Development of 5hmC and 5mC biomarkers in cell-free circulating DNA for sensitive colon cancer detection and prognosis

开发无细胞循环 DNA 中的 5hmC 和 5mC 生物标志物，用于敏感的结肠癌检测和预后

• 批准号: 10220895
• 负责人: Bruce Marc Bissonnette
• 金额: $ 59.98万
• 依托单位: UNIVERSITY OF CHICAGO
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-08-01 至 2023-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10220895
• 关键词: Achievement; Age; Algorithms; Archives; Bar Codes; Biological Assay; Biological Markers; Blood; Blood Tests; Cancer Control; Cancer Detection; Cancer Etiology; Cancer Prognosis; Cells; Cessation of life; Chemicals; Clinical; Colon Carcinoma; Colonic Neoplasms; Colonoscopy; Colorectal Cancer; Cost efficiency; Custom; Cytosine; DNA; DNA Modification Process; Data; Detection; Development; Diagnosis; Disease; Early Diagnosis; Enhancers; Epigenetic Process; FDA approved; Feces; Future; Gender; Gene Expression; Gene Expression Regulation; Gene Mutation; Genes; Genetic Transcription; Genomics; Goals; Human Genome; Immunoprecipitation; Individual; Label; Location; Malignant Neoplasms; Maps; Modification; Monitoring for Recurrence; Mutation; Neoplasm Metastasis; Outcome; Patients; Pattern; Plasma; Positioning Attribute; Prevalence; Prognosis; Prospective cohort; Public Health; Recurrence; Research Personnel; Resources; Role; Sampling; Study Subject; Technology; Testing; Training; Tumor Biology; Tumor Markers; Tumor Tissue; Unresectable; Validation; Vimentin; base; biobank; bisulfite; blood-based biomarker; cancer biomarkers; cancer diagnosis; cancer prevention; case control; cell free DNA; chemical stability; colon cancer patients; colon cancer screening; colorectal cancer screening; cost efficient; demethylation; differential expression; epigenetic marker; epigenomics; genetic signature; indexing; innovation; liquid biopsy; minimal risk; minimally invasive; nano; neoplasm registry; neoplastic cell; next generation sequencing; oxidation; procedure cost; prognostic; promoter; prospective; rare cancer; recruit; relapse patients; repository; response; sample archive; screening; seal; standard of care; treatment response; tumor; tumor DNA

PROJECT SUMMARY/ABSTRACT Colorectal cancer (CRC) is a major cause of cancer-related deaths. Screening colonoscopy is the standard of care for CRC detection, but compliance remains below 50% because of challenging preps, procedural costs and potential complications. Specific mutations are rare in CRC, precluding their utility as screening biomarkers. Epigenetic changes, including DNA 5-methylcytosine (5mC), contribute to CRC and are interrogated in several FDA-approved tests, but have limited sensitivity and no prognostic information. Sensitive blood tests for biomarkers in circulating cell-free DNA (cfDNA) could offer greater convenience and higher compliance. In addition to 5mC, changes in 5-hydroxymethylcytosine (5hmC) are important in normal and disease states. 5hmC is an abundant, stable modified cytosine that is generated by DNA demethylation and frequently marks active gene transcription. 5hmC and 5mC could serve as superior biomarkers, given their widespread genomic prevalence, distinct roles in gene regulation, and robust chemical stability. We developed a highly sensitive and selective chemical labeling technology (nano-hmC-Seal) to capture 5hmC bases, and using next generation sequencing (NGS), map their genomic positions. In preliminary studies, we captured and profiled 5hmC and 5mC in cfDNA and paired tumor tissues from 47 controls and 136 patients with recently diagnosed cancers, including 46 with CRC. We developed a classifier to identify genes with differential 5hmC changes in CRC patients and identified consistent cancer-specific epigenetic signatures in tumors and cfDNA. Because of the high sensitivity (~1ng DNA), robustness, clinical convenience and cost-efficiency, we hypothesize that unique cell-free 5hmC and 5mC profiles might be useful as plasma biomarkers to detect CRC and ultimately predict tumor prognosis. We propose to use PLCO biorepository samples and our own archived CRC with annotated clinical outcomes, and newly recruited prospective CRC patients to refine and validate the sensitivity of differentially expressed 5hmC and 5mC gene signatures for CRC diagnosis and prognosis. We propose: Aim 1 to profile 5hmC and 5mC in cfDNA from PLCO samples (CRC and control), using nano-hmC- Seal and NGS and refine algorithms for sensitive CRC blood test, using 200 CRC cases and 400 controls for training set, and an additional 200 cases and 400 controls from our prospective cohort for validation set. We will develop discriminators of 5hmC and 5mC modifications to diagnose CRC and control analyses by tumor location, stage, patient age and gender that likely modulate 5hmC and 5mC distributions; Aim 2a to profile 100 PLCO tumors for 5hmC and 5mC distributions and compare distributions to cfDNA (aim 1 samples); In aim 2b, we will study 150 tumors from archived samples with recurrence data (60 relapsed patients vs. 90 clinical feature-matched non-relapsed patients), to detect a predictive index for tumor prognosis. In aim 2c, we will compare markers determined in tumors to markers detected in cfDNA to assess whether we can develop a minimally-invasive, cost-efficient, clinically convenient cfDNA-based marker for tumor prognosis.

项目摘要/摘要 结直肠癌(CRC)是癌症相关死亡的主要原因。筛查结肠镜检查是诊断结肠镜的标准 关注CRC检测，但由于具有挑战性的准备和程序成本，合规性保持在50%以下 以及潜在的并发症。在结直肠癌中，特定的突变是罕见的，这排除了它们作为筛查的用途 生物标志物。表观遗传学改变，包括DNA 5-甲基胞嘧啶(5mC)，有助于结直肠癌和 在FDA批准的几项测试中进行了讯问，但敏感性有限，没有预后信息。 对循环中的无细胞DNA(CfDNA)中的生物标记物进行敏感的血液检测可以提供更大的便利和 更高的合规性。除了5mC外，5-羟甲基胞嘧啶(5hmC)的变化在正常人群中也很重要 和疾病状态。5HmC是一种丰富、稳定的修饰胞嘧啶，由DNA去甲基化生成 并经常标记活跃的基因转录。5hmC和5mC可以作为卓越的生物标志物，因为它们 广泛的基因组流行，在基因调控中的独特作用，以及强大的化学稳定性。我们开发了 一种高灵敏度和选择性的化学标记技术(Nano-HMC-Seal)以捕获5hmC碱基，以及 使用下一代测序(NGS)，绘制它们的基因组位置。在初步研究中，我们捕获了 从47名对照组和136名新近发现的癌症患者的cfDNA和配对的肿瘤组织中分析了5hmC和5mC 确诊的癌症，包括46例结直肠癌。我们开发了一种分类器来识别差异5hmC的基因 结直肠癌患者的变化，并在肿瘤和cfDNA中发现一致的癌症特异性表观遗传学特征。 由于高灵敏度(~1 ng DNA)、健壮性、临床方便性和成本效益，我们 假设独特的无细胞5hmC和5mC图谱可能作为检测结直肠癌的血浆生物标志物有用 并最终预测肿瘤的预后。我们建议使用PLCO生物库样本和我们自己的归档 带注释的临床结果的结直肠癌，以及新招募的预期结直肠癌患者，以完善和验证 差异表达的5hmC和5mC基因信号对结直肠癌诊断和预后的敏感性我们 建议：目的1从PLCO样本(结直肠癌和对照)中分析cfDNA中的5hmC和5mC，使用纳米HMC- 用于敏感的CRC血液检测的SEAL和NGS和REFINE算法，使用200例CRC病例和400名对照 训练集，以及来自我们用于验证集的预期队列中的另外200个病例和400个对照。我们 将开发5hmC和5mC改进的鉴别器来诊断结直肠癌并根据肿瘤进行对照分析 可能调节5hmC和5mC分布的位置、分期、患者年龄和性别；目标2a至配置文件100 PLCO肿瘤的5hmC和5mC分布，并与cfDNA(Aim 1样本)进行比较；在Aim 2b中， 我们将从有复发数据的存档样本中研究150个肿瘤(60名复发患者与90名临床患者 特征匹配的非复发患者)，以检测肿瘤预后的预测指标。在Aim 2c中，我们将 将在肿瘤中确定的标记与在cfDNA中检测到的标记进行比较，以评估我们是否可以开发出 基于cfDNA的微创、经济高效、临床方便的肿瘤预后标记物。

项目成果

Analysis of genome-wide 5-hydroxymethylation of blood samples stored in different anticoagulants: opportunities for the expansion of clinical resources for epigenetic research.

• DOI: 10.1080/15592294.2023.2271692
• 发表时间: 2023-12
• 期刊: EPIGENETICS
• 影响因子: 3.7
• 作者: Gao, Lu;Zhang, Zhou;Cui, Xiao-Long;West-Szymanski, Diana;Ye, Chang;He, Chuan;Zhang, Wei;Bissonnette, Marc
• 通讯作者: Bissonnette, Marc