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

Osteogenesis is modulated by multipleregulatory networks. Recentstudies showed that RNA modifications and their reader, writer, anderaser (RWE) proteins are involved in regulating various biologicalprocesses. Few studies, however, were conducted to investigate thefunctions of RNA modifications and their RWE proteins in osteogenesis.By using LC-MS/MS in parallel-reaction monitoring (PRM) mode, we performeda comprehensive quantitative assessment of 154 epitranscriptomic RWEproteins throughout the entire time course of osteogenic differentiationin H9 human embryonic stem cells (ESCs). We found that approximatelyhalf of the 127 detected RWE proteins were down-regulated during osteogenicdifferentiation, and they included mainly proteins involved in RNAmethylation and pseudouridylation. Protein-protein interaction(PPI) network analysis unveiled significant associations between thedown-regulated epitranscriptomic RWE proteins and osteogenesis-relatedproteins. Gene set enrichment analysis (GSEA) of publicly availableRNA-seq data obtained from osteogenesis imperfecta patients suggesteda potential role of METTL1 in osteogenesis through the cytokine network.Together, this is the first targeted profiling of epitranscriptomicRWE proteins during osteogenic differentiation of human ESCs, andour work unveiled potential regulatory roles of these proteins inosteogenesis. LC-MS/MS data were deposited on ProteomeXchange (PXD039249).