Kim Stephanie S, Lee Seung Cho, Lim Bumjin, Shin Seung-Ho, Kim Mee Young, Kim Sol-Yi, Lim Hyeyeun, Charton Clémentine, Shin Dongho, Moon Hyong Woo, Kim Jinho, Park Donghyun, Park Woong-Yang, Lee Ji Youl
Precision Medicine Center, Future Innovation Research Division, Seoul National University Bundang Hospital, Seongnam, Korea.
GENINUS Inc., Seoul, Korea.
Prostate Int. 2023 Jun;11(2):113-121. doi: 10.1016/j.prnil.2023.01.001. Epub 2023 Jan 5.
DNA methylation markers are considered robust diagnostic features in various cancer types, as epigenetic marks are commonly altered during cancer progression. Differentiation between benign prostatic hyperplasia (BPH) and early-stage prostate cancer (PCa) is clinically difficult, relying on the information of the patient's symptoms or levels of prostate-specific antigen.
A total of 42 PCa patients and 11 BPH patients were recruited. Genomic DNA was purified from tissues and used for the library preparation of the target-enriched methylome with enzymatic conversion and a Twist 85 Mbp EM-seq panel. Paired-end sequencing (150 bp) was performed using NovaSeq 6000 or NextSeq 550. After quality control, including adapter trimming and de-duplication of raw sequencing data, differential methylation patterns were analyzed between the BPH and PCa groups.
We report DNA methylation patterns existing between BPH and PCa. The major finding is that broad hypermethylation occurred at genic loci in PCa tissues as compared to the BPH. Gene ontology analysis suggested that hypermethylation of genic loci involved in chromatin and transcriptional regulation is involved in cancer progression. We also compared PCa tissues with high Gleason scores to tissues with low Gleason scores. The high-Gleason PCa tissues showed hundreds of focal differentially methylated CpG sites corresponding to genes functioning in cancer cell proliferation or metastasis. This suggests that dissecting early-to-advanced-grade cancer stages requires an in-depth analysis of differential methylation at the single CpG site level.
Our study reports that enzymatic methylome sequencing data can be used to distinguish PCa from BPH and advanced PCa from early-stage PCa. The stage-specific methylation patterns in this study will be valuable resources for diagnostic purposes as well as further development of liquid biopsy approaches for the early detection of PCa.
DNA甲基化标记被认为是多种癌症类型中可靠的诊断特征，因为表观遗传标记在癌症进展过程中通常会发生改变。良性前列腺增生（BPH）和早期前列腺癌（PCa）之间的鉴别在临床上具有挑战性，主要依赖于患者症状或前列腺特异性抗原水平等信息。
共招募了42例PCa患者和11例BPH患者。从组织中纯化基因组DNA，并用于通过酶促转化和Twist 85 Mbp EM-seq面板制备目标富集甲基化组文库。使用NovaSeq 6000或NextSeq 550进行双端测序（150 bp）。在进行包括接头修剪和原始测序数据去重在内的质量控制后，分析BPH组和PCa组之间的差异甲基化模式。
我们报告了BPH和PCa之间存在的DNA甲基化模式。主要发现是，与BPH相比，PCa组织中的基因位点普遍发生高甲基化。基因本体分析表明，参与染色质和转录调控的基因位点高甲基化与癌症进展有关。我们还将高Gleason评分的PCa组织与低Gleason评分的组织进行了比较。高Gleason评分的PCa组织显示出数百个与癌细胞增殖或转移相关基因对应的局灶性差异甲基化CpG位点。这表明剖析早期到晚期癌症阶段需要在单个CpG位点水平上深入分析差异甲基化。
我们的研究报告称，酶促甲基化组测序数据可用于区分PCa与BPH以及晚期PCa与早期PCa。本研究中阶段特异性的甲基化模式将成为诊断目的以及进一步开发用于PCa早期检测的液体活检方法的宝贵资源。
