Leveraging canine spontaneous cancer to optimize the power of blood biopsy

利用犬自发癌优化血液活检的功效

• 批准号: 10844821
• 负责人: Elinor Karlsson
• 金额: $ 4.5万
• 依托单位: UNIV OF MASSACHUSETTS MED SCH WORCESTER
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-06-07 至 2026-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10844821
• 关键词: Address; Administrative Supplement; Affect; Award; Biopsy; Blood; Cancer Patient; Canis familiaris; Cells; Circulation; Clinical; Collecting Cell; Collection; Custom; DNA; DNA Methylation; DNA analysis; DNA copy number; DNA methylation profiling; Data; Data Correlations; Data Set; Detection; Diagnosis; Diagnostic; Disease; Elements; Evaluation; Goals; Hemangiosarcoma; Hematopoiesis; Histologic; Human; Incidence; Length; Licorice; Location; Lymphoma; Machine Learning; Malignant Neoplasms; Methodology; Methylation; Monitor; Mutation; Patient-Focused Outcomes; Patients; Peripheral; Plasma; Point Mutation; Procedures; Proteins; RNA; Recurrence; Relapse; Residual state; Sampling; Sensitivity and Specificity; Standardization; Techniques; Technology; Tissues; Tumor Burden; Tumor-Derived; Veins; Work; cancer therapy; design; diagnostic platform; exosome; genome sequencing; improved; interest; large cell Diffuse non-Hodgkin' s lymphoma; liquid biopsy; methylome; multimodality; neoplastic cell; osteosarcoma; outcome prediction; prevent; prospective; tool; tumor; tumor DNA; whole genome

ABSTRACT Blood biopsy is a rapidly advancing technology in which circulating elements (DNA, RNA, proteins, exosomes) released from tumor cells are collected and assessed. In most cases, the circulating free DNA (cfDNA) is collected, and the circulating tumor DNA (ctDNA) within the cfDNA is quantified and analyzed. Blood biopsy has the potential to transform cancer treatment, but several challenges remain that prevent widespread application including the need to standardize collection and processing procedures, optimize sequencing/analysis platforms, and correlate data generated with long-term patient outcomes. Our current NCI R01 award (CA255319) leverages pet dogs with spontaneous cancer as a tool for improving blood biopsy technologies and as a tool for advancing effective implementation in human patients. The aims of this work award are to 1) assess ctDNA/tumor mutation concordance and optimize the parameters for diagnostic sampling; 2) utilize cancer in pet dogs to improve ctDNA deep duplex sequencing diagnostics; and 3) determine the accuracy of blood biopsy for monitoring disease status and predicting outcome in affected dogs. Over the past 2 years we have made significant progress on these goals, including sequencing more than 260 samples from over 110 dogs. Our data demonstrate that location of blood draw (central versus peripheral vein) influences ctDNA yield, and that ctDNA becomes detectable an average of 90 days prior to clinical relapse in dogs with lymphoma. We further identified clonal hematopoiesis of indeterminate potential (CHIP) mutations in 10.8% of samples, supporting the routine incorporation of CHIP detection in blood biopsy diagnostics. However, up to 20% of canine samples had no detectable copy number changes and a low tumor fraction, despite a very high clinical tumor burden. These data are concordant with recent findings in human cancer patients, creating a diagnostic challenge, particularly in tumors with high structural complexity and low incidence of recurrent point mutations. To address these issues, there is broad interest in evaluating other factors affecting cfDNA, such as methylation. Indeed, unique tissue- specific methylation signatures can determine the cell of origin of DNA in circulation, and in combination with tumor fraction and copy number analysis, have the potential to increase sensitivity and accuracy of liquid biopsy detection. As such, the purpose of this administrative supplement is to analyze the methylome of cfDNA from dogs with histologically confirmed cancers and incorporate these results into our existing ctDNA copy number pipeline. To accomplish this, we propose to first validate the methylation signatures of cfDNA in canine cancers, then characterize the accuracy of multi-modal cfDNA analysis for detection and monitoring of these cancers. All necessary samples have already been collected, along with associated patient outcome data, permitting completion of planned studies within 12 months. Data generated from this administrative supplement will support prospective incorporation of tumor methylome analytics into a multi-parameter blood biopsy diagnostic platform designed to enhance clinical impact in human cancer patients.

摘要 血液活检是一项快速发展的技术，其中循环元素（DNA，RNA，蛋白质，外来体） 收集并评估从肿瘤细胞释放的细胞。在大多数情况下，循环游离DNA（cfDNA）是 收集，并定量和分析cfDNA内的循环肿瘤DNA（ctDNA）。血液活检有 改变癌症治疗的潜力，但仍存在一些挑战，阻碍了广泛应用 包括需要标准化收集和处理程序，优化测序/分析平台， 并将生成的数据与长期患者结果相关联。我们目前的NCI R 01奖项（CA 255319） 利用患有自发性癌症的宠物狗作为改善血液活检技术的工具， 促进在人类患者中的有效实施。该奖项的目的是：（1）评估 ctDNA/肿瘤突变一致性并优化诊断采样的参数; 2）在宠物中利用癌症 狗，以改善ctDNA深度双链测序诊断;和3）确定血液活检的准确性， 监测患病犬的疾病状态并预测结果。在过去的两年里，我们取得了 这些目标取得了重大进展，包括对110多只狗的260多个样本进行测序。我们的数据 证明了抽血的位置（中心静脉与外周静脉）影响ctDNA产量，并且ctDNA 在患有淋巴瘤的狗的临床复发前平均90天可检测到。我们进一步确认 在10.8%的样本中发现了不确定潜能的克隆性造血（CHIP）突变，支持常规 在血液活检诊断中结合CHIP检测。然而，高达20%的犬样本没有 可检测的拷贝数变化和低肿瘤分数，尽管临床肿瘤负荷非常高。这些数据 与最近在人类癌症患者中的发现一致，创造了诊断挑战，特别是在 具有高结构复杂性和低复发性点突变发生率的肿瘤。为了解决这些问题， 人们对评价影响cfDNA的其它因素如甲基化有广泛的兴趣。实际上，独特的组织- 特异性甲基化标记可以确定循环中DNA的细胞来源，并与 肿瘤分数和拷贝数分析，有可能增加液体活检的灵敏度和准确性 侦测因此，本行政补充的目的是分析来自以下的cfDNA的甲基化组： 组织学证实患有癌症的狗，并将这些结果纳入我们现有的ctDNA拷贝数 渠道.为了实现这一点，我们建议首先验证犬癌症中cfDNA的甲基化特征， 然后表征用于检测和监测这些癌症的多模式cfDNA分析的准确性。所有 已经收集了必要的样本，沿着相关的患者结局数据， 在12个月内完成计划的研究。本行政补充文件生成的数据将支持 肿瘤甲基化组分析的前瞻性合并到多参数血液活检诊断平台中 旨在增强对人类癌症患者的临床影响。

项目成果

Lifetime prevalence of owner-reported medical conditions in the 25 most common dog breeds in the Dog Aging Project pack.

• DOI: 10.3389/fvets.2023.1140417
• 发表时间: 2023
• 期刊: Frontiers in veterinary science
• 影响因子: 3.2

Using evolutionary constraint to define novel candidate driver genes in medulloblastoma.

• DOI: 10.1073/pnas.2300984120
• 发表时间: 2023-08-15
• 期刊: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• 影响因子: 11.1
• 作者: Roy, Ananya;Sakthikumar, Sharadha;Kozyrev, Sergey V.;Nordin, Jessika;Pensch, Raphaela;Makelainen, Suvi;Pettersson, Mats;Karlsson, Elinor K.;Lindblad-Toh, Kerstin;Forsberg-Nilsson, Karin
• 通讯作者: Forsberg-Nilsson, Karin

Dog size and patterns of disease history across the canine age spectrum: Results from the Dog Aging Project.

• DOI: 10.1371/journal.pone.0295840
• 发表时间: 2024
• 期刊: PloS one
• 影响因子: 3.7

​Comparative genomics of Balto, a famous historic dog, captures lost diversity of 1920s sled dogs.

• DOI: 10.1126/science.abn5887
• 发表时间: 2023-04-28
• 期刊: Science (New York, N.Y.)