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脑肿瘤研究中脑脊液蛋白质组学的综合工作流程

A Comprehensive Workflow for Cerebrospinal Fluid Proteomics in the Study of Brain Tumors.

作者信息

Halder Ankit, Dutta Suhisna, Srivastava Sanjeeva

机构信息

Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India.

出版信息

Methods Mol Biol. 2025;2914:183-199. doi: 10.1007/978-1-0716-4462-1_14.

DOI:10.1007/978-1-0716-4462-1_14
PMID:40167919
Abstract

The cerebrospinal fluid (CSF) plays a critical role in maintaining homeostasis within the central nervous system (CNS). Detecting protein alterations in CSF associated with brain tumors offers a unique opportunity to enhance diagnosis, prognosis, recurrence monitoring, and treatment response. As an extracellular component of the CNS, it serves as a valuable reservoir of biomarkers that reflect changes associated with brain tumors-biomarkers that are often difficult to detect in the systemic circulation due to the blood-brain barrier. Advances in liquid biopsy techniques for CSF, coupled with high-throughput technologies, have the potential to significantly benefit patients. Here, we provide a comprehensive overview of methodologies for studying the CSF proteome to identify brain tumor-associated alterations.

摘要

脑脊液(CSF)在维持中枢神经系统(CNS)内的稳态中起着关键作用。检测与脑肿瘤相关的脑脊液中的蛋白质变化为提高诊断、预后、复发监测和治疗反应提供了独特的机会。作为中枢神经系统的细胞外成分,它是反映与脑肿瘤相关变化的生物标志物的宝贵储存库——由于血脑屏障,这些生物标志物在体循环中往往难以检测到。脑脊液液体活检技术的进展,再加上高通量技术,有可能使患者显著受益。在此,我们全面概述了研究脑脊液蛋白质组以识别脑肿瘤相关变化的方法。

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本文引用的文献

1
Proteomic profiling of cerebrospinal fluid reveals TKT as a potential biomarker for medulloblastoma.脑脊液蛋白质组学分析显示 TKT 可能成为髓母细胞瘤的潜在生物标志物。
Sci Rep. 2024 Sep 10;14(1):21053. doi: 10.1038/s41598-024-71738-z.
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Mass spectrometry-based proteomics of cerebrospinal fluid in pediatric central nervous system malignancies: a systematic review with meta-analysis of individual patient data.基于质谱的小儿中枢神经系统恶性肿瘤脑脊液蛋白质组学:一项基于个体患者数据的系统评价和荟萃分析。
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Analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform.
使用 MSFragger-DIA 和 FragPipe 计算平台分析 DIA 蛋白质组学数据。
Nat Commun. 2023 Jul 12;14(1):4154. doi: 10.1038/s41467-023-39869-5.
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Recent advances in mass-spectrometry based proteomics software, tools and databases.基于质谱的蛋白质组学软件、工具和数据库的最新进展。
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Data-independent acquisition (DIA): An emerging proteomics technology for analysis of drug-metabolizing enzymes and transporters.数据非依赖采集(DIA):一种新兴的蛋白质组学技术,用于分析药物代谢酶和转运体。
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Use of Hybrid Data-Dependent and -Independent Acquisition Spectral Libraries Empowers Dual-Proteome Profiling.使用混合数据相关和非相关采集谱库实现双蛋白质组分析。
J Proteome Res. 2021 Feb 5;20(2):1165-1177. doi: 10.1021/acs.jproteome.0c00350. Epub 2021 Jan 19.
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Brief Bioinform. 2021 Jan 18;22(1):315-333. doi: 10.1093/bib/bbz160.
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In silico spectral libraries by deep learning facilitate data-independent acquisition proteomics.深度学习构建的虚拟光谱库促进了数据非依赖采集蛋白质组学的发展。
Nat Commun. 2020 Jan 9;11(1):146. doi: 10.1038/s41467-019-13866-z.
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Affinity depletion versus relative protein enrichment: a side-by-side comparison of two major strategies for increasing human cerebrospinal fluid proteome coverage.亲和去除与相对蛋白质富集:两种增加人类脑脊液蛋白质组覆盖率的主要策略的并列比较。
Clin Proteomics. 2019 Feb 26;16:9. doi: 10.1186/s12014-019-9229-1. eCollection 2019.