Longitudinal therapeutic monitoring of colorectal cancer patients using exosome-based liquid biopsies

使用基于外泌体的液体活检对结直肠癌患者进行纵向治疗监测

基本信息

批准号：
10439595
负责人：
Scott Kopetz
金额：
$ 65.07万
依托单位：
UNIVERSITY OF TX MD ANDERSON CAN CTR
依托单位国家：
美国
项目类别：
财政年份：
2018
资助国家：
美国
起止时间：
2018-07-01 至 2024-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10439595
关键词：
Bioinformatics Biological Biological Assay Biological Markers Biology Biometry Biopsy Blood Blood Circulation CLIA certified Cell Communication Cell Line Cell physiology Cell surface Cells Classification Clinical Clinical Trials Collaborations Colorectal Cancer Computational Biology Consensus DNA Data Development Disease Disease model Distant Epidermal Growth Factor Receptor Frequencies Genetic Transcription Genomics Goals Histones Immunosuppression KRAS2 gene Laboratories Length Letters Lipids Malignant Neoplasms Mass Spectrum Analysis Medical Oncology Membrane Membrane Proteins Methodology Modeling Molecular Molecular Weight Monitor Monitoring Clinical Trials Mutation Neoplasm Circulating Cells Nucleic Acids Oncologist Operative Surgical Procedures Organoids Pathologist Pathology Patients Peptide Vaccines Peptides Performance Plasma Proteins Proteomics RNA Recurrence Reproducibility Resected Residual Neoplasm Resistance Sampling Series Site Solid Neoplasm Surface Technology Text Therapeutic Tissue Sample Tissues Transcript Translating Translations Tumor Debulking Tumor Tissue Tumor Volume Ultracentrifugation Visceral Work actionable mutation base bioinformatics tool biomarker discovery cancer cell cancer genome clinical translation cohort colon cancer patients exosome genomic profiles immunotherapy trials innovation liquid biopsy meetings metastatic colorectal microvesicles molecular diagnostics molecular marker molecular subtypes multidisciplinary neoantigens next generation sequencing preservation prospective standard of care therapy resistant tool transcriptome transcriptome sequencing transcriptomics treatment response treatment stratification tumor tumor microenvironment tumor progression validation studies

项目摘要

Project Summary and Relevance: Exosomes are bi-layered lipid microvesicles containing DNA, RNA and proteins, which have emerged as an important avenue for cell-cell communication in cancer. Our team has performed pioneering studies on the utility of circulating exosomes for genomic and transcriptomic profiling of visceral cancers that are challenging to sample longitudinally. Specifically, we have demonstrated the remarkable integrity of the nucleic acid cargo (exoDNA and exoRNA) contained within exosomes, which makes them readily amenable to next generation sequencing (NGS). The objective of this proposal is to establish the utility of liquid biopsies that enrich for high quality exosomes as a platform for therapeutic stratification and disease monitoring in advanced colorectal cancer (CRC). In Aim 1 will meticulously evaluate the most appropriate methodology for reproducible and sensitive isolation of circulating exosomes from metastatic CRC patients using gradient ultracentrifugation versus two of the most commonly used commercial kits. We will develop perform rigorous biological and technical reproducibility assays on the isolated exosomes and nucleic acid cargo that will develop standards necessary for translation of exosomal-based “liquid biopsy” to a clinical molecular diagnostics laboratory (MDL). We will also perform mass spectrometry-based proteomic profiling of exosomes isolated from a panel of CRC organoid models versus control organoids and cell lines, in order to identify the surface proteins (“surfaceome”) present on CRC-derived exosomes. The surfaceome data will serve as an invaluable tool for enrichment of cancer- specific exosomes in low-volume tumor settings, such as minimal residual disease monitoring. In Aim 2, we will compare targeted mutation panel and copy number profiles of tissue samples in patients undergoing surgical debulking for metastatic (m)CRC, with that of corresponding plasma exoDNA-derived profiles. The remarkable preservation of exoRNA within exosomes will allow us to perform RNA-Seq and compare the consensus molecular subtype (CMS) classification obtained by shed exosomes versus metastatic tissues. Finally, in Aim 3, we will longitudinally monitor cohorts of surgically resected CRC patients, or mCRC patients on two prospective clinical trials, using exosomes as a molecular tool for identifying disease recurrence and emergence of treatment resistance, respectively. The first trial will evaluate for emergence of low frequency KRAS mutations and other secondary drivers of resistance to EGFR-based therapies. The second trial is an immunotherapy trial of multivalent peptide vaccine, where exoRNA data will also be used to predict, and then monitor, expressed neoantigens in mCRC samples, using bioinformatics tools we have developed for mapping transcript data to HLA-presented peptides on the cancer cell surface. The long-term goal of these studies is to generate the compendium of standards and assays needed for successful translation of exosomes as a liquid biopsy platform to the clinical realm.

项目摘要和相关性：外泌体是含有DNA，RNA和蛋白质的双层脂质微囊泡，它们已成为一种癌症细胞传播的重要途径。我们的团队已经对公用事业进行了开创性研究内脏癌的基因组和转录谱分析的循环外泌体的挑战纵向样品。特别是，我们证明了核酸货物的显着完整性（Exodna和Exorna）包含在外泌体内，这使得它们很容易被下一代测序（NGS）。该提案的目的是建立富含高度的液体活检的效用质量外泌体作为治疗分层和疾病监测的平台癌症（CRC）。在AIM 1中，将精心评估可再现和使用梯度超速离心与转移性CRC患者循环外泌体的敏感隔离最常用的两个商业套件。我们将开发执行严格的生物学和技术对孤立的外泌体和核酸货物的可重复性测定将制定必要的标准用于将基于外Nes的“液体活检”转换为临床分子诊断实验室（MDL）。我们将还对从一系列CRC类器官分离的外泌体进行基于质谱的蛋白质组学分析模型与对照器官和细胞系，以识别存在的表面蛋白（“表面”）在CRC衍生的外泌体上。 Surfaceome数据将成为丰富癌症的宝贵工具小体外肿瘤环境中的特定外泌体，例如最小残留疾病监测。在AIM 2中，我们将比较接受手术的患者的靶向突变面板和组织样品的拷贝数谱图延迟转移（M）CRC，其具有相应的等离子体出埃及纳衍生的特征。杰出的在外泌体内保存exorna将使我们能够执行RNA-seq并比较共识通过棚外泌体与转移组织获得的分子亚型（CMS）分类。最后，目标 3，我们将纵向监测手术切除的CRC患者的同类，或两名MCRC患者前瞻性临床试验，使用外泌体作为鉴定疾病复发和出现的分子工具治疗耐药性分别。第一个试验将评估低频KRAS突变的出现以及其他对基于EGFR的疗法的耐药驱动因素。第二次试验是免疫疗法试验多价肽疫苗，其中还将使用Exorna数据预测，然后监测表达 MCRC样品中的新抗原，使用生物信息学工具，我们开发了用于将转录本数据映射到癌细胞表面上的HLA呈现肽。这些研究的长期目标是产生成功翻译外泌体作为液体活检平台所需的标准和测定法到临床领域。