2025-11-04 東京大学,聖マリアンナ医科大学,国立がん研究センター
Web要約 の発言:
t-nanoEM法の概略図
<関連情報>
- https://www.k.u-tokyo.ac.jp/information/category/press/0028264.html
- https://www.k.u-tokyo.ac.jp/assets/files/わずかながん検体から染色体上の狙った部分の長いDNAのメチル化の検出が可能に_WEB.pdf
- https://www.sciencedirect.com/science/article/pii/S2667237525002516
臨床検体に適したハイブリダイゼーションキャプチャーを用いた標的ロングリードメチル化解析 Targeted long-read methylation analysis using hybridization capture suitable for clinical specimens
Keisuke Kunigo, Satoi Nagasawa, Keiko Kajiya, Yoshitaka Sakamoto, Suzuko Zaha, Yuta Kuze, Akinori Kanai, Kotaro Nomura, Masahiro Tsuboi, Genichiro Ishii, Ai Motoyoshi, Koichiro Tsugawa, Motohiro Chosokabe, Junki Koike, Ayako Suzuki, Yutaka Suzuki, Masahide Seki
Cell Reports methods Available online 3 November 2025
DOI:https://doi.org/10.1016/j.crmeth.2025.101215
Highlights
- T-nanoEM enables target region-specific long-read methylation analysis
- The method achieves high-depth methylation analysis with high sensitivity
- We provide a workflow for haplotype and mutated allele-specific methylation analysis
- We apply t-nanoEM to clinical breast and lung cancer tissue sections
Motivation
Existing methods for targeted long-read methylation analysis, such as PCR, Cas9-based approaches, and adaptive sampling, are limited by the number of target sites and/or the amount of input DNA. While hybridization capture enables the analysis of numerous target genomic regions from small amounts of input DNA, its application to long-read methylation analysis has remained challenging. To address this limitation, we developed targeted nanoEM (t-nanoEM). T-nanoEM combines nanoEM, a method that enzymatically converts long DNA fragments to differentiate methylated and unmethylated cytosines for nanopore sequencing, with a hybridization capture system capable of capturing target DNA even after the conversion.
Summary
To detect precise DNA methylation patterns in long-read DNA sequencing analysis, an efficient target enrichment method is needed. In this study, we established t-nanoEM, a practical method that integrates a hybridization-based capture step into a long-read enzymatic methyl (EM)-seq library for nanopore sequencing. We achieved a high sequencing coverage of up to ×570 at 5 kb N50 in length. We applied this method to the long-read methylation analysis of cancers. Using breast cancer as an example, we demonstrated that the signature changes in DNA methylation occurring in local cell populations could be displayed in a haplotype-aware manner. In lung cancer, the spatial diversity in gene expression as detected by the spatial expression profiling analysis may be associated with changes in DNA methylation.
