Novel Technologies to Isolate and Analyze Extrachromosomal DNAs for Diagnostic Applications

总结/摘要 染色体外环状DNA（eccDNA）元件是DNA的物理和拓扑学上不同的组分， 真核生物基因组，可以有助于细胞间的拷贝数变异，环境适应， 功能基因组多样性最近，高通量测序已经使广泛的基因组图谱， 可能的eccDNA序列。尽管这一重大进展，有关这些生物成因的信息， 循环DNA和这些DNA元素与人类病理学之间的因果关系，仍然非常重要。 有限公司eccDNA分子的序列、结构和生物学特性构成了一个主要的知识 缺口，有关信息可以导致针对疾病特异性eccDNA结构和功能的策略。 eccDNA代表大范围的分子（~100 bp至> 1 Mbp），并与正常组织中发现的eccDNA共存。 体细胞;分离和表征不同类别的eccDNA伴随着它们自己独特的宿主 挑战为了解决这些知识差距，可以直接询问所有环状DNA物种的方法， 细胞是非常需要的。 在这份FastTrack SBIR提案中，Phinomics，Inc.正在开发一种创新的基于尿液的测试， 将以完整状态分离eccDNA分子，适合下一代测序和表观遗传学 表征，并辅以一套生物物理和新的生物信息学方法，以确定和 定义这些分子。在第一阶段，Phinomics将1）展示Phinomics专有技术的能力， 从人细胞系中分离全面/无偏倚eccDNA库（环组）的技术;和2） 展示Phinomics的技术强大的测序，绘图，组装和信息化的能力 对分离的环状组进行分析。在满足第一阶段的“进行/不进行”里程碑后，在第二阶段，Phinomics将3） Phinomics的技术作为膀胱癌诊断应用的分子平台; 4）扩展 将Phinomics的技术应用于生物流体样品;以及5）开发PCR测试以检测循环 非肌肉浸润性膀胱癌中的DNA种类，以实现CLIA认证。 初步数据已经开始阐明正常体细胞系和组织中的环组，胶质母细胞瘤 肿瘤样品和血浆，增强eccDNA作为固体和液体中有价值的生物标志物的用途， 活检应用。基于eccDNA生物标志物的监测旨在采用微创策略， 确定对治疗的免疫反应，预测复发的可能性，并监测残留疾病。

SUMMARY/ABSTRACT Extrachromosomal circular DNA (eccDNA) elements are physically and topologically distinct components of eukaryotic genomes that can contribute to intercellular copy-number variation, environmental adaptations, and functional genomic diversity. Recently, high-throughput sequencing has made extensive genomic mapping of eccDNA sequences possible. Notwithstanding this major advance, information regarding biogenesis of these circular DNAs and causal connections between these DNA elements and human pathologies, remains extremely limited. The sequences, structure, and biological properties of eccDNA molecules constitute a major knowledge gap, information about which can lead to strategies targeting disease-specific eccDNA structure and function. eccDNAs represent a large range of molecules (~100 bp to >1 Mbp) and coexist with eccDNAs found in normal somatic cells; isolating and characterizing different classes of eccDNA comes with their own host of unique challenges. To address these knowledge gaps, methods that can directly interrogate all circular DNA species in the cell are critically needed. In this FastTrack SBIR proposal, Phinomics, Inc. is developing is developing an innovative urine-based test that will isolate eccDNA molecules in an intact state suitable for next-generation sequencing and epigenetic characterization, and is complemented by a suite of biophysical and novel bioinformatic methods to identify and define these molecules. In Phase I, Phinomics will 1) Demonstrate the capability of Phinomics’ proprietary technology to isolate comprehensive/unbiased eccDNA repertoires (circulomes) from human cell lines; and 2) Demonstrate the capability of Phinomics’ technology to robustly sequence, map, assemble, and informatically profile the isolated circulome. Upon meeting Phase I Go/No-Go milestones, in Phase II Phinomics will 3) Validate Phinomics’ technology as a molecular platform for bladder cancer diagnostic applications; 4) Extend the application of Phinomics’ technologies to biological fluid samples; and 5) Develop a PCR test to detect circular DNA species in non-muscle invasive bladder cancer to enable CLIA certification. Preliminary data has begun to illuminate the circulome in normal somatic cell lines and tissues, glioblastoma tumor samples, and plasma, potentiating the use of eccDNA as a valuable biomarker in both solid- and liquid- biopsy applications. Surveillance based on eccDNA biomarkers is aimed at a minimally invasive strategy to determine the immune response to therapies, predict recurrence likelihood, and monitor residual disease.