HRD-IA signatures in pancreatic ductal adenocarcinoma

胰腺导管腺癌中的 HRD-IA 特征

• 批准号: 10515859
• 负责人: Michael T Barrett
• 金额: $ 31万
• 依托单位: MAYO CLINIC ARIZONA
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-02-01 至 2025-01-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10515859
• 关键词: Address; American; Aneuploidy; BRCA mutations; BRCA1 gene; BRCA2 gene; Base Excision Repairs; Biological Assay; Biological Models; Biopsy; CLIA certified; Cancer Etiology; Cells; Cellularity; Cessation of life; Chemotherapy-Oncologic Procedure; Chromosome abnormality; Clinic; Clinical; Clinical Research; Clinical Trials; Complex; Copy Number Polymorphism; DNA Damage; DNA Double Strand Break; DNA Repair; Development; Diagnosis; Disease; Environment; Flow Cytometry; Formalin; Freezing; Genome; Genomic Instability; Genomics; Genotype; Lesion; Malignant Neoplasms; Measures; Mediating; Mediator of activation protein; Methods; Molecular; Morphology; Nature; Necrosis; PALB2 gene; Pancreatic Ductal Adenocarcinoma; Paraffin Embedding; Pathogenicity; Patients; Phase; Phenotype; Ploidies; Poly(ADP-ribose) Polymerases; Population; Prediction of Response to Therapy; Procedures; Protocols documentation; Publishing; Quality Control; Research; Resistance; Resources; Sampling; Series; Solid Neoplasm; Sorting - Cell Movement; Tissue Embedding; Tissues; Variant; Work; base; brca gene; cancer cell; cancer genome; chemotherapy; clinical application; clinically relevant; detection assay; genome analysis; genomic aberrations; genomic signature; homologous recombination; inhibitor; interstitial; neoplastic; neoplastic cell; novel; patient biomarkers; patient response; personalized medicine; predictive signature; prospective; response; standard of care; targeted agent; targeted treatment; triple-negative invasive breast carcinoma; tumor; whole genome

ABSTRACT Tumors deficient in homologous recombination display high levels of copy number variants (CNVs) including amplifications, deletions, and breakpoints in their genomes. This homologous recombination deficiency (HRD) phenotype has been associated with pathogenic BRCA mutations in multiple cancers and can be exploited clinically through a synthetic lethal interaction with agents, such as inhibitors of poly ADP- ribose polymerase (PARP) and chemotherapy regimens such as FOLFIRINOX, that increase the level of DNA damage in tumor genomes. Strikingly, subsets of tumors that are wild type for BRCA1 and BRCA2 have shown similar clinical responses to these agents. Preliminary studies suggest that responder tumors have elevated numbers of genomic aberrations even in the absence of variants in the BRCA genes or in other mediators of homologous recombination mediated DNA repair (e.g. PALB2, ATM, and BRIP1). Thus the nature and extent of these lesions in tumor genomes, regardless of genotype, provides a biomarker for patients who will respond to DNA damage and repair targeting therapies. It is estimated that in 2019, 56,770 Americans will be diagnosed with pancreatic ductal adenocarcinoma (PDA) and 45,750 will die from the disease, making PDA the third most common cause of cancer death. Recent clinical trials have made modest improvements in overall survival. Studies suggest that similar to other tumors, elevated numbers of chromosomal aberrations define a HRD signature in a subset of PDAs. A fundamental hypothesis is that this genomic signature predicts those PDA patients likely to respond to PARP inhibitors and to DNA damaging agents. However PDA biopsies are difficult to characterize due to complex genomes and heterogeneous cellularity, as cancer cells represent on average only 25% of the cells within the tumor. Furthermore, biopsies frequently contain multiple neoplastic populations that cannot be distinguished by morphology based methods. To address these clinical challenges we validated DNA content based flow sorting of PDA tissues. Our published methods yield highly purified (>95%) samples suitable for whole genome analyses from a variety of clinical samples. These include both fresh frozen and formalin fixed paraffin embedded (FFPE) tissues with low tumor cell content (<10-20%) and high amounts (>90%) of necrosis and debris. We have identified PDAs with extensive numbers of interstitial aberrations (IAs) in their genomes similar to those observed in HRD-positive BRCAmut tumors. Our results suggest that elevated numbers of IAs correlate with clinical response in PDA. In this study we will establish analytical and processing procedures for our HRD-IA assay then establish a score that distinguishes HRD+ BRCAmut tumors. We will then exploit samples treated with FOLFIRINOX to validate the application of our HRD-IA assay to identify those PDA patients, BRCAmut and BRCAwt, who respond to DNA damage targeting agents. The final phase of this work will validate our sorting and CNV based HRD-IA assay for CLIA application and clinical use.

同源重组缺陷的肿瘤表现出高水平的拷贝数变异 CNVs包括其基因组中的扩增、缺失和断裂点。这种同源重组 缺乏（HRD）表型与多种癌症中的致病性BRCA突变相关， 可以通过与药剂（例如聚ADP的抑制剂）的合成致死相互作用而在临床上开发。 核糖聚合酶（PARP）和化疗方案，如FOLFIRINOX，增加DNA水平 肿瘤基因组的损伤。引人注目的是，BRCA 1和BRCA 2野生型肿瘤的亚群已经显示出 对这些药物的临床反应相似。初步研究表明，反应性肿瘤已经升高， 即使在BRCA基因或其他介体中没有变异的情况下， 同源重组介导的DNA修复（例如PALB 2、ATM和BRIP 1）。因此， 肿瘤基因组中的这些病变，无论基因型如何，都为患者提供了生物标志物， 对DNA损伤和修复靶向治疗有反应。 预计2019年将有56,770名美国人被诊断为胰腺导管腺癌 (PDA)45，750人将死于这种疾病，使PDA成为第三大癌症死亡原因。 最近的临床试验在总体生存率方面取得了适度的改善。研究表明，类似于 在其它肿瘤中，染色体畸变数目的增加定义了PDA亚组中的HRD特征。 一个基本的假设是，这种基因组特征预测那些PDA患者可能对 PARP抑制剂和DNA损伤剂。然而，PDA活检难以表征，因为 复杂的基因组和异质的细胞结构，因为癌细胞平均只占细胞的25%， 在肿瘤内。此外，活组织检查经常包含多个肿瘤群体， 通过基于形态学的方法区分。为了应对这些临床挑战，我们验证了DNA含量 基于PDA组织的流式分选。我们公布的方法产生高度纯化（>95%）的样品，适用于 对各种临床样本进行全基因组分析。这些包括新鲜冷冻和福尔马林固定 石蜡包埋（FFPE）组织，肿瘤细胞含量低（<10-20%），坏死量高（>90%） 和碎片。我们已经发现PDA的基因组中存在大量的间质畸变（IA） 与HRD阳性BRCAmut肿瘤中观察到的相似。我们的研究结果表明， 与PDA的临床反应相关。在这项研究中，我们将建立分析和处理程序， 然后我们的HRD-IA测定建立区分HRD+ BRCAmut肿瘤的评分。然后我们将利用 用FOLFIRINOX处理的样本，以验证我们的HRD-IA检测法在鉴定这些PDA中的应用 BRCAmut和BRCAwt患者，他们对DNA损伤靶向药物有反应。这项工作的最后阶段将 验证我们的分选和基于CNV的HRD-IA测定用于CLIA应用和临床使用。