Evidence map›Paper›PMID 39260367›Full record

ArticleMolecular cell2024

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

Teodorus Theo Susanto, Victoria Hung, Andrew G Levine, Yuxiang Chen, Craig H Kerr, Yongjin Yoo, Juan A Oses-Prieto, Lisa Fromm, Zijian Zhang, Travis C Lantz and 5 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Molecular cell, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.

0numbers the graph read from it
0cells of the map it votes in
15citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

15 citing papers in PubMed.

  1. Article
  2. Article
  3. RiboScreenBiomedicines · 2026
    Review
  4. Article
  5. Article
  6. Article
  7. Article
  8. Article
  9. Review
  10. World journal of gastrointestinal oncology · 2025
    Article
  11. Article
  12. Ribosome-associated proteins: unwRAPping ribosome heterogeneity in the twenty-first century.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025
    Review
  13. Ribosomal protein paralogues in ribosome specialization.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025
    Review
  14. Ribosome heterogeneity and specialization.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025
    Article
  15. Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

15 authors.

Teodorus Theo SusantoDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Victoria HungDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Andrew G LevineDepartment 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 ChenDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Craig H KerrDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Yongjin YooInstitute for Stem Cell Biology and Regenerative Medicine and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
Juan A Oses-PrietoDepartment of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
Lisa FrommDepartment 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 ZhangDepartment 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 LantzDepartment 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 FujiiDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Marius WernigInstitute 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 BurlingameDepartment of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
Davide RuggeroDepartment 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 BarnaDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address: mbarna@stanford.edu.

Funding

Mechanisms of regulated translation control in cancer and its therapeutic implicationsR35CA242986 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI RUGGERO, DAVIDE · 2019 to 2025
$6.4M
Specialized Translational Control of Stem Cell Differentiation and Embryonic DevelopmentR01HD086634 · NICHD · STANFORD UNIVERSITY · PI BARNA, MARIA · 2016 to 2025
$5.5M
Rapid remodeling of the translatome underlying wound healing and regenerationR01HD105731 · NICHD · STANFORD UNIVERSITY · PI Maria Barna · 2022 to 2026
$1.7M
Enhancing Resident Investigation and Career Advancement in Cardiovascular and Pulmonary ScienceR38HL143581 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI BIBBINS-DOMINGO, KIRSTEN, HUANG, ALISON · 2018 to 2021
$1.4M
A ribosome interactome that regulates local translation and neural functionR21MH130323 · NIMH · STANFORD UNIVERSITY · PI BARNA, MARIA · 2022 to 2023
$433k
Control of ribosomal function in cells of the hematopoietic systemK38HL165490 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI LEVINE, ANDREW · 2022 to 2023
$222k
NCI NIH HHS R35 CA242986NHLBI NIH HHS K38 HL165490NHLBI NIH HHS R38 HL143581NICHD NIH HHS R01 HD086634NICHD NIH HHS R01 HD105731NIMH NIH HHS R21 MH130323
6 · The paper itself

Abstract

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.

Indexed as

MacrophagesRibosomal ProteinsRibosomesAnimalsCell Line, TumorDEAD-box RNA HelicasesGene Expression Regulation, DevelopmentalHumansMiceMice, Inbred C57BLNeoplasmsProtein BiosynthesisDEAD-box RNA HelicasesRibosomal Proteinscancerembryonic developmentmacrophagesproteomicsribosomeribosome-associated proteinsribosome heterogeneitytranslational control

Identifiers

PMID39260367
PMCPMC11460945

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.