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Minor Allele Frequencies and Molecular Pathways Differences for SNPs Associated with Amyotrophic Lateral Sclerosis in Subjects Participating in the UKBB and 1000 Genomes Project. J Clin Med 2021; 10:jcm10153394. [PMID: 34362180 PMCID: PMC8348602 DOI: 10.3390/jcm10153394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/12/2021] [Accepted: 07/28/2021] [Indexed: 12/25/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a complex disease with a late onset and is characterized by the progressive loss of muscular and respiratory functions. Although recent studies have partially elucidated ALS's mechanisms, many questions remain such as what the most important molecular pathways involved in ALS are and why there is such a large difference in ALS onset among different populations. In this study, we addressed this issue with a bioinformatics approach, using the United Kingdom Biobank (UKBB) and the European 1000 Genomes Project (1KG) in order to analyze the most ALS-representative single nucleotide polymorphisms (SNPs) that differ for minor allele frequency (MAF) between the United Kingdom population and some European populations including Finnish in Finland, Iberian population in Spain, and Tuscans in Italy. We found 84 SNPs associated with 46 genes that are involved in different pathways including: "Ca2+ activated K+ channels", "cGMP effects", "Nitric oxide stimulates guanylate cyclase", "Proton/oligopeptide cotransporters", and "Signaling by MAPK mutants". In addition, we revealed that 83% of the 84 SNPs can alter transcription factor-motives binding sites of 224 genes implicated in "Regulation of beta-cell development", "Transcription-al regulation by RUNX3", "Transcriptional regulation of pluripotent stem cells", and "FOXO-mediated transcription of cell death genes". In conclusion, the genes and pathways analyzed could explain the cause of the difference of ALS onset.
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Salinas-Jazmín N, Rosas-Cruz A, Velasco-Velázquez M. Reporter gene systems for the identification and characterization of cancer stem cells. World J Stem Cells 2021; 13:861-876. [PMID: 34367481 PMCID: PMC8316869 DOI: 10.4252/wjsc.v13.i7.861] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/19/2021] [Accepted: 07/05/2021] [Indexed: 02/06/2023] Open
Abstract
Cancer stem cells (CSCs) are tumor cells that share functional characteristics with normal and embryonic stem cells. CSCs have increased tumor-initiating capacity and metastatic potential and lower sensitivity to chemo- and radiotherapy, with important roles in tumor progression and the response to therapy. Thus, a current goal of cancer research is to eliminate CSCs, necessitating an adequate phenotypic and functional characterization of CSCs. Strategies have been developed to identify, enrich, and track CSCs, many of which distinguish CSCs by evaluating the expression of surface markers, the initiation of specific signaling pathways, and the activation of master transcription factors that control stemness in normal cells. We review and discuss the use of reporter gene systems for identifying CSCs. Reporters that are under the control of aldehyde dehydrogenase 1A1, CD133, Notch, Nanog homeobox, Sex-determining region Y-box 2, and POU class 5 homeobox can be used to identify CSCs in many tumor types, track cells in real time, and screen for drugs. Thus, reporter gene systems, in combination with in vitro and in vivo functional assays, can assess changes in the CSCs pool. We present relevant examples of these systems in the evaluation of experimental CSCs-targeting therapeutics, demonstrating their value in CSCs research.
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Affiliation(s)
- Nohemí Salinas-Jazmín
- Department of Pharmacology, School of Medicine, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Arely Rosas-Cruz
- Department of Pharmacology, School of Medicine, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Marco Velasco-Velázquez
- Department of Pharmacology, School of Medicine, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico.
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53
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Phattarataratip E, Panitkul T, Khodkaew W, Anupuntanun P, Jaroonvechatam J, Pitarangsikul S. Expression of SOX2 and OCT4 in odontogenic cysts and tumors. Head Face Med 2021; 17:29. [PMID: 34261507 PMCID: PMC8278639 DOI: 10.1186/s13005-021-00283-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/08/2021] [Indexed: 11/20/2022] Open
Abstract
Background Aberrant expression of stem cell markers has been observed in several types of neoplasms. This trait attributes to the acquired stem-like property of tumor cells and can impact patient prognosis. The objective of this study was to comparatively analyze the expression and significance of SOX2 and OCT4 in various types of odontogenic cysts and tumors. Methods Fifty-five cases of odontogenic cysts and tumors, including 15 ameloblastomas (AM), 5 adenomatoid odontogenic tumors (AOT), 5 ameloblastic fibromas (AF), 5 calcifying odontogenic cysts (COC), 10 dentigerous cysts (DC) and 15 odontogenic keratocysts (OKC) were investigated for the expression of SOX2 and OCT4 immunohistochemically. Results Most OKCs (86.7 %) and all AFs expressed SOX2 in more than 50 % of epithelial cells. Its immunoreactivity was moderate-to-strong in all epithelial cell types in both lesions. In contrast, SOX2 expression was undetectable in AOTs and limited to the ameloblast-like cells in a minority of AM and COC cases. Most DCs showed positive staining in less than 25 % of cystic epithelium. Significantly greater SOX2 expression was noted in OKC compared with DC or AM, and in AF compared with COC or AOT. OCT4 rarely expressed in odontogenic lesions with the immunoreactivity being mild and present exclusively in OKCs. Conclusions SOX2 is differentially expressed in odontogenic cysts and tumors. This could be related to their diverse cells of origin or stages of histogenesis. The overexpression of SOX2 and OCT4 in OKC indicates the acquired stem-like property. Future studies should investigate whether the overexpression of OCT4 and SOX2 contributes to the aggressive behaviors of the tumors.
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Affiliation(s)
- Ekarat Phattarataratip
- Department of Oral Pathology, Faculty of Dentistry, Chulalongkorn University, Henri-Dunant Road, Pathumwan, 10330, Bangkok, Thailand.
| | - Tarit Panitkul
- Faculty of Dentistry, Chulalongkorn University, Henri-Dunant Road, Pathumwan, 10330, Bangkok, Thailand
| | - Watunyoo Khodkaew
- Faculty of Dentistry, Chulalongkorn University, Henri-Dunant Road, Pathumwan, 10330, Bangkok, Thailand
| | - Pattarapong Anupuntanun
- Faculty of Dentistry, Chulalongkorn University, Henri-Dunant Road, Pathumwan, 10330, Bangkok, Thailand
| | - Jirapat Jaroonvechatam
- Faculty of Dentistry, Chulalongkorn University, Henri-Dunant Road, Pathumwan, 10330, Bangkok, Thailand
| | - Sirawit Pitarangsikul
- Faculty of Dentistry, Chulalongkorn University, Henri-Dunant Road, Pathumwan, 10330, Bangkok, Thailand
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54
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Pluripotency-State-Dependent Role of Dax1 in Embryonic Stem Cells Self-Renewal. Stem Cells Int 2021; 2021:5522723. [PMID: 34335791 PMCID: PMC8286181 DOI: 10.1155/2021/5522723] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/18/2021] [Accepted: 06/14/2021] [Indexed: 11/24/2022] Open
Abstract
Dax1(also known as Nr0b1) is regarded as an important component of the transcription factor network in mouse embryonic stem cells (ESCs). However, the role and the molecular mechanism of Dax1 in the maintenance of different pluripotency states are poorly understood. Here, we constructed a stable Dax1 knockout (KO) cell line using the CRISPR/Cas9 system to analyze the precise function of Dax1. We reported that 2i/LIF-ESCs had significantly lower Dax1 expression than LIF/serum-ESCs. Dax1KO ES cell lines could be established in 2i/LIF and their pluripotency was confirmed. In contrast, Dax1-null ESCs could not be continuously passaged in LIF/serum due to severe differentiation and apoptosis. In LIF/serum, the activities of the Core module and Myc module were significantly reduced, while the PRC2 module was activated after Dax1KO. The expression of most proapoptotic genes and lineage-commitment genes were drastically increased, while the downregulated expression of antiapoptotic genes and many pluripotency genes was observed. Our research on the pluripotent state-dependent role of Dax1 provides clues to understand the molecular regulation mechanism at different stages of early embryonic development.
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55
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Pachano T, Sánchez-Gaya V, Ealo T, Mariner-Faulí M, Bleckwehl T, Asenjo HG, Respuela P, Cruz-Molina S, Muñoz-San Martín M, Haro E, van IJcken WFJ, Landeira D, Rada-Iglesias A. Orphan CpG islands amplify poised enhancer regulatory activity and determine target gene responsiveness. Nat Genet 2021; 53:1036-1049. [PMID: 34183853 PMCID: PMC7611182 DOI: 10.1038/s41588-021-00888-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 05/17/2021] [Indexed: 12/12/2022]
Abstract
CpG islands (CGIs) represent a widespread feature of vertebrate genomes, being associated with ~70% of all gene promoters. CGIs control transcription initiation by conferring nearby promoters with unique chromatin properties. In addition, there are thousands of distal or orphan CGIs (oCGIs) whose functional relevance is barely known. Here we show that oCGIs are an essential component of poised enhancers that augment their long-range regulatory activity and control the responsiveness of their target genes. Using a knock-in strategy in mouse embryonic stem cells, we introduced poised enhancers with or without oCGIs within topologically associating domains harboring genes with different types of promoters. Analysis of the resulting cell lines revealed that oCGIs act as tethering elements that promote the physical and functional communication between poised enhancers and distally located genes, particularly those with large CGI clusters in their promoters. Therefore, by acting as genetic determinants of gene-enhancer compatibility, CGIs can contribute to gene expression control under both physiological and potentially pathological conditions.
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Affiliation(s)
- Tomas Pachano
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria/SODERCAN, Santander, Spain
| | - Víctor Sánchez-Gaya
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria/SODERCAN, Santander, Spain
| | - Thais Ealo
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria/SODERCAN, Santander, Spain
| | - Maria Mariner-Faulí
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria/SODERCAN, Santander, Spain
| | - Tore Bleckwehl
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Helena G Asenjo
- Centre for Genomics and Oncological Research (GENYO), Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Hospital Virgen de las Nieves, Granada, Spain
| | - Patricia Respuela
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria/SODERCAN, Santander, Spain
| | - Sara Cruz-Molina
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany
| | - María Muñoz-San Martín
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria/SODERCAN, Santander, Spain
| | - Endika Haro
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria/SODERCAN, Santander, Spain
| | | | - David Landeira
- Centre for Genomics and Oncological Research (GENYO), Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Hospital Virgen de las Nieves, Granada, Spain
| | - Alvaro Rada-Iglesias
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria/SODERCAN, Santander, Spain.
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.
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56
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Wszoła M, Nitarska D, Cywoniuk P, Gomółka M, Klak M. Stem Cells as a Source of Pancreatic Cells for Production of 3D Bioprinted Bionic Pancreas in the Treatment of Type 1 Diabetes. Cells 2021; 10:1544. [PMID: 34207441 PMCID: PMC8234129 DOI: 10.3390/cells10061544] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/10/2021] [Accepted: 06/15/2021] [Indexed: 12/14/2022] Open
Abstract
Type 1 diabetes (T1D) is the third most common autoimmune disease which develops due to genetic and environmental risk factors. Often, intensive insulin therapy is insufficient, and patients require a pancreas or pancreatic islets transplant. However, both solutions are associated with many possible complications, including graft rejection. The best approach seems to be a donor-independent T1D treatment strategy based on human stem cells cultured in vitro and differentiated into insulin and glucagon-producing cells (β and α cells, respectively). Both types of cells can then be incorporated into the bio-ink used for 3D printing of the bionic pancreas, which can be transplanted into T1D patients to restore glucose homeostasis. The aim of this review is to summarize current knowledge about stem cells sources and their transformation into key pancreatic cells. Last, but not least, we comment on possible solutions of post-transplant immune response triggered stem cell-derived pancreatic cells and their potential control mechanisms.
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Affiliation(s)
- Michał Wszoła
- Foundation of Research and Science Development, 01-793 Warsaw, Poland; (M.W.); (P.C.); (M.G.)
- Polbionica Ltd., 01-793 Warsaw, Poland;
- Medispace Medical Centre, 01-044 Warsaw, Poland
| | | | - Piotr Cywoniuk
- Foundation of Research and Science Development, 01-793 Warsaw, Poland; (M.W.); (P.C.); (M.G.)
| | - Magdalena Gomółka
- Foundation of Research and Science Development, 01-793 Warsaw, Poland; (M.W.); (P.C.); (M.G.)
| | - Marta Klak
- Foundation of Research and Science Development, 01-793 Warsaw, Poland; (M.W.); (P.C.); (M.G.)
- Polbionica Ltd., 01-793 Warsaw, Poland;
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57
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Alavi S, Ghadiri H, Dabirmanesh B, Moriyama K, Khajeh K, Masai H. G-quadruplex binding protein Rif1, a key regulator of replication timing. J Biochem 2021; 169:1-14. [PMID: 33169133 DOI: 10.1093/jb/mvaa128] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/18/2020] [Indexed: 12/19/2022] Open
Abstract
DNA replication is spatially and temporally regulated during S phase to execute efficient and coordinated duplication of entire genome. Various epigenomic mechanisms operate to regulate the timing and locations of replication. Among them, Rif1 plays a major role to shape the 'replication domains' that dictate which segments of the genome are replicated when and where in the nuclei. Rif1 achieves this task by generating higher-order chromatin architecture near nuclear membrane and by recruiting a protein phosphatase. Rif1 is a G4 binding protein, and G4 binding activity of Rif1 is essential for replication timing regulation in fission yeast. In this article, we first summarize strategies by which cells regulate their replication timing and then describe how Rif1 and its interaction with G4 contribute to regulation of chromatin architecture and replication timing.
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Affiliation(s)
| | - Hamed Ghadiri
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Bahareh Dabirmanesh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Kenji Moriyama
- Genome Dynamics Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, Japan
| | - Khosro Khajeh
- Department of Nanobiotechnology.,Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Hisao Masai
- Genome Dynamics Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, Japan
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58
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Lee BK, Kim J. Integrating High-Throughput Approaches and in vitro Human Trophoblast Models to Decipher Mechanisms Underlying Early Human Placenta Development. Front Cell Dev Biol 2021; 9:673065. [PMID: 34150768 PMCID: PMC8206641 DOI: 10.3389/fcell.2021.673065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/04/2021] [Indexed: 12/13/2022] Open
Abstract
The placenta is a temporary but pivotal organ for human pregnancy. It consists of multiple specialized trophoblast cell types originating from the trophectoderm of the blastocyst stage of the embryo. While impaired trophoblast differentiation results in pregnancy disorders affecting both mother and fetus, the molecular mechanisms underlying early human placenta development have been poorly understood, partially due to the limited access to developing human placentas and the lack of suitable human in vitro trophoblast models. Recent success in establishing human trophoblast stem cells and other human in vitro trophoblast models with their differentiation protocols into more specialized cell types, such as syncytiotrophoblast and extravillous trophoblast, has provided a tremendous opportunity to understand early human placenta development. Unfortunately, while high-throughput research methods and omics tools have addressed numerous molecular-level questions in various research fields, these tools have not been widely applied to the above-mentioned human trophoblast models. This review aims to provide an overview of various omics approaches that can be utilized in the study of human in vitro placenta models by exemplifying some important lessons obtained from omics studies of mouse model systems and introducing recently available human in vitro trophoblast model systems. We also highlight some key unknown questions that might be addressed by such techniques. Integrating high-throughput omics approaches and human in vitro model systems will facilitate our understanding of molecular-level regulatory mechanisms underlying early human placenta development as well as placenta-associated complications.
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Affiliation(s)
- Bum-Kyu Lee
- Department of Biomedical Sciences, Cancer Research Center, University at Albany-State University of New York, Rensselaer, NY, United States
| | - Jonghwan Kim
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, United States
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59
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Muhr J, Hagey DW. The cell cycle and differentiation as integrated processes: Cyclins and CDKs reciprocally regulate Sox and Notch to balance stem cell maintenance. Bioessays 2021; 43:e2000285. [PMID: 34008221 DOI: 10.1002/bies.202000285] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 04/15/2021] [Accepted: 04/21/2021] [Indexed: 12/18/2022]
Abstract
Development and maintenance of diverse organ systems require context-specific regulation of stem cell behaviour. We hypothesize that this is achieved via reciprocal regulation between the cell cycle machinery and differentiation factors. This idea is supported by the parallel evolutionary emergence of differentiation pathways, cell cycle components and complex multicellularity. In addition, the activities of different cell cycle phases have been found to bias cells towards stem cell maintenance or differentiation. Finally, several direct mechanistic links between these two processes have been established. Here, we focus on interactions between cyclin-CDK complexes and differentiation regulators of the Notch pathway and Sox family of transcription factors within the context of pluripotent and neural stem cells. Thus, this hypothesis formalizes the links between these two processes as an integrated network. Since such factors are common to all stem cells, better understanding their interconnections will help to explain their behaviour in health and disease.
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Affiliation(s)
- Jonas Muhr
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Daniel W Hagey
- Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
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60
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PHC1 maintains pluripotency by organizing genome-wide chromatin interactions of the Nanog locus. Nat Commun 2021; 12:2829. [PMID: 33990559 PMCID: PMC8121881 DOI: 10.1038/s41467-021-22871-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 04/03/2021] [Indexed: 12/13/2022] Open
Abstract
Polycomb group (PcG) proteins maintain cell identity by repressing gene expression during development. Surprisingly, emerging studies have recently reported that a number of PcG proteins directly activate gene expression during cell fate determination process. However, the mechanisms by which they direct gene activation in pluripotency remain poorly understood. Here, we show that Phc1, a subunit of canonical polycomb repressive complex 1 (cPRC1), can exert its function in pluripotency maintenance via a PRC1-independent activation of Nanog. Ablation of Phc1 reduces the expression of Nanog and overexpression of Nanog partially rescues impaired pluripotency caused by Phc1 depletion. We find that Phc1 interacts with Nanog and activates Nanog transcription by stabilizing the genome-wide chromatin interactions of the Nanog locus. This adds to the already known canonical function of PRC1 in pluripotency maintenance via a PRC1-dependent repression of differentiation genes. Overall, our study reveals a function of Phc1 to activate Nanog transcription through regulating chromatin architecture and proposes a paradigm for PcG proteins to maintain pluripotency. Phc1 is a subunit of the polycomb repressive complex 1 (PRC1), which represses gene expression during development. Here the authors show that Phc1 acts independently from PRC1 to activate Nanog transcription by stabilizing genome-wide chromatin interactions of the Nanog locus, and in turn stabilize pluripotency.
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61
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Wang X, Ruan Y, Zhang J, Tian Y, Liu L, Wang J, Liu G, Cheng Y, Xu Y, Yang Y, Yu M, Zhao B, Zhang Y, Wang J, Wang J, Wu W, He P, Xiao L, Xiong J, Jian R. Expression levels and activation status of Yap splicing isoforms determine self-renewal and differentiation potential of embryonic stem cells. STEM CELLS (DAYTON, OHIO) 2021; 39:1178-1191. [PMID: 33938099 DOI: 10.1002/stem.3389] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 03/30/2021] [Indexed: 11/10/2022]
Abstract
Yap is the key effector of Hippo signaling; however, its role in embryonic stem cells (ESCs) remains controversial. Here, we identify two Yap splicing isoforms (Yap472 and Yap488), which show equal expression levels but heterogeneous distribution in ESCs. Knockout (KO) of both isoforms reduces ESC self-renewal, accelerates pluripotency exit, but arrests terminal differentiation, while overexpression of each isoform leads to the reverse phenotype. The effect of both Yap isoforms on self-renewal is Teads-dependent and mediated by c-Myc. Nonetheless, different isoforms are found to affect overlapping yet distinct genes, and confer different developmental potential to Yap-KO cells, with Yap472 exerting a more pronounced biological effect and being more essential for neuroectoderm differentiation. Constitutive activation of Yaps, particularly Yap472, dramatically upregulates p53 and Cdx2, inducing trophectoderm trans-differentiation even under self-renewal conditions. These findings reveal the combined roles of different Yap splicing isoforms and mechanisms in regulating self-renewal efficiency and differentiation potential of ESCs.
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Affiliation(s)
- Xueyue Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Army Medical University, Chongqing, People's Republic of China.,Department of Paediatrics, The General Hospital of PLA Tibet Military Area Command, Lhasa, People's Republic of China
| | - Yan Ruan
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Army Medical University, Chongqing, People's Republic of China
| | - Junlei Zhang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Army Medical University, Chongqing, People's Republic of China
| | - Yanping Tian
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Army Medical University, Chongqing, People's Republic of China
| | - Lianlian Liu
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Army Medical University, Chongqing, People's Republic of China
| | - JiaLi Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Army Medical University, Chongqing, People's Republic of China
| | - Gaoke Liu
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Army Medical University, Chongqing, People's Republic of China
| | - Yuda Cheng
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Army Medical University, Chongqing, People's Republic of China
| | - Yixiao Xu
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Army Medical University, Chongqing, People's Republic of China.,Southwest Hospital/Southwest Eye Hospital, The First Hospital Affiliated to Army Medical University, Chongqing, People's Republic of China
| | - Yi Yang
- Experimental Center of Basic Medicine, College of Basic Medical Sciences, Army Medical University, Chongqing, People's Republic of China
| | - Meng Yu
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Army Medical University, Chongqing, People's Republic of China
| | - Binyu Zhao
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Army Medical University, Chongqing, People's Republic of China
| | - Yue Zhang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Army Medical University, Chongqing, People's Republic of China.,Southwest Hospital/Southwest Eye Hospital, The First Hospital Affiliated to Army Medical University, Chongqing, People's Republic of China
| | - Jiaqi Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Army Medical University, Chongqing, People's Republic of China
| | - Jiangjun Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Army Medical University, Chongqing, People's Republic of China
| | - Wei Wu
- Thoracic Surgery Department, Southwest Hospital, The First Hospital Affiliated to Army Medical University, Chongqing, People's Republic of China
| | - Ping He
- Cardiac Surgery Department, Southwest Hospital, The First Hospital Affiliated to Army Medical University, Chongqing, People's Republic of China
| | - Lan Xiao
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Army Medical University, Chongqing, People's Republic of China
| | - Jiaxiang Xiong
- Experimental Center of Basic Medicine, College of Basic Medical Sciences, Army Medical University, Chongqing, People's Republic of China
| | - Rui Jian
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Army Medical University, Chongqing, People's Republic of China
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62
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Paonessa M, Borini A, Coticchio G. Genetic causes of preimplantation embryo developmental failure. Mol Reprod Dev 2021; 88:338-348. [PMID: 33843124 DOI: 10.1002/mrd.23471] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/27/2021] [Accepted: 03/23/2021] [Indexed: 12/13/2022]
Abstract
Embryo development requires orchestrated events, finely regulated at the molecular and cellular level by mechanisms which are progressively emerging from animal studies. With progress in genetic technologies-such as genome editing and single-cell RNA analysis-we can now assess embryo gene expression with increased precision and gain new insights into complex processes until recently difficult to explore. Multiple genes and regulative pathways have been identified for each developmental stage. We have learned that embryos with undisturbed and timely gene expression have higher chances of successful development. For example, selected genes are highly expressed during the first stages, being involved in cell adhesion, cell cycle, and regulation of transcription; other genes are instead crucial for lineage specification and therefore expressed at later stages. Due to ethical constraints, studies on human embryos remain scarce, mainly descriptive, and unable to provide functional evidence. This highlights the importance of animal studies as basic knowledge to test and appraise in a clinical context. In this review, we report on preimplantation development with a focus on genes whose impairment leads to developmental arrest. Preconceptional genetic screening could identify loss-of-function mutations of these genes; thereby, novel biomarkers of embryo quality could be adopted to improve diagnosis and treatment of infertility.
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Affiliation(s)
- Mariagrazia Paonessa
- 9.Baby, Family and Fertility Center, Bologna, Italy.,Casa di Cura Candela Spa, Palermo, Italy
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63
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Iyer AA, Groves AK. Transcription Factor Reprogramming in the Inner Ear: Turning on Cell Fate Switches to Regenerate Sensory Hair Cells. Front Cell Neurosci 2021; 15:660748. [PMID: 33854418 PMCID: PMC8039129 DOI: 10.3389/fncel.2021.660748] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/08/2021] [Indexed: 12/15/2022] Open
Abstract
Non-mammalian vertebrates can restore their auditory and vestibular hair cells naturally by triggering the regeneration of adjacent supporting cells. The transcription factor ATOH1 is a key regulator of hair cell development and regeneration in the inner ear. Following the death of hair cells, supporting cells upregulate ATOH1 and give rise to new hair cells. However, in the mature mammalian cochlea, such natural regeneration of hair cells is largely absent. Transcription factor reprogramming has been used in many tissues to convert one cell type into another, with the long-term hope of achieving tissue regeneration. Reprogramming transcription factors work by altering the transcriptomic and epigenetic landscapes in a target cell, resulting in a fate change to the desired cell type. Several studies have shown that ATOH1 is capable of reprogramming cochlear non-sensory tissue into cells resembling hair cells in young animals. However, the reprogramming ability of ATOH1 is lost with age, implying that the potency of individual hair cell-specific transcription factors may be reduced or lost over time by mechanisms that are still not clear. To circumvent this, combinations of key hair cell transcription factors have been used to promote hair cell regeneration in older animals. In this review, we summarize recent findings that have identified and studied these reprogramming factor combinations for hair cell regeneration. Finally, we discuss the important questions that emerge from these findings, particularly the feasibility of therapeutic strategies using reprogramming factors to restore human hearing in the future.
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Affiliation(s)
- Amrita A. Iyer
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Program in Genetics & Genomics, Houston, TX, United States
| | - Andrew K. Groves
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Program in Genetics & Genomics, Houston, TX, United States
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
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64
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Sevilla A, Papatsenko D, Mazloom AR, Xu H, Vasileva A, Unwin RD, LeRoy G, Chen EY, Garrett-Bakelman FE, Lee DF, Trinite B, Webb RL, Wang Z, Su J, Gingold J, Melnick A, Garcia BA, Whetton AD, MacArthur BD, Ma'ayan A, Lemischka IR. An Esrrb and Nanog Cell Fate Regulatory Module Controlled by Feed Forward Loop Interactions. Front Cell Dev Biol 2021; 9:630067. [PMID: 33816475 PMCID: PMC8017264 DOI: 10.3389/fcell.2021.630067] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/17/2021] [Indexed: 01/02/2023] Open
Abstract
Cell fate decisions during development are governed by multi-factorial regulatory mechanisms including chromatin remodeling, DNA methylation, binding of transcription factors to specific loci, RNA transcription and protein synthesis. However, the mechanisms by which such regulatory “dimensions” coordinate cell fate decisions are currently poorly understood. Here we quantified the multi-dimensional molecular changes that occur in mouse embryonic stem cells (mESCs) upon depletion of Estrogen related receptor beta (Esrrb), a key pluripotency regulator. Comparative analyses of expression changes subsequent to depletion of Esrrb or Nanog, indicated that a system of interlocked feed-forward loops involving both factors, plays a central part in regulating the timing of mESC fate decisions. Taken together, our meta-analyses support a hierarchical model in which pluripotency is maintained by an Oct4-Sox2 regulatory module, while the timing of differentiation is regulated by a Nanog-Esrrb module.
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Affiliation(s)
- Ana Sevilla
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Departament de Biología Cellular, Fisiología i Immunología, Facultat de Biología, Universitat de Barcelona, Barcelona, Spain
| | - Dimitri Papatsenko
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Amin R Mazloom
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Huilei Xu
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Ana Vasileva
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Richard D Unwin
- Stem Cell and Leukaemia Proteomics Laboratory, School of Cancer and Enabling Sciences, Faculty of Medical and Human Sciences, University of Manchester, Manchester, United Kingdom.,Academic Health Science Centre, Wolfson Molecular Imaging Centre, Manchester, United Kingdom.,Centre for Advanced Discovery and Experimental Therapeutics, Central Manchester University Hospitals NHS Foundation Trust, Institute of Human Development, Faculty of Medical and Human Sciences, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
| | - Gary LeRoy
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States
| | - Edward Y Chen
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Francine E Garrett-Bakelman
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, United States
| | - Dung-Fang Lee
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Benjamin Trinite
- Institut de Recerca de La Sida, IrsiCaixa AIDS Research Institute, Germans Trias I Pujol Research Institute, Hospital Universitari Germans Trias I Pujol, Catalonia, Spain
| | - Ryan L Webb
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Zichen Wang
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jie Su
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Julian Gingold
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Ari Melnick
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, United States
| | - Benjamin A Garcia
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States
| | - Anthony D Whetton
- Stem Cell and Leukaemia Proteomics Laboratory, School of Cancer and Enabling Sciences, Faculty of Medical and Human Sciences, University of Manchester, Manchester, United Kingdom.,Academic Health Science Centre, Wolfson Molecular Imaging Centre, Manchester, United Kingdom
| | - Ben D MacArthur
- The Centre for Human Development, Stem Cells and Regeneration, Institute of Developmental Sciences, University of Southampton, Southampton, United Kingdom
| | - Avi Ma'ayan
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Ihor R Lemischka
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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65
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Choi HJ, Jin SD, Rengaraj D, Kim JH, Pain B, Han JY. Differential transcriptional regulation of the NANOG gene in chicken primordial germ cells and embryonic stem cells. J Anim Sci Biotechnol 2021; 12:40. [PMID: 33658075 PMCID: PMC7931612 DOI: 10.1186/s40104-021-00563-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 01/26/2021] [Indexed: 01/06/2023] Open
Abstract
Background NANOG is a core transcription factor (TF) in embryonic stem cells (ESCs) and primordial germ cells (PGCs). Regulation of the NANOG gene by TFs, epigenetic factors, and autoregulatory factors is well characterized in ESCs, and transcriptional regulation of NANOG is well established in these cells. Although NANOG plays a key role in germ cells, the molecular mechanism underlying its transcriptional regulation in PGCs has not been studied. Therefore, we investigated the mechanism that regulates transcription of the chicken NANOG (cNANOG) gene in PGCs and ESCs. Results We first identified the transcription start site of cNANOG by 5′-rapid amplification of cDNA ends PCR analysis. Then, we measured the promoter activity of various 5′ flanking regions of cNANOG in chicken PGCs and ESCs using the luciferase reporter assay. cNANOG expression required transcriptional regulatory elements, which were positively regulated by POU5F3 (OCT4) and SOX2 and negatively regulated by TP53 in PGCs. The proximal region of the cNANOG promoter contains a positive transcriptional regulatory element (CCAAT/enhancer-binding protein (CEBP)-binding site) in ESCs. Furthermore, small interfering RNA-mediated knockdown demonstrated that POU5F3, SOX2, and CEBP played a role in cell type-specific transcription of cNANOG. Conclusions We show for the first time that different trans-regulatory elements control transcription of cNANOG in a cell type-specific manner. This finding might help to elucidate the mechanism that regulates cNANOG expression in PGCs and ESCs.
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Affiliation(s)
- Hee Jung Choi
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - So Dam Jin
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Deivendran Rengaraj
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Jin Hwa Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Bertrand Pain
- Univ Lyon, Universite ́Lyon 1, INSERM, INRAE, Stem Cell and Brain Research Institute, U1208, USC1361, 69500, Bron, France
| | - Jae Yong Han
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea. .,Institute for Biomedical Sciences, Shinshu University, Minamiminowa, Nagano, 399-4598, Japan.
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66
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Abstract
In the past several decades, the establishment of in vitro models of pluripotency has ushered in a golden era for developmental and stem cell biology. Research in this arena has led to profound insights into the regulatory features that shape early embryonic development. Nevertheless, an integrative theory of the epigenetic principles that govern the pluripotent nucleus remains elusive. Here, we summarize the epigenetic characteristics that define the pluripotent state. We cover what is currently known about the epigenome of pluripotent stem cells and reflect on the use of embryonic stem cells as an experimental system. In addition, we highlight insights from super-resolution microscopy, which have advanced our understanding of the form and function of chromatin, particularly its role in establishing the characteristically "open chromatin" of pluripotent nuclei. Further, we discuss the rapid improvements in 3C-based methods, which have given us a means to investigate the 3D spatial organization of the pluripotent genome. This has aided the adaptation of prior notions of a "pluripotent molecular circuitry" into a more holistic model, where hotspots of co-interacting domains correspond with the accumulation of pluripotency-associated factors. Finally, we relate these earlier hypotheses to an emerging model of phase separation, which posits that a biophysical mechanism may presuppose the formation of a pluripotent-state-defining transcriptional program.
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Affiliation(s)
| | - Eran Meshorer
- Department of Genetics, the Institute of Life Sciences
- Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem, Israel 9190400
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67
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Wu Y, Zhang W. The Role of E3s in Regulating Pluripotency of Embryonic Stem Cells and Induced Pluripotent Stem Cells. Int J Mol Sci 2021; 22:1168. [PMID: 33503896 PMCID: PMC7865285 DOI: 10.3390/ijms22031168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 01/15/2021] [Accepted: 01/20/2021] [Indexed: 12/14/2022] Open
Abstract
Pluripotent embryonic stem cells (ESCs) are derived from early embryos and can differentiate into any type of cells in living organisms. Induced pluripotent stem cells (iPSCs) resemble ESCs, both of which serve as excellent sources to study early embryonic development and realize cell replacement therapies for age-related degenerative diseases and other cell dysfunction-related illnesses. To achieve these valuable applications, comprehensively understanding of the mechanisms underlying pluripotency maintenance and acquisition is critical. Ubiquitination modifies proteins with Ubiquitin (Ub) at the post-translational level to monitor protein stability and activity. It is extensively involved in pluripotency-specific regulatory networks in ESCs and iPSCs. Ubiquitination is achieved by sequential actions of the Ub-activating enzyme E1, Ub-conjugating enzyme E2, and Ub ligase E3. Compared with E1s and E2s, E3s are most abundant, responsible for substrate selectivity and functional diversity. In this review, we focus on E3 ligases to discuss recent progresses in understanding how they regulate pluripotency and somatic cell reprogramming through ubiquitinating core ESC regulators.
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Affiliation(s)
| | - Weiwei Zhang
- College of Life Sciences, Capital Normal University, Beijing 100048, China;
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68
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Deng Z, Jin J, Wang S, Qi F, Chen X, Liu C, Li Y, Ma Y, Lyu F, Zheng Q. Narrative review of the choices of stem cell sources and hydrogels for cartilage tissue engineering. ANNALS OF TRANSLATIONAL MEDICINE 2021; 8:1598. [PMID: 33437797 PMCID: PMC7791208 DOI: 10.21037/atm-20-2342] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Stem cell-based therapy is a promising treatment for cartilage defects due to the pluripotency, abundant sources and low immunogenicity of stem cells. Hydrogels are a promising class of biomaterials for cartilage engineering and are characterized by bioactivity, degradability and elasticity as well as provide water content and mechanical support. The combination of stem cells and hydrogels opens new possibilities for cartilage tissue engineering. However, the selection of suitable types of stem cells and hydrogels is difficult. Currently, various types of stem cells, such as embryonic stem cells (ESCs), mesenchymal stem cells (MSCs), induced pluripotent stem cells (iPSCs), and peripheral blood mononuclear cells (PBMSCs), and various types of hydrogels, including natural polymers, chemically modified natural polymers and synthetic polymers, have been explored based on their potential for cartilage tissue engineering. These materials are used independently or in combination; however, there is no clear understanding of their merits and disadvantages with regard to their suitability for cartilage repair. In this article, we aim to review recent progress in the use of stem cell-hydrogel hybrid constructs for cartilage tissue engineering. We focus on the effects of stem cell types and hydrogel types on efficient chondrogenesis from cellular, preclinical and clinical perspectives. We compare and analyze the advantages and disadvantages of these cells and hydrogels with the hope of increasing discussion of their suitability for cartilage repair and present our perspective on their use for the improvement of physical and biological properties for cartilage tissue engineering.
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Affiliation(s)
- Zhantao Deng
- Department of Orthopedics, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jiewen Jin
- Department of Endocrinology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shuai Wang
- Department of Orthopedics, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Fangjie Qi
- Department of Orthopedics, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xuepan Chen
- Department of Orthopedics, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Chang Liu
- Department of Orthopedics, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yanbing Li
- Department of Endocrinology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yuanchen Ma
- Department of Orthopedics, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Fengjuan Lyu
- Department of Orthopedics, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,South China University of Technology-the University of Western Australia Joint Center for Regenerative Medicine Research, School of Medicine, South China University of Technology, Guangzhou, China
| | - Qiujian Zheng
- Department of Orthopedics, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
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69
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Emisoglu-Kulahli H, Gul S, Morgil H, Ozcan O, Aygenli F, Selvi S, Kavakli IH, Ozturk N. Transcriptome analysis of the circadian clock gene BMAL1 deletion with opposite carcinogenic effects. Funct Integr Genomics 2021; 21:1-16. [PMID: 33111200 DOI: 10.1007/s10142-020-00757-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/14/2020] [Accepted: 10/21/2020] [Indexed: 12/26/2022]
Abstract
We have previously reported that the deletion of BMAL1 gene has opposite effects in respect to its contribution to the pathways that are effective in the multistage carcinogenesis process. BMAL1 deletion sensitized nearly normal breast epithelial (MCF10A) and invasive breast cancer cells (MDA-MB-231) to cisplatin- and doxorubicin-induced apoptosis, while this deletion also aggravated the invasive potential of MDA-MB-231 cells. However, the mechanistic relationship of the seemingly opposite contribution of BMAL1 deletion to carcinogenesis process is not known at genome-wide level. In this study, an RNA-seq approach was taken to uncover the differentially expressed genes (DEGs) and pathways after treating BMAL1 knockout (KO) or wild-type (WT) MDA-MB-231 cells with cisplatin and doxorubicin to initiate apoptosis. Gene set enrichment analysis with the DEGs demonstrated that enrichment in multiple genes/pathways contributes to sensitization to cisplatin- or doxorubicin-induced apoptosis in BMAL1-dependent manner. Additionally, our DEG analysis suggested that non-coding transcript RNA (such as lncRNA and processed pseudogenes) may have role in cisplatin- or doxorubicin-induced apoptosis. Protein-protein interaction network obtained from common DEGs in cisplatin and doxorubicin treatments revealed that GSK3β, NACC1, and EGFR are the principal genes regulating the response of the KO cells. Moreover, the analysis of DEGs among untreated BMAL1 KO and WT cells revealed that epithelial-mesenchymal transition genes are up-regulated in KO cells. As a negative control, we have also analyzed the DEGs following treatment with an endoplasmic reticulum (ER) stress-inducing agent, tunicamycin, which was affected by BMAL1 deletion minimally. Collectively, the present study suggests that BMAL1 regulates many genes/pathways of which the alteration in BMAL1 KO cells may shed light on pleotropic phenotype observed.
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Affiliation(s)
- Handan Emisoglu-Kulahli
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Seref Gul
- Department of Molecular Biology and Genetics, Koc University, Istanbul, Turkey
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
| | - Hande Morgil
- Department of Biology, Istanbul University, Istanbul, Turkey
- Istanbul University Centre for Plant and Herbal Products Research-Development, 34126, Istanbul, Turkey
| | - Onur Ozcan
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
| | - Fatih Aygenli
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey
- Institute of Medical Psychology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Saba Selvi
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Ibrahim Halil Kavakli
- Department of Molecular Biology and Genetics, Koc University, Istanbul, Turkey
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
| | - Nuri Ozturk
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey.
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70
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Auer JMT, Stoddart JJ, Christodoulou I, Lima A, Skouloudaki K, Hall HN, Vukojević V, Papadopoulos DK. Of numbers and movement - understanding transcription factor pathogenesis by advanced microscopy. Dis Model Mech 2020; 13:dmm046516. [PMID: 33433399 PMCID: PMC7790199 DOI: 10.1242/dmm.046516] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Transcription factors (TFs) are life-sustaining and, therefore, the subject of intensive research. By regulating gene expression, TFs control a plethora of developmental and physiological processes, and their abnormal function commonly leads to various developmental defects and diseases in humans. Normal TF function often depends on gene dosage, which can be altered by copy-number variation or loss-of-function mutations. This explains why TF haploinsufficiency (HI) can lead to disease. Since aberrant TF numbers frequently result in pathogenic abnormalities of gene expression, quantitative analyses of TFs are a priority in the field. In vitro single-molecule methodologies have significantly aided the identification of links between TF gene dosage and transcriptional outcomes. Additionally, advances in quantitative microscopy have contributed mechanistic insights into normal and aberrant TF function. However, to understand TF biology, TF-chromatin interactions must be characterised in vivo, in a tissue-specific manner and in the context of both normal and altered TF numbers. Here, we summarise the advanced microscopy methodologies most frequently used to link TF abundance to function and dissect the molecular mechanisms underlying TF HIs. Increased application of advanced single-molecule and super-resolution microscopy modalities will improve our understanding of how TF HIs drive disease.
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Affiliation(s)
- Julia M T Auer
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 1XU, UK
| | - Jack J Stoddart
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 1XU, UK
| | | | - Ana Lima
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 1XU, UK
| | | | - Hildegard N Hall
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 1XU, UK
| | - Vladana Vukojević
- Center for Molecular Medicine (CMM), Department of Clinical Neuroscience, Karolinska Institutet, 17176 Stockholm, Sweden
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71
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Sohn EJ, Moon HJ, Lim JK, Kim DS, Kim JH. Regulation of the protein stability and transcriptional activity of OCT4 in stem cells. Adv Biol Regul 2020; 79:100777. [PMID: 33451972 DOI: 10.1016/j.jbior.2020.100777] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/15/2020] [Accepted: 12/21/2020] [Indexed: 12/31/2022]
Abstract
OCT4 (also known as Oct3 and Oct3/4), which is encoded by Pou5f1, is expressed in early embryonic cells and plays an important role in early development, pluripotency maintenance, and self-renewal of embryonic stem cells. It also regulates the reprogramming of somatic cells into induced pluripotent stem cells. Several OCT4-binding proteins, including SOX2 and NANOG, reportedly regulate gene transcription in stem cells. An increasing number of evidence suggests that not only gene transcription but also post-translational modifications of OCT4 play a pivotal role in regulating the expression and activity of OCT4. For instance, ubiquitination and sumoylation have been reported to regulate OCT4 protein stability. In addition, the phosphorylation of Ser347 in OCT4 also stabilizes the OCT4 protein level. Recently, we identified KAP1 as an OCT4-binding protein and reported the KAP1-mediated regulation of OCT4 protein stability. KAP1 overexpression led to an increased proliferation of mouse embryonic stem cells and promoted the reprogramming of somatic cells resulting in induced pluripotent stem cells. In this review, we discuss how the protein stability and function of OCT4 are regulated by protein-protein interaction in stem cells.
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Affiliation(s)
- Eun Jung Sohn
- Medical Research Center for Ischemic Tissue Regeneration, Pusan National University, Yangsan, 50612, Republic of Korea; Department of Physiology, School of Medicine, Pusan National University, Yangsan, 50612, Republic of Korea
| | - Hye Ji Moon
- Medical Research Center for Ischemic Tissue Regeneration, Pusan National University, Yangsan, 50612, Republic of Korea; Department of Physiology, School of Medicine, Pusan National University, Yangsan, 50612, Republic of Korea
| | - Jae Kyong Lim
- Medical Research Center for Ischemic Tissue Regeneration, Pusan National University, Yangsan, 50612, Republic of Korea; Department of Physiology, School of Medicine, Pusan National University, Yangsan, 50612, Republic of Korea
| | - Da Sol Kim
- Medical Research Center for Ischemic Tissue Regeneration, Pusan National University, Yangsan, 50612, Republic of Korea; Department of Physiology, School of Medicine, Pusan National University, Yangsan, 50612, Republic of Korea
| | - Jae Ho Kim
- Medical Research Center for Ischemic Tissue Regeneration, Pusan National University, Yangsan, 50612, Republic of Korea.
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72
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Nucleus Accumbens-Associated Protein 1 Binds DNA Directly through the BEN Domain in a Sequence-Specific Manner. Biomedicines 2020; 8:biomedicines8120608. [PMID: 33327466 PMCID: PMC7764960 DOI: 10.3390/biomedicines8120608] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/10/2020] [Accepted: 12/10/2020] [Indexed: 01/03/2023] Open
Abstract
Nucleus accumbens-associated protein 1 (NAC1) is a nuclear protein that harbors an amino-terminal BTB domain and a carboxyl-terminal BEN domain. NAC1 appears to play significant and diverse functions in cancer and stem cell biology. Here we demonstrated that the BEN domain of NAC1 is a sequence-specific DNA-binding domain. We selected the palindromic 6 bp motif ACATGT as a target sequence by using a PCR-assisted random oligonucleotide selection approach. The interaction between NAC1 and target DNA was characterized by gel shift assays, pull-down assays, isothermal titration calorimetry (ITC), chromatin-immunoprecipitation assays, and NMR chemical shifts perturbation (CSP). The solution NMR structure revealed that the BEN domain of human NAC-1 is composed of five conserved α helices and two short β sheets, with an additional hitherto unknown N-terminal α helix. In particular, ITC clarified that there are two sequential events in the titration of the BEN domain of NAC1 into the target DNA. The ITC results were further supported by CSP data and structure analyses. Furthermore, live cell photobleaching analyses revealed that the BEN domain of NAC1 alone was unable to interact with chromatin/other proteins in cells.
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73
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Pelham-Webb B, Murphy D, Apostolou E. Dynamic 3D Chromatin Reorganization during Establishment and Maintenance of Pluripotency. Stem Cell Reports 2020; 15:1176-1195. [PMID: 33242398 PMCID: PMC7724465 DOI: 10.1016/j.stemcr.2020.10.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 10/25/2020] [Accepted: 10/27/2020] [Indexed: 12/12/2022] Open
Abstract
Higher-order chromatin structure is tightly linked to gene expression and therefore cell identity. In recent years, the chromatin landscape of pluripotent stem cells has become better characterized, and unique features at various architectural levels have been revealed. However, the mechanisms that govern establishment and maintenance of these topological characteristics and the temporal and functional relationships with transcriptional or epigenetic features are still areas of intense study. Here, we will discuss progress and limitations of our current understanding regarding how the 3D chromatin topology of pluripotent stem cells is established during somatic cell reprogramming and maintained during cell division. We will also discuss evidence and theories about the driving forces of topological reorganization and the functional links with key features and properties of pluripotent stem cell identity.
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Affiliation(s)
- Bobbie Pelham-Webb
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10021, USA
| | - Dylan Murphy
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Effie Apostolou
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA.
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Lezmi E, Weissbein U, Golan-Lev T, Nissim-Rafinia M, Meshorer E, Benvenisty N. The Chromatin Regulator ZMYM2 Restricts Human Pluripotent Stem Cell Growth and Is Essential for Teratoma Formation. Stem Cell Reports 2020; 15:1275-1286. [PMID: 32559458 PMCID: PMC7724477 DOI: 10.1016/j.stemcr.2020.05.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 05/19/2020] [Accepted: 05/19/2020] [Indexed: 01/13/2023] Open
Abstract
Chromatin regulators play fundamental roles in controlling pluripotency and differentiation. We examined the effect of mutations in 703 genes from nearly 70 chromatin-modifying complexes on human embryonic stem cell (ESC) growth. While the vast majority of chromatin-associated complexes are essential for ESC growth, the only complexes that conferred growth advantage upon mutation of their members, were the repressive complexes LSD-CoREST and BHC. Both complexes include the most potent growth-restricting chromatin-related protein, ZMYM2. Interestingly, while ZMYM2 expression is rather low in human blastocysts, its expression peaks in primed ESCs and is again downregulated upon differentiation. ZMYM2-null ESCs overexpress pluripotency genes and show genome-wide promotor-localized histone H3 hyper-acetylation. These mutant cells were also refractory to differentiate in vitro and failed to produce teratomas upon injection into immunodeficient mice. Our results suggest a central role for ZMYM2 in the transcriptional regulation of the undifferentiated state and in the exit-from-pluripotency of human ESCs.
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Affiliation(s)
- Elyad Lezmi
- The Azrieli Center for Stem Cells and Genetic Research, The Hebrew University, Jerusalem, Israel
| | - Uri Weissbein
- The Azrieli Center for Stem Cells and Genetic Research, The Hebrew University, Jerusalem, Israel
| | - Tamar Golan-Lev
- The Azrieli Center for Stem Cells and Genetic Research, The Hebrew University, Jerusalem, Israel; Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Malka Nissim-Rafinia
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel; Edmond and Lily Center for Brain Sciences (ELSC), The Hebrew University, Jerusalem, Israel
| | - Eran Meshorer
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel; Edmond and Lily Center for Brain Sciences (ELSC), The Hebrew University, Jerusalem, Israel.
| | - Nissim Benvenisty
- The Azrieli Center for Stem Cells and Genetic Research, The Hebrew University, Jerusalem, Israel; Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel.
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75
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Donada A, Basso-Valentina F, Arkoun B, Monte-Mor B, Plo I, Raslova H. Induced pluripotent stem cells and hematological malignancies: A powerful tool for disease modeling and drug development. Stem Cell Res 2020; 49:102060. [PMID: 33142254 DOI: 10.1016/j.scr.2020.102060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 10/09/2020] [Accepted: 10/16/2020] [Indexed: 01/12/2023] Open
Abstract
The derivation of human pluripotent stem cell (iPSC) lines by in vitro reprogramming of somatic cells revolutionized research: iPSCs have been used for disease modeling, drug screening and regenerative medicine for many disorders, especially when combined with cutting-edge genome editing technologies. In hematology, malignant transformation is often a multi-step process, that starts with either germline or acquired genetic alteration, followed by progressive acquisition of mutations combined with the selection of one or more pre-existing clones. iPSCs are an excellent model to study the cooperation between different genetic alterations and to test relevant therapeutic drugs. In this review, we will describe the use of iPSCs for pathophysiological studies and drug testing in inherited and acquired hematological malignancies.
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Affiliation(s)
- A Donada
- INSERM, UMR1287, Université Paris Sud, Université Paris Saclay, Gustave Roussy, Equipe Labellisée LNCC, Villejuif, France
| | - F Basso-Valentina
- INSERM, UMR1287, Université Paris Sud, Université Paris Saclay, Gustave Roussy, Equipe Labellisée LNCC, Villejuif, France
| | - B Arkoun
- INSERM, UMR1287, Université Paris Sud, Université Paris Saclay, Gustave Roussy, Equipe Labellisée LNCC, Villejuif, France
| | - B Monte-Mor
- Brazilian National Cancer Institute, Rio de Janeiro, Brazil
| | - I Plo
- INSERM, UMR1287, Université Paris Sud, Université Paris Saclay, Gustave Roussy, Equipe Labellisée LNCC, Villejuif, France
| | - H Raslova
- INSERM, UMR1287, Université Paris Sud, Université Paris Saclay, Gustave Roussy, Equipe Labellisée LNCC, Villejuif, France.
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76
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Yi JK, Park S, Ha JJ, Kim DH, Huang H, Park SJ, Lee MH, Ryoo ZY, Kim SH, Kim MO. Effects of Dimethyl Sulfoxide on the Pluripotency and Differentiation Capacity of Mouse Embryonic Stem Cells. Cell Reprogram 2020; 22:244-253. [DOI: 10.1089/cell.2020.0006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Affiliation(s)
- Jun-Koo Yi
- Department of Embryo Transfer Research, Gyeongbuk Livestock Research Institute, Yeongju, Korea
| | - Song Park
- Core Protein Resources Center, DGIST, Daegu, Republic of Korea
| | - Jae-Jung Ha
- Department of Embryo Transfer Research, Gyeongbuk Livestock Research Institute, Yeongju, Korea
| | - Dae-Hyun Kim
- Department of Embryo Transfer Research, Gyeongbuk Livestock Research Institute, Yeongju, Korea
| | - Hai Huang
- Department of Animal Science and Biotechnology, Kyungpook National University, Sangju, Korea
| | - Si-Jun Park
- Department of Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Kyungpook National University, Daegu, Korea
| | - Mee-Hyun Lee
- College of Korean Medicine, Dongshin University, Naju, Jeollanamdo, Korea
- China-US (Henan) Hormel Cancer Institute, No. 127 Dongming Road, Zhengzhou, Henan, China
| | - Zae-Young Ryoo
- Department of Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Kyungpook National University, Daegu, Korea
| | - Sung-Hyun Kim
- Life Medicine Analysis Korea Polytechnics Institute, Nonsan, Korea
| | - Myoung-Ok Kim
- Department of Animal Science and Biotechnology, Kyungpook National University, Sangju, Korea
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77
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Li B, Chen M, Pan MX. Sex determining region Y-box 2 is a prognostic factor for head and neck squamous cell carcinoma: Evidence from 11 published investigations. J Cancer Res Ther 2020; 16:434-439. [PMID: 32719247 DOI: 10.4103/0973-1482.189238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Objective The aim of this study was to review the published literature and investigate whether sex determining region Y-box 2 (SOX2) is a prognostic factor in head and neck squamous cell carcinoma (HNSCC) by conduct a meta-analysis. Materials and Methods Trials were identified from the major electronic databases (MEDLINE, EMBASE, and Cochrane Library) using the key words "HNSCC" and "SOX2." The overall survival (OS), disease-specific survival (DPS), and disease-free survival (DFS) were the primary outcome measures. Results We identified 371 articles, 9 articles 11 studies with a total number of 1334 cases were eligible for inclusion of this meta-analysis. The results showed that OS (DPS) in low-expression group was higher than that in high-expression group. However, the difference between the two groups was not significant (hazard ratio [HR] = 1.30, 95% confidence interval [95% CI] = [0.88, 1.91]; P = 0.18), and there was great statistical heterogeneity (I2 = 66%, P = 0.002). After subgroup analysis, the HR for OS of the patients with reduced expression of SOX2 was 1.34 (95% CI = [1.04, 1.74], P = 0.03), and the heterogeneity became acceptable (I2 = 32%, P = 0.16). The HR for DFS of the patients with reduced expression of SOX2 was 1.39 (95% CI = [1.00, 1.93]; P = 0.05). Conclusion The findings of this meta-analysis are indicative of that high SOX2 expression is a negative prognostic factor of HNSCC and exhibit both worse OS and DFS. However, the small sample size available for this systematic review limited the power of this quantitative meta-analysis. It may therefore be too early to place complete confidence in these results.
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Affiliation(s)
- Bo Li
- Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi Zhuang Autonomous Region, 541001, China
| | - Mei Chen
- Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi Zhuang Autonomous Region, 541001, China
| | - Meng-Xiong Pan
- Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi Zhuang Autonomous Region, 541001, China
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78
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Hao J, Yang X, Zhang C, Zhang XT, Shi M, Wang SH, Mi L, Zhao YT, Cao H, Wang Y. KLF3 promotes the 8-cell-like transcriptional state in pluripotent stem cells. Cell Prolif 2020; 53:e12914. [PMID: 32990380 PMCID: PMC7653263 DOI: 10.1111/cpr.12914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/05/2020] [Accepted: 09/06/2020] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVES Mouse embryonic stem cell (mESC) culture contains various heterogeneous populations, which serve as excellent models to study gene regulation in early embryo development. The heterogeneity is typically defined by transcriptional activities, for example, the expression of Nanog or Rex1 mRNA. Our objectives were to identify mESC heterogeneity that are caused by mechanisms other than transcriptional control. MATERIALS AND METHODS Klf3 mRNA and protein were analysed by RT-qPCR, Western blotting or immunofluorescence in mESCs, C2C12 cells, early mouse embryos and various mouse tissues. An ESC reporter line expressing KLF3-GFP fusion protein was made to study heterogeneity of KLF3 protein expression in ESCs. GFP-positive mESCs were sorted for further analysis including RT-qPCR and RNA-seq. RESULTS In the majority of mESCs, KLF3 protein is actively degraded due to its proline-rich sequence and highly disordered structure. Interestingly, KLF3 protein is stabilized in a small subset of mESCs. Transcriptome analysis indicates that KLF3-positive mESCs upregulate genes that are initially activated in 8-cell embryos. Consistently, KLF3 protein but not mRNA is dramatically increased in 8-cell embryos. Forced expression of KLF3 protein in mESCs promotes the expression of 8-cell-embryo activated genes. CONCLUSIONS Our study identifies previously unrecognized heterogeneity due to KLF3 protein expression in mESCs.
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Affiliation(s)
- Jing Hao
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Xi Yang
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Chao Zhang
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Xue-Tao Zhang
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Ming Shi
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Shao-Hua Wang
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Li Mi
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Yu-Ting Zhao
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Huiqing Cao
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Yangming Wang
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
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79
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Chen T, Ali Al-Radhawi M, Sontag ED. A mathematical model exhibiting the effect of DNA methylation on the stability boundary in cell-fate networks. Epigenetics 2020; 16:436-457. [PMID: 32842865 DOI: 10.1080/15592294.2020.1805686] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Cell-fate networks are traditionally studied within the framework of gene regulatory networks. This paradigm considers only interactions of genes through expressed transcription factors and does not incorporate chromatin modification processes. This paper introduces a mathematical model that seamlessly combines gene regulatory networks and DNA methylation (DNAm), with the goal of quantitatively characterizing the contribution of epigenetic regulation to gene silencing. The 'Basin of Attraction percentage' is introduced as a metric to quantify gene silencing abilities. As a case study, a computational and theoretical analysis is carried out for a model of the pluripotent stem cell circuit as well as a simplified self-activating gene model. The results confirm that the methodology quantitatively captures the key role that DNAm plays in enhancing the stability of the silenced gene state.
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Affiliation(s)
- Tianchi Chen
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - M Ali Al-Radhawi
- Department of Electrical and Computer Engineering, Northeastern University, Boston, MA, USA
| | - Eduardo D Sontag
- Department of Bioengineering, Northeastern University, Boston, MA, USA.,Department of Electrical and Computer Engineering, Northeastern University, Boston, MA, USA.,Laboratory of Systems Pharmacology, Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
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80
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Hendrijantini N, Hartono CK, Daniati RP, Hong G, Sitalaksmi RM, Kuntjoro M, Ari MDA. Human Umbilical Cord Mesenchymal Stem Cell-induced Osterix, Bone Morphogenetic Protein-2, and Tartrate-resistant Acid Phosphatase Expression in Osteoporotic Mandibular Bone. Eur J Dent 2020; 15:84-89. [PMID: 32898872 PMCID: PMC7902117 DOI: 10.1055/s-0040-1715987] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
OBJECTIVES The aim of this study was to prove that human umbilical cord mesenchymal stem cell (hUCMSC) therapy conducted according to the mandibular osteoporotic model will increase Osterix (Osx) and bone morphogenetic protein-2 (BMP-2) expression, while reducing tartrate-resistant acid phosphatase (TRAP) expression. PKH26 labeling proves that mandibular bone regeneration is produced by hUCMSCs induction. MATERIALS AND METHODS This study incorporated a true posttest only control group design. Twenty-five female Wistar rats were randomly divided into five groups consisting of the sham surgery (N) group, osteoporotic groups injected with gelatin for 4 weeks (G4) and 8 weeks (G8), and osteoporotic groups injected with hUCMSC-gelatin for 4weeks (SC4) and 8 weeks (SC8). All subjects were provided for BMP-2, Osx, and TRAP on immunohistochemistry examination and PKH-26 labeling. STATISTICAL ANALYSIS All data were analyzed using ANOVA and Tukey HSD tests with p < 0.05 being considered as statistically significant. RESULTS Compared with other groups, the highest level of BMP-2 and Osx occurred in the sham surgery (N) and osteoporotic groups injected with hUCMSCs-gelatin (SC), while the lowest level of TRAP was found in SC4. During 4- and 8-week observation periods, the PKH 26 appeared green (fluorescent). CONCLUSIONS hUCMSC demonstrates high-osteogenic activity and increased osteoporotic mandibular bone regeneration, as shown by increased expression of Osx and BMP-2 and decreased TRAP expression. From the labeling, PKH-26 proved that viable hUCMSCs in gelatin solvent can be present in the mandibular bone and be capable of promoting osteogenic differentiation and increasing mineralization and bone formation in the osteoporotic mandibular bone.
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Affiliation(s)
- Nike Hendrijantini
- Department of Prosthodontic, Faculty of Dental Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Cindy Karina Hartono
- Department of Prosthodontic, Faculty of Dental Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Reni Puspa Daniati
- Department of Prosthodontic, Faculty of Dental Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Guang Hong
- Liaison Center for Innovative Dentistry, Graduate School of Dentistry, Tohoku University, Aoba-ku, Sendai, Japan
| | - Ratri Maya Sitalaksmi
- Department of Prosthodontic, Faculty of Dental Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Mefina Kuntjoro
- Department of Prosthodontic, Faculty of Dental Medicine, Universitas Airlangga, Surabaya, Indonesia
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81
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Tegginamani AS, Shivakumar VH, Kallarakkal TG, Ismail SM, Abraham MT, Bin Zamzuri AT. Analysis of octamer-binding transcription factor-4 expression in oral leukoplakia. J Oral Maxillofac Pathol 2020; 24:400. [PMID: 33456258 PMCID: PMC7802831 DOI: 10.4103/jomfp.jomfp_272_19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 06/12/2020] [Accepted: 06/24/2020] [Indexed: 11/14/2022] Open
Abstract
Background: Oral potentially malignant disorders have a risk for malignant transformation but are difficult to reliably identify and predict which patients are at the risk for malignant transformation. OCT4 has been hypothesized to play a key oncogenic driver in a variety of solid tumors. A deeper understanding of the aberrant molecular pathways which lead to carcinogenesis needs to be identified by the potential markers. Aims: To assess the OCT4 stemness factor in oral leukoplakia for its potential risk to malignant transformation. Settings and Design: 20 cases of oral leukoplakia were obtained from archives at Oral Cancer Research & Coordinating center (OCRCC) Malaysia Subjects and Methods: 20 cases of oral leukoplakia were assessed by OCT4 immunohistochemically. Oral squamous cell carcinoma was used as a control. Result: no expression of OCT 4 was observed in any cases of oral leukoplakia. Conclusion: The molecular mechanisms of Oct4 regulation and in particular of its switch on and off in tissues depends upon its microenvironment, which makes it challenging in fundamental and applied research fields of regenerative medicine and cancer therapy. It's better that patients should undergo multiple biopsies for the early detection of malignant transformation with close follow-up during the first two to three years, a large amount of work remains to be done with multi-marker panel investigation, as cure rates have remained constant over three decades.
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82
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Sundaravinayagam D, Rahjouei A, Andreani M, Tupiņa D, Balasubramanian S, Saha T, Delgado-Benito V, Coralluzzo V, Daumke O, Di Virgilio M. 53BP1 Supports Immunoglobulin Class Switch Recombination Independently of Its DNA Double-Strand Break End Protection Function. Cell Rep 2020; 28:1389-1399.e6. [PMID: 31390554 PMCID: PMC6693562 DOI: 10.1016/j.celrep.2019.06.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 05/16/2019] [Accepted: 06/07/2019] [Indexed: 01/29/2023] Open
Abstract
Class switch recombination (CSR) is a DNA recombination reaction that diversifies the effector functions of antibodies. CSR occurs via the formation and non-homologous end joining (NHEJ) repair of programmed DNA double-strand breaks (DSBs) at the immunoglobulin heavy chain locus. The DNA repair factors 53BP1 and Rif1 promote NHEJ and CSR by protecting DSBs against resection. However, to what extent repression of DNA end resection contributes to CSR is unknown. Here, we show that B lymphocytes devoid of 53BP1-Rif1-dependent DSB end protection activity undergo robust CSR. Inactivation of specific sets of phospho-sites within 53BP1 N-terminal SQ/TQ motifs abrogates Rif1 recruitment and inhibition of resection but only mildly reduces CSR. Furthermore, mutations within 53BP1 oligomerization domain abolish CSR without substantially affecting DNA end processing. Thus, inhibition of DNA end resection does not correlate with CSR efficiency, indicating that regulation of DSB processing is not a key determinant step in CSR. 53BP1 oligomerization is largely dispensable for inhibition of DSB resection 53BP1 higher order oligomerization is a pre-requisite for CSR B lymphocytes devoid of 53BP1-Rif1 DSB end protection activity undergo robust CSR 53BP1-mediated DSB end mobility is dispensable for CSR
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Affiliation(s)
- Devakumar Sundaravinayagam
- Laboratory of DNA Repair and Maintenance of Genome Stability, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Ali Rahjouei
- Laboratory of DNA Repair and Maintenance of Genome Stability, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Matteo Andreani
- Laboratory of DNA Repair and Maintenance of Genome Stability, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Dagnija Tupiņa
- Laboratory of Structural Biology of Membrane-Associated Processes, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Sandhya Balasubramanian
- Laboratory of DNA Repair and Maintenance of Genome Stability, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Tannishtha Saha
- Laboratory of DNA Repair and Maintenance of Genome Stability, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Verónica Delgado-Benito
- Laboratory of DNA Repair and Maintenance of Genome Stability, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Violeta Coralluzzo
- Laboratory of DNA Repair and Maintenance of Genome Stability, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Oliver Daumke
- Laboratory of Structural Biology of Membrane-Associated Processes, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Michela Di Virgilio
- Laboratory of DNA Repair and Maintenance of Genome Stability, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany.
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Zhu Y, Yan Z, Tang Z, Li W. Novel Approaches to Profile Functional Long Noncoding RNAs Associated with Stem Cell Pluripotency. Curr Genomics 2020; 21:37-45. [PMID: 32655297 PMCID: PMC7324891 DOI: 10.2174/1389202921666200210142840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 01/17/2020] [Accepted: 01/31/2020] [Indexed: 12/11/2022] Open
Abstract
The pluripotent state of stem cells depends on the complicated network orchestrated by thousands of factors and genes. Long noncoding RNAs (lncRNAs) are a class of RNA longer than 200 nt without a protein-coding function. Single-cell sequencing studies have identified hundreds of lncRNAs with dynamic changes in somatic cell reprogramming. Accumulating evidence suggests that they participate in the initiation of reprogramming, maintenance of pluripotency, and developmental processes by cis and/or trans mechanisms. In particular, they may interact with proteins, RNAs, and chromatin modifier complexes to form an intricate pluripotency-associated network. In this review, we focus on recent progress in approaches to profiling functional lncRNAs in somatic cell reprogramming and cell differentiation.
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Affiliation(s)
- Yanbo Zhu
- 1Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin130021, China; 2Division of Endocrinology and Metabolism, The First Hospital of Jilin University, Changchun, Jilin130021, China; 3Department of Thoracic Surgery, The First Hospital of Jilin University, Changchun, Jilin130021, China
| | - Zi Yan
- 1Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin130021, China; 2Division of Endocrinology and Metabolism, The First Hospital of Jilin University, Changchun, Jilin130021, China; 3Department of Thoracic Surgery, The First Hospital of Jilin University, Changchun, Jilin130021, China
| | - Ze Tang
- 1Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin130021, China; 2Division of Endocrinology and Metabolism, The First Hospital of Jilin University, Changchun, Jilin130021, China; 3Department of Thoracic Surgery, The First Hospital of Jilin University, Changchun, Jilin130021, China
| | - Wei Li
- 1Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin130021, China; 2Division of Endocrinology and Metabolism, The First Hospital of Jilin University, Changchun, Jilin130021, China; 3Department of Thoracic Surgery, The First Hospital of Jilin University, Changchun, Jilin130021, China
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84
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Muñoz-Galván S, Carnero A. Targeting Cancer Stem Cells to Overcome Therapy Resistance in Ovarian Cancer. Cells 2020; 9:cells9061402. [PMID: 32512891 PMCID: PMC7349391 DOI: 10.3390/cells9061402] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 06/02/2020] [Indexed: 12/18/2022] Open
Abstract
Ovarian cancer is the most lethal gynecological malignancy due to its late detection and high recurrence rate. Resistance to conventional platinum-based therapies and metastasis are attributed to a population of cells within tumors called cancer stem cells, which possess stem-like features and are able to recapitulate new tumors. Recent studies have deepened the understanding of the biology of ovarian cancer stem cells and their special properties and have identified multiple markers and signaling pathways responsible for their self-renewal abilities. Targeting cancer stem cells represents the most promising strategy for overcoming therapy resistance and reducing mortality in ovarian cancer, but further efforts must be made to improve our understanding of the mechanisms involved in therapy resistance. In this review, we summarize our current knowledge about ovarian cancer stem cells, their involvement in metastasis and their interactions with the tumor microenvironment; we also discuss the therapeutic approaches that are being developed to target them to prevent tumor relapse.
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Affiliation(s)
- Sandra Muñoz-Galván
- Instituto de Biomedicina de Sevilla, IBIS, Hospital Universitario Virgen del Rocío, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Avda. Manuel Siurot s/n, 41013 Seville, Spain
- CIBERONC, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Correspondence: (S.M.-G.); (A.C.); Tel.: +34-955-923-115 (S.M.-G); +34-955-923-110 (A.C.)
| | - Amancio Carnero
- Instituto de Biomedicina de Sevilla, IBIS, Hospital Universitario Virgen del Rocío, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Avda. Manuel Siurot s/n, 41013 Seville, Spain
- CIBERONC, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Correspondence: (S.M.-G.); (A.C.); Tel.: +34-955-923-115 (S.M.-G); +34-955-923-110 (A.C.)
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Abstract
BACKGROUND SALL4 is a zinc finger transcription factor that exerts its physiological role during embryo-fetal development. Analyses of SALL4 expression have shown its oncogenic role in precursor B-cell lymphoblastic lymphoma, acute and chronic myeloid leukemia, gastrointestinal, breast, and lung cancers. The aim of this study was to determine the immunohistochemical profile of SALL4 in pediatric yolk sac tumors (YSTs). METHODS AND RESULTS Immunohistochemistry detection of SALL4 was performed in 22 cases of pediatric YSTs and 10 mature teratomas. The percentage of tumor cells stained was scored as 0, 1+ (1-30% cells), 2+ (31-60%), 3+ (61-90%), and 4+ (> 90%). To compare its sensitivity and specificity with Glypican-3 and α-fetoprotein (AFP), we also stained tumors from these cases for Glypican-3 and AFP. In contrast to AFP and glypican-3, SALL4 staining in more than 90% of the tumor cells was seen in all 22 pediatric YSTs (100% sensitivity) (P < 0.001 for both SALL4 vs. AFP and SALL4 vs. glypican-3). CONCLUSIONS SALL4 is a sensitive marker for pediatric YSTs and it can be used to distinguish them from mature teratomas. SALL4 is likely to become a new and valuable biomarker for the diagnosis of pediatric YST.
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86
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Ghazi N, Aali N, Shahrokhi VR, Mohajertehran F, Saghravanian N. Relative Expression of SOX2 and OCT4 in Oral Squamous Cell Carcinoma and Oral Epithelial Dysplasia. Rep Biochem Mol Biol 2020; 9:171-179. [PMID: 33178866 DOI: 10.29252/rbmb.9.2.171] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Background Over 90% of oral cancers including oral squamous cell carcinoma (OSCC), originate from the oral cavity epithelium. Early detection for this lesion is as important. Evaluating cancer stem cell markers can improve the accuracy of early diagnosis, and be used as an OSCC prognostic indicator. We aimed to evaluate SOX2 and OCT4 gene expression among different grades of OSCC and oral epithelial dysplasia (OED) lesions. Methods Sixty samples that contains 45 OSCC and 15 OED samples were retrieved from the pathology department archives at the dental school of Mashhad. Demographic and pathological patient data including the tumor stage and tumor grade were assessed. Finally, SOX2 and OCT4 expression was examined using qRT-PCR. Results There was a significant difference in SOX2 and OCT4 expression between OSCC and OED samples (p< 0.001). The mean expression of SOX2 and OCT4 in OSCC samples were significantly higher than in the OED group (p< 0.001). The mean expression of SOX2 and OCT4 was higher in grade II and grade III OSCC compared to grade I. There was no significant relationship between the gene expression of SOX2 or OCT4 to the demographic, site and stage of tumors. The correlation between SOX2 and OCT4 expression (p= 0.001) was significant in grade III OSCC specimens compared to other grades (p= 0.005, r= 0.68). Conclusion The increased expression of SOX2 and OCT4 in higher grades and the significant correlation of these genes with each other among OSCC specimens could suggest the role of SOX2 or OCT4 in oral mucosal carcinogenesis.
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Affiliation(s)
- Narges Ghazi
- Department of Oral and Maxillofacial Pathology, School of Dentistry, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Narges Aali
- Oral and Maxillofacial Disease Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Vahid-Reza Shahrokhi
- Oral and Maxillofacial Disease Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Farnaz Mohajertehran
- Department of Oral and Maxillofacial Pathology, School of Dentistry, Mashhad University of Medical Sciences, Mashhad, Iran.,Oral and Maxillofacial Disease Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Nasrollah Saghravanian
- Oral and Maxillofacial Disease Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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87
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Che J, Wu P, Wang G, Yao X, Zheng J, Guo C. Expression and clinical value of SALL4 in renal cell carcinomas. Mol Med Rep 2020; 22:819-827. [PMID: 32468053 PMCID: PMC7339774 DOI: 10.3892/mmr.2020.11170] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 03/30/2020] [Indexed: 12/17/2022] Open
Abstract
The aim of the present study was to investigate the expression of spalt like transcription factor 4 (SALL4) in the three most common types of renal cell carcinomas (RCC) [clear cell RCC (ccRCC), papillary renal cell carcinoma (pRCC) and chromophobe RCC (chRCC)], and the association with the overall survival (OS) of patients. The Cancer Genome Atlas (TCGA) database and RCC samples were used to investigate the expression levels of the SALL4 gene and its association with the OS in the three types of RCC based on the analysis of the transcriptome, copy number and survival data. It was found that SALL4 was highly expressed in ccRCC and pRCC tumor tissue, and low mRNA expression level of SALL4 indicated a prolonged survival in both ccRCC and pRCC. This mRNA expression level was associated with pathological Tumor-Node-Metastasis stage, M and T stages in both ccRCC and pRCC. The analysis of the enriched pathway results suggested that SALL4 may act via translation initiation, and that the related genes promoted the progression of RCC. Moreover, the high expression level of SALL4 was detected in RCC samples and serum from patients. It was demonstrated that SALL4 promotes increased viability in RCC cells. Therefore, the present results suggest that SALL4 may be a sensitive and specific cancer biomarker in ccRCC and pRCC. Furthermore, targeting of SALL4 may improve RCC therapy and prolong the survival of patients with ccRCC or pRCC.
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Affiliation(s)
- Jianping Che
- Department of Urology, The Affiliated Shanghai Tenth People's Hospital, Nanjing Medical University, Shanghai 200072, P.R. China
| | - Pengfei Wu
- Department of Urology, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, P.R. China
| | - Guangchun Wang
- Department of Urology, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, P.R. China
| | - Xudong Yao
- Department of Urology, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, P.R. China
| | - Junhua Zheng
- Department of Urology, The Affiliated Shanghai Tenth People's Hospital, Nanjing Medical University, Shanghai 200072, P.R. China
| | - Changcheng Guo
- Department of Urology, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, P.R. China
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88
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Gao M, Herlinger AL, Wu R, Wang TL, Shih IM, Kong B, Rangel LBA, Yang JM. NAC1 attenuates BCL6 negative autoregulation and functions as a BCL6 coactivator of FOXQ1 transcription in cancer cells. Aging (Albany NY) 2020; 12:9275-9291. [PMID: 32412910 PMCID: PMC7288929 DOI: 10.18632/aging.103203] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/09/2020] [Indexed: 01/08/2023]
Abstract
Background: Nucleus accumbens-associated protein 1 (NAC1) has multifaceted roles in cancer pathogenesis and progression, including the development of drug resistance, promotion of cytokinesis, and maintenance of “stem cell-like” phenotypes. NAC1 is a transcriptional co-regulator belonging to the bric-a-brac tramtrack broad (BTB) family of proteins, although it lacks the characteristic DNA binding motif of the BTB family. The formation of higher-order transcription complexes likely depends on its interaction with other DNA-binding co-factors. Results: NAC1 interacts with BCL6 via its C-terminal BEN domain and forms a complex that binds the promoter region and activates transcription of the NAC1 target gene, FOXQ1. NAC1 and BCL6 were coordinately upregulated. Our analysis also identified a novel function of NAC1 in attenuating BCL6 auto-downregulation in ovarian cancer. Lastly, we found a significant overlap among NAC1- and BCL6-regulated genes in tumor cells, suggesting that NAC1 and BCL6 coordinately control transcription in cancer. Conclusions: The results of this study provide a novel mechanistic insight into the oncogenic roles of NAC1 and underline the importance of developing the NAC1/BCL6-targeted cancer therapy. Methods: Using the Cistrome database and Chromatin Immunoprecipitation (ChIP) analyses, we identified BCL6 as a potential NAC1- interacting molecule. Co-immunoprecipitation (Co-IP), luciferase reporter assay, immunohistochemistry and microarray analysis were performed to analyze the interaction between NAC1 and BCL6 and the mechanisms by which they regulate the downstream genes including FOXQ1.
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Affiliation(s)
- Min Gao
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, PR China.,Departments of Gynecology and Obstetrics, Oncology and Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
| | - Alice Laschuk Herlinger
- Departments of Gynecology and Obstetrics, Oncology and Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA.,Biotechnology Program/Renorbio, Health Science Center, Federal University of Espírito Santo, Vitória, Brazil.,Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Renchin Wu
- Departments of Gynecology and Obstetrics, Oncology and Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
| | - Tian-Li Wang
- Departments of Gynecology and Obstetrics, Oncology and Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
| | - Ie-Ming Shih
- Departments of Gynecology and Obstetrics, Oncology and Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
| | - Beihua Kong
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, PR China
| | - Leticia Batista Azevedo Rangel
- Biotechnology Program/Renorbio, Health Science Center, Federal University of Espírito Santo, Vitória, Brazil.,Biochemistry and Pharmacology Program, Health Science Center, Federal University of Espírito Santo, Vitória, Brazil.,Department of Pharmaceutical Sciences, Federal University of Espírito Santo, Vitória, Brazil
| | - Jin-Ming Yang
- Department of Toxicology and Cancer Biology, College of Medicine, Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
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89
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Lynch-Sutherland CF, Chatterjee A, Stockwell PA, Eccles MR, Macaulay EC. Reawakening the Developmental Origins of Cancer Through Transposable Elements. Front Oncol 2020; 10:468. [PMID: 32432029 PMCID: PMC7214541 DOI: 10.3389/fonc.2020.00468] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/16/2020] [Indexed: 12/12/2022] Open
Abstract
Transposable elements (TEs) have an established role as important regulators of early human development, functioning as tissue-specific genes and regulatory elements. Functional TEs are highly active during early development, and interact with important developmental genes, some of which also function as oncogenes. Dedifferentiation is a hallmark of cancer, and is characterized by genetic and epigenetic changes that enable proliferation, self-renewal and a metabolism reminiscent of embryonic stem cells. There is also compelling evidence suggesting that the path to dedifferentiation in cancer can contribute to invasion and metastasis. TEs are frequently expressed in cancer, and recent work has identified a newly proposed mechanism involving extensive recruitment of TE-derived promoters to drive expression of oncogenes and subsequently promote oncogenesis—a process termed onco-exaptation. However, the mechanism by which this phenomenon occurs, and the extent to which it contributes to oncogenesis remains unknown. Initial hypotheses have proposed that onco-exaptation events are cancer-specific and arise randomly due to the dysregulated and hypomethylated state of cancer cells and abundance of TEs across the genome. However, we suspect that exaptation-like events may not just arise due to chance activation of novel regulatory relationships as proposed previously, but as a result of the reestablishment of early developmental regulatory relationships. Dedifferentiation in cancer is well-documented, along with expression of TEs. The known interactions between TEs and pluripotency factors such as NANOG and OCTt4 during early development, along with the expression of some placental-specific TE-derived transcripts in cancer support a possible link between TEs and dedifferentiation of tumor cells. Thus, we hypothesize that onco-exaptation events can be associated with the epigenetic reawakening of early developmental TEs to regulate expression of oncogenes and promote oncogenesis. We also suspect that activation of these early developmental regulatory TEs may promote dedifferentiation, although at this stage it is hard to predict whether TE activation is one of the initial drivers of dedifferentiation. We expect that developmental TE activation occurs as a result of the establishment of an epigenetic landscape in cancer that resembles that of early development and that developmental TE activation may also enable cancers to exploit early developmental pathways, repurposing them to promote malignancy.
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Affiliation(s)
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Peter A Stockwell
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Michael R Eccles
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Erin C Macaulay
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
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90
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Gao M, Bai H, Jethava Y, Wu Y, Zhu Y, Yang Y, Xia J, Cao H, Franqui-Machin R, Nadiminti K, Thomas GS, Salama ME, Altevogt P, Bishop G, Tomasson M, Janz S, Shi J, Chen L, Frech I, Tricot G, Zhan F. Identification and Characterization of Tumor-Initiating Cells in Multiple Myeloma. J Natl Cancer Inst 2020; 112:507-515. [PMID: 31406992 PMCID: PMC7225664 DOI: 10.1093/jnci/djz159] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 07/11/2019] [Accepted: 08/07/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Treatment failures in cancers, including multiple myeloma (MM), are most likely due to the persistence of a minor population of tumor-initiating cells (TICs), which are noncycling or slowly cycling and very drug resistant. METHODS Gene expression profiling and real-time quantitative reverse transcription polymerase chain reaction were employed to define genes differentially expressed between the side-population cells, which contain the TICs, and the main population of MM cells derived from 11 MM patient samples. Self-renewal potential was analyzed by clonogenicity and drug resistance of CD24+ MM cells. Flow cytometry (n = 60) and immunofluorescence (n = 66) were applied on MM patient samples to determine CD24 expression. Therapeutic effects of CD24 antibodies were tested in xenograft MM mouse models containing three to six mice per group. RESULTS CD24 was highly expressed in the side-population cells, and CD24+ MM cells exhibited high expression of induced pluripotent or embryonic stem cell genes. CD24+ MM cells showed increased clonogenicity, drug resistance, and tumorigenicity. Only 10 CD24+ MM cells were required to develop plasmacytomas in mice (n = three of five mice after 27 days). The frequency of CD24+ MM cells was highly variable in primary MM samples, but the average of CD24+ MM cells was 8.3% after chemotherapy and in complete-remission MM samples with persistent minimal residual disease compared with 1.0% CD24+ MM cells in newly diagnosed MM samples (n = 26). MM patients with a high initial percentage of CD24+ MM cells had inferior progression-free survival (hazard ratio [HR] = 3.81, 95% confidence interval [CI] = 5.66 to 18.34, P < .001) and overall survival (HR = 3.87, 95% CI = 16.61 to 34.39, P = .002). A CD24 antibody inhibited MM cell growth and prevented tumor progression in vivo. CONCLUSION Our studies demonstrate that CD24+ MM cells maintain the TIC features of self-renewal and drug resistance and provide a target for myeloma therapy.
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Affiliation(s)
- Minjie Gao
- Division of Hematology, Oncology, and Blood and Marrow Transplantation, Department of Internal Medicine, University of Iowa, Iowa City, IA.,Department of Hematology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Hua Bai
- Division of Hematology, Oncology, and Blood and Marrow Transplantation, Department of Internal Medicine, University of Iowa, Iowa City, IA
| | - Yogesh Jethava
- Division of Hematology, Oncology, and Blood and Marrow Transplantation, Department of Internal Medicine, University of Iowa, Iowa City, IA
| | - Yujie Wu
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
| | - Yuqi Zhu
- Division of Hematology, Oncology, and Blood and Marrow Transplantation, Department of Internal Medicine, University of Iowa, Iowa City, IA
| | - Ye Yang
- Division of Hematology, Oncology, and Blood and Marrow Transplantation, Department of Internal Medicine, University of Iowa, Iowa City, IA
| | - Jiliang Xia
- Division of Hematology, Oncology, and Blood and Marrow Transplantation, Department of Internal Medicine, University of Iowa, Iowa City, IA
| | - Huojun Cao
- Iowa Institute for Oral Health Research, College of Dentistry, The University of Iowa, Iowa City, IA
| | - Reinaldo Franqui-Machin
- Division of Hematology, Oncology, and Blood and Marrow Transplantation, Department of Internal Medicine, University of Iowa, Iowa City, IA
| | - Kalyan Nadiminti
- Division of Hematology, Oncology, and Blood and Marrow Transplantation, Department of Internal Medicine, University of Iowa, Iowa City, IA
| | - Gregory S Thomas
- Division of Hematology, Oncology, and Blood and Marrow Transplantation, Department of Internal Medicine, University of Iowa, Iowa City, IA
| | - Mohamed E Salama
- Department of Pathology, University of Utah, and Associated Regional University Pathologists Laboratories, Salt Lake City, UT
| | - Peter Altevogt
- Skin Cancer Unit, German Cancer Research Center, and University Medical Center Mannheim, Germany
| | - Gail Bishop
- Department of Microbiology and Immunology, University of Iowa and VA Medical Center, Iowa City, IA
| | - Michael Tomasson
- Division of Hematology, Oncology, and Blood and Marrow Transplantation, Department of Internal Medicine, University of Iowa, Iowa City, IA
| | - Siegfried Janz
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI
| | - Jumei Shi
- Department of Hematology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Lijuan Chen
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
| | - Ivana Frech
- Division of Hematology, Oncology, and Blood and Marrow Transplantation, Department of Internal Medicine, University of Iowa, Iowa City, IA
| | - Guido Tricot
- Division of Hematology, Oncology, and Blood and Marrow Transplantation, Department of Internal Medicine, University of Iowa, Iowa City, IA
| | - Fenghuang Zhan
- Division of Hematology, Oncology, and Blood and Marrow Transplantation, Department of Internal Medicine, University of Iowa, Iowa City, IA
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Behrens A, Jousheghany F, Yao-Borengasser A, Siegel ER, Kieber-Emmons T, Monzavi-Karbassi B. Carbohydrate (Chondroitin 4) Sulfotransferase-11-Mediated Induction of Epithelial-Mesenchymal Transition and Generation of Cancer Stem Cells. Pharmacology 2020; 105:246-259. [PMID: 32344408 DOI: 10.1159/000506710] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 02/20/2020] [Indexed: 11/19/2022]
Abstract
INTRODUCTION We have previously shown that the expression of carbohydrate (chondroitin 4) sulfotransferase-11 (CHST11) is elevated in human breast cancer tissues, and that its expression in human breast cancer cell lines is associated with aggressive behavior of cells. The clinical significance of CHST11 expression is unknown, and its function in breast cancer cells is not fully understood. OBJECTIVE The current study was performed to define the clinical significance of this gene and address its biological function in promoting the aggressive behavior of breast cancer cells. METHODS Publicly available datasets were analyzed to determine the correlation of CHST11 expression with breast cancer survival. MCF-7 cells were transfected with the human CHST11 gene, and MCF-7-CHST11 cells with stable expression of the gene were established. Morphology and metastatic capacity of transfected cells were monitored in vitro. E-cadherin and β-catenin expression was compared by immunofluorescence. The expression of genes involved in epithelial-mesenchymal transition (EMT) and pluripotency was determined using real-time PCR. The Wnt inhibitor, Wnt-C59, was used to examine the involvement of Wnt in CHST11-mediated morphology. RESULTS The elevated expression of CHST11 in breast tumor specimens was significantly associated with poor survival among patients. MCF-7-CHST11 cells displayed morphological characteristics consistent with EMT, together with a significantly higher proliferation rate, enhanced migratory potential, and more robust anchorage-independent growth. MCF-7-CHST11 cells showed decreased expression of E-cadherin and increased accumulation of β-catenin, as assessed by immunofluorescence. Consistently, increased expression of CHST11 resulted in upregulation of key EMT and stem cell markers. Morphological transition in MCF-7-CHST11 cells was partially reversed by co-incubation with an inhibitor of the Wnt pathway. CONCLUSIONS Our findings support a role for CHST11 in induction of EMT and stem cell-like properties. Our data also associate the expression levels of CHST11 in breast tumor specimens with patients' survival. The results have a significant implication for CHST11 expression level as a novel molecular signature for predictive and prognostic purposes in breast cancer. Moreover, with a possible role in driving tumor cell aggressiveness, CHST11 expression might be further considered as a potential therapeutic target for breast cancer.
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Affiliation(s)
- Alice Behrens
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Fariba Jousheghany
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Aiwei Yao-Borengasser
- Department of Medical Genetics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Eric R Siegel
- Department of Biostatistics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Thomas Kieber-Emmons
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.,Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Behjatolah Monzavi-Karbassi
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA, .,Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA,
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92
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Rizzo D, Graziani C, Gallus R, Zannoni GF, Lucchetti D, Parrilla C, Boninsegna A, Galli J, Paludetti G, Bussu F, Sgambato A. Stem cell markers in oral and oropharyngeal squamous cell carcinomas in relation to the site of origin and HPV infection: clinical implications. ACTA OTORHINOLARYNGOLOGICA ITALICA : ORGANO UFFICIALE DELLA SOCIETA ITALIANA DI OTORINOLARINGOLOGIA E CHIRURGIA CERVICO-FACCIALE 2020; 40:90-98. [PMID: 32469002 PMCID: PMC7256905 DOI: 10.14639/0392-100x-2419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 08/26/2019] [Indexed: 01/06/2023]
Abstract
The expression of potential stem cell markers in HNSCCs was investigated to assess their potential clinical role. 69 primary, previously untreated oral (OSCC) and oropharyngeal squamous cell carcinomas (OPSCC) were enrolled; personal, clinical and follow-up data were collected. HPV infection and expression of 5 potential stem cell markers (CD44, CD133, Oct-4, Nanog, and Sox-2) were evaluated. HPV+ OPSCC showed lower expression of Nanog. The cytoplasmic expression of Nanog was associated with significantly worse prognosis in OPSCC, but not in OSCC. Sox-2 staining was more intense among OPSCCs. Sox-2 nuclear staining was associated with worse prognosis. Nanog expression was associated with HPV- OPSCC and may have a role as a surrogate diagnostic marker. In general, the expression profile of some stem cell markers in HNSCC seems to vary according to the site of origin and HPV infection. Nanog and Sox-2 may also have prognostic value.
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Affiliation(s)
- Davide Rizzo
- Otolaryngology Division, Azienda Ospedaliera Universitaria, Sassari, Italy
| | - Cristina Graziani
- Department of General Pathology, Università Cattolica del S. Cuore, Rome, Italy
| | - Roberto Gallus
- Department of Otolaryngology, Università Cattolica del S. Cuore, Rome, Italy
| | - Gian Franco Zannoni
- Department of Histopathology, Università Cattolica del S. Cuore, Rome, Italy
| | - Donatella Lucchetti
- Department of General Pathology, Università Cattolica del S. Cuore, Rome, Italy
| | - Claudio Parrilla
- Department of Otolaryngology, Università Cattolica del S. Cuore, Rome, Italy
| | - Alma Boninsegna
- Department of General Pathology, Università Cattolica del S. Cuore, Rome, Italy
| | - Jacopo Galli
- Department of Otolaryngology, Università Cattolica del S. Cuore, Rome, Italy
| | - Gaetano Paludetti
- Department of Otolaryngology, Università Cattolica del S. Cuore, Rome, Italy
| | - Francesco Bussu
- Otolaryngology Division, Azienda Ospedaliera Universitaria, Sassari, Italy
- Department of Otolaryngology, Università Cattolica del S. Cuore, Rome, Italy
| | - Alessandro Sgambato
- Department of General Pathology, Università Cattolica del S. Cuore, Rome, Italy
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93
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Cell Biology of Intracellular Adaptation of Mycobacterium leprae in the Peripheral Nervous System. Microbiol Spectr 2020; 7. [PMID: 31322104 DOI: 10.1128/microbiolspec.bai-0020-2019] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The mammalian nervous system is invaded by a number of intracellular bacterial pathogens which can establish and progress infection in susceptible individuals. Subsequent clinical manifestation is apparent with the impairment of the functional units of the nervous system, i.e., the neurons and the supporting glial cells that produce myelin sheaths around axons and provide trophic support to axons and neurons. Most of these neurotrophic bacteria display unique features, have coevolved with the functional sophistication of the nervous system cells, and have adapted remarkably to manipulate neural cell functions for their own advantage. Understanding how these bacterial pathogens establish intracellular adaptation by hijacking endogenous pathways in the nervous system, initiating myelin damage and axonal degeneration, and interfering with myelin maintenance provides new knowledge not only for developing strategies to combat neurodegenerative conditions induced by these pathogens but also for gaining novel insights into cellular and molecular pathways that regulate nervous system functions. Since the pathways hijacked by bacterial pathogens may also be associated with other neurodegenerative diseases, it is anticipated that detailing the mechanisms of bacterial manipulation of neural systems may shed light on common mechanisms, particularly of early disease events. This chapter details a classic example of neurodegeneration, that caused by Mycobacterium leprae, which primarily infects glial cells of the peripheral nervous system (Schwann cells), and how it targets and adapts intracellularly by reprogramming Schwann cells to stem cells/progenitor cells. We also discuss implications of this host cell reprogramming by leprosy bacilli as a model in a wider context.
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ARID3A and ARID3B induce stem promoting pathways in ovarian cancer cells. Gene 2020; 738:144458. [PMID: 32061921 DOI: 10.1016/j.gene.2020.144458] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 02/05/2020] [Accepted: 02/07/2020] [Indexed: 12/14/2022]
Abstract
ARID3A and ARID3B are paralogs from the AT-Rich interactive Domain (ARID) family. ARID3A and ARID3B associate to regulate genes in B-cells and cancer. We were the first to demonstrate that ARID3B regulates stem cell genes and promotes the cancer stem cell phenotype. Importantly, different knockout phenotypes in mice and distinct patterns of expression in adult animals suggests that ARID3A and ARID3B may have unique functions. In addition, high levels of ARID3B but not ARID3A induce cell death. Our goal was to express ARID3A, ARID3B, or both genes at a moderate level (as can be observed in cancer) and then identify ARID3 regulated genes. We transduced ovarian cancer cells with ARID3A-GFP, ARID3B-RFP, or both. RNA-sequencing was conducted. ARID3A and ARID3B regulated nearly identical sets of genes. Few genes (<5%) were uniquely regulated by ARID3A or ARID3B. ARID3A/B induced genes involved in cancer and stem cell processes including: Twist, MYCN, MMP2, GLI2, TIMP3, and WNT5B. We found that ARID3A and ARID3B also induced expression of each other, providing evidence of the cooperativity. While ARID3A and ARID3B likely have unique functions in distinct contexts, they are largely capable of regulating the same stem cell genes in cancer cells. This study provides a comprehensive list of genes and pathways regulated by ARID3A and ARID3B in ovarian cancer cells.
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95
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Liu G, David BT, Trawczynski M, Fessler RG. Advances in Pluripotent Stem Cells: History, Mechanisms, Technologies, and Applications. Stem Cell Rev Rep 2020; 16:3-32. [PMID: 31760627 PMCID: PMC6987053 DOI: 10.1007/s12015-019-09935-x] [Citation(s) in RCA: 228] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Over the past 20 years, and particularly in the last decade, significant developmental milestones have driven basic, translational, and clinical advances in the field of stem cell and regenerative medicine. In this article, we provide a systemic overview of the major recent discoveries in this exciting and rapidly developing field. We begin by discussing experimental advances in the generation and differentiation of pluripotent stem cells (PSCs), next moving to the maintenance of stem cells in different culture types, and finishing with a discussion of three-dimensional (3D) cell technology and future stem cell applications. Specifically, we highlight the following crucial domains: 1) sources of pluripotent cells; 2) next-generation in vivo direct reprogramming technology; 3) cell types derived from PSCs and the influence of genetic memory; 4) induction of pluripotency with genomic modifications; 5) construction of vectors with reprogramming factor combinations; 6) enhancing pluripotency with small molecules and genetic signaling pathways; 7) induction of cell reprogramming by RNA signaling; 8) induction and enhancement of pluripotency with chemicals; 9) maintenance of pluripotency and genomic stability in induced pluripotent stem cells (iPSCs); 10) feeder-free and xenon-free culture environments; 11) biomaterial applications in stem cell biology; 12) three-dimensional (3D) cell technology; 13) 3D bioprinting; 14) downstream stem cell applications; and 15) current ethical issues in stem cell and regenerative medicine. This review, encompassing the fundamental concepts of regenerative medicine, is intended to provide a comprehensive portrait of important progress in stem cell research and development. Innovative technologies and real-world applications are emphasized for readers interested in the exciting, promising, and challenging field of stem cells and those seeking guidance in planning future research direction.
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Affiliation(s)
- Gele Liu
- Department of Neurosurgery, Rush University Medical College, 1725 W. Harrison St., Suite 855, Chicago, IL, 60612, USA.
| | - Brian T David
- Department of Neurosurgery, Rush University Medical College, 1725 W. Harrison St., Suite 855, Chicago, IL, 60612, USA
| | - Matthew Trawczynski
- Department of Neurosurgery, Rush University Medical College, 1725 W. Harrison St., Suite 855, Chicago, IL, 60612, USA
| | - Richard G Fessler
- Department of Neurosurgery, Rush University Medical College, 1725 W. Harrison St., Suite 855, Chicago, IL, 60612, USA
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96
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Thiagalingam S. Epigenetic memory in development and disease: Unraveling the mechanism. Biochim Biophys Acta Rev Cancer 2020; 1873:188349. [PMID: 31982403 DOI: 10.1016/j.bbcan.2020.188349] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 01/22/2020] [Accepted: 01/22/2020] [Indexed: 01/14/2023]
Abstract
Epigenetic memory is an essential process of life that governs the inheritance of predestined functional characteristics of normal cells and the newly acquired properties of cells affected by cancer and other diseases from parental to progeny cells. Unraveling the molecular basis of epigenetic memory dictated by protein and RNA factors in conjunction with epigenetic marks that are erased and re-established during embryogenesis/development during the formation of somatic, stem and disease cells will have far reaching implications to our understanding of embryogenesis/development and various diseases including cancer. While there has been enormous progress made, there are still gaps in knowledge which includes, the identity of unique epigenetic memory factors (EMFs) and epigenome coding enzymes/co-factors/scaffolding proteins involved in the assembly of defined "epigenetic memorysomes" and the epigenome marks that constitute collections of gene specific epigenetic memories corresponding to specific cell types and physiological conditions. A better understanding of the molecular basis for epigenetic memory will play a central role in improving diagnostics and prognostics of disease states and aid the development of targeted therapeutics of complex diseases.
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Affiliation(s)
- Sam Thiagalingam
- Department of Medicine (Biomedical Genetics Section and Cancer Center), Department of Pathology & Laboratory Medicine, Department of Pharmacology & Experimental Therapeutics, Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, United States of America.
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97
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In Vivo Quantitative Estimation of DNA-Dependent Interaction of Sox2 and Oct4 Using BirA-Catalyzed Site-Specific Biotinylation. Biomolecules 2020; 10:biom10010142. [PMID: 31963153 PMCID: PMC7022529 DOI: 10.3390/biom10010142] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/03/2020] [Accepted: 01/09/2020] [Indexed: 11/25/2022] Open
Abstract
Protein–protein interactions of core pluripotency transcription factors play an important role during cell reprogramming. Cell identity is controlled by a trio of transcription factors: Sox2, Oct4, and Nanog. Thus, methods that help to quantify protein–protein interactions may be useful for understanding the mechanisms of pluripotency at the molecular level. Here, a detailed protocol for the detection and quantitative analysis of in vivo protein–protein proximity of Sox2 and Oct4 using the proximity-utilizing biotinylation (PUB) method is described. The method is based on the coexpression of two proteins of interest fused to a biotin acceptor peptide (BAP)in one case and a biotin ligase enzyme (BirA) in the other. The proximity between the two proteins leads to more efficient biotinylation of the BAP, which can be either detected by Western blotting or quantified using proteomics approaches, such as a multiple reaction monitoring (MRM) analysis. Coexpression of the fusion proteins BAP-X and BirA-Y revealed strong biotinylation of the target proteins when X and Y were, alternatively, the pluripotency transcription factors Sox2 and Oct4, compared with the negative control where X or Y was green fluorescent protein (GFP), which strongly suggests that Sox2 and Oct4 come in close proximity to each other and interact.
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98
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Yang J, Bashkenova N, Zang R, Huang X, Wang J. The roles of TET family proteins in development and stem cells. Development 2020; 147:147/2/dev183129. [PMID: 31941705 DOI: 10.1242/dev.183129] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Ten-eleven translocation (TET) methylcytosine dioxygenases are enzymes that catalyze the demethylation of 5-methylcytosine on DNA. Through global and site-specific demethylation, they regulate cell fate decisions during development and in embryonic stem cells by maintaining pluripotency or by regulating differentiation. In this Primer, we provide an updated overview of TET functions in development and stem cells. We discuss the catalytic and non-catalytic activities of TETs, and their roles as epigenetic regulators of both DNA and RNA hydroxymethylation, highlighting how TET proteins function in regulating gene expression at both the transcriptional and post-transcriptional levels.
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Affiliation(s)
- Jihong Yang
- Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Nazym Bashkenova
- Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Ruge Zang
- Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY 10032, USA.,Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xin Huang
- Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jianlong Wang
- Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY 10032, USA
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99
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Nicolai S, Mahen R, Raschellà G, Marini A, Pieraccioli M, Malewicz M, Venkitaraman AR, Melino G. ZNF281 is recruited on DNA breaks to facilitate DNA repair by non-homologous end joining. Oncogene 2020; 39:754-766. [PMID: 31570788 PMCID: PMC6976523 DOI: 10.1038/s41388-019-1028-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 08/19/2019] [Accepted: 08/24/2019] [Indexed: 02/06/2023]
Abstract
Efficient repair of DNA double-strand breaks (DSBs) is of critical importance for cell survival. Although non-homologous end joining (NHEJ) is the most used DSBs repair pathway in the cells, how NHEJ factors are sequentially recruited to damaged chromatin remains unclear. Here, we identify a novel role for the zinc-finger protein ZNF281 in participating in the ordered recruitment of the NHEJ repair factor XRCC4 at damage sites. ZNF281 is recruited to DNA lesions within seconds after DNA damage through a mechanism dependent on its DNA binding domain and, at least in part, on poly-ADP ribose polymerase (PARP) activity. ZNF281 binds XRCC4 through its zinc-finger domain and facilitates its recruitment to damaged sites. Consequently, depletion of ZNF281 impairs the efficiency of the NHEJ repair pathway and decreases cell viability upon DNA damage. Survival analyses from datasets of commonly occurring human cancers show that higher levels of ZNF281 correlate with poor prognosis of patients treated with DNA-damaging therapies. Thus, our results define a late ZNF281-dependent regulatory step of NHEJ complex assembly at DNA lesions and suggest additional possibilities for cancer patients' stratification and for the development of personalised therapeutic strategies.
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Affiliation(s)
- Sara Nicolai
- Medical Research Council, Toxicology Unit, University of Cambridge, Leicester, LE1 9HN, UK
| | - Robert Mahen
- Medical Research Council, Cancer Unit, University of Cambridge, Cambridge, CB2 0XZ, UK
| | | | - Alberto Marini
- Medical Research Council, Toxicology Unit, University of Cambridge, Leicester, LE1 9HN, UK
| | - Marco Pieraccioli
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Michal Malewicz
- Medical Research Council, Toxicology Unit, University of Cambridge, Leicester, LE1 9HN, UK
| | - Ashok R Venkitaraman
- Medical Research Council, Cancer Unit, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - Gerry Melino
- Medical Research Council, Toxicology Unit, University of Cambridge, Leicester, LE1 9HN, UK.
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133, Rome, Italy.
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100
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Li QV, Rosen BP, Huangfu D. Decoding pluripotency: Genetic screens to interrogate the acquisition, maintenance, and exit of pluripotency. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2020; 12:e1464. [PMID: 31407519 PMCID: PMC6898739 DOI: 10.1002/wsbm.1464] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 05/31/2019] [Accepted: 07/17/2019] [Indexed: 01/25/2023]
Abstract
Pluripotent stem cells have the ability to unlimitedly self-renew and differentiate to any somatic cell lineage. A number of systems biology approaches have been used to define this pluripotent state. Complementary to systems level characterization, genetic screens offer a unique avenue to functionally interrogate the pluripotent state and identify the key players in pluripotency acquisition and maintenance, exit of pluripotency, and lineage differentiation. Here we review how genetic screens have helped us decode pluripotency regulation. We will summarize results from RNA interference (RNAi) based screens, discuss recent advances in CRISPR/Cas-based genetic perturbation methods, and how these advances have made it possible to more comprehensively interrogate pluripotency and differentiation through genetic screens. Such investigations will not only provide a better understanding of this unique developmental state, but may enhance our ability to use pluripotent stem cells as an experimental model to study human development and disease progression. Functional interrogation of pluripotency also provides a valuable roadmap for utilizing genetic perturbation to gain systems level understanding of additional cellular states, from later stages of development to pathological disease states. This article is categorized under: Developmental Biology > Stem Cell Biology and Regeneration Developmental Biology > Developmental Processes in Health and Disease Biological Mechanisms > Cell Fates.
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Affiliation(s)
- Qing V. Li
- Sloan Kettering Institute, 1275 York Avenue, New York, New York 10065, USA
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA
- These authors contributed equally
| | - Bess P. Rosen
- Sloan Kettering Institute, 1275 York Avenue, New York, New York 10065, USA
- Weill Graduate School of Medical Sciences at Cornell University, 1300 York Avenue, New York, New York 10065, USA
- These authors contributed equally
| | - Danwei Huangfu
- Sloan Kettering Institute, 1275 York Avenue, New York, New York 10065, USA
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