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Saini P, Anugula S, Fong YW. The Role of ATP-Binding Cassette Proteins in Stem Cell Pluripotency. Biomedicines 2023; 11:1868. [PMID: 37509507 PMCID: PMC10377311 DOI: 10.3390/biomedicines11071868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/20/2023] [Accepted: 06/22/2023] [Indexed: 07/30/2023] Open
Abstract
Pluripotent stem cells (PSCs) are highly proliferative cells that can self-renew indefinitely in vitro. Upon receiving appropriate signals, PSCs undergo differentiation and can generate every cell type in the body. These unique properties of PSCs require specific gene expression patterns that define stem cell identity and dynamic regulation of intracellular metabolism to support cell growth and cell fate transitions. PSCs are prone to DNA damage due to elevated replicative and transcriptional stress. Therefore, mechanisms to prevent deleterious mutations in PSCs that compromise stem cell function or increase the risk of tumor formation from becoming amplified and propagated to progenitor cells are essential for embryonic development and for using PSCs including induced PSCs (iPSCs) as a cell source for regenerative medicine. In this review, we discuss the role of the ATP-binding cassette (ABC) superfamily in maintaining PSC homeostasis, and propose how their activities can influence cellular signaling and stem cell fate decisions. Finally, we highlight recent discoveries that not all ABC family members perform only canonical metabolite and peptide transport functions in PSCs; rather, they can participate in diverse cellular processes from genome surveillance to gene transcription and mRNA translation, which are likely to maintain the pristine state of PSCs.
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Affiliation(s)
- Prince Saini
- Brigham Regenerative Medicine Center, Brigham and Women’s Hospital, Boston, MA 02115, USA; (P.S.); (S.A.)
- Department of Medicine, Cardiovascular Medicine Division, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Sharath Anugula
- Brigham Regenerative Medicine Center, Brigham and Women’s Hospital, Boston, MA 02115, USA; (P.S.); (S.A.)
- Department of Medicine, Cardiovascular Medicine Division, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Yick W. Fong
- Brigham Regenerative Medicine Center, Brigham and Women’s Hospital, Boston, MA 02115, USA; (P.S.); (S.A.)
- Department of Medicine, Cardiovascular Medicine Division, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
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2
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PSCRIdb: A database of regulatory interactions and networks of pluripotent stem cell lines. J Biosci 2020. [DOI: 10.1007/s12038-020-00027-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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3
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Albuquerque-Souza E, Schulte F, Chen T, Hardt M, Hasturk H, Van Dyke TE, Holzhausen M, Kantarci A. Maresin-1 and Resolvin E1 Promote Regenerative Properties of Periodontal Ligament Stem Cells Under Inflammatory Conditions. Front Immunol 2020; 11:585530. [PMID: 33101318 PMCID: PMC7546375 DOI: 10.3389/fimmu.2020.585530] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/08/2020] [Indexed: 12/23/2022] Open
Abstract
Maresin-1 (MaR1) and Resolvin E1 (RvE1) are specialized pro-resolving lipid mediators (SPMs) that regulate inflammatory processes. We have previously demonstrated the hard and soft tissue regenerative capacity of RvE1 in an in vivo model of the periodontal disease characterized by inflammatory tissue destruction. Regeneration of periodontal tissues requires a well-orchestrated process mediated by periodontal ligament stem cells. However, limited data are available on how SPMs can regulate the regenerative properties of human periodontal ligament stem cells (hPDLSCs) under inflammatory conditions. Thus, we measured the impact of MaR1 and RvE1 in an in vitro model of hPDLSC under stimulation with IL-1β and TNF-α by evaluating pluripotency, migration, viability/cell death, periodontal ligament markers (α-smooth muscle actin, tenomodulin, and periostin), cementogenic-osteogenic differentiation, and phosphoproteomic perturbations. The data showed that the pro-inflammatory milieu suppresses pluripotency, viability, and migration of hPDLSCs; MaR1 and RvE1 both restored regenerative capacity by increasing hPDLSC viability, accelerating wound healing/migration, and up-regulating periodontal ligament markers and cementogenic-osteogenic differentiation. Protein phosphorylation perturbations were associated with the SPM-induced regenerative capacity of hPDLSCs. Together, these results demonstrate that MaR1 and RvE1 restore or improve the regenerative properties of highly specialized stem cells when inflammation is present and offer opportunities for direct pharmacologic treatment of lost tissue integrity.
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Affiliation(s)
- Emmanuel Albuquerque-Souza
- The Forsyth Institute, Cambridge, MA, United States.,Division of Periodontics, Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Fabian Schulte
- The Forsyth Institute, Cambridge, MA, United States.,Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA, United States
| | - Tsute Chen
- The Forsyth Institute, Cambridge, MA, United States
| | - Markus Hardt
- The Forsyth Institute, Cambridge, MA, United States.,Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA, United States
| | | | | | - Marinella Holzhausen
- Division of Periodontics, Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo, Brazil
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4
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Meta-Analysis of Gene Expressions in Testicular Germ Cell Tumor Histologies. Int J Mol Sci 2020; 21:ijms21124487. [PMID: 32599785 PMCID: PMC7349960 DOI: 10.3390/ijms21124487] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 02/02/2023] Open
Abstract
There is no consensus as to how a precursor lesion, germ cell neoplasia in situ (GCNIS), develops into the histologic types of testicular germ cell tumor type II (TGCT). The present meta-analysis examined RNA expressions of 24 candidate genes in three datasets. They included 203 samples of normal testis (NT) and histologic types of TGCT. The Fisher’s test for combined p values was used for meta-analysis of the RNA expressions in the three datasets. The histologic types differed in RNA expression of PRAME, KIT, SOX17, NANOG, KLF4, POU5F1, RB1, DNMT3B, and LIN28A (p < 0.01). The histologic types had concordant differences in RNA expression of the genes in the three datasets. Eight genes had overlap with a high RNA expression in at least two histologic types. In contrast, only seminoma (SE) had a high RNA expression of KLF4 and only embryonal carcinoma (EC) had a high RNA expression of DNMT3B. In conclusion, the meta-analysis showed that the development of the histologic types of TGCT was driven by changes in RNA expression of candidate genes. According to the RNA expressions of the ten genes, TGCT develops from NT over GCNIS, SE, EC, to the differentiated types of TGCT.
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5
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Banerjee K, Jana T, Ghosh Z, Saha S. PSCRIdb: A database of regulatory interactions and networks of pluripotent stem cell lines. J Biosci 2020; 45:53. [PMID: 32345779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Pluripotency in stem cells is regulated by a complex network between the transcription factors, signaling molecules, mRNAs, and epigenetic regulators like non-coding RNAs. Different pluripotent stem cell (PSC) lines were isolated and characterized to study the regulatory network topology to understand the mechanism that control developmental potential of pluripotent cells. PSCRIdb is a manually curated database of regulatory interactions including protein-protein, protein-DNA, gene-gene, and miRNA-mRNA interactions in mouse and human pluripotent stem cells including embryonic stem cells and embryonic carcinoma cells. At present, 22 different mouse and human pluripotent stem-cell-line-specific regulatory interactions are compiled in the database. Detailed information of the four types of interaction data are presented in tabular format and graphical network view in Cytoscape layout. The database is available at http://bicresources.jcbose.ac.in/ ssaha4/pscridb. The database contains 3037 entries of experimentally validated molecular interactions that can be useful for systematic study of pluripotency integrating multi-omics data. In summary, the database can be a useful resource for identification of regulatory networks present in different pluripotent stem cell lines.
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Gordeeva O. TGFβ Family Signaling Pathways in Pluripotent and Teratocarcinoma Stem Cells' Fate Decisions: Balancing Between Self-Renewal, Differentiation, and Cancer. Cells 2019; 8:cells8121500. [PMID: 31771212 PMCID: PMC6953027 DOI: 10.3390/cells8121500] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 11/19/2019] [Accepted: 11/21/2019] [Indexed: 12/11/2022] Open
Abstract
The transforming growth factor-β (TGFβ) family factors induce pleiotropic effects and are involved in the regulation of most normal and pathological cellular processes. The activity of different branches of the TGFβ family signaling pathways and their interplay with other signaling pathways govern the fine regulation of the self-renewal, differentiation onset and specialization of pluripotent stem cells in various cell derivatives. TGFβ family signaling pathways play a pivotal role in balancing basic cellular processes in pluripotent stem cells and their derivatives, although disturbances in their genome integrity induce the rearrangements of signaling pathways and lead to functional impairments and malignant transformation into cancer stem cells. Therefore, the identification of critical nodes and targets in the regulatory cascades of TGFβ family factors and other signaling pathways, and analysis of the rearrangements of the signal regulatory network during stem cell state transitions and interconversions, are key issues for understanding the fundamental mechanisms of both stem cell biology and cancer initiation and progression, as well as for clinical applications. This review summarizes recent advances in our understanding of TGFβ family functions in naїve and primed pluripotent stem cells and discusses how these pathways are involved in perturbations in the signaling network of malignant teratocarcinoma stem cells with impaired differentiation potential.
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Affiliation(s)
- Olga Gordeeva
- Kol'tsov Institute of Developmental Biology, Russian Academy of Sciences, 26 Vavilov str., 119334 Moscow, Russia
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Hashimoto Y, Greco TM, Cristea IM. Contribution of Mass Spectrometry-Based Proteomics to Discoveries in Developmental Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:143-154. [PMID: 31347046 DOI: 10.1007/978-3-030-15950-4_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Understanding multicellular organism development from a molecular perspective is no small feat, yet this level of comprehension affords clinician-scientists the ability to identify root causes and mechanisms of congenital diseases. Inarguably, the maturation of molecular biology tools has significantly contributed to the identification of genetic loci that underlie normal and aberrant developmental programs. In combination with cell biology approaches, these tools have begun to elucidate the spatiotemporal expression and function of developmentally-regulated proteins. The emergence of quantitative mass spectrometry (MS) for biological applications has accelerated the pace at which these proteins can be functionally characterized, driving the construction of an increasingly detailed systems biology picture of developmental processes. Here, we review the quantitative MS-based proteomic technologies that have contributed significantly to understanding the role of proteome regulation in developmental processes. We provide a brief overview of these methodologies, focusing on their ability to provide precise and accurate proteome measurements. We then highlight the use of discovery-based and targeted mass spectrometry approaches in model systems to study cellular differentiation states, tissue phenotypes, and spatiotemporal subcellular organization. We also discuss the current application and future perspectives of MS proteomics to study PTM coordination and the role of protein complexes during development.
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Affiliation(s)
- Yutaka Hashimoto
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA
| | - Todd M Greco
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA.
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8
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Mitochondrial Metabolism in Cancer. A Tangled Topic. Which Role for Proteomics? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1158:1-16. [DOI: 10.1007/978-981-13-8367-0_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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9
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Nettersheim D, Berger D, Jostes S, Kristiansen G, Lochnit G, Schorle H. N6-Methyladenosine detected in RNA of testicular germ cell tumors is controlled by METTL3, ALKBH5, YTHDC1/F1/F2, and HNRNPC as writers, erasers, and readers. Andrology 2019; 7:498-506. [PMID: 30903744 DOI: 10.1111/andr.12612] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/18/2019] [Accepted: 02/24/2019] [Indexed: 12/18/2022]
Abstract
BACKGROUND Type II testicular germ cell tumors (GCTs) arise from a common precursor lesion (germ cell neoplasia in situ) and are stratified into seminomas and non-seminomas, which differ considerably in morphology, gene expression, and epigenetic landscape. The N6-methyladenosine (6mA) epigenetic modification is the most abundant modification in mRNA and is also detectable in eukaryotic DNA. The functional role of 6mA is not fully understood, but 6mA residues may influence transcription by affecting splicing, miRNA processing, and mRNA stability. Additionally, the methyl group of 6mA destabilizes Watson-Crick base-pairing affecting RNA structure and protein binding. OBJECTIVES Here, we analyzed the presence of the 6mA epigenetic modification in germ cells and GCT tissues and cell lines. MATERIALS AND METHODS We screened for the presence of 6mA in DNA and RNA by immunohistochemistry, mass spectrometry or ELISA-based quantification assays. Additionally, expression of 6mA writer-, eraser- and reader-factors was analyzed by microarrays, qRT-PCR, western blotting and screening of public databases. RESULTS We demonstrate that 6mA is detectable in RNA, but not DNA, of GCT cell lines and tissues, fibroblasts, and Sertoli cells as well as germ cells of different developmental stages. Based on expression analyses, our results suggest METTL3, ALKBH5, YTHDC1, YTHDF1, YTHDF2 and HNRNPC as main writers, erasers, and readers of the 6mA modification in GCTs. DISCUSSION Owing to the lack of 6mA in DNA of GCTs, a functional role in regulating DNA transcription can be excluded. Interestingly, expression levels of 6mA regulators are comparable between tumor and normal tissues/cells, suggesting a similar mechanism of 6mA regulation in RNA. Finally, we demonstrate that 6mA levels in RNA increase upon differentiation of GCT cell lines, suggesting a role of 6mA in cell fate decisions. CONCLUSION In summary, our data provide the starting point for further experiments deciphering the role of 6mA in the RNA of GCTs.
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Affiliation(s)
- D Nettersheim
- Department of Urology, Urological Research Lab, Translational Urooncology, University Medical School Düsseldorf, Düsseldorf, Germany
| | - D Berger
- Department of Developmental Pathology, Institute of Pathology, Bonn University Medical School, Bonn, Germany
| | - S Jostes
- Department of Developmental Pathology, Institute of Pathology, Bonn University Medical School, Bonn, Germany
| | - G Kristiansen
- Institute of Pathology, Bonn University Medical School, Bonn, Germany
| | - G Lochnit
- Institute of Biochemistry, Protein Analytics, Justus-Liebig University Giessen, Giessen, Germany
| | - H Schorle
- Department of Developmental Pathology, Institute of Pathology, Bonn University Medical School, Bonn, Germany
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10
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Kerr CL, Bol GM, Vesuna F, Raman V. Targeting RNA helicase DDX3 in stem cell maintenance and teratoma formation. Genes Cancer 2019; 10:11-20. [PMID: 30899416 PMCID: PMC6420792 DOI: 10.18632/genesandcancer.187] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
DDX3 is an RNA helicase that has antiapoptotic properties, and promotes proliferation and transformation. Besides the role of DDX3 in transformed cells, there is evidence to indicate that DDX3 expression is at its highest levels during early embryonic development and is also expressed in germ cells of adults. Even though there is a distinct pattern of DDX3 expression during embryonic development and in adults, very little is known regarding its role in embryonic stem cells and pluripotency. In this work, we examined the relationship between DDX3 and human embryonic stem cells and its differentiated lineages. DDX3 expression was analyzed by immunohistochemistry in human embryonic stem cells and embryonal carcinoma cells. From the data obtained, it was evident that DDX3 was overexpressed in undifferentiated stem cells compared to differentiated cells. Moreover, when DDX3 expression was abrogated in multiple stem cells, proliferation was decreased, but differentiation was facilitated. Importantly, this resulted in reduced potency to induce teratoma formation. Taken together, these findings indicate a distinct role for DDX3 in stem cell maintenance.
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Affiliation(s)
- Candace L Kerr
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Guus M Bol
- Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Oncology, University Medical Center Utrecht Cancer Center, GA Utrecht, The Netherlands
| | - Farhad Vesuna
- Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Oncology, University Medical Center Utrecht Cancer Center, GA Utrecht, The Netherlands
| | - Venu Raman
- Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Pathology, University Medical Center Utrecht Cancer Center, GA Utrecht, The Netherlands
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11
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Jung J, Kim Y, Song J, Yoon YJ, Kim DE, Kim JA, Jin Y, Lee YJ, Kim S, Kwon BM, Han DC. KRIBB53 binds to OCT4 and enhances its degradation through the proteasome, causing apoptotic cell death of OCT4-positive testicular germ cell tumors. Carcinogenesis 2018; 39:838-849. [DOI: 10.1093/carcin/bgy054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/11/2018] [Indexed: 12/20/2022] Open
Affiliation(s)
- Jiyae Jung
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
- University of Science and Technology in Korea, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
| | - Youngmi Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
- University of Science and Technology in Korea, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
| | - Jinhoi Song
- University of Science and Technology in Korea, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
- Aging Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
| | - Yae Jin Yoon
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
| | - Da-Eun Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
- University of Science and Technology in Korea, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
| | - Joo Ae Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
- University of Science and Technology in Korea, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
| | - Yena Jin
- University of Science and Technology in Korea, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
- Aging Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
| | - Yu-Jin Lee
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
| | - Seokho Kim
- Aging Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
| | - Byoung-Mog Kwon
- University of Science and Technology in Korea, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
| | - Dong Cho Han
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
- University of Science and Technology in Korea, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
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12
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Epigenetics and testicular germ cell tumors. Gene 2018; 661:22-33. [PMID: 29605605 DOI: 10.1016/j.gene.2018.03.072] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 02/07/2018] [Accepted: 03/21/2018] [Indexed: 11/20/2022]
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13
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Somanath P, Bush KM, Knoepfler PS. ERBB3-Binding Protein 1 (EBP1) Is a Novel Developmental Pluripotency-Associated-4 (DPPA4) Cofactor in Human Pluripotent Cells. Stem Cells 2018; 36:671-682. [PMID: 29327467 DOI: 10.1002/stem.2776] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 12/04/2017] [Accepted: 12/09/2017] [Indexed: 12/31/2022]
Abstract
Developmental Pluripotency-Associated-4 (DPPA4) is one of the few core pluripotency genes lacking clearly defined molecular and cellular functions. Here, we used a proteomics screening approach of human embryonic stem cell (hESC) nuclear extract to determine DPPA4 molecular functions through identification of novel cofactors. Unexpectedly, the signaling molecule ERBB3-binding protein 1 (EBP1) was the strongest candidate binding partner for DPPA4 in hESC. EBP1 is a growth factor signaling mediator present in two isoforms, p48 and p42. The two isoforms generally have opposing functions, however their roles in pluripotent cells have not been established. We found that DPPA4 preferentially binds p48 in pluripotent and NTERA-2 cells, but this interaction is largely absent in non-pluripotent cells and is reduced with differentiation. The DPPA4-EBP1 interaction is mediated at least in part in DPPA4 by the highly conserved SAF-A/B, Acinus and PIAS (SAP) domain. Functionally, we found that DPPA4 transcriptional repressive function in reporter assays is significantly increased by specific p48 knockdown, an effect that was abolished with an interaction-deficient DPPA4 ΔSAP mutant. Thus, DPPA4 and EBP1 may cooperate in transcriptional functions through their physical association in a pluripotent cell specific context. Our study identifies EBP1 as a novel pluripotency cofactor and provides insight into potential mechanisms used by DPPA4 in regulating pluripotency through its association with EBP1. Stem Cells 2018;36:671-682.
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Affiliation(s)
- Priyanka Somanath
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, California, USA.,Institute of Pediatric Regenerative Medicine, Shriners Hospital for Children Northern California, Sacramento, California, USA
| | - Kelly M Bush
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, California, USA.,Institute of Pediatric Regenerative Medicine, Shriners Hospital for Children Northern California, Sacramento, California, USA
| | - Paul S Knoepfler
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, California, USA.,Institute of Pediatric Regenerative Medicine, Shriners Hospital for Children Northern California, Sacramento, California, USA
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14
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Nettersheim D, Jostes S, Schneider S, Schorle H. Elucidating human male germ cell development by studying germ cell cancer. Reproduction 2017; 152:R101-13. [PMID: 27512122 DOI: 10.1530/rep-16-0114] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 06/07/2016] [Indexed: 12/19/2022]
Abstract
Human germ cell development is regulated in a spatio-temporal manner by complex regulatory networks. Here, we summarize results obtained in germ cell tumors and respective cell lines and try to pinpoint similarities to normal germ cell development. This comparison allows speculating about the critical and error-prone mechanisms, which when disturbed, lead to the development of germ cell tumors. Short after specification, primordial germ cells express markers of pluripotency, which, in humans, persists up to the stage of fetal/infantile spermatogonia. Aside from the rare spermatocytic tumors, virtually all seminomas and embryonal carcinomas express markers of pluripotency and show signs of pluripotency or totipotency. Therefore, it appears that proper handling of the pluripotency program appears to be the most critical step in germ cell development in terms of tumor biology. Furthermore, data from mice reveal that germline cells display an epigenetic signature, which is highly similar to pluripotent cells. This signature (poised histone code, DNA hypomethylation) is required for the rapid induction of toti- and pluripotency upon fertilization. We propose that adult spermatogonial cells, when exposed to endocrine disruptors or epigenetic active substances, are prone to reinitiate the pluripotency program, giving rise to a germ cell tumor. The fact that pluripotent cells can be derived from adult murine and human testicular cells further corroborates this idea.
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Affiliation(s)
- Daniel Nettersheim
- Department of Developmental PathologyInstitute of Pathology, University of Bonn Medical School, Bonn, Germany
| | - Sina Jostes
- Department of Developmental PathologyInstitute of Pathology, University of Bonn Medical School, Bonn, Germany
| | - Simon Schneider
- Department of Developmental PathologyInstitute of Pathology, University of Bonn Medical School, Bonn, Germany
| | - Hubert Schorle
- Department of Developmental PathologyInstitute of Pathology, University of Bonn Medical School, Bonn, Germany
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15
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Govaert E, Van Steendam K, Willems S, Vossaert L, Dhaenens M, Deforce D. Comparison of fractionation proteomics for local SWATH library building. Proteomics 2017; 17:1700052. [PMID: 28664598 PMCID: PMC5601298 DOI: 10.1002/pmic.201700052] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 05/23/2017] [Accepted: 06/28/2017] [Indexed: 01/08/2023]
Abstract
For data-independent acquisition by means of sequential window acquisition of all theoretical fragment ion spectra (SWATH), a reference library of data-dependent acquisition (DDA) runs is typically used to correlate the quantitative data from the fragment ion spectra with peptide identifications. The quality and coverage of such a reference library is therefore essential when processing SWATH data. In general, library sizes can be increased by reducing the impact of DDA precursor selection with replicate runs or fractionation. However, these strategies can affect the match between the library and SWATH measurement, and thus larger library sizes do not necessarily correspond to improved SWATH quantification. Here, three fractionation strategies to increase local library size were compared to standard library building using replicate DDA injection: protein SDS-PAGE fractionation, peptide high-pH RP-HPLC fractionation and MS-acquisition gas phase fractionation. The impact of these libraries on SWATH performance was evaluated in terms of the number of extracted peptides and proteins, the match quality of the peptides and the extraction reproducibility of the transitions. These analyses were conducted using the hydrophilic proteome of differentiating human embryonic stem cells. Our results show that SWATH quantitative results and interpretations are affected by choice of fractionation technique. Data are available via ProteomeXchange with identifier PXD006190.
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Affiliation(s)
- Elisabeth Govaert
- Laboratory of Pharmaceutical BiotechnologyGhent UniversityGhentBelgium
| | | | - Sander Willems
- Laboratory of Pharmaceutical BiotechnologyGhent UniversityGhentBelgium
| | - Liesbeth Vossaert
- Laboratory of Pharmaceutical BiotechnologyGhent UniversityGhentBelgium
| | - Maarten Dhaenens
- Laboratory of Pharmaceutical BiotechnologyGhent UniversityGhentBelgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical BiotechnologyGhent UniversityGhentBelgium
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Huwe1 Sustains Normal Ovarian Epithelial Cell Transformation and Tumor Growth through the Histone H1.3-H19 Cascade. Cancer Res 2017; 77:4773-4784. [DOI: 10.1158/0008-5472.can-16-2597] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 02/09/2017] [Accepted: 06/29/2017] [Indexed: 11/16/2022]
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17
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Tomasello L, Musso R, Cillino G, Pitrone M, Pizzolanti G, Coppola A, Arancio W, Di Cara G, Pucci-Minafra I, Cillino S, Giordano C. Donor age and long-term culture do not negatively influence the stem potential of limbal fibroblast-like stem cells. Stem Cell Res Ther 2016; 7:83. [PMID: 27296060 PMCID: PMC4906894 DOI: 10.1186/s13287-016-0342-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 01/14/2016] [Accepted: 05/16/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND In regenerative medicine the maintenance of stem cell properties is of crucial importance. Ageing is considered a cause of reduced stemness capability. The limbus is a stem niche of easy access and harbors two stem cell populations: epithelial stem cells and fibroblast-like stem cells. Our aim was to investigate whether donor age and/or long-term culture have any influence on stem cell marker expression and the profiles in the fibroblast-like stem cell population. METHODS Fibroblast-like stem cells were isolated and digested from 25 limbus samples of normal human corneo-scleral rings and long-term cultures were obtained. SSEA4 expression and sphere-forming capability were evaluated; cytofluorimetric assay was performed to detect the immunophenotypes HLA-DR, CD45, and CD34 and the principle stem cell markers ABCG2, OCT3/4, and NANOG. Molecular expression of the principal mesenchymal stem cell genes was investigated by real-time PCR. Two-dimensional gel electrophoresis and mass spectrometric sequencing were performed and a stable proteomic profile was identified. The proteins detected were explored by gene ontology and STRING analysis. The data were reported as means ± SD, compared by Student's unpaired t test and considering p < 0.05 as statistically significant. RESULTS The isolated cells did not display any hematopoietic surface marker (CD34 and CD45) and HLA-DR and they maintained these features in long-term culture. The expression of the stemness genes and the multilineage differentiation under in-vitro culture conditions proved to be well maintained. Proteomic analysis revealed a fibroblast-like stem cell profile of 164 proteins with higher expression levels. Eighty of these showed stable expression levels and were involved in maintenance of "the stem gene profile"; 84 were differentially expressed and were involved in structural activity. CONCLUSIONS The fibroblast-like limbal stem cells confirmed that they are a robust source of adult stem cells and that they have good plasticity, good proliferative capability, and long-term maintenance of stem cell properties, independently of donor age and long-term culture conditions. Our findings confirm that limbal fibroblast-like stem cells are highly promising for application in regenerative medicine and that in-vitro culture steps do not influence their stem cell properties. Moreover, the proteomic data enrich our knowledge of fibroblast-like stem cells.
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Affiliation(s)
- Laura Tomasello
- Laboratory of Regenerative Medicine, Section of Endocrinology, Diabetology and Metabolism, Di.Bi.M.I.S., University of Palermo, Piazza delle Cliniche 2, 90127, Palermo, Italy
| | - Rosa Musso
- Centro di Oncobiologia Sperimentale (COBS), Palermo, Italy
| | - Giovanni Cillino
- Department of Ophthalmology, University of Palermo, Palermo, Italy
| | - Maria Pitrone
- Laboratory of Regenerative Medicine, Section of Endocrinology, Diabetology and Metabolism, Di.Bi.M.I.S., University of Palermo, Piazza delle Cliniche 2, 90127, Palermo, Italy
| | - Giuseppe Pizzolanti
- Laboratory of Regenerative Medicine, Section of Endocrinology, Diabetology and Metabolism, Di.Bi.M.I.S., University of Palermo, Piazza delle Cliniche 2, 90127, Palermo, Italy
- ATeN (Advanced Technologies Network Center), University of Palermo, Palermo, Italy
| | - Antonina Coppola
- Laboratory of Regenerative Medicine, Section of Endocrinology, Diabetology and Metabolism, Di.Bi.M.I.S., University of Palermo, Piazza delle Cliniche 2, 90127, Palermo, Italy
| | - Walter Arancio
- Laboratory of Regenerative Medicine, Section of Endocrinology, Diabetology and Metabolism, Di.Bi.M.I.S., University of Palermo, Piazza delle Cliniche 2, 90127, Palermo, Italy
| | | | | | | | - Carla Giordano
- Laboratory of Regenerative Medicine, Section of Endocrinology, Diabetology and Metabolism, Di.Bi.M.I.S., University of Palermo, Piazza delle Cliniche 2, 90127, Palermo, Italy.
- ATeN (Advanced Technologies Network Center), University of Palermo, Palermo, Italy.
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18
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Two Effective Routes for Removing Lineage Restriction Roadblocks: From Somatic Cells to Hepatocytes. Int J Mol Sci 2015; 16:20873-95. [PMID: 26340624 PMCID: PMC4613233 DOI: 10.3390/ijms160920873] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 08/24/2015] [Accepted: 08/24/2015] [Indexed: 12/31/2022] Open
Abstract
The conversion of somatic cells to hepatocytes has fundamentally re-shaped traditional concepts regarding the limited resources for hepatocyte therapy. With the various induced pluripotent stem cell (iPSC) generation routes, most somatic cells can be effectively directed to functional stem cells, and this strategy will supply enough pluripotent material to generate promising functional hepatocytes. However, the major challenges and potential applications of reprogrammed hepatocytes remain under investigation. In this review, we provide a summary of two effective routes including direct reprogramming and indirect reprogramming from somatic cells to hepatocytes and the general potential applications of the resulting hepatocytes. Through these approaches, we are striving toward the goal of achieving a robust, mature source of clinically relevant lineages.
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Bazley FA, Liu CF, Yuan X, Hao H, All AH, De Los Angeles A, Zambidis ET, Gearhart JD, Kerr CL. Direct Reprogramming of Human Primordial Germ Cells into Induced Pluripotent Stem Cells: Efficient Generation of Genetically Engineered Germ Cells. Stem Cells Dev 2015; 24:2634-48. [PMID: 26154167 DOI: 10.1089/scd.2015.0100] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Primordial germ cells (PGCs) share many properties with embryonic stem cells (ESCs) and innately express several key pluripotency-controlling factors, including OCT4, NANOG, and LIN28. Therefore, PGCs may provide a simple and efficient model for studying somatic cell reprogramming to induced pluripotent stem cells (iPSCs), especially in determining the regulatory mechanisms that fundamentally define pluripotency. Here, we report a novel model of PGC reprogramming to generate iPSCs via transfection with SOX2 and OCT4 using integrative lentiviral. We also show the feasibility of using nonintegrative approaches for generating iPSC from PGCs using only these two factors. We show that human PGCs express endogenous levels of KLF4 and C-MYC protein at levels similar to embryonic germ cells (EGCs) but lower levels of SOX2 and OCT4. Transfection with both SOX2 and OCT4 together was required to induce PGCs to a pluripotent state at an efficiency of 1.71%, and the further addition of C-MYC increased the efficiency to 2.33%. Immunohistochemical analyses of the SO-derived PGC-iPSCs revealed that these cells were more similar to ESCs than EGCs regarding both colony morphology and molecular characterization. Although leukemia inhibitory factor (LIF) was not required for the generation of PGC-iPSCs like EGCs, the presence of LIF combined with ectopic exposure to C-MYC yielded higher efficiencies. Additionally, the SO-derived PGC-iPSCs exhibited differentiation into representative cell types from all three germ layers in vitro and successfully formed teratomas in vivo. Several lines were generated that were karyotypically stable for up to 24 subcultures. Their derivation efficiency and survival in culture significantly supersedes that of EGCs, demonstrating their utility as a powerful model for studying factors regulating pluripotency in future studies.
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Affiliation(s)
- Faith A Bazley
- 1 Department of Biomedical Engineering, The Johns Hopkins University School of Medicine , Baltimore, Maryland
| | - Cyndi F Liu
- 2 Department of Genecology and Obstetrics, The Johns Hopkins University School of Medicine , Baltimore, Maryland.,3 Institute for Cell Engineering, The Johns Hopkins University School of Medicine , Baltimore, Maryland
| | - Xuan Yuan
- 4 Department of Medicine, Division of Hematology, The Johns Hopkins University School of Medicine , Baltimore, Maryland
| | - Haiping Hao
- 5 JHMI Deep Sequencing and Microarray Core, High Throughput Biology Center, Johns Hopkins University , Baltimore, Maryland
| | - Angelo H All
- 1 Department of Biomedical Engineering, The Johns Hopkins University School of Medicine , Baltimore, Maryland
| | - Alejandro De Los Angeles
- 6 Stem Cell Transplantation Program, Division of Pediatric Hematology Oncology, Children's Hospital Boston , Massachusetts.,7 Department of Biological Chemistry and Molecular Pharmacology, Dana-Farber Cancer Institute , Harvard Medical School, Boston, Massachusetts.,8 Harvard Stem Cell Institute , Cambridge, Massachusetts
| | - Elias T Zambidis
- 3 Institute for Cell Engineering, The Johns Hopkins University School of Medicine , Baltimore, Maryland.,9 Division of Pediatric Oncology at the Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine , Baltimore, Maryland
| | - John D Gearhart
- 10 Department of Cell and Developmental Biology, School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania.,11 Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania , Philadelphia, Pennsylvania
| | - Candace L Kerr
- 2 Department of Genecology and Obstetrics, The Johns Hopkins University School of Medicine , Baltimore, Maryland.,12 Department of Biochemistry and Molecular Biology, University of Maryland , Baltimore, Maryland
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20
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McNamara LE, Turner LA, Burgess KV. Systems Biology Approaches Applied to Regenerative Medicine. CURRENT PATHOBIOLOGY REPORTS 2015; 3:37-45. [PMID: 25722955 PMCID: PMC4333234 DOI: 10.1007/s40139-015-0072-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Systems biology is the creation of theoretical and mathematical models for the study of biological systems, as an engine for hypothesis generation and to provide context to experimental data. It is underpinned by the collection and analysis of complex datasets from different biological systems, including global gene, RNA, protein and metabolite profiles. Regenerative medicine seeks to replace or repair tissues with compromised function (for example, through injury, deficiency or pathology), in order to improve their functionality. In this paper, we will address the application of systems biology approaches to the study of regenerative medicine, with a particular focus on approaches to study modifications to the genome, transcripts and small RNAs, proteins and metabolites.
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Affiliation(s)
- Laura E. McNamara
- Centre for Cell Engineering, University of Glasgow, Glasgow, G12 8QQ UK
| | | | - Karl V. Burgess
- Glasgow Polyomics, TCRC, University of Glasgow, Garscube Campus, Glasgow, G61 1QH UK
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21
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Mansouri A, Esmaeili F, Nejatpour A, Houshmand F, Shabani L, Ebrahimie E. Differentiation of P19 embryonal carcinoma stem cells into insulin-producing cells promoted by pancreas-conditioned medium. J Tissue Eng Regen Med 2014; 10:600-12. [DOI: 10.1002/term.1927] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 04/25/2014] [Accepted: 05/05/2014] [Indexed: 12/27/2022]
Affiliation(s)
- Akram Mansouri
- Department of Biology, Faculty of Basic Sciences; Shahrekord University; Iran
| | - Fariba Esmaeili
- Research Institute of Biotechnology; Shahrekord University; Iran
- Department of Biology, Faculty of Basic Sciences; University of Isfahan; Iran
| | | | - Fariba Houshmand
- Department of Physiology, Faculty of Medical Sciences; Shahrekord University of Medical Sciences; Iran
| | - Leila Shabani
- Department of Biology, Faculty of Basic Sciences; Shahrekord University; Iran
- Research Institute of Biotechnology; Shahrekord University; Iran
| | - Esmaeil Ebrahimie
- Institute of Biotechnology; Shiraz University; Shiraz Iran
- School of Molecular and Biomedical Science; The University of Adelaide; Adelaide Australia
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22
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23
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Sun Y, Yang Y, Zeng S, Tan Y, Lu G, Lin G. Identification of proteins related to epigenetic regulation in the malignant transformation of aberrant karyotypic human embryonic stem cells by quantitative proteomics. PLoS One 2014; 9:e85823. [PMID: 24465727 PMCID: PMC3895013 DOI: 10.1371/journal.pone.0085823] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 12/02/2013] [Indexed: 11/19/2022] Open
Abstract
Previous reports have demonstrated that human embryonic stem cells (hESCs) tend to develop genomic alterations and progress to a malignant state during long-term in vitro culture. This raises concerns of the clinical safety in using cultured hESCs. However, transformed hESCs might serve as an excellent model to determine the process of embryonic stem cell transition. In this study, ITRAQ-based tandem mass spectrometry was used to quantify normal and aberrant karyotypic hESCs proteins from simple to more complex karyotypic abnormalities. We identified and quantified 2583 proteins, and found that the expression levels of 316 proteins that represented at least 23 functional molecular groups were significantly different in both normal and abnormal hESCs. Dysregulated protein expression in epigenetic regulation was further verified in six pairs of hESC lines in early and late passage. In summary, this study is the first large-scale quantitative proteomic analysis of the malignant transformation of aberrant karyotypic hESCs. The data generated should serve as a useful reference of stem cell-derived tumor progression. Increased expression of both HDAC2 and CTNNB1 are detected as early as the pre-neoplastic stage, and might serve as prognostic markers in the malignant transformation of hESCs.
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Affiliation(s)
- Yi Sun
- Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China
- National Engineering and Research Center of Human Stem Cells, Changsha, China
- Key Laboratory of Stem Cells and Reproductive Engineering, Ministry of Health, Changsha, China
| | - Yixuan Yang
- Key Laboratory of Molecular Biology for Infectious Diseases of Ministry of Education of China, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Sicong Zeng
- Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China
| | - Yueqiu Tan
- Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China
- National Engineering and Research Center of Human Stem Cells, Changsha, China
- Key Laboratory of Stem Cells and Reproductive Engineering, Ministry of Health, Changsha, China
| | - Guangxiu Lu
- Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China
- National Engineering and Research Center of Human Stem Cells, Changsha, China
- * E-mail: (G. Lin); (G. Lu)
| | - Ge Lin
- Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China
- National Engineering and Research Center of Human Stem Cells, Changsha, China
- Key Laboratory of Stem Cells and Reproductive Engineering, Ministry of Health, Changsha, China
- * E-mail: (G. Lin); (G. Lu)
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Pryzhkova MV, Harris GM, Ma S, Jabbarzadeh E. Patterning Pluripotent Stem Cells at a Single Cell Level. J BIOMATER TISS ENG 2013; 3:461-471. [PMID: 30135745 DOI: 10.1166/jbt.2013.1106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Studies of cell-extracellular matrix (ECM) interactions at a single cell level have drawn interest from scientists around the world. Subcellular ECM micropatterning techniques allow researchers to control cell shape, migration, and spindle orientation during mitosis potentially influencing the stem cell fate. Generally these studies have been limited to somatic cells rather than human pluripotent stem cells (hPSCs) which are capable of enormous differentiation potential. hPSCs require a defined ECM for attachment and express characteristic integrins mediating cell-substrate interactions. hPSCs also rely on cell-cell contacts for survival and to maintain self-renewal properties, but these circumstances also significantly limit hPSC observation at a single cell level. In addition, currently available methods for ECM micropatterning generally require a facility with trained personnel and intricate equipment to produce protein micropatterns. To overcome this problem, we have developed a protocol for vitronectin micropatterning using simple UV/ozone modification of polystyrene. Single hPSCs were able to attach and form characteristic stress fibers and focal adhesions similar to somatic cell types which demonstrate hPSC responsiveness to extracellular adhesive cues. Micropatterned hPSCs were able to be cultured for up to 48 hours while maintaining expression of pluripotency-associated transcription factor OCT4. Although further studies are necessary, the results of our investigation will potentially have a large impact on cell regenerative medicine and tissue engineering.
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Affiliation(s)
- Marina V Pryzhkova
- Department of Chemical Engineering, University of South Carolina, SC 29208, USA
| | - Greg M Harris
- Department of Chemical Engineering, University of South Carolina, SC 29208, USA
| | - Shuguo Ma
- Department of Chemical Engineering, University of South Carolina, SC 29208, USA
| | - Ehsan Jabbarzadeh
- Department of Chemical Engineering, University of South Carolina, SC 29208, USA.,Department of Orthopaedic Surgery, University of South Carolina, SC 29208, USA.,Biomedical Engineering Program, University of South Carolina, SC 29208, USA
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25
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Hao J, Li W, Dan J, Ye X, Wang F, Zeng X, Wang L, Wang H, Cheng Y, Liu L, Shui W. Reprogramming- and pluripotency-associated membrane proteins in mouse stem cells revealed by label-free quantitative proteomics. J Proteomics 2013; 86:70-84. [DOI: 10.1016/j.jprot.2013.04.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 03/10/2013] [Accepted: 04/07/2013] [Indexed: 12/15/2022]
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26
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Alagaratnam S, Harrison N, Bakken AC, Hoff AM, Jones M, Sveen A, Moore HD, Andrews PW, Lothe RA, Skotheim RI. Transforming pluripotency: an exon-level study of malignancy-specific transcripts in human embryonal carcinoma and embryonic stem cells. Stem Cells Dev 2013; 22:1136-46. [PMID: 23137282 DOI: 10.1089/scd.2012.0369] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
To circumvent difficulties of isolating pure populations of cancer stem cells (CSCs) for the purpose of identifying malignancy-specific gene expression, we have compared exon-resolution transcriptomic profiles of 5 embryonal carcinoma (EC) cell lines, a histological subtype of germ cell tumor (GCT), to their nonmalignant caricature, specifically 6 human embryonic stem (ES) cell lines. Both cell types are readily accessible, and were purified for undifferentiated cells only. We identified a set of 28 differentially expressed genes, many of which had cancer and stemness roles. Overexpression of the recently discovered pluripotency gene NR5A2 in malignant EC cells revealed an intriguing indication of how WNT-mediated dysregulation of pluripotency is involved with malignancy. Expression of these 28 genes was further explored within 2 publically available data sets of primary EC tumors and normal testis. At the exon-level, alternative splicing events were detected in ZNF195, DNMT3B, and PMF1, and alternative promoters were detected for ASH2L and ETV5. These events were validated by reverse transcriptase-polymerase chain reaction-based methods in EC and ES lines, where the alternative splicing event in the de novo DNA methyltransferase DNMT3B may have functional consequences. In conclusion, we have identified malignancy-specific gene expression differences within a rigorous pluripotent stem cell context. These findings are of particular interest for both GCT and ES cell biology, and, in general, to the concept of CSCs.
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Affiliation(s)
- Sharmini Alagaratnam
- Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
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Kranenburg O, Emmink BL, Knol J, van Houdt WJ, Rinkes IHMB, Jimenez CR. Proteomics in studying cancer stem cell biology. Expert Rev Proteomics 2013; 9:325-36. [PMID: 22809210 DOI: 10.1586/epr.12.24] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Normal multipotent tissue stem cells (SCs) are the driving force behind tissue turnover and repair. The cancer stem cell theory holds that tumors also contain stem-like cells that drive tumor growth and metastasis formation. However, very little is known about the regulation of SC maintenance pathways in cancer and how these are affected by cancer-specific genetic alterations and by treatment. Proteomics is emerging as a powerful tool to identify the signaling complexes and pathways that control multi- and pluri-potency and SC differentiation. Here, the authors review the novel insights that these studies have provided and present a comprehensive strategy for the use of proteomics in studying cancer SC biology.
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Affiliation(s)
- Onno Kranenburg
- Department of Surgery, University Medical Center Utrecht, Heidelberglaan 100, 3584CX, The Netherlands.
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28
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Malecki M, Tombokan X, Anderson M, Malecki R, Beauchaine M. TRA-1-60 +, SSEA-4 +, POU5F1 +, SOX2 +, NANOG + Clones of Pluripotent Stem Cells in the Embryonal Carcinomas of the Testes. ACTA ACUST UNITED AC 2013; 3. [PMID: 23772337 DOI: 10.4172/2157-7633.1000134] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
INTRODUCTION Cancer of the testes is currently the most frequent neoplasm and a leading cause of morbidity in men 15-35 years of age. Its incidence is increasing. Embryonal carcinoma is its most malignant form, which either may be resistant or may develop resistance to therapies, which results in relapses. Cancer stem cells are hypothesized to be drivers of these phenomena. SPECIFIC AIM The specific aim of this work was identification and isolation of spectra of single, living cancer stem cells, which were acquired directly from the patients' biopsies, followed by testing of their pluripotency. PATIENTS METHODS Biopsies were obtained from the patients with the clinical and histological diagnoses of the primary, pure embryonal carcinomas of the testes. The magnetic and fluorescent antibodies were genetically engineered. The SSEA-4 and TRA-1-60 cell surface display was analyzed by multiphoton fluorescence spectroscopy (MPFS), flow cytometry (FCM), immunoblotting (IB), nuclear magnetic resonance spectroscopy (NMRS), energy dispersive x-ray spectroscopy (EDXS), and total reflection x-ray spectroscopy (TRXFS). The single, living cells were isolated by magnetic or fluorescent sorting followed by their clonal expansion. The OCT4A, SOX2, and NANOG genes' transcripts were analyzed by qRTPCR and the products by IB and MPFS. RESULTS The clones of cells, with the strong surface display of TRA-1-60 and SSEA-4, were identified and isolated directly from the biopsies acquired from the patients diagnosed with the pure embryonal carcinomas of the testes. These cells demonstrated high levels of transcription and translation of the pluripotency genes: OCT4A, SOX2, and NANOG. They formed embryoid bodies, which differentiated into ectoderm, mesoderm, and endoderm. CONCLUSION In the pure embryonal carcinomas of the testes, acquired directly from the patients, we identified, isolated with high viability and selectivity, and profiled the clones of the pluripotent stem cells. These results may help in explaining therapy-resistance and relapses of these neoplasms, as well as, in designing targeted, personalized therapy.
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Affiliation(s)
- Marek Malecki
- Phoenix Biomolecular Engineering Foundation, San Francisco, CA, USA ; University of Wisconsin, Madison, WI, USA
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29
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Nguyen HT, Geens M, Spits C. Genetic and epigenetic instability in human pluripotent stem cells. Hum Reprod Update 2012; 19:187-205. [PMID: 23223511 DOI: 10.1093/humupd/dms048] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND There is an increasing body of evidence that human pluripotent stem cells (hPSCs) are prone to (epi)genetic instability during in vitro culture. This review aims at giving a comprehensive overview of the current knowledge on culture-induced (epi)genetic alterations in hPSCs and their phenotypic consequences. METHODS Combinations of the following key words were applied as search criteria: human induced pluripotent stem cells and human embryonic stem cells in combination with malignancy, tumorigenicity, X inactivation, mitochondrial mutations, genomic integrity, chromosomal abnormalities, culture adaptation, aneuploidy and CD30. Only studies in English, on hPSCs and focused on (epi)genomic integrity were included. Further manuscripts were added from cross-references. RESULTS Numerous (epi)genetic aberrations have been detected in hPSCs. Recurrent genetic alterations give a selective advantage in culture to the altered cells leading to overgrowth of abnormal, culture-adapted cells. The functional effects of these alterations are not yet fully understood, but suggest a (pre)malignant transformation of abnormal cells with decreased differentiation and increased proliferative capacity. CONCLUSIONS Given the high degree of (epi)genetic alterations reported in the literature and altered phenotypic characteristics of the abnormal cells, controlling for the (epi)genetic integrity of hPSCs before any clinical application is an absolute necessity.
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Affiliation(s)
- H T Nguyen
- Research Group Reproduction and Genetics, Vrije Universiteit Brussel, Laarbeeklaan 101, 1090 Jette, Brussels, Belgium
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30
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Malecki M, Anderson M, Beauchaine M, Seo S, Tombokan X, Malecki R. TRA-1-60 +, SSEA-4 +, Oct4A +, Nanog + Clones of Pluripotent Stem Cells in the Embryonal Carcinomas of the Ovaries. JOURNAL OF STEM CELL RESEARCH & THERAPY 2012; 2:130. [PMID: 23293749 PMCID: PMC3535320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
INTRODUCTION Embryonal carcinoma of the ovary (ECO), pure or admixed to other tumors, is the deadly gynecological cancer. SPECIFIC AIM The specific aim of this work was identification, isolation, clonal expansion, and molecular profiling of the pluripotent cells in the embryonal carcinomas of the ovaries. PATIENTS METHODS The samples were acquired from the patients, who were clinically and histopathologically diagnosed with the advanced, pure embryonal carcinomas of the ovaries. The cell surface display of the TRA-1-60 and SSEA-4 was analyzed by flow cytometry (FCM), immunoblotting (IB), multiphoton fluorescence spectroscopy (MPFS), nuclear magnetic resonance spectroscopy (NMRS), and total reflection x-ray spectroscopy (TRXFS). The transcripts of the Oct4A and Nanog were analyzed by qRTPCR and MPFS and the products by MPFS. The human pluripotent, embryonic stem cells (ESC), human pluripotent, embryonal carcinoma of the testes (ECT), healthy tissues of the ovary (HTO), healthy tissue of testes (HTT), peripheral blood mononuclear cells (PBMC), and bone marrow mononuclear cells (BMMC) served as the controls. RESULTS The studied embryonal carcinomas of the ovaries (ECOs) contained the cells with the strong surface display of the TRA-1-60 and SSEA-4, which was similar to the pluripotent ESC and ECT. Their morphology was consistent with the histopathological diagnosis. Moreover, these cells showed strong expression of the Oct4A and Nanog, which was similar to the pluripotent ESC and ECT. The ECO cells formed embryoid bodies, which differentiated into ectoderm, mesoderm, and endoderm. These cells were induced to differentiate into muscles, epithelia, and neurons. CONCLUSION Herein, we revealed presence and identified molecular profiles of the clones of the pluripotent stem cells in the embryonal carcinomas of the ovaries. These results should help us with refining molecular diagnoses of these deadly neoplasms and design biomarker-targeted, patient-centered, personalized therapy.
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Affiliation(s)
- Marek Malecki
- University of Wisconsin, Madison, WI, USA
- Phoenix Biomolecular Engineering Foundation, San Francisco, CA, USA
| | - Mark Anderson
- University of Wisconsin, Madison, WI, USA
- National Institutes of Health, National Nuclear Magnetic Resonance Facility, Madison, WI, USA
| | | | | | | | - Raf Malecki
- San Francisco State University, San Francisco, CA, USA
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31
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Shah SN, Kerr C, Cope L, Zambidis E, Liu C, Hillion J, Belton A, Huso DL, Resar LMS. HMGA1 reprograms somatic cells into pluripotent stem cells by inducing stem cell transcriptional networks. PLoS One 2012; 7:e48533. [PMID: 23166588 PMCID: PMC3499526 DOI: 10.1371/journal.pone.0048533] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 09/26/2012] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Although recent studies have identified genes expressed in human embryonic stem cells (hESCs) that induce pluripotency, the molecular underpinnings of normal stem cell function remain poorly understood. The high mobility group A1 (HMGA1) gene is highly expressed in hESCs and poorly differentiated, stem-like cancers; however, its role in these settings has been unclear. METHODS/PRINCIPAL FINDINGS We show that HMGA1 is highly expressed in fully reprogrammed iPSCs and hESCs, with intermediate levels in ECCs and low levels in fibroblasts. When hESCs are induced to differentiate, HMGA1 decreases and parallels that of other pluripotency factors. Conversely, forced expression of HMGA1 blocks differentiation of hESCs. We also discovered that HMGA1 enhances cellular reprogramming of somatic cells to iPSCs together with the Yamanaka factors (OCT4, SOX2, KLF4, cMYC - OSKM). HMGA1 increases the number and size of iPSC colonies compared to OSKM controls. Surprisingly, there was normal differentiation in vitro and benign teratoma formation in vivo of the HMGA1-derived iPSCs. During the reprogramming process, HMGA1 induces the expression of pluripotency genes, including SOX2, LIN28, and cMYC, while knockdown of HMGA1 in hESCs results in the repression of these genes. Chromatin immunoprecipitation shows that HMGA1 binds to the promoters of these pluripotency genes in vivo. In addition, interfering with HMGA1 function using a short hairpin RNA or a dominant-negative construct blocks cellular reprogramming to a pluripotent state. CONCLUSIONS Our findings demonstrate for the first time that HMGA1 enhances cellular reprogramming from a somatic cell to a fully pluripotent stem cell. These findings identify a novel role for HMGA1 as a key regulator of the stem cell state by inducing transcriptional networks that drive pluripotency. Although further studies are needed, these HMGA1 pathways could be exploited in regenerative medicine or as novel therapeutic targets for poorly differentiated, stem-like cancers.
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Affiliation(s)
- Sandeep N. Shah
- Hematology Division, the Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Medicine, the Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Candace Kerr
- Obstetrics & Gynecology, the Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Leslie Cope
- Oncology, the Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Biostatistics, the Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Elias Zambidis
- Oncology, the Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Comparative Molecular & Pathobiology, the Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Cyndi Liu
- Obstetrics & Gynecology, the Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Joelle Hillion
- Hematology Division, the Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Amy Belton
- Hematology Division, the Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Medicine, the Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - David L. Huso
- Oncology, the Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Comparative Molecular & Pathobiology, the Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Pathology, the Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Linda M. S. Resar
- Hematology Division, the Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Medicine, the Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Oncology, the Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Pediatrics, the Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
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Lin Y, Yang Y, Li W, Chen Q, Li J, Pan X, Zhou L, Liu C, Chen C, He J, Cao H, Yao H, Zheng L, Xu X, Xia Z, Ren J, Xiao L, Li L, Shen B, Zhou H, Wang YJ. Reciprocal regulation of Akt and Oct4 promotes the self-renewal and survival of embryonal carcinoma cells. Mol Cell 2012; 48:627-40. [PMID: 23041284 DOI: 10.1016/j.molcel.2012.08.030] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Revised: 07/05/2012] [Accepted: 08/20/2012] [Indexed: 10/27/2022]
Abstract
Signaling via the Akt serine/threonine protein kinase plays critical roles in the self-renewal of embryonic stem cells and their malignant counterpart, embryonal carcinoma cells (ECCs). Here we show that in ECCs, Akt phosphorylated the master pluripotency factor Oct4 at threonine 235, and that the levels of phosphorylated Oct4 in ECCs correlated with resistance to apoptosis and tumorigenic potential. Phosphorylation of Oct4 increased its stability and facilitated its nuclear localization and its interaction with Sox2, which promoted the transcription of the core stemness genes POU5F1 and NANOG. Furthermore, in ECCs, unphosphorylated Oct4 bound to the AKT1 promoter and repressed its transcription. Phosphorylation of Oct4 by Akt resulted in dissociation of Oct4 from the AKT1 promoter, which activated AKT1 transcription and promoted cell survival. Therefore, a site-specific, posttranslational modification of the Oct4 protein orchestrates the regulation of its stability, subcellular localization, and transcriptional activities, which collectively promotes the survival and tumorigenicity of ECCs.
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Affiliation(s)
- Yuanji Lin
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, 79 QingChun Road, Hangzhou, Zhejiang 310003, China
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Pashai N, Hao H, All A, Gupta S, Chaerkady R, De Los Angeles A, Gearhart JD, Kerr CL. Genome-wide profiling of pluripotent cells reveals a unique molecular signature of human embryonic germ cells. PLoS One 2012; 7:e39088. [PMID: 22737227 PMCID: PMC3380858 DOI: 10.1371/journal.pone.0039088] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 05/18/2012] [Indexed: 11/18/2022] Open
Abstract
Human embryonic germ cells (EGCs) provide a powerful model for identifying molecules involved in the pluripotent state when compared to their progenitors, primordial germ cells (PGCs), and other pluripotent stem cells. Microarray and Principal Component Analysis (PCA) reveals for the first time that human EGCs possess a transcription profile distinct from PGCs and other pluripotent stem cells. Validation with qRT-PCR confirms that human EGCs and PGCs express many pluripotency-associated genes but with quantifiable differences compared to pluripotent embryonic stem cells (ESCs), induced pluripotent stem cells (IPSCs), and embryonal carcinoma cells (ECCs). Analyses also identified a number of target genes that may be potentially associated with their unique pluripotent states. These include IPO7, MED7, RBM26, HSPD1, and KRAS which were upregulated in EGCs along with other pluripotent stem cells when compared to PGCs. Other potential target genes were also found which may contribute toward a primed ESC-like state. These genes were exclusively up-regulated in ESCs, IPSCs and ECCs including PARP1, CCNE1, CDK6, AURKA, MAD2L1, CCNG1, and CCNB1 which are involved in cell cycle regulation, cellular metabolism and DNA repair and replication. Gene classification analysis also confirmed that the distinguishing feature of EGCs compared to ESCs, ECCs, and IPSCs lies primarily in their genetic contribution to cellular metabolism, cell cycle, and cell adhesion. In contrast, several genes were found upregulated in PGCs which may help distinguish their unipotent state including HBA1, DMRT1, SPANXA1, and EHD2. Together, these findings provide the first glimpse into a unique genomic signature of human germ cells and pluripotent stem cells and provide genes potentially involved in defining different states of germ-line pluripotency.
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Affiliation(s)
- Nikta Pashai
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Haiping Hao
- Deep Sequencing and Microarray Core, High Throughput Biology Center, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Angelo All
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Neurology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Siddharth Gupta
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Raghothama Chaerkady
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Alejandro De Los Angeles
- Stem Cell Transplantation Program, Division of Pediatric Hematology Oncology, Children’s Hospital Boston, Massachusetts, United States of America
- Department of Biological Chemistry and Molecular Pharmacology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Harvard Stem Cell Institute, Cambridge, Massachusetts, United States of America
| | - John D. Gearhart
- Department of Cell and Developmental Biology, Institute of Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Animal Biology, Institute of Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Candace L. Kerr
- Stem Cell Program, Institute for Cell Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Gynecology and Obstetrics, Institute for Cell Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail:
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Huang X, Tian C, Liu M, Wang Y, Tolmachev AV, Sharma S, Yu F, Fu K, Zheng J, Ding SJ. Quantitative proteomic analysis of mouse embryonic fibroblasts and induced pluripotent stem cells using 16O/18O labeling. J Proteome Res 2012; 11:2091-102. [PMID: 22375802 DOI: 10.1021/pr300155r] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Induced pluripotent stem cells (iPSC) hold great promise for regenerative medicine as well as for investigations into the pathogenesis and treatment of various diseases. Understanding of key intracellular signaling pathways and protein targets that control development of iPSC from somatic cells is essential for designing new approaches to improve reprogramming efficiency. Here, we report the development and application of an integrated quantitative proteomics platform for investigating differences in protein expressions between mouse embryonic fibroblasts (MEF) and MEF-derived iPSC. This platform consists of 16O/18O labeling, multidimensional peptide separation coupled with tandem mass spectrometry, and data analysis with UNiquant software. With this platform, a total of 2481 proteins were identified and quantified from the 16O/18O-labeled MEF-iPSC proteome mixtures with a false discovery rate of 0.01. Among them, 218 proteins were significantly upregulated, while 247 proteins were significantly downregulated in iPSC compared to MEF. Many nuclear proteins, including Hdac1, Dnmt1, Pcna, Ccnd1, Smarcc1, and subunits in DNA replication and RNA polymerase II complex, were found to be enhanced in iPSC. Protein network analysis revealed that Pcna functions as a hub orchestrating complicated mechanisms including DNA replication, epigenetic inheritance (Dnmt1), and chromatin remodeling (Smarcc1) to reprogram MEF and maintain stemness of iPSC.
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Affiliation(s)
- Xin Huang
- Department of Pathology and Microbiology, Mass Spectrometry and Proteomics Core Facility, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
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Scatena R, Bottoni P, Pontoglio A, Giardina B. The proteomics of cancer stem cells. Potential clinical applications for innovative research in oncology. Proteomics Clin Appl 2011; 5:590-602. [DOI: 10.1002/prca.201000142] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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Gundry RL, Burridge PW, Boheler KR. Pluripotent stem cell heterogeneity and the evolving role of proteomic technologies in stem cell biology. Proteomics 2011; 11:3947-61. [PMID: 21834136 DOI: 10.1002/pmic.201100100] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Revised: 04/29/2011] [Accepted: 06/08/2011] [Indexed: 12/13/2022]
Abstract
Stem cells represent obvious choices for regenerative medicine and are invaluable for studies of human development and drug testing. The proteomic landscape of pluripotent stem cells (PSCs), in particular, is not yet clearly defined; consequently, this field of research would greatly benefit from concerted efforts designed to better characterize these cells. In this concise review, we provide an overview of stem cell potency, highlight the types and practical implications of heterogeneity in PSCs and provide a detailed analysis of the current view of the pluripotent proteome in a unique resource for this rapidly evolving field. Our goal in this review is to provide specific insights into the current status of the known proteome of both mouse and human PSCs. This has been accomplished by integrating published data into a unified PSC proteome to facilitate the identification of proteins, which may be informative for the stem cell state as well as to reveal areas where our current view is limited. These analyses provide insight into the challenges faced in the proteomic analysis of PSCs and reveal one area--the cell surface subproteome--that would especially benefit from enhanced research efforts.
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Affiliation(s)
- Rebekah L Gundry
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
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37
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Chaerkady R, Letzen B, Renuse S, Sahasrabuddhe NA, Kumar P, All AH, Thakor NV, Delanghe B, Gearhart JD, Pandey A, Kerr CL. Quantitative temporal proteomic analysis of human embryonic stem cell differentiation into oligodendrocyte progenitor cells. Proteomics 2011; 11:4007-20. [PMID: 21770034 DOI: 10.1002/pmic.201100107] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 06/19/2011] [Accepted: 07/01/2011] [Indexed: 11/11/2022]
Abstract
Oligodendrocytes (OLs) are glial cells of the central nervous system, which produce myelin. Cultured OLs provide immense therapeutic opportunities for treating a variety of neurological conditions. One of the most promising sources for such therapies is human embryonic stem cells (ESCs) as well as providing a model to study human OL development. For these purposes, an investigation of proteome level changes is critical for understanding the process of OL differentiation. In this report, an iTRAQ-based quantitative proteomic approach was used to study multiple steps during OL differentiation including neural progenitor cells, glial progenitor cells and oligodendrocyte progenitor cells (OPCs) compared to undifferentiated ESCs. Using a 1% false discovery rate cutoff, ∼3145 proteins were quantitated and several demonstrated progressive stage-specific expression. Proteins such as transferrin, neural cell adhesion molecule 1, apolipoprotein E and wingless-related MMTV integration site 5A showed increased expression from the neural progenitor cell to the OPC stage. Several proteins that have demonstrated evidence or been suspected in OL maturation were also found upregulated in OPCs including fatty acid-binding protein 4, THBS1, bone morphogenetic protein 1, CRYAB, transferrin, tenascin C, COL3A1, TGFBI and EPB41L3. Thus, by providing the first extensive proteomic profiling of human ESC differentiation into OPCs, this study provides many novel proteins that are potentially involved in OL development.
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Affiliation(s)
- Raghothama Chaerkady
- McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Tenga MJ, Lazar IM. Impact of peptide modifications on the isobaric tags for relative and absolute quantitation method accuracy. Anal Chem 2011; 83:701-7. [PMID: 21210697 PMCID: PMC3717298 DOI: 10.1021/ac100775s] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In this study, the impact of amino acid modifications on the accuracy of the iTRAQ (isobaric tags for relative and absolute quantitation) method was evaluated. MCF-7 breast cancer cells, cultured in the presence of 17β-estradiol and tamoxifen, were used as a model system. The cells were labeled and analyzed by reversed-phase liquid chromatography and pulsed Q dissociation ion trap tandem mass spectrometry detection. Database searching was performed by using various combinations of amino acid modification allowances, i.e, Lys/Tyr/Cys and amino terminal iTRAQ labeling, Lys methylation, acetylation and carbamylation, and Cys/Met oxidation. Other than the intended Lys/amino terminal iTRAQ labeling, such modifications occur as a result of either enzymatic or sample preparation related reactions and are typically ignored in quantitation analysis to minimize the rate of false-positive peptide identifications. The study revealed that the modifications with the greatest impact on protein identification and quantitation pertain to Lys and Tyr amino acid residues, that by enabling such modifications the number and type of identified proteins will change (by up to 10%), and that the rate of false-positive protein identifications can be maintained below an upper threshold of 5% if appropriate data filtering conditions are used. In addition, the interference of possible posttranslational modifications (i.e., phosphorylation) with iTRAQ quantitation was examined.
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Affiliation(s)
- Milagros J. Tenga
- Department of Biological Sciences Virginia Polytechnic Institute and State University 1981 Kraft Drive, Blacksburg, VA 24061, USA
| | - Iulia M. Lazar
- Department of Biological Sciences Virginia Polytechnic Institute and State University 1981 Kraft Drive, Blacksburg, VA 24061, USA
- Virginia Bioinformatics Institute Virginia Polytechnic Institute and State University 1981 Kraft Drive, Blacksburg, VA 24061, USA
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39
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Hughes CS, Nuhn AA, Postovit LM, Lajoie GA. Proteomics of human embryonic stem cells. Proteomics 2011; 11:675-90. [DOI: 10.1002/pmic.201000407] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Revised: 09/13/2010] [Accepted: 10/14/2010] [Indexed: 01/01/2023]
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40
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Lo JF, Yu CC, Chiou SH, Huang CY, Jan CI, Lin SC, Liu CJ, Hu WY, Yu YH. The epithelial-mesenchymal transition mediator S100A4 maintains cancer-initiating cells in head and neck cancers. Cancer Res 2010; 71:1912-23. [PMID: 21169409 DOI: 10.1158/0008-5472.can-10-2350] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Cancer-initiating cells (CIC) comprise a rare subpopulation of cells in tumors that are proposed to be responsible for tumor growth. Starting from CICs identified in head and neck squamous cell carcinomas (HNSCC), termed head and neck cancer-initiating cells (HN-CIC), we determined as a candidate stemness-maintaining molecule for HN-CICs the proinflammatory mediator S100A4, which is also known to be an inducer of epithelial-mesenchymal transition. S100A4 knockdown in HN-CICs reduced their self-renewal capability and their stemness and tumorigenic properties, both in vitro and in vivo. Conversely, S100A4 overexpression in HNSCC cells enhanced their stem cell properties. Mechanistic investigations indicated that attenuation of endogenous S100A4 levels in HNSCC cells caused downregulation of Notch2 and PI3K (phosphoinositide 3-kinase)/pAKT along with upregulation of PTEN, consistent with biological findings. Immunohistochemical analysis of HNSCC clinical specimens showed that S100A4 expression was positively correlated with clinical grading, stemness markers, and poorer patient survival. Together, our findings reveal a crucial role for S100A4 signaling pathways in maintaining the stemness properties and tumorigenicity of HN-CICs. Furthermore, our findings suggest that targeting S100A4 signaling may offer a new targeted strategy for HNSCC treatment by eliminating HN-CICs.
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Affiliation(s)
- Jeng-Fan Lo
- Institute of Oral Biology, National Yang-Ming University, Taipei, Taiwan, ROC.
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