abnormal patterns of DNA methylation, disrupted patterns of histone modifications, and changes in chromatin components. More than 17 types of modification in DNA and 160 posttranscriptional modifications in RNA have been found, respectively (Zhao et al, 2020), among which the commonest modification type is methylation modification (Jenjaroenpun et al, 2021). The commonest epigenetic change in cancers is 5-methylcytosine (5mC) DNA modification. For the detection of 5mC in DNA, bisulfite converted sequencing is the most commonly applied method. Bisulfite-based sequencing remains the gold-standard method for DNA
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