Effect of methodological and biological variability on molecular profiling of extracellular vesicles in cancer detection

方法学和生物学变异对癌症检测中细胞外囊泡分子谱的影响

• 批准号: 10509911
• 负责人: IONITA Calin GHIRAN
• 金额: $ 41.47万
• 依托单位: NORTHEASTERN UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-03-15 至 2024-02-29
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10509911
• 关键词: Behavior; Biogenesis; Biological; Biology; Blood; Blood specimen; Cancer Detection; Cancer Patient; Cell physiology; Clinical Medicine; Collection; Data; Diagnostic; Disease; Excision; Gene Expression; Goals; Grant; Health; Immune response; Lipids; Malignant Neoplasms; Methodology; Methods; Molecular; Molecular Profiling; Neoplasm Metastasis; Organ; Paracrine Communication; Pathologic; Patients; Post-Translational Protein Processing; Preparation; Proteins; Proteomics; Publishing; RNA; Reproducibility; Sampling; Screening for cancer; Signal Transduction; Source; Specificity; Techniques; Time; Tissues; analytical method; base; biomarker discovery; cell type; disease diagnosis; extracellular vesicles; glycoproteomics; insight; nanoflow cytometry; novel; personalized medicine; prognostic

Project Summary A novel paradigm in paracrine signaling has recently emerged based on the findings identifying extracellular vesicles (EVs) as intercellular conveyors of biological information both in normal and pathological conditions such as cancer. EVs and their cargo have been shown by us and others to regulate gene expression and alter cell function in various cell types. Moreover, during pathological conditions such as cancer, the number and compositions of EVs alter the host immune response as well as synchronize the behavior of secondary tumors. Isolation and molecular profiling of EVs (i.e. RNAs, proteins, post-translational modifications, lipids, metabolites) both in health and disease are critical for understanding EVs' biogenesis and effector functions. Currently, the study of EVs as biological entities relevant for intracellular signaling and disease diagnosis is based on the assumption that the biogenesis and removal of EVs happen at a steady state rate, being modified mostly by the healthy/diseased status of the host. Our published results show that that is not the case. Our data indicate that the tissue-origin, number, size distribution, as well as protein, lipid, metabolite and RNA composition of EVs isolated by standard techniques depend not just on the blood collection methods, but also on the time of the day the blood samples were collected. Therefore, systematic assessment of these factors and other sources of variability in EV profiles are important for enabling basic biology, clinical and personalized medicine applications. Although it is beyond the purpose of this grant, the long-term goal of our team is to establish reproducible methods for blood collection and sample processing that would allow us to identify the specific molecular EV signatures during the day/night cycle, with the aim of pinpointing the ideal, organ-specific times for blood collection, which would increase the reliability and specificity of early cancer detection. We believe that establishing biological and methodological baselines are absolutely vital for correctly comparing proteomics and glycomics data obtained in various studies, as well as interpreting the data obtained from patients’ samples.

项目摘要 旁分泌信号传导中的一种新型范式最近根据发现细胞外的发现而出现 在正常和病理条件下，蔬菜（EV）作为生物信息的细胞间输送体 例如癌症。 EV及其货物已由我们和其他人显示，以调节基因表达并改变 各种细胞类型中的细胞功能。此外，在癌症，数量和数量等病理状况下 EV的组成改变了宿主免疫响应，并同步次级肿瘤的行为。 EV的分离和分子分析（即RNA，蛋白质，翻译后修饰，脂质， 健康和疾病中的代谢物对于理解电动汽车的生物发生和效应子功能至关重要。 目前，将电动汽车作为与细胞内信号传导和疾病诊断相关的生物实体的研究是 基于以下假设：EV的生物发生和去除以稳态速率发生， 主要是由宿主的健康/患病状况进行修改。我们发表的结果表明，那不是 案件。我们的数据表明组织 - 原始数量，数量，尺寸分布以及蛋白质，脂质，代谢物和 标准技术分离的电动汽车的RNA组成不仅取决于血液收集方法，还取决于 同样在一天中收集血液样本。因此，对这些的系统评估 EV轮廓中的因素和其他可变性来源对于启用基本生物学，临床和 个性化医学应用。 尽管这超出了这笔赠款的目的，但我们团队的长期目标是建立可重现的 血液收集和样品加工的方法，使我们能够识别特定的分子EV 白天/夜间周期的签名，目的是指出理想的特定器官特定时间的血液 收集，这将增加早期癌症检测的可靠性和特异性。我们相信 建立生物学和方法论基准对于正确比较蛋白质组学绝对至关重要 以及在各种研究中获得的数据，以及解释从患者获得的数据 样品。

项目成果

Capillary Electrophoresis Coupled to Electrospray Ionization Tandem Mass Spectrometry for Ultra-Sensitive Proteomic Analysis of Limited Samples.

• DOI: 10.1021/acs.analchem.1c02929
• 发表时间: 2022-01-18
• 期刊: Analytical chemistry
• 影响因子: 7.4
• 作者: Johnson KR;Greguš M;Kostas JC;Ivanov AR
• 通讯作者: Ivanov AR

Experimental and data analysis advances in thermal proteome profiling.

热蛋白质组分析的实验和数据分析取得了进展。

• DOI: 10.1016/j.crmeth.2024.100717
• 发表时间: 2024
• 期刊: Cell reports methods
• 作者: Figueroa-Navedo,AmandaM;Ivanov,AlexanderR
• 通讯作者: Ivanov,AlexanderR

Extracellular Vesicle Refractive Index Derivation Utilizing Orthogonal Characterization.

• DOI: 10.1021/acs.nanolett.3c00562
• 发表时间: 2023-10-25
• 期刊: NANO LETTERS
• 影响因子: 10.8
• 作者: Pleet, Michelle L.;Cook, Sean;Tang, Vera A.;Stack, Emily;Ford, Verity J.;Lannigan, Joanne;Do, Ngoc;Wenger, Ellie;Fraikin, Jean-Luc;Jacobson, Steven;Jones, Jennifer C.;Welsh, Joshua A.
• 通讯作者: Welsh, Joshua A.

SnRNA sequencing defines signaling by RBC-derived extracellular vesicles in the murine heart.

• DOI: 10.26508/lsa.202101048
• 发表时间: 2021-12
• 期刊: Life science alliance
• 影响因子: 4.4
• 作者: Valkov N;Das A;Tucker NR;Li G;Salvador AM;Chaffin MD;Pereira De Oliveira Junior G;Kur I;Gokulnath P;Ziegler O;Yeri A;Lu S;Khamesra A;Xiao C;Rodosthenous R;Srinivasan S;Toxavidis V;Tigges J;Laurent LC;Momma S;Kitchen R;Ellinor P;Ghiran I;Das S
• 通讯作者: Das S

A systematic approach to development of analytical scale and microflow-based liquid chromatography coupled to mass spectrometry metabolomics methods to support drug discovery and development.

• DOI: 10.1016/j.chroma.2021.462047
• 发表时间: 2021-04-12
• 期刊: Journal of chromatography. A
• 作者: Geller S;Lieberman H;Kloss A;Ivanov AR
• 通讯作者: Ivanov AR