Characterization of microRNAs involved in embryonic stem cell states.
Bradford M. Stadler,Irena Ivanovska,Kshama Mehta,Sunny Song,Angelique M. Nelson,Yunbing Tan,Julie Mathieu,Christopher Darby,C. Anthony Blau,Carol B. Ware,Garrick Peters,Daniel G. Miller,Lanlan Shen,Michele A. Cleary,Hannele Ruohola-Baker +14 more
TLDR
The results raise the possibility that the relative expression of related miRNAs might serve as diagnostic indicators in defining the developmental state of embryonic cells and other stem cell lines, such as iPSCs, and raise the possibilities that mi RNAs bearing identical seed sequences could have specific functions during separable stages of early embryonic development.Abstract:
Studies of embryonic stem cells (ESCs) reveal that these cell lines can be derived from differing stages of embryonic development. We analyzed common changes in the expression of microRNAs (miRNAs)...read more
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HIF Induces Human Embryonic Stem Cell Markers in Cancer Cells
Julie Mathieu,Zhan Zhang,Wenyu Zhou,Amy Wang,John M. Heddleston,Claudia M A Pinna,Alexis Hubaud,Bradford M. Stadler,Michael Choi,Merav Bar,Muneesh Tewari,Alvin Y. Liu,Robert L. Vessella,Robert C. Rostomily,Donald E. Born,Marshall S. Horwitz,Carol B. Ware,C. Anthony Blau,Michele A. Cleary,Jeremy N. Rich,Hannele Ruohola-Baker +20 more
TL;DR: Hypoxia, through hypoxia-inducible factor (HIF), can induce an hESC-like transcriptional program, including the induced pluripotent stem cell (iPSC) inducers, OCT4, NANOG, SOX2, KLF4, cMYC, and microRNA-302 in 11 cancer cell lines.
Journal ArticleDOI
Derivation of naive human embryonic stem cells.
Carol B. Ware,Angelique M. Nelson,Brigham H. Mecham,Jennifer Hesson,Wenyu Zhou,Erica C. Jonlin,Antonio J. Jimenez-Caliani,Xinxian Deng,Christopher Cavanaugh,Savannah Cook,Paul J. Tesar,Jeffrey Okada,Lilyana Margaretha,Henrik Sperber,Michael Choi,C. Anthony Blau,Piper M. Treuting,R. David Hawkins,Vincenzo Cirulli,Hannele Ruohola-Baker +19 more
TL;DR: The naïve state in humans is described and it is shown that naïve human ES cells have expanded endoderm developmental capacity and meet mouse criteria for the naïve state by growth characteristics, antibody labeling profile, gene expression, X-inactivation profile, mitochondrial morphology, microRNA profile and development in the context of teratomas.
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The metabolome regulates the epigenetic landscape during naive-to-primed human embryonic stem cell transition
Henrik Sperber,Julie Mathieu,Yuliang Wang,Amy Ferreccio,Jennifer Hesson,Zhuojin Xu,Karin A. Fischer,Arikketh Devi,Arikketh Devi,Damien Detraux,Haiwei Gu,Stephanie L. Battle,Megan R. Showalter,Cristina Valensisi,Jason H. Bielas,Jason H. Bielas,Nolan G. Ericson,Lilyana Margaretha,Aaron M. Robitaille,Daciana Margineantu,Oliver Fiehn,Oliver Fiehn,David M. Hockenbery,C. Anthony Blau,Daniel Raftery,Daniel Raftery,Adam A. Margolin,R. David Hawkins,Randall T. Moon,Randall T. Moon,Carol B. Ware,Hannele Ruohola-Baker +31 more
TL;DR: It is shown that nicotinamide N-methyltransferase (NNMT) and the metabolic state regulate pluripotency in human embryonic stem cells (hESCs), supporting the hypothesis that the metabolome regulates the epigenetic landscape of the earliest steps in human development.
Journal ArticleDOI
Analysis of CDS-located miRNA target sites suggests that they can effectively inhibit translation
TL;DR: This study suggests that miRNAs may combine targeting of CDS and 3' UTR to flexibly tune the time scale and magnitude of their post-transcriptional regulatory effects.
Journal ArticleDOI
The primate-specific microRNA gene cluster (C19MC) is imprinted in the placenta
Marie Noguer-Dance,Marie Noguer-Dance,Sayeda Abu-Amero,Mohamed Al-Khtib,Annick Lefèvre,Philippe Coullin,Gudrun E. Moore,Jérôme Cavaillé,Jérôme Cavaillé +8 more
TL;DR: The unexpected finding that the chromosome 19 microRNA cluster (C19MC), the largest human microRNA gene cluster discovered so far, is regulated by genomic imprinting with only the paternally inherited allele being expressed in the placenta is reported.
References
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Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors.
TL;DR: Induction of pluripotent stem cells from mouse embryonic or adult fibroblasts by introducing four factors, Oct3/4, Sox2, c-Myc, and Klf4, under ES cell culture conditions is demonstrated and iPS cells, designated iPS, exhibit the morphology and growth properties of ES cells and express ES cell marker genes.
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Induction of Pluripotent Stem Cells from Adult Human Fibroblasts by Defined Factors
Kazutoshi Takahashi,Koji Tanabe,Mari Ohnuki,Megumi Narita,Tomoko Ichisaka,Kiichiro Tomoda,Shinya Yamanaka +6 more
TL;DR: It is demonstrated that iPS cells can be generated from adult human fibroblasts with the same four factors: Oct3/4, Sox2, Klf4, and c-Myc.
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Embryonic Stem Cell Lines Derived from Human Blastocysts
James A. Thomson,Joseph Itskovitz-Eldor,Sander S. Shapiro,Michelle A. Waknitz,Swiergiel Jennifer J,Vivienne S. Marshall,Jeffrey M. Jones +6 more
TL;DR: Human blastocyst-derived, pluripotent cell lines are described that have normal karyotypes, express high levels of telomerase activity, and express cell surface markers that characterize primate embryonic stem cells but do not characterize other early lineages.
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Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments
TL;DR: The hierarchical model of Lonnstedt and Speed (2002) is developed into a practical approach for general microarray experiments with arbitrary numbers of treatments and RNA samples and the moderated t-statistic is shown to follow a t-distribution with augmented degrees of freedom.
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The functions of animal microRNAs
TL;DR: Evidence is mounting that animal miRNAs are more numerous, and their regulatory impact more pervasive, than was previously suspected.