Perturbations in Osteogenic Cell Fate Following Exposure to Constituents Present in Tobacco: A Combinatorial Study.

Tobacco smoke contains between 7000 and 10,000 constituents, and only an evanescently low number of which have been identified, let alone been evaluated for their toxicity. Recently, the Food and Drug Administration has published a list of 93 chemical tobacco constituents that are harmful or potentially harmful to a number of cellular processes. However, their effect on developing skeletal cells is unknown. In this study, we used ToxPI, a computational tool, to prioritize constituents on this list for screening in osteogenically differentiating human embryonic stem cells and fibroblasts. In selected endpoint assays, we evaluated the potential of these chemicals to inhibit osteogenic differentiation success as well as their cytotoxicity. Six of these chemicals, which were ascribed an embryotoxic potential in our screen, as well as nicotine, which was not found to be osteotoxic in vitro, were then evaluated in combinatorial exposures, either in pairs of two or three. No one single chemical could be pinpointed as the culprit of reduced calcification in response to tobacco exposure. Combining chemicals at their half-maximal inhibitory concentration of differentiation often elicited expected decreases in calcification over the individual exposures; however, cytotoxicity was improved in many of the dual combinations. A reverse response was also noted, in which calcification output improved in combinatorial exposures. Results from ternary combinations reflected those from double combinations. Thus, the results from this study suggest that it may be difficult to isolate single chemicals as the primary drivers of skeletal embryotoxicity and that the full combination of chemicals in tobacco smoke may produce the hypomineralization phenotype that we have so far observed in vitro in human embryonic stem cells as well as in vivo in zebrafish.

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

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).

Targeted Proteomic Profiling Revealed Roles of Small GTPases during Osteogenic Differentiation.

The small GTPase superfamily of proteins are crucial for numerous cellular processes, including early development. The roles of these proteins in osteogenic differentiation, however, remained poorly explored. In this study, we employed a high-throughput targeted proteomic method, relying on scheduled liquid chromatography-multiple-reaction monitoring (LC-MRM) coupled with synthetic stable isotope-labeled peptides, to interrogate systematically the temporal responses of the entire small GTPase proteome during the course of osteogenic differentiation of H9 human embryonic stem cells. Our results demonstrated that the method offers high quantification accuracy, reproducibility, and throughput. In addition, the quantification results revealed altered expression of a large number of small GTPases accompanied with osteogenic differentiation, especially those involved with autophagy. We also documented a previously unrecognized role of KRAS in osteogenesis, where it regulates the accumulation of extracellular matrix for mineralization through attenuating the activity of secreted matrix metalloproteinase 9 (MMP9). Together, this study represents a novel application of a state-of-the-art analytical method, i.e., targeted quantitative proteomics, for revealing the progressive reprogramming of the small GTPase proteome during osteogenic differentiation of human embryonic stem cells, and our results revealed KRAS as a new regulator for osteogenesis.