Efficient Endoderm Induction from Human Pluripotent Stem Cells by Logically Directing Signals Controlling Lineage Bifurcations

Loh, Kyle M.; Ang, Lay Teng; Zhang, Jingyao; Kumar, Vibhor; Ang, Jasmin; Auyeong, Jun Qiang; Lee, Kian Leong; Choo, Siew Hua; Lim, Christina Ying Yan; Nichane, Massimo; Tan, Junru; Noghabi, Monireh Soroush; Azzola, Lisa; Ng, Elizabeth; Durruthy-Durruthy, Jens; Sebastiano, Vittorio; Poellinger, Lorenz; Elefanty, Andrew G.; Chen, Yi‐Ping Phoebe; Prabhakar, Shyam; Weissman, Irving L.; Lim, Bing

doi:10.1016/j.stem.2013.12.007

Cited by 345 publications

(498 citation statements)

References 58 publications

(140 reference statements)

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“…4 B and C). It seems, however, that Activin A alone induced a biased destabilization of the E attractor toward the En states and resulted in low iCM efficiency (<30%); this observation is consistent with use of Activin A in definitive endoderm (hepatocytes and pancreatic) differentiation protocols (26).…”

Section: Resultssupporting

confidence: 77%

Cell population structure prior to bifurcation predicts efficiency of directed differentiation in human induced pluripotent cells

Bargaje

Trachana

Shelton

et al. 2017

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

120

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Steering the differentiation of induced pluripotent stem cells (iPSCs) toward specific cell types is crucial for patient-specific disease modeling and drug testing. This effort requires the capacity to predict and control when and how multipotent progenitor cells commit to the desired cell fate. Cell fate commitment represents a critical state transition or "tipping point" at which complex systems undergo a sudden qualitative shift. To characterize such transitions during iPSC to cardiomyocyte differentiation, we analyzed the gene expression patterns of 96 developmental genes at single-cell resolution. We identified a bifurcation event early in the trajectory when a primitive streak-like cell population segregated into the mesodermal and endodermal lineages. Before this branching point, we could detect the signature of an imminent critical transition: increase in cell heterogeneity and coordination of gene expression. Correlation analysis of gene expression profiles at the tipping point indicates transcription factors that drive the state transition toward each alternative cell fate and their relationships with specific phenotypic readouts. The latter helps us to facilitate small molecule screening for differentiation efficiency. To this end, we set up an analysis of cell population structure at the tipping point after systematic variation of the protocol to bias the differentiation toward mesodermal or endodermal cell lineage. We were able to predict the proportion of cardiomyocytes many days before cells manifest the differentiated phenotype. The analysis of cell populations undergoing a critical state transition thus affords a tool to forecast cell fate outcomes and can be used to optimize differentiation protocols to obtain desired cell populations.single-cell analysis | critical state transitions | iPSC to cardiomyocyte differentiation | differentiation efficiency | prediction

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Section: Resultssupporting

confidence: 77%

Cell population structure prior to bifurcation predicts efficiency of directed differentiation in human induced pluripotent cells

Bargaje

Trachana

Shelton

et al. 2017

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

120

View full text Add to dashboard Cite

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“…We therefore hypothesized that TGF-beta signaling could be responsible for some of the observed differential histone acetylation in response to LPS. To test this prediction, we treated BV2 cells with the TGFBR1 inhibitor A83-01, which inhibits TGF-beta signaling (Loh et al 2014), and repeated the LPS induction assay (TGF-KD:LPS BV2). As predicted, TGF-beta inhibition rendered a substantial fraction (33%) of C3 regions unresponsive to LPS (C3S1 subcluster) ( Fig.…”

Section: Histone Acetylation Dynamics Of Cell-state Transitionsmentioning

confidence: 99%

“…The current paradigm is that enhancers exist in multiple poised or primed chromatin states characterized by various combinations of H2A.Z, H3K4me1, H3K4me2, and H3K27me3 (Rada-Iglesias et al 2011;Loh et al 2014) before they become active. A similar model holds for promoters, with H3K4me3 taking the place of H3K4me1 (Mikkelsen et al 2007).…”

mentioning

confidence: 99%

Comprehensive benchmarking reveals H2BK20 acetylation as a distinctive signature of cell-state-specific enhancers and promoters

et al. 2016

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Although over 35 different histone acetylation marks have been described, the overwhelming majority of regulatory genomics studies focus exclusively on H3K27ac and H3K9ac. In order to identify novel epigenomic traits of regulatory elements, we constructed a benchmark set of validated enhancers by performing 140 enhancer assays in human T cells. We tested 40 chromatin signatures on this unbiased enhancer set and identified H2BK20ac, a little-studied histone modification, as the most predictive mark of active enhancers. Notably, we detected a novel class of functionally distinct enhancers enriched in H2BK20ac but lacking H3K27ac, which was present in all examined cell lines and also in embryonic forebrain tissue. H2BK20ac was also unique in highlighting cell-type-specific promoters. In contrast, other acetylation marks were present in all active promoters, regardless of cell-type specificity. In stimulated microglial cells, H2BK20ac was more correlated with cell-state-specific expression changes than H3K27ac, with TGF-beta signaling decoupling the two acetylation marks at a subset of regulatory elements. In summary, our study reveals a previously unknown connection between histone acetylation and cell-type-specific gene regulation and indicates that H2BK20ac profiling can be used to uncover new dimensions of gene regulation.

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“…This is a story of a very long trip from tolerance to T and B cell maturation to stem cells. [I have discussed HSCs, but we have also isolated and transplanted human central nervous system stem cells in clinical trials (254); we have isolated a number of other tissue and cancer stem cells (124,127,193,(255)(256)(257)(258)(259)(260)(261)(262)(263)(264)(265)(266), and many are in progress to investigational therapies.] It is a story with some cautions about human motivations, commerce, and clinical translation.…”

Section: Cancer Stem Cells and The Therapeutics That Come From Them: mentioning

confidence: 99%

How One Thing Led to Another

Weissman

2016

Annu. Rev. Immunol.

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I started research in high school, experimenting on immunological tolerance to transplantation antigens. This led to studies of the thymus as the site of maturation of T cells, which led to the discovery, isolation, and clinical transplantation of purified hematopoietic stem cells (HSCs). The induction of immune tolerance with HSCs has led to isolation of other tissue-specific stem cells for regenerative medicine. Our studies of circulating competing germline stem cells in colonial protochordates led us to document competing HSCs. In human acute myelogenous leukemia we showed that all preleukemic mutations occur in HSCs, and determined their order; the final mutations occur in a multipotent progenitor derived from the preleukemic HSC clone. With these, we discovered that CD47 is an upregulated gene in all human cancers and is a “don't eat me” signal; blocking it with antibodies leads to cancer cell phagocytosis. CD47 is the first known gene common to all cancers and is a target for cancer immunotherapy.

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Efficient Endoderm Induction from Human Pluripotent Stem Cells by Logically Directing Signals Controlling Lineage Bifurcations

Cited by 345 publications

References 58 publications

Cell population structure prior to bifurcation predicts efficiency of directed differentiation in human induced pluripotent cells

Cell population structure prior to bifurcation predicts efficiency of directed differentiation in human induced pluripotent cells

Comprehensive benchmarking reveals H2BK20 acetylation as a distinctive signature of cell-state-specific enhancers and promoters

How One Thing Led to Another

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