Dissecting the variation in transcriptional circuits between naive and primed pluripotent states

Deb, Aritra; Sarkar, Arijita; Ghosh, Zhumur

doi:10.1002/1873-3468.12732

Cited by 5 publications

(4 citation statements)

References 44 publications

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“…In contrast, pluripotent (NANOG, OCT3/4, and SOX2) and surface markers (TRA-1-60 and TRA-1-81) were expressed in both naïve-and primed-state hESCs (SI Appendix, Fig. S1C), as reported previously (3).…”

Section: Resultssupporting

confidence: 83%

B3GALT5 knockout alters glycosphingolipid profile and facilitates transition to human naïve pluripotency

Lin

Kuo

Yang

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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Conversion of human pluripotent stem cells from primed to naïve state is accompanied by altered transcriptome and methylome, but glycosphingolipid (GSL) profiles in naïve human embryonic stem cells (hESCs) have not been systematically characterized. Here we showed a switch from globo-(SSEA-3, SSEA-4, and Globo H) and lacto-series (fucosyl-Lc4Cer) to neolacto-series GSLs (SSEA-1 and H type 2 antigen), along with marked down-regulation of β-1,3-galactosyltransferase (B3GALT5) upon conversion to naïve state. CRISPR/Cas9-generated B3GALT5-knockout (KO) hESCs displayed an altered GSL profile, increased cloning efficiency and intracellular Ca2+, reminiscent of the naïve state, while retaining differentiation ability. The altered GSLs could be rescued through overexpression of B3GALT5. B3GALT5-KO cells cultured with 2iLAF exhibited naïve-like transcriptome, global DNA hypomethylation, and X-chromosome reactivation. In addition, B3GALT5-KO rendered hESCs more resistant to calcium chelator in blocking entry into naïve state. Thus, loss of B3GALT5 induces a distinctive state of hESCs displaying unique GSL profiling with expression of neolacto-glycans, increased Ca2+, and conducive for transition to naïve pluripotency.

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Section: Resultssupporting

confidence: 83%

B3GALT5 knockout alters glycosphingolipid profile and facilitates transition to human naïve pluripotency

Lin

Kuo

Yang

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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“…The naive pluripotent cells are assumed to be completely unrestricted and free from any epigenetic constraints. On the other hand, primed pluripotent cells are developmentally advanced and have lineage bias during differentiation [3,4]. This often limits the application of conventional hESCs for biomedical applications [5].…”

Section: Introductionmentioning

confidence: 99%

Decoding molecular markers and transcriptional circuitry of naive and primed states of human pluripotency

Ghosh

Som

2020

Preprint

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Pluripotent stem cells (PSCs) have been observed to occur in two distinct states -naive and primed. Both naive and primed state PSCs can give rise to tissues of all the three germ layers in vitro but differ in their potential to generate germline chimera in vivo. Understanding the molecular mechanisms that govern these two states of pluripotency in human can open up a plethora of opportunities for studying early embryonic development and in biomedical applications. In this work, we use weighted gene co-expression network (WGCN) approach to identify the key molecular makers and their interactions that define the two distinct pluripotency states. Signed-hybrid WGCN was reconstructed from transcriptomic data (RNA-seq) of naive and primed state pluripotent samples. Our analysis revealed two sets of genes that are involved in establishment and maintenance of naive (4791 genes) and primed (5066 genes) states. The naive state genes were found to be enriched for biological processes and pathways related to metabolic processes while primed state genes were associated with system development. Further, we identified the top 10% genes by intra-modular connectivity as hubs and the hub transcription factors for each group, thus providing a three-tier list of genes associated with naive and primed states of pluripotency in human. HIGHLIGHTS Weighted gene co-expression network analysis (WGCNA) identified 4791 and 5066 genes to be involved in naive and primed states of human pluripotency respectively.  Functional and pathway enrichment analysis revealed the naive genes were mostly related to metabolic processes and primed genes to system development. The top 10% genes based on intra-modular connectivity from each group were defined as hubs.  Identified 52 and 33 transcription factors among the naive and primed module hubs respectively. The transcription factors might play a switch on-off mechanism in induction of the two pluripotent states.

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“…ESCs originated from distinct organism present different features or states. Mouse ESCs (mESCs) could be classified into a naive and a primed pluripotent states in vitro, where the naive mESCs exhibit a grounder state pluripotency while the primed mESCs show a limited pluripotency and are primed for lineage specification [12, 13]. Many biological features differ significantly between these two states, such as colony morphology, growth factor requirement for maintaining undifferentiated growth, gene expression profile, and X chromosome inactivation [14].…”

Section: Introductionmentioning

confidence: 99%

Flow-enhanced priming of hESCs through H2B acetylation and chromatin decondensation

Wang

Zhang

et al. 2019

Stem Cell Res Ther

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BackgroundDistinct mechanical stimuli are known to manipulate the behaviors of embryonic stem cells (ESCs). Fundamental rationale of how ESCs respond to mechanical forces and the potential biological effects remain elusive. Here we conducted the mechanobiological study for hESCs upon mechanomics analysis to unravel typical mechanosensitive processes on hESC-specific fluid shear.MethodshESC line H1 was subjected to systematically varied shear flow, and mechanosensitive proteins were obtained by mass spectrometry (MS) analysis. Then, function enrichment analysis was performed to identify the enriched gene sets. Under a steady shear flow of 1.1 Pa for 24 h, protein expressions were further detected using western blotting (WB), quantitative real-time PCR (qPCR), and immunofluorescence (IF) staining. Meanwhile, the cells were treated with 200 nM trichostatin (TSA) for 1 h as positive control to test chromatin decondensation. Actin, DNA, and RNA were then visualized with TRITC-labeled phalloidin, Hoechst 33342, and SYTO® RNASelect™ green fluorescent cell stain (Life Technologies), respectively. In addition, cell stiffness was determined with atomic force microscopy (AFM) and annexin V-PE was used to determine the apoptosis with a flow cytometer (FCM).ResultsTypical mechanosensitive proteins were unraveled upon mechanomics analysis under fluid shear related to hESCs in vivo. Functional analyses revealed significant alterations in histone acetylation, nuclear size, and cytoskeleton for hESC under shear flow. Shear flow was able to induce H2B acetylation and nuclear spreading by CFL2/F-actin cytoskeletal reorganization. The resulting chromatin decondensation and a larger nucleus readily accommodate signaling molecules and transcription factors.ConclusionsShear flow regulated chromatin dynamics in hESCs via cytoskeleton and nucleus alterations and consolidated their primed state.

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Dissecting the variation in transcriptional circuits between naive and primed pluripotent states

Cited by 5 publications

References 44 publications

B3GALT5 knockout alters glycosphingolipid profile and facilitates transition to human naïve pluripotency

B3GALT5 knockout alters glycosphingolipid profile and facilitates transition to human naïve pluripotency

Decoding molecular markers and transcriptional circuitry of naive and primed states of human pluripotency

Flow-enhanced priming of hESCs through H2B acetylation and chromatin decondensation

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