Genomic approaches to deconstruct pluripotency

BioEssays, 2009

The phenomenal proliferation of scientific studies into the nature o nduced pluripotent stem (iPS) cells following publication of the findings of Takahashi and Yamanaka little more than 2 years ago, have significantly expanded our understanding of cellular mechanisms relating to cell lineage, di erentiation, and proliferation. While the full potential o PS cell lineages for both scientific tool and therapeutic applications is as yet unclear, findings from several lines o nvestigation suggests that multipotential and terminally di erentiated cells from an array of cell types are competent to undergo epigenetic reprogramming to a pluripotential state. The nature of this pluripotential state appears to be similar to, but not identical with that previously described for embryonic stem (ES) cells. Understanding the nature of this induced reprogrammed state will be critical to determining the full potential o PS cells. Recently, this issue has been examined through an integrated analysis of the genome in fully and partially reprogrammed iPS cell lineages. These results provide a window onto the temporal components of reprogramming and suggest mechanisms by which the efficacy of reprogramming can be enhanced.

Cell Cycle, 2015

I dentification of functionally relevant differences between induced pluripotent stem cells (iPSC) and reference embryonic stem cells (ESC) remains a central question for therapeutic applications. Differences in gene expression between iPSC and ESC have been examined by microarray and more recently with RNA-SEQ technologies. We here report an in depth analyses of nuclear and cytoplasmic transcriptomes, using the CAGE (cap analysis of gene expression) technology, for 5 iPSC clones derived from mouse lymphocytes B and 3 ESC lines. This approach reveals nuclear transcriptomes significantly more complex in ESC than in iPSC. Hundreds of yet not annotated putative non-coding RNAs and enhancer-associated transcripts specifically transcribed in ESC have been detected and supported with epigenetic and chromatin-chromatin interactions data. We identified superenhancers transcriptionally active specifically in ESC and associated with genes implicated in the maintenance of pluripotency. Similarly, we detected non-coding transcripts of yet unknown function being regulated by ESC specific superenhancers. Taken together, these results demonstrate that current protocols of iPSC reprogramming do not trigger activation of numerous cis-regulatory regions. It thus reinforces the need for already suggested deeper monitoring of the non-coding transcriptome when characterizing iPSC clones. Such differences in regulatory transcript expression may indeed impact their potential for clinical applications.

Epigenomics, 2016

Enforced ectopic expression of a cocktail of pluripotency-associated genes such as Oct4, Sox2, Klf4 and c-Myc can reprogram somatic cells into induced pluripotent stem cells (iPSCs). The remarkable proliferation ability of iPSCs and their aptitude to redifferentiate into any cell lineage makes these cells a promising tool for generating a variety of human tissue in vitro. Yet, pluripotency induction is an inefficient process, as cells undergoing reprogramming need to overcome developmentally imposed epigenetic barriers. Recent work has shed new light on the molecular mechanisms that drive the reprogramming of somatic cells to iPSCs. Here, we present current knowledge on the transcriptional and epigenetic regulation of pluripotency induction and discuss how variability in epigenetic states impacts iPSCs' inherent biological properties.

Pluripotent stem cells (PSCs) have the potential to differentiate into many cell types and therefore can be a valuable source for cell therapy. Embryonic stem cells (ESCs), which are derived from the inner cell mass (ICM) of the blastocyst, are representative of PSCs. However, use of these cells has some limitations, especially ethical restrictions and immune response. As a result, researchers have been looking for other cell sources or strategies to overcome these limitations. One kind of cellular reprogramming is the process of guiding mature cells into a state of gene expression similar to PSCs. It has been demonstrated that somatic cells can be reprogrammed by various methods, including somatic cell nuclear transfer (SCNT) and cell fusion with ESCs or treatment with their extracts. This implies that some factors in oocytes and ESCs are able to initiate the reprogramming process. Accordingly, induced pluripotent stem cells (iPSCs) have been derived from somatic cells by ectopic expression of some transcription factors. This discovery has resulted in raising several important questions about the mechanisms by which these factors influence the reprogramming and epigenetic status of the cells. iPSCs hold great promise for regenerative medicine, developmental biology, and drug discovery because they circumvent problems associated with both ethical issues and immunological rejection. Here we review the experiments involved in the discovery of iPSCs, important factors in their reprogramming, and their future perspectives in cell therapy.

Development (Cambridge, England), 2017

Pluripotent stem cells have broad utility in biomedical research and their molecular regulation has thus garnered substantial interest. While the principles that establish and regulate pluripotency have been well defined in the mouse, it has been difficult to extrapolate these insights to the human system due to species-specific differences and the distinct developmental identities of mouse versus human embryonic stem cells. In this Review, we examine genome-wide approaches to elucidate the regulatory principles of pluripotency in human embryos and stem cells, and highlight where differences exist in the regulation of pluripotency in mice and humans. We review recent insights into the nature of human pluripotent cells , obtained by the deep sequencing of pre-implantation embryos. We also present an integrated overview of the principal layers of global gene regulation in human pluripotent stem cells. Finally, we discuss the transcriptional and epigenomic remodeling events associated ...

Journal of Population Therapeutics & Clinical Pharmacology, 2024

Human embryology holds immense promise for medical science, offering insights into the initial establishment of human growth and the potential for regenerative medicine. This paper delves into the captivating realm of self-renewing pluripotent stem cells, which lie at the heart of unlocking the mysteries of human embryology. Pluripotent stem cells hold the outstanding capacity to form into any cell type inside the body, presenting unprecedented opportunities for understanding development, modeling diseases, and facilitating therapeutic interventions. With recent advancements in cellular reprogramming techniques and genome editing technologies, researchers have made significant strides in connecting the potential of pluripotent stem cells for various bids. This paper aims to explore the journey of pluripotent stem cells, from their discovery to current state-of-the-art methodologies, while highlighting the challenges and ethical considerations inherent in their utilization. By elucidating the mechanisms governing pluripotency and differentiation, this research seeks to provide valuable insights into human embryology and pave the way for innovative approaches in regenerative medicine and disease modeling.

Human Molecular Genetics, 2008

Embryonic stem (ES) cells are pluripotent and capable of self-renewal, thus holding promise for regenerative medicine. Recent studies have begun to provide insights into the molecular mechanisms underlying pluripotency and self-renewal. In this article, we discuss the roles of transcriptional regulation, epigenetic regulation and miRNAs in the maintenance of pluripotency and the differentiation of ES cells.

Acta Naturae, 2010

Mammalian embryonic stem cells (ESC) have a number of specific properties that make them a unique object of fundamental and applied studies. In culture, ESC can remain in an infinitely undifferentiated state and differentiate into descendants of all three germ layers-ectoderm, endoderm, and mesoderm-that is, they can potentially produce more than 200 cell types comprising the body of an adult mammal. These properties of ESC are refered to as self-renewal and pluripotency. In this review, the basic signal pathways implicated in the maintenance of ESC pluripotency are considered. The major genes comprising a subsystem of "internal regulators of pluripotency," their protein products and regulators, are characterized, and interaction with other factors is described as well. The role of epigenetic mechanisms and microRNAs in the system of ESC self-renewal and pluripotency, as well as the relationship between pluripotency and X-chromosome inactivation in female mammals, is discussed.

Stem Cells, 2010

Pluripotent stem cells (PSCs) have been derived from the embryos of mice and humans, representing the two major sources of PSCs. These cells are universally defined by their developmental properties, specifically their self-renewal capacity and differentiation potential which are regulated in mice and humans by complex transcriptional networks orchestrated by conserved transcription factors. However, significant differences exist in the transcriptional networks and signaling pathways that control mouse and human PSC self-renewal and lineage development. To distinguish between universally applicable and species-specific features, we collated and compared the molecular and cellular descriptions of mouse and human PSCs. Here we compare and contrast the response to signals dictated by the transcriptome and epigenome of mouse and human PSCs that will hopefully act as a critical resource to the field. These analyses underscore the importance of accounting for species differences when desi...

Cell Stem Cell, 2008

The molecular mechanisms underlying pluripotency and lineage specification from embryonic stem (ES) cells are largely unclear. Differentiation pathways may be determined by the targeted activation of lineage specific genes or by selective silencing of genome regions during differentiation. Here we show that the ES cell genome is transcriptionally globally hyperactive and undergoes global silencing as cells differentiate. Normally silent repeat regions are active in ES cells and tissue-specific genes are sporadically expressed at low levels. Whole genome tiling arrays demonstrate widespread transcription in both coding and non-coding regions in pluripotent ES cells whereas the transcriptional landscape becomes more discrete as differentiation proceeds. The transcriptional hyperactivity in ES cells is accompanied by disproportionate expression of chromatin-remodeling genes and the general transcription machinery, but not histone modifying activities. Interference with several chromatin remodeling activities in ES cells affects their proliferation and differentiation behavior. We propose that global transcriptional activity is a hallmark of pluripotent ES cells that contributes to their plasticity and that lineage specification is strongly driven by reduction of the actively transcribed portion of the genome. *Correspondence: [email protected] (E.M.), [email protected] (T.M.). 7 Current address :