Dataset Information

1H NMR metabolite monitoring during the differentiation of human induced pluripotent stem cells provides new insights into the molecular events that regulate embryonic chondrogenesis

ABSTRACT: The integration of cell metabolism with signalling pathways, transcription factor networks and epigenetic mediators is critical in coordinating molecular and cellular events during embryogenesis. Induced pluripotent stem cells (IPSCs) are an established model for embryogenesis, germ layer specification and cell lineage differentiation, advancing the study of human embryonic development and the translation of innovations in drug discovery, disease modelling and cell-based therapies. The metabolic regulation of IPSC pluripotency is mediated by balancing glycolysis and oxidative phosphorylation, but there is a paucity of data regarding the influence of individual metabolite changes during cell lineage differentiation. We used ¹H NMR metabolite fingerprinting and footprinting to monitor metabolite levels as IPSCs are directed in a three-stage protocol through primitive streak/mesendoderm, mesoderm and chondrogenic populations. Metabolite changes were associated with central metabolism, with aerobic glycolysis predominant in IPSC, elevated oxidative phosphorylation during differentiation and fatty acid oxidation and ketone body use in chondrogenic cells. Metabolites were also implicated in the epigenetic regulation of pluripotency, cell signalling and biosynthetic pathways. Our results show that ¹H NMR metabolomics is an effective tool for monitoring metabolite changes during the differentiation of pluripotent cells with implications on optimising media and environmental parameters for the study of embryogenesis and translational applications.

INSTRUMENT(S): Nuclear Magnetic Resonance (NMR) -

PROVIDER: MTBLS4854 | MetaboLights | 2023-05-24

REPOSITORIES: MetaboLights

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<sup>1</sup>H NMR Metabolite Monitoring during the Differentiation of Human Induced Pluripotent Stem Cells Provides New Insights into the Molecular Events That Regulate Embryonic Chondrogenesis.

Coope Ashley A Ghanameh Zain Z Kingston Olivia O Sheridan Carl M CM Barrett-Jolley Richard R Phelan Marie M MM Oldershaw Rachel A RA

International journal of molecular sciences 20220817 16

The integration of cell metabolism with signalling pathways, transcription factor networks and epigenetic mediators is critical in coordinating molecular and cellular events during embryogenesis. Induced pluripotent stem cells (IPSCs) are an established model for embryogenesis, germ layer specification and cell lineage differentiation, advancing the study of human embryonic development and the translation of innovations in drug discovery, disease modelling and cell-based therapies. The metabolic ...[more]

PMID: 36012540

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Project description:At the blastocyst stage, the embryo invades the uterine and the pluripotent epiblast cells get reshaped from an amorphous ball into a polarized cup-shaped epithelium. At the same time, the transiently established naïve pluripotency is dismantled, transforming into a more developmentally advanced post-implantation pluripotent state. The major driver of the differentiation process is the autocrine Fgf/Mek/Erk singling which promotes the exit of naïve pluripotency. However, inhibiting Mek alone is not sufficient to maintain the cells in the naïve state suggesting the contribution of additional, as yet unidentified, pro-differentiation signals. Using a 3D embryonic stem cells (ESC) based model of epiblast development we established an automated pipeline for cell culture and analysis and performed a large-scale functional screen to identify factors regulating the development of the pluripotent lineage. We found that the mitotic kinases – Aurora kinase A (Aurka) and Polo-like kinase (PLK) positively regulate Erk signalling in a Mek-independent manner. We determined that Aurka and Erk form a complex in ESCs and suppression of Aurka activity delays the exit of naïve pluripotency. Moreover, a combination of Aurka and Mek inhibition enabled the de novo derivation of ESC lines from mouse embryos. Interestingly, during cell division, we found that phospho-Erk (pErk) localizes on the spindle poles at prophase and metaphase, gradually decreasing its signal at anaphase and telophase. Proximity biotinylation analysis of the pErk interactome identified the formation of PLK/pErk complex in metaphase cells. Moreover, inhibition of PLK, but not Mek or Aurka, resulted in a substantial decrease in Erk phosphorylation at the mitotic spindle. In summary, our findings demonstrate that the pluripotent cells continuously generate and perceive two types of Erk-mediated pro-differentiation cues - autocrine signals of the Fgf/Mek cascade and cell-intrinsic cues via the mitotic kinase Aurka and PLK. Altogether, these signals promote the exit of naïve pluripotency, driving the transient pace of embryonic development.

Project description:Epigenetic priming factors establish a permissive epigenetic landscape which is not required until a later developmental or physiological time point, temporally uncoupling the presence of these factors with their phenotypic effects. One classic example of epigenetic priming is in the context of bivalent chromatin, found in pluripotent stem cells and early embryos at key developmental gene promoters marked by both activating-associated H3K4me3 and repressive-associated H3K27me3 histone modifications. It is currently unknown how these bivalent domains are targeted, or precisely how they impact on lineage commitment. Here we show that the small heterodimerising non-enzymatic DNA binding proteins Developmental Pluripotency Associated 2 (Dppa2) and 4 (Dppa4) act as epigenetic priming factors to establish bivalency at a subset of developmental genes. Dppa2/4 localise to the +1 nucleosome position of bivalent genes and while they are not required for pluripotency in embryonic stem cells (ESCs), double knockout cells fail to exit pluripotency and to differentiate efficiently, with delays in upregulating bivalently marked lineage genes. Proteomics reveal that Dppa2/4 interact on chromatin with members of the COMPASS and Polycomb complexes important for H3K4me3 and H3K27me3 deposition, respectively. Epigenetic profiling reveals a striking loss of H3K4me3, H3K27me3, and their associated enzymatic machinery at a significant subset of bivalent promoters in Dppa2/4 mutants, in addition to loss of H2A.Z and chromatin accessibility. In wild-type ESCs, these “Dppa2/4-dependent” bivalent promoters are characterised by low H3K4me3 enrichment and breadth, near-absent expression levels and initiating but not elongating RNA polymerase. Notably, Dppa2/4-dependent promoters are less evolutionarily conserved suggesting that they lack additional safeguard measures to maintain bivalency at these genes in the absence of Dppa2/4. Concomitantly with the loss of bivalency, Dppa2/4-dependent bivalent promoters gain DNA methylation and consequently are no longer able to be effectively activated upon ESC differentiation, leading to defects in cell fate acquisition. Our findings reveal a targeting principle for bivalency to developmental gene promoters poising them for future lineage specific gene activation.

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Dataset Information

1H NMR metabolite monitoring during the differentiation of human induced pluripotent stem cells provides new insights into the molecular events that regulate embryonic chondrogenesis

Dataset's files

Publications

<sup>1</sup>H NMR Metabolite Monitoring during the Differentiation of Human Induced Pluripotent Stem Cells Provides New Insights into the Molecular Events That Regulate Embryonic Chondrogenesis.

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Dataset Information

1H NMR metabolite monitoring during the differentiation of human induced pluripotent stem cells provides new insights into the molecular events that regulate embryonic chondrogenesis

Dataset's files

Publications

&lt;sup&gt;1&lt;/sup&gt;H NMR Metabolite Monitoring during the Differentiation of Human Induced Pluripotent Stem Cells Provides New Insights into the Molecular Events That Regulate Embryonic Chondrogenesis.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

<sup>1</sup>H NMR Metabolite Monitoring during the Differentiation of Human Induced Pluripotent Stem Cells Provides New Insights into the Molecular Events That Regulate Embryonic Chondrogenesis.