Functional Genomics and Epigenomics of Stem Cells

A special issue of Cells (ISSN 2073-4409). This special issue belongs to the section "Stem Cells".

Deadline for manuscript submissions: closed (31 October 2022) | Viewed by 3036

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Department of Environmental Health Sciences, Florida International University, Miami, FL 33199, USA
Interests: cancer biology; developmental biology; transcription factors; cellular senescence; precision medicine
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Scientist, Cancer Commons, 650 Castro Street, Suite 120-522, Mountain View, CA 94041, USA
Interests: cancer biology; developmental biology; transcription factors; cellular senescence; precision medicine

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Postdoctoral Scholar, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
Interests: cancer biology; developmental biology; transcription factors; cellular senescence; precision medicine

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Independent Researcher, Miami, FL, USA
Interests: cancer biology; developmental biology; transcription factors; cellular senescence; precision medicine

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Department of Health and Natural Sciences, Florida Memorial University, Miami Gardens, FL 33054, USA
Interests: cancer and molecular biology; toxicology; cancer stem cells; anti-cancer drug designs

Special Issue Information

Dear Colleagues,

Emerging genomic and epigenomic functional landscapes of different origins of cells offer an opportunity for the enrichment of precise personalized medicine. Functional genomic, transcriptomic, epigenomic, and proteomic landscapes in single cells are tremendously advancing our understanding of the networks of genes and epigenetic patterns regulating development and diseases. Stem cells have the capacity to self-replicate as well as to differentiate into a variety of cell types that form the basis for organ development and tissue regeneration. These cells are important during the embryonic phase and throughout adulthood and are known to play an active role in cancer development, progression, and treatment resistance. Recent advances in technology have allowed the use of stem cells for disease modeling, drug screening, and personalized medicine. Isolation and propagation of human stem cells including embryonic stem cells (ESCs), fetal progenitors, and adult stem cells (ASCs), as well as generation of induced pluripotent stem cells (iPSCs), have led to key discoveries about human developmental and disease processes. Newly developed single-cell transcriptomics and epigenomics techniques allow for the study of individual stem cells in the context of their surroundings. It is critical to integrate new findings with known markers of health and disease for advancing treatment approaches. In this Special Issue on “Functional Genomics and Epigenomics of Stem Cells”, we are soliciting both original research articles and reviews that will update our readers on novel findings, current understanding as well as perspectives on the topic. 

Sincerely,

Prof. Dr. Deodutta Roy
Dr. Kaumudi Bhawe
Dr. Jairo Ramos
Dr. Priti Roy
Dr. Jayanta Kumar Das
Guest Editors

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Keywords

  • genomics
  • epigenomics
  • stem cells
  • cell therapy

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Published Papers (1 paper)

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Research

19 pages, 7495 KiB  
Article
Padi2/3 Deficiency Alters the Epigenomic Landscape and Causes Premature Differentiation of Mouse Trophoblast Stem Cells
by Noura N. Ballasy, Elizabeth A. Bering, Caroline Kokorudz, Bethany N. Radford, Xiang Zhao, Wendy Dean and Myriam Hemberger
Cells 2022, 11(16), 2466; https://doi.org/10.3390/cells11162466 - 9 Aug 2022
Cited by 5 | Viewed by 2481
Abstract
Histone citrullination is a relatively poorly studied epigenetic modification that involves the irreversible conversion of arginine residues into citrulline. It is conferred by a small family of enzymes known as protein arginine deiminases (PADIs). PADI function supports the pluripotent state of embryonic stem [...] Read more.
Histone citrullination is a relatively poorly studied epigenetic modification that involves the irreversible conversion of arginine residues into citrulline. It is conferred by a small family of enzymes known as protein arginine deiminases (PADIs). PADI function supports the pluripotent state of embryonic stem cells, but in other contexts, also promotes efficient cellular differentiation. In the current study, we sought to gain deeper insights into the possible roles of PADIs in mouse trophoblast stem cells (TSCs). We show that Padi2 and Padi3 are the most highly expressed PADI family members in TSCs and are rapidly down-regulated upon differentiation. Padi2/3 double knockout (DKO) TSCs express lower levels of stem cell transcription factors CDX2 and SOX2 and are prone to differentiate into extremely large trophoblast giant cells, an effect that may be mediated by centrosome duplication defects. Interestingly, Padi2/3 DKO TSCs display alterations to their epigenomic landscape, with fewer H3K9me3-marked chromocentric foci and globally reduced 5-methylcytosine levels. DNA methylation profiling identifies that this effect is specifically evident at CpG islands of critical trophoblast genes, such as Gata3, Peg3, Socs3 and Hand1. As a consequence of the hypomethylated state, these factors are up-regulated in Padi2/3 DKO TSCs, driving their premature differentiation. Our data uncover a critical epigenetic role for PADI2/3 in safeguarding the stem cell state of TSCs by modulating the DNA methylation landscape to restrict precocious trophoblast differentiation. Full article
(This article belongs to the Special Issue Functional Genomics and Epigenomics of Stem Cells)
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