Analysis of genome-wide 5-hydroxymethylation of blood samples stored in different anticoagulants: opportunities for the expansion of clinical resources for epigenetic research.
Analysis of genome-wide 5-hydroxymethylation of blood samples stored in different anticoagulants: opportunities for the expansion of clinical resources for epigenetic research.
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DOI：
10.1080/15592294.2023.2271692
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发表时间：
2023-12
期刊：
影响因子：
3.7
通讯作者：
Bissonnette, Marc
中科院分区：
文献类型：
--
作者：
Gao, Lu;Zhang, Zhou;Cui, Xiao-Long;West-Szymanski, Diana;Ye, Chang;He, Chuan;Zhang, Wei;Bissonnette, Marc
背景：阐明表观遗传机制可以为疾病的诊断和预后提供新的生物标志物。技术进步允许在液体活检中对5-羟甲基胞嘧啶（5hmC）进行全基因组分析。5hmC- seal后加NGS是一种高灵敏度的cfDNA中5hmC生物标志物发现技术。目前，5hmC Seal对EDTA血液采集进行了优化。我们询问肝素是否与5hmC Seal兼容，因为许多临床和生物样本都储存在肝素中。方法：我们从前列腺、肺、结直肠和卵巢（PLCO）癌症筛查试验中获得60例EDTA样本与60例肝素样本相匹配。样本由30个对照组和30个后来被诊断患有结肠癌的个体组成。我们在cfDNA中使用5hmC- seal测定和NGS分析全基因组5hmC。从EDTA收集的样本中收集的5hmC分析数据与肝素中收集的数据进行了系统的比较，这些数据具有不同的基因组特征。结果：肝素与EDTA的cfDNA分离和文库构建具有可比性。典型的5hmC基因组分布模式，包括基因体和增强子标记，在肝素和EDTA中具有可比性。病例和对照组的5hmC分析产生了高度相关的差异特征，表明这两种抗凝剂与5hmC Seal试验兼容。结论：虽然目前不推荐用于5hmC- seal方案，但储存在肝素中的血液样本已成功用于生成可分析的和生物学相关的全基因组5hmC分析。我们的发现是第一个支持将生物标本资源扩展到5hmC Seal的肝素样本以及其他基于pcr的表观遗传学研究技术的机会。
Background: Elucidating epigenetic mechanisms could provide new biomarkers for disease diagnosis and prognosis. Technological advances allow genome-wide profiling of 5-hydroxymethylcytosines (5hmC) in liquid biopsies. 5hmC-Seal followed by NGS is a highly sensitive technique for 5hmC biomarker discovery in cfDNA. Currently, 5hmC Seal is optimized for EDTA blood collection. We asked whether heparin was compatible with 5hmC Seal as many clinical and biobanked samples are stored in heparin. Methods: We obtained 60 samples in EDTA matched to 60 samples in heparin from the Prostate, Lung, Colorectal, and Ovarian (PLCO) Cancer Screening Trial. Samples were comprised of 30 controls and 30 individuals who were later diagnosed with colon cancer. We profiled genome-wide 5hmC in cfDNA using 5hmC-Seal assay followed by NGS. The 5hmC profiling data from samples collected in EDTA were systematically compared to those in heparin across various genomic features. Results: cfDNA isolation and library construction appeared comparable in heparin vs. EDTA. Typical genomic distribution patterns of 5hmC, including gene bodies and enhancer markers, were comparable in heparin vs. EDTA. 5hmC analysis of cases and controls yielded highly correlated differential features suggesting that both anticoagulants were compatible with 5hmC Seal assay. Conclusions: While not currently recommended for the 5hmC-Seal protocol, blood samples stored in heparin were successfully used to generate analysable and biologically relevant genome-wide 5hmC profiling. Our findings are the first to support opportunities to expand the biospecimen resource to heparin samples for 5hmC Seal and perhaps other PCR-based technologies in epigenetic research.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
7
作者：
Harrow J;Frankish A;Gonzalez JM;Tapanari E;Diekhans M;Kokocinski F;Aken BL;Barrell D;Zadissa A;Searle S;Barnes I;Bignell A;Boychenko V;Hunt T;Kay M;Mukherjee G;Rajan J;Despacio-Reyes G;Saunders G;Steward C;Harte R;Lin M;Howald C;Tanzer A;Derrien T;Chrast J;Walters N;Balasubramanian S;Pei B;Tress M;Rodriguez JM;Ezkurdia I;van Baren J;Brent M;Haussler D;Kellis M;Valencia A;Reymond A;Gerstein M;Guigó R;Hubbard TJ
通讯作者：
Hubbard TJ
影响因子：
4.4
作者：
Han, Liyuan;Chen, Chang;Duan, Shiwei
通讯作者：
Duan, Shiwei
结直肠癌患者基因组和游离 DNA 的 5-羟甲基胞嘧啶分析
影响因子：
5.3
作者：
Gao, Pingting;Lin, Shengli;Zhou, Pinghong
通讯作者：
Zhou, Pinghong
影响因子：
7.5
作者：
Chiu, Brian C-H;Zhang, Zhou;Zhang, Wei
通讯作者：
Zhang, Wei