Summary

基于化学亲和力的生物流体细胞外囊泡分离用于蛋白质组学和磷酸化蛋白质组学分析

Published: October 27, 2023
doi:

Summary

本方案为利用功能化磁珠有效分离尿细胞外囊泡提供了详细的描述。此外,它还包括后续分析,包括蛋白质印迹、蛋白质组学和磷酸化蛋白质组学。

Abstract

来自生物流体的细胞外囊泡 (EV) 最近在液体活检领域引起了极大的关注。它们由几乎所有类型的细胞释放,提供宿主细胞的实时快照,并包含丰富的分子信息,包括蛋白质,特别是那些具有翻译后修饰 (PTM) 的蛋白质,如磷酸化,作为细胞功能和疾病发生和进展的主要参与者。然而,由于当前 EV 分离方法的产量和杂质低,从生物流体中分离 EV 仍然具有挑战性,这使得 EV 货物(如 EV 磷蛋白)的下游分析变得困难。在这里,我们描述了一种基于功能化磁珠的快速有效的 EV 分离方法,用于从生物流体(如人尿液)中分离 EV 和 EV 分离后的下游蛋白质组学和磷酸化蛋白质组学分析。该方案实现了尿 EV 的高回收率以及 EV 蛋白质组和磷酸化蛋白质组的敏感谱。此外,本文还讨论了该协议的多功能性和相关技术考虑因素。

Introduction

细胞外囊泡 (EV) 是由所有类型的细胞分泌的膜包膜纳米颗粒,存在于血液、尿液、唾液等生物流体1,2,3,4。EV 携带多种生物活性分子,这些分子反映了宿主细胞的生理和病理状态,因此是疾病进展的关键因素 4,5,6此外,广泛的研究已经确定,基于 EV 的疾病标志物可以在症状出现或肿瘤生理检测之前被识别出来 5,6,7

磷酸化是细胞信号传导和调节的关键机制。因此,磷蛋白为生物标志物的发现提供了有价值的来源,因为异常的磷酸化事件与失调的细胞信号通路和转移性疾病的发展(如癌症)有关8,9,10。尽管分析磷酸化动力学可以识别疾病特异性磷蛋白特征作为潜在的生物标志物,但磷蛋白的低丰度和动态性质对开发磷蛋白作为生物标志物构成了重大挑战11,12。值得注意的是,封装在 EV 中的低丰度磷蛋白在细胞外环境中受到保护,免受外部酶消化的影响8。因此,EV 和 EV 衍生的磷蛋白为癌症和其他疾病的早期检测中的生物标志物发现提供了理想的来源。

尽管对 EV 中蛋白质磷酸化的分析为了解癌症信号传导和早期疾病诊断提供了宝贵的资源,但缺乏有效的 EV 分离方法是一个主要障碍。EV 隔离通常通过差示超速离心 (DUC)13 实现。然而,这种方法耗时且由于通量低和重现性差而不适合临床意义13,14。替代 EV 分离方法(例如聚合物诱导沉淀15)由于非 EV 蛋白的共沉淀而受到低特异性的限制。基于亲和力的方法,包括基于抗体的亲和力捕获16 和亲和力过滤17,可提供增强的特异性,但由于体积小,回收率相对较低。

为了解决探索 EV 中磷蛋白动力学的问题,我们课题组开发了基于化学亲和力的细胞外囊泡全回收和纯化 (EVtrap) 技术,将 EV 捕获到功能化的磁珠上18。先前的结果表明,与DUC和其他现有分离方法相比,这种基于磁珠的EV分离方法在从各种生物流体样品中分离EV方面非常有效,并且能够实现更高的EV产量,同时最大限度地减少污染18,19。我们已经成功地利用了 EVtrap 和我们小组20 开发的钛基磷酸肽富集方法来分析来自不同生物流体的 EV 的磷酸化蛋白质组,并检测各种疾病的潜在磷蛋白生物标志物192122

在这里,我们提出了一种基于EVtrap的协议,用于分离循环的EV。该协议侧重于泌尿 EV。我们还演示了使用蛋白质印迹法对分离的 EV 进行表征。然后,我们详细介绍了蛋白质组学和磷酸化蛋白质组学分析的样品制备和质谱 (MS) 采集。该协议为分析尿液 EV 蛋白质组和磷酸化蛋白质组提供了高效且可重复的工作流程,这将有助于对 EV 及其临床应用的进一步研究23

Protocol

所有尿液样本均在知情同意后从健康个体中收集。这些实验符合涉及人体样本的所有伦理标准,并符合普渡大学人类研究保护计划的指导方针。 1. 样品采集 在2,500× g,4°C下将12mL尿液样品在15mL锥形离心管中离心10分钟,以除去细胞碎片和大凋亡体。 将 10 mL 上清液转移到新的 15 mL 试管中,然后进行 EV 分离。注意:方案可以在这里暂停,?…

Representative Results

该协议展示了从EV分离到下游蛋白质组学和磷酸化蛋白质组学分析的综合工作流程(图1)。对一式三份的尿液样本进行EV分离。分离的 EV 通过蛋白质印迹进行表征,随后进行基于质谱的蛋白质组学样品制备,包括蛋白质提取、酶消化和肽纯化。对于磷酸化蛋白质组学分析,基于金属离子功能化的可溶性纳米聚合物进一步富集了磷酸肽。多肽和磷酸肽样品均在数据无关模式下?…

Discussion

有效的EV分离是检测EV中低丰度蛋白质和磷蛋白的重要先决条件。尽管开发了许多方法来满足这一需求,但大多数方法仍然存在局限性,例如恢复率差或可重复性低,这阻碍了它们在大规模研究和常规临床环境中的使用。DUC 通常被认为是最常见的 EV 隔离方法,通常应用额外的洗涤步骤来帮助提高目标 EV 的纯度27,28。此过程会导致更繁琐和耗时的 DUC 过程…

Disclosures

The authors have nothing to disclose.

Acknowledgements

这项工作部分由 NIH 赠款 3RF1AG064250 和 R44CA239845资助。

Materials

1.5 mL microcentrifuge tube Life Science Products M-1700C-LB
1.5 mL tube magnetic separator rack Sergi Lab Supplies 1005
15 mL conical centrifuge tube Corning  352097
15 mL tube magnetic separator rack Sergi Lab Supplies 1002
Anti-rabbit IgG, HRP-linked Antibody Cell Signaling Technology 7074P2
Benchtop incubated shaker Bioer DIS-87999-3367802 Bioer Thermocell Mixing Block MB-101
CD9 (D3H4P) Rabbit mAb Cell Signaling Technology 13403S
Chloroacetamide Sigma -Aldrich C0267-100G Used for alkylation of reduced sulfide groups. Freshly prepare 400 mM in water as stock solution.
Ethyl acetate  Fisher Scientific  E145-4 Precipitates detergents
Evosep One  Evosep Liquid chromatography system
Evotips Evosep EV2013 Sample loading for Evosep One system 
EVtrap Tymora Analytical Functionalized magnetic beads, loading buffer, and washing buffer 
Immobilon-FL PVDF Membrane Sigma -Aldrich IPFL00010 Blotting membrane 
NuPAGE 4-12% Bis-Tris Gel Invitrogen NP0322BOX Invitrogen NuPAGE 4 to 12%, Bis-Tris, 1.0 mm, Mini Protein Gel, 12-well
NuPAGE LDS Sample Buffer (4X) Invitrogen NP0007
PBS ThermoFisher 10010023
Pepsep C18 15 x 75 x 1.9 Bruker  1893473 Separation column 
Phosphatase Inhibitor Cocktail 2 Sigma -Aldrich P5726-5ML 100X, Phosphotase inhibitor.
Phosphatase Inhibitor Cocktail 3 Sigma -Aldrich P0044-1ML 100X,  Phosphotase inhibitor. 
Pierce BCA Protein Assay Kit ThermoFisher 23225
Pierce ECL Western Blotting Substrate ThermoFisher 32106 HRP substrate 
PolyMAC phosphopeptide enrichment kit Tymora Analytical Polymer-based metal ion affinity capture (PolyMAC) for phosphopeptide enrichment
Sodium deoxycholate  Sigma -Aldrich D6750-10G Detergent for lysis buffer. Prepare 120 mM in water as stock solution.
Sodium lauroyl sarcosinate  Sigma -Aldrich L9150-50G Detergent for lysis buffer. Prepare 120 mM in water as stock solution.
timsTOF HT Bruker Trapped ion-mobility time-of-flight mass spectrometry
TopTip C-18 (10-200 μL) tips  Glygen TT2C18.96 Desalting method
Triethylamine Sigma -Aldrich 471283-100ML For EV elution. 
Triethylammonium bicabonate buffer Sigma -Aldrich T7408-100ML 1 M
Trifluoroacetic acid Sigma -Aldrich 302031-100ML
Tris-(2-carboxyethyl)phosphine hydrochloride Sigma -Aldrich C4706 Used for reducion of disulfide bonds. Prepare 200 mM in water as stock solution. Aliquot the stock solution into small volume and store it in at-20°C (avoid multiple freeze-thaw cycles).
Trypsin/Lys-C MIX ThermoFisher PIA41007

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Cite This Article
Liu, Y., Luo, Z., Iliuk, A., Tao, W. A. Chemical Affinity-Based Isolation of Extracellular Vesicles from Biofluids for Proteomics and Phosphoproteomics Analysis. J. Vis. Exp. (200), e65844, doi:10.3791/65844 (2023).

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