Enhanced In Situ Spatial Proteomics by Effective Combination of MALDI Imaging and LC-MS/MS.

IF 6.1 2区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS
Molecular & Cellular Proteomics Pub Date : 2024-08-01 Epub Date: 2024-07-11 DOI:10.1016/j.mcpro.2024.100811
Frederike Schäfer, Archana Tomar, Shogo Sato, Raffaele Teperino, Axel Imhof, Shibojyoti Lahiri
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引用次数: 0

Abstract

Highly specialized cells are fundamental for the proper functioning of complex organs. Variations in cell-type-specific gene expression and protein composition have been linked to a variety of diseases. Investigation of the distinctive molecular makeup of these cells within tissues is therefore critical in biomedical research. Although several technologies have emerged as valuable tools to address this cellular heterogeneity, most workflows lack sufficient in situ resolution and are associated with high costs and extremely long analysis times. Here, we present a combination of experimental and computational approaches that allows a more comprehensive investigation of molecular heterogeneity within tissues than by either shotgun LC-MS/MS or MALDI imaging alone. We applied our pipeline to the mouse brain, which contains a wide variety of cell types that not only perform unique functions but also exhibit varying sensitivities to insults. We explored the distinct neuronal populations within the hippocampus, a brain region crucial for learning and memory that is involved in various neurological disorders. As an example, we identified the groups of proteins distinguishing the neuronal populations of the dentate gyrus (DG) and the cornu ammonis (CA) in the same brain section. Most of the annotated proteins matched the regional enrichment of their transcripts, thereby validating the method. As the method is highly reproducible, the identification of individual masses through the combination of MALDI-IMS and LC-MS/MS methods can be used for the much faster and more precise interpretation of MALDI-IMS measurements only. This greatly speeds up spatial proteomic analyses and allows the detection of local protein variations within the same population of cells. The method's general applicability has the potential to be used to investigate different biological conditions and tissues and a much higher throughput than other techniques making it a promising approach for clinical routine applications.

通过有效结合 MALDI 成像和 LC-MS/MS,增强原位空间蛋白质组学。
高度特化的细胞是复杂器官正常运作的基础。细胞类型特异性基因表达和蛋白质组成的变化与多种疾病有关。因此,研究组织内这些细胞的独特分子构成在生物医学研究中至关重要。虽然有几种技术已成为解决这种细胞异质性的重要工具,但大多数工作流程缺乏足够的原位分辨率,而且成本高昂,分析时间极长。在这里,我们介绍了一种实验与计算相结合的方法,它能比单独使用枪式 LC-MS/MS 或 MALDI 成像更全面地研究组织内的分子异质性。我们在小鼠大脑中应用了我们的方法,小鼠大脑包含多种细胞类型,它们不仅具有独特的功能,而且对损伤的敏感性也各不相同。我们探索了海马区内不同的神经元群,海马区是一个对学习和记忆至关重要的脑区,与各种神经系统疾病有关。例如,我们确定了在同一脑切片中区分齿状回(DG)和胼胝体(CA)神经元群的蛋白质组。大多数被注释的蛋白质与其转录本的区域富集相匹配,从而验证了该方法的有效性。由于该方法具有很高的可重复性,因此通过 MALDI-IMS 和 LC-MS/MS 方法的结合对单个质量进行鉴定,可用于更快、更精确地解释仅 MALDI-IMS 测量结果。这大大加快了空间蛋白质组分析的速度,并能检测同一细胞群中局部蛋白质的变化。该方法具有普遍适用性,可用于研究不同的生物条件和组织,而且比其他技术的通量要高得多,因此在临床常规应用中大有可为。
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来源期刊
Molecular & Cellular Proteomics
Molecular & Cellular Proteomics 生物-生化研究方法
CiteScore
11.50
自引率
4.30%
发文量
131
审稿时长
84 days
期刊介绍: The mission of MCP is to foster the development and applications of proteomics in both basic and translational research. MCP will publish manuscripts that report significant new biological or clinical discoveries underpinned by proteomic observations across all kingdoms of life. Manuscripts must define the biological roles played by the proteins investigated or their mechanisms of action. The journal also emphasizes articles that describe innovative new computational methods and technological advancements that will enable future discoveries. Manuscripts describing such approaches do not have to include a solution to a biological problem, but must demonstrate that the technology works as described, is reproducible and is appropriate to uncover yet unknown protein/proteome function or properties using relevant model systems or publicly available data. Scope: -Fundamental studies in biology, including integrative "omics" studies, that provide mechanistic insights -Novel experimental and computational technologies -Proteogenomic data integration and analysis that enable greater understanding of physiology and disease processes -Pathway and network analyses of signaling that focus on the roles of post-translational modifications -Studies of proteome dynamics and quality controls, and their roles in disease -Studies of evolutionary processes effecting proteome dynamics, quality and regulation -Chemical proteomics, including mechanisms of drug action -Proteomics of the immune system and antigen presentation/recognition -Microbiome proteomics, host-microbe and host-pathogen interactions, and their roles in health and disease -Clinical and translational studies of human diseases -Metabolomics to understand functional connections between genes, proteins and phenotypes
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