Methylation Sequencing: Unraveling the Epigenetic Code with Targeted Solutions

Understanding DNA Methylation: The Epigenetic Cornerstone

DNA methylation is a key epigenetic mechanism controlling gene expression and plays a fundamental role in cellular development, differentiation, and disease progression. The addition of methyl groups to DNA molecules typically occurs at cytosine bases within CpG dinucleotides, altering gene activity without changing the underlying DNA sequence. This epigenetic mechanism serves as an important regulatory system, influencing which genes are expressed or silenced in specific cells.

Aberrant methylation patterns have been implicated in various diseases, particularly cancer, where hypermethylation of tumor suppressor genes or hypomethylation of oncogenes can contribute to disease progression. Advances in developing targeted drugs that modulate DNA methylation have opened promising avenues for epigenetic therapies in oncology. As researchers continue to explore the complex relationship between methylation patterns and human health, methylation sequencing has become critical for understanding these epigenetic landscapes.¹

The power of targeted methylation sequencing

Comprehensive genome-wide methylation analysis through whole genome bisulfite sequencing (WGBS) represents the premier approach for uncovering methylation patterns across diverse biological samples. While this technique provides a wide breadth of coverage, when research transitions from discovery to targeted validation, the practical utility of WGBS diminishes. High sequencing costs and excessive data generation make WGBS impractical for large sample cohorts and routine clinical analysis where focused investigation is more relevant.

For these studies, targeted methylation sequencing that focuses only on genomic regions of interest emerges as a transformative approach. This method employs the use of probes to bind to specific sequences within a next-generation sequencing library, with subsequent hybridization capture to enrich the library prior to methylation sequencing.

A targeted methylation sequencing approach offers several distinct advantages:

1. Cost-effectiveness: By focusing on specific regions of interest rather than the entire genome, targeted methylation sequencing significantly reduces sequencing costs while still capturing the most relevant information
2. Increased sequencing depth: The focused approach allows for higher coverage of target regions, enabling more accurate detection of subtle methylation changes and rare methylation events
3. Enhanced sensitivity: Targeted methods can detect low-frequency methylation signatures in complex samples, making them ideal for applications like liquid biopsy where informative methylated DNA molecules may be present in low abundance
4. Streamlined analysis: By limiting analysis to specific genomic regions, targeted approaches simplify data processing and interpretation, accelerating the path from sequencing to meaningful insights

myBaits® technology: advancing targeted methylation sequencing

Targeting methylated regions presents unique technical challenges due to the reduced sequence complexity following bisulfite or enzymatic conversion. The myBaits Custom Methyl-Seq system addresses these challenges through a proprietary methylation-specific probe design algorithm that simulates various potential methylation configurations on both strands from converted genomic templates, while thoroughly filtering for specificity. This approach ensures high on-target efficiency while minimizing bias toward either methylated or unmethylated DNA.

The system’s performance metrics are impressive, with custom panels demonstrated to achieve over 80% of reads on-target following hybridization capture, representing an 8000- to 9000-fold enrichment. Furthermore, the system demonstrates compatibility with low-input samples, as little as 1 ng of starting DNA, to maximize sensitivity.

Applications in cancer research and beyond

Targeted methylation sequencing has proven particularly valuable in cancer research applications, where methylation signatures can serve as biomarkers for early detection, prognosis, and treatment response.² Underscoring the clinical potential of targeted methylation sequencing is the rise in cell-free DNA (cfDNA) signatures as a promising tool in oncology. Tumor cells release DNA fragments into the bloodstream that carry distinct methylation signatures, enabling identification and monitoring of tumors through minimally invasive cfDNA-based liquid biopsies rather than traditional tissue biopsies.³ Powerful data presented in a recent webinar, demonstrated the characterization of cancer-associated methylation states in cfDNA. This study leveraged targeted methylation sequencing using the myBaits Custom Methyl-Seq system and revealed accurate measurement of site-specific methylation levels.

Beyond oncology, targeted methylation sequencing supports diverse research areas including developmental biology studies examining dynamic methylation changes during cellular differentiation, neurological research investigating epigenetic contributions to brain development and neurodegeneration, and environmental health studies assessing how environmental exposures influence the epigenome.

The path forward with precision epigenetics

As our understanding of epigenetics continues to evolve, targeted methylation sequencing stands as an essential tool for unraveling the complex role of DNA methylation in health and disease. The precision of a hybridization capture approach to methylation sequencing is enabling researchers to interrogate methylation patterns with unprecedented detail, accuracy, and efficiency.

The continued advancement of technologies like Arbor Biosciences’ myBaits Custom Methyl-Seq system promises to further enhance our ability to detect and interpret methylation signatures, ultimately translating epigenetic insights into improved diagnostic approaches and therapeutic strategies.

References:

1. Saghafinia, S. et al. “Pan-cancer landscape of aberrant DNA methylation across human tumors” Cell Reports. (2022) Oct; 39(2). doi: 10.1016/j.celrep.2018.09.082
2. Liang, G. et al. “DNA methylation aberrancies as a guide for surveillance and treatment of human cancers” Epigenetics. (2017) Mar; 12(6):416–432. doi: 1080/15592294.2017.1311434
3. Buckley, D. et al. “Targeted DNA methylation from cell-free DNA using hybridization probe capture” NAR Genomics and Bioinformatics. (2022) Dec; 4(4). doi:10.1093/nargab/lqac099