1
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Wang ZH, Wang J, Liu F, Sun S, Zheng Q, Hu X, Yin Z, Xie C, Wang H, Wang T, Zhang S, Wang YP. THAP3 recruits SMYD3 to OXPHOS genes and epigenetically promotes mitochondrial respiration in hepatocellular carcinoma. FEBS Lett 2024; 598:1513-1531. [PMID: 38664231 DOI: 10.1002/1873-3468.14889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/27/2024] [Accepted: 03/31/2024] [Indexed: 06/27/2024]
Abstract
Mitochondria harbor the oxidative phosphorylation (OXPHOS) system to sustain cellular respiration. However, the transcriptional regulation of OXPHOS remains largely unexplored. Through the cancer genome atlas (TCGA) transcriptome analysis, transcription factor THAP domain-containing 3 (THAP3) was found to be strongly associated with OXPHOS gene expression. Mechanistically, THAP3 recruited the histone methyltransferase SET and MYND domain-containing protein 3 (SMYD3) to upregulate H3K4me3 and promote OXPHOS gene expression. The levels of THAP3 and SMYD3 were altered by metabolic cues. They collaboratively supported liver cancer cell proliferation and colony formation. In clinical human liver cancer, both of them were overexpressed. THAP3 positively correlated with OXPHOS gene expression. Together, THAP3 cooperates with SMYD3 to epigenetically upregulate cellular respiration and liver cancer cell proliferation.
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Affiliation(s)
- Zi-Hao Wang
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jingyi Wang
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai Key Laboratory of Pancreatic Disease, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, China
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, China
| | - Fuchen Liu
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Third Affiliated Hospital, Naval Medical University, Shanghai, China
| | - Sijun Sun
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai Key Laboratory of Pancreatic Disease, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, China
- Department of Gastrointestinal Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, China
| | - Quan Zheng
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, China
| | - Xiaotian Hu
- Department of Gastrointestinal Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, China
| | - Zihan Yin
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai Key Laboratory of Pancreatic Disease, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, China
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, China
| | - Chengmei Xie
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai Key Laboratory of Pancreatic Disease, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, China
| | - Haiyan Wang
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, China
| | - Tianshi Wang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, China
| | - Shengjie Zhang
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai Key Laboratory of Pancreatic Disease, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, China
| | - Yi-Ping Wang
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai Key Laboratory of Pancreatic Disease, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, China
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2
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Zhou Z, Jiang T, Zhu Y, Ling Z, Yang B, Huang L. A comparative investigation on
H3K27ac
enhancer activities in the brain and liver tissues between wild boars and domesticated pigs. Evol Appl 2022; 15:1281-1290. [PMID: 36051459 PMCID: PMC9423090 DOI: 10.1111/eva.13461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 06/28/2022] [Accepted: 07/20/2022] [Indexed: 11/29/2022] Open
Abstract
Dramatic phenotypic differences between domestic pigs and wild boars (Sus scrofa) provide opportunities to investigate molecular mechanisms underlying the formation of complex traits, including morphology, physiology and behaviour. Most studies comparing domestic pigs and wild boars have focused on variations in DNA sequences and mRNA expression, but not on epigenetic changes. Here, we present a genome‐wide comparative study on H3K27ac enhancer activities and the corresponding mRNA profiling in the brain and liver tissues of adult Bama Xiang pigs (BMXs) and Chinese wild boars (CWBs). We identified a total of 1,29,487 potential regulatory elements, among which 11,241 H3K27ac peaks showed differential activity between CWBs and BMXs in at least one tissue. These peaks were overrepresented by binding motifs of FOXA1, JunB, ATF3 and BATF, and overlapped with differentially expressed genes that are involved in female mating behaviour, response to growth factors and hormones, and lipid metabolism. We also identified 4118 nonredundant super‐enhancers from ChIP‐Seq data on H3K27ac. Notably, we identified differentially active peaks located close to or within candidate genes, including TBX19, MSTN, AHR and P2RY1, which were identified in DNA sequence‐based population differentiation studies. This study generates a valuable dataset on H3K27ac profiles of the brain and liver from domestic pigs and wild boars, which helps gain insights into the changes in enhancer activities from wild boars to domestic pigs.
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Affiliation(s)
- Zhimin Zhou
- State Key Laboratory of Swine Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Tao Jiang
- State Key Laboratory of Swine Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Yaling Zhu
- State Key Laboratory of Swine Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Ziqi Ling
- State Key Laboratory of Swine Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Bin Yang
- State Key Laboratory of Swine Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Lusheng Huang
- State Key Laboratory of Swine Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
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3
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The role of NURR1 in metabolic abnormalities of Parkinson's disease. Mol Neurodegener 2022; 17:46. [PMID: 35761385 PMCID: PMC9235236 DOI: 10.1186/s13024-022-00544-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 05/21/2022] [Indexed: 11/30/2022] Open
Abstract
A constant metabolism and energy supply are crucial to all organs, particularly the brain. Age-dependent neurodegenerative diseases, such as Parkinson’s disease (PD), are associated with alterations in cellular metabolism. These changes have been recognized as a novel hot topic that may provide new insights to help identify risk in the pre-symptomatic phase of the disease, understand disease pathogenesis, track disease progression, and determine critical endpoints. Nuclear receptor-related factor 1 (NURR1), an orphan member of the nuclear receptor superfamily of transcription factors, is a major risk factor in the pathogenesis of PD, and changes in NURR1 expression can have a detrimental effect on cellular metabolism. In this review, we discuss recent evidence that suggests a vital role of NURR1 in dopaminergic (DAergic) neuron development and the pathogenesis of PD. The association between NURR1 and cellular metabolic abnormalities and its implications for PD therapy have been further highlighted.
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4
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Zhou Z, Zhu Y, Zhang Z, Jiang T, Ling Z, Yang B, Li W. Comparative Analysis of Promoters and Enhancers in the Pituitary Glands of the Bama Xiang and Large White Pigs. Front Genet 2021; 12:697994. [PMID: 34367256 PMCID: PMC8343535 DOI: 10.3389/fgene.2021.697994] [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: 04/20/2021] [Accepted: 06/29/2021] [Indexed: 12/14/2022] Open
Abstract
The epigenetic regulation of gene expression is implicated in complex diseases in humans and various phenotypes in other species. There has been little exploration of regulatory elements in the pig. Here, we performed chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) to profile histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine 27 acetylation (H3K27ac) in the pituitary gland of adult Bama Xiang and Large White pigs, which have divergent evolutionary histories and large phenotypic differences. We identified a total of 65,044 non-redundant regulatory regions, including 23,680 H3K4me3 peaks and 61,791 H3K27ac peaks (12,318 proximal and 49,473 distal), augmenting the catalog of pituitary regulatory elements in pigs. We found 793 H3K4me3 and 3,602 H3K27ac peaks that show differential activity between the two breeds, overlapping with genes involved in the Notch signaling pathway, response to growth hormone (GH), thyroid hormone signaling pathway, and immune system, and enriched for binding motifs of transcription factors (TFs), including JunB, ATF3, FRA1, and BATF. We further identified 2,025 non-redundant super enhancers from H3K27ac ChIP-seq data, among which 302 were shared in all samples of cover genes enriched for biological processes related to pituitary function. This study generated a valuable dataset of H3K4me3 and H3K27ac regions in porcine pituitary glands and revealed H3K4me3 and H3K27ac peaks with differential activity between Bama Xiang and Large White pigs.
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Affiliation(s)
- Zhimin Zhou
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Yaling Zhu
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China.,Laboratory Animal Research Center, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Zhen Zhang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Tao Jiang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Ziqi Ling
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Bin Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Wanbo Li
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China.,Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen, China
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5
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Li G, Xie Q, Yang Z, Wang L, Zhang X, Zuo B, Zhang S, Yang A, Jia L. Sp1-mediated epigenetic dysregulation dictates HDAC inhibitor susceptibility of HER2-overexpressing breast cancer. Int J Cancer 2019; 145:3285-3298. [PMID: 31111958 DOI: 10.1002/ijc.32425] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 04/23/2019] [Accepted: 05/13/2019] [Indexed: 12/17/2023]
Abstract
Human epidermal growth factor receptor 2 (HER2/erbB2) is a key driver and therapeutic target for breast cancer. The treatment of HER2-positive breast cancer remains a clinical challenge largely due to the limited understanding of HER2-driving oncogenic signaling and the frequent resistance to simply HER2-targeted therapy. Here, we show that the histone deacetylase inhibitor, trichostatin A (TSA), suppresses HER2-overexpressing breast cancer via upregulation of miR-146a and the resultant repression of its oncogenic targets, interleukin-1 receptor-associated kinase 1 and the chemokine receptor CXCR4. Mechanistically, histone H3K56 acetylation and deacetylation on the MIR146A promoter are catalyzed respectively by the acetyltransferase p300 and histone deacetylase 1 (HDAC1), both of which are recruited to the genomic loci by the transcription factor specificity protein 1 (Sp1). HER2 signaling phosphorylates Sp1 and induces its predominant association with HDAC1, but not p300, leading to histone hypoacetylation and silencing of MIR146A. In addition, the death receptor Fas is similarly downregulated by the aforementioned epigenetic paradigm, indicating its wide involvement in impairing tumor suppressor gene expression. Consequently, TSA synergizes with lapatinib, a tyrosine kinase inhibitor of HER2, to suppress breast cancer in vitro and in rodent models. These findings demonstrate a novel mechanism of HER2-driven carcinogenesis and suggest the applicability of combined HER2 and HDAC targeting in breast cancer therapy.
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MESH Headings
- Animals
- Breast Neoplasms/drug therapy
- Breast Neoplasms/genetics
- Cell Line, Tumor
- Down-Regulation/drug effects
- Down-Regulation/genetics
- Epigenesis, Genetic/genetics
- Female
- Gene Expression Regulation, Neoplastic/drug effects
- Gene Expression Regulation, Neoplastic/genetics
- Histone Deacetylase 1/genetics
- Histone Deacetylase Inhibitors/pharmacology
- Histone Deacetylases/genetics
- Humans
- MCF-7 Cells
- Mice
- Mice, Inbred BALB C
- Mice, Nude
- Promoter Regions, Genetic/drug effects
- Promoter Regions, Genetic/genetics
- Receptor, ErbB-2/genetics
- Sp1 Transcription Factor/genetics
- Transcription, Genetic/drug effects
- Transcription, Genetic/genetics
- Transcriptional Activation/drug effects
- Transcriptional Activation/genetics
- Up-Regulation/drug effects
- Up-Regulation/genetics
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Affiliation(s)
- Guoyin Li
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Qiaosheng Xie
- Department of Immunology, Fourth Military Medical University, Xi'an, China
- Department of Radiation Oncology, China-Japan Friendship Hospital, Beijing, China
| | - Zhiwei Yang
- Department of Applied Physics, School of Science, Xi'an Jiaotong University, Xi'an, China
| | - Lei Wang
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
| | - Xiang Zhang
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
| | - Baile Zuo
- Department of Immunology, Fourth Military Medical University, Xi'an, China
| | - Shengli Zhang
- Department of Applied Physics, School of Science, Xi'an Jiaotong University, Xi'an, China
| | - Angang Yang
- Department of Immunology, Fourth Military Medical University, Xi'an, China
| | - Lintao Jia
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
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6
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Pennings S, Revuelta A, McLaughlin KA, Abd Hadi NA, Petchreing P, Ottaviano R, Meehan RR. Dynamics and Mechanisms of DNA Methylation Reprogramming. EPIGENETICS AND REGENERATION 2019:19-45. [DOI: 10.1016/b978-0-12-814879-2.00002-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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7
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Wang S, Xiao S, Cheng X, Chen S, Zhu X, Lin F, Chen S. Construction and rescue of Muscovy duck-origin goose parvovirus from an infectious clone containing an E-box deletion within the left terminal region. Mol Cell Probes 2018; 42:32-35. [PMID: 30240819 DOI: 10.1016/j.mcp.2018.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 09/07/2018] [Accepted: 09/17/2018] [Indexed: 01/24/2023]
Abstract
To obtain a deletion mutant of Muscovy duck-origin goose parvovirus (MDGPV) and to analyze its biological characteristics, the pMDGPVPT plasmid, which contains a full-length DNA infectious clone of the MDGPV PT strain, was used in this study as the template. The E-box at nt 315 of the left inverted terminal repeat sequence (L-ITR) was deleted by overlap extension PCR to obtain the infectious recombinant plasmid p-PTΔE315. The p-PTΔE315 plasmid was transfected into 9-day-old non-immune Muscovy duck embryos via the yolk sac and the rescued deletion mutant virus r-PTΔE315 was generated. Experiments to demonstrate the novel deletion mutant virus' biological characteristics showed that r-PTΔE315 can cause typical lesions after infection of Muscovy duck embryos. Compared with its parent strain PT, the virulence of r-PTΔE315 and its proliferation ability in Muscovy duck embryos were attenuated, but its ability to replicate in MDEF cells was enhanced. This study laid the foundation for further understanding of the relationship between E-box deletion in the L-ITR and MDGPV virulence.
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Affiliation(s)
- Shao Wang
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, 350013, China; Fujian Animal Diseases Control Technology Development Center, Fuzhou, 350013, China
| | - Shifeng Xiao
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, 350013, China; Fujian Animal Diseases Control Technology Development Center, Fuzhou, 350013, China
| | - Xiaoxia Cheng
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, 350013, China; Fujian Animal Diseases Control Technology Development Center, Fuzhou, 350013, China
| | - Shaoying Chen
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, 350013, China; Fujian Animal Diseases Control Technology Development Center, Fuzhou, 350013, China.
| | - Xiaoli Zhu
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, 350013, China; Fujian Animal Diseases Control Technology Development Center, Fuzhou, 350013, China
| | - Fengqiang Lin
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, 350013, China; Fujian Animal Diseases Control Technology Development Center, Fuzhou, 350013, China
| | - Shilong Chen
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, 350013, China; Fujian Animal Diseases Control Technology Development Center, Fuzhou, 350013, China
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8
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Schmitt CE, Morales BM, Schmitz EMH, Hawkins JS, Lizama CO, Zape JP, Hsiao EC, Zovein AC. Fluorescent tagged episomals for stoichiometric induced pluripotent stem cell reprogramming. Stem Cell Res Ther 2017; 8:132. [PMID: 28583172 PMCID: PMC5460403 DOI: 10.1186/s13287-017-0581-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 04/28/2017] [Accepted: 05/08/2017] [Indexed: 12/31/2022] Open
Abstract
Background Non-integrating episomal vectors have become an important tool for induced pluripotent stem cell reprogramming. The episomal vectors carrying the “Yamanaka reprogramming factors” (Oct4, Klf, Sox2, and L-Myc + Lin28) are critical tools for non-integrating reprogramming of cells to a pluripotent state. However, the reprogramming process remains highly stochastic, and is hampered by an inability to easily identify clones that carry the episomal vectors. Methods We modified the original set of vectors to express spectrally separable fluorescent proteins to allow for enrichment of transfected cells. The vectors were then tested against the standard original vectors for reprogramming efficiency and for the ability to enrich for stoichiometric ratios of factors. Results The reengineered vectors allow for cell sorting based on reprogramming factor expression. We show that these vectors can assist in tracking episomal expression in individual cells and can select the reprogramming factor dosage. Conclusions Together, these modified vectors are a useful tool for understanding the reprogramming process and improving induced pluripotent stem cell isolation efficiency. Electronic supplementary material The online version of this article (doi:10.1186/s13287-017-0581-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christopher E Schmitt
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Blanca M Morales
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA.,Division of Endocrinology and Metabolism, Institute for Human Genetics, Department of Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Ellen M H Schmitz
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA
| | - John S Hawkins
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Carlos O Lizama
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Joan P Zape
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Edward C Hsiao
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA. .,Division of Endocrinology and Metabolism, Institute for Human Genetics, Department of Medicine, University of California San Francisco, San Francisco, CA, 94143, USA.
| | - Ann C Zovein
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA. .,Division of Neonatology, Department of Pediatrics, University of California San Francisco School of Medicine, San Francisco, CA, 94143, USA.
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9
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Retinoic acid combined with spermatogonial stem cell conditions facilitate the generation of mouse germ-like cells. Biosci Rep 2017; 37:BSR20170637. [PMID: 28314787 PMCID: PMC5398254 DOI: 10.1042/bsr20170637] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 03/10/2017] [Accepted: 03/17/2017] [Indexed: 11/23/2022] Open
Abstract
Spermatogenic lineage has been directly generated in spermatogonial stem cell (SSC) conditions from human pluripotent stem cells (PSCs). However, it remains unknown whether mouse embryonic stem cells (ESCs) can directly differentiate into advanced male germ cell lineage in the same conditions. Here, we showed rather low efficiency of germ-like cell generation from mouse ESCs in SSC conditions. Interestingly, addition of retinoic acid (RA) into SSC conditions enabled efficient differentiation of mouse ESCs into germ-like cells, as shown by the activation of spermatogenesis-associated genes such as Mvh, Dazl, Prdm14, Stella, Scp1, Scp3, Stra8 and Rec8. In contrast, for cells cultured in control medium, the activation of the above genes barely occurred. In addition, RA with SSC conditions yielded colonies of Acrosin-expressing cells and the positive ratio reached a peak at day 6. Our work thus establishes a simple and cost-efficient approach for male germ like cell differentiation from mouse PSCs and may propose a useful strategy for studying spermatogenesis in vitro.
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10
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Becker SF, Jarriault S. Natural and induced direct reprogramming: mechanisms, concepts and general principles-from the worm to vertebrates. Curr Opin Genet Dev 2016; 40:154-163. [PMID: 27690213 DOI: 10.1016/j.gde.2016.06.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 05/31/2016] [Accepted: 06/23/2016] [Indexed: 12/19/2022]
Abstract
Elucidating the mechanisms underlying cell fate determination, cell identity maintenance and cell reprogramming in vivo is one of the main challenges in today's science. Such knowledge of fundamental importance will further provide new leads for early diagnostics and targeted therapy approaches both in regenerative medicine and cancer research. This review focuses on recent mechanistic findings and factors that influence the differentiated state of cells in direct reprogramming events, aka transdifferentiation. In particular, we will look at the mechanistic and conceptual advances brought by the use of the nematode Caenorhabditis elegans and highlight common themes across phyla.
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Affiliation(s)
- Sarah F Becker
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR7104, INSERM U964, Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch Cu Strasbourg, France
| | - Sophie Jarriault
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR7104, INSERM U964, Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch Cu Strasbourg, France.
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11
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Martovetsky G, Bush KT, Nigam SK. Kidney versus Liver Specification of SLC and ABC Drug Transporters, Tight Junction Molecules, and Biomarkers. ACTA ACUST UNITED AC 2016; 44:1050-60. [PMID: 27044799 DOI: 10.1124/dmd.115.068254] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 03/30/2016] [Indexed: 01/04/2023]
Abstract
The hepatocyte nuclear factors, Hnf1a and Hnf4a, in addition to playing key roles in determining hepatocyte fate, have been implicated as candidate lineage-determining transcription factors in the kidney proximal tubule (PT) [Martovetsky et. al., (2012) Mol Pharmacol 84:808], implying an additional level of regulation that is potentially important in developmental and/or tissue-engineering contexts. Mouse embryonic fibroblasts (MEFs) transduced with Hnf1a and Hnf4a form tight junctions and express multiple PT drug transporters (e.g., Slc22a6/Oat1, Slc47a1/Mate1, Slc22a12/Urat1, Abcg2/Bcrp, Abcc2/Mrp2, Abcc4/Mrp4), nutrient transporters (e.g., Slc34a1/NaPi-2, Slco1a6), and tight junction proteins (occludin, claudin 6, ZO-1/Tjp1, ZO-2/Tjp2). In contrast, the coexpression (with Hnf1a and Hnf4a) of GATA binding protein 4 (Gata4), as well as the forkhead box transcription factors, Foxa2 and Foxa3, in MEFs not only downregulates PT markers but also leads to upregulation of several hepatocyte markers, including albumin, apolipoprotein, and transferrin. A similar result was obtained with primary mouse PT cells. Thus, the presence of Gata4 and Foxa2/Foxa3 appears to alter the effect of Hnf1a and Hnf4a by an as-yet unidentified mechanism, leading toward the generation of more hepatocyte-like cells as opposed to cells exhibiting PT characteristics. The different roles of Hnf4a in the kidney and liver was further supported by reanalysis of ChIP-seq data, which revealed Hnf4a colocalization in the kidney near PT-enriched genes compared with those genes enriched in the liver. These findings provide valuable insight, not only into the developmental, and perhaps organotypic, regulation of drug transporters, drug-metabolizing enzymes, and tight junctions, but also for regenerative medicine strategies aimed at restoring the function of the liver and/or kidney (acute kidney injury, AKI; chronic kidney disease, CKD).
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Affiliation(s)
- Gleb Martovetsky
- Department of Pediatrics (G.M., K.T.B., S.K.N.), Department of Medicine, Division of Nephrology and Hypertension, (S.K.N.), and Department of Cellular and Molecular Medicine (S.K.N.), University of California, San Diego, La Jolla, California
| | - Kevin T Bush
- Department of Pediatrics (G.M., K.T.B., S.K.N.), Department of Medicine, Division of Nephrology and Hypertension, (S.K.N.), and Department of Cellular and Molecular Medicine (S.K.N.), University of California, San Diego, La Jolla, California
| | - Sanjay K Nigam
- Department of Pediatrics (G.M., K.T.B., S.K.N.), Department of Medicine, Division of Nephrology and Hypertension, (S.K.N.), and Department of Cellular and Molecular Medicine (S.K.N.), University of California, San Diego, La Jolla, California
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12
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Physical Interactions and Functional Coordination between the Core Subunits of Set1/Mll Complexes and the Reprogramming Factors. PLoS One 2015; 10:e0145336. [PMID: 26691508 PMCID: PMC4686221 DOI: 10.1371/journal.pone.0145336] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 12/02/2015] [Indexed: 11/19/2022] Open
Abstract
Differentiated cells can be reprogrammed to the pluripotent state by overexpression of defined factors, and this process is profoundly influenced by epigenetic mechanisms including dynamic histone modifications. Changes in H3K4 methylation have been shown to be the predominant activating response in the early stage of cellular reprogramming. Mechanisms underlying such epigenetic priming, however, are not well understood. Here we show that the expression of the reprogramming factors (Yamanaka factors, Oct4, Sox2, Klf4 and Myc), especially Myc, directly promotes the expression of certain core subunits of the Set1/Mll family of H3K4 methyltransferase complexes. A dynamic recruitment of the Set1/Mll complexes largely, though not sufficiently in its own, explains the dynamics of the H3K4 methylation during cellular reprogramming. We then demonstrate that the core subunits of the Set1/Mll complexes physically interact with mainly Sox2 and Myc among the Yamanaka factors. We further show that Sox2 directly binds the Ash2l subunit in the Set1/Mll complexes and this binding is mediated by the HMG domain of Sox2. Functionally, we show that the Set1/Mll complex core subunits are required for efficient cellular reprogramming. We also show that Dpy30, one of the core subunits in the complexes, is required for the efficient target binding of the reprogramming factors. Interestingly, such requirement is not necessarily dependent on locus-specific H3K4 methylation. Our work provides a better understanding of how the reprogramming factors physically interact and functionally coordinate with a key group of epigenetic modulators to mediate transitions of the chromatin state involved in cellular reprogramming.
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Transcriptional Pause Release Is a Rate-Limiting Step for Somatic Cell Reprogramming. Cell Stem Cell 2014; 15:574-88. [DOI: 10.1016/j.stem.2014.09.018] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 08/07/2014] [Accepted: 09/26/2014] [Indexed: 02/07/2023]
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Eid JE, Garcia CB. Reprogramming of mesenchymal stem cells by oncogenes. Semin Cancer Biol 2014; 32:18-31. [PMID: 24938913 DOI: 10.1016/j.semcancer.2014.05.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 05/21/2014] [Accepted: 05/22/2014] [Indexed: 12/18/2022]
Abstract
Mesenchymal stem cells (MSCs) originate from embryonic mesoderm and give rise to the multiple lineages of connective tissues. Transformed MSCs develop into aggressive sarcomas, some of which are initiated by specific chromosomal translocations that generate fusion proteins with potent oncogenic properties. The sarcoma oncogenes typically prime MSCs through aberrant reprogramming. They dictate commitment to a specific lineage but prevent mature differentiation, thus locking the cells in a state of proliferative precursors. Deregulated expression of lineage-specific transcription factors and controllers of chromatin structure play a central role in MSC reprogramming and sarcoma pathogenesis. This suggests that reversing the epigenetic aberrancies created by the sarcoma oncogenes with differentiation-related reagents holds great promise as a beneficial addition to sarcoma therapies.
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Affiliation(s)
- Josiane E Eid
- Department of Cancer Biology, Vanderbilt University Medical Center, 771 Preston, Research Building, 2220 Pierce Avenue, Nashville, TN 37232, USA.
| | - Christina B Garcia
- Department of Pediatrics-Nutrition, Baylor College of Medicine, BCM320, Huston, TX 77030, USA
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Mirakhori F, Zeynali B, Salekdeh GH, Baharvand H. Induced Neural Lineage Cells as Repair Kits: So Close, Yet So Far Away. J Cell Physiol 2014; 229:728-42. [DOI: 10.1002/jcp.24509] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 11/06/2013] [Indexed: 12/15/2022]
Affiliation(s)
- Fahimeh Mirakhori
- School of Biology, College of Science; University of Tehran; Tehran Iran
- Department of Stem Cells and Developmental Biology at the Cell Science Research Center; Royan Institute for Stem Cell Biology and Technology, ACECR; Tehran Iran
| | - Bahman Zeynali
- School of Biology, College of Science; University of Tehran; Tehran Iran
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology at Cell Science Research Center; Royan Institute for Stem Cell Biology and Technology, ACECR; Tehran Iran
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology at the Cell Science Research Center; Royan Institute for Stem Cell Biology and Technology, ACECR; Tehran Iran
- Department of Developmental Biology; University of Science and Culture, ACECR; Tehran Iran
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Abstract
In the past several years, human genetics studies have progressed from monogenic to complex and common diseases because of the advancement in technologies. There is increased knowledge of the pharmacokinetics and pharmacogenomics of the drugs in adults as well as in children. These technological developments provided new diagnostic, prognostic, and therapeutic opportunities. We are now in a position to address many additional ambitious questions. For instance, in clinical medicine, interindividual variation in drug response is a major problem. Some of the heterogeneity of drug safety and efficacy among individuals can be explained by pharmacogenomics. It has also the potential to improve the treatment in both adults and children. In pediatrics however, there is ontogeny and metabolic capacity in children is different compared to adults. Several specific developmental changes may underlie some of the variability in drug response seen in children. They may also be responsible for adverse drug reactions (ADRs). Therefore, much of the diversity in drug effects cannot be explained by studying the genomic diversity alone. It is necessary to include the effect of growth (involves variations in gene expression) along with genetic differences when explaining the variability in treatment response. In this respect epigenomics may expand the scope of pharmacogenomics towards optimization of drug therapy. Future studies must focus on periods of maturation of the drug-metabolizing enzymes and polymorphisms in their genes by using candidate gene approach, gene expression analysis, genome-wide haplotype mapping, and proteomics. The integration of genetic data and clinical phenotypes along with the role of other factors is necessary to evaluate both efficacy and ADRs of any drug. It may require extensive genetic epidemiological studies spanning over many years.
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Sun X, Jiao X, Pestell TG, Fan C, Qin S, Mirabelli E, Ren H, Pestell RG. MicroRNAs and cancer stem cells: the sword and the shield. Oncogene 2013; 33:4967-77. [PMID: 24240682 DOI: 10.1038/onc.2013.492] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 10/11/2013] [Accepted: 10/11/2013] [Indexed: 12/18/2022]
Abstract
Emerging chemotherapy drugs and targeted therapies have been widely applied in anticancer treatment and have given oncologists a promising future. Nevertheless, regeneration and recurrence are still huge obstacles on the way to cure cancer. Cancer stem cells (CSCs) are capable of self-renewal, tumor initiation, recurrence, metastasis, therapy resistance, and reside as a subset in many, if not all, cancers. Therefore, therapeutics specifically targeting and killing CSCs are being identified, and may be promising and effective strategies to eliminate cancer. MicroRNAs (miRNAs, miRs), small noncoding RNAs regulating gene expression in a post-transcriptional manner, are dysregulated in most malignancies and are identified as important regulators of CSCs. However, limited knowledge exists for biological and molecular mechanism by which miRNAs regulate CSCs. In this article, we review CSCs, miRNAs and the interactions between miRNA regulation and CSCs, with a specific focus on the molecular mechanisms and clinical applications. This review will help us to know in detail how CSCs are regulated by miRNAs networks and also help to develop more effective and secure miRNA-based clinical therapies.
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Affiliation(s)
- X Sun
- 1] Oncology Department of the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China [2] Departments of Cancer Biology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - X Jiao
- Departments of Cancer Biology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - T G Pestell
- Department of Stem Cell Biology and Regenerative Medicine, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - C Fan
- Cardiovascular Department of the Second Affiliated Hospital of Tianjin Medical University, Tianjin, China
| | - S Qin
- 1] Oncology Department of the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China [2] New York University Medical Center, New York, NY, USA
| | - E Mirabelli
- Departments of Cancer Biology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - H Ren
- Oncology Department of the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - R G Pestell
- Departments of Cancer Biology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
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The use of small molecules in somatic-cell reprogramming. Trends Cell Biol 2013; 24:179-87. [PMID: 24183602 DOI: 10.1016/j.tcb.2013.09.011] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 09/20/2013] [Accepted: 09/23/2013] [Indexed: 12/27/2022]
Abstract
Pioneering work over the past years has highlighted the remarkable ability of manipulating cell states through exogenous, mostly transcription factor-induced reprogramming. The use of small molecules and reprogramming by transcription factors share a common history starting with the early AZA and MyoD experiments in fibroblast cells. Recent work shows that a combination of small molecules can replace all of the reprogramming factors and many previous studies have demonstrated their use in enhancing efficiencies or replacing individual factors. Here we provide a brief introduction to reprogramming followed by a detailed review of the major classes of small molecules that have been used to date and what future opportunities can be expected from these.
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Nestor MW, Noggle SA. Standardization of human stem cell pluripotency using bioinformatics. Stem Cell Res Ther 2013; 4:37. [PMID: 23680084 PMCID: PMC3707009 DOI: 10.1186/scrt185] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The study of cell differentiation, embryonic development, and personalized regenerative medicine are all possible through the use of human stem cells. The propensity for these cells to differentiate into all three germ layers of the body with the potential to generate any cell type opens a number of promising avenues for studying human development and disease. One major hurdle to the development of high-throughput production of human stem cells for use in regenerative medicine has been standardization of pluripotency assays. In this review we discuss technologies currently being deployed to produce standardized, high-quality stem cells that can be scaled for high-throughput derivation and screening in regenerative medicine applications. We focus on assays for pluripotency using bioinformatics and gene expression profiling. We review a number of approaches that promise to improve unbiased prediction of utility of both human induced pluripotent stem cells and embryonic stem cells.
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