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Daks A, Parfenyev S, Shuvalov O, Fedorova O, Nazarov A, Melino G, Barlev NA. Lysine-specific methyltransferase Set7/9 in stemness, differentiation, and development. Biol Direct 2024; 19:41. [PMID: 38812048 PMCID: PMC11137904 DOI: 10.1186/s13062-024-00484-z] [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: 04/17/2024] [Accepted: 05/21/2024] [Indexed: 05/31/2024] Open
Abstract
The enzymes performing protein post-translational modifications (PTMs) form a critical post-translational regulatory circuitry that orchestrates literally all cellular processes in the organism. In particular, the balance between cellular stemness and differentiation is crucial for the development of multicellular organisms. Importantly, the fine-tuning of this balance on the genetic level is largely mediated by specific PTMs of histones including lysine methylation. Lysine methylation is carried out by special enzymes (lysine methyltransferases) that transfer the methyl group from S-adenosyl-L-methionine to the lysine residues of protein substrates. Set7/9 is one of the exemplary protein methyltransferases that however, has not been fully studied yet. It was originally discovered as histone H3 lysine 4-specific methyltransferase, which later was shown to methylate a number of non-histone proteins that are crucial regulators of stemness and differentiation, including p53, pRb, YAP, DNMT1, SOX2, FOXO3, and others. In this review we summarize the information available to date on the role of Set7/9 in cellular differentiation and tissue development during embryogenesis and in adult organisms. Finally, we highlight and discuss the role of Set7/9 in pathological processes associated with aberrant cellular differentiation and self-renewal, including the formation of cancer stem cells.
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Affiliation(s)
- Alexandra Daks
- Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russian Federation, 194064.
| | - Sergey Parfenyev
- Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russian Federation, 194064
| | - Oleg Shuvalov
- Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russian Federation, 194064
| | - Olga Fedorova
- Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russian Federation, 194064
| | - Alexander Nazarov
- Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russian Federation, 194064
| | - Gerry Melino
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Nickolai A Barlev
- Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russian Federation, 194064.
- Department of Biomedical Sciences, School of Medicine, Nazarbayev University, 001000, Astana, Kazakhstan.
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2
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García-Andrade F, Vigueras-Villaseñor RM, Chávez-Saldaña MD, Rojas-Castañeda JC, Bahena-Ocampo IU, Aréchaga-Ocampo E, Flores-Fortis M, Díaz-Chávez J, Herrera LA, Landero-Huerta DA. Molecular Characterization of Patients with Cryptorchidism: Preliminary Search for an Expression Profile Related to That of Testicular Germ-Cell Tumors. Diagnostics (Basel) 2023; 13:3020. [PMID: 37761387 PMCID: PMC10529510 DOI: 10.3390/diagnostics13183020] [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: 06/16/2023] [Revised: 08/30/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023] Open
Abstract
Cryptorchidism (CO) is a risk factor for the development of testicular germ-cell tumors (TGCT). This is supported by reports showing the persistence of gonocytes in CO patients. These cells are proposed to be related to the development of germ-cell neoplasia in situ (GCNIS), which is considered the precursor stage/lesion of TGCT. Therefore, it is proposed that some patients with CO could express some molecular markers related to TGCT. In this study, we analyzed testicular tissue samples from CO, TGCT, and controls. We determined the expression of POU5F1, PLAP, and KIT by immunohistochemistry and that of the hsa-miR-371-373 cluster, hsa-miR-367, and LATS2, PTEN, and IGFR1 genes by RT-qPCR. We then carried out a bioinformatic analysis to identify other possible candidate genes as tumor biomarkers. We found that 16.7% (2/12) of the CO patients presented increased expression of POU5F1, KIT, PLAP, hsa-miR-371-373, and hsa-miR-367 and decreased expression of LATS2 and IGF1R. Finally, the genes ARID4B, GALNT3, and KPNA6 were identified as other possible candidate tumor biomarkers. This is the first report describing the expression of the hsa-miR-371-373 cluster, hsa-miR-367, LATS2, and IGF1R in the testicular tissues of two CO patients with cells immune-positive to POU5F1, PLAP, and KIT, which is similar to what is observed in TGCT.
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Affiliation(s)
- Fabiola García-Andrade
- Laboratorio de Biología de la Reproducción, Instituto Nacional de Pediatría, Ciudad de Mexico 04530, Mexico
- Posgrado en Biología Experimental, Universidad Autónoma Metropolitana, Unidad Iztapalapa, Ciudad de Mexico 09310, Mexico
| | | | | | | | - Ivan Uriel Bahena-Ocampo
- Departamento de Ciencias de la Salud, Universidad Autónoma Metropolitana, Unidad Iztapalapa, Ciudad de Mexico 09310, Mexico
| | - Elena Aréchaga-Ocampo
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Ciudad de Mexico 05348, Mexico
| | - Mauricio Flores-Fortis
- Posgrado en Ciencias Naturales e Ingeniería, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Ciudad de Mexico 05348, Mexico
| | - José Díaz-Chávez
- Unidad de Investigación en Cáncer, Instituto de Investigaciones Biomédicas-Universidad Nacional Autónoma de México, Instituto Nacional de Cancerología, Ciudad de Mexico 14080, Mexico
| | - Luis Alonso Herrera
- Unidad de Investigación en Cáncer, Instituto de Investigaciones Biomédicas-Universidad Nacional Autónoma de México, Instituto Nacional de Cancerología, Ciudad de Mexico 14080, Mexico
- Escuela de Medicina y Ciencias de la Salud-Tecnológico de Monterrey, Ciudad de Mexico 14380, Mexico
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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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4
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Saliyeva S, Boranbayeva R, Konoplya N, Bulegenova M, Blau O, Belousov V, Granica J, Mukushkina D, Altynbayeva G. Pediatric Extracranial Germ Cell Tumors: Expression of microRNA. J Pediatr Hematol Oncol 2023; 45:e174-e179. [PMID: 35700382 DOI: 10.1097/mph.0000000000002495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 05/11/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND Germ cell tumors (GCTs) may occur from the neonatal period to late adulthood, characterized by extensive clinical and pathologic heterogeneity. MicroRNAs are a family of small noncoding RNAs that regulate a wide array of biological processes including carcinogenesis. MicroRNAs may be used for many purposes in clinical diagnostics. Numerous studies have proven the diagnostic value of microRNA371-373 and microRNA302/367 expression in malignant GCT. The diagnostic value of microRNA375 is disputable, because while its value is confirmed by some research data, there are still others denying it. METHODS The results of our own research on the relative expression of 10 microRNAs, including microRNA375, associated with GCT in the tumor tissues of 84 children and adolescents are presented. RESULTS In our research, overexpression of microRNA 371-373, 302/367 detected in the group of malignant GCT subtypes. Statistically significant expression of microRNA375 have been defined not only in the group of malignant GCT subtypes, but also in the group of immature teratomas. Among malignant GCTs, high expression of microRNA375 is specific for yolk sac tumors. In the group of seminomas, embryonic carcinomas, and mature teratomas expression of microRNA375 was observed imperceptible, even so the results were statistically insignificant. CONCLUSION Expression of microRNA 371-373, 302/367 is representative of malignant GCT subtypes. Statistically significant and high expression of microRNA375 attributable for yolk sac tumors and immature teratomas.
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Affiliation(s)
- Symbat Saliyeva
- "Scientific Center of Pediatrics and Pediatric Surgery"
- "Kazakh National Medical University named after S.D. Asfendiyarov"
| | - Riza Boranbayeva
- "Scientific Center of Pediatrics and Pediatric Surgery"
- "Kazakh National Medical University named after S.D. Asfendiyarov"
| | - Natalya Konoplya
- "N. N. Alexandrov National Cancer Centre of Belarus", Minsk, Belarus
| | | | - Olga Blau
- Clinic for Hematology, Oncology and Tumorimmunology, Charite University Berlin, Berlin, Germany
| | | | | | | | - Gulmira Altynbayeva
- "Scientific Center of Pediatrics and Pediatric Surgery"
- "Kazakh National Medical University named after S.D. Asfendiyarov"
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5
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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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6
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Machado HC, Bispo S, Dallagiovanna B. miR-6087 Might Regulate Cell Cycle–Related mRNAs During Cardiomyogenesis of hESCs. Bioinform Biol Insights 2023; 17:11779322231161918. [PMID: 37020502 PMCID: PMC10069004 DOI: 10.1177/11779322231161918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/16/2023] [Indexed: 04/03/2023] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that act as negative regulators of gene expression at the post-transcriptional level, promoting mRNA degradation or translation repression. Despite the well-described presence of miRNAs in various human tissues, there is still a lack of information about the relationship between miRNAs and the translation regulation in human embryonic stem cells (hESCs) during cardiomyogenesis. Here, we investigate RNA-seq data from hESCs, focusing on distinct stages of cardiomyogenesis and searching for polysome-bound miRNAs that could be involved in translational regulation. We identify miR-6087 as a differentially expressed miRNA at latest steps of cardiomyocyte differentiation. We analyzed the coexpression pattern between the differentially expressed mRNAs and miR-6087, evaluating whether they are predicted targets of the miRNA. We arranged the genes into an interaction network and identified BLM, RFC4, RFC3, and CCNA2 as key genes of the network. A post hoc analysis of the key genes suggests that miR-6087 could act as a regulator of the cell cycle in hESC during cardiomyogenesis.
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Affiliation(s)
- Hellen Cristine Machado
- Laboratory of Basic Stem-Cell Biology,
Instituto Carlos Chagas – FIOCRUZ-PR, Curitiba, Brazil
| | - Saloe Bispo
- Laboratory of Molecular and Systems
Biology of Trypanosomatids, Instituto Carlos Chagas – FIOCRUZ-PR, Curitiba,
Brazil
| | - Bruno Dallagiovanna
- Laboratory of Basic Stem-Cell Biology,
Instituto Carlos Chagas – FIOCRUZ-PR, Curitiba, Brazil
- Bruno Dallagiovanna, Laboratory of Basic
Stem-Cell Biology, Instituto Carlos Chagas – FIOCRUZ-PR, Rua Professor Algacyr
Munhoz Mader, 3775, Curitiba 81350-010, Brazil.
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7
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Kulthanaamondhita P, Kornsuthisopon C, Photichailert S, Manokawinchoke J, Limraksasin P, Osathanon T. Specific microRNAs regulate dental pulp stem cell behavior. J Endod 2022; 48:688-698. [PMID: 35271859 DOI: 10.1016/j.joen.2022.02.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 02/10/2022] [Accepted: 02/25/2022] [Indexed: 02/07/2023]
Abstract
INTRODUCTION MicroRNAs (miRNAs), small non-coding RNA, control the translation of messenger RNAs into proteins. miRNAs have a crucial role in regulating the diverse biological processes of many physiological and pathological activities. The aim of this systematic review is to explore various functions of miRNAs in the regulation of dental pulp stem cells (DPSCs) behavior. METHODS The articles were searched in PubMed, SCOPUS and ISI Web of Science database using designated keywords. Full-length manuscripts published in English in peer-reviewed journals relevant to the role of miRNAs in DPSC functions were included and reviewed by 2 independent researchers. RESULTS The original search of the database generated 299 studies. One hundred and two duplicate studies were removed. After their exclusion, 48 studies were selected for review. miRNAs have shown to modulate the stemness and differentiation of various mesenchymal stem cells. The miRNAs expression profiles in DPSCs were differed compared with other cell types and have been demonstrated to regulate the levels of proteins crucial for promoting or inhibiting DPSC proliferation as well as differentiation. Further, miRNAs also modulate inflammatory processes in dental pulp. CONCLUSION miRNAs have various function upon the regulation of DPSCs and understanding these roles of miRNAs is crucial for the development of new therapeutics in regenerative dental medicine. With the advancing technologies, the utilization of miRNA technology could revolutionarily change the future of regenerative endodontics.
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Affiliation(s)
- Promphakkon Kulthanaamondhita
- Dental Stem Cell Biology Research Unit and Department of Anatomy, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Chatvadee Kornsuthisopon
- Dental Stem Cell Biology Research Unit and Department of Anatomy, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Suphalak Photichailert
- Dental Stem Cell Biology Research Unit and Department of Anatomy, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Jeeranan Manokawinchoke
- Dental Stem Cell Biology Research Unit and Department of Anatomy, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Phoonsuk Limraksasin
- Dental Stem Cell Biology Research Unit and Department of Anatomy, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand; Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai, Miyagi, Japan
| | - Thanaphum Osathanon
- Dental Stem Cell Biology Research Unit and Department of Anatomy, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand.
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8
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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: 5] [Impact Index Per Article: 1.7] [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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9
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Building Pluripotency Identity in the Early Embryo and Derived Stem Cells. Cells 2021; 10:cells10082049. [PMID: 34440818 PMCID: PMC8391114 DOI: 10.3390/cells10082049] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 07/27/2021] [Accepted: 08/06/2021] [Indexed: 12/13/2022] Open
Abstract
The fusion of two highly differentiated cells, an oocyte with a spermatozoon, gives rise to the zygote, a single totipotent cell, which has the capability to develop into a complete, fully functional organism. Then, as development proceeds, a series of programmed cell divisions occur whereby the arising cells progressively acquire their own cellular and molecular identity, and totipotency narrows until when pluripotency is achieved. The path towards pluripotency involves transcriptome modulation, remodeling of the chromatin epigenetic landscape to which external modulators contribute. Both human and mouse embryos are a source of different types of pluripotent stem cells whose characteristics can be captured and maintained in vitro. The main aim of this review is to address the cellular properties and the molecular signature of the emerging cells during mouse and human early development, highlighting similarities and differences between the two species and between the embryos and their cognate stem cells.
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10
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Patel M, Wang Y, Bartom ET, Dhir R, Nephew KP, Matei D, Murmann AE, Lengyel E, Peter ME. The Ratio of Toxic-to-Nontoxic miRNAs Predicts Platinum Sensitivity in Ovarian Cancer. Cancer Res 2021; 81:3985-4000. [PMID: 34224372 PMCID: PMC8338879 DOI: 10.1158/0008-5472.can-21-0953] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/10/2021] [Accepted: 06/14/2021] [Indexed: 01/09/2023]
Abstract
Ovarian cancer remains one of the deadliest gynecologic malignancies affecting women, and development of resistance to platinum remains a major barrier to achieving a cure. Multiple mechanisms have been identified to confer platinum resistance. Numerous miRNAs have been linked to platinum sensitivity and resistance in ovarian cancer. miRNA activity occurs mainly when the guide strand of the miRNA, with its seed sequence at position 2-7/8, is loaded into the RNA-induced silencing complex (RISC) and targets complementary short seed matches in the 3' untranslated region of mRNAs. Toxic 6mer seeds, which target genes critical for cancer cell survival, have been found in tumor-suppressive miRNAs. Many siRNAs and short hairpin RNAs (shRNA) can also kill cancer cells via toxic seeds, the most toxic of which carry G-rich 6mer seed sequences. We showed here that treatment of ovarian cancer cells with platinum led to increased RISC-bound miRNAs carrying toxic 6mer seeds and decreased miRNAs with nontoxic seeds. Platinum-tolerant cells did not exhibit this toxicity shift but retained sensitivity to cell death mediated by siRNAs carrying toxic 6mer seeds. Analysis of RISC-bound miRNAs in tumors from patients with ovarian cancer revealed that the ratio between miRNAs with toxic versus nontoxic seeds was predictive of treatment outcome. Application of the 6mer seed toxicity concept to cancer relevant miRNAs provides a new framework for understanding and predicting cancer therapy responses. SIGNIFICANCE: These findings demonstrate that the balance of miRNAs that carry toxic and nontoxic 6mer seeds contributes to platinum resistance in ovarian cancer.
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Affiliation(s)
- Monal Patel
- Department of Medicine/Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Yinu Wang
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Elizabeth T Bartom
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Rohin Dhir
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, Illinois
| | - Kenneth P Nephew
- Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana
| | - Daniela Matei
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
- Robert H. Lurie Comprehensive Cancer Center, Chicago, Illinois
| | - Andrea E Murmann
- Department of Medicine/Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Ernst Lengyel
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, Illinois
| | - Marcus E Peter
- Department of Medicine/Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
- Robert H. Lurie Comprehensive Cancer Center, Chicago, Illinois
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11
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Li C, Jiang Z, Hao J, Liu D, Hu H, Gao Y, Wang D. Role of N6-methyl-adenosine modification in mammalian embryonic development. Genet Mol Biol 2021; 44:e20200253. [PMID: 33999093 PMCID: PMC8127566 DOI: 10.1590/1678-4685-gmb-2020-0253] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 04/07/2021] [Indexed: 11/21/2022] Open
Abstract
N6-methyl-adenosine (m6A) methylation is one of the most common and abundant modifications of RNA molecules in eukaryotes. Although various biological roles of m6A methylation have been elucidated, its role in embryonic development is still unclear. In this review, we focused on the function and expression patterns of m6A-related genes in mammalian embryonic development and the role of m6A modification in the embryonic epigenetic reprogramming process. The modification of m6A is regulated by the combined activities of methyltransferases, demethylases, and m6A-binding proteins. m6A-related genes act synergistically to form a dynamic, reversible m6A pattern, which exists in several physiological processes in various stages of embryonic development. The lack of one of these enzymes affects embryonic m6A levels, leading to abnormal embryonic development and even death. Moreover, m6A is a positive regulator of reprogramming to pluripotency and can affect embryo reprogramming by affecting activation of the maternal-to-zygotic transition. In conclusion, m6A is involved in the regulation of gene expression during embryonic development and the metabolic processes of RNA and plays an important role in the epigenetic modification of embryos.
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Affiliation(s)
- Chengshun Li
- Jilin University, College of Animal Science, Laboratory Animal Center, Changchun, China
| | - Ziping Jiang
- The First Hospital of Jilin University, Department of hand surgery, Changchun, China
| | - Jindong Hao
- Jilin University, College of Animal Science, Laboratory Animal Center, Changchun, China
| | - Da Liu
- Changchun University of Chinese Medicine, Department of Pharmacy, Changchun, China
| | - Haobo Hu
- Jilin University, College of Animal Science, Laboratory Animal Center, Changchun, China
| | - Yan Gao
- Jilin University, College of Animal Science, Laboratory Animal Center, Changchun, China
| | - Dongxu Wang
- Jilin University, College of Animal Science, Laboratory Animal Center, Changchun, China
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12
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Xu P, Ma Y, Wu H, Wang YL. Placenta-Derived MicroRNAs in the Pathophysiology of Human Pregnancy. Front Cell Dev Biol 2021; 9:646326. [PMID: 33777951 PMCID: PMC7991791 DOI: 10.3389/fcell.2021.646326] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 02/22/2021] [Indexed: 12/11/2022] Open
Abstract
In placental mammals, reproductive success, and maternal-fetal health substantially depend on a well-being placenta, the interface between the fetus and the mother. Disorders in placental cells are tightly associated with adverse pregnancy outcomes including preeclampsia (PE), fetal growth restriction, etc. MicroRNAs (miRNAs) represent small non-coding RNAs that regulate post-transcriptional gene expression and are integral to a wide range of healthy or diseased cellular proceedings. Numerous miRNAs have been detected in human placenta and increasing evidence is revealing their important roles in regulating placental cell behaviors. Recent studies indicate that placenta-derived miRNAs can be released to the maternal circulation via encapsulating into the exosomes, and they potentially target various maternal cells to provide a hormone-like means of intercellular communication between the mother and the fetus. These placental exosome miRNAs are attracting more and more attention due to their differential expression in pregnant complications, which may provide novel biomarkers for prediction of the diseases. In this review, we briefly summarize the current knowledge and the perspectives of the placenta-derived miRNAs, especially the exosomal transfer of placental miRNAs and their pathophysiological relevance to PE. The possible exosomal-miRNA-targeted strategies for diagnosis, prognosis or therapy of PE are highlighted.
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Affiliation(s)
- Peng Xu
- School of Life Science, Shanxi University, Taiyuan, China
| | - Yeling Ma
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Hongyu Wu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Yan-Ling Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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13
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Keuls RA, Kojima K, Lozzi B, Steele JW, Chen Q, Gross SS, Finnell RH, Parchem RJ. MiR-302 Regulates Glycolysis to Control Cell-Cycle during Neural Tube Closure. Int J Mol Sci 2020; 21:E7534. [PMID: 33066028 PMCID: PMC7589003 DOI: 10.3390/ijms21207534] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 09/26/2020] [Accepted: 10/06/2020] [Indexed: 01/03/2023] Open
Abstract
Neural tube closure is a critical early step in central nervous system development that requires precise control of metabolism to ensure proper cellular proliferation and differentiation. Dysregulation of glucose metabolism during pregnancy has been associated with neural tube closure defects (NTDs) in humans suggesting that the developing neuroepithelium is particularly sensitive to metabolic changes. However, it remains unclear how metabolic pathways are regulated during neurulation. Here, we used single-cell mRNA-sequencing to analyze expression of genes involved in metabolism of carbon, fats, vitamins, and antioxidants during neurulation in mice and identify a coupling of glycolysis and cellular proliferation to ensure proper neural tube closure. Using loss of miR-302 as a genetic model of cranial NTD, we identify misregulated metabolic pathways and find a significant upregulation of glycolysis genes in embryos with NTD. These findings were validated using mass spectrometry-based metabolite profiling, which identified increased glycolytic and decreased lipid metabolites, consistent with a rewiring of central carbon traffic following loss of miR-302. Predicted miR-302 targets Pfkp, Pfkfb3, and Hk1 are significantly upregulated upon NTD resulting in increased glycolytic flux, a shortened cell cycle, and increased proliferation. Our findings establish a critical role for miR-302 in coordinating the metabolic landscape of neural tube closure.
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Affiliation(s)
- Rachel A. Keuls
- Development, Disease Models & Therapeutics Graduate Program, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA;
- Center for Cell and Gene Therapy, Stem Cells and Regenerative Medicine Center, One Baylor Plaza, Houston, TX 77030, USA;
| | - Karin Kojima
- Center for Cell and Gene Therapy, Stem Cells and Regenerative Medicine Center, One Baylor Plaza, Houston, TX 77030, USA;
| | - Brittney Lozzi
- Genetics and Genomics Graduate Program, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA;
| | - John W. Steele
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; (J.W.S.); (R.H.F.)
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology and Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Qiuying Chen
- Department of Pharmacology, Weill Cornell Medicine, New York, NY 10065, USA; (Q.C.); (S.S.G.)
| | - Steven S. Gross
- Department of Pharmacology, Weill Cornell Medicine, New York, NY 10065, USA; (Q.C.); (S.S.G.)
| | - Richard H. Finnell
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; (J.W.S.); (R.H.F.)
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology and Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ronald J. Parchem
- Development, Disease Models & Therapeutics Graduate Program, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA;
- Center for Cell and Gene Therapy, Stem Cells and Regenerative Medicine Center, One Baylor Plaza, Houston, TX 77030, USA;
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; (J.W.S.); (R.H.F.)
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14
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Giroux P, Bhajun R, Segard S, Picquenot C, Charavay C, Desquilles L, Pinna G, Ginestier C, Denis J, Cherradi N, Guyon L. miRViz: a novel webserver application to visualize and interpret microRNA datasets. Nucleic Acids Res 2020; 48:W252-W261. [PMID: 32319523 PMCID: PMC7319447 DOI: 10.1093/nar/gkaa259] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/20/2020] [Accepted: 04/06/2020] [Indexed: 01/06/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that are involved in the regulation of major pathways in eukaryotic cells through their binding to and repression of multiple mRNAs. With high-throughput methodologies, various outcomes can be measured that produce long lists of miRNAs that are often difficult to interpret. A common question is: after differential expression or phenotypic screening of miRNA mimics, which miRNA should be chosen for further investigation? Here, we present miRViz (http://mirviz.prabi.fr/), a webserver application designed to visualize and interpret large miRNA datasets, with no need for programming skills. MiRViz has two main goals: (i) to help biologists to raise data-driven hypotheses and (ii) to share miRNA datasets in a straightforward way through publishable quality data representation, with emphasis on relevant groups of miRNAs. MiRViz can currently handle datasets from 11 eukaryotic species. We present real-case applications of miRViz, and provide both datasets and procedures to reproduce the corresponding figures. MiRViz offers rapid identification of miRNA families, as demonstrated here for the miRNA-320 family, which is significantly exported in exosomes of colon cancer cells. We also visually highlight a group of miRNAs associated with pluripotency that is particularly active in control of a breast cancer stem-cell population in culture.
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Affiliation(s)
- Pierre Giroux
- Univ. Grenoble Alpes, CEA, IRIG, Inserm, BCI, 38000 Grenoble, France
| | - Ricky Bhajun
- Univ. Grenoble Alpes, CEA, IRIG, Inserm, BGE, 38000 Grenoble, France
| | - Stéphane Segard
- Univ. Grenoble Alpes, CEA, IRIG, Inserm, BGE, 38000 Grenoble, France
| | - Claire Picquenot
- Univ. Grenoble Alpes, CEA, IRIG, Inserm, BGE, 38000 Grenoble, France
| | - Céline Charavay
- Univ. Grenoble Alpes, CEA, IRIG, Inserm, BGE, 38000 Grenoble, France
| | - Lise Desquilles
- Univ. Grenoble Alpes, CEA, IRIG, Inserm, BCI, 38000 Grenoble, France
| | - Guillaume Pinna
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Sud, University Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - Christophe Ginestier
- Aix-Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Epithelial Stem Cells and Cancer lab, F-13273 Marseille, France
| | - Josiane Denis
- Univ. Grenoble Alpes, CEA, IRIG, Inserm, BCI, 38000 Grenoble, France
| | - Nadia Cherradi
- Univ. Grenoble Alpes, CEA, IRIG, Inserm, BCI, 38000 Grenoble, France
| | - Laurent Guyon
- Univ. Grenoble Alpes, CEA, IRIG, Inserm, BCI, 38000 Grenoble, France.,Univ. Grenoble Alpes, CEA, IRIG, Inserm, BGE, 38000 Grenoble, France
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15
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Cimadomo D, Rienzi L, Giancani A, Alviggi E, Dusi L, Canipari R, Noli L, Ilic D, Khalaf Y, Ubaldi FM, Capalbo A. Definition and validation of a custom protocol to detect miRNAs in the spent media after blastocyst culture: searching for biomarkers of implantation. Hum Reprod 2020; 34:1746-1761. [PMID: 31419301 DOI: 10.1093/humrep/dez119] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/09/2019] [Indexed: 12/18/2022] Open
Abstract
STUDY QUESTION Can miRNAs be reliably detected in the spent blastocyst media (SBM) after IVF as putative biomarkers of the implantation potential of euploid embryos? SUMMARY ANSWER Adjustment of the data for blastocyst quality and the day of full-expansion hinders the predictive power of a fast, inexpensive, reproducible and user-friendly protocol based on the detection of 10 selected miRNAs from SBM. WHAT IS KNOWN ALREADY Euploidy represents so far the strongest predictor of blastocyst competence. Nevertheless, ~50% of the euploid blastocysts fail to implant. Several studies across the years have suggested that a dialogue exists between the embryo and the endometrium aimed at the establishment of a pregnancy. MicroRNAs have been proposed as mediators of such a dialogue and investigated in this respect. Several expensive, time-consuming and complex protocols have been adopted and promising results have been produced, but conclusive evidence from large clinical studies is missing. STUDY DESIGN, SIZE, DURATION This study was conducted in two phases from September 2015 to December 2017. In Phase 1, the human blastocyst miRNome profile was defined from the inner cell mass (ICM) and the corresponding whole-trophectoderm (TE) of six donated blastocysts. Two different protocols were adopted to this end. In parallel, 6 pools of 10 SBM each were run (3 from only implanted euploid blastocysts, IEBs; and 3 from only not-implanted euploid blastocysts, not-IEBs). A fast, inexpensive and user-friendly custom protocol for miRNA SBM profiling was designed. In Phase 2, 239 SBM from IEB and not-IEB were collected at three IVF centres. After 18 SBM from poor-quality blastocysts were excluded from the analysis, data from 107 SBM from not-IEB and 114 from IEB were produced through the previously developed custom protocol and compared. The data were corrected through logistic regressions. PARTICIPANT/MATERIALS, SETTINGS, METHODS Donated blastocysts underwent ICM and whole-TE isolation. SBM were collected during IVF cycles characterized by ICSI, blastocyst culture in a continuous media, TE biopsy without zona pellucida opening in Day 3, quantitative PCR (qPCR)-based aneuploidy testing and vitrified-warmed single euploid embryo transfer. Not-IEB and IEB were clustered following a negative pregnancy test and a live birth, respectively. The Taqman Low Density Array (TLDA) cards and the Exiqon microRNA human panel I+II qPCR analysis protocols were adopted to analyse the ICM and whole-TE. The latter was used also for SBM pools. A custom protocol and plate was then designed based on the Exiqon workflow, validated and finally adopted for SBM analysis in study Phase 2. This custom protocol allows the analysis of 10 miRNAs from 10 SBM in 3 hours from sample collection to data inspection. MAIN RESULTS AND ROLE OF THE CHANCE The TLDA cards protocol involved a higher rate of false positive results (5.6% versus 2.8% with Exiqon). There were 44 miRNAs detected in the ICM and TE from both the protocols. One and 24 miRNAs were instead detected solely in the ICM and the TE, respectively. Overall, 29 miRNAs were detected in the pooled SBM: 8 only from not-IEB, 8 only from IEB and 13 from both. Most of them (N = 24/29, 82.7%) were also detected previously in both the ICM and TE with the Exiqon protocol; two miRNAs (N = 2/29, 6.9%) were previously detected only in the TE, and three (N = 3/29, 10.3%) were never detected previously. In study Phase 2, significant differences were shown between not-IEB and IEB in terms of both miRNA detection and relative quantitation. However, when the data were corrected for embryo morphology and day of full development (i.e. SBM collection), no significant association was confirmed. LIMITATIONS, REASONS FOR CAUTION This study did not evaluate specifically exosomal miRNAs, thereby reducing the chance of identifying the functional miRNAs. Ex-vivo experiments are required to confirm the role of miRNAs in mediating the dialogue with endometrial cells, and higher throughput technologies need to be further evaluated for miRNA profiling from clinical SBM samples. WIDER IMPLICATIONS OF THE FINDINGS Although no clinical predictive power was reported in this study, the absence of invasiveness related with SBM analysis and the evidence that embryonic genetic material can be reliably detected and analysed from SBM make this waste product of IVF an important source for further investigations aimed at improving embryo selection. STUDY FUNDING/COMPETING INTEREST(S) This project has been financially supported by Merck KgaA (Darmstadt, Germany) with a Grant for Fertility Innovation (GFI) 2015. The authors have no conflict of interest to declare related with this study. TRIAL REGISTRATION NUMBER None.
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Affiliation(s)
- Danilo Cimadomo
- Clinica Valle Giulia, G.en.e.r.a. center for reproductive medicine, Rome, Italy.,Clinica Ruesch, G.en.e.r.a. Center for Reproductive Medicine, Naples, Italy.,G.en.e.r.a. Veneto, G.en.e.r.a. Center for Reproductive Medicine, Marostica, Italy
| | - Laura Rienzi
- Clinica Valle Giulia, G.en.e.r.a. center for reproductive medicine, Rome, Italy.,Clinica Ruesch, G.en.e.r.a. Center for Reproductive Medicine, Naples, Italy.,G.en.e.r.a. Veneto, G.en.e.r.a. Center for Reproductive Medicine, Marostica, Italy
| | - Adriano Giancani
- Clinica Valle Giulia, G.en.e.r.a. center for reproductive medicine, Rome, Italy.,DAHFMO, Unit of Histology and Medical Embryology, Sapienza, University of Rome, Italy
| | - Erminia Alviggi
- Clinica Ruesch, G.en.e.r.a. Center for Reproductive Medicine, Naples, Italy
| | - Ludovica Dusi
- G.en.e.r.a. Veneto, G.en.e.r.a. Center for Reproductive Medicine, Marostica, Italy
| | - Rita Canipari
- DAHFMO, Unit of Histology and Medical Embryology, Sapienza, University of Rome, Italy
| | - Laila Noli
- Fakeeh College of Medical Sciences, Jeddah, Saudi Arabia.,Division of Women's Health and Assisted Conception Unit, King's College of London, Guy's Hospital, London, United Kingdom
| | - Dusko Ilic
- Division of Women's Health and Assisted Conception Unit, King's College of London, Guy's Hospital, London, United Kingdom
| | - Yacoub Khalaf
- Division of Women's Health and Assisted Conception Unit, King's College of London, Guy's Hospital, London, United Kingdom
| | - Filippo Maria Ubaldi
- Clinica Valle Giulia, G.en.e.r.a. center for reproductive medicine, Rome, Italy.,Clinica Ruesch, G.en.e.r.a. Center for Reproductive Medicine, Naples, Italy.,G.en.e.r.a. Veneto, G.en.e.r.a. Center for Reproductive Medicine, Marostica, Italy
| | - Antonio Capalbo
- DAHFMO, Unit of Histology and Medical Embryology, Sapienza, University of Rome, Italy.,Igenomix, Marostica, Italy
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16
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The Key Role of MicroRNAs in Self-Renewal and Differentiation of Embryonic Stem Cells. Int J Mol Sci 2020; 21:ijms21176285. [PMID: 32877989 PMCID: PMC7504502 DOI: 10.3390/ijms21176285] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/21/2020] [Accepted: 08/28/2020] [Indexed: 12/17/2022] Open
Abstract
Naïve pluripotent embryonic stem cells (ESCs) and epiblast stem cells (EpiSCs) represent distinctive developmental stages, mimicking the pre- and the post-implantation events during the embryo development, respectively. The complex molecular mechanisms governing the transition from ESCs into EpiSCs are orchestrated by fluctuating levels of pluripotency transcription factors (Nanog, Oct4, etc.) and wide-ranging remodeling of the epigenetic landscape. Recent studies highlighted the pivotal role of microRNAs (miRNAs) in balancing the switch from self-renewal to differentiation of ESCs. Of note, evidence deriving from miRNA-based reprogramming strategies underscores the role of the non-coding RNAs in the induction and maintenance of the stemness properties. In this review, we revised recent studies concerning the functions mediated by miRNAs in ESCs, with the aim of giving a comprehensive view of the highly dynamic miRNA-mediated tuning, essential to guarantee cell cycle progression, pluripotency maintenance and the proper commitment of ESCs.
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17
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MicroRNA-dependent inhibition of PFN2 orchestrates ERK activation and pluripotent state transitions by regulating endocytosis. Proc Natl Acad Sci U S A 2020; 117:20625-20635. [PMID: 32788350 DOI: 10.1073/pnas.2002750117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Profilin2 (PFN2) is a target of the embryonic stem cell (ESC)-enriched miR-290 family of microRNAs (miRNAs) and an actin/dynamin-binding protein implicated in endocytosis. Here we show that the miR-290-PFN2 pathway regulates many aspects of ESC biology. In the absence of miRNAs, PFN2 is up-regulated in ESCs, with a resulting decrease in endocytosis. Reintroduction of miR-290, knockout of Pfn2, or disruption of the PFN2-dynamin interaction domain in miRNA-deficient cells reverses the endocytosis defect. The reduced endocytosis is associated with impaired extracellular signal-regulated kinase (ERK) signaling, delayed ESC cell cycle progression, and repressed ESC differentiation. Mutagenesis of the single canonical conserved 3' UTR miR-290-binding site of Pfn2 or overexpression of the Pfn2 open reading frame alone in otherwise wild-type cells largely recapitulates these phenotypes. Taken together, these findings define an axis of posttranscriptional control, endocytosis, and signal transduction that is important for ESC proliferation and differentiation.
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18
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Radtke A, Dieckmann KP, Grobelny F, Salzbrunn A, Oing C, Schulze W, Belge G. Expression of miRNA-371a-3p in seminal plasma and ejaculate is associated with sperm concentration. Andrology 2020; 7:469-474. [PMID: 31310058 DOI: 10.1111/andr.12664] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 05/06/2019] [Accepted: 05/12/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND The microRNAs of the miR-371-3 cluster are novel serum markers for testicular germ cell tumors. Sporadic reports suggested the expression of this miRNA in semen. OBJECTIVES To verify the expression of miR-371a-3p in seminal plasma and unprocessed ejaculate; to compare seminal plasma miRNA levels in germ cell tumors patients with those of controls; to look for an association of miRNA levels with semen quality. MATERIALS AND METHODS The miR-371a-3p expression was analyzed with qPCR. The study population consisted of 100 participants: seminal plasma samples from 20 germ cell tumors patients and 30 controls, serum samples from 12 healthy men, ejaculate samples from 38 men undergoing fertility testing. RESULTS The seminal plasma miR-371a-3p levels of germ cell tumors patients were not different from controls. The miRNA expression was very low in serum but much higher in seminal plasma. In ejaculate samples, the miRNA expression significantly correlated with sperm concentration and the total sperm count. DISCUSSION miR-371-a-3p is present in sperm-containing fluids. Seminal plasma levels cannot be used to distinguish germ cell tumors from controls. The correlation with sperm concentration in ejaculate samples suggests the spermatozoa as possible source of miR-371a-3p production. CONCLUSION The miR-371a-3p levels in ejaculate could represent a novel biomarker for the non-invasive evaluation of male infertility.
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Affiliation(s)
- A Radtke
- Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany
| | - K-P Dieckmann
- Department of Urology, Asklepios Klinik Altona, Hamburg, Germany.,Amedes Group, MVZ Fertility Center GmbH, Hamburg, Germany
| | - F Grobelny
- Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany
| | - A Salzbrunn
- Institute of Andrology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - C Oing
- Department of Oncology, Hematology and Bone Marrow Transplantation with Division of Pneumology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - W Schulze
- Amedes Group, MVZ Fertility Center GmbH, Hamburg, Germany
| | - G Belge
- Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany
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19
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Mong EF, Yang Y, Akat KM, Canfield J, VanWye J, Lockhart J, Tsibris JCM, Schatz F, Lockwood CJ, Tuschl T, Kayisli UA, Totary-Jain H. Chromosome 19 microRNA cluster enhances cell reprogramming by inhibiting epithelial-to-mesenchymal transition. Sci Rep 2020; 10:3029. [PMID: 32080251 PMCID: PMC7033247 DOI: 10.1038/s41598-020-59812-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 02/04/2020] [Indexed: 02/08/2023] Open
Abstract
During implantation, cytotrophoblasts undergo epithelial-to-mesenchymal transition (EMT) as they differentiate into invasive extravillous trophoblasts (EVTs). The primate-specific microRNA cluster on chromosome 19 (C19MC) is exclusively expressed in the placenta, embryonic stem cells and certain cancers however, its role in EMT gene regulation is unknown. In situ hybridization for miR-517a/c, a C19MC cistron microRNA, in first trimester human placentas displayed strong expression in villous trophoblasts and a gradual decrease from proximal to distal cell columns as cytotrophoblasts differentiate into invasive EVTs. To investigate the role of C19MC in the regulation of EMT genes, we employed the CRISPR/dCas9 Synergistic Activation Mediator (SAM) system, which induced robust transcriptional activation of the entire C19MC cistron and resulted in suppression of EMT associated genes. Exposure of human iPSCs to hypoxia or differentiation of iPSCs into either cytotrophoblast-stem-like cells or EVT-like cells under hypoxia reduced C19MC expression and increased EMT genes. Furthermore, transcriptional activation of the C19MC cistron induced the expression of OCT4 and FGF4 and accelerated cellular reprogramming. This study establishes the CRISPR/dCas9 SAM as a powerful tool that enables activation of the entire C19MC cistron and uncovers its novel role in suppressing EMT genes critical for maintaining the epithelial cytotrophoblasts stem cell phenotype.
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Affiliation(s)
- Ezinne F Mong
- Department of Molecular Pharmacology and Physiology, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
| | - Ying Yang
- Department of Molecular Pharmacology and Physiology, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
| | - Kemal M Akat
- Howard Hughes Medical Institute and Laboratory for RNA Molecular Biology, The Rockefeller University, New York, New York, USA
| | - John Canfield
- Department of Molecular Pharmacology and Physiology, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
| | - Jeffrey VanWye
- Department of Molecular Pharmacology and Physiology, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
| | - John Lockhart
- Department of Molecular Pharmacology and Physiology, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
| | - John C M Tsibris
- Department of Obstetrics and Gynecology, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
| | - Frederick Schatz
- Department of Obstetrics and Gynecology, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
| | - Charles J Lockwood
- Department of Obstetrics and Gynecology, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
| | - Thomas Tuschl
- Howard Hughes Medical Institute and Laboratory for RNA Molecular Biology, The Rockefeller University, New York, New York, USA
| | - Umit A Kayisli
- Department of Obstetrics and Gynecology, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
| | - Hana Totary-Jain
- Department of Molecular Pharmacology and Physiology, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA.
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20
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Sastre D, Baiochi J, de Souza Lima IM, Canto de Souza F, Corveloni AC, Thomé CH, Faça VM, Schiavinato JLDS, Covas DT, Panepucci RA. Focused screening reveals functional effects of microRNAs differentially expressed in colorectal cancer. BMC Cancer 2019; 19:1239. [PMID: 31864341 PMCID: PMC6925883 DOI: 10.1186/s12885-019-6468-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 12/16/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is still a leading cause of death worldwide. Recent studies have pointed to an important role of microRNAs in carcinogenesis. Several microRNAs are described as aberrantly expressed in CRC tissues and in the serum of patients. However, functional outcomes of microRNA aberrant expression still need to be explored at the cellular level. Here, we aimed to investigate the effects of microRNAs aberrantly expressed in CRC samples in the proliferation and cell death of a CRC cell line. METHODS We transfected 31 microRNA mimics into HCT116 cells. Total number of live propidium iodide negative (PI-) and dead (PI+) cells were measured 4 days post-transfection by using a high content screening (HCS) approach. HCS was further used to evaluate apoptosis (via Annexin V and PI staining), and to discern between intrinsic and extrinsic apoptotic pathways, by detecting cleaved Caspase 9 and 8, respectively. To reveal mRNA targets and potentially involved mechanisms, we performed microarray gene expression and functional pathway enrichment analysis. Quantitative PCR and western blot were used to validate potential mRNA targets. RESULTS Twenty microRNAs altered the proliferation of HCT116 cells in comparison to control. miR-22-3p, miR-24-3p, and miR-101-3p significantly repressed cell proliferation and induced cell death. Interestingly, all anti-proliferative microRNAs in our study had been previously described as poorly expressed in the CRC samples. Predicted miR-101-3p targets that were also downregulated by in our microarray were enriched for genes associated with Wnt and cancer pathways, including MCL-1, a member of the BCL-2 family, involved in apoptosis. Interestingly, miR-101-3p preferentially downregulated the long anti-apoptotic MCL-1 L isoform, and reduced cell survival specifically by activating the intrinsic apoptosis pathway. Moreover, miR-101-3p also downregulated IL6ST, STAT3A/B, and MYC mRNA levels, genes associated with stemness properties of CRC cells. CONCLUSIONS microRNAs upregulated in CRC tend to induce proliferation in vitro, whereas microRNAs poorly expressed in CRC halt proliferation and induce cell death. We provide novel evidence linking preferential inhibition of the anti-apoptotic MCL-1 L isoform by miR-101-3p and consequent activation of the intrinsic apoptotic pathway as potential mechanisms for its antitumoral activity, likely due to the inhibition of the IL-6/JAK/STAT signaling pathway.
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Affiliation(s)
- Danuta Sastre
- Laboratory of Human and Medical Genetics, Federal University of Pará, Rua Augusto Corrêa, 01. Guamá., Belém, Pará CEP 66075-110 Brazil
- Laboratory of Functional Biology (LFBio), Center for Cell-Based Therapy (CTC), Regional Blood Center, Ribeirao Preto Medical School, University of São Paulo (USP), R. Ten. Catão Roxo, 2501., Ribeirão Preto, SP 14051-140 Brazil
| | - João Baiochi
- Laboratory of Functional Biology (LFBio), Center for Cell-Based Therapy (CTC), Regional Blood Center, Ribeirao Preto Medical School, University of São Paulo (USP), R. Ten. Catão Roxo, 2501., Ribeirão Preto, SP 14051-140 Brazil
| | - Ildercilio Mota de Souza Lima
- Laboratory of Functional Biology (LFBio), Center for Cell-Based Therapy (CTC), Regional Blood Center, Ribeirao Preto Medical School, University of São Paulo (USP), R. Ten. Catão Roxo, 2501., Ribeirão Preto, SP 14051-140 Brazil
| | - Felipe Canto de Souza
- Laboratory of Functional Biology (LFBio), Center for Cell-Based Therapy (CTC), Regional Blood Center, Ribeirao Preto Medical School, University of São Paulo (USP), R. Ten. Catão Roxo, 2501., Ribeirão Preto, SP 14051-140 Brazil
| | - Amanda Cristina Corveloni
- Laboratory of Functional Biology (LFBio), Center for Cell-Based Therapy (CTC), Regional Blood Center, Ribeirao Preto Medical School, University of São Paulo (USP), R. Ten. Catão Roxo, 2501., Ribeirão Preto, SP 14051-140 Brazil
| | - Carolina Hassib Thomé
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo (USP), Av. Bandeirantes, 3900 - Vila Monte Alegre, Ribeirão Preto, SP 14049-900 Brazil
| | - Vitor Marcel Faça
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo (USP), Av. Bandeirantes, 3900 - Vila Monte Alegre, Ribeirão Preto, SP 14049-900 Brazil
| | - Josiane Lilian dos Santos Schiavinato
- Laboratory of Functional Biology (LFBio), Center for Cell-Based Therapy (CTC), Regional Blood Center, Ribeirao Preto Medical School, University of São Paulo (USP), R. Ten. Catão Roxo, 2501., Ribeirão Preto, SP 14051-140 Brazil
| | - Dimas Tadeu Covas
- Laboratory of Functional Biology (LFBio), Center for Cell-Based Therapy (CTC), Regional Blood Center, Ribeirao Preto Medical School, University of São Paulo (USP), R. Ten. Catão Roxo, 2501., Ribeirão Preto, SP 14051-140 Brazil
| | - Rodrigo Alexandre Panepucci
- Laboratory of Functional Biology (LFBio), Center for Cell-Based Therapy (CTC), Regional Blood Center, Ribeirao Preto Medical School, University of São Paulo (USP), R. Ten. Catão Roxo, 2501., Ribeirão Preto, SP 14051-140 Brazil
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21
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Wang Y, Hussein AM, Somasundaram L, Sankar R, Detraux D, Mathieu J, Ruohola-Baker H. microRNAs Regulating Human and Mouse Naïve Pluripotency. Int J Mol Sci 2019; 20:E5864. [PMID: 31766734 PMCID: PMC6929104 DOI: 10.3390/ijms20235864] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/07/2019] [Accepted: 11/13/2019] [Indexed: 12/16/2022] Open
Abstract
microRNAs are ~22bp nucleotide non-coding RNAs that play important roles in the post-transcriptional regulation of gene expression. Many studies have established that microRNAs are important for cell fate choices, including the naïve to primed pluripotency state transitions, and their intermediate state, the developmentally suspended diapause state in early development. However, the full extent of microRNAs associated with these stage transitions in human and mouse remain under-explored. By meta-analysis of microRNA-seq, RNA-seq, and metabolomics datasets from human and mouse, we found a set of microRNAs, and importantly, their experimentally validated target genes that show consistent changes in naïve to primed transitions (microRNA up, target genes down, or vice versa). The targets of these microRNAs regulate developmental pathways (e.g., the Hedgehog-pathway), primary cilium, and remodeling of metabolic processes (oxidative phosphorylation, fatty acid metabolism, and amino acid transport) during the transition. Importantly, we identified 115 microRNAs that significantly change in the same direction in naïve to primed transitions in both human and mouse, many of which are novel candidate regulators of pluripotency. Furthermore, we identified 38 microRNAs and 274 target genes that may be involved in diapause, where embryonic development is temporarily suspended prior to implantation to uterus. The upregulated target genes suggest that microRNAs activate stress response in the diapause stage. In conclusion, we provide a comprehensive resource of microRNAs and their target genes involved in naïve to primed transition and in the paused intermediate, the embryonic diapause stage.
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Affiliation(s)
- Yuliang Wang
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; (A.M.H.); (L.S.); (R.S.); (D.D.)
| | - Abdiasis M. Hussein
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; (A.M.H.); (L.S.); (R.S.); (D.D.)
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Logeshwaran Somasundaram
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; (A.M.H.); (L.S.); (R.S.); (D.D.)
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Rithika Sankar
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; (A.M.H.); (L.S.); (R.S.); (D.D.)
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Damien Detraux
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; (A.M.H.); (L.S.); (R.S.); (D.D.)
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Department of Comparative Medicine, University of Washington, Seattle, WA 98195, USA
| | - Julie Mathieu
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; (A.M.H.); (L.S.); (R.S.); (D.D.)
- Department of Comparative Medicine, University of Washington, Seattle, WA 98195, USA
| | - Hannele Ruohola-Baker
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; (A.M.H.); (L.S.); (R.S.); (D.D.)
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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22
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Nasr MA, Salah RA, Abd Elkodous M, Elshenawy SE, El-Badri N. Dysregulated MicroRNA Fingerprints and Methylation Patterns in Hepatocellular Carcinoma, Cancer Stem Cells, and Mesenchymal Stem Cells. Front Cell Dev Biol 2019; 7:229. [PMID: 31681762 PMCID: PMC6811506 DOI: 10.3389/fcell.2019.00229] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 09/26/2019] [Indexed: 12/14/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the top causes of cancer mortality worldwide. Although HCC has been researched extensively, there is still a need for novel and effective therapeutic interventions. There is substantial evidence that initiation of carcinogenesis in liver cirrhosis, a leading cause of HCC, is mediated by cancer stem cells (CSCs). CSCs were also shown to be responsible for relapse and chemoresistance in several cancers, including HCC. MicroRNAs (miRNAs) constitute important epigenetic markers that regulate carcinogenesis by acting post-transcriptionally on mRNAs, contributing to the progression of HCC. We have previously shown that co-culture of cancer cells with mesenchymal stem cells (MSCs) could induce the reprogramming of MSCs into CSC-like cells. In this review, we evaluate the available data concerning the epigenetic regulation of miRNAs through methylation and the possible role of this regulation in stem cell and somatic reprogramming in HCC.
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Affiliation(s)
- Mohamed A Nasr
- Center of Excellence for Stem Cells and Regenerative Medicine (CESC), Zewail City of Science and Technology, 6th of October City, Egypt
| | - Radwa Ayman Salah
- Center of Excellence for Stem Cells and Regenerative Medicine (CESC), Zewail City of Science and Technology, 6th of October City, Egypt
| | - M Abd Elkodous
- Center of Excellence for Stem Cells and Regenerative Medicine (CESC), Zewail City of Science and Technology, 6th of October City, Egypt
| | - Shimaa E Elshenawy
- Center of Excellence for Stem Cells and Regenerative Medicine (CESC), Zewail City of Science and Technology, 6th of October City, Egypt
| | - Nagwa El-Badri
- Center of Excellence for Stem Cells and Regenerative Medicine (CESC), Zewail City of Science and Technology, 6th of October City, Egypt
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23
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Mawaribuchi S, Aiki Y, Ikeda N, Ito Y. mRNA and miRNA expression profiles in an ectoderm-biased substate of human pluripotent stem cells. Sci Rep 2019; 9:11910. [PMID: 31417139 PMCID: PMC6695399 DOI: 10.1038/s41598-019-48447-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 08/05/2019] [Indexed: 12/27/2022] Open
Abstract
The potential applications of human pluripotent stem cells, embryonic stem (ES) cells, and induced pluripotent stem (iPS) cells in cell therapy and regenerative medicine have been widely studied. The precise definition of pluripotent stem cell status during culture using biomarkers is essential for basic research and regenerative medicine. Culture conditions, including extracellular matrices, influence the balance between self-renewal and differentiation. Accordingly, to explore biomarkers for defining and monitoring the pluripotent substates during culture, we established different substates in H9 human ES cells by changing the extracellular matrix from vitronectin to Matrigel. The substate was characterised by low and high expression of the pluripotency marker R-10G epitope and the mesenchymal marker vimentin, respectively. Immunohistochemistry, induction of the three germ layers, and exhaustive expression analysis showed that the substate was ectoderm-biased, tended to differentiate into nerves, but retained the potential to differentiate into the three germ layers. Further integrated analyses of mRNA and miRNA microarrays and qPCR analysis showed that nine genes (COL9A2, DGKI, GBX2, KIF26B, MARCH1, PLXNA4, SLC24A4, TLR4, and ZHX3) were upregulated in the ectoderm-biased cells as ectoderm-biased biomarker candidates in pluripotent stem cells. Our findings provide important insights into ectoderm-biased substates of human pluripotent stem cells in the fields of basic research and regenerative medicine.
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Affiliation(s)
- Shuuji Mawaribuchi
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8565, Japan
| | - Yasuhiko Aiki
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8565, Japan
| | - Nozomi Ikeda
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8565, Japan
| | - Yuzuru Ito
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8565, Japan.
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24
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de Souza Lima IM, Schiavinato JLDS, Paulino Leite SB, Sastre D, Bezerra HLDO, Sangiorgi B, Corveloni AC, Thomé CH, Faça VM, Covas DT, Zago MA, Giacca M, Mano M, Panepucci RA. High-content screen in human pluripotent cells identifies miRNA-regulated pathways controlling pluripotency and differentiation. Stem Cell Res Ther 2019; 10:202. [PMID: 31287022 PMCID: PMC6615276 DOI: 10.1186/s13287-019-1318-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 06/11/2019] [Accepted: 06/30/2019] [Indexed: 01/13/2023] Open
Abstract
Background By post-transcriptionally regulating multiple target transcripts, microRNAs (miRNAs or miR) play important biological functions. H1 embryonic stem cells (hESCs) and NTera-2 embryonal carcinoma cells (ECCs) are two of the most widely used human pluripotent model cell lines, sharing several characteristics, including the expression of miRNAs associated to the pluripotent state or with differentiation. However, how each of these miRNAs functionally impacts the biological properties of these cells has not been systematically evaluated. Methods We investigated the effects of 31 miRNAs on NTera-2 and H1 hESCs, by transfecting miRNA mimics. Following 3–4 days of culture, cells were stained for the pluripotency marker OCT4 and the G2 cell-cycle marker Cyclin B1, and nuclei and cytoplasm were co-stained with Hoechst and Cell Mask Blue, respectively. By using automated quantitative fluorescence microscopy (i.e., high-content screening (HCS)), we obtained several morphological and marker intensity measurements, in both cell compartments, allowing the generation of a multiparametric miR-induced phenotypic profile describing changes related to proliferation, cell cycle, pluripotency, and differentiation. Results Despite the overall similarities between both cell types, some miRNAs elicited cell-specific effects, while some related miRNAs induced contrasting effects in the same cell. By identifying transcripts predicted to be commonly targeted by miRNAs inducing similar effects (profiles grouped by hierarchical clustering), we were able to uncover potentially modulated signaling pathways and biological processes, likely mediating the effects of the microRNAs on the distinct groups identified. Specifically, we show that miR-363 contributes to pluripotency maintenance, at least in part, by targeting NOTCH1 and PSEN1 and inhibiting Notch-induced differentiation, a mechanism that could be implicated in naïve and primed pluripotent states. Conclusions We present the first multiparametric high-content microRNA functional screening in human pluripotent cells. Integration of this type of data with similar data obtained from siRNA screenings (using the same HCS assay) could provide a large-scale functional approach to identify and validate microRNA-mediated regulatory mechanisms controlling pluripotency and differentiation. Electronic supplementary material The online version of this article (10.1186/s13287-019-1318-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ildercílio Mota de Souza Lima
- Laboratory of Functional Biology (LFBio), Center for Cell-Based Therapy (CTC), Regional Blood Center of Ribeirão Preto, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, SP, CEP: 14051-140, Brazil.,Department of Genetics and Internal Medicine, Ribeirao Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, SP, Brazil
| | - Josiane Lilian Dos Santos Schiavinato
- Laboratory of Functional Biology (LFBio), Center for Cell-Based Therapy (CTC), Regional Blood Center of Ribeirão Preto, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, SP, CEP: 14051-140, Brazil.,Department of Genetics and Internal Medicine, Ribeirao Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, SP, Brazil
| | - Sarah Blima Paulino Leite
- Laboratory of Functional Biology (LFBio), Center for Cell-Based Therapy (CTC), Regional Blood Center of Ribeirão Preto, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, SP, CEP: 14051-140, Brazil.,Department of Genetics and Internal Medicine, Ribeirao Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, SP, Brazil
| | - Danuta Sastre
- Laboratory of Functional Biology (LFBio), Center for Cell-Based Therapy (CTC), Regional Blood Center of Ribeirão Preto, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, SP, CEP: 14051-140, Brazil
| | - Hudson Lenormando de Oliveira Bezerra
- Laboratory of Functional Biology (LFBio), Center for Cell-Based Therapy (CTC), Regional Blood Center of Ribeirão Preto, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, SP, CEP: 14051-140, Brazil.,Department of Genetics and Internal Medicine, Ribeirao Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, SP, Brazil
| | - Bruno Sangiorgi
- Laboratory of Functional Biology (LFBio), Center for Cell-Based Therapy (CTC), Regional Blood Center of Ribeirão Preto, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, SP, CEP: 14051-140, Brazil.,Department of Genetics and Internal Medicine, Ribeirao Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, SP, Brazil
| | - Amanda Cristina Corveloni
- Laboratory of Functional Biology (LFBio), Center for Cell-Based Therapy (CTC), Regional Blood Center of Ribeirão Preto, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, SP, CEP: 14051-140, Brazil.,Department of Genetics and Internal Medicine, Ribeirao Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, SP, Brazil
| | - Carolina Hassibe Thomé
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, Brazil
| | - Vitor Marcel Faça
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, Brazil
| | - Dimas Tadeu Covas
- Laboratory of Functional Biology (LFBio), Center for Cell-Based Therapy (CTC), Regional Blood Center of Ribeirão Preto, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, SP, CEP: 14051-140, Brazil.,Department of Genetics and Internal Medicine, Ribeirao Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, SP, Brazil
| | - Marco Antônio Zago
- Laboratory of Functional Biology (LFBio), Center for Cell-Based Therapy (CTC), Regional Blood Center of Ribeirão Preto, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, SP, CEP: 14051-140, Brazil.,Department of Genetics and Internal Medicine, Ribeirao Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, SP, Brazil
| | - Mauro Giacca
- Molecular Medicine Laboratory, International Centre for Genetic and Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Miguel Mano
- Molecular Medicine Laboratory, International Centre for Genetic and Engineering and Biotechnology (ICGEB), Trieste, Italy.,Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal
| | - Rodrigo Alexandre Panepucci
- Laboratory of Functional Biology (LFBio), Center for Cell-Based Therapy (CTC), Regional Blood Center of Ribeirão Preto, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, SP, CEP: 14051-140, Brazil. .,Department of Genetics and Internal Medicine, Ribeirao Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, SP, Brazil.
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25
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Apicella C, Ruano CSM, Méhats C, Miralles F, Vaiman D. The Role of Epigenetics in Placental Development and the Etiology of Preeclampsia. Int J Mol Sci 2019; 20:ijms20112837. [PMID: 31212604 PMCID: PMC6600551 DOI: 10.3390/ijms20112837] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/03/2019] [Accepted: 06/03/2019] [Indexed: 12/12/2022] Open
Abstract
In this review, we comprehensively present the function of epigenetic regulations in normal placental development as well as in a prominent disease of placental origin, preeclampsia (PE). We describe current progress concerning the impact of DNA methylation, non-coding RNA (with a special emphasis on long non-coding RNA (lncRNA) and microRNA (miRNA)) and more marginally histone post-translational modifications, in the processes leading to normal and abnormal placental function. We also explore the potential use of epigenetic marks circulating in the maternal blood flow as putative biomarkers able to prognosticate the onset of PE, as well as classifying it according to its severity. The correlation between epigenetic marks and impacts on gene expression is systematically evaluated for the different epigenetic marks analyzed.
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Affiliation(s)
- Clara Apicella
- Institut Cochin, U1016 INSERM, UMR8104 CNRS, Université Paris Descartes, 24 rue du faubourg St Jacques, 75014 Paris, France.
| | - Camino S M Ruano
- Institut Cochin, U1016 INSERM, UMR8104 CNRS, Université Paris Descartes, 24 rue du faubourg St Jacques, 75014 Paris, France.
| | - Céline Méhats
- Institut Cochin, U1016 INSERM, UMR8104 CNRS, Université Paris Descartes, 24 rue du faubourg St Jacques, 75014 Paris, France.
| | - Francisco Miralles
- Institut Cochin, U1016 INSERM, UMR8104 CNRS, Université Paris Descartes, 24 rue du faubourg St Jacques, 75014 Paris, France.
| | - Daniel Vaiman
- Institut Cochin, U1016 INSERM, UMR8104 CNRS, Université Paris Descartes, 24 rue du faubourg St Jacques, 75014 Paris, France.
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26
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Vilela-Salgueiro B, Barros-Silva D, Lobo J, Costa AL, Guimarães R, Cantante M, Lopes P, Braga I, Oliveira J, Henrique R, Jerónimo C. Germ cell tumour subtypes display differential expression of microRNA371a-3p. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0338. [PMID: 29685967 DOI: 10.1098/rstb.2017.0338] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2018] [Indexed: 12/15/2022] Open
Abstract
Testicular germ cell tumours (TGCTs) are a heterogeneous group of neoplasms, mostly affecting young men. Curability rates are high and adequate treatment relies on careful and accurate pathological and clinical assessment. Indeed, TGCTs' histopathological subtyping is critical for adequate therapeutic decision. Considering the limitation of currently available serum biomarkers, novel candidates have been proposed, most notably miR-371a-3p, which outperformed classical serum markers, but no detailed information concerning TGCT subtype was available. Thus, we carried out evaluation of miR-371a-3p expression levels among TGCT subtypes using a consecutive cohort of tissue samples. MiR-371a-3p discriminated TGCTs from control tissues with high sensitivity and specificity (AUC = 0.99). Furthermore, seminomas displayed higher miR-371a-3p expression levels compared to non-seminomatous TGCTs, which also showed significant differences among them. Nonetheless, prepubertal TGCTs depicted lower miR-371a-3p expression levels than postpubertal TGCTs. Globally, miR-371a-3p expression levels decreased in parallel with progressive cell differentiation. We concluded that miR-371a-3p is TGCTs-specific and it might be clinically useful for early detection and disease monitoring.This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'.
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Affiliation(s)
- Bárbara Vilela-Salgueiro
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de almeida, 4200-072, Porto, Portugal
| | - Daniela Barros-Silva
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de almeida, 4200-072, Porto, Portugal.,Master in Oncology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira n.° 228, 4050-313, Porto, Portugal
| | - João Lobo
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de almeida, 4200-072, Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de almeida, 4200-072, Porto, Portugal.,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira n.° 228, 4050-313, Porto, Portugal
| | - Ana Laura Costa
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de almeida, 4200-072, Porto, Portugal.,Master in Oncology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira n.° 228, 4050-313, Porto, Portugal
| | - Rita Guimarães
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de almeida, 4200-072, Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de almeida, 4200-072, Porto, Portugal
| | - Mariana Cantante
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de almeida, 4200-072, Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de almeida, 4200-072, Porto, Portugal
| | - Paula Lopes
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de almeida, 4200-072, Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de almeida, 4200-072, Porto, Portugal
| | - Isaac Braga
- Department of Urology, Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de almeida, 4200-072, Porto, Portugal
| | - Jorge Oliveira
- Department of Urology, Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de almeida, 4200-072, Porto, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de almeida, 4200-072, Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de almeida, 4200-072, Porto, Portugal.,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira n.° 228, 4050-313, Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de almeida, 4200-072, Porto, Portugal .,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira n.° 228, 4050-313, Porto, Portugal
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27
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Macrin D, Alghadeer A, Zhao YT, Miklas JW, Hussein AM, Detraux D, Robitaille AM, Madan A, Moon RT, Wang Y, Devi A, Mathieu J, Ruohola-Baker H. Metabolism as an early predictor of DPSCs aging. Sci Rep 2019; 9:2195. [PMID: 30778087 PMCID: PMC6379364 DOI: 10.1038/s41598-018-37489-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 11/30/2018] [Indexed: 02/07/2023] Open
Abstract
Tissue resident adult stem cells are known to participate in tissue regeneration and repair that follows cell turnover, or injury. It has been well established that aging impedes the regeneration capabilities at the cellular level, but it is not clear if the different onset of stem cell aging between individuals can be predicted or prevented at an earlier stage. Here we studied the dental pulp stem cells (DPSCs), a population of adult stem cells that is known to participate in the repair of an injured tooth, and its properties can be affected by aging. The dental pulp from third molars of a diverse patient group were surgically extracted, generating cells that had a high percentage of mesenchymal stem cell markers CD29, CD44, CD146 and Stro1 and had the ability to differentiate into osteo/odontogenic and adipogenic lineages. Through RNA seq and qPCR analysis we identified homeobox protein, Barx1, as a marker for DPSCs. Furthermore, using high throughput transcriptomic and proteomic analysis we identified markers for DPSC populations with accelerated replicative senescence. In particular, we show that the transforming growth factor-beta (TGF-β) pathway and the cytoskeletal proteins are upregulated in rapid aging DPSCs, indicating a loss of stem cell characteristics and spontaneous initiation of terminal differentiation. Importantly, using metabolic flux analysis, we identified a metabolic signature for the rapid aging DPSCs, prior to manifestation of senescence phenotypes. This metabolic signature therefore can be used to predict the onset of replicative senescence. Hence, the present study identifies Barx1 as a DPSCs marker and dissects the first predictive metabolic signature for DPSCs aging.
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Affiliation(s)
- Dannie Macrin
- Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA, 98195, USA.,Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA, 98109, USA.,Department of Genetic Engineering, SRM Institute of Science and Technology, Chennai, 603203, India
| | - Ammar Alghadeer
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA, 98109, USA.,Department of Oral Health Sciences, University of Washington, School of Dentistry, Seattle, WA, 98109, USA.,Department of Biomedical Dental Sciences, Imam Abdulrahman bin Faisal University, College of Dentistry, Dammam, 31441, Saudi Arabia
| | - Yan Ting Zhao
- Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA, 98195, USA.,Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA, 98109, USA.,Department of Oral Health Sciences, University of Washington, School of Dentistry, Seattle, WA, 98109, USA
| | - Jason W Miklas
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA, 98109, USA.,Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Abdiasis M Hussein
- Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA, 98195, USA.,Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA, 98109, USA
| | - Damien Detraux
- Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA, 98195, USA.,Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA, 98109, USA
| | - Aaron M Robitaille
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA, 98109, USA.,Department of Pharmacology, University of Washington, Seattle, WA, 98109, USA
| | - Anup Madan
- Covance Genomics Laboratory, Redmond, WA, 98052, USA
| | - Randall T Moon
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA, 98109, USA.,Department of Pharmacology, University of Washington, Seattle, WA, 98109, USA
| | - Yuliang Wang
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA, 98109, USA.,Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Arikketh Devi
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA, 98109, USA.,Department of Genetic Engineering, SRM Institute of Science and Technology, Chennai, 603203, India
| | - Julie Mathieu
- Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA, 98195, USA.,Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA, 98109, USA.,Department of Comparative Medicine, University of Washington, School of Medicine, Seattle, WA, 98195, USA
| | - Hannele Ruohola-Baker
- Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA, 98195, USA. .,Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA, 98109, USA. .,Department of Oral Health Sciences, University of Washington, School of Dentistry, Seattle, WA, 98109, USA. .,Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA.
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28
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Panepucci RA, de Souza Lima IM. Arrayed functional genetic screenings in pluripotency reprogramming and differentiation. Stem Cell Res Ther 2019; 10:24. [PMID: 30635073 PMCID: PMC6330485 DOI: 10.1186/s13287-018-1124-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Thoroughly understanding the molecular mechanisms responsible for the biological properties of pluripotent stem cells, as well as for the processes involved in reprograming, differentiation, and transition between Naïve and Primed pluripotent states, is of great interest in basic and applied research. Although pluripotent cells have been extensively characterized in terms of their transcriptome and miRNome, a comprehensive understanding of how these gene products specifically impact their biology, depends on gain- or loss-of-function experimental approaches capable to systematically interrogate their function. We review all studies carried up to date that used arrayed screening approaches to explore the function of these genetic elements on those biological contexts, using focused or genome-wide genetic libraries. We further discuss the limitations and advantages of approaches based on assays with population-level primary readouts, derived from single-parameter plate readers, or cell-level primary readouts, obtained using multiparametric flow cytometry or quantitative fluorescence microscopy (i.e., high-content screening). Finally, we discuss technical limitation and future perspectives, highlighting how the integration of screening data may lead to major advances in the field of stem cell research and therapy.
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Affiliation(s)
- Rodrigo Alexandre Panepucci
- Laboratory of Functional Biology (LFBio), Center for Cell-Based Therapy (CTC), Regional Blood Center of Ribeirão Preto, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, SP CEP: 14051-140 Brazil
- Department of Genetics, Ribeirao Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, SP Brazil
| | - Ildercílio Mota de Souza Lima
- Laboratory of Functional Biology (LFBio), Center for Cell-Based Therapy (CTC), Regional Blood Center of Ribeirão Preto, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, SP CEP: 14051-140 Brazil
- Department of Genetics, Ribeirao Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, SP Brazil
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29
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Chen EYY, Chen JS, Ying SY. The microRNA and the perspectives of miR-302. Heliyon 2019; 5:e01167. [PMID: 30723835 PMCID: PMC6351428 DOI: 10.1016/j.heliyon.2019.e01167] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 12/18/2018] [Accepted: 01/22/2019] [Indexed: 12/24/2022] Open
Abstract
MiRNAs are naturally occurring, small, non-coding RNA molecules that post-transcriptionally regulate the expression of a large number of genes involved in various biological processes, either through mRNA degradation or through translation inhibition. MiRNAs play important roles in many aspects of physiology and pathology throughout the body, particularly in cancer, which have made miRNAs attractive tools and targets for translational research. The types of non-coding RNAs, biogenesis of miRNAs, circulating miRNAs, and direct delivery of miRNA were briefly reviewed. As a case of point, the role and perspective of miR-302, a family of ES-specific miRNA, on cancer, iPSCs, heart disease were presented.
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Affiliation(s)
- Emily Yen Yu Chen
- Department of Integrative Anatomical Sciences, Keck School of Medicine, BMT-403, University of Southern California, 1333 San Pablo Street, Los Angeles, CA 90033, USA
- WJWU & LYNN Institute for Stem Cell Research, Santa Fe Springs, CA 90670, USA
| | - Jack S. Chen
- WJWU & LYNN Institute for Stem Cell Research, Santa Fe Springs, CA 90670, USA
| | - Shao-Yao Ying
- Department of Integrative Anatomical Sciences, Keck School of Medicine, BMT-403, University of Southern California, 1333 San Pablo Street, Los Angeles, CA 90033, USA
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30
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Vanhauwaert S, Decaesteker B, De Brouwer S, Leonelli C, Durinck K, Mestdagh P, Vandesompele J, Sermon K, Denecker G, Van Neste C, Speleman F, De Preter K. In silico discovery of a FOXM1 driven embryonal signaling pathway in therapy resistant neuroblastoma tumors. Sci Rep 2018; 8:17468. [PMID: 30504901 PMCID: PMC6269481 DOI: 10.1038/s41598-018-35868-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 11/09/2018] [Indexed: 12/21/2022] Open
Abstract
Chemotherapy resistance is responsible for high mortality rates in neuroblastoma. MYCN, an oncogenic driver in neuroblastoma, controls pluripotency genes including LIN28B. We hypothesized that enhanced embryonic stem cell (ESC) gene regulatory programs could mark tumors with high pluripotency capacity and subsequently increased risk for therapy failure. An ESC miRNA signature was established based on publicly available data. In addition, an ESC mRNA signature was generated including the 500 protein coding genes with the highest positive expression correlation with the ESC miRNA signature score in 200 neuroblastomas. High ESC m(i)RNA expression signature scores were significantly correlated with poor neuroblastoma patient outcome specifically in the subgroup of MYCN amplified tumors and stage 4 nonamplified tumors. Further data-mining identified FOXM1, as the major predicted driver of this ESC signature, controlling a large set of genes implicated in cell cycle control and DNA damage response. Of further interest, re-analysis of published data showed that MYCN transcriptionally activates FOXM1 in neuroblastoma cells. In conclusion, a novel ESC m(i)RNA signature stratifies neuroblastomas with poor prognosis, enabling the identification of therapy-resistant tumors. The finding that this signature is strongly FOXM1 driven, warrants for drug design targeted at FOXM1 or key components controlling this pathway.
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Affiliation(s)
- Suzanne Vanhauwaert
- Center for Medical Genetics (CMGG), Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Bieke Decaesteker
- Center for Medical Genetics (CMGG), Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Sara De Brouwer
- Center for Medical Genetics (CMGG), Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Carina Leonelli
- Center for Medical Genetics (CMGG), Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Kaat Durinck
- Center for Medical Genetics (CMGG), Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Pieter Mestdagh
- Center for Medical Genetics (CMGG), Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Jo Vandesompele
- Center for Medical Genetics (CMGG), Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Karen Sermon
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Brussels, Belgium
| | - Geertrui Denecker
- Center for Medical Genetics (CMGG), Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Christophe Van Neste
- Center for Medical Genetics (CMGG), Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Frank Speleman
- Center for Medical Genetics (CMGG), Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Katleen De Preter
- Center for Medical Genetics (CMGG), Ghent University, Ghent, Belgium. .,Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium.
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31
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Vahidian F, Mohammadi H, Ali-Hasanzadeh M, Derakhshani A, Mostaan M, Hemmatzadeh M, Baradaran B. MicroRNAs and breast cancer stem cells: Potential role in breast cancer therapy. J Cell Physiol 2018; 234:3294-3306. [PMID: 30362508 DOI: 10.1002/jcp.27246] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 07/24/2018] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs) can control cancer and cancer stem cells (CSCs), and this topic has drawn immense attention recently. Stem cells are a tiny population of a bulk of tumor cells that have enormous potential in expansion and metastasis of the tumor. miRNA have a crucial role in the management of the function of stem cells. This role is to either promote or suppress the tumor. In this review, we investigated the function and different characteristics of CSCs and function of the miRNAs that are related to them. We also demonstrated the role and efficacy of these miRNAs in breast cancer and breast cancer stem cells (BCSC). Eventually, we revealed the metastasis, tumor formation, and their role in the apoptosis process. Also, the therapeutic potential of miRNA as an effective method for the treatment of BCSC was described. Extensive research is required to investigate the employment or suppression of these miRNAs for therapeutics approached in different cancers in the future.
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Affiliation(s)
- Fatemeh Vahidian
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Immunology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.,Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hamed Mohammadi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Immunology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Ali-Hasanzadeh
- Department of Immunology, School of Medicine, Jiroft University of Medical Sciences, Jiroft, Iran
| | - Afshin Derakhshani
- Department of Immunology, Birjand University of Medical Sciences, Birjand, Iran.,Student Research Committee, Birjand University of Medical Sciences, Birjand, Iran
| | - Masoud Mostaan
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Islamic Azad university, Tabriz, Iran
| | - Maryam Hemmatzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Immunology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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32
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Ishikawa D, Diekmann U, Fiedler J, Just A, Thum T, Lenzen S, Naujok O. miRNome Profiling of Purified Endoderm and Mesoderm Differentiated from hESCs Reveals Functions of miR-483-3p and miR-1263 for Cell-Fate Decisions. Stem Cell Reports 2018; 9:1588-1603. [PMID: 29141233 PMCID: PMC5688239 DOI: 10.1016/j.stemcr.2017.10.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 10/12/2017] [Accepted: 10/12/2017] [Indexed: 12/20/2022] Open
Abstract
Pluripotent stem cells hold great promise for regenerative medicine since they can differentiate into all somatic cells. MicroRNAs (miRNAs) could be important for the regulation of these cell-fate decisions. Profiling of miRNAs revealed 19 differentially expressed miRNAs in the endoderm and 29 in the mesoderm when analyzing FACS-purified cells derived from human embryonic stem cells. The mesodermal-enriched miR-483-3p was identified as an important regulator for the generation of mesodermal PDGFRA+ paraxial cells. Repression of its target PGAM1 significantly increased the number of PDGFRA+ cells. Furthermore, miR-483-3p, miR-199a-3p, and miR-214-3p might also have functions for the mesodermal progenitors. The endoderm-specific miR-489-3p and miR-1263 accelerated and increased endoderm differentiation upon overexpression. KLF4 was identified as a target of miR-1263. RNAi-mediated downregulation of KLF4 partially mimicked miR-1263 overexpression. Thus, the effects of this miRNA were mediated by facilitating differentiation through destabilization of pluripotency along with other not yet defined targets.
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Affiliation(s)
- Daichi Ishikawa
- Institute of Clinical Biochemistry, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany; Department of Surgery, Tokushima University, 3-18-15, Kuramoto, Tokushima 770-8503, Japan
| | - Ulf Diekmann
- Institute of Clinical Biochemistry, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Jan Fiedler
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Annette Just
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany; National Heart and Lung Institute, Imperial College London, Sydney Street, London SW3 6NP, UK
| | - Sigurd Lenzen
- Institute of Clinical Biochemistry, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Ortwin Naujok
- Institute of Clinical Biochemistry, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany.
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33
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Li L, Miu KK, Gu S, Cheung HH, Chan WY. Comparison of multi-lineage differentiation of hiPSCs reveals novel miRNAs that regulate lineage specification. Sci Rep 2018; 8:9630. [PMID: 29941943 PMCID: PMC6018499 DOI: 10.1038/s41598-018-27719-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 06/07/2018] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) are known to be crucial players in governing the differentiation of human induced pluripotent stem cells (hiPSCs). Despite their utter importance, identifying key lineage specifiers among the myriads of expressed miRNAs remains challenging. We believe that the current practice in mining miRNA specifiers via delineating dynamic fold-changes only is inadequate. Our study, therefore, provides evidence to pronounce "lineage specificity" as another important attribute to qualify for these lineage specifiers. Adopted hiPSCs were differentiated into representative lineages (hepatic, nephric and neuronal) over all three germ layers whilst the depicted miRNA expression changes compiled into an integrated atlas. We demonstrated inter-lineage analysis shall aid in the identification of key miRNAs with lineage-specificity, while these shortlisted candidates were collectively known as "lineage-specific miRNAs". Subsequently, we followed through the fold-changes along differentiation via computational analysis to identify miR-192 and miR-372-3p, respectively, as representative candidate key miRNAs for the hepatic and nephric lineages. Indeed, functional characterization validated that miR-192 and miR-372-3p regulate lineage differentiation via modulation of the expressions of lineage-specific genes. In summary, our presented miRNA atlas is a resourceful ore for the mining of key miRNAs responsible for lineage specification.
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Affiliation(s)
- Lu Li
- CUHK-CAS GIBH Joint Research Laboratory on Stem Cell and Regenerative Medicine, School of Biomedical Sciences, the Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR
- School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Kai-Kei Miu
- CUHK-CAS GIBH Joint Research Laboratory on Stem Cell and Regenerative Medicine, School of Biomedical Sciences, the Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR
| | - Shen Gu
- CUHK-CAS GIBH Joint Research Laboratory on Stem Cell and Regenerative Medicine, School of Biomedical Sciences, the Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR
- M&H Genetics/Baylor Genetics Laboratories, Baylor College of Medicine, Houston, TX, USA
| | - Hoi-Hung Cheung
- CUHK-CAS GIBH Joint Research Laboratory on Stem Cell and Regenerative Medicine, School of Biomedical Sciences, the Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR.
| | - Wai-Yee Chan
- CUHK-CAS GIBH Joint Research Laboratory on Stem Cell and Regenerative Medicine, School of Biomedical Sciences, the Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR.
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34
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Chen TY, Lee SH, Dhar SS, Lee MG. Protein arginine methyltransferase 7-mediated microRNA-221 repression maintains Oct4, Nanog, and Sox2 levels in mouse embryonic stem cells. J Biol Chem 2018; 293:3925-3936. [PMID: 29378844 DOI: 10.1074/jbc.ra117.000425] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 01/09/2018] [Indexed: 11/06/2022] Open
Abstract
The stemness maintenance of embryonic stem cells (ESCs) requires pluripotency transcription factors, including Oct4, Nanog, and Sox2. We have previously reported that protein arginine methyltransferase 7 (PRMT7), an epigenetic modifier, is an essential pluripotency factor that maintains the stemness of mouse ESCs, at least in part, by down-regulating the expression of the anti-stemness microRNA (miRNA) miR-24-2. To gain greater insight into the molecular basis underlying PRMT7-mediated maintenance of mouse ESC stemness, we searched for new PRMT7-down-regulated anti-stemness miRNAs. Here, we show that miR-221 gene-encoded miR-221-3p and miR-221-5p are anti-stemness miRNAs whose expression levels in mouse ESCs are directly repressed by PRMT7. Notably, both miR-221-3p and miR-221-5p targeted the 3' untranslated regions of mRNA transcripts of the major pluripotency factors Oct4, Nanog, and Sox2 to antagonize mouse ESC stemness. Moreover, miR-221-5p silenced also the expression of its own transcriptional repressor PRMT7. Transfection of miR-221-3p and miR-221-5p mimics induced spontaneous differentiation of mouse ESCs. CRISPR-mediated deletion of the miR-221 gene, as well as specific antisense inhibitors of miR-221-3p and miR-221-5p, inhibited the spontaneous differentiation of PRMT7-depleted mouse ESCs. Taken together, these findings reveal that the PRMT7-mediated repression of miR-221-3p and miR-221-5p expression plays a critical role in maintaining mouse ESC stemness. Our results also establish miR-221-3p and miR-221-5p as anti-stemness miRNAs that target Oct4, Nanog, and Sox2 mRNAs in mouse ESCs.
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Affiliation(s)
- Tsai-Yu Chen
- From the Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030 and.,Cancer Biology Program, The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, Texas 77030
| | - Sung-Hun Lee
- From the Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030 and
| | - Shilpa S Dhar
- From the Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030 and
| | - Min Gyu Lee
- From the Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030 and .,Cancer Biology Program, The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, Texas 77030
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35
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Abstract
MicroRNAs (miRNAs), widely distributed, small regulatory RNA genes, target both messenger RNA (mRNA) degradation and suppression of protein translation based on sequence complementarity between the miRNA and its targeted mRNA. Different names have been used to describe various types of miRNA. During evolution, RNA retroviruses or transgenes invaded the eukaryotic genome and were inserted itself in the noncoding regions of DNA, conceivably acting as transposon-like jumping genes, providing defense from viral invasion and fine-tuning of gene expression as a secondary level of gene modulation in eukaryotes. When a transposon is inserted in the intron, it becomes an intronic miRNA, taking advantage of the protein synthesis machinery, i.e., mRNA transcription and splicing, as a means for processing and maturation. MiRNAs have been found to play an important, but not life-threatening, role in embryonic development. They might play a pivotal role in diverse biological systems in various organisms, facilitating a quick response and accurate plotting of body physiology and structures. Based on these unique properties, manufactured intronic miRNAs have been developed for in vitro evaluation of gene function, in vivo gene therapy, and generation of transgenic animal models. The biogenesis of miRNAs, circulating miRNAs, miRNAs and cancer, iPSCs, and heart disease are presented in this chapter, highlighting some recent studies on these topics.
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Affiliation(s)
- Shao-Yao Ying
- Department of Integrative Anatomical Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - Donald C Chang
- WJWU & LYNN Institute for Stem Cell Research, Santa Fe Springs, CA, USA
| | - Shi-Lung Lin
- Division of Regenerative Medicine, WJWU & LYNN Institute for Stem Cell Research, Santa Fe Springs, CA, USA
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36
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Nguyen PNN, Choo KB, Huang CJ, Sugii S, Cheong SK, Kamarul T. miR-524-5p of the primate-specific C19MC miRNA cluster targets TP53IPN1- and EMT-associated genes to regulate cellular reprogramming. Stem Cell Res Ther 2017; 8:214. [PMID: 28962647 PMCID: PMC5622517 DOI: 10.1186/s13287-017-0666-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 08/29/2017] [Accepted: 09/12/2017] [Indexed: 12/26/2022] Open
Abstract
Background Introduction of the transcription factors Oct4, Sox2, Klf4, and c-Myc (OSKM) is able to ‘reprogram’ somatic cells to become induced pluripotent stem cells (iPSCs). Several microRNAs (miRNAs) are known to enhance reprogramming efficiency when co-expressed with the OSKM factors. The primate-specific chromosome 19 miRNA cluster (C19MC) is essential in primate reproduction, development, and differentiation. miR-524-5p, a C19MC member, is highly homologous to the reprogramming miR-520d-5p; we also reported that miR-524-5p was expressed in iPSCs but not mesenchymal stem cells (MSCs). This study aimed to elucidate possible contributions of miR-524-5p to the reprogramming process. Methods A miR-524-5p precursor was introduced into human fibroblast HFF-1 in the presence of OSKM, and the relative number of embryonic stem cell (ESC)-like colonies that stained positively with alkaline phosphatase (AP) and Nanog were quantified to determine reprogramming efficiency. A miR-524-5p mimic was transfected to MSCs to investigate the effects of miR-524-5p on TP53INP1, ZEB2, and SMAD4 expression by real-time polymerase chain reaction (PCR) and Western blot. Direct gene targeting was confirmed by luciferase activity. A phylogenetic tree of TP53INP1 was constructed by the Clustal method. Contribution of miR-524-5p to cell proliferation and apoptosis was examined by cell counts, BrdU, MTT, and cell death assays, and pluripotency gene expression by real-time PCR. Results Co-expressing the miR-524 precursor with OSKM resulted in a two-fold significant increase in the number of AP- and Nanog-positive ESC-like colonies, indicating a role for miR-524-5p in reprogramming. The putative target, TP53INP1, showed an inverse expression relationship with miR-524-5p; direct TP53INP1 targeting was confirmed in luciferase assays. miR-524-5p-induced TP53INP1 downregulation enhanced cell proliferation, suppressed apoptosis, and upregulated the expression of pluripotency genes, all of which are critical early events of the reprogramming process. Interestingly, the TP53INP1 gene may have co-evolved late with the primate-specific miR-524-5p. miR-524-5p also promoted mesenchymal-to-epithelial transition (MET), a required initial event of reprogramming, by directly targeting the epithelial-to-mesenchymal transition (EMT)-related genes, ZEB2 and SMAD4. Conclusions Via targeting TP53INP1, ZEB2, and SMAD4, miR-524-5p contributes to the early stage of inducing pluripotency by promoting cell proliferation, inhibiting apoptosis, upregulating expression of pluripotency genes, and enhancing MET. Other C19MC miRNAs may have similar reprogramming functions. Electronic supplementary material The online version of this article (doi:10.1186/s13287-017-0666-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Phan Nguyen Nhi Nguyen
- Centre for Stem Cell Research, Universiti Tunku Abdul Rahman, Sungai Long, Kajang, Selangor DE, Malaysia.,Department of Preclinical Sciences, Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Sungai Long Campus, Bandar Sungai Long, Cheras, 43000, Kajang, Selangor DE, Malaysia
| | - Kong Bung Choo
- Centre for Stem Cell Research, Universiti Tunku Abdul Rahman, Sungai Long, Kajang, Selangor DE, Malaysia. .,Department of Preclinical Sciences, Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Sungai Long Campus, Bandar Sungai Long, Cheras, 43000, Kajang, Selangor DE, Malaysia.
| | - Chiu-Jung Huang
- Department of Animal Science, Chinese Culture University, Taipei, Taiwan.,Graduate Institute of Biotechnology, Chinese Culture University, Taipei, Taiwan
| | - Shigeki Sugii
- Singapore BioImaging Consortium A*Star, Singapore, Singapore.,Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Soon Keng Cheong
- Centre for Stem Cell Research, Universiti Tunku Abdul Rahman, Sungai Long, Kajang, Selangor DE, Malaysia.,Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Sungai Long, Kajang, Selangor DE, Malaysia
| | - Tunku Kamarul
- Tissue Engineering Group, National Orthopaedic Centre of Excellence for Research and Learning, Kuala Lumpur, Malaysia.,Department of Orthopaedic Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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37
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Hashemzadeh MR. Role of micro RNAs in stem cells, cardiac differentiation and cardiovascular diseases. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.04.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Chen H, Zhang Z, Lu Y, Song K, Liu X, Xia F, Sun W. Downregulation of ULK1 by microRNA-372 inhibits the survival of human pancreatic adenocarcinoma cells. Cancer Sci 2017; 108:1811-1819. [PMID: 28677209 PMCID: PMC5581518 DOI: 10.1111/cas.13315] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 06/28/2017] [Accepted: 07/02/2017] [Indexed: 12/12/2022] Open
Abstract
Dysregulation of microRNA (miRNA) expression in various cancers and their role in cancer progression is well documented. The purpose of this study was to investigate the biological role of miR‐372 in human pancreatic adenocarcinoma (HPAC). We collected 20 pairs of HPAC tissues and adjacent non‐cancerous tissues to detect miR‐372 expression levels. We transfected BXPC‐3 and PANC‐1 cells with miR‐372 inhibitor/mimics to study their effect on cell proliferation, apoptosis, invasion, migration and autophagy. In addition, miR‐372 mimics and a tumor protein UNC51‐like kinase 1 (ULK1) siRNA were co‐transfected into BXPC‐3 and PANC‐1 cells to explore the mechanism of miR‐372 and ULK1 on HPAC tumorigenesis. We found that the expression of miR‐372 was markedly downregulated in HPAC cells compared to adjacent normal tissues. Furthermore, functional assays showed that miR‐372 inhibited cell proliferation, invasion, migration and autophagy in BXPC‐3 and PANC‐1 cells. An inverse correlation between miR‐372 expression and ULK1 expression was observed in HPAC tissues. Downregulation of ULK1 inhibited the overexpression effects of miR‐372, and upregulation of ULK1 reversed the effects of overexpressed miR‐372. Finally, we found that silencing ULK1 or inhibiting autophagy partly rescued the effects of miR‐372 knockdown in HPAC cells, which may explain the influence of miR‐372/ULK1 in HPAC development. Taken together, these results revealed a significant role of the miR‐372/ULK1 axis in suppressing HPAC cell proliferation, migration, invasion and autophagy.
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Affiliation(s)
- Hongxi Chen
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Zhipeng Zhang
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Yebin Lu
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Kun Song
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Xiwu Liu
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Fada Xia
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Weijia Sun
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
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39
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Zhou W, Yuan T, Gao Y, Yin P, Liu W, Pan C, Liu Y, Yu X. IL-1β-induces NF-κB and upregulates microRNA-372 to inhibit spinal cord injury recovery. J Neurophysiol 2017; 117:2282-2291. [PMID: 28298306 DOI: 10.1152/jn.00936.2016] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 01/27/2017] [Accepted: 03/10/2017] [Indexed: 12/14/2022] Open
Abstract
Excessive inflammation including IL-1β-initiated signaling is among the earlies reactions that can cause neuronal damage following spinal cord injury (SCI). It has been suggested that microRNAs may participate in stem cell repair to facilitate functional recovery following SCI. In this study we have shown that in cultured human neural stem cells (hNSC), IL-1β reduced the expression of both KIF3B (kinesin family member 3B) and NOSIP (nitric oxide synthase-interacting protein), two key modulators for restricting inflammation and promoting neuronal regeneration. The induction of microRNA-372 (miR-372) by IL-1β is specifically responsible for the inhibition of KIF3B and NOSIP. The 3'-untranslated regions (UTRs) of both KIF3B and NOSIP contain targeting sequences to miR-372 that directly inhibit their expression. Moreover, we found that the expression of miR-372 was stimulated in hNSC by IL-1β through an NF-κB binding site at its promoter region. Finally, stable overexpression of miR-372 inhibitor in hNSC rescued the IL-1β-induced impairment as shown by significant improvements in tissue water content, myeloperoxidase activity, and behavioral assessments in SCI rats. These findings suggest a critical role of miR-372 in inflammatory signaling and pinpoint a novel target for the treatment of acute SCI.NEW & NOTEWORTHY Our data demonstrate that IL-1β can impair the functional recovery of neural stem cell transplant therapy for spinal cord injury (SCI) treatment in rats. This effect is dependent on microRNA-372 (miR-372)-dependent gene repression of KIF3B and NOSIP. Therefore, specific knockdown of miR-372 may provide benefits for SCI treatments.
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Affiliation(s)
- Wei Zhou
- Department of Orthopaedic Surgery, Shanghai Sixth People's Hospital East Affiliated to Shanghai University of Medicine & Health Sciences, Shanghai, People's Republic of China.,Department of Orthopaedic Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, People's Republic of China; and
| | - Tongzhou Yuan
- Department of Orthopaedic Surgery, Second Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Youshui Gao
- Department of Orthopaedic Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, People's Republic of China; and
| | - Peipei Yin
- Department of Orthopaedic Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, People's Republic of China; and
| | - Wei Liu
- Department of Orthopaedic Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, People's Republic of China; and
| | - Chenhao Pan
- Department of Orthopaedic Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, People's Republic of China; and
| | - Yingjie Liu
- Department of Orthopaedic Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, People's Republic of China; and
| | - Xiaowei Yu
- Department of Orthopaedic Surgery, Shanghai Sixth People's Hospital East Affiliated to Shanghai University of Medicine & Health Sciences, Shanghai, People's Republic of China; .,Department of Orthopaedic Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, People's Republic of China; and
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Mathai J, Mittal SPK, Alam A, Ranade P, Mogare D, Patel S, Saxena S, Ghorai S, Kulkarni AP, Chattopadhyay S. SMAR1 binds to T(C/G) repeat and inhibits tumor progression by regulating miR-371-373 cluster. Sci Rep 2016; 6:33779. [PMID: 27671416 PMCID: PMC5037395 DOI: 10.1038/srep33779] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 08/18/2016] [Indexed: 12/19/2022] Open
Abstract
Chromatin architecture and dynamics are regulated by various histone and non-histone proteins. The matrix attachment region binding proteins (MARBPs) play a central role in chromatin organization and function through numerous regulatory proteins. In the present study, we demonstrate that nuclear matrix protein SMAR1 orchestrates global gene regulation as determined by massively parallel ChIP-sequencing. The study revealed that SMAR1 binds to T(C/G) repeat and targets genes involved in diverse biological pathways. We observe that SMAR1 binds and targets distinctly different genes based on the availability of p53. Our data suggest that SMAR1 binds and regulates one of the imperative microRNA clusters in cancer and metastasis, miR-371-373. It negatively regulates miR-371-373 transcription as confirmed by SMAR1 overexpression and knockdown studies. Further, deletion studies indicate that a ~200 bp region in the miR-371-373 promoter is necessary for SMAR1 binding and transcriptional repression. Recruitment of HDAC1/mSin3A complex by SMAR1, concomitant with alteration of histone marks results in downregulation of the miRNA cluster. The regulation of miR-371-373 by SMAR1 inhibits breast cancer tumorigenesis and metastasis as determined by in vivo experiments. Overall, our study highlights the binding of SMAR1 to T(C/G) repeat and its role in cancer through miR-371-373.
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Affiliation(s)
- Jinumary Mathai
- Chromatin and Disease Biology Lab, National Centre for Cell Science, Savitribai Phule Pune University Campus, Ganeshkhind, Pune-411007, India
| | - Smriti P K Mittal
- Department of Zoology, Savitribai Phule Pune University Campus, Pune 411007, India
| | - Aftab Alam
- Chromatin and Disease Biology Lab, National Centre for Cell Science, Savitribai Phule Pune University Campus, Ganeshkhind, Pune-411007, India
| | - Payal Ranade
- Chromatin and Disease Biology Lab, National Centre for Cell Science, Savitribai Phule Pune University Campus, Ganeshkhind, Pune-411007, India
| | - Devraj Mogare
- Chromatin and Disease Biology Lab, National Centre for Cell Science, Savitribai Phule Pune University Campus, Ganeshkhind, Pune-411007, India
| | - Sonal Patel
- Chromatin and Disease Biology Lab, National Centre for Cell Science, Savitribai Phule Pune University Campus, Ganeshkhind, Pune-411007, India
| | - Smita Saxena
- Bioinformatics Centre, Savitribai Phule Pune University Campus, Pune 411007, India
| | - Suvankar Ghorai
- Chromatin and Disease Biology Lab, National Centre for Cell Science, Savitribai Phule Pune University Campus, Ganeshkhind, Pune-411007, India
| | - Abhijeet P Kulkarni
- Bioinformatics Centre, Savitribai Phule Pune University Campus, Pune 411007, India
| | - Samit Chattopadhyay
- Chromatin and Disease Biology Lab, National Centre for Cell Science, Savitribai Phule Pune University Campus, Ganeshkhind, Pune-411007, India
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Mature Let-7 miRNAs fine tune expression of LIN28B in pluripotent human embryonic stem cells. Stem Cell Res 2016; 17:498-503. [PMID: 27776272 DOI: 10.1016/j.scr.2016.09.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 08/22/2016] [Accepted: 09/22/2016] [Indexed: 01/02/2023] Open
Abstract
MicroRNAs (miRNA) are central regulators of diverse biological processes and are important in the regulation of stem cell self-renewal. One of the widely studied miRNA-protein regulators is the Lin28-Let-7 pair. In this study, we demonstrate that contrary to the well-established models of mouse ES cells (mESC) and transformed human cancer cells, the pluripotent state of human ES cells (hESC) involves expression of mature Let-7 family miRNAs with concurrent expression of all LIN28 proteins. We show that mature Let-7 miRNAs are regulated during hESC differentiation and have opposite expression profile with LIN28B. Moreover, mature Let-7 miRNAs fine tune the expression levels of LIN28B protein in pluripotent hESCs, whereas silencing of LIN28 proteins have no effect on mature Let-7 levels. These results bring novel information to the highly complex network of human pluripotency and suggest that maintenance of hESC pluripotency differs greatly from the mESCs in regard to LIN28-Let-7 regulation.
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42
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Dieckmann KP, Radtke A, Spiekermann M, Balks T, Matthies C, Becker P, Ruf C, Oing C, Oechsle K, Bokemeyer C, Hammel J, Melchior S, Wosniok W, Belge G. Serum Levels of MicroRNA miR-371a-3p: A Sensitive and Specific New Biomarker for Germ Cell Tumours. Eur Urol 2016; 71:213-220. [PMID: 27495845 DOI: 10.1016/j.eururo.2016.07.029] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 07/20/2016] [Indexed: 11/30/2022]
Abstract
BACKGROUND Clinical management of germ cell tumours (GCTs) relies on monitoring of serum tumour markers. However, the markers α-fetoprotein (AFP), the β-subunit of human chorionic gonadotropin (bHCG), and lactate dehydrogenase (LDH) are expressed in <60% of GCT cases. OBJECTIVE To test the utility of the microRNAs (miRNAs) miR-371a-3p, miR-372-3p, miR-373-3p, and miR-367-3p as sensitive and specific GCT serum biomarkers. DESIGN, SETTING, AND PARTICIPANTS Serum levels of miRNAs were measured in 166 consecutive patients with GCT before and after treatment and in 106 male controls. In the first 50 consecutive patients, all four miRNAs were measured. In the main study, only the most sensitive miRNA was further analysed. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS The specificity and sensitivity of the four miRNAs were studied using receiver operating characteristic curves. miRNA sensitivities were compared to those of classical markers. Statistical cross-comparisons of miRNA levels for GCT subgroups and controls were performed at various time points during treatment. RESULTS AND LIMITATIONS Overall, miR-371a-3p performed best, with 88.7% sensitivity (95% confidence interval [CI] 82.5-93.3%) and 93.4% specificity (95% CI 86.9-97.3%) and an area under the curve of 0.94, outperforming AFP, bHCG, and LDH (combined sensitivity 50%). According to Kernel density estimation, the sensitivity and specificity were 86.3% and 92.5%, respectively. miR-371a-3p levels dropped to normal after completion of treatment. The miRNA levels correlated with treatment failure and relapse. Teratoma did not express miR-371a-3p. CONCLUSIONS The miRNA miR-371a-3p is a specific and sensitive novel serum GCT biomarker that accurately correlates with disease activity. Validation of this test in a large-scale prospective study is needed. PATIENT SUMMARY: miR-371a-3p is a novel serum marker for germ cell tumours that is expressed by 88.7% of patients and thus is far more sensitive and specific than classical serum markers. It correlates with tumour burden and treatment results. Validation in a large patient cohort is needed.
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Affiliation(s)
| | - Arlo Radtke
- Centre for Human Genetics, University of Bremen, Bremen, Germany
| | | | - Thomas Balks
- Department of Urology, Albertinen Krankenhaus, Hamburg, Germany
| | - Cord Matthies
- Department of Urology, Bundeswehr Krankenhaus, Hamburg, Germany
| | - Pascal Becker
- Department of Urology, Bundeswehr Krankenhaus, Hamburg, Germany
| | - Christian Ruf
- Department of Urology, Bundeswehr Krankenhaus, Hamburg, Germany
| | - Christoph Oing
- Department of Medical Oncology, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Karin Oechsle
- Department of Medical Oncology, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Carsten Bokemeyer
- Department of Medical Oncology, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Johannes Hammel
- Department of Urology, Zentralklinikum Bremen, Bremen, Germany
| | | | - Werner Wosniok
- Institute of Statistics, University of Bremen, Bremen, Germany
| | - Gazanfer Belge
- Centre for Human Genetics, University of Bremen, Bremen, Germany
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Hysolli E, Tanaka Y, Su J, Kim KY, Zhong T, Janknecht R, Zhou XL, Geng L, Qiu C, Pan X, Jung YW, Cheng J, Lu J, Zhong M, Weissman SM, Park IH. Regulation of the DNA Methylation Landscape in Human Somatic Cell Reprogramming by the miR-29 Family. Stem Cell Reports 2016; 7:43-54. [PMID: 27373925 PMCID: PMC4945581 DOI: 10.1016/j.stemcr.2016.05.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Revised: 05/31/2016] [Accepted: 05/31/2016] [Indexed: 02/05/2023] Open
Abstract
Reprogramming to pluripotency after overexpression of OCT4, SOX2, KLF4, and MYC is accompanied by global genomic and epigenomic changes. Histone modification and DNA methylation states in induced pluripotent stem cells (iPSCs) have been shown to be highly similar to embryonic stem cells (ESCs). However, epigenetic differences still exist between iPSCs and ESCs. In particular, aberrant DNA methylation states found in iPSCs are a major concern when using iPSCs in a clinical setting. Thus, it is critical to find factors that regulate DNA methylation states in reprogramming. Here, we found that the miR-29 family is an important epigenetic regulator during human somatic cell reprogramming. Our global DNA methylation and hydroxymethylation analysis shows that DNA demethylation is a major event mediated by miR-29a depletion during early reprogramming, and that iPSCs derived from miR-29a depletion are epigenetically closer to ESCs. Our findings uncover an important miRNA-based approach to generate clinically robust iPSCs.
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Affiliation(s)
- Eriona Hysolli
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, 10 Amistad, 201B, New Haven, CT 06520, USA
| | - Yoshiaki Tanaka
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, 10 Amistad, 201B, New Haven, CT 06520, USA
| | - Juan Su
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, 10 Amistad, 201B, New Haven, CT 06520, USA; Department of Cell Biology, Second Military Medical University, Shanghai 200433, P.R. China
| | - Kun-Yong Kim
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, 10 Amistad, 201B, New Haven, CT 06520, USA
| | - Tianyu Zhong
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, 10 Amistad, 201B, New Haven, CT 06520, USA; Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi 341000, P.R. China
| | - Ralf Janknecht
- Department of Cell Biology, University of Oklahoma Health Sciences Center, 975 Northeast, 10th Street, Oklahoma City, OK 73104, USA
| | - Xiao-Ling Zhou
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, 10 Amistad, 201B, New Haven, CT 06520, USA; Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, 515041, P.R. China
| | - Lin Geng
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, 10 Amistad, 201B, New Haven, CT 06520, USA
| | - Caihong Qiu
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, 10 Amistad, 201B, New Haven, CT 06520, USA
| | - Xinghua Pan
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, 10 Amistad, 201B, New Haven, CT 06520, USA
| | - Yong-Wook Jung
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, 10 Amistad, 201B, New Haven, CT 06520, USA; Department of Obstetrics and Gynecology, CHA Gangnam Medical Center, CHA University, Seoul 135-081, Republic of Korea
| | - Jijun Cheng
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, 10 Amistad, 201B, New Haven, CT 06520, USA
| | - Jun Lu
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, 10 Amistad, 201B, New Haven, CT 06520, USA
| | - Mei Zhong
- Department of Cell Biology, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Sherman M Weissman
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, 10 Amistad, 201B, New Haven, CT 06520, USA
| | - In-Hyun Park
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, 10 Amistad, 201B, New Haven, CT 06520, USA.
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Jin S, Collin J, Zhu L, Montaner D, Armstrong L, Neganova I, Lako M. A Novel Role for miR-1305 in Regulation of Pluripotency-Differentiation Balance, Cell Cycle, and Apoptosis in Human Pluripotent Stem Cells. Stem Cells 2016; 34:2306-17. [PMID: 27339422 PMCID: PMC5031214 DOI: 10.1002/stem.2444] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 05/24/2016] [Accepted: 06/07/2016] [Indexed: 12/13/2022]
Abstract
Human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSCs) are defined as pluripotent in view of their self‐renewal ability and potential to differentiate to cells of all three germ layers. Recent studies have indicated that microRNAs (miRNAs) play an important role in the maintenance of pluripotency and cell cycle regulation. We used a microarray based approach to identify miRNAs that were enriched in hESCs when compared to differentiated cells and at the same time showed significant expression changes between different phases of cell cycle. We identified 34 candidate miRNAs and performed functional studies on one of these, miR‐1305, which showed the highest expression change during cell cycle transition. Overexpression of miR‐1305 induced differentiation of pluripotent stem cells, increased cell apoptosis and sped up G1/S transition, while its downregulation facilitated the maintenance of pluripotency and increased cell survival. Using target prediction software and luciferase based reporter assays we identified POLR3G as a downstream target by which miR‐1305 regulates the fine balance between maintenance of pluripotency and onset of differentiation. Overexpression of POLR3G rescued pluripotent stem cell differentiation induced by miR‐1305 overexpression. In contrast, knock‐down of POLR3G expression abolished the miR‐1305‐knockdown mediated enhancement of pluripotency, thus validating its role as miR‐1305 target in human pluripotent stem cells. Together our data point to an important role for miR‐1305 as a novel regulator of pluripotency, cell survival and cell cycle and uncovers new mechanisms and networks by which these processes are intertwined in human pluripotent stem cells. Stem Cells2016;34:2306–2317
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Affiliation(s)
- Shibo Jin
- Institute of Genetic Medicine, Newcastle University, UK
| | - Joseph Collin
- Institute of Genetic Medicine, Newcastle University, UK
| | - Lili Zhu
- Institute of Genetic Medicine, Newcastle University, UK
| | - David Montaner
- Centro De Investigacion Principe Felipe, Valencia, Spain
| | | | - Irina Neganova
- Institute of Genetic Medicine, Newcastle University, UK.
| | - Majlinda Lako
- Institute of Genetic Medicine, Newcastle University, UK.
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Zhang W, Zhong L, Wang J, Han J. Distinct MicroRNA Expression Signatures of Porcine Induced Pluripotent Stem Cells under Mouse and Human ESC Culture Conditions. PLoS One 2016; 11:e0158655. [PMID: 27384321 PMCID: PMC4934789 DOI: 10.1371/journal.pone.0158655] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 06/20/2016] [Indexed: 12/15/2022] Open
Abstract
It is well known that microRNAs play a very important role in regulating reprogramming, pluripotency and cell fate decisions. Porcine induced pluripotent stem cells (piPSCs) are now available for studying the pluripotent regulation network in pigs. Two types of piPSCs have been derived from human and mouse embryonic stem cell (ESC) culture conditions: hpiPSCs and mpiPSCs, respectively. The hpiPSCs were morphologically similar to human ESCs, and the mpiPSCs resembled mouse ESCs. However, our current understanding of the role of microRNAs in the development of piPSCs is still very limited. Here, we performed small RNA sequencing to profile the miRNA expression in porcine fibroblasts (pEFs), hpiPSCs and mpiPSCs. There were 22 differential expressed (DE) miRNAs down-regulated in both types of piPSCs compared with pEFs, such as ssc-miR-145-5p and ssc-miR-98. There were 27 DE miRNAs up-regulated in both types of piPSCs compared with pEFs. Among these up-regulated DE miRNAs in piPSCs, ssc-miR-217, ssc-miR-216, ssc-miR-142-5p, ssc-miR-182, ssc-miR-183 and ssc-miR-96-5p have much higher expression levels in mpiPSCs, while ssc-miR-106a, ssc-miR-363, ssc-miR-146b, ssc-miR-195, ssc-miR-497, ssc-miR-935 and ssc-miR-20b highly expressed in hpiPSCs. Quantitative stem-loop RT-PCR was performed to confirm selected DE miRNAs expression levels. The results were consistent with small RNA sequencing. Different expression patterns were observed for key miRNA clusters, such as the miR-17-92 cluster, the let-7 family, the miR-106a-363 cluster and the miR-182-183 cluster, in the mpiPSCs and hpiPSCs. Novel miRNAs were also predicted in this study, including a putative porcine miR-302 cluster: ssc_38503, ssc_38503 and ssc_38501 (which resemble human miR-302a and miR-302b) found in both types of piPSCs. The miR-106a-363 cluster and putative miR-302 cluster increased the reprogramming efficiency of pEFs. The study revealed significant differences in the miRNA signatures of hpiPSCs and mpiPSCs under different pluripotent states that were derived from different culture conditions. These differentially expressed miRNAs may play important roles in pluripotent regulation in pigs, and this information will facilitate the understanding of the mechanism of pluripotency in pigs.
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Affiliation(s)
- Wei Zhang
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Liang Zhong
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jing Wang
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jianyong Han
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- * E-mail:
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46
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Profiling of differentially expressed microRNAs in arrhythmogenic right ventricular cardiomyopathy. Sci Rep 2016; 6:28101. [PMID: 27307080 PMCID: PMC4910108 DOI: 10.1038/srep28101] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/27/2016] [Indexed: 02/04/2023] Open
Abstract
Arrhythmogenic right ventricular cardiomyopathy (ARVC) is a kind of primary cardiomyopathy characterized by the fibro-fatty replacement of right ventricular myocardium. Currently, myocardial microRNAs have been reported to play critical role in the pathophysiology of cardiovascular pathophysiology. So far, the profiling of microRNAs in ARVC has not been described. In this study, we applied S-Poly (T) Plus method to investigate the expression profile of microRNAs in 24 ARVC patients heart samples. The tissue levels of 1078 human microRNAs were assessed and were compared with levels in a group of 24 healthy controls. Analysis of the area under the receiver operating characteristic curve (ROC) supported the 21 validated microRNAs to be miRNA signatures of ARVC, eleven microRNAs were significantly increased in ARVC heart tissues and ten microRNAs were significantly decreased. After functional enrichment analysis, miR-21-5p and miR-135b were correlated with Wnt and Hippo pathway, which might involve in the molecular pathophysiology of ARVC. Overall, our data suggested that myocardial microRNAs were involved in the pathophysiology of ARVC, miR-21-5p and miR-135b were significantly associated with both the myocardium adipose and fibrosis, which was a potential disease pathway for ARVC and might to be useful as therapeutic targets for ARVC.
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47
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Cellular Reprogramming Using Defined Factors and MicroRNAs. Stem Cells Int 2016; 2016:7530942. [PMID: 27382371 PMCID: PMC4921148 DOI: 10.1155/2016/7530942] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 03/08/2016] [Accepted: 04/10/2016] [Indexed: 01/07/2023] Open
Abstract
Development of human bodies, organs, and tissues contains numerous steps of cellular differentiation including an initial zygote, embryonic stem (ES) cells, three germ layers, and multiple expertized lineages of cells. Induced pluripotent stem (iPS) cells have been recently developed using defined reprogramming factors such as Nanog, Klf5, Oct3/4 (Pou5f1), Sox2, and Myc. This outstanding innovation is largely changing life science and medicine. Methods of direct reprogramming of cells into myocytes, neurons, chondrocytes, and osteoblasts have been further developed using modified combination of factors such as N-myc, L-myc, Sox9, and microRNAs in defined cell/tissue culture conditions. Mesenchymal stem cells (MSCs) and dental pulp stem cells (DPSCs) are also emerging multipotent stem cells with particular microRNA expression signatures. It was shown that miRNA-720 had a role in cellular reprogramming through targeting the pluripotency factor Nanog and induction of DNA methyltransferases (DNMTs). This review reports histories, topics, and idea of cellular reprogramming.
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48
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Lee YJ, Ramakrishna S, Chauhan H, Park WS, Hong SH, Kim KS. Dissecting microRNA-mediated regulation of stemness, reprogramming, and pluripotency. ACTA ACUST UNITED AC 2016; 5:2. [PMID: 27006752 PMCID: PMC4802578 DOI: 10.1186/s13619-016-0028-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 02/20/2016] [Indexed: 02/06/2023]
Abstract
Increasing evidence indicates that microRNAs (miRNAs), endogenous short non-coding RNAs 19–24 nucleotides in length, play key regulatory roles in various biological events at the post-transcriptional level. Embryonic stem cells (ESCs) represent a valuable tool for disease modeling, drug discovery, developmental studies, and potential cell-based therapies in regenerative medicine due to their unlimited self-renewal and pluripotency. Therefore, remarkable progress has been made in recent decades toward understanding the expression and functions of specific miRNAs in the establishment and maintenance of pluripotency. Here, we summarize the recent knowledge regarding the regulatory roles of miRNAs in self-renewal of pluripotent ESCs and during cellular reprogramming, as well as the potential role of miRNAs in two distinct pluripotent states (naïve and primed).
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Affiliation(s)
- Young Jin Lee
- iDream Research Center, MizMedi Women's Hospital, Seoul, 07639 South Korea
| | - Suresh Ramakrishna
- Department of Biomedical Science, Graduate School of Biomedical Science and Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 04763 South Korea.,College of Medicine, Hanyang University, Seoul, South Korea
| | | | - Won Sun Park
- Department of Physiology, School of Medicine, Kangwon National University, Chuncheon, 24341 South Korea
| | - Seok-Ho Hong
- Department of Internal Medicine, School of Medicine, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do 24341 South Korea.,Stem Cell Institute, Kangwon National University, Chuncheon, 24341 South Korea
| | - Kye-Seong Kim
- Department of Biomedical Science, Graduate School of Biomedical Science and Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 04763 South Korea.,College of Medicine, Hanyang University, Seoul, South Korea
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49
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Ling H, Krassnig L, Bullock MD, Pichler M. MicroRNAs in Testicular Cancer Diagnosis and Prognosis. Urol Clin North Am 2016; 43:127-34. [PMID: 26614035 DOI: 10.1016/j.ucl.2015.08.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Testicular cancer processes a unique and clear miRNA expression signature. This differentiates testicular cancer from most other cancer types, which are usually more ambiguous when assigning miRNA patterns. As such, testicular cancer may represent a unique cancer type in which miRNAs find their use as biomarkers for cancer diagnosis and prognosis, with a potential to surpass the current available markers usually with low sensitivity. In this review, we present literature findings on miRNAs associated with testicular cancer, and discuss their potential diagnostic and prognostic values, as well as their potential as indicators of drug response in patients with testicular cancer.
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Affiliation(s)
- Hui Ling
- Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77054, USA
| | - Lisa Krassnig
- Division of Oncology, Department of Internal Medicine, Medical University of Graz (MUG), Graz, Austria
| | - Marc D Bullock
- Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77054, USA
| | - Martin Pichler
- Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77054, USA; Division of Oncology, Department of Internal Medicine, Medical University of Graz (MUG), Graz, Austria.
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50
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Li HL, Wei JF, Fan LY, Wang SH, Zhu L, Li TP, Lin G, Sun Y, Sun ZJ, Ding J, Liang XL, Li J, Han Q, Zhao RCH. miR-302 regulates pluripotency, teratoma formation and differentiation in stem cells via an AKT1/OCT4-dependent manner. Cell Death Dis 2016; 7:e2078. [PMID: 26821070 PMCID: PMC4816169 DOI: 10.1038/cddis.2015.383] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 10/20/2015] [Accepted: 11/20/2015] [Indexed: 12/12/2022]
Abstract
Pluripotency makes human pluripotent stem cells (hPSCs) promising for regenerative medicine, but the teratoma formation has been considered to be a major obstacle for their clinical applications. Here, we determined that the downregulation of miR-302 suppresses the teratoma formation, hampers the self-renewal and pluripotency, and promotes hPSC differentiation. The underlying mechanism is that the high endogenous expression of miR-302 suppresses the AKT1 expression by directly targeting its 3'UTR and subsequently maintains the pluripotent factor OCT4 at high level. Our findings reveal that miR-302 regulates OCT4 by suppressing AKT1, which provides hPSCs two characteristics related to their potential for clinical applications: the benefit of pluripotency and the hindrance of teratoma formation. More importantly, we demonstrate that miR-302 upregulation cannot lead OCT4 negative human adult mesenchymal stem cells (hMSCs) to acquire the teratoma formation in vivo. Whether miR-302 upregulation can drive hMSCs to acquire a higher differentiation potential is worthy of deep investigation.
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Affiliation(s)
- H-L Li
- Department of Cell Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Tissue Engineering Center of Chinese Academy of Medical Sciences, Beijing, China
| | - J-F Wei
- Department of Cell Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Tissue Engineering Center of Chinese Academy of Medical Sciences, Beijing, China.,Department of Histology and Embryology, School of Basic Medical Sciences, Xuzhou Medical University, Xuzhou, China
| | - L-Y Fan
- Department of Cell Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Tissue Engineering Center of Chinese Academy of Medical Sciences, Beijing, China
| | - S-H Wang
- Department of Cell Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Tissue Engineering Center of Chinese Academy of Medical Sciences, Beijing, China
| | - L Zhu
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Beijing, China
| | - T-P Li
- Department of Cell Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Tissue Engineering Center of Chinese Academy of Medical Sciences, Beijing, China
| | - G Lin
- Institute of Reproductive and Stem Cell Engineering, Key Laboratory of Stem Cells and Reproductive Engineering, Ministry of Health, Central South University, Changsha, China
| | - Y Sun
- Department of Nuclear Medicine, Peking Union Medical College Hospital, Beijing, China
| | - Z-J Sun
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Beijing, China
| | - J Ding
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Beijing, China
| | - X-L Liang
- Department of Cell Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Tissue Engineering Center of Chinese Academy of Medical Sciences, Beijing, China
| | - J Li
- Department of Cell Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Tissue Engineering Center of Chinese Academy of Medical Sciences, Beijing, China
| | - Q Han
- Department of Cell Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Tissue Engineering Center of Chinese Academy of Medical Sciences, Beijing, China
| | - R-C-H Zhao
- Department of Cell Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Tissue Engineering Center of Chinese Academy of Medical Sciences, Beijing, China.,Peking Union Medical College Hospital, Beijing, China
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