Circulating DNA methylation biomarkers in micrometastatic breast cancer

微转移乳腺癌中的循环 DNA 甲基化生物标志物

基本信息

批准号：
10224828
负责人：
Bodour Salhia
金额：
$ 38.07万
依托单位：
UNIVERSITY OF SOUTHERN CALIFORNIA
依托单位国家：
美国
项目类别：
财政年份：
2017
资助国家：
美国
起止时间：
2017-09-15 至 2023-08-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10224828
关键词：
Affect Attention Biological Markers Blood Blood Circulation Blood Tests Blood specimen Brain Breast Cancer Patient Breast Carcinoma Breast cancer metastasis Clinical Clinical Management Cohort Studies Consent Coupled CpG Islands DNA DNA Methylation Detection Disease Disease Management Enrollment Frequencies Future Genes Human Hypermethylation Individual Lead Liquid substance Liver Lung Malignant Neoplasms Measures Metastatic breast cancer Methylation Microscopic Neoadjuvant Therapy Neoplasm Metastasis Newly Diagnosed Nucleic Acids Operative Surgical Procedures Organ PAX5 gene Patient-derived xenograft models of breast cancer Patients Pilot Projects Plasma Postoperative Period Pre-Clinical Model Prognostic Marker Prospective Studies Publishing RUNX3 gene Recurrence Refractory Relapse Reporting Research Residual Tumors Residual state Risk Risk Assessment Sampling Sensitivity and Specificity Serum Survivors Systemic Therapy Testing Time Tissues Tumor Burden Tumor Debulking Tumor Tissue Validation base bisulfite bisulfite sequencing bone cell free DNA chemotherapy circulating DNA cohort curative treatments detection limit disorder risk effective therapy experimental study high risk improved in vivo malignant breast neoplasm methylation biomarker methylation pattern methylome next generation sequencing non-invasive monitor patient derived xenograft model predicting response predictive marker prognostic prognostic assays protocadherin 10 risk prediction therapeutically effective tumor whole genome

项目摘要

Abstract Metastatic breast cancer (MBC) is an incurable disease, affecting 10-15% of breast cancer patients, and is often refractory to therapy. Since tumor tissue is not always available after therapy is complete, there is a need for biomarkers that can be monitored noninvasively such as from blood to measure risk of recurrence due to microscopic metastatic residual disease. Numerous studies suggest that DNA methylation could be a useful biomarker for improving the clinical management of disease. Recently circulating cell-free (cf)DNA has attracted attention for clinical use in the context of risk prediction, prognostication and prediction of response to chemotherapy in human cancer and several groups have now reported the detection of tumor-associated DNA methylation patterns in plasma or serum. We identified by whole genome bisulfite sequencing hypermethylation of 21 CpG islands (CGI) in plasma of MBC compared with disease free survivors or healthy cases. Our hypothesis is that a 21-gene DNA hypermethylation signature involving rationally selected hotspots detectable in circulation can be used to detect micrometastatic disease at the end of therapy in patients with early stage breast cancer. In Aim 1 we plan to determine the frequency and the sensitivity and specificity of this DNA methylation signature as a prognostic test in retrospectively collected plasma samples with targeted bisulfite amplicon sequencing. In Aim 2 we will determine the analytical limit of detection and track how different degrees of tumor burden impacts the methylation status of the signature in cell-free DNA in preclinical models of breast cancer metastasis. To clinically validate the biomarker, in Aim 3 we will analyze samples collected as part of prospective study already initiated where we plan to enroll 100 newly diagnosed high-risk breast cancer patients. Blood will be collected after neoadjuvant therapy and surgery and CpG4C in cfDNA will be tested by bAmplicon-seq. We have already collected blood from 20/39 consented patients after their neoadjuvant therapy and subsequent surgery. We will classify patients as positive or negative for CpG4C at the end of neo-adjuvant therapy and additionally at the post-operative blood draw based on cut-off criteria defined in Aim 1 and statistically determine the utility of the marker to prognosticate recurrence. In time such a blood test would also be advantageous at the time of surgery and/or after the completion of chemotherapy to predict which patients could benefit from additional and curative therapies.

抽象的转移性乳腺癌（MBC）是一种无法治愈的疾病，影响10-15％的乳腺癌患者，并且通常对治疗难治。由于治疗完成后，肿瘤组织并不总是可用，因此需要对可以非侵入性监测的生物标志物，例如从血液中衡量复发的风险由于微观转移性残留疾病。大量研究表明，DNA甲基化可能是有用的生物标志物来改善疾病的临床管理。最近循环无细胞（CF）DNA具有在风险预测，预测和对对的反应预测的背景下，引起了人们对临床使用的关注现在，人类癌症的化学疗法和几个组报告了与肿瘤相关的DNA的检测血浆或血清中的甲基化模式。我们通过整个基因组Bisulfite测序确定与无疾病幸存者相比，MBC血浆中21个CpG岛（CGI）的高甲基化案例。我们的假设是21基因DNA高甲基化特征涉及合理选择的热点可检测到的循环中可用于在治疗结束时在患者中检测微转移疾病早期乳腺癌。在AIM 1中，我们计划确定此的频率和敏感性和特异性 DNA甲基化签名作为回顾性收集的血浆样品的预后测试亚硫酸盐扩增子测序。在AIM 2中，我们将确定检测的分析极限，并跟踪不同程度的肿瘤负担会影响临床前无细胞DNA的特征的甲基化状态乳腺癌转移的模型。为了临床验证生物标志物，在AIM 3中，我们将分析样品作为前瞻性研究的一部分收集的已经开始，我们计划注册100个新诊断的高风险乳腺癌患者。新辅助治疗和手术以及CFDNA中的CPG4C将收集血液由Bamplicon-Seq测试。我们已经从20/39例同意患者那里收集了血液新辅助治疗和随后的手术。我们将对患者分类为阳性或为CPG4C阳性或阴性新辅助疗法的结束，并根据临界标准在术后抽血处在AIM 1中定义，并在统计上确定标记对预后复发的效用。随着时间的流逝在手术和/或化学疗法完成后，血液检查也将是有利的预测哪些患者可以受益于其他治疗疗法。