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Multi-Omics of Pluripotent Stem Cells
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Multi-Omics of Pluripotent Stem Cells

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (30 June 2021) | Viewed by 9480

Special Issue Editor

Prof. Dr. Man Ryul Lee

E-Mail Website
Guest Editor
Soonchunhyang Institute of Medi-bio Science, Soon Chun Hyang University, Korea
Interests: Human Embryonic Stem Cell; Induced Pluripotent Stem Cell; Metabolic reprogramming; Cell fate determination; Single cell analysis

Special Issue Information

Pluripotent stem cells (PSCs) offer great clinical potential because of their dual capacity to self-renew and to differentiate into all cell types of the body. To characterize the subsets of PSCs that represent functionally distinct states during differentiation, a detailed molecular analysis is required, particularly when the cells are used for cell-based regenerative therapy. Recently, there have been significant advances in integrative analytical approaches, combining molecular data collected from the analyses of genome, transcriptomes (including single-cell mRNA-Seq), proteomes, metabolomes, epigenomes, and liposomes, collectively called multi-omics analysis. In addition, the availability of high-throughput analytical techniques at lower costs, and the development of supercomputers, have contributed to the integration of information on PSCs at an unprecedented scale and detail. Vast information acquired through such comprehensive data analyses greatly advances our understanding of not only the basic nature of PSCs but also their potential applications in developing stem-cell-based regenerative therapies without concerns about their biosafety. To recognize this new, growing field of research, the Special Issue focuses on areas of single- and multi-omics analyses of PSCs and the cell types differentiated from them. To this end, the International Journal of Molecular Science invites investigators to present their novel findings in the field of multi-omics of PSCs.

Prof. Dr. Man Ryul Lee
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • pluripotent stem cell
  • embryonic stem cell
  • induced pluripotent stem cell
  • transcriptomes
  • genome
  • proteomes
  • metabolomes
  • epigenomes
  • multi-omics

Published Papers (3 papers)

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Research

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13 pages, 1739 KiB  
Article
Complement C4 Is Reduced in iPSC-Derived Astrocytes of Autism Spectrum Disorder Subjects
by Fernanda Mansur, André Luiz Teles e Silva, Ana Karolyne Santos Gomes, Juliana Magdalon, Janaina Sena de Souza, Karina Griesi-Oliveira, Maria Rita Passos-Bueno and Andréa Laurato Sertié
Int. J. Mol. Sci. 2021, 22(14), 7579; https://doi.org/10.3390/ijms22147579 - 15 Jul 2021
Cited by 11 | Viewed by 2912
Abstract
In recent years, accumulating evidence has shown that the innate immune complement system is involved in several aspects of normal brain development and in neurodevelopmental disorders, including autism spectrum disorder (ASD). Although abnormal expression of complement components was observed in post-mortem brain samples [...] Read more.
In recent years, accumulating evidence has shown that the innate immune complement system is involved in several aspects of normal brain development and in neurodevelopmental disorders, including autism spectrum disorder (ASD). Although abnormal expression of complement components was observed in post-mortem brain samples from individuals with ASD, little is known about the expression patterns of complement molecules in distinct cell types in the developing autistic brain. In the present study, we characterized the mRNA and protein expression profiles of a wide range of complement system components, receptors and regulators in induced pluripotent stem cell (iPSC)-derived neural progenitor cells, neurons and astrocytes of individuals with ASD and neurotypical controls, which constitute in vitro cellular models that recapitulate certain features of both human brain development and ASD pathophysiology. We observed that all the analyzed cell lines constitutively express several key complement molecules. Interestingly, using different quantification strategies, we found that complement C4 mRNA and protein are expressed in significantly lower levels by astrocytes derived from ASD individuals compared to control astrocytes. As astrocytes participate in synapse elimination, and diminished C4 levels have been linked to defective synaptic pruning, our findings may contribute to an increased understanding of the atypically enhanced brain connectivity in ASD. Full article
(This article belongs to the Special Issue Multi-Omics of Pluripotent Stem Cells)
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20 pages, 7866 KiB  
Article
Chronically Elevated Exogenous Glucose Elicits Antipodal Effects on the Proteome Signature of Differentiating Human iPSC-Derived Pancreatic Progenitors
by Luiza Ghila, Thomas Aga Legøy, Andreas Frøslev Mathisen, Shadab Abadpour, Joao A. Paulo, Hanne Scholz, Helge Ræder and Simona Chera
Int. J. Mol. Sci. 2021, 22(7), 3698; https://doi.org/10.3390/ijms22073698 - 2 Apr 2021
Cited by 2 | Viewed by 2137
Abstract
The past decade revealed that cell identity changes, such as dedifferentiation or transdifferentiation, accompany the insulin-producing β-cell decay in most diabetes conditions. Mapping and controlling the mechanisms governing these processes is, thus, extremely valuable for managing the disease progression. Extracellular glucose is known [...] Read more.
The past decade revealed that cell identity changes, such as dedifferentiation or transdifferentiation, accompany the insulin-producing β-cell decay in most diabetes conditions. Mapping and controlling the mechanisms governing these processes is, thus, extremely valuable for managing the disease progression. Extracellular glucose is known to influence cell identity by impacting the redox balance. Here, we use global proteomics and pathway analysis to map the response of differentiating human pancreatic progenitors to chronically increased in vitro glucose levels. We show that exogenous high glucose levels impact different protein subsets in a concentration-dependent manner. In contrast, regardless of concentration, glucose elicits an antipodal effect on the proteome landscape, inducing both beneficial and detrimental changes in regard to achieving the desired islet cell fingerprint. Furthermore, we identified that only a subgroup of these effects and pathways are regulated by changes in redox balance. Our study highlights a complex effect of exogenous glucose on differentiating pancreas progenitors characterized by a distinct proteome signature. Full article
(This article belongs to the Special Issue Multi-Omics of Pluripotent Stem Cells)
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Review

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11 pages, 603 KiB  
Review
Single-Cell Transcriptome Analysis as a Promising Tool to Study Pluripotent Stem Cell Reprogramming
by Hyun Kyu Kim, Tae Won Ha and Man Ryul Lee
Int. J. Mol. Sci. 2021, 22(11), 5988; https://doi.org/10.3390/ijms22115988 - 1 Jun 2021
Cited by 6 | Viewed by 3759
Abstract
Cells are the basic units of all organisms and are involved in all vital activities, such as proliferation, differentiation, senescence, and apoptosis. A human body consists of more than 30 trillion cells generated through repeated division and differentiation from a single-cell fertilized egg [...] Read more.
Cells are the basic units of all organisms and are involved in all vital activities, such as proliferation, differentiation, senescence, and apoptosis. A human body consists of more than 30 trillion cells generated through repeated division and differentiation from a single-cell fertilized egg in a highly organized programmatic fashion. Since the recent formation of the Human Cell Atlas consortium, establishing the Human Cell Atlas at the single-cell level has been an ongoing activity with the goal of understanding the mechanisms underlying diseases and vital cellular activities at the level of the single cell. In particular, transcriptome analysis of embryonic stem cells at the single-cell level is of great importance, as these cells are responsible for determining cell fate. Here, we review single-cell analysis techniques that have been actively used in recent years, introduce the single-cell analysis studies currently in progress in pluripotent stem cells and reprogramming, and forecast future studies. Full article
(This article belongs to the Special Issue Multi-Omics of Pluripotent Stem Cells)
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