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Chandrasekaran V, Wellens S, Bourguignon A, Djidrovski I, Fransen L, Ghosh S, Mazidi Z, Murphy C, Nunes C, Singh P, Zana M, Armstrong L, Dinnyés A, Grillari J, Grillari-Voglauer R, Leonard MO, Verfaillie C, Wilmes A, Zurich MG, Exner T, Jennings P, Culot M. Evaluation of the impact of iPSC differentiation protocols on transcriptomic signatures. Toxicol In Vitro 2024; 98:105826. [PMID: 38615723 DOI: 10.1016/j.tiv.2024.105826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 04/09/2024] [Indexed: 04/16/2024]
Abstract
Human induced pluripotent stem cells (iPSC) have the potential to produce desired target cell types in vitro and allow for the high-throughput screening of drugs/chemicals at population level thereby minimising the cost of drug discovery and drug withdrawals after clinical trials. There is a substantial need for the characterisation of the iPSC derived models to better understand and utilise them for toxicological relevant applications. In our study, iPSC (SBAD2 or SBAD3 lines obtained from StemBANCC project) were differentiated towards toxicologically relevant cell types: alveolar macrophages, brain capillary endothelial cells, brain cells, endothelial cells, hepatocytes, lung airway epithelium, monocytes, podocytes and renal proximal tubular cells. A targeted transcriptomic approach was employed to understand the effects of differentiation protocols on these cell types. Pearson correlation and principal component analysis (PCA) separated most of the intended target cell types and undifferentiated iPSC models as distinct groups with a high correlation among replicates from the same model. Based on PCA, the intended target cell types could also be separated into the three germ layer groups (ectoderm, endoderm and mesoderm). Differential expression analysis (DESeq2) presented the upregulated genes in each intended target cell types that allowed the evaluation of the differentiation to certain degree and the selection of key differentiation markers. In conclusion, these data confirm the versatile use of iPSC differentiated cell types as standardizable and relevant model systems for in vitro toxicology.
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Affiliation(s)
- Vidya Chandrasekaran
- Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081HZ Amsterdam, the Netherlands
| | - Sara Wellens
- University of Artois, UR 2465, Laboratoire de la Barrière Hémato-Encéphalique (LBHE), Faculté des sciences Jean Perrin, Rue Jean Souvraz SP18, F-62300 Lens, France
| | - Aurore Bourguignon
- BioTalentum Ltd, Gödöllő, Hungary; Department of Physiology and Animal Health, Institute of Physiology and Animal Nutrition, Hungarian University of Agriculture and Life Sciences, H-2100, Gödöllő, Hungary
| | - Ivo Djidrovski
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, UK
| | - Leonie Fransen
- Toxicology Department, Radiation, Chemical and Environmental Hazards (RCE) Directorate, UK Health Security Agency, Harwell Campus, OX11 0RQ, UK
| | - Sreya Ghosh
- Department of Development and Regeneration, Stem Cell Institute, KU Leuven, Leuven, Belgium
| | - Zahra Mazidi
- Evercyte GmbH, Vienna, Austria; Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Cormac Murphy
- Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081HZ Amsterdam, the Netherlands
| | - Carolina Nunes
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland; Swiss Centre for Applied Human Toxicology (SCAHT), University of Basel, Basel, Switzerland
| | - Pranika Singh
- Edelweiss Connect GmbH, Technology Park Basel, Hochbergerstrasse 60C, 4057 Basel, Switzerland; Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | | | - Lyle Armstrong
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, UK
| | - András Dinnyés
- BioTalentum Ltd, Gödöllő, Hungary; Department of Physiology and Animal Health, Institute of Physiology and Animal Nutrition, Hungarian University of Agriculture and Life Sciences, H-2100, Gödöllő, Hungary
| | - Johannes Grillari
- Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria; Ludwig Boltzmann Institute for Traumatology in cooperation with AUVA, Vienna, Austria
| | | | - Martin O Leonard
- Toxicology Department, Radiation, Chemical and Environmental Hazards (RCE) Directorate, UK Health Security Agency, Harwell Campus, OX11 0RQ, UK
| | - Catherine Verfaillie
- Department of Development and Regeneration, Stem Cell Institute, KU Leuven, Leuven, Belgium
| | - Anja Wilmes
- Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081HZ Amsterdam, the Netherlands
| | - Marie-Gabrielle Zurich
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland; Swiss Centre for Applied Human Toxicology (SCAHT), University of Basel, Basel, Switzerland
| | | | - Paul Jennings
- Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081HZ Amsterdam, the Netherlands.
| | - Maxime Culot
- University of Artois, UR 2465, Laboratoire de la Barrière Hémato-Encéphalique (LBHE), Faculté des sciences Jean Perrin, Rue Jean Souvraz SP18, F-62300 Lens, France.
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2
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Abujarour R, Dinella J, Pribadi M, Fong LK, Denholtz M, Gutierrez A, Haynes M, Mahmood E, Lee TT, Ding S, Valamehr B. A chemical approach facilitates CRISPRa-only human iPSC generation and minimizes the number of targeted loci required. Future Sci OA 2024; 10:FSO964. [PMID: 38817352 PMCID: PMC11137772 DOI: 10.2144/fsoa-2023-0257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/19/2024] [Indexed: 06/01/2024] Open
Abstract
Aim: We explored the generation of human induced pluripotent stem cells (iPSCs) solely through the transcriptional activation of endogenous genes by CRISPR activation (CRISPRa). Methods: Minimal number of human-specific guide RNAs targeting a limited set of loci were used with a unique cocktail of small molecules (CRISPRa-SM). Results: iPSC clones were efficiently generated by CRISPRa-SM, expressed general and naive iPSC markers and clustered with high-quality iPSCs generated using conventional reprogramming methods. iPSCs showed genomic stability and robust pluripotent potential as assessed by in vitro and in vivo. Conclusion: CRISPRa-SM-generated human iPSCs by direct and multiplexed loci activation facilitating a unique and potentially safer cellular reprogramming process to aid potential applications in cellular therapy and regenerative medicine.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Tom T Lee
- Fate Therapeutics, San Diego, CA 92121, USA
| | - Sheng Ding
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
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3
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Tahmasebi F, Asl ER, Vahidinia Z, Barati S. Stem Cell-Derived Exosomal MicroRNAs as Novel Potential Approach for Multiple Sclerosis Treatment. Cell Mol Neurobiol 2024; 44:44. [PMID: 38713302 PMCID: PMC11076329 DOI: 10.1007/s10571-024-01478-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 04/09/2024] [Indexed: 05/08/2024]
Abstract
Multiple Sclerosis (MS) is an autoimmune disease of the central nervous system (CNS) characterized by inflammation and demyelination of CNS neurons. Up to now, there are many therapeutic strategies for MS but they are only being able to reduce progression of diseases and have not got any effect on repair and remyelination. Stem cell therapy is an appropriate method for regeneration but has limitations and problems. So recently, researches were used of exosomes that facilitate intercellular communication and transfer cell-to-cell biological information. MicroRNAs (miRNAs) are a class of short non-coding RNAs that we can used to their dysregulation in order to diseases diagnosis. The miRNAs of microvesicles obtained stem cells may change the fate of transplanted cells based on received signals of injured regions. The miRNAs existing in MSCs may be displayed the cell type and their biological activities. Current studies show also that the miRNAs create communication between stem cells and tissue-injured cells. In the present review, firstly we discuss the role of miRNAs dysregulation in MS patients and miRNAs expression by stem cells. Finally, in this study was confirmed the relationship of microRNAs involved in MS and miRNAs expressed by stem cells and interaction between them in order to find appropriate treatment methods in future for limit to disability progression.
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Affiliation(s)
- Fatemeh Tahmasebi
- Department of Anatomy, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Elmira Roshani Asl
- Department of Biochemistry, Saveh University of Medical Sciences, Saveh, Iran
| | - Zeinab Vahidinia
- Anatomical Sciences Research Center, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Shirin Barati
- Department of Anatomy, Saveh University of Medical Sciences, Saveh, Iran.
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4
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Mote RD, Tiwari M, Yadavalli N, Rajan R, Subramanyam D. A high-throughput screen in mESCs to identify the cross-talk between signaling, endocytosis, and pluripotency. Cell Biol Int 2024. [PMID: 38706123 DOI: 10.1002/cbin.12168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 03/23/2024] [Accepted: 04/14/2024] [Indexed: 05/07/2024]
Abstract
Embryonic stem cell fate is regulated by various cellular processes. Recently, the process of endocytosis has been implicated in playing a role in the maintenance of self-renewal and pluripotency of mouse embryonic stem cells. A previous siRNA-based screen interrogated the function of core components of the endocytic machinery in maintaining the pluripotency of embryonic stem cells, revealing a crucial role for clathrin mediated endocytosis. A number of other proteins involved in key signaling pathways have also been shown to both regulate and be regulated by endocytosis. We collated a list of 1141 genes in connection to the term "endocytosis" from Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO), excluding those previously interrogated, and examined the effect of their knockdown on the pluripotency of mouse embryonic stem cells (mESCs) using levels of green fluorescent protein driven by the Oct4 promoter. We used high-throughput screening followed by an automated MATrix LABoratory (MATLAB)-based analysis pipeline and assessed changes in GFP fluorescence as a readout for ESC pluripotency. Through this screen we identified a number of genes, many hitherto not associated with stem cell pluripotency, which upon knockdown either resulted in a significant increase or decrease of GFP fluorescence. We further present validation for some of these hits. We present a workflow aimed to identify genes involved in signaling pathways which can be regulated by endocytosis, and that affect the pluripotency of ESCs.
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Affiliation(s)
- Ridim D Mote
- Stem Cell Biology Lab, National Centre for Cell Science, SP Pune University Campus, Pune, India
| | - Mahak Tiwari
- Stem Cell Biology Lab, National Centre for Cell Science, SP Pune University Campus, Pune, India
- SP Pune University, Pune, India
| | - Narayana Yadavalli
- Stem Cell Biology Lab, National Centre for Cell Science, SP Pune University Campus, Pune, India
| | - Raghav Rajan
- Indian Institute of Science Education and Research, Pune, India
| | - Deepa Subramanyam
- Stem Cell Biology Lab, National Centre for Cell Science, SP Pune University Campus, Pune, India
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5
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Pazzin DB, Previato TTR, Budelon Gonçalves JI, Zanirati G, Xavier FAC, da Costa JC, Marinowic DR. Induced Pluripotent Stem Cells and Organoids in Advancing Neuropathology Research and Therapies. Cells 2024; 13:745. [PMID: 38727281 PMCID: PMC11083827 DOI: 10.3390/cells13090745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/19/2024] [Accepted: 03/19/2024] [Indexed: 05/13/2024] Open
Abstract
This review delves into the groundbreaking impact of induced pluripotent stem cells (iPSCs) and three-dimensional organoid models in propelling forward neuropathology research. With a focus on neurodegenerative diseases, neuromotor disorders, and related conditions, iPSCs provide a platform for personalized disease modeling, holding significant potential for regenerative therapy and drug discovery. The adaptability of iPSCs, along with associated methodologies, enables the generation of various types of neural cell differentiations and their integration into three-dimensional organoid models, effectively replicating complex tissue structures in vitro. Key advancements in organoid and iPSC generation protocols, alongside the careful selection of donor cell types, are emphasized as critical steps in harnessing these technologies to mitigate tumorigenic risks and other hurdles. Encouragingly, iPSCs show promising outcomes in regenerative therapies, as evidenced by their successful application in animal models.
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Affiliation(s)
- Douglas Bottega Pazzin
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul, Porto Alegre 90610-000, Brazil; (D.B.P.); (T.T.R.P.); (J.I.B.G.); (G.Z.); (F.A.C.X.); (J.C.d.C.)
- Graduate Program in Pediatrics and Child Health, School of Medicine, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre 90619-900, Brazil
| | - Thales Thor Ramos Previato
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul, Porto Alegre 90610-000, Brazil; (D.B.P.); (T.T.R.P.); (J.I.B.G.); (G.Z.); (F.A.C.X.); (J.C.d.C.)
- Graduate Program in Biomedical Gerontology, School of Medicine, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre 90619-900, Brazil
| | - João Ismael Budelon Gonçalves
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul, Porto Alegre 90610-000, Brazil; (D.B.P.); (T.T.R.P.); (J.I.B.G.); (G.Z.); (F.A.C.X.); (J.C.d.C.)
| | - Gabriele Zanirati
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul, Porto Alegre 90610-000, Brazil; (D.B.P.); (T.T.R.P.); (J.I.B.G.); (G.Z.); (F.A.C.X.); (J.C.d.C.)
| | - Fernando Antonio Costa Xavier
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul, Porto Alegre 90610-000, Brazil; (D.B.P.); (T.T.R.P.); (J.I.B.G.); (G.Z.); (F.A.C.X.); (J.C.d.C.)
| | - Jaderson Costa da Costa
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul, Porto Alegre 90610-000, Brazil; (D.B.P.); (T.T.R.P.); (J.I.B.G.); (G.Z.); (F.A.C.X.); (J.C.d.C.)
| | - Daniel Rodrigo Marinowic
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul, Porto Alegre 90610-000, Brazil; (D.B.P.); (T.T.R.P.); (J.I.B.G.); (G.Z.); (F.A.C.X.); (J.C.d.C.)
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6
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Bao Q, Tay NL, Lim CY, Chua DHH, Kee SK, Choolani M, Loh YH, Ng SC, Chai C. Integration-free induced pluripotent stem cells from three endangered Southeast Asian non-human primate species. Sci Rep 2024; 14:2391. [PMID: 38287040 PMCID: PMC10825216 DOI: 10.1038/s41598-023-50510-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 12/20/2023] [Indexed: 01/31/2024] Open
Abstract
Advanced molecular and cellular technologies provide promising tools for wildlife and biodiversity conservation. Induced pluripotent stem cell (iPSC) technology offers an easily accessible and infinite source of pluripotent stem cells, and have been derived from many threatened wildlife species. This paper describes the first successful integration-free reprogramming of adult somatic cells to iPSCs, and their differentiation, from three endangered Southeast Asian primates: the Celebes Crested Macaque (Macaca nigra), the Lar Gibbon (Hylobates lar), and the Siamang (Symphalangus syndactylus). iPSCs were also generated from the Proboscis Monkey (Nasalis larvatus). Differences in mechanisms could elicit new discoveries regarding primate evolution and development. iPSCs from endangered species provides a safety net in conservation efforts and allows for sustainable sampling for research and conservation, all while providing a platform for the development of further in vitro models of disease.
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Affiliation(s)
- Qiuye Bao
- Institute of Molecular and Cell Biology-Endangered Species Conservation By Assisted Reproduction (IMCB-ESCAR) Joint Laboratory, Agency for Science, Technology, and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Nicole Liling Tay
- Institute of Molecular and Cell Biology-Endangered Species Conservation By Assisted Reproduction (IMCB-ESCAR) Joint Laboratory, Agency for Science, Technology, and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119074, Singapore
| | - Christina Yingyan Lim
- Institute of Molecular and Cell Biology-Endangered Species Conservation By Assisted Reproduction (IMCB-ESCAR) Joint Laboratory, Agency for Science, Technology, and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
| | | | - Su Keyau Kee
- Cytogenetics Laboratory, Department of Pathology, Singapore General Hospital, 20 College Road, Singapore, 169856, Singapore
| | - Mahesh Choolani
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119074, Singapore
| | - Yuin-Han Loh
- Institute of Molecular and Cell Biology-Endangered Species Conservation By Assisted Reproduction (IMCB-ESCAR) Joint Laboratory, Agency for Science, Technology, and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117593, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
| | - Soon Chye Ng
- Institute of Molecular and Cell Biology-Endangered Species Conservation By Assisted Reproduction (IMCB-ESCAR) Joint Laboratory, Agency for Science, Technology, and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore.
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119074, Singapore.
- Sincere Healthcare Group, 8 Sinaran Drive, Singapore, 307470, Singapore.
| | - Chou Chai
- Institute of Molecular and Cell Biology-Endangered Species Conservation By Assisted Reproduction (IMCB-ESCAR) Joint Laboratory, Agency for Science, Technology, and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore
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7
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Inagaki M. Cell Reprogramming and Differentiation Utilizing Messenger RNA for Regenerative Medicine. J Dev Biol 2023; 12:1. [PMID: 38535481 PMCID: PMC10971469 DOI: 10.3390/jdb12010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/06/2023] [Accepted: 12/19/2023] [Indexed: 06/16/2024] Open
Abstract
The COVID-19 pandemic generated interest in the medicinal applications of messenger RNA (mRNA). It is expected that mRNA will be applied, not only to vaccines, but also to regenerative medicine. The purity of mRNA is important for its medicinal applications. However, the current mRNA synthesis techniques exhibit problems, including the contamination of undesired 5'-uncapped mRNA and double-stranded RNA. Recently, our group developed a completely capped mRNA synthesis technology that contributes to the progress of mRNA research. The introduction of chemically modified nucleosides, such as N1-methylpseudouridine and 5-methylcytidine, has been reported by Karikó and Weissman, opening a path for the practical application of mRNA for vaccines and regenerative medicine. Yamanaka reported the production of induced pluripotent stem cells (iPSCs) by introducing four types of genes using a retrovirus vector. iPSCs are widely used for research on regenerative medicine and the preparation of disease models to screen new drug candidates. Among the Yamanaka factors, Klf4 and c-Myc are oncogenes, and there is a risk of tumor development if these are integrated into genomic DNA. Therefore, regenerative medicine using mRNA, which poses no risk of genome insertion, has attracted attention. In this review, the author summarizes techniques for synthesizing mRNA and its application in regenerative medicine.
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Affiliation(s)
- Masahito Inagaki
- Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
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8
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Conrad JV, Meyer S, Ramesh PS, Neira JA, Rusteika M, Mamott D, Duffin B, Bautista M, Zhang J, Hiles E, Higgins EM, Steill J, Freeman J, Ni Z, Liu S, Ungrin M, Rancourt D, Clegg DO, Stewart R, Thomson JA, Chu LF. Efficient derivation of transgene-free porcine induced pluripotent stem cells enables in vitro modeling of species-specific developmental timing. Stem Cell Reports 2023; 18:2328-2343. [PMID: 37949072 PMCID: PMC10724057 DOI: 10.1016/j.stemcr.2023.10.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 11/12/2023] Open
Abstract
Sus scrofa domesticus (pig) has served as a superb large mammalian model for biomedical studies because of its comparable physiology and organ size to humans. The derivation of transgene-free porcine induced pluripotent stem cells (PiPSCs) will, therefore, benefit the development of porcine-specific models for regenerative biology and its medical applications. In the past, this effort has been hampered by a lack of understanding of the signaling milieu that stabilizes the porcine pluripotent state in vitro. Here, we report that transgene-free PiPSCs can be efficiently derived from porcine fibroblasts by episomal vectors along with microRNA-302/367 using optimized protocols tailored for this species. PiPSCs can be differentiated into derivatives representing the primary germ layers in vitro and can form teratomas in immunocompromised mice. Furthermore, the transgene-free PiPSCs preserve intrinsic species-specific developmental timing in culture, known as developmental allochrony. This is demonstrated by establishing a porcine in vitro segmentation clock model that, for the first time, displays a specific periodicity at ∼3.7 h, a timescale recapitulating in vivo porcine somitogenesis. We conclude that the transgene-free PiPSCs can serve as a powerful tool for modeling development and disease and developing transplantation strategies. We also anticipate that they will provide insights into conserved and unique features on the regulations of mammalian pluripotency and developmental timing mechanisms.
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Affiliation(s)
- J Vanessa Conrad
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada
| | - Susanne Meyer
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Pranav S Ramesh
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada
| | - Jaime A Neira
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada; Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Margaret Rusteika
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada; Department of Biomedical Engineering, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Daniel Mamott
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Bret Duffin
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Monica Bautista
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada
| | - Jue Zhang
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Emily Hiles
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada
| | - Eve M Higgins
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada
| | - John Steill
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Jack Freeman
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Zijian Ni
- Department of Statistics, University of Wisconsin, Madison, WI 53706, USA
| | - Shiying Liu
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Mark Ungrin
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada; Department of Biomedical Engineering, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Derrick Rancourt
- Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada; Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Dennis O Clegg
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; Department of Molecular, Cellular, & Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Ron Stewart
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - James A Thomson
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Molecular, Cellular, & Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Li-Fang Chu
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada; Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada.
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9
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Li Z, Duan Y, Yan S, Zhang Y, Wu Y. The miR-302/367 cluster: Aging, inflammation, and cancer. Cell Biochem Funct 2023; 41:752-766. [PMID: 37555645 DOI: 10.1002/cbf.3836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 07/25/2023] [Indexed: 08/10/2023]
Abstract
MicroRNAs (miRNAs) are a class of noncoding RNAs that occupy a significant role in biological processes as important regulators of intracellular homeostasis. First, we will discuss the biological genesis and functions of the miR-302/367 cluster, including miR-302a, miR-302b, miR-302c, miR-302d, and miR-367, as well as their roles in physiologically healthy tissues. The second section of this study reviews the progress of the miR-302/367 cluster in the treatment of cancer, inflammation, and diseases associated with aging. This cluster's aberrant expression in cells and/or tissues exhibits similar or different effects in various diseases through molecular mechanisms such as proliferation, apoptosis, cycling, drug resistance, and invasion. This article also discusses the upstream and downstream regulatory networks of miR-302/367 clusters and their related mechanisms. Particularly because studies on the upstream regulatory molecules of miR-302/367 clusters, which include age-related macular degeneration, myocardial infarction, and cancer, have become more prevalent in recent years. MiR-302/367 cluster can be an important therapeutic target and the use of miRNAs in combination with other molecular markers may improve diagnostic or therapeutic capabilities, providing unique insights and a more dynamic view of various diseases. It is noted that miRNAs can be an important bio-diagnostic target and offer a promising method for illness diagnosis, prevention, and treatment.
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Affiliation(s)
- Zhou Li
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi Province, China
| | - Yan Duan
- Department of Stomatology, Shanxi Provincial People's Hospital, Taiyuan, Shanxi Province, China
| | - Shaofu Yan
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi Province, China
| | - Yao Zhang
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi Province, China
| | - Yunxia Wu
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi Province, China
- Department of Stomatology, First Hospital of Shanxi Medical University, Taiyuan, Shanxi Province, China
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10
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Sahito JZA, Deng S, Qin L, Xiao L, Zhang D, Huang B. CeRNA Network Reveals the Circular RNA Characterization in Goat Ear Fibroblasts Reprogramming into Mammary Epithelial Cells. Genes (Basel) 2023; 14:1831. [PMID: 37895180 PMCID: PMC10606430 DOI: 10.3390/genes14101831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/18/2023] [Accepted: 08/22/2023] [Indexed: 10/29/2023] Open
Abstract
Circular RNAs (circRNAs) are a type of non-coding RNA that play a crucial role in the development and lactation of mammary glands in mammals. A total of 107 differentially expressed circRNAs (DE circRNAs) were found, of which 52 were up-regulated and 55 were down-regulated. We also found that DE circRNA host genes were mainly involved in GO terms related to the development process of mammary epithelial cells and KEGG pathways were mostly related to mammary epithelial cells, lactation, and gland development. Protein network analysis found that DE circRNAs can competitively bind to miRNAs as key circRNAs by constructing a circRNA-miRNA-mRNA network. CircRNAs competitively bind to miRNAs (miR-10b-3p, miR-671-5p, chi-miR-200c, chi-miR-378-3p, and chi-miR-30e-5p) involved in goat mammary gland development, mammary epithelial cells, and lactation, affecting the expression of core genes (CDH2, MAPK1, ITGB1, CAMSAP2, and MAPKAPK5). Here, we generated CiMECs and systematically explored the differences in the transcription profile for the first time using whole-transcriptome sequencing. We also analyzed the interaction among mRNA, miRNA, and cirRNA and predicted that circRNA plays an important role in the maintenance of mammary epithelial cells.
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Affiliation(s)
- Jam Zaheer Ahmed Sahito
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (J.Z.A.S.); (S.D.); (L.Q.); (L.X.); (D.Z.)
| | - Shan Deng
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (J.Z.A.S.); (S.D.); (L.Q.); (L.X.); (D.Z.)
| | - Liangshan Qin
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (J.Z.A.S.); (S.D.); (L.Q.); (L.X.); (D.Z.)
| | - Lianggui Xiao
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (J.Z.A.S.); (S.D.); (L.Q.); (L.X.); (D.Z.)
| | - Dandan Zhang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (J.Z.A.S.); (S.D.); (L.Q.); (L.X.); (D.Z.)
- Guangxi Key Laboratory of Eye Health, The People’s Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical Sciences, Nanning, 530021, China
| | - Ben Huang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (J.Z.A.S.); (S.D.); (L.Q.); (L.X.); (D.Z.)
- Guangxi Key Laboratory of Eye Health, The People’s Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical Sciences, Nanning, 530021, China
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11
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Ware AP, Satyamoorthy K, Paul B. Integrated multiomics analysis of chromosome 19 miRNA cluster in bladder cancer. Funct Integr Genomics 2023; 23:266. [PMID: 37542643 PMCID: PMC10404189 DOI: 10.1007/s10142-023-01191-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/07/2023]
Abstract
With 46 microRNAs (miRNAs) embedded tandemly over a distance of ~100 kb, chromosome 19 microRNA cluster (C19MC) is the largest miRNA cluster in the human genome. The C19MC is transcribed from a long noncoding genomic region and is usually expressed simultaneously at a higher level. Hence, we performed an integrative multiomics data analysis to examine C19MC regulation, expression patterns, and their impact on bladder cancer (BCa). We found that 43 members of C19MC were highly expressed in BCa. However, its co-localization with recurrent copy number variation (CNV) gain was not statistically significant to implicate its upregulation. It has been reported that C19MC expression is regulated by a well-established CpG island situated 17.6 kb upstream of the transcription start site, but we found that CpG probes at this island were hypomethylated, which was not statistically significant in the BCa cohort. In addition, the promoter region of C19MC is strongly regulated by a group of seven transcription factors (NR2F6, SREBF1, TBP, GATA3, GABPB1, ETV4, and ZNF444) and five chromatin modifiers (SMC3, KDMA1, EZH2, RAD21, and CHD7). Interestingly, these 12 genes were found to be overexpressed in BCa patients. Further, C19MC targeted 42 tumor suppressor (TS) genes that were downregulated, of which 15 were significantly correlated with patient survival. Our findings suggest that transcription factors and chromatin modifiers at the promoter region may regulate C19MC overexpression. The upregulated C19MC members, transcription regulators, and TS genes can be further exploited as potential diagnostic and prognostic indicators as well as for therapeutic management of BCa.
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Affiliation(s)
- Akshay Pramod Ware
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
- SDM College of Medical Sciences and Hospital, Shri Dharmasthala Manjunatheshwara (SDM) University, Manjushree Nagar, Sattur, Dharwad, Karnataka, 580009, India
| | - Bobby Paul
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.
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12
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Hoetker MS, Yagi M, Di Stefano B, Langerman J, Cristea S, Wong LP, Huebner AJ, Charlton J, Deng W, Haggerty C, Sadreyev RI, Meissner A, Michor F, Plath K, Hochedlinger K. H3K36 methylation maintains cell identity by regulating opposing lineage programmes. Nat Cell Biol 2023; 25:1121-1134. [PMID: 37460697 PMCID: PMC10896483 DOI: 10.1038/s41556-023-01191-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/19/2023] [Indexed: 08/12/2023]
Abstract
The epigenetic mechanisms that maintain differentiated cell states remain incompletely understood. Here we employed histone mutants to uncover a crucial role for H3K36 methylation in the maintenance of cell identities across diverse developmental contexts. Focusing on the experimental induction of pluripotency, we show that H3K36M-mediated depletion of H3K36 methylation endows fibroblasts with a plastic state poised to acquire pluripotency in nearly all cells. At a cellular level, H3K36M facilitates epithelial plasticity by rendering fibroblasts insensitive to TGFβ signals. At a molecular level, H3K36M enables the decommissioning of mesenchymal enhancers and the parallel activation of epithelial/stem cell enhancers. This enhancer rewiring is Tet dependent and redirects Sox2 from promiscuous somatic to pluripotency targets. Our findings reveal a previously unappreciated dual role for H3K36 methylation in the maintenance of cell identity by integrating a crucial developmental pathway into sustained expression of cell-type-specific programmes, and by opposing the expression of alternative lineage programmes through enhancer methylation.
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Affiliation(s)
- Michael S Hoetker
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Masaki Yagi
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bruno Di Stefano
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Justin Langerman
- David Geffen School of Medicine, Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - Simona Cristea
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Lai Ping Wong
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Aaron J Huebner
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jocelyn Charlton
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Department of Genome Regulation, Max-Planck Institute for Molecular Genetics, Berlin, Germany
| | - Weixian Deng
- David Geffen School of Medicine, Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - Chuck Haggerty
- Department of Genome Regulation, Max-Planck Institute for Molecular Genetics, Berlin, Germany
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School and Massachusetts General Hospital, Boston, MA, USA
| | - Alexander Meissner
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Department of Genome Regulation, Max-Planck Institute for Molecular Genetics, Berlin, Germany
| | - Franziska Michor
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- The Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA, USA
- The Ludwig Center at Harvard, Boston, MA, USA
| | - Kathrin Plath
- David Geffen School of Medicine, Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - Konrad Hochedlinger
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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13
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Maraghechi P, Aponte MTS, Ecker A, Lázár B, Tóth R, Szabadi NT, Gócza E. Pluripotency-Associated microRNAs in Early Vertebrate Embryos and Stem Cells. Genes (Basel) 2023; 14:1434. [PMID: 37510338 PMCID: PMC10379376 DOI: 10.3390/genes14071434] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
MicroRNAs (miRNAs), small non-coding RNA molecules, regulate a wide range of critical biological processes, such as proliferation, cell cycle progression, differentiation, survival, and apoptosis, in many cell types. The regulatory functions of miRNAs in embryogenesis and stem cell properties have been extensively investigated since the early years of miRNA discovery. In this review, we will compare and discuss the impact of stem-cell-specific miRNA clusters on the maintenance and regulation of early embryonic development, pluripotency, and self-renewal of embryonic stem cells, particularly in vertebrates.
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Affiliation(s)
- Pouneh Maraghechi
- Department of Animal Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences; Agrobiotechnology and Precision Breeding for Food Security National Laboratory, Szent-Györgyi Albert str. 4, 2100 Gödöllő, Hungary
| | - Maria Teresa Salinas Aponte
- Department of Animal Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences; Agrobiotechnology and Precision Breeding for Food Security National Laboratory, Szent-Györgyi Albert str. 4, 2100 Gödöllő, Hungary
| | - András Ecker
- Department of Animal Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences; Agrobiotechnology and Precision Breeding for Food Security National Laboratory, Szent-Györgyi Albert str. 4, 2100 Gödöllő, Hungary
| | - Bence Lázár
- Department of Animal Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences; Agrobiotechnology and Precision Breeding for Food Security National Laboratory, Szent-Györgyi Albert str. 4, 2100 Gödöllő, Hungary
- National Centre for Biodiversity and Gene Conservation, Institute for Farm Animal Gene Conservation (NBGK-HGI), Isaszegi str. 200, 2100 Gödöllő, Hungary
| | - Roland Tóth
- Department of Animal Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences; Agrobiotechnology and Precision Breeding for Food Security National Laboratory, Szent-Györgyi Albert str. 4, 2100 Gödöllő, Hungary
| | - Nikolett Tokodyné Szabadi
- Department of Animal Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences; Agrobiotechnology and Precision Breeding for Food Security National Laboratory, Szent-Györgyi Albert str. 4, 2100 Gödöllő, Hungary
| | - Elen Gócza
- Department of Animal Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences; Agrobiotechnology and Precision Breeding for Food Security National Laboratory, Szent-Györgyi Albert str. 4, 2100 Gödöllő, Hungary
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14
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Kosanović M, Milutinović B, Kutzner TJ, Mouloud Y, Bozic M. Clinical Prospect of Mesenchymal Stromal/Stem Cell-Derived Extracellular Vesicles in Kidney Disease: Challenges and the Way Forward. Pharmaceutics 2023; 15:1911. [PMID: 37514097 PMCID: PMC10384614 DOI: 10.3390/pharmaceutics15071911] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/23/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
Kidney disease is a growing public health problem worldwide, including both acute and chronic forms. Existing therapies for kidney disease target various pathogenic mechanisms; however, these therapies only slow down the progression of the disease rather than offering a cure. One of the potential and emerging approaches for the treatment of kidney disease is mesenchymal stromal/stem cell (MSC) therapy, shown to have beneficial effects in preclinical studies. In addition, extracellular vesicles (EVs) released by MSCs became a potent cell-free therapy option in various preclinical models of kidney disease due to their regenerative, anti-inflammatory, and immunomodulatory properties. However, there are scarce clinical data available regarding the use of MSC-EVs in kidney pathologies. This review article provides an outline of the renoprotective effects of MSC-EVs in different preclinical models of kidney disease. It offers a comprehensive analysis of possible mechanisms of action of MSC-EVs with an emphasis on kidney disease. Finally, on the journey toward the implementation of MSC-EVs into clinical practice, we highlight the need to establish standardized methods for the characterization of an EV-based product and investigate the adequate dosing, safety, and efficacy of MSC-EVs application, as well as the development of suitable potency assays.
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Affiliation(s)
- Maja Kosanović
- Institute for the Application of Nuclear Energy (INEP), University of Belgrade, 11 000 Belgrade, Serbia
| | - Bojana Milutinović
- Department of Neurosurgery, MD Anderson Cancer Center, University of Texas, Houston, TX 770302, USA
| | - Tanja J Kutzner
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, 45355 Essen, North Rhine-Westhpalia, Germany
| | - Yanis Mouloud
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, 45355 Essen, North Rhine-Westhpalia, Germany
| | - Milica Bozic
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, 45355 Essen, North Rhine-Westhpalia, Germany
- Vascular and Renal Translational Research Group, Biomedical Research Institute of Lleida Dr. Pifarré Foundation (IRBLLEIDA), 25196 Lleida, Spain
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15
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Lucchini M, De Arcangelis V, Santoro M, Morosetti R, Broccolini A, Mirabella M. Serum-Circulating microRNAs in Sporadic Inclusion Body Myositis. Int J Mol Sci 2023; 24:11139. [PMID: 37446317 DOI: 10.3390/ijms241311139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/25/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND Sporadic inclusion body myositis (s-IBM) represents a unique disease within idiopathic inflammatory myopathies with a dual myodegenerative-autoimmune physiopathology and a lack of an efficacious treatment. Circulating miRNA expression could expand our knowledge of s-IBM patho-mechanisms and provide new potential disease biomarkers. To evaluate the expression of selected pre-amplified miRNAs in the serum of s-IBM patients compared to those of a sex- and age-matched healthy control group, we enrolled 14 consecutive s-IBM patients and 8 sex- and age-matched healthy controls. By using two different normalization approaches, we found one downregulated and three upregulated miRNAs. hsa-miR-192-5p was significantly downregulated, while hsa-miR-372-3p was found to be upregulated more in the s-IBM patients compared to the level of the controls. The other two miRNAs had a very low expression levels (raw Ct data > 29). hsa-miR-192-5p and hsa-miR-372-3p were found to be significantly dysregulated in the serum of s-IBM patients. These miRNAs are involved in differentiation and regeneration processes, thus possibly reflecting pathological mechanisms in s-IBM muscles and potentially representing disease biomarkers.
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Affiliation(s)
- Matteo Lucchini
- UOC Neurologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
- Dipartimento di Neuroscienze, Sezione di Neurologia, Catholic University of Sacred Heart, 00168 Rome, Italy
| | - Valeria De Arcangelis
- UOC Neurologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Massimo Santoro
- Energy and Sustainable Economic Development, Division of Health Protection Technologies ENEA-Italian National Agency for New Technologies, 00123 Rome, Italy
| | - Roberta Morosetti
- UOC Neurologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Aldobrando Broccolini
- UOC Neurologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
- Dipartimento di Neuroscienze, Sezione di Neurologia, Catholic University of Sacred Heart, 00168 Rome, Italy
| | - Massimiliano Mirabella
- UOC Neurologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
- Dipartimento di Neuroscienze, Sezione di Neurologia, Catholic University of Sacred Heart, 00168 Rome, Italy
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16
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Ishida T, Ueyama T, Ihara D, Harada Y, Nakagawa S, Saito K, Nakao S, Kawamura T. c-Myc/microRNA-17-92 Axis Phase-Dependently Regulates PTEN and p21 Expression via ceRNA during Reprogramming to Mouse Pluripotent Stem Cells. Biomedicines 2023; 11:1737. [PMID: 37371832 DOI: 10.3390/biomedicines11061737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/08/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Induced pluripotent stem cells (iPSCs) are promising cell sources for regenerative medicine and disease modeling. iPSCs are commonly established by introducing the defined reprogramming factors Oct4, Sox2, Klf4, and c-Myc. However, iPSC reprogramming efficiency remains low. Although recent studies have identified microRNAs that contribute to efficient reprogramming, the underlying molecular mechanisms are not completely understood. miR-17-92 is highly expressed in embryonic stem cells and may play an important role in regulating stem cell properties. Therefore, we examined the role of miR-17-92 in the induction of mouse iPSC production. c-Myc-mediated miR-17-92 upregulation increased reprogramming efficiency, whereas CRISPR/Cas9-based deletion of the miR-17-92 cluster decreased reprogramming efficiency. A combination of in silico and microarray analyses revealed that Pten and cyclin-dependent kinase inhibitor 1 (known as p21) are common target genes of miR-17 and miR-20a, which are transcribed from the miR-17-92 cluster. Moreover, miR-17-92 downregulated p21 in the early phase and PTEN in the mid-to-late phase of reprogramming. These downregulations were perturbed by introducing the 3' UTR of PTEN and p21, respectively, suggesting that PTEN and p21 mRNAs are competing endogenous RNAs (ceRNA) against miR-17-92. Collectively, we propose that the c-Myc-mediated expression of miR-17-92 is involved in iPSC reprogramming through the phase-dependent inhibition of PTEN and p21 in a ceRNA manner, thus elucidating an underlying mechanism of iPSC reprogramming.
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Affiliation(s)
- Tomoaki Ishida
- Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu 525-8577, Shiga, Japan
- Ritsumeikan Global Innovation Research Organization, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu 525-8577, Shiga, Japan
| | - Tomoe Ueyama
- Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu 525-8577, Shiga, Japan
- Ritsumeikan Global Innovation Research Organization, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu 525-8577, Shiga, Japan
| | - Dai Ihara
- Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu 525-8577, Shiga, Japan
| | - Yukihiro Harada
- Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu 525-8577, Shiga, Japan
| | - Sae Nakagawa
- Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu 525-8577, Shiga, Japan
| | - Kaho Saito
- Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu 525-8577, Shiga, Japan
| | - Shu Nakao
- Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu 525-8577, Shiga, Japan
- Ritsumeikan Global Innovation Research Organization, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu 525-8577, Shiga, Japan
- Department of Physiology, Tokai University School of Medicine, 143 Shimokasuya, Isehara 259-1193, Kanagawa, Japan
| | - Teruhisa Kawamura
- Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu 525-8577, Shiga, Japan
- Ritsumeikan Global Innovation Research Organization, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu 525-8577, Shiga, Japan
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17
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Kshirsagar A, Doroshev SM, Gorelik A, Olender T, Sapir T, Tsuboi D, Rosenhek-Goldian I, Malitsky S, Itkin M, Argoetti A, Mandel-Gutfreund Y, Cohen SR, Hanna JH, Ulitsky I, Kaibuchi K, Reiner O. LIS1 RNA-binding orchestrates the mechanosensitive properties of embryonic stem cells in AGO2-dependent and independent ways. Nat Commun 2023; 14:3293. [PMID: 37280197 DOI: 10.1038/s41467-023-38797-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/15/2023] [Indexed: 06/08/2023] Open
Abstract
Lissencephaly-1 (LIS1) is associated with neurodevelopmental diseases and is known to regulate the molecular motor cytoplasmic dynein activity. Here we show that LIS1 is essential for the viability of mouse embryonic stem cells (mESCs), and it governs the physical properties of these cells. LIS1 dosage substantially affects gene expression, and we uncovered an unexpected interaction of LIS1 with RNA and RNA-binding proteins, most prominently the Argonaute complex. We demonstrate that LIS1 overexpression partially rescued the extracellular matrix (ECM) expression and mechanosensitive genes conferring stiffness to Argonaute null mESCs. Collectively, our data transforms the current perspective on the roles of LIS1 in post-transcriptional regulation underlying development and mechanosensitive processes.
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Affiliation(s)
- Aditya Kshirsagar
- Departments of Molecular Genetics and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Svetlana Maslov Doroshev
- Departments of Molecular Genetics and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Anna Gorelik
- Departments of Molecular Genetics and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Tsviya Olender
- Departments of Molecular Genetics and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Tamar Sapir
- Departments of Molecular Genetics and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Daisuke Tsuboi
- International Center for Brain Science, Fujita Health University, Toyoake, Japan
| | - Irit Rosenhek-Goldian
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Sergey Malitsky
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Maxim Itkin
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Amir Argoetti
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | | | - Sidney R Cohen
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Jacob H Hanna
- Departments of Molecular Genetics and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Igor Ulitsky
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Kozo Kaibuchi
- International Center for Brain Science, Fujita Health University, Toyoake, Japan
| | - Orly Reiner
- Departments of Molecular Genetics and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel.
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18
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Tajik F, Alian F, Yousefi M, Azadfallah A, Hoseini A, Mohammadi F, Karimi-Dehkordi M, Alizadeh-Fanalou S. MicroRNA-372 acts as a double-edged sword in human cancers. Heliyon 2023; 9:e15991. [PMID: 37251909 PMCID: PMC10208947 DOI: 10.1016/j.heliyon.2023.e15991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 04/26/2023] [Accepted: 04/28/2023] [Indexed: 05/31/2023] Open
Abstract
MicroRNAs (miRNAs or miRs) are non-coding, single-stranded, endogenous RNAs that regulate various biological processes, most notably the pathophysiology of many human malignancies. It process is accomplished by binding to 3'-UTR mRNAs and controlling gene expression at the post-transcriptional level. As an oncogene, miRNAs can either accelerate cancer progression or slow it down as a tumor suppressor. MicroRNA-372 (miR-372) has been found to have an abnormal expression in numerous human malignancies, implying that the miRNA plays a role in carcinogenesis. It is both increased and downregulated in various cancers, and it serves as both a tumor suppressor and an oncogene. This study examines the functions of miR-372 as well as the LncRNA/CircRNA-miRNA-mRNA signaling pathways in various malignancies and analyses its potential prognostic, diagnostic, and therapeutic implications.
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Affiliation(s)
- Fatemeh Tajik
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Alian
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Mohammad Yousefi
- Department of Medicine, School of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Ali Azadfallah
- Department of Medicine, School of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Aref Hoseini
- Student Research Committee, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Forogh Mohammadi
- Department of Veterinary, Agriculture Faculty, Kermanshah Branch, Islamic Azad University, Kermanshah, Iran
| | - Maryam Karimi-Dehkordi
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Shahin Alizadeh-Fanalou
- Department of Clinical Biochemistry, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran
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19
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Yu Y, Li W, Xian T, Tu M, Wu H, Zhang J. Human Embryonic Stem-Cell-Derived Exosomes Repress NLRP3 Inflammasome to Alleviate Pyroptosis in Nucleus Pulposus Cells by Transmitting miR-302c. Int J Mol Sci 2023; 24:ijms24087664. [PMID: 37108824 PMCID: PMC10141109 DOI: 10.3390/ijms24087664] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/03/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Recent studies have shown that the NOD-, LRR-, and pyrin domain-containing protein 3 (NLRP3) inflammasome is extensively activated in the process of intervertebral disc degeneration (IVDD), leading to the pyroptosis of nucleus pulposus cells (NPCs) and the exacerbation of the pathological development of the intervertebral disc (IVD). Exosomes derived from human embryonic stem cells (hESCs-exo) have shown great therapeutic potential in degenerative diseases. We hypothesized that hESCs-exo could alleviate IVDD by downregulating NLRP3. We measured the NLRP3 protein levels in different grades of IVDD and the effect of hESCs-exo on the H2O2-induced pyroptosis of NPCs. Our results indicate that the expression of NLRP3 was upregulated with the increase in IVD degeneration. hESCs-exo were able to reduce the H2O2-mediated pyroptosis of NPCs by downregulating the expression levels of NLRP3 inflammasome-related genes. Bioinformatics software predicted that miR-302c, an embryonic stem-cell-specific RNA, can inhibit NLRP3, thereby alleviating the pyroptosis of NPCs, and this was further verified by the overexpression of miR-302c in NPCs. In vivo experiments confirmed the above results in a rat caudal IVDD model. Our study demonstrates that hESCs-exo could inhibit excessive NPC pyroptosis by downregulating the NLRP3 inflammasome during IVDD, and miR-302c may play a key role in this process.
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Affiliation(s)
- Yawen Yu
- Department of Biochemistry and Molecular Biology, School of Preclinical Medicine, Jinan University, 601 West Huangpu Avenue, Guangzhou 510632, China
| | - Wenting Li
- Department of Biochemistry and Molecular Biology, School of Preclinical Medicine, Jinan University, 601 West Huangpu Avenue, Guangzhou 510632, China
| | - Tinghui Xian
- Department of Biochemistry and Molecular Biology, School of Preclinical Medicine, Jinan University, 601 West Huangpu Avenue, Guangzhou 510632, China
| | - Mei Tu
- Department of Materials Science and Engineering, Jinan University, Guangzhou 510632, China
| | - Hao Wu
- Department of Orthopedic Surgery, The First Affiliated Hospital, Jinan University, Guangzhou 510632, China
| | - Jiaqing Zhang
- Department of Biochemistry and Molecular Biology, School of Preclinical Medicine, Jinan University, 601 West Huangpu Avenue, Guangzhou 510632, China
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20
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Keuls RA, Oh YS, Patel I, Parchem RJ. Post-transcriptional regulation in cranial neural crest cells expands developmental potential. Proc Natl Acad Sci U S A 2023; 120:e2212578120. [PMID: 36724256 PMCID: PMC9963983 DOI: 10.1073/pnas.2212578120] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 12/20/2022] [Indexed: 02/03/2023] Open
Abstract
Developmental potential is progressively restricted after germ layer specification during gastrulation. However, cranial neural crest cells challenge this paradigm, as they develop from anterior ectoderm, yet give rise to both ectodermal derivatives of the peripheral nervous system and ectomesenchymal bone and cartilage. How cranial neural crest cells differentiate into multiple lineages is poorly understood. Here, we demonstrate that cranial neural crest cells possess a transient state of increased chromatin accessibility. We profile the spatiotemporal emergence of premigratory neural crest and find evidence of lineage bias toward either a neuronal or ectomesenchymal fate, with each expressing distinct factors from earlier stages of development. We identify the miR-302 miRNA family to be highly expressed in cranial neural crest cells and genetic deletion leads to precocious specification of the ectomesenchymal lineage. Loss of mir-302 results in reduced chromatin accessibility in the neuronal progenitor lineage of neural crest and a reduction in peripheral neuron differentiation. Mechanistically, we find that mir-302 directly targets Sox9 to slow the timing of ectomesenchymal neural crest specification and represses multiple genes involved in chromatin condensation to promote accessibility required for neuronal differentiation. Our findings reveal a posttranscriptional mechanism governed by miRNAs to expand developmental potential of cranial neural crest.
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Affiliation(s)
- Rachel A. Keuls
- Development, Disease Models & Therapeutics Graduate Program, Baylor College of Medicine, Houston, TX77030
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX77030
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX77030
- Department of Neuroscience, Baylor College of Medicine, Houston, TX77030
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX77030
| | - Young Sun Oh
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX77030
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX77030
- Department of Neuroscience, Baylor College of Medicine, Houston, TX77030
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX77030
| | - Ivanshi Patel
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX77030
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX77030
- Department of Neuroscience, Baylor College of Medicine, Houston, TX77030
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX77030
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX77030
| | - Ronald J. Parchem
- Development, Disease Models & Therapeutics Graduate Program, Baylor College of Medicine, Houston, TX77030
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX77030
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX77030
- Department of Neuroscience, Baylor College of Medicine, Houston, TX77030
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX77030
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX77030
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21
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Peng J, Zhang WJ, Zhang Q, Su YH, Tang LP. The dynamics of chromatin states mediated by epigenetic modifications during somatic cell reprogramming. Front Cell Dev Biol 2023; 11:1097780. [PMID: 36727112 PMCID: PMC9884706 DOI: 10.3389/fcell.2023.1097780] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/05/2023] [Indexed: 01/17/2023] Open
Abstract
Somatic cell reprogramming (SCR) is the conversion of differentiated somatic cells into totipotent or pluripotent cells through a variety of methods. Somatic cell reprogramming also provides a platform to investigate the role of chromatin-based factors in establishing and maintaining totipotency or pluripotency, since high expression of totipotency- or pluripotency-related genes usually require an active chromatin state. Several studies in plants or mammals have recently shed light on the molecular mechanisms by which epigenetic modifications regulate the expression of totipotency or pluripotency genes by altering their chromatin states. In this review, we present a comprehensive overview of the dynamic changes in epigenetic modifications and chromatin states during reprogramming from somatic cells to totipotent or pluripotent cells. In addition, we illustrate the potential role of DNA methylation, histone modifications, histone variants, and chromatin remodeling during somatic cell reprogramming, which will pave the way to developing reliable strategies for efficient cellular reprogramming.
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Affiliation(s)
| | | | | | - Ying Hua Su
- *Correspondence: Ying Hua Su, ; Li Ping Tang,
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22
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Benati D, Leung A, Perdigao P, Toulis V, van der Spuy J, Recchia A. Induced Pluripotent Stem Cells and Genome-Editing Tools in Determining Gene Function and Therapy for Inherited Retinal Disorders. Int J Mol Sci 2022; 23:ijms232315276. [PMID: 36499601 PMCID: PMC9735568 DOI: 10.3390/ijms232315276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Inherited retinal disorders (IRDs) affect millions of people worldwide and are a major cause of irreversible blindness. Therapies based on drugs, gene augmentation or transplantation approaches have been widely investigated and proposed. Among gene therapies for retinal degenerative diseases, the fast-evolving genome-editing CRISPR/Cas technology has emerged as a new potential treatment. The CRISPR/Cas system has been developed as a powerful genome-editing tool in ophthalmic studies and has been applied not only to gain proof of principle for gene therapies in vivo, but has also been extensively used in basic research to model diseases-in-a-dish. Indeed, the CRISPR/Cas technology has been exploited to genetically modify human induced pluripotent stem cells (iPSCs) to model retinal disorders in vitro, to test in vitro drugs and therapies and to provide a cell source for autologous transplantation. In this review, we will focus on the technological advances in iPSC-based cellular reprogramming and gene editing technologies to create human in vitro models that accurately recapitulate IRD mechanisms towards the development of treatments for retinal degenerative diseases.
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Affiliation(s)
- Daniela Benati
- Centre for Regenerative Medicine, Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Amy Leung
- UCL Institute of Ophthalmology, London EC1V 9EL, UK
| | - Pedro Perdigao
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | | | | | - Alessandra Recchia
- Centre for Regenerative Medicine, Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
- Correspondence: (J.v.d.S.); (A.R.)
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23
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Sugawara T, Kawamoto Y, Kawasaki T, Umezawa A, Akutsu H. A single allele of the hsa-miR-302/367 cluster maintains human pluripotent stem cells. Regen Ther 2022; 21:37-45. [PMID: 35702483 PMCID: PMC9162946 DOI: 10.1016/j.reth.2022.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/13/2022] [Accepted: 05/15/2022] [Indexed: 12/03/2022] Open
Abstract
Introduction In a diploid organism, two alleles from a single genetic locus are expressed to generate a normal phenotype. Heterozygous deleterious mutation causes a reduction of functional proteins to a half dose and insufficient amounts of functional proteins can occur to generate an in–normal phenotype, namely haploinsufficiency. Heterozygous deleterious mutation of microRNAs (miRs), non-coding RNAs that regulate the expression level of target transcripts, is still not well understood. The hsa-miR-302/367 cluster is the most abundant and specifically up-regulated miR cluster in human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) and plays an important role in the maintenance of pluripotency. Methods We targeted the hsa-miR-302/367 region via a Cas9 nuclease complex with guide RNA and replaced that region with green fluorescent protein (GFP). Using a homologous donor, consisting of left and right arms and GFP, we confirmed deletion of the hsa-miR-302/367 cluster by homologous recombination without cellular destruction by microscopy. We sub-cloned GFP-positive colonies and checked the genotype of each sub-clone by genomic PCR. We then analyzed the pluripotency of heterozygous knockout cells with a hsa-miR-302/367 cluster by assessing cell proliferation ratio, morphology, and undifferentiated marker gene expression. We also used an embryoid body formation assay and transplanted wild-type and heterozygous knockout cells into immune-deficient mice. Furthermore, to analyze the lineage-specific differentiation potential of heterozygous knockout cells, we differentiated both wild-type and heterozygous knockout cells into neural stem cells. Results Here, we show that the half dose of mature miRs from the hsa-miR-302/367 cluster loci was sufficient for the continued self-renewal of hiPSCs. All GFP-positive clones were revealed to be heterozygous knockout cells, suggesting hsa-miR-302/367 cluster homozygous knockout cells were not maintained. The cell proliferation ratio, morphology, and expression of undifferentiated marker genes were comparable between wild-type and heterozygous knockout of undifferentiated human iPSCs. In addition, we found that heterozygous knockout human iPSCs have the capacity to differentiate into three germ layers, including neural stem cells. Conclusions Taken together, a single allele of the hsa-miR-302/367 cluster expresses a sufficient amount of miRs to maintain the pluripotent properties of human stem cells. hsa-miR-302/367 cluster was deleted with CRISPR/Cas9 in human pluripotent stem cells. Homozygous hsa-miR-302/367 knockout cell was not generated.
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Affiliation(s)
| | | | | | | | - Hidenori Akutsu
- Corresponding author. Department of Reproductive Medicine, Center for Regenerative Medicine, National Center for Child Health and Development (NCCHD), Okura 2-10-1, Setagaya, Tokyo, 157-8535, Japan. Tel: +81-3-5494-7047, Fax: +81-3-5494-7048.
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24
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Matrix from urine stem cells boosts tissue-specific stem cell mediated functional cartilage reconstruction. Bioact Mater 2022; 23:353-367. [PMID: 36474659 PMCID: PMC9709166 DOI: 10.1016/j.bioactmat.2022.11.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 11/27/2022] Open
Abstract
Articular cartilage has a limited capacity to self-heal once damaged. Tissue-specific stem cells are a solution for cartilage regeneration; however, ex vivo expansion resulting in cell senescence remains a challenge as a large quantity of high-quality tissue-specific stem cells are needed for cartilage regeneration. Our previous report demonstrated that decellularized extracellular matrix (dECM) deposited by human synovium-derived stem cells (SDSCs), adipose-derived stem cells (ADSCs), urine-derived stem cells (UDSCs), or dermal fibroblasts (DFs) provided an ex vivo solution to rejuvenate human SDSCs in proliferation and chondrogenic potential, particularly for dECM deposited by UDSCs. To make the cell-derived dECM (C-dECM) approach applicable clinically, in this study, we evaluated ex vivo rejuvenation of rabbit infrapatellar fat pad-derived stem cells (IPFSCs), an easily accessible alternative for SDSCs, by the abovementioned C-dECMs, in vivo application for functional cartilage repair in a rabbit osteochondral defect model, and potential cellular and molecular mechanisms underlying this rejuvenation. We found that C-dECM rejuvenation promoted rabbit IPFSCs' cartilage engineering and functional regeneration in both ex vivo and in vivo models, particularly for the dECM deposited by UDSCs, which was further confirmed by proteomics data. RNA-Seq analysis indicated that both mesenchymal-epithelial transition (MET) and inflammation-mediated macrophage activation and polarization are potentially involved in the C-dECM-mediated promotion of IPFSCs' chondrogenic capacity, which needs further investigation.
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25
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Paloviita P, Vuoristo S. The non-coding genome in early human development - Recent advancements. Semin Cell Dev Biol 2022; 131:4-13. [PMID: 35177347 DOI: 10.1016/j.semcdb.2022.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/08/2022] [Accepted: 02/08/2022] [Indexed: 12/14/2022]
Abstract
Not that long ago, the human genome was discovered to be mainly non-coding, that is comprised of DNA sequences that do not code for proteins. The initial paradigm that non-coding is also non-functional was soon overturned and today the work to uncover the functions of non-coding DNA and RNA in human early embryogenesis has commenced. Early human development is characterized by large-scale changes in genomic activity and the transcriptome that are partly driven by the coordinated activation and repression of repetitive DNA elements scattered across the genome. Here we provide examples of recent novel discoveries of non-coding DNA and RNA interactions and mechanisms that ensure accurate non-coding activity during human maternal-to-zygotic transition and lineage segregation. These include studies on small and long non-coding RNAs, transposable element regulation, and RNA tailing in human oocytes and early embryos. High-throughput approaches to dissect the non-coding regulatory networks governing early human development are a foundation for functional studies of specific genomic elements and molecules that has only begun and will provide a wider understanding of early human embryogenesis and causes of infertility.
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Affiliation(s)
- Pauliina Paloviita
- Department of Obstetrics and Gynaecology, University of Helsinki, 00014 Helsinki, Finland
| | - Sanna Vuoristo
- Department of Obstetrics and Gynaecology, University of Helsinki, 00014 Helsinki, Finland.
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26
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Xie J, He C, Su Y, Ding Y, Zhu X, Xu Y, Ding J, Zhou H, Wang H. Research progress on microRNA in gout. Front Pharmacol 2022; 13:981799. [PMID: 36339582 PMCID: PMC9631428 DOI: 10.3389/fphar.2022.981799] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/26/2022] [Indexed: 07/30/2023] Open
Abstract
Gout is a common form of arthritis caused by the deposition of sodium urate crystals in the joints and tissues around them. MicroRNAs (miRNAs) are noncoding RNAs that have been shown to be involved in regulating the pathogenesis of gout through multiple cellular signaling pathways, which may be potential targets for the treatment of gout. In this review, we systematically discuss the regulatory roles of related miRNAs in gout, which will provide help for the treatment of gout and miRNAs is expected to become a potential biomarker for gout diagnosis.
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Affiliation(s)
- Jing Xie
- Clinical Trials Center, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
| | - Cuixia He
- Clinical Trials Center, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
- School of Pharmacy, Bengbu Medical College, Bengbu, Anhui, China
| | - Yue Su
- Clinical Trials Center, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
- School of Public Foundation, Bengbu Medical College, Bengbu, Anhui, China
| | - Yuzhou Ding
- Clinical Trials Center, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
| | - Xingyu Zhu
- Clinical Trials Center, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
- School of Pharmacy, Bengbu Medical College, Bengbu, Anhui, China
| | - Yuanyuan Xu
- Clinical Trials Center, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
- School of Pharmacy, Bengbu Medical College, Bengbu, Anhui, China
| | - Jiaxiang Ding
- Clinical Trials Center, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
- School of Public Foundation, Bengbu Medical College, Bengbu, Anhui, China
| | - Huan Zhou
- Clinical Trials Center, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
- School of Pharmacy, Bengbu Medical College, Bengbu, Anhui, China
- School of Public Foundation, Bengbu Medical College, Bengbu, Anhui, China
| | - Hongju Wang
- Clinical Trials Center, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
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27
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Bi Y, Qiao X, Liu Q, Song S, Zhu K, Qiu X, Zhang X, Jia C, Wang H, Yang Z, Zhang Y, Ji G. Systemic proteomics and miRNA profile analysis of exosomes derived from human pluripotent stem cells. Stem Cell Res Ther 2022; 13:449. [PMID: 36064647 PMCID: PMC9444124 DOI: 10.1186/s13287-022-03142-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/16/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Increasing studies have reported the therapeutic effect of mesenchymal stem cell (MSC)-derived exosomes by which protein and miRNA are clearly characterized. However, the proteomics and miRNA profiles of exosomes derived from human embryonic stem cells (hESCs) and human-induced pluripotent stem cells (hiPSCs) remain unclear. METHODS In this study, we isolated exosomes from hESCs, hiPSCs, and human umbilical cord mesenchymal stem cells (hUC-MSCs) via classic ultracentrifugation and a 0.22-μm filter, followed by the conservative identification. Tandem mass tag labeling and label-free relative peptide quantification together defined their proteomics. High-throughput sequencing was performed to determine miRNA profiles. Then, we conducted a bioinformatics analysis to identify the dominant biological processes and pathways modulated by exosome cargos. Finally, the western blot and RT-qPCR were performed to detect the actual loads of proteins and miRNAs in three types of exosomes. RESULTS Based on our study, the cargos from three types of exosomes contribute to sophisticated biological processes. In comparison, hESC exosomes (hESC-Exos) were superior in regulating development, metabolism, and anti-aging, and hiPSC exosomes (hiPSC-Exos) had similar biological functions as hESC-Exos, whereas hUC-MSCs exosomes (hUC-MSC-Exos) contributed more to immune regulation. CONCLUSIONS The data presented in our study help define the protein and miRNA landscapes of three exosomes, predict their biological functions via systematic and comprehensive network analysis at the system level, and reveal their respective potential applications in different fields so as to optimize exosome selection in preclinical and clinical trials.
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Affiliation(s)
- Youkun Bi
- Key Laboratory of Interdisciplinary Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xinlong Qiao
- Key Laboratory of Interdisciplinary Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qun Liu
- Key Laboratory of Interdisciplinary Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shaole Song
- Key Laboratory of Interdisciplinary Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Keqi Zhu
- Key Laboratory of Interdisciplinary Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xun Qiu
- Department of Medical Oncology, The Second Affiliated Hospital of Dalian Medical University, Dalian, 116023, China
| | - Xiang Zhang
- Key Laboratory of Interdisciplinary Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ce Jia
- Key Laboratory of Interdisciplinary Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huiwen Wang
- Key Laboratory of Interdisciplinary Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhiguang Yang
- Key Laboratory of Interdisciplinary Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ying Zhang
- Sixth Department of Liver Disease, Dalian Public Health Clinical Center, Dalian Medical University, Dalian, 116023, China.
| | - Guangju Ji
- Key Laboratory of Interdisciplinary Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
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miR-106b enhances human mesenchymal stem cell differentiation to spermatogonial stem cells under germ cell profile genes involved in TGF-b signaling pathways. In Vitro Cell Dev Biol Anim 2022; 58:539-548. [PMID: 35939226 DOI: 10.1007/s11626-022-00688-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 02/24/2022] [Indexed: 11/05/2022]
Abstract
Mesenchymal stem cells can be differentiated into tissue-specific cells. MicroRNAs (miRNAs) regulate the translation of mRNAs involved in the growth and development of a variety of cells, including primordial germ cells (PGCs). This study evaluated male germ cell differentiation from human MSCs by miR-106b. The MSCs were obtained from human adipose tissue. The differentiation of MSCs into PGCs was accomplished by transfection of a lentiviral vector expressing miR-106b. MSCs were treated with bone morphogenic factor 4 as a control and also as a putative inducer of PGC differentiation. PGC was differentiated into spermatogonial-like cells by retinoic acid. Moreover, Dazl, Plzf, Stra8, Gfra, and Thy1 gene expressions were investigated using real-time PCR. Our results showed that Dazl, Plzf, and Stra8 genes that were treated with BMP4 and miR-106b did not show any significant difference, meaning that miR-106b, like BMP4, is able to differentiate PGC cells from MSCs. In spermatogonial-like cells, Thy1 was significantly unregulated in both the miR-106b and BMP4 groups. Our findings showed that miR-106b regulates the differentiation of MSCs into PGCs. miR-106b influences on the expression of Dazl, Plzf, and Stra8 genes in PGC and Gfra, Stra8, and Thy1 genes.
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Hall JC, Paull D, Pébay A, Lidgerwood GE. Human pluripotent stem cells for the modelling of retinal pigment epithelium homeostasis and disease: A review. Clin Exp Ophthalmol 2022; 50:667-677. [PMID: 35739648 PMCID: PMC9546239 DOI: 10.1111/ceo.14128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/06/2022] [Accepted: 06/19/2022] [Indexed: 12/05/2022]
Abstract
Human pluripotent stem cells (hPSCs), which include induced pluripotent stem cells and embryonic stem cells, are powerful tools for studying human development, physiology and disease, including those affecting the retina. Cells from selected individuals, or specific genetic backgrounds, can be differentiated into distinct cell types allowing the modelling of diseases in a dish for therapeutic development. hPSC‐derived retinal cultures have already been used to successfully model retinal pigment epithelium (RPE) degeneration for various retinal diseases including monogenic conditions and complex disease such as age‐related macular degeneration. Here, we will review the current knowledge gained in understanding the molecular events involved in retinal disease using hPSC‐derived retinal models, in particular RPE models. We will provide examples of various conditions to illustrate the scope of applications associated with the use of hPSC‐derived RPE models.
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Affiliation(s)
- Jenna C Hall
- Department of Anatomy and Physiology The University of Melbourne Parkville Victoria Australia
| | - Daniel Paull
- The New York Stem Cell Foundation Research Institute New York New York USA
| | - Alice Pébay
- Department of Anatomy and Physiology The University of Melbourne Parkville Victoria Australia
- Department of Surgery, Royal Melbourne Hospital The University of Melbourne Parkville Victoria Australia
| | - Grace E. Lidgerwood
- Department of Anatomy and Physiology The University of Melbourne Parkville Victoria Australia
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30
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Exosome-Associated circRNAs as Key Regulators of EMT in Cancer. Cells 2022; 11:cells11101716. [PMID: 35626752 PMCID: PMC9140110 DOI: 10.3390/cells11101716] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 12/12/2022] Open
Abstract
Epithelial-to-mesenchymal transition (EMT) is a dynamic program of cell plasticity aberrantly reactivated in cancer. The crosstalk between tumor cells and the tumoral microenvironment (TME) has a pivotal importance for the induction of the EMT and the progression toward a malignant phenotype. Notably, exosomes are key mediators of this crosstalk as vehicles of specific molecular signals that include the class of circular RNAs (circRNAs). This review specifically focuses on the role of exosome-associated circRNAs as key regulators of EMT in cancer. The relevance of these molecules in regulating the intercellular communication in TME and tumor progression is highlighted. Moreover, the here-presented evidence indicates that exosome-associated circRNA modulation should be taken in account for cancer diagnostic and therapeutic approaches.
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31
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Zeng Q, Qi X, Ma J, Hu F, Wang X, Qin H, Li M, Huang S, Yang Y, Li Y, Bai H, Jiang M, Ren D, Kang Y, Zhao Y, Chen X, Ding X, Ye D, Wang Y, Jiang J, Li D, Chen X, Hu K, Zhang B, Shi B, Zhang C. Distinct miRNAs associated with various clinical presentations of SARS-CoV-2 infection. iScience 2022; 25:104309. [PMID: 35502319 PMCID: PMC9044631 DOI: 10.1016/j.isci.2022.104309] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 01/04/2022] [Accepted: 04/22/2022] [Indexed: 01/08/2023] Open
Abstract
MicroRNAs (miRNAs) have been shown to play important roles in viral infections, but their associations with SARS-CoV-2 infection remain poorly understood. Here, we detected 85 differentially expressed miRNAs (DE-miRNAs) from 2,336 known and 361 novel miRNAs that were identified in 233 plasma samples from 61 healthy controls and 116 patients with COVID-19 using the high-throughput sequencing and computational analysis. These DE-miRNAs were associated with SASR-CoV-2 infection, disease severity, and viral persistence in the patients with COVID-19, respectively. Gene ontology and KEGG pathway analyses of the DE-miRNAs revealed their connections to viral infections, immune responses, and lung diseases. Finally, we established a machine learning model using the DE-miRNAs between various groups for classification of COVID-19 cases with different clinical presentations. Our findings may help understand the contribution of miRNAs to the pathogenesis of COVID-19 and identify potential biomarkers and molecular targets for diagnosis and treatment of SARS-CoV-2 infection. 2,336 known and 361 novel miRNAs identified in this study 85 miRNAs associated with COVID-19 A panel of miRNAs targeting the viral or cellular genes Machine learning using miRNAs for classification of COVID-19
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Affiliation(s)
- Qiqi Zeng
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China
| | - Xin Qi
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China
| | - Junpeng Ma
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China
| | - Fang Hu
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China
| | - Xiaorui Wang
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China
| | - Hongyu Qin
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China
| | - Mengyang Li
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China
| | - Shaoxin Huang
- SpecAlly Life Technology Co, Ltd, Wuhan East Lake High-tech Development Zone, 666 Gaoxin Road, Wuhan 430075, China
| | - Yong Yang
- SpecAlly Life Technology Co, Ltd, Wuhan East Lake High-tech Development Zone, 666 Gaoxin Road, Wuhan 430075, China
| | - Yixin Li
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China
| | - Han Bai
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China
| | - Meng Jiang
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China
| | - Doudou Ren
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China
| | - Ye Kang
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China
| | - Yang Zhao
- Department of Respiratory and Critical Care Medicine, Renmin Hospital of Wuhan University, 99 Zhangzhidong Road, Wuhan 430060, China
| | - Xiaobei Chen
- Department of Infectious Diseases, The Renmin Hospital of Wuhan University, East Campus, East Lake New Technology Development Zone, Gaoxin 6th Road, Wuhan 430040, China
| | - Xi Ding
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China
| | - Di Ye
- Department of Rehabilitation, The Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuchang District, Wuhan 430060, China
| | - Yankui Wang
- Dialysis Center, The Renmin Hospital of Wuhan University, East Campus, East Lake New Technology Development Zone, Gaoxin 6th Road, Wuhan 430040, China
| | - Jianguo Jiang
- LC-Bio Technologies (Hangzhou) Co., Ltd., Hanghzhou 310000, China
| | - Dong Li
- Department of Clinical Laboratory, The Renmin Hospital of Wuhan University, East Campus, East Lake New Technology Development Zone, Gaoxin 6th Road, Wuhan 430040, China
| | - Xi Chen
- SpecAlly Life Technology Co, Ltd, Wuhan East Lake High-tech Development Zone, 666 Gaoxin Road, Wuhan 430075, China.,Wuhan Institute of Biotechnology, Wuhan East Lake High-tech Development Zone, 666 Gaoxin Road, Wuhan 430040, China
| | - Ke Hu
- Department of Respiratory and Critical Care Medicine, Renmin Hospital of Wuhan University, 99 Zhangzhidong Road, Wuhan 430060, China
| | - Binghong Zhang
- The Renmin Hospital of Wuhan University, East Campus, East Lake New Technology Development Zone, Gaoxin 6th Road, Wuhan 430040, China
| | - Bingyin Shi
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China
| | - Chengsheng Zhang
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China.,Cancer Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
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32
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Rezania MA, Eghtedari A, Taha MF, Ardekani AM, Javeri A. A novel role for aspirin in enhancing the reprogramming function of miR-302/367 cluster and breast tumor suppression. J Cell Biochem 2022; 123:1077-1090. [PMID: 35535453 DOI: 10.1002/jcb.30264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 04/04/2022] [Accepted: 04/07/2022] [Indexed: 11/06/2022]
Abstract
Recent studies have provided evidence for tumor suppressive function of the embryonic stem cell-specific miR-302/367 cluster through induction of a reprogramming process. Aspirin has been found to induce reprogramming factors of mesenchymal-to-epithelial transition in breast cancer cells. Therefore, we aimed to investigate whether overexpression of miR-302/367 cluster and aspirin treatment cooperate in the induction of reprogramming and tumor suppression in breast cancer cells. MDA-MB-231 and SK-BR-3 human breast cancer cell lines were transfected with a miR-302/367 expressing vector and treated with aspirin. The cells were evaluated for indices of apoptosis, proliferation, migration, and invasion. In both cell lines, treatment of miR-302/367-transfected cells with aspirin upregulated expression of some main pluripotency factors such as OCT4, SOX2, NANOG, and KLF4, and downregulated expression of some invasion and angiogenesis markers at gene and protein levels. Aspirin increased the apoptotic rate in both cell lines transfected with miR-302/367. Both miR-302/367 and aspirin upregulated the expression of FOXD3 protein which is a known inducer of OCT4 and NANOG. Our results demonstrate that aspirin can enhance miR-302/367-induced reprogramming of breast cancer cells possibly through upregulation of FOXD3 expression. This can further augment the reversal of epithelial-mesenchymal transition and inhibits migration, invasion, and angiogenic signaling in breast cancer cells reprogrammed by miR-302/367. Therefore, aspirin may serve as a useful adjuvant for reprogramming of cancer cells.
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Affiliation(s)
- Mohammad A Rezania
- Department of Stem Cells and Regenerative Medicine, Institute for Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Azadeh Eghtedari
- Department of Stem Cells and Regenerative Medicine, Institute for Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Masoumeh F Taha
- Department of Stem Cells and Regenerative Medicine, Institute for Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | | | - Arash Javeri
- Department of Stem Cells and Regenerative Medicine, Institute for Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
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33
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Esmaeilivand M, Abedelahi A, Hamdi K, Farzadi L, Goharitaban S, Fattahi A, Niknafs B. Role of miRNAs in preimplantation embryo development and their potential as embryo selection biomarkers. Reprod Fertil Dev 2022; 34:589-597. [PMID: 35440361 DOI: 10.1071/rd21274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 01/05/2022] [Indexed: 12/20/2022] Open
Abstract
CONTEXT MicroRNAs (miRNAs) play different roles in oocyte fertilisation, degradation of maternal transcripts, embryo development, and implantation. During in vitro fertilisation (IVF), different miRNAs are released from embryos into the spent culture media (SCM) that can potentially reflect the status of the embryo. AIMS This study is the assessment of miRNAs, which secreted in SCM during the IVF cycles can be used as noninvasive biomarkers to predict an embryo's ability to form a blastocyst, implant, and give live birth. METHODS Systematic literature search was conducted to review all recent studies about miRNAs as potential non-invasive biomarkers for selecting the best embryos in the assisted reproductive technology (ART) cycle. KEY RESULTS Studies have shown that levels of some miRNAs in the SCM have an association with the implantation potential and pregnancy outcome of the embryo. CONCLUSIONS Embryo-secreted miRNAs can be used as potential non-invasive biomarkers for selecting the best embryos in the ART cycle. Unfortunately, few human studies evaluated the association between ART outcomes and miRNAs in SCM. IMPLICATIONS This review can pave the way for further miRNAs transcriptomic studies on human embryo culture media and introducing a specific miRNA profile as a multivariable prediction model for embryo selection in IVF cycles.
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Affiliation(s)
- Masoumeh Esmaeilivand
- Immunology Research Center, Tabriz University of Medical Science, Tabriz, Iran; and Department of Reproductive Biology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Abedelahi
- Department of Anatomical Sciences, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Kobra Hamdi
- Women's Reproductive Health Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Laya Farzadi
- Women's Reproductive Health Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sepide Goharitaban
- Immunology Research Center, Tabriz University of Medical Science, Tabriz, Iran; and Department of Anatomical Sciences, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Amir Fattahi
- Immunology Research Center, Tabriz University of Medical Science, Tabriz, Iran; and Department of Reproductive Biology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran; and Women's Reproductive Health Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behrooz Niknafs
- Immunology Research Center, Tabriz University of Medical Science, Tabriz, Iran; and Department of Reproductive Biology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran; and Department of Anatomical Sciences, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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34
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Pascale E, Caiazza C, Paladino M, Parisi S, Passaro F, Caiazzo M. MicroRNA Roles in Cell Reprogramming Mechanisms. Cells 2022; 11:cells11060940. [PMID: 35326391 PMCID: PMC8946776 DOI: 10.3390/cells11060940] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/28/2022] [Accepted: 03/08/2022] [Indexed: 02/01/2023] Open
Abstract
Cell reprogramming is a groundbreaking technology that, in few decades, generated a new paradigm in biomedical science. To date we can use cell reprogramming to potentially generate every cell type by converting somatic cells and suitably modulating the expression of key transcription factors. This approach can be used to convert skin fibroblasts into pluripotent stem cells as well as into a variety of differentiated and medically relevant cell types, including cardiomyocytes and neural cells. The molecular mechanisms underlying such striking cell phenotypes are still largely unknown, but in the last decade it has been proven that cell reprogramming approaches are significantly influenced by non-coding RNAs. Specifically, this review will focus on the role of microRNAs in the reprogramming processes that lead to the generation of pluripotent stem cells, neurons, and cardiomyocytes. As highlighted here, non-coding RNA-forced expression can be sufficient to support some cell reprogramming processes, and, therefore, we will also discuss how these molecular determinants could be used in the future for biomedical purposes.
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Affiliation(s)
- Emilia Pascale
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, Via Pansini 5, 80131 Naples, Italy; (E.P.); (C.C.); (M.P.); (S.P.)
| | - Carmen Caiazza
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, Via Pansini 5, 80131 Naples, Italy; (E.P.); (C.C.); (M.P.); (S.P.)
| | - Martina Paladino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, Via Pansini 5, 80131 Naples, Italy; (E.P.); (C.C.); (M.P.); (S.P.)
| | - Silvia Parisi
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, Via Pansini 5, 80131 Naples, Italy; (E.P.); (C.C.); (M.P.); (S.P.)
| | - Fabiana Passaro
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, Via Pansini 5, 80131 Naples, Italy; (E.P.); (C.C.); (M.P.); (S.P.)
- Correspondence: (F.P.); (M.C.)
| | - Massimiliano Caiazzo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, Via Pansini 5, 80131 Naples, Italy; (E.P.); (C.C.); (M.P.); (S.P.)
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
- Correspondence: (F.P.); (M.C.)
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35
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Rallabandi R, Sharp B, Cruz C, Wang Q, Locsin A, Driscoll CB, Lee E, Nelson T, Devaux P. miRNA-mediated control of exogenous OCT4 during mesenchymal-epithelial transition increases measles vector reprogramming efficiency. Mol Ther Methods Clin Dev 2022; 24:48-61. [PMID: 34977272 PMCID: PMC8683617 DOI: 10.1016/j.omtm.2021.11.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/27/2021] [Indexed: 12/14/2022]
Abstract
OCT4 is a key mediator of induced pluripotent stem cell (iPSC) reprogramming, but the mechanistic insights into the role of exogenous OCT4 and timelines that initiate pluripotency remain to be resolved. Here, using measles reprogramming vectors, we present microRNA (miRNA) targeting of exogenous OCT4 to shut down its expression during the mesenchymal to the epithelial transition phase of reprogramming. We showed that exogenous OCT4 is required only for the initiation of reprogramming and is dispensable for the maturation stage. However, the continuous expression of SOX2, KLF4, and c-MYC is necessary for the maturation stage of the iPSC. Additionally, we demonstrate a novel application of miRNA targeting in a viral vector to contextually control the vector/transgene, ultimately leading to an improved reprogramming efficiency. This novel approach could be applied to other systems for improving the efficiency of vector-induced processes.
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Affiliation(s)
- Ramya Rallabandi
- Virology and Gene Therapy Graduate Track, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN 55905, USA
- Regenerative Sciences PhD Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Brenna Sharp
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Conrad Cruz
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Qi Wang
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Alexis Locsin
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Christopher B. Driscoll
- Virology and Gene Therapy Graduate Track, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Ella Lee
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Tim Nelson
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester MN 55905, USA
| | - Patricia Devaux
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Virology and Gene Therapy Graduate Track, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN 55905, USA
- Regenerative Sciences PhD Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN 55905, USA
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36
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Shah V, Shah J. Restoring Ravaged Heart: Molecular Mechanisms and Clinical Application of miRNA in Heart Regeneration. Front Cardiovasc Med 2022; 9:835138. [PMID: 35224063 PMCID: PMC8866653 DOI: 10.3389/fcvm.2022.835138] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/17/2022] [Indexed: 11/28/2022] Open
Abstract
Human heart development is a complex and tightly regulated process, conserving proliferation, and multipotency of embryonic cardiovascular progenitors. At terminal stage, progenitor cell type gets suppressed for terminal differentiation and maturation. In the human heart, most cardiomyocytes are terminally differentiated and so have limited proliferation capacity. MicroRNAs (miRNAs) are non-coding single-stranded RNA that regulate gene expression and mRNA silencing at the post-transcriptional level. These miRNAs play a crucial role in numerous biological events, including cardiac development, and cardiomyocyte proliferation. Several cardiac cells specific miRNAs have been discovered. Inhibition or overexpression of these miRNAs could induce cardiac regeneration, cardiac stem cell proliferation and cardiomyocyte proliferation. Clinical application of miRNAs extends to heart failure, wherein the cell cycle arrest of terminally differentiated cardiac cells inhibits the heart regeneration. The regenerative capacity of the myocardium can be enhanced by cardiomyocyte specific miRNAs controlling the cell cycle. In this review, we focus on cardiac-specific miRNAs involved in cardiac regeneration and cardiomyocyte proliferation, and their potential as a new clinical therapy for heart regeneration.
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37
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Bailly A, Milhavet O, Lemaitre JM. RNA-Based Strategies for Cell Reprogramming toward Pluripotency. Pharmaceutics 2022; 14:pharmaceutics14020317. [PMID: 35214051 PMCID: PMC8876983 DOI: 10.3390/pharmaceutics14020317] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/16/2022] [Accepted: 01/25/2022] [Indexed: 02/04/2023] Open
Abstract
Cell therapy approaches to treat a wide range of pathologies have greatly benefited from cell reprogramming techniques that allow the conversion of a somatic cell into a pluripotent cell. Many technological developments have been made since the initial major discovery of this biological process. Recently reprogramming methods based on the use of RNA have emerged and seem very promising. Thus, in this review we will focus on presenting the interest of such methods for cell reprogramming but also how these RNA-based strategies can be extended to eventually lead to medical applications to improve healthspan and longevity.
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Affiliation(s)
- Anaëlle Bailly
- IRMB, University Montpellier, INSERM, 34295 Montpellier, France
- INGRAALYS, SA, IRMB, Incubator Cyborg, 34295 Montpellier, France
| | - Ollivier Milhavet
- IRMB, University Montpellier, INSERM, CNRS, 34295 Montpellier, France
- SAFE-iPSC Facility, CHU Montpellier, 34295 Montpellier, France
- Correspondence: (O.M.); (J.-M.L.)
| | - Jean-Marc Lemaitre
- IRMB, University Montpellier, INSERM, 34295 Montpellier, France
- SAFE-iPSC Facility, CHU Montpellier, 34295 Montpellier, France
- Correspondence: (O.M.); (J.-M.L.)
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38
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Sokka J, Yoshihara M, Kvist J, Laiho L, Warren A, Stadelmann C, Jouhilahti EM, Kilpinen H, Balboa D, Katayama S, Kyttälä A, Kere J, Otonkoski T, Weltner J, Trokovic R. CRISPR activation enables high-fidelity reprogramming into human pluripotent stem cells. Stem Cell Reports 2022; 17:413-426. [PMID: 35063129 PMCID: PMC8828555 DOI: 10.1016/j.stemcr.2021.12.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 12/19/2022] Open
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39
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Li X, Liu Y, Mu Q, Tian J, Yu H. MiR-290 family maintains developmental potential by targeting p21 in mouse pre-implantation embryos. Biol Reprod 2021; 106:425-440. [PMID: 34907414 DOI: 10.1093/biolre/ioab227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/29/2021] [Accepted: 12/03/2021] [Indexed: 11/15/2022] Open
Abstract
The miR-290 family is a mouse-specific microRNA cluster, which maintains mouse embryonic stem cells (ESCs) pluripotency by increasing OCT3/4 and C-MYC expression. However, its functions in mouse pre-implantation embryos remain unclear, especially during zygotic genome activation (ZGA). In this study, miR-290 family expression increased from the two-cell embryo stage through the blastocyst stage. Inhibition of miR-294-3p/5p did not affect ZGA initiation or embryo development, whereas pri-miR-290 knockdown decreased ZGA gene expression and slowed embryonic development. In addition, pluripotency decreased in ESCs derived from pri-miR-290 knockdown blastocysts. To clarify the mechanism of action, 33 candidate miR-294-3p target genes were screened from three databases, and miR-294-3p directly targeted the 3'-untranslated region of Cdkn1a (p21) mRNA. Similar to pri-miR-290 knockdown, P21 overexpression impeded embryonic development, whereas simultaneous overexpression of P21 and pri-miR-290 partially rescued embryonic development. The results indicate that the miR-290 family participates in promoting ZGA process and maintaining developmental potency in embryos by targeting p21.
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Affiliation(s)
- Xiangnan Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (RRBGL), Inner Mongolia University, 010070 Hohhot, China
| | - Yueshi Liu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (RRBGL), Inner Mongolia University, 010070 Hohhot, China
| | - Qier Mu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (RRBGL), Inner Mongolia University, 010070 Hohhot, China
| | - Junliang Tian
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (RRBGL), Inner Mongolia University, 010070 Hohhot, China
| | - Haiquan Yu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (RRBGL), Inner Mongolia University, 010070 Hohhot, China
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Wang J, Zhang T, Yu Z, Tan WT, Wen M, Shen Y, Lambert FRP, Huber RG, Wan Y. Genome-wide RNA structure changes during human neurogenesis modulate gene regulatory networks. Mol Cell 2021; 81:4942-4953.e8. [PMID: 34655516 DOI: 10.1016/j.molcel.2021.09.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 08/01/2021] [Accepted: 09/24/2021] [Indexed: 11/18/2022]
Abstract
The distribution, dynamics, and function of RNA structures in human development are under-explored. Here, we systematically assayed RNA structural dynamics and their relationship with gene expression, translation, and decay during human neurogenesis. We observed that the human ESC transcriptome is globally more structurally accessible than differentiated cells and undergoes extensive RNA structure changes, particularly in the 3' UTR. Additionally, RNA structure changes during differentiation are associated with translation and decay. We observed that RBP and miRNA binding is associated with RNA structural changes during early neuronal differentiation, and splicing is associated during later neuronal differentiation. Furthermore, our analysis suggests that RBPs are major factors in structure remodeling and co-regulate additional RBPs and miRNAs through structure. We demonstrated an example of this by showing that PUM2-induced structure changes on LIN28A enable miR-30 binding. This study deepens our understanding of the widespread and complex role of RNA-based gene regulation during human development.
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Affiliation(s)
- Jiaxu Wang
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore
| | - Tong Zhang
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore
| | - Zhang Yu
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore
| | - Wen Ting Tan
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore
| | - Ming Wen
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore
| | - Yang Shen
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore
| | - Finnlay R P Lambert
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore; Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Roland G Huber
- Bioinformatics Institute, A(∗)STAR, Singapore 138671, Singapore
| | - Yue Wan
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore; Department of Biochemistry, National University of Singapore, Singapore 117596, Singapore.
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41
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Xu D, Zhou C, Lin J, Cai W, Lin W. MicroRNA-367-3p suppresses sevoflurane-induced adult rat astrocyte apoptosis by targeting BCL2L11. Exp Ther Med 2021; 23:9. [PMID: 34815761 PMCID: PMC8593860 DOI: 10.3892/etm.2021.10931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 07/30/2021] [Indexed: 11/21/2022] Open
Abstract
The present study aimed to characterize the effect of microRNA (miR)-367-3p on sevoflurane anesthesia and elucidate the underlying mechanism. A total of 36 4-month-old adult Sprague-Dawley rats were divided into six groups. Sevoflurane was inhaled at concentrations of 0, 1, 2, 4, 8 and 16% for a total of 6 h; the hippocampus of the brain was subsequently minced and digested, and astrocytes were isolated. Various methods, including reverse transcription-quantitative (RT-q)PCR, western blotting and TUNEL staining, were used to determine the expression levels of Bax, BCL-2 and BCL-2-like protein 11 (BCL2L11), as well as the level of apoptosis. The rats were treated with 8% sevoflurane and the astrocytes from the rats were transfected with miR-367-3p or anti-miR-367-3p. The present study demonstrated that sevoflurane promoted astrocytes apoptosis. Western blotting revealed that with an increase of sevoflurane concentration, the expression levels of the apoptotic proteins Bax and BCL2L11 were significantly increased, whereas the protein expression levels of BCL-2 were significantly decreased. However, overexpression of miR-367-3p reversed these effects. TUNEL staining revealed that sevoflurane promoted the apoptosis of astrocytes, while apoptosis was reversed by miR-367-3p overexpression. RT-qPCR demonstrated that sevoflurane inhibited the expression of miR-367-3p. Notably, miR-367-3p reduced the expression of BCL2L11, thereby inhibiting the apoptosis of astrocytes originating from the hippocampal area of adult rats induced by sevoflurane. Therefore, miR-367-3p and BCL2L11 may act as effective targets for the study of anesthesia.
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Affiliation(s)
- Deming Xu
- Department of Anesthesiology, The Affiliated Hospital of Putian University, Putian, Fujian 351100, P.R. China
| | - Changbi Zhou
- Department of Anesthesiology, The Affiliated Hospital of Putian University, Putian, Fujian 351100, P.R. China
| | - Juanyun Lin
- Department of Anesthesiology, The Affiliated Hospital of Putian University, Putian, Fujian 351100, P.R. China
| | - Wenhui Cai
- Department of Anesthesiology, The Affiliated Hospital of Putian University, Putian, Fujian 351100, P.R. China
| | - Wei Lin
- Department of General Surgery, The Affiliated Hospital of Putian University, Putian, Fujian 351100, P.R. China
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Induced Pluripotent Stem Cells to Model Juvenile Myelomonocytic Leukemia: New Perspectives for Preclinical Research. Cells 2021; 10:cells10092335. [PMID: 34571984 PMCID: PMC8465353 DOI: 10.3390/cells10092335] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/24/2021] [Accepted: 08/31/2021] [Indexed: 11/16/2022] Open
Abstract
Juvenile myelomonocytic leukemia (JMML) is a malignant myeloproliferative disorder arising in infants and young children. The origin of this neoplasm is attributed to an early deregulation of the Ras signaling pathway in multipotent hematopoietic stem/progenitor cells. Since JMML is notoriously refractory to conventional cytostatic therapy, allogeneic hematopoietic stem cell transplantation remains the mainstay of curative therapy for most cases. However, alternative therapeutic approaches with small epigenetic molecules have recently entered the stage and show surprising efficacy at least in specific subsets of patients. Hence, the establishment of preclinical models to test novel agents is a priority. Induced pluripotent stem cells (IPSCs) offer an opportunity to imitate JMML ex vivo, after attempts to generate immortalized cell lines from primary JMML material have largely failed in the past. Several research groups have previously generated patient-derived JMML IPSCs and successfully differentiated these into myeloid cells with extensive phenotypic similarities to primary JMML cells. With infinite self-renewal and the capability to differentiate into multiple cell types, JMML IPSCs are a promising resource to advance the development of treatment modalities targeting specific vulnerabilities. This review discusses current reprogramming techniques for JMML stem/progenitor cells, related clinical applications, and the challenges involved.
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Rombaut M, Boeckmans J, Rodrigues RM, van Grunsven LA, Vanhaecke T, De Kock J. Direct reprogramming of somatic cells into induced hepatocytes: Cracking the Enigma code. J Hepatol 2021; 75:690-705. [PMID: 33989701 DOI: 10.1016/j.jhep.2021.04.048] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/29/2021] [Accepted: 04/30/2021] [Indexed: 01/10/2023]
Abstract
There is an unmet need for functional primary human hepatocytes to support the pharmaceutical and (bio)medical demand. The unique discovery, a decade ago, that somatic cells can be drawn out of their apparent biological lockdown to reacquire a pluripotent state has revealed a completely new avenue of possibilities for generating surrogate human hepatocytes. Since then, the number of papers reporting the direct conversion of somatic cells into induced hepatocytes (iHeps) has burgeoned. A hepatic cell fate can be established via the ectopic expression of native liver-enriched transcription factors in somatic cells, thereby bypassing the need for an intermediate (pluripotent) stem cell state. That said, understanding and eventually controlling the processes that give rise to functional iHeps remains challenging. In this review, we provide an overview of the state-of-the-art reprogramming cocktails and techniques, as well as their corresponding conversion efficiencies. Special attention is paid to the role of liver-enriched transcription factors as hepatogenic reprogramming tools and small molecules as facilitators of hepatic transdifferentiation. To conclude, we formulate recommendations to optimise, standardise and enrich the in vitro production of iHeps to reach clinical standards, and propose minimal criteria for their characterisation.
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Affiliation(s)
- Matthias Rombaut
- Department of In Vitro Toxicology and Dermato-Cosmetology, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, B-1090 Brussels, Belgium.
| | - Joost Boeckmans
- Department of In Vitro Toxicology and Dermato-Cosmetology, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, B-1090 Brussels, Belgium
| | - Robim M Rodrigues
- Department of In Vitro Toxicology and Dermato-Cosmetology, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, B-1090 Brussels, Belgium
| | - Leo A van Grunsven
- Liver Cell Biology Research Group, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, B-1090 Brussels, Belgium
| | - Tamara Vanhaecke
- Department of In Vitro Toxicology and Dermato-Cosmetology, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, B-1090 Brussels, Belgium
| | - Joery De Kock
- Department of In Vitro Toxicology and Dermato-Cosmetology, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, B-1090 Brussels, Belgium.
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Afshari A, Yaghobi R, Rezaei G. Inter-regulatory role of microRNAs in interaction between viruses and stem cells. World J Stem Cells 2021; 13:985-1004. [PMID: 34567421 PMCID: PMC8422934 DOI: 10.4252/wjsc.v13.i8.985] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/11/2021] [Accepted: 07/13/2021] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are well known for post-transcriptional regulatory ability over specific mRNA targets. miRNAs exhibit temporal or tissue-specific expression patterns and regulate the cell and tissue developmental pathways. They also have determinative roles in production and differentiation of multiple lineages of stem cells and might have therapeutic advantages. miRNAs are a part of some viruses’ regulatory machinery, not a byproduct. The trace of miRNAs was detected in the genomes of viruses and regulation of cell reprograming and viral pathogenesis. Combination of inter-regulatory systems has been detected for miRNAs during viral infections in stem cells. Contraction between viruses and stem cells may be helpful in therapeutic tactics, pathogenesis, controlling viral infections and defining stem cell developmental strategies that is programmed by miRNAs as a tool. Therefore, in this review we intended to study the inter-regulatory role of miRNAs in the interaction between viruses and stem cells and tried to explain the advantages of miRNA regulatory potentials, which make a new landscape for future studies.
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Affiliation(s)
- Afsoon Afshari
- Shiraz Nephro-Urology Research Center, Shiraz University of Medical Sciences, Shiraz 7193711351, Iran
| | - Ramin Yaghobi
- Shiraz Transplant Research Center, Shiraz University of Medical Sciences, Shiraz 7193711351, Iran
| | - Ghazal Rezaei
- Shiraz Transplant Research Center, Shiraz University of Medical Sciences, Shiraz 7193711351, Iran
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45
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iPSC Preparation and Epigenetic Memory: Does the Tissue Origin Matter? Cells 2021; 10:cells10061470. [PMID: 34208270 PMCID: PMC8230744 DOI: 10.3390/cells10061470] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/06/2021] [Accepted: 06/10/2021] [Indexed: 02/07/2023] Open
Abstract
The production of induced pluripotent stem cells (iPSCs) represent a breakthrough in regenerative medicine, providing new opportunities for understanding basic molecular mechanisms of human development and molecular aspects of degenerative diseases. In contrast to human embryonic stem cells (ESCs), iPSCs do not raise any ethical concerns regarding the onset of human personhood. Still, they present some technical issues related to immune rejection after transplantation and potential tumorigenicity, indicating that more steps forward must be completed to use iPSCs as a viable tool for in vivo tissue regeneration. On the other hand, cell source origin may be pivotal to iPSC generation since residual epigenetic memory could influence the iPSC phenotype and transplantation outcome. In this paper, we first review the impact of reprogramming methods and the choice of the tissue of origin on the epigenetic memory of the iPSCs or their differentiated cells. Next, we describe the importance of induction methods to determine the reprogramming efficiency and avoid integration in the host genome that could alter gene expression. Finally, we compare the significance of the tissue of origin and the inter-individual genetic variation modification that has been lightly evaluated so far, but which significantly impacts reprogramming.
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46
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What we can learn from embryos to understand the mesenchymal-to-epithelial transition in tumor progression. Biochem J 2021; 478:1809-1825. [PMID: 33988704 DOI: 10.1042/bcj20210083] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/06/2021] [Accepted: 04/23/2021] [Indexed: 12/15/2022]
Abstract
Epithelial plasticity involved the terminal and transitional stages that occur during epithelial-to-mesenchymal transition (EMT) and mesenchymal-to-epithelial transition (MET), both are essential at different stages of early embryonic development that have been co-opted by cancer cells to undergo tumor metastasis. These processes are regulated at multiple instances, whereas the post-transcriptional regulation of key genes mediated by microRNAs is gaining major attention as a common and conserved pathway. In this review, we focus on discussing the latest findings of the cellular and molecular basis of the less characterized process of MET during embryonic development, with special attention to the role of microRNAs. Although we take in consideration the necessity of being cautious when extrapolating the obtained evidence, we propose some commonalities between early embryonic development and cancer progression that can shed light into our current understanding of this complex event and might aid in the design of specific therapeutic approaches.
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Xie N, Pan Y, Wu J, Bai Y, Xiao C, Gao X, Wang J, Liu N. MicroRNA-302s Might Regulate ARL4C-Mediated Gastric Cancer Progression via p53 Signaling: Bioinformatics Analysis and Experiments Validation. Onco Targets Ther 2021; 14:2541-2553. [PMID: 33880033 PMCID: PMC8053516 DOI: 10.2147/ott.s282992] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 01/18/2021] [Indexed: 11/23/2022] Open
Abstract
Background Our previous studies demonstrate that ARL4C is the most critical clinical biomarker for gastric cancer (GC) patients among ARL family members (ARLs) and functions as an oncogene in GC. However, its underlying mechanisms in GC need to be further illustrated. In this study, we aim to explore the upstream and downstream molecular mechanisms of ARL4C in GC cells. Methods The genetic alteration of ARL4C in GC is analyzed by cBioPortal database. Potential ARL4C-targeted microRNAs (miRs) are predicted by three databases. The high-throughput RNA sequencing is performed to explore the underlying mechanisms of ARL4C in GC cells. The effects of predicted microRNAs on ARL4C, the RNA-sequencing results validation and the biological functions of ARL4C in GC cells are illustrated by in vitro experiments. Results Genetic analyses indicate that ARL4C is significantly upregulated in GC, which is not caused by gene amplification. MicroRNAs prediction shows the high relevance between ARL4C and miR-302 members. Moreover, miR-302c or miR-302d transfection reduces ARL4C protein expression in GC cells. Based on the high-throughput RNA sequencing of ARL4C-knockdown cells, enrichment analyses demonstrate that ARL4C is closely related to cell growth and involved in p53 signaling. Moreover, there are strong gene–gene interactions between ARL4C and genes in p53 signaling, and ARL4C downregulation could inhibit the protein expression of MDM2, a critical gene in p53 pathway. Further functional experiments demonstrate that ARL4C silencing leads to cell cycle arrest and increased cell apoptosis in AGS and MKN45 cells. Conclusion Our data suggest that miR-302c and miR-302d may function as the upstream regulators of ARL4C. And, ARL4C might promote GC cell cycle progression via regulating p53 signaling. Our findings provide novel insights into the key role of ARL4C and the underlying mechanisms in GC progression, thus facilitating the development of ARL4C-targeted therapy.
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Affiliation(s)
- Ning Xie
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China.,Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Yifei Pan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
| | - Jian Wu
- Xijing Hospital of Digestive Diseases, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, People's Republic of China
| | - Yunfan Bai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
| | - Cailan Xiao
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China.,Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Xiaoliang Gao
- Xijing Hospital of Digestive Diseases, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, People's Republic of China
| | - Jinhai Wang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China.,Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Na Liu
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China.,Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
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48
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Maali A, Maroufi F, Sadeghi F, Atashi A, Kouchaki R, Moghadami M, Azad M. Induced pluripotent stem cell technology: trends in molecular biology, from genetics to epigenetics. Epigenomics 2021; 13:631-647. [PMID: 33823614 DOI: 10.2217/epi-2020-0409] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Induced pluripotent stem cell (iPSC) technology, based on autologous cells' reprogramming to the embryonic state, is a new approach in regenerative medicine. Current advances in iPSC technology have opened up new avenues for multiple applications, from basic research to clinical therapy. Thus, conducting iPSC trials have attracted increasing attention and requires an extensive understanding of the molecular basis of iPSCs. Since iPSC reprogramming is based on the methods inducing the expression of specific genes involved in pluripotency states, it can be concluded that iPSC reprogramming is strongly influenced by epigenetics. In this study, we reviewed the molecular basis of reprogramming, including the reprogramming factors (OCT4, SOX2, KLF4, c-MYC, NANOG, ESRRB, LIN28 as well as their regulatory networks), applied vectors (retroviral vectors, adenoviral vectors, Sendaiviral vectors, episomal plasmids, piggyBac, simple vectors, etc.) and epigenetic modifications (miRNAs, histones and DNA methylation states) to provide a comprehensive guide for reprogramming studies.
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Affiliation(s)
- Amirhosein Maali
- Student Research Committee, Pasteur Institute of Iran, Tehran, Iran.,Department of Medical Biotechnology, Faculty of Allied Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Faezeh Maroufi
- Department of Medical Laboratory Sciences, Faculty of Allied Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Farzin Sadeghi
- Cellular & Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Amir Atashi
- Stem Cells & Tissue Engineering Research Center, Shahroud University of Medical Sciences, Shahroud, Iran
| | - Reza Kouchaki
- Department of Medical Laboratory Sciences, Faculty of Allied Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Mona Moghadami
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
| | - Mehdi Azad
- Department of Medical Laboratory Sciences, Faculty of Allied Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
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Altundag Ö, Çelebi-Saltik B. From Embryo to Adult: One Carbon Metabolism in Stem Cells. Curr Stem Cell Res Ther 2021; 16:175-188. [PMID: 32652922 DOI: 10.2174/1574888x15666200712191308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/16/2020] [Accepted: 04/23/2020] [Indexed: 11/22/2022]
Abstract
Stem cells are undifferentiated cells with self-renewal property and varying differentiation potential that allow the regeneration of tissue cells of an organism throughout adult life beginning from embryonic development. Through the asymmetric cell divisions, each stem cell replicates itself and produces an offspring identical with the mother cell, and a daughter cell that possesses the characteristics of a progenitor cell and commits to a specific lineage to differentiate into tissue cells to maintain homeostasis. To maintain a pool of stem cells to ensure tissue regeneration and homeostasis, it is important to regulate the metabolic functioning of stem cells, progenitor cells and adult tissue stem cells that will meet their internal and external needs. Upon fertilization, the zygote transforms metabolic reprogramming while implantation, embryonic development, organogenesis processes and after birth through adult life. Metabolism in stem cells is a concept that is relatively new to be enlightened. There are no adequate and comprehensive in vitro studies on the comparative analysis of the effects of one-carbon (1-C) metabolism on fetal and adult stem cells compared to embryonic and cancer stem cells' studies that have been reported recently. Since 1-C metabolism is linking parental environmental/ dietary factors and fetal development, investigating the epigenetic, genetic, metabolic and developmental effects on adult period is necessary. Several mutations and abnormalities in 1-C metabolism have been noted in disease changing from diabetes, cancer, pregnancy-related outcomes such as pre-eclampsia, spontaneous abortion, placental abruption, premature delivery, and cardiovascular diseases. In this review, the effects of 1-C metabolism, mainly the methionine and folate metabolism, in stem cells that exist in different developmental stages will be discussed.
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Affiliation(s)
- Özlem Altundag
- Department of Stem Cell Sciences, Hacettepe University Graduate School of Health Sciences, 06100, Sihhiye, Ankara, Turkey
| | - Betül Çelebi-Saltik
- Department of Stem Cell Sciences, Hacettepe University Graduate School of Health Sciences, 06100, Sihhiye, Ankara, Turkey
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50
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Sun S, Wang J, Liu J, Yin F, Xin C, Zeng X, Li J, Chen Q. MiR-302b Suppresses Tumor Metastasis by Targeting Frizzled 6 in OSCC. J Dent Res 2021; 100:739-745. [PMID: 33478325 DOI: 10.1177/0022034520986551] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Oral squamous cell carcinoma (OSCC) accounts for approximately 90% of malignant epithelial tumors of the oral and maxillofacial region. OSCC has high rate of metastasis and poor prognosis. Tobacco and/or alcohol consumption and human papillomavirus infection are relatively exact susceptibility factors for OSCC, but the specific process of oral mucosal carcinogenesis and progression is very complicated. microRNA-302b (miR-302b) could regulate various characteristics of many tumor cells, such as proliferation and apoptosis, but its role and mechanism in OSCC have not been reported. This research aims to study the effect of miR-302b on the invasion and migration ability of OSCC and the mechanism by which it functions as well as to identify new prognostic indicators and therapeutic targets for OSCC patients. Functional studies showed that the miR-302b level was negatively correlated with the invasion and migration ability of OSCC. The studies also showed that the overexpression of miR-302b could attenuate the invasion and migration ability of OSCC cells and reduce lymphangiogenesis and the lung metastasis rate of OSCC cells in a mouse model. Mechanistic studies were performed by quantitative polymerase chain reactions, luciferase assays, and RNA pull-down experiments. The results verified that frizzled class receptor 6 (FZD6) is a target gene of miR-302b in OSCC that could promote cell invasion and migration. Clinical studies demonstrate that the protein expression level of FZD6 was higher in OSCC and metastatic lymph nodes than in normal oral mucosa epithelium. Taken together, these data showed that miR-302b could inhibit the invasion and migration ability of OSCC cells by targeting and downregulating FZD6, thereby inhibiting OSCC metastasis. As a new target gene of miR-302b, FZD6 has the potential to become a prognostic and therapeutic target for OSCC patients.
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Affiliation(s)
- S Sun
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - J Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - J Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China.,Stomatological Hospital of Chongqing Medical University, Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - F Yin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - C Xin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - X Zeng
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - J Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Q Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
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