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Article: Transcriptome Encyclopedia of Early Human Development

Sahakyan, Anna / Kathrin Plath

Cell. 2016 May 05, v. 165

2016

Abstract: Our understanding of human pre-implantation development is limited by the availability of human embryos and cannot completely rely on mouse studies. Petropoulos etÂ al. now provide an extensive transcriptome analysis of a large number of human pre- ... ...

Abstract	Our understanding of human pre-implantation development is limited by the availability of human embryos and cannot completely rely on mouse studies. Petropoulos etÂ al. now provide an extensive transcriptome analysis of a large number of human pre-implantation embryos at single-cell resolution, revealing previously unrecognized features unique to early human development.
Keywords	human development ; humans ; mice ; transcriptome ; transcriptomics
Language	English
Dates of publication	2016-0505
Size	p. 777-779.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2016.04.042
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: DNA methylation estimation using methylation-sensitive restriction enzyme bisulfite sequencing (MREBS).

Giancarlo Bonora / Liudmilla Rubbi / Marco Morselli / Feiyang Ma / Constantinos Chronis / Kathrin Plath / Matteo Pellegrini

PLoS ONE, Vol 14, Iss 4, p e

2019 Volume 0214368

Abstract: Whole-genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS) are widely used for measuring DNA methylation levels on a genome-wide scale. Both methods have limitations: WGBS is expensive and prohibitive for most large- ... ...

Abstract	Whole-genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS) are widely used for measuring DNA methylation levels on a genome-wide scale. Both methods have limitations: WGBS is expensive and prohibitive for most large-scale projects; RRBS only interrogates 6-12% of the CpGs in the human genome. Here, we introduce methylation-sensitive restriction enzyme bisulfite sequencing (MREBS) which has the reduced sequencing requirements of RRBS, but significantly expands the coverage of CpG sites in the genome. We built a multiple regression model that combines the two features of MREBS: the bisulfite conversion ratios of single cytosines (as in WGBS and RRBS) as well as the number of reads that cover each locus (as in MRE-seq). This combined approach allowed us to estimate differential methylation across 60% of the genome using read count data alone, and where counts were sufficiently high in both samples (about 1.5% of the genome), our estimates were significantly improved by the single CpG conversion information. We show that differential DNA methylation values based on MREBS data correlate well with those based on WGBS and RRBS. This newly developed technique combines the sequencing cost of RRBS and DNA methylation estimates on a portion of the genome similar to WGBS, making it ideal for large-scale projects of mammalian genomes.
Keywords	Medicine ; R ; Science ; Q
Subject code	310
Language	English
Publishing date	2019-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Transcriptional, Electrophysiological, and Metabolic Characterizations of hESC-Derived First and Second Heart Fields Demonstrate a Potential Role of TBX5 in Cardiomyocyte Maturation

Arash Pezhouman / Ngoc B. Nguyen / Alexander J. Sercel / Thang L. Nguyen / Ali Daraei / Shan Sabri / Douglas J. Chapski / Melton Zheng / Alexander N. Patananan / Jason Ernst / Kathrin Plath / Thomas M. Vondriska / Michael A. Teitell / Reza Ardehali

Frontiers in Cell and Developmental Biology, Vol

2021 Volume 9

Abstract: Background: Human embryonic stem cell-derived cardiomyocytes (hESC-CMs) can be used as a source for cell delivery to remuscularize the heart after myocardial infarction. Despite their therapeutic potential, the emergence of ventricular arrhythmias has ... ...

Abstract	Background: Human embryonic stem cell-derived cardiomyocytes (hESC-CMs) can be used as a source for cell delivery to remuscularize the heart after myocardial infarction. Despite their therapeutic potential, the emergence of ventricular arrhythmias has limited their application. We previously developed a double reporter hESC line to isolate first heart field (FHF: TBX5+NKX2-5+) and second heart field (SHF: TBX5-NKX2-5+) CMs. Herein, we explore the role of TBX5 and its effects on underlying gene regulatory networks driving phenotypical and functional differences between these two populations.Methods: We used a combination of tools and techniques for rapid and unsupervised profiling of FHF and SHF populations at the transcriptional, translational, and functional level including single cell RNA (scRNA) and bulk RNA sequencing, atomic force and quantitative phase microscopy, respirometry, and electrophysiology.Results: Gene ontology analysis revealed three biological processes attributed to TBX5 expression: sarcomeric structure, oxidative phosphorylation, and calcium ion handling. Interestingly, migratory pathways were enriched in SHF population. SHF-like CMs display less sarcomeric organization compared to FHF-like CMs, despite prolonged in vitro culture. Atomic force and quantitative phase microscopy showed increased cellular stiffness and decreased mass distribution over time in FHF compared to SHF populations, respectively. Electrophysiological studies showed longer plateau in action potentials recorded from FHF-like CMs, consistent with their increased expression of calcium handling genes. Interestingly, both populations showed nearly identical respiratory profiles with the only significant functional difference being higher ATP generation-linked oxygen consumption rate in FHF-like CMs. Our findings suggest that FHF-like CMs display more mature features given their enhanced sarcomeric alignment, calcium handling, and decreased migratory characteristics. Finally, pseudotime analyses revealed a closer association ...
Keywords	first and second heart fields ; single cell RNA seq ; action potential ; hESC-derived cardiomyocyte ; maturity ; regenerative medicine ; Biology (General) ; QH301-705.5
Subject code	621
Language	English
Publishing date	2021-12-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: SARS-CoV-2 infection rewires host cell metabolism and is potentially susceptible to mTORC1 inhibition

Peter J. Mullen / Gustavo Garcia / Arunima Purkayastha / Nedas Matulionis / Ernst W. Schmid / Milica Momcilovic / Chandani Sen / Justin Langerman / Arunachalam Ramaiah / David B. Shackelford / Robert Damoiseaux / Samuel W. French / Kathrin Plath / Brigitte N. Gomperts / Vaithilingaraja Arumugaswami / Heather R. Christofk

Nature Communications, Vol 12, Iss 1, Pp 1-

2021 Volume 10

Abstract: The pandemic of COVID-19, caused by SARS-CoV-2 infection, warrants immediate investigation for therapy options. Here the authors show, using epithelial and air-liquid interface cultures, that SARS-CoV-2 hijacks host cell metabolism to facilitate viral ... ...

Abstract	The pandemic of COVID-19, caused by SARS-CoV-2 infection, warrants immediate investigation for therapy options. Here the authors show, using epithelial and air-liquid interface cultures, that SARS-CoV-2 hijacks host cell metabolism to facilitate viral replication, and that inhibition of mTORC1, a master metabolic regulator, suppresses viral replication.
Keywords	Science ; Q
Language	English
Publishing date	2021-03-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Stage-Specific Regulation of Reprogramming to Induced Pluripotent Stem Cells by Wnt Signaling and T Cell Factor Proteins

Ritchie Ho / Bernadett Papp / Jackson A. Hoffman / Bradley J. Merrill / Kathrin Plath

Cell Reports, Vol 3, Iss 6, Pp 2113-

2013 Volume 2126

Abstract: Wnt signaling is intrinsic to mouse embryonic stem cell self-renewal. Therefore, it is surprising that reprogramming of somatic cells to induced pluripotent stem cells (iPSCs) is not strongly enhanced by Wnt signaling. Here, we demonstrate that active ... ...

Abstract	Wnt signaling is intrinsic to mouse embryonic stem cell self-renewal. Therefore, it is surprising that reprogramming of somatic cells to induced pluripotent stem cells (iPSCs) is not strongly enhanced by Wnt signaling. Here, we demonstrate that active Wnt signaling inhibits the early stage of reprogramming to iPSCs, whereas it is required and even stimulating during the late stage. Mechanistically, this biphasic effect of Wnt signaling is accompanied by a change in the requirement of all four of its transcriptional effectors: T cell factor 1 (Tcf1), Lef1, Tcf3, and Tcf4. For example, Tcf3 and Tcf4 are stimulatory early but inhibitory late in the reprogramming process. Accordingly, ectopic expression of Tcf3 early in reprogramming combined with its loss of function late enables efficient reprogramming in the absence of ectopic Sox2. Together, our data indicate that the stepwise process of reprogramming to iPSCs is critically dependent on the stage-specific control and action of all four Tcfs and Wnt signaling.
Keywords	Biology (General) ; QH301-705.5
Subject code	570 ; 571
Language	English
Publishing date	2013-06-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: X Chromosome Dosage Influences DNA Methylation Dynamics during Reprogramming to Mouse iPSCs

Vincent Pasque / Rahul Karnik / Constantinos Chronis / Paula Petrella / Justin Langerman / Giancarlo Bonora / Juan Song / Lotte Vanheer / Anupama Sadhu Dimashkie / Alexander Meissner / Kathrin Plath

Stem Cell Reports, Vol 10, Iss 5, Pp 1537-

2018 Volume 1550

Abstract: Summary: A dramatic difference in global DNA methylation between male and female cells characterizes mouse embryonic stem cells (ESCs), unlike somatic cells. We analyzed DNA methylation changes during reprogramming of male and female somatic cells and in ...

Abstract	Summary: A dramatic difference in global DNA methylation between male and female cells characterizes mouse embryonic stem cells (ESCs), unlike somatic cells. We analyzed DNA methylation changes during reprogramming of male and female somatic cells and in resulting induced pluripotent stem cells (iPSCs). At an intermediate reprogramming stage, somatic and pluripotency enhancers are targeted for partial methylation and demethylation. Demethylation within pluripotency enhancers often occurs at ESC binding sites of pluripotency transcription factors. Late in reprogramming, global hypomethylation is induced in a female-specific manner. Genome-wide hypomethylation in female cells affects many genomic landmarks, including enhancers and imprint control regions, and accompanies the reactivation of the inactive X chromosome. The loss of one of the two X chromosomes in propagating female iPSCs is associated with genome-wide methylation gain. Collectively, our findings highlight the dynamic regulation of DNA methylation at enhancers during reprogramming and reveal that X chromosome dosage dictates global DNA methylation levels in iPSCs. : Somatic cells can be reprogrammed to iPSCs, inducing reactivation of the inactive X chromosome. Using genome-scale DNA methylation analyses, Plath, Pasque, and colleagues show that iPSCs adopt sex-specific differences in global DNA methylation that correlate with the presence of two active X chromosomes. Upon culture, female iPSCs lose one of the two X chromosomes and adopt male-like DNA methylation. Keywords: induced pluripotency, iPSC, DNA methylation, epigenetics, embryonic stem cells, ESC, pluripotency, reprogramming, X chromosome inactivation
Keywords	Medicine (General) ; R5-920 ; Biology (General) ; QH301-705.5
Subject code	570
Language	English
Publishing date	2018-05-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Loss of MECP2 Leads to Activation of P53 and Neuronal Senescence

Minori Ohashi / Elena Korsakova / Denise Allen / Peiyee Lee / Kai Fu / Benni S. Vargas / Jessica Cinkornpumin / Carlos Salas / Jenny C. Park / Igal Germanguz / Justin Langerman / Contantinos Chronis / Edward Kuoy / Stephen Tran / Xinshu Xiao / Matteo Pellegrini / Kathrin Plath / William E. Lowry

Stem Cell Reports, Vol 10, Iss 5, Pp 1453-

2018 Volume 1463

Abstract: Summary: To determine the role for mutations of MECP2 in Rett syndrome, we generated isogenic lines of human induced pluripotent stem cells, neural progenitor cells, and neurons from patient fibroblasts with and without MECP2 expression in an attempt to ... ...

Abstract	Summary: To determine the role for mutations of MECP2 in Rett syndrome, we generated isogenic lines of human induced pluripotent stem cells, neural progenitor cells, and neurons from patient fibroblasts with and without MECP2 expression in an attempt to recapitulate disease phenotypes in vitro. Molecular profiling uncovered neuronal-specific gene expression changes, including induction of a senescence-associated secretory phenotype (SASP) program. Patient-derived neurons made without MECP2 showed signs of stress, including induction of P53, and senescence. The induction of P53 appeared to affect dendritic branching in Rett neurons, as P53 inhibition restored dendritic complexity. The induction of P53 targets was also detectable in analyses of human Rett patient brain, suggesting that this disease-in-a-dish model can provide relevant insights into the human disorder. : In this report, Lowry and colleagues found that loss of MECP2 has a more profound effect as pluripotent stem cells are terminally differentiated toward neurons. The loss of MECP2 leads to induction of P53 protein and subsequent senescence pathways including an SASP gene program, which appears to be a cause of diminished dendritic branching in Rett neurons. Keywords: MECP2, Rett syndrome, disease in a dish, senescence
Keywords	Medicine (General) ; R5-920 ; Biology (General) ; QH301-705.5
Subject code	572
Language	English
Publishing date	2018-05-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The Pluripotency Factor-Bound Intron 1 of Xist Is Dispensable for X Chromosome Inactivation and Reactivation In Vitro and In Vivo

Alissa Minkovsky / Tahsin Stefan Barakat / Nadia Sellami / Mark Henry Chin / Nilhan Gunhanlar / Joost Gribnau / Kathrin Plath

Cell Reports, Vol 3, Iss 3, Pp 905-

2013 Volume 918

Abstract: X chromosome inactivation (XCI) is a dynamically regulated developmental process with inactivation and reactivation accompanying the loss and gain of pluripotency, respectively. A functional relationship between pluripotency and lack of XCI has been ... ...

Abstract	X chromosome inactivation (XCI) is a dynamically regulated developmental process with inactivation and reactivation accompanying the loss and gain of pluripotency, respectively. A functional relationship between pluripotency and lack of XCI has been suggested, whereby pluripotency transcription factors repress the master regulator of XCI, the noncoding transcript Xist, by binding to its first intron (intron 1). To test this model, we have generated intron 1 mutant embryonic stem cells (ESCs) and two independent mouse models. We found that Xist’s repression in ESCs, its transcriptional upregulation upon differentiation, and its silencing upon reprogramming to pluripotency are not dependent on intron 1. Although we observed subtle effects of intron 1 deletion on the randomness of XCI and in the absence of the antisense transcript Tsix in differentiating ESCs, these have little relevance in vivo because mutant mice do not deviate from Mendelian ratios of allele transmission. Altogether, our findings demonstrate that intron 1 is dispensable for the developmental dynamics of Xist expression.
Keywords	Biology (General) ; QH301-705.5
Subject code	570
Language	English
Publishing date	2013-03-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Post-translational regulation of Oct4 transcriptional activity.

Jonathan P Saxe / Alexey Tomilin / Hans R Schöler / Kathrin Plath / Jing Huang

PLoS ONE, Vol 4, Iss 2, p e

2009 Volume 4467

Abstract: Oct4 is a key component of the molecular circuitry which regulates embryonic stem cell proliferation and differentiation. It is essential for maintenance of undifferentiated, pluripotent cell populations, and accomplishes these tasks by binding DNA in ... ...

Abstract	Oct4 is a key component of the molecular circuitry which regulates embryonic stem cell proliferation and differentiation. It is essential for maintenance of undifferentiated, pluripotent cell populations, and accomplishes these tasks by binding DNA in multiple heterodimer and homodimer configurations. Very little is known about how formation of these complexes is regulated, or the mechanisms through which Oct4 proteins respond to complex extracellular stimuli which regulate pluripotency. Here, we provide evidence for a phosphorylation-based mechanism which regulates specific Oct4 homodimer conformations. Point mutations of a putative phosphorylation site can specifically abrogate transcriptional activity of a specific homodimer assembly, with little effect on other configurations. Moreover, we performed bioinformatic predictions to identify a subset of Oct4 target genes which may be regulated by this specific assembly, and show that altering Oct4 protein levels affects transcription of Oct4 target genes which are regulated by this assembly but not others. Finally, we identified several signaling pathways which may mediate this phosphorylation and act in combination to regulate Oct4 transcriptional activity and protein stability. These results provide a mechanism for rapid and reversible alteration of Oct4 transactivation potential in response to extracellular signals.
Keywords	Medicine ; R ; Science ; Q
Subject code	570
Language	English
Publishing date	2009-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Analysis of cardiomyocyte clonal expansion during mouse heart development and injury

Konstantina-Ioanna Sereti / Ngoc B. Nguyen / Paniz Kamran / Peng Zhao / Sara Ranjbarvaziri / Shuin Park / Shan Sabri / James L. Engel / Kevin Sung / Rajan P. Kulkarni / Yichen Ding / Tzung K. Hsiai / Kathrin Plath / Jason Ernst / Debashis Sahoo / Hanna K.A. Mikkola / M. Luisa Iruela-Arispe / Reza Ardehali

Nature Communications, Vol 9, Iss 1, Pp 1-

2018 Volume 13

Abstract: During cardiac tissue formation it is unclear whether newly generated myocytes originate from cardiac progenitor cells or from pre-existing cardiomyocytes. Here, the authors use a stochastic four-colour reporter system (Rainbow) to identify the source of ...

Abstract	During cardiac tissue formation it is unclear whether newly generated myocytes originate from cardiac progenitor cells or from pre-existing cardiomyocytes. Here, the authors use a stochastic four-colour reporter system (Rainbow) to identify the source of new cardiomyocytes during mouse development.
Keywords	Science ; Q
Language	English
Publishing date	2018-02-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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