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FrozONE：用于冷冻组织全面蛋白质组学分析的快速细胞核富集法

FrozONE: quick cell nucleus enrichment for comprehensive proteomics analysis of frozen tissues.

作者信息

Huschet Lukas A, Kliem Fabian P, Wienand Peter, Wunderlich Claudia M, Ribeiro Andrea, Bustos-Martínez Isabel, Barco Ángel, Wunderlich F Thomas, Lech Maciej, Robles Maria S

机构信息

Institute of Medical Psychology and Biomedical Center (BMC), Faculty of Medicine, LMU, Munich, Germany.

Max Planck Institute for Metabolism Research, Center for Molecular Medicine Cologne (CMMC) and Policlinic for Endocrinology, Diabetes, and Preventive Medicine (PEDP), University Hospital Cologne, Cologne, Germany.

出版信息

Life Sci Alliance. 2024 Dec 12;8(3). doi: 10.26508/lsa.202403130. Print 2025 Mar.

DOI:10.26508/lsa.202403130
PMID:39667914
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11638322/
Abstract

Subcellular fractionation allows for the investigation of compartmentalized processes in individual cellular organelles. Nuclear enrichment methods commonly employ the use of density gradients combined with ultracentrifugation for freshly isolated tissues. Although it is broadly used in combination with proteomics, this approach poses several challenges when it comes to scalability and applicability for frozen material. To overcome these limitations, we developed FrozONE (Frozen Organ Nucleus Enrichment), a nucleus enrichment and proteomics workflow for frozen tissues. By extensively benchmarking our workflow against alternative methods, we showed that FrozONE is a faster, simpler, and more scalable alternative to conventional ultracentrifugation methods. FrozONE allowed for the study, profiling, and classification of nuclear proteomes in different tissues with complex cellular heterogeneity, ensuring optimal nucleus enrichment from different cell types and quantitative resolution for low abundant proteins. In addition to its performance in healthy mouse tissues, FrozONE proved to be very efficient for the characterization of liver nuclear proteome alterations in a pathological condition, diet-induced nonalcoholic steatohepatitis.

摘要

亚细胞分级分离能够研究单个细胞器中分隔化的过程。细胞核富集方法通常将密度梯度与超速离心结合用于新鲜分离的组织。尽管它广泛与蛋白质组学结合使用，但在可扩展性和对冷冻材料的适用性方面，这种方法存在一些挑战。为了克服这些限制，我们开发了FrozONE（冷冻器官细胞核富集），这是一种用于冷冻组织的细胞核富集和蛋白质组学工作流程。通过将我们的工作流程与其他方法进行广泛的基准测试，我们表明FrozONE是一种比传统超速离心方法更快、更简单且更具可扩展性的替代方法。FrozONE能够对具有复杂细胞异质性的不同组织中的细胞核蛋白质组进行研究、分析和分类，确保从不同细胞类型中实现最佳的细胞核富集，并对低丰度蛋白质具有定量分辨率。除了在健康小鼠组织中的性能外，FrozONE在病理状态（饮食诱导的非酒精性脂肪性肝炎）下对肝脏细胞核蛋白质组变化的表征方面也被证明非常有效。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f6d/11638322/891aea523dd1/LSA-2024-03130_FigS7.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f6d/11638322/a6a76c1fc487/LSA-2024-03130_Fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f6d/11638322/f91aa7d82883/LSA-2024-03130_FigS1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f6d/11638322/c79275b06913/LSA-2024-03130_FigS2.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f6d/11638322/c4e95ec3bc8e/LSA-2024-03130_Fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f6d/11638322/e59ef5e9a26d/LSA-2024-03130_FigS4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f6d/11638322/4105f6152239/LSA-2024-03130_Fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f6d/11638322/4ea12a5bbe52/LSA-2024-03130_FigS5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f6d/11638322/5fcbebb59ddd/LSA-2024-03130_FigS6.jpg
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Characterization of cell-fate decision landscapes by estimating transcription factor dynamics.通过估计转录因子动力学来描绘细胞命运决定景观。
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