RAPIDASH: Tag-free enrichment of ribosome-associated proteins reveals composition dynamics in embryonic tissue, cancer cells, and macrophages,Molecular Cell

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RAPIDASH: Tag-free enrichment of ribosome-associated proteins reveals composition dynamics in embryonic tissue, cancer cells, and macrophages
Molecular Cell ( IF 14.5 ) Pub Date : 2024-09-10 , DOI: 10.1016/j.molcel.2024.08.023
Teodorus Theo Susanto ₁ , Victoria Hung ₁ , Andrew G Levine ₂ , Yuxiang Chen ₁ , Craig H Kerr ₁ , Yongjin Yoo ₃ , Juan A Oses-Prieto ₄ , Lisa Fromm ₅ , Zijian Zhang ₆ , Travis C Lantz ₆ , Kotaro Fujii ₁ , Marius Wernig ₇ , Alma L Burlingame ₄ , Davide Ruggero ₅ , Maria Barna ₁

Affiliation

Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
Institute for Stem Cell Biology and Regenerative Medicine and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
Department of Urology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
Institute for Stem Cell Biology and Regenerative Medicine and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.

Ribosomes are emerging as direct regulators of gene expression, with ribosome-associated proteins (RAPs) allowing ribosomes to modulate translation. Nevertheless, a lack of technologies to enrich RAPs across sample types has prevented systematic analysis of RAP identities, dynamics, and functions. We have developed a label-free methodology called RAPIDASH to enrich ribosomes and RAPs from any sample. We applied RAPIDASH to mouse embryonic tissues and identified hundreds of potential RAPs, including Dhx30 and Llph, two forebrain RAPs important for neurodevelopment. We identified a critical role of LLPH in neural development linked to the translation of genes with long coding sequences. In addition, we showed that RAPIDASH can identify ribosome changes in cancer cells. Finally, we characterized ribosome composition remodeling during immune cell activation and observed extensive changes post-stimulation. RAPIDASH has therefore enabled the discovery of RAPs in multiple cell types, tissues, and stimuli and is adaptable to characterize ribosome remodeling in several contexts.

中文翻译：

RAPIDASH：核糖体相关蛋白的无标签富集揭示了胚胎组织、癌细胞和巨噬细胞的组成动力学

核糖体正在成为基因表达的直接调节因子，核糖体相关蛋白（RAP）允许核糖体调节翻译。然而，缺乏跨样本类型富集 RAP 的技术阻碍了对 RAP 身份、动力学和功能的系统分析。我们开发了一种称为 RAPIDASH 的无标记方法，用于富集任何样品中的核糖体和 RAP。我们将 RAPIDASH 应用于小鼠胚胎组织并确定了数百种潜在的 RAP，包括 Dhx30 和 Llph，这两种前脑 RAP 对神经发育很重要。我们确定了 LLPH 在神经发育中的关键作用，该作用与具有长编码序列的基因的翻译有关。此外，我们表明 RAPIDASH 可以识别癌细胞中的核糖体变化。最后，我们表征了免疫细胞激活过程中核糖体组成重塑，并观察到刺激后的广泛变化。因此，RAPIDASH 能够在多种细胞类型、组织和刺激中发现 RAP，并且适用于在多种情况下表征核糖体重塑。

更新日期：2024-09-10

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