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

cancer embryonic development macrophages proteomics ribosome ribosome heterogeneity ribosome-associated proteins translational control

Journal

Molecular cell
ISSN: 1097-4164
Titre abrégé: Mol Cell
Pays: United States
ID NLM: 9802571

Informations de publication

Date de publication:
05 Sep 2024
Historique:
received: 08 12 2023
revised: 25 06 2024
accepted: 20 08 2024
medline: 12 9 2024
pubmed: 12 9 2024
entrez: 11 9 2024
Statut: aheadofprint

Résumé

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.

Identifiants

DOI: 10.1016/j.molcel.2024.08.023 PMID: 39260367
pubmed: 39260367
pii: S1097-2765(24)00700-7
doi: 10.1016/j.molcel.2024.08.023
pii:
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Informations de copyright

Copyright © 2024 Elsevier Inc. All rights reserved.

Déclaration de conflit d'intérêts

Declaration of interests The authors declare no competing interests.

Auteurs

Teodorus Theo Susanto (TT)

Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.

Victoria Hung (V)

Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.

Andrew G Levine (AG)

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.

Yuxiang Chen (Y)

Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.

Craig H Kerr (CH)

Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.

Yongjin Yoo (Y)

Institute for Stem Cell Biology and Regenerative Medicine and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.

Juan A Oses-Prieto (JA)

Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.

Lisa Fromm (L)

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.

Zijian Zhang (Z)

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.

Travis C Lantz (TC)

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.

Kotaro Fujii (K)

Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.

Marius Wernig (M)

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.

Alma L Burlingame (AL)

Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.

Davide Ruggero (D)

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. Electronic address: davide.ruggero@ucsf.edu.

Maria Barna (M)

Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address: mbarna@stanford.edu.

Classifications MeSH