Victoria Hung

All Publications

• RAPIDASH: Tag-free enrichment of ribosome-associated proteins reveals composition dynamics in embryonic tissue, cancer cells, and macrophages. Molecular cell Susanto, T. T., Hung, V., Levine, A. G., Chen, Y., Kerr, C. H., Yoo, Y., Oses-Prieto, J. A., Fromm, L., Zhang, Z., Lantz, T. C., Fujii, K., Wernig, M., Burlingame, A. L., Ruggero, D., Barna, M. 2024

  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.

  View details for DOI 10.1016/j.molcel.2024.08.023

  View details for PubMedID 39260367

• RAPIDASH: A tag-free enrichment of ribosome-associated proteins reveals compositional dynamics in embryonic tissues and stimulated macrophages. bioRxiv : the preprint server for biology Susanto, T. T., Hung, V., Levine, A. G., Kerr, C. H., Yoo, Y., Chen, Y., Oses-Prieto, J. A., Fromm, L., Fujii, K., Wernig, M., Burlingame, A. L., Ruggero, D., Barna, M. 2023

  Abstract

  Ribosomes are emerging as direct regulators of gene expression, with ribosome-associated proteins (RAPs) allowing ribosomes to modulate translational control. However, a lack of technologies to enrich RAPs across many sample types has prevented systematic analysis of RAP number, dynamics, and functions. Here, 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 that is linked to the translation of genes with long coding sequences. Finally, we characterized ribosome composition remodeling during immune activation and observed extensive changes post-stimulation. RAPIDASH has therefore enabled the discovery of RAPs ranging from those with neuroregulatory functions to those activated by immune stimuli, thereby providing critical insights into how ribosomes are remodeled.

  View details for DOI 10.1101/2023.12.07.570613

  View details for PubMedID 38106052

  View details for PubMedCentralID PMC10723405

• A stem cell roadmap of ribosome heterogeneity reveals a function for RPL10A in mesoderm production. Nature communications Genuth, N. R., Shi, Z., Kunimoto, K., Hung, V., Xu, A. F., Kerr, C. H., Tiu, G. C., Oses-Prieto, J. A., Salomon-Shulman, R. E., Axelrod, J. D., Burlingame, A. L., Loh, K. M., Barna, M. 2022; 13 (1): 5491

  Abstract

  Recent findings suggest that the ribosome itself modulates gene expression. However, whether ribosomes change composition across cell types or control cell fate remains unknown. Here, employing quantitative mass spectrometry during human embryonic stem cell differentiation, we identify dozens of ribosome composition changes underlying cell fate specification. We observe upregulation of RPL10A/uL1-containing ribosomes in the primitive streak followed by progressive decreases during mesoderm differentiation. An Rpl10a loss-of-function allele in mice causes striking early mesodermal phenotypes, including posterior trunk truncations, and inhibits paraxial mesoderm production in culture. Ribosome profiling in Rpl10a loss-of-function mice reveals decreased translation of mesoderm regulators, including Wnt pathway mRNAs, which are also enriched on RPL10A/uL1-containing ribosomes. We further show that RPL10A/uL1 regulates canonical and non-canonical Wnt signaling during stem cell differentiation and in the developing embryo. These findings reveal unexpected ribosome composition modularity that controls differentiation and development through the specialized translation of key signaling networks.

  View details for DOI 10.1038/s41467-022-33263-3

  View details for PubMedID 36123354

• Tag-free rapid enrichment of ribosome-associated proteins across cell types, tissues, and species Susanto, T., Hung, V., Fujii, K., Barna, M. AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC. 2019: S78

  View details for Web of Science ID 000516535000127

• Characterizing the role of ribosomal protein phosphorylation in control of gene regulation and cell fate Hung, V., Oses-Prieto, J. A., Moss, S. M., Stevenson, J., Shokat, K. M., Burlingame, A. L., Barna, M. AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC. 2019: S77

  View details for Web of Science ID 000516535000125

• Ribosome Heterogeneity in Translating the Genetic Code Genuth, N., Hung, V., Shi, Z., Simsek, D., Oses-Prieto, J. A., Burlingame, A. L., Barna, M. AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC. 2019: S23

  View details for Web of Science ID 000516535000018

• Proteomic mapping of cytosol-facing outer mitochondrial and ER membranes in living human cells by proximity biotinylation ELIFE Hung, V., Lam, S. S., Udeshi, N. D., Svinkina, T., Guzman, G., Mootha, V. K., Carr, S. A., Ting, A. Y. 2017; 6

  Abstract

  The cytosol-facing membranes of cellular organelles contain proteins that enable signal transduction, regulation of morphology and trafficking, protein import and export, and other specialized processes. Discovery of these proteins by traditional biochemical fractionation can be plagued with contaminants and loss of key components. Using peroxidase-mediated proximity biotinylation, we captured and identified endogenous proteins on the outer mitochondrial membrane (OMM) and endoplasmic reticulum membrane (ERM) of living human fibroblasts. The proteomes of 137 and 634 proteins, respectively, are highly specific and highlight 94 potentially novel mitochondrial or ER proteins. Dataset intersection identified protein candidates potentially localized to mitochondria-ER contact sites. We found that one candidate, the tail-anchored, PDZ-domain-containing OMM protein SYNJ2BP, dramatically increases mitochondrial contacts with rough ER when overexpressed. Immunoprecipitation-mass spectrometry identified ribosome-binding protein 1 (RRBP1) as SYNJ2BP's ERM binding partner. Our results highlight the power of proximity biotinylation to yield insights into the molecular composition and function of intracellular membranes.

  View details for DOI 10.7554/eLife.24463

  View details for Web of Science ID 000400017500001

  View details for PubMedID 28441135

  View details for PubMedCentralID PMC5404927