Developing ATAC-array as a novel epigenetic biomarker to guide personalized therapy in pancreatic cancer

开发 ATAC 阵列作为新型表观遗传生物标志物来指导胰腺癌的个性化治疗

• 批准号: 10512502
• 负责人: Steven D Leach
• 金额: $ 42.17万
• 依托单位: DARTMOUTH COLLEGE
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-21 至 2024-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10512502
• 关键词: 3-Dimensional; ATAC-seq; Adjuvant Chemotherapy; Algorithms; Binding; Binding Sites; Cancer Patient; Cells; Chemoresistance; Chromatin; Clinic; Clinical; Clinical Trials; Diagnosis; Disease; Disease-Free Survival; Drug Targeting; Epigenetic Process; Event; Genome; Glass; Goals; Grant; Histone Deacetylase Inhibitor; Hybrids; In Vitro; Label; Legal patent; Libraries; Malignant - descriptor; Malignant Epithelial Cell; Malignant neoplasm of pancreas; Methodology; Methods; Molecular; Nature; Needle biopsy procedure; Neoplasm Metastasis; Noise; Nuclear; Operative Surgical Procedures; Organoids; Outcome; Pancreatic Ductal Adenocarcinoma; Patient Selection; Patients; Pattern; Prognosis; Prognostic Marker; Publishing; Quality of life; Recurrence; Regimen; Resected; Resistance; Routine Diagnostic Tests; Sampling; Signal Transduction; Slide; Specimen; Stains; Stratification; Systemic Therapy; TACSTD1 gene; Technology; Testing; Therapeutic; Time; Training; Work; XCL1 gene; base; chemotherapeutic agent; chemotherapy; clinical application; clinically relevant; cohort; cost; cost effective; epigenetic drug; epigenetic marker; epigenetic therapy; epigenome; genome-wide; improved outcome; individual patient; individualized medicine; mRNA Differential Displays; neoplastic cell; next generation; next generation sequencing; novel; novel therapeutics; pancreatic cancer patients; pancreatic ductal adenocarcinoma cell; patient prognosis; personalized medicine; predictive test; prognostic; relapse patients; response; therapeutic biomarker; transcription factor; tumor

ABSTRACT: Although chemotherapy remains the mainstay of systemic therapy, a large number of cancer patients fail to respond to. About half of surgically resected pancreatic ductal adenocarcinoma (PDAC) patients relapse within a year despite adjuvant chemotherapy. Using genome-wide ATAC-Seq to comprehensively analyze tumor cell-intrinsic chromatin accessibility patterns of resected PDAC, we discovered a signature of 1092 chromatin loci displaying differential accessibility between patients with disease free survival (DFS) < 1 year and patients with DFS > 1 year. Based on this signature, we developed “ATAC-array” – a novel, clinically applicable microarray platform that reads chromatin accessibility without the time and cost associated with Next Generation Sequencing. Using this novel platform, we developed a chromatin-based Prognosis Score, derived from the ATAC-array results from our training set samples, which was further validated on an independent cohort of PDAC patient-derived 3D organoids. By analyzing over-represented transcription factor binding sites among chromatin loci found to be accessible in patients with prolonged DFS, we also identified HNF1b as a transcription factor displaying differential nuclear localization between patients with short vs. long DFS. Combining these two simple methodologies (i.e., the ATAC-array “Prognosis Score” and immunohistochemical determination or HNF1b nuclear localization), we have developed an algorithm that at the time of diagnosis stratifies PDAC patients into prognostic groups with more than seven-fold differences in DFS. Our stratification algorithm provides a simple and clinically achievable prediction of favorable vs unfavorable epigenetic states in PDAC. Based on this work, we now hypothesize that ATAC-array based analysis of chromatin accessibility will provide a clinically relevant means of predicting prognosis in both localized and metastatic pancreatic cancer, and further allow rational selection of patients for clinical trials of epigenetic therapy. Through this R21 grant, we now aim to optimize ATAC-array for clinical use and expand it to all stages of pancreatic cancer. Our goal is to optimize methodologies allowing ATAC-array to be applied to scant tumor specimens retrieved from needle biopsies. We additionally plan to screen epigenetic drugs in vitro in patient-derived 3D organoids to determine whether adverse patterns of chromatin accessibility might be amenable to epigenetic “reprogramming” therapy, such that ATAC- array could provide a therapeutic biomarker selecting patients for epigenetic therapy. The long-term goal of this project is to enhance the feasibility of genome-wide assessment of chromatin accessibility as a clinically relevant indicator of outcome in PDAC patients, and to facilitate the rational inclusion of epigenetic drugs into the therapeutic regimens of patients displaying poor-prognosis epigenetic signatures.

摘要：尽管化学疗法仍然是全身疗法的支柱，但大量癌症 患者无法做出反应。大约一半的手术切除的胰腺导管腺癌（PDAC）患者 一年内的复发调整化疗。使用全基因组ATAC-SEQ全面 分析切除的PDAC的肿瘤细胞中性染色质可及性模式，我们发现 1092染色质基因素，在无疾病生存的患者（DFS）之间显示出差异可及性<1 年份和DFS> 1年的患者。基于此签名，我们开发了“ ATAC-Array” - 一种小说的诊所 适用的微阵列平台，可以读取染色质访问性，而无需与接下来相关的时间和成本 生成测序。使用这个新颖的平台，我们开发了基于染色质的预后评分 从我们的训练集样品的ATAC阵列结果中，该结果在独立队列上得到了进一步验证 PDAC患者衍生的3D器官的。通过分析过多代表的转录因子结合位点 染色质位置发现在长时间DF的患者中可以访问，我们还确定HNF1B是转录 短与长DF的患者之间显示出差异性核定位的因子。结合这两个 简单的方法（即，ATAC阵列“预后评分”和免疫组织化学测定或 HNF1B核定位），我们开发了一种算法，该算法在诊断时对PDAC进行了分层 患者进入了DFS差异超过七倍以上的预后组。我们的分层算法 对PDAC中有利与不利的表观遗传状态提供了简单且在临床上可实现的预测。 基于这项工作，我们现在假设基于ATAC阵列的染色质可及性分析将提供 预测局部和转移性胰腺癌预后的临床相关手段，并进一步 允许合理选择患者进行表观遗传疗法的临床试验。通过此R21赠款，我们现在瞄准 为了优化临床使用的ATAC阵列，并将其扩展到胰腺癌的所有阶段。我们的目标是优化 允许将ATAC阵列应用于从针头活检中获取的较少肿瘤标本的方法。我们 此外，计划在患者衍生的3D器官中在体外筛选表观遗传药物，以确定是否广告 染色质可及性的模式可能适合表观遗传“重编程”疗法，以便使ATAC- 阵列可以提供治疗性生物标志物，以选择表观遗传疗法的患者。这个长期目标 项目是为了提高全基因组评估染色质可及性作为临床相关的可行性 PDAC患者预后的指标，并促进将表观遗传药物合理纳入 表现出较差的表观遗传学特征的患者的治疗方案。