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Temporal Profiling of Epitranscriptomic Modulators during Osteogenic Differentiation of Human Embryonic Stem Cells

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Download Hi-Res ImageDownload to MS-PowerPointCite This:J. Proteome Res. 2023, 22, 7, 2179-2185
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    Temporal Profiling of Epitranscriptomic Modulators during Osteogenic Differentiation of Human Embryonic Stem Cells
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    • Jiekai Yin
      Jiekai Yin
      Environmental Toxicology Graduate Program, University of California Riverside, Riverside, California 92521-0403, United States,
      More by Jiekai Yin
    • Tianyu F. Qi
      Tianyu F. Qi
      Environmental Toxicology Graduate Program, University of California Riverside, Riverside, California 92521-0403, United States,
      More by Tianyu F. Qi
    • Yen-Yu Yang
      Yen-Yu Yang
      Department of Chemistry, University of California Riverside, Riverside, California 92521-0403, United States
      More by Yen-Yu Yang
    • Madeline Vera-Colón
      Madeline Vera-Colón
      Environmental Toxicology Graduate Program, University of California Riverside, Riverside, California 92521-0403, United States,
      More by Madeline Vera-Colón
      Orcidhttps://orcid.org/0000-0002-5276-2782
    • Nicole I. zur Nieden
      Nicole I. zur Nieden
      Environmental Toxicology Graduate Program, University of California Riverside, Riverside, California 92521-0403, United States,
      Department of Molecular, Cell, and Systems Biology, University of California, Riverside, California 92521-0403, United States
      More by Nicole I. zur Nieden
    • Yinsheng Wang*
      Yinsheng Wang
      Environmental Toxicology Graduate Program, University of California Riverside, Riverside, California 92521-0403, United States,
      Department of Chemistry, University of California Riverside, Riverside, California 92521-0403, United States
      *Phone (951) 827-2700. Email: [email protected]
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      Orcidhttps://orcid.org/0000-0001-5565-283X
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    Journal of Proteome Research

    Cite this: J. Proteome Res. 2023, 22, 7, 2179–2185
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    https://doi.org/10.1021/acs.jproteome.3c00215
    Published June 22, 2023
    Copyright © 2023 American Chemical Society
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    Abstract

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    Osteogenesis is modulated by multiple regulatory networks. Recent studies showed that RNA modifications and their reader, writer, and eraser (RWE) proteins are involved in regulating various biological processes. Few studies, however, were conducted to investigate the functions of RNA modifications and their RWE proteins in osteogenesis. By using LC-MS/MS in parallel-reaction monitoring (PRM) mode, we performed a comprehensive quantitative assessment of 154 epitranscriptomic RWE proteins throughout the entire time course of osteogenic differentiation in H9 human embryonic stem cells (ESCs). We found that approximately half of the 127 detected RWE proteins were down-regulated during osteogenic differentiation, and they included mainly proteins involved in RNA methylation and pseudouridylation. Protein–protein interaction (PPI) network analysis unveiled significant associations between the down-regulated epitranscriptomic RWE proteins and osteogenesis-related proteins. Gene set enrichment analysis (GSEA) of publicly available RNA-seq data obtained from osteogenesis imperfecta patients suggested a potential role of METTL1 in osteogenesis through the cytokine network. Together, this is the first targeted profiling of epitranscriptomic RWE proteins during osteogenic differentiation of human ESCs, and our work unveiled potential regulatory roles of these proteins in osteogenesis. LC-MS/MS data were deposited on ProteomeXchange (PXD039249).

    Copyright © 2023 American Chemical Society

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    Supporting Information

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    The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.jproteome.3c00215.

    • Supplementary experimental section; Figure S1, LC-PRM quantification results; Figure S2, GO analysis of the down-regulated RWE proteins in Group 1; Figure S3, Quantification results of methyltransferases and pseudouridine synthases; Figure S4, PPI network analysis of the down-regulated RWE proteins; Figure S5, Western blot validation of quantification results for METTL1; Figure S6, GSEA enrichment plots; Figure S7, Uncropped Western blot images; Table S2, Top 3 functionally enriched terms of each MCODE complex (PDF)

    • Table S1, LC-PRM quantification results of epitranscriptomic RWE proteins during the osteogenesis of human embryonic stem cells (XLSX)

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    Journal of Proteome Research

    Cite this: J. Proteome Res. 2023, 22, 7, 2179–2185
    Click to copy citationCitation copied!
    https://doi.org/10.1021/acs.jproteome.3c00215
    Published June 22, 2023
    Copyright © 2023 American Chemical Society
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