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Yao X, Xu K, Tao N, Cheng S, Chen H, Zhang D, Yang M, Tan M, Yu H, Chen P, Zhan Z, He S, Li R, Wang C, Wu D, Ren J. ZNF148 inhibits HBV replication by downregulating RXRα transcription. Virol J 2024; 21:35. [PMID: 38297280 PMCID: PMC10832224 DOI: 10.1186/s12985-024-02291-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 01/08/2024] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND Progressive hepatitis B virus (HBV) infection can result in cirrhosis, hepatocellular cancer, and chronic hepatitis. While antiviral drugs that are now on the market are efficient in controlling HBV infection, finding a functional cure is still quite difficult. Identifying host factors involved in regulating the HBV life cycle will contribute to the development of new antiviral strategies. Zinc finger proteins have a significant function in HBV replication, according to earlier studies. Zinc finger protein 148 (ZNF148), a zinc finger transcription factor, regulates the expression of various genes by specifically binding to GC-rich sequences within promoter regions. The function of ZNF148 in HBV replication was investigated in this study. METHODS HepG2-Na+/taurocholate cotransporting polypeptide (HepG2-NTCP) cells and Huh7 cells were used to evaluate the function of ZNF148 in vitro. Northern blotting and real-time PCR were used to quantify the amount of viral RNA. Southern blotting and real-time PCR were used to quantify the amount of viral DNA. Viral protein levels were elevated, according to the Western blot results. Dual-luciferase reporter assays were used to examine the transcriptional activity of viral promoters. ZNF148's impact on HBV in vivo was investigated using an established rcccDNA mouse model. RESULTS ZNF148 overexpression significantly decreased the levels of HBV RNAs and HBV core DNA in HBV-infected HepG2-NTCP cells and Huh7 cells expressing prcccDNA. Silencing ZNF148 exhibited the opposite effects in both cell lines. Furthermore, ZNF148 inhibited the activity of HBV ENII/Cp and the transcriptional activity of cccDNA. Mechanistic studies revealed that ZNF148 attenuated retinoid X receptor alpha (RXRα) expression by binding to the RXRα promoter sequence. RXRα binding site mutation or RXRα overexpression abolished the suppressive effect of ZNF148 on HBV replication. The inhibitory effect of ZNF148 was also observed in the rcccDNA mouse model. CONCLUSIONS ZNF148 inhibited HBV replication by downregulating RXRα transcription. Our findings reveal that ZNF148 may be a new target for anti-HBV strategies.
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Affiliation(s)
- Xinyan Yao
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chong Yi Building, 1 YiXueYuan Road, Yuzhong District, Chongqing, 400016, China
| | - Kexin Xu
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chong Yi Building, 1 YiXueYuan Road, Yuzhong District, Chongqing, 400016, China
| | - Nana Tao
- Department of Clinical Laboratory, Chongqing Traditional Chinese Medicine Hospital, Chongqing, China
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China
| | - Shengtao Cheng
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chong Yi Building, 1 YiXueYuan Road, Yuzhong District, Chongqing, 400016, China
| | - Huajian Chen
- Department of Clinical Laboratory, Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing, China
| | - Dapeng Zhang
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chong Yi Building, 1 YiXueYuan Road, Yuzhong District, Chongqing, 400016, China
| | - Minli Yang
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chong Yi Building, 1 YiXueYuan Road, Yuzhong District, Chongqing, 400016, China
| | - Ming Tan
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chong Yi Building, 1 YiXueYuan Road, Yuzhong District, Chongqing, 400016, China
| | - Haibo Yu
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chong Yi Building, 1 YiXueYuan Road, Yuzhong District, Chongqing, 400016, China
| | - Peng Chen
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chong Yi Building, 1 YiXueYuan Road, Yuzhong District, Chongqing, 400016, China
| | - Zongzhu Zhan
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chong Yi Building, 1 YiXueYuan Road, Yuzhong District, Chongqing, 400016, China
| | - Siyi He
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chong Yi Building, 1 YiXueYuan Road, Yuzhong District, Chongqing, 400016, China
| | - Ranran Li
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chong Yi Building, 1 YiXueYuan Road, Yuzhong District, Chongqing, 400016, China
| | - Chunduo Wang
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chong Yi Building, 1 YiXueYuan Road, Yuzhong District, Chongqing, 400016, China
| | - Daiqing Wu
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chong Yi Building, 1 YiXueYuan Road, Yuzhong District, Chongqing, 400016, China.
| | - Jihua Ren
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chong Yi Building, 1 YiXueYuan Road, Yuzhong District, Chongqing, 400016, China.
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2
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Kim M, Singh M, Lee BK, Hibbs M, Richardson K, Ellies L, Wintle L, Stuart LM, Wang JY, Voon DC, Blancafort P, Wang J, Kim J, Leedman PJ, Woo AJ. A MYC-ZNF148-ID1/3 regulatory axis modulating cancer stem cell traits in aggressive breast cancer. Oncogenesis 2022; 11:60. [PMID: 36207293 PMCID: PMC9546828 DOI: 10.1038/s41389-022-00435-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 09/17/2022] [Accepted: 09/22/2022] [Indexed: 11/13/2022] Open
Abstract
The MYC proto-oncogene (MYC) is one of the most frequently overexpressed genes in breast cancer that drives cancer stem cell-like traits, resulting in aggressive disease progression and poor prognosis. In this study, we identified zinc finger transcription factor 148 (ZNF148, also called Zfp148 and ZBP-89) as a direct target of MYC. ZNF148 suppressed cell proliferation and migration and was transcriptionally repressed by MYC in breast cancer. Depletion of ZNF148 by short hairpin RNA (shRNA) and CRISPR/Cas9 increased triple-negative breast cancer (TNBC) cell proliferation and migration. Global transcriptome and chromatin occupancy analyses of ZNF148 revealed a central role in inhibiting cancer cell de-differentiation and migration. Mechanistically, we identified the Inhibitor of DNA binding 1 and 3 (ID1, ID3), drivers of cancer stemness and plasticity, as previously uncharacterized targets of transcriptional repression by ZNF148. Silencing of ZNF148 increased the stemness and tumorigenicity in TNBC cells. These findings uncover a previously unknown tumor suppressor role for ZNF148, and a transcriptional regulatory circuitry encompassing MYC, ZNF148, and ID1/3 in driving cancer stem cell traits in aggressive breast cancer.
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Affiliation(s)
- Mijeong Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Manjot Singh
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Perth, WA, 6000, Australia
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, 6027, Australia
| | - Bum-Kyu Lee
- Department of Biomedical Sciences, Cancer Research Center, University at Albany, State University of New York, Rensselaer, NY, 12144, USA
| | - Moira Hibbs
- RPH Research Centre, Royal Perth Hospital, Perth, WA, 6000, Australia
| | - Kirsty Richardson
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Perth, WA, 6000, Australia
| | - Lesley Ellies
- Division of Pharmacology and Toxicology, School of Biomedical Sciences, The University of Western Australia, Perth, WA, 6000, Australia
| | - Larissa Wintle
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Perth, WA, 6000, Australia
| | - Lisa M Stuart
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Perth, WA, 6000, Australia
| | - Jenny Y Wang
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, 2006, Australia
| | - Dominic C Voon
- Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, 920-1192, Japan
- Cancer Research Institute, Kanazawa University, Kanazawa, 920-1192, Japan
| | - Pilar Blancafort
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Perth, WA, 6000, Australia
- School of Human Sciences, The University of Western Australia, Perth, WA, 6000, Australia
- The Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Jianlong Wang
- Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Jonghwan Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Peter J Leedman
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Perth, WA, 6000, Australia.
| | - Andrew J Woo
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Perth, WA, 6000, Australia.
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, 6027, Australia.
- School of Medical and Health Sciences, Edith Cowan University, Perth, WA, 6000, Australia.
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3
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Emfinger CH, de Klerk E, Schueler KL, Rabaglia ME, Stapleton DS, Simonett SP, Mitok KA, Wang Z, Liu X, Paulo JA, Yu Q, Cardone RL, Foster HR, Lewandowski SL, Perales JC, Kendziorski CM, Gygi SP, Kibbey RG, Keller MP, Hebrok M, Merrins MJ, Attie AD. β Cell-specific deletion of Zfp148 improves nutrient-stimulated β cell Ca2+ responses. JCI Insight 2022; 7:e154198. [PMID: 35603790 PMCID: PMC9220824 DOI: 10.1172/jci.insight.154198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 04/20/2022] [Indexed: 12/05/2022] Open
Abstract
Insulin secretion from pancreatic β cells is essential for glucose homeostasis. An insufficient response to the demand for insulin results in diabetes. We previously showed that β cell-specific deletion of Zfp148 (β-Zfp148KO) improves glucose tolerance and insulin secretion in mice. Here, we performed Ca2+ imaging of islets from β‑Zfp148KO and control mice fed both a chow and a Western-style diet. β-Zfp148KO islets demonstrated improved sensitivity and sustained Ca2+ oscillations in response to elevated glucose levels. β-Zfp148KO islets also exhibited elevated sensitivity to amino acid-induced Ca2+ influx under low glucose conditions, suggesting enhanced mitochondrial phosphoenolpyruvate-dependent (PEP-dependent), ATP-sensitive K+ channel closure, independent of glycolysis. RNA-Seq and proteomics of β-Zfp148KO islets revealed altered levels of enzymes involved in amino acid metabolism (specifically, SLC3A2, SLC7A8, GLS, GLS2, PSPH, PHGDH, and PSAT1) and intermediary metabolism (namely, GOT1 and PCK2), consistent with altered PEP cycling. In agreement with this, β-Zfp148KO islets displayed enhanced insulin secretion in response to l-glutamine and activation of glutamate dehydrogenase. Understanding pathways controlled by ZFP148 may provide promising strategies for improving β cell function that are robust to the metabolic challenge imposed by a Western diet.
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Affiliation(s)
| | | | - Kathryn L. Schueler
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Mary E. Rabaglia
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Donnie S. Stapleton
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Shane P. Simonett
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kelly A. Mitok
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ziyue Wang
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina, USA
| | - Xinyue Liu
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Qing Yu
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Rebecca L. Cardone
- Department of Internal Medicine (Endocrinology), Yale University, New Haven, Connecticut, USA
| | - Hannah R. Foster
- Department of Medicine, Division of Endocrinology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Sophie L. Lewandowski
- Department of Medicine, Division of Endocrinology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - José C. Perales
- Department of Physiological Sciences, School of Medicine, University of Barcelona, L’Hospitalet del Llobregat, Barcelona, Spain
| | - Christina M. Kendziorski
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Richard G. Kibbey
- Department of Internal Medicine (Endocrinology), Yale University, New Haven, Connecticut, USA
- Department of Cellular and Molecular Physiology, Yale University, New Haven, Connecticut, USA
| | - Mark P. Keller
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - Matthew J. Merrins
- Department of Medicine, Division of Endocrinology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- William S. Middleton Memorial Veterans Hospital, Madison, Wisconsin, USA
| | - Alan D. Attie
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
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4
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Beveridge DJ, Richardson KL, Epis MR, Brown RAM, Stuart LM, Woo AJ, Leedman PJ. The tumor suppressor miR-642a-5p targets Wilms Tumor 1 gene and cell-cycle progression in prostate cancer. Sci Rep 2021; 11:18003. [PMID: 34504167 PMCID: PMC8429423 DOI: 10.1038/s41598-021-97190-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 08/17/2021] [Indexed: 12/19/2022] Open
Abstract
RNA-based therapeutics are emerging as innovative options for cancer treatment, with microRNAs being attractive targets for therapy development. We previously implicated microRNA-642a-5p (miR-642a-5p) as a tumor suppressor in prostate cancer (PCa), and here we characterize its mode of action, using 22Rv1 PCa cells. In an in vivo xenograft tumor model, miR-642a-5p induced a significant decrease in tumor growth, compared to negative control. Using RNA-Sequencing, we identified gene targets of miR-642a-5p which were enriched for gene sets controlling cell cycle; downregulated genes included Wilms Tumor 1 gene (WT1), NUAK1, RASSF3 and SKP2; and upregulated genes included IGFBP3 and GPS2. Analysis of PCa patient datasets showed a higher expression of WT1, NUAK1, RASSF3 and SKP2; and a lower expression of GPS2 and IGFBP3 in PCa tissue compared to non-malignant prostate tissue. We confirmed the prostatic oncogene WT1, as a direct target of miR-642a-5p, and treatment of 22Rv1 and LNCaP PCa cells with WT1 siRNA or a small molecule inhibitor of WT1 reduced cell proliferation. Taken together, these data provide insight into the molecular mechanisms by which miR-642a-5p acts as a tumor suppressor in PCa, an effect partially mediated by regulating genes involved in cell cycle control; and restoration of miR-642-5p in PCa could represent a novel therapeutic approach.
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Affiliation(s)
- Dianne J Beveridge
- Laboratory for Cancer Medicine, Harry Perkins Institute of Medical Research, QEII Medical Centre, 6 Verdun St, Nedlands, 6009, Australia
- Centre for Medical Research, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Kirsty L Richardson
- Laboratory for Cancer Medicine, Harry Perkins Institute of Medical Research, QEII Medical Centre, 6 Verdun St, Nedlands, 6009, Australia
- Centre for Medical Research, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Michael R Epis
- Laboratory for Cancer Medicine, Harry Perkins Institute of Medical Research, QEII Medical Centre, 6 Verdun St, Nedlands, 6009, Australia
- Centre for Medical Research, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Rikki A M Brown
- Laboratory for Cancer Medicine, Harry Perkins Institute of Medical Research, QEII Medical Centre, 6 Verdun St, Nedlands, 6009, Australia
- Centre for Medical Research, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Lisa M Stuart
- Laboratory for Cancer Medicine, Harry Perkins Institute of Medical Research, QEII Medical Centre, 6 Verdun St, Nedlands, 6009, Australia
- Centre for Medical Research, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Andrew J Woo
- Laboratory for Cancer Medicine, Harry Perkins Institute of Medical Research, QEII Medical Centre, 6 Verdun St, Nedlands, 6009, Australia
- Centre for Medical Research, The University of Western Australia, Crawley, WA, 6009, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, 6027, Australia
| | - Peter J Leedman
- Laboratory for Cancer Medicine, Harry Perkins Institute of Medical Research, QEII Medical Centre, 6 Verdun St, Nedlands, 6009, Australia.
- Centre for Medical Research, The University of Western Australia, Crawley, WA, 6009, Australia.
- School of Medicine and Pharmacology, The University of Western Australia, Crawley, WA, 6009, Australia.
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5
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Identification of the transcription factor MAZ as a regulator of erythropoiesis. Blood Adv 2021; 5:3002-3015. [PMID: 34351390 DOI: 10.1182/bloodadvances.2021004609] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/11/2021] [Indexed: 12/28/2022] Open
Abstract
Erythropoiesis requires a combination of ubiquitous and tissue-specific transcription factors (TFs). Here, through DNA affinity purification followed by mass spectrometry, we have identified the widely expressed protein MAZ (Myc-associated zinc finger) as a TF that binds to the promoter of the erythroid-specific human α-globin gene. Genome-wide mapping in primary human erythroid cells revealed that MAZ also occupies active promoters as well as GATA1-bound enhancer elements of key erythroid genes. Consistent with an important role during erythropoiesis, knockdown of MAZ reduces α-globin expression in K562 cells and impairs differentiation in primary human erythroid cells. Genetic variants in the MAZ locus are associated with changes in clinically important human erythroid traits. Taken together, these findings reveal the zinc-finger TF MAZ to be a previously unrecognized regulator of the erythroid differentiation program.
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Zinghirino F, Pappalardo XG, Messina A, Nicosia G, De Pinto V, Guarino F. VDAC Genes Expression and Regulation in Mammals. Front Physiol 2021; 12:708695. [PMID: 34421651 PMCID: PMC8374620 DOI: 10.3389/fphys.2021.708695] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/02/2021] [Indexed: 11/13/2022] Open
Abstract
VDACs are pore-forming proteins, coating the mitochondrial outer membrane, and playing the role of main regulators for metabolites exchange between cytosol and mitochondria. In mammals, three isoforms have evolutionary originated, VDAC1, VDAC2, and VDAC3. Despite similarity in sequence and structure, evidence suggests different biological roles in normal and pathological conditions for each isoform. We compared Homo sapiens and Mus musculus VDAC genes and their regulatory elements. RNA-seq transcriptome analysis shows that VDAC isoforms are expressed in human and mouse tissues at different levels with a predominance of VDAC1 and VDAC2 over VDAC3, with the exception of reproductive system. Numerous transcript variants for each isoform suggest specific context-dependent regulatory mechanisms. Analysis of VDAC core promoters has highlighted that, both in a human and a mouse, VDAC genes show features of TATA-less ones. The level of CG methylation of the human VDAC genes revealed that VDAC1 promoter is less methylated than other two isoforms. We found that expression of VDAC genes is mainly regulated by transcription factors involved in controlling cell growth, proliferation and differentiation, apoptosis, and bioenergetic metabolism. A non-canonical initiation site termed "the TCT/TOP motif," the target for translation regulation by the mTOR pathway, was identified in human VDAC2 and VDAC3 and in every murine VDACs promoter. In addition, specific TFBSs have been identified in each VDAC promoter, supporting the hypothesis that there is a partial functional divergence. These data corroborate our experimental results and reinforce the idea that gene regulation could be the key to understanding the evolutionary specialization of VDAC isoforms.
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Affiliation(s)
- Federica Zinghirino
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Xena Giada Pappalardo
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Angela Messina
- Section of Molecular Biology, Department of Biological, Geological and Environmental Sciences, University of Catania, Catania, Italy
- we.MitoBiotech.srl, Catania, Italy
| | - Giuseppe Nicosia
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Vito De Pinto
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
- we.MitoBiotech.srl, Catania, Italy
- Section of Catania, National Institute of Biostructures and Biosystems, Catania, Italy
| | - Francesca Guarino
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
- we.MitoBiotech.srl, Catania, Italy
- Section of Catania, National Institute of Biostructures and Biosystems, Catania, Italy
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De Pinto V. Renaissance of VDAC: New Insights on a Protein Family at the Interface between Mitochondria and Cytosol. Biomolecules 2021; 11:biom11010107. [PMID: 33467485 PMCID: PMC7831034 DOI: 10.3390/biom11010107] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/10/2021] [Accepted: 01/12/2021] [Indexed: 12/14/2022] Open
Abstract
It has become impossible to review all the existing literature on Voltage-Dependent Anion selective Channel (VDAC) in a single article. A real Renaissance of studies brings this protein to the center of decisive knowledge both for cell physiology and therapeutic application. This review, after highlighting the similarities between the cellular context and the study methods of the solute carriers present in the inner membrane and VDAC in the outer membrane of the mitochondria, will focus on the isoforms of VDAC and their biochemical characteristics. In particular, the possible reasons for their evolutionary onset will be discussed. The variations in their post-translational modifications and the differences between the regulatory regions of their genes, probably the key to understanding the current presence of these genes, will be described. Finally, the situation in the higher eukaryotes will be compared to that of yeast, a unicellular eukaryote, where there is only one active isoform and the role of VDAC in energy metabolism is better understood.
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Affiliation(s)
- Vito De Pinto
- Department of Biomedicine and Biotechnology Sciences, University of Catania, Via S. Sofia 64, 95123 Catania, Italy; ; Tel.: +39-095-73842444
- we.MitoBiotech.srl, c.so Italia 172, 95129 Catania, Italy
- National Institute of Biostructures and Biosystems, Section of Catania, 00136 Rome, Italy
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Is the secret of VDAC Isoforms in their gene regulation? Characterization of human VDAC genes expression profile, promoter activity, and transcriptional regulators. Int J Mol Sci 2020; 21:ijms21197388. [PMID: 33036380 PMCID: PMC7582299 DOI: 10.3390/ijms21197388] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/02/2020] [Accepted: 10/03/2020] [Indexed: 02/07/2023] Open
Abstract
VDACs (voltage-dependent anion-selective channels) are pore-forming proteins of the outer mitochondrial membrane, whose permeability is primarily due to VDACs’ presence. In higher eukaryotes, three isoforms are raised during the evolution: they have the same exon–intron organization, and the proteins show the same channel-forming activity. We provide a comprehensive analysis of the three human VDAC genes (VDAC1–3), their expression profiles, promoter activity, and potential transcriptional regulators. VDAC isoforms are broadly but also specifically expressed in various human tissues at different levels, with a predominance of VDAC1 and VDAC2 over VDAC3. However, an RNA-seq cap analysis gene expression (CAGE) approach revealed a higher level of transcription activation of VDAC3 gene. We experimentally confirmed this information by reporter assay of VDACs promoter activity. Transcription factor binding sites (TFBSs) distribution in the promoters were investigated. The main regulators common to the three VDAC genes were identified as E2F-myc activator/cell cycle (E2FF), Nuclear respiratory factor 1 (NRF1), Krueppel-like transcription factors (KLFS), E-box binding factors (EBOX) transcription factor family members. All of them are involved in cell cycle and growth, proliferation, differentiation, apoptosis, and metabolism. More transcription factors specific for each VDAC gene isoform were identified, supporting the results in the literature, indicating a general role of VDAC1, as an actor of apoptosis for VDAC2, and the involvement in sex determination and development of VDAC3. For the first time, we propose a comparative analysis of human VDAC promoters to investigate their specific biological functions. Bioinformatics and experimental results confirm the essential role of the VDAC protein family in mitochondrial functionality. Moreover, insights about a specialized function and different regulation mechanisms arise for the three isoform gene.
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Guarino F, Zinghirino F, Mela L, Pappalardo XG, Ichas F, De Pinto V, Messina A. NRF-1 and HIF-1α contribute to modulation of human VDAC1 gene promoter during starvation and hypoxia in HeLa cells. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148289. [PMID: 32810507 DOI: 10.1016/j.bbabio.2020.148289] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/05/2020] [Accepted: 08/11/2020] [Indexed: 02/07/2023]
Abstract
VDAC (Voltage Dependent Anion Channel) is a family of pore forming protein located in the outer mitochondrial membrane. Its channel property ensures metabolites exchange between mitochondria and the rest of the cell resulting in metabolism and bioenergetics regulation, and in cell death and life switch. VDAC1 is the best characterized and most abundant isoform, and is involved in many pathologies, as cancer or neurodegenerative diseases. However, little information is available about its gene expression regulation in normal and/or pathological conditions. In this work, we explored VDAC1 gene expression regulation in normal conditions and in the contest of some metabolic and energetic mitochondrial dysfunction and cell stress as example. The core of the putative promoter region was characterized in terms of transcription factors responsive elements both by bioinformatic studies and promoter activity experiments. In particular, we found an abundant presence of NRF-1 sites, together with other transcription factors binding sites involved in cell growth, proliferation, development, and we studied their prevalence in gene activity. Furthermore, upon depletion of nutrients or controlled hypoxia, as detected in various pathologies, we found that VDAC1 transcripts levels were significantly increased in a time related manner. VDAC1 promoter activity was also validated by gene reporter assays. According to PCR real-time experiments, it was confirmed that VDAC1 promoter activity is further stimulated when cells are exposed to stress. A bioinformatic survey suggested HIF-1α, besides NRF-1, as a most active TFBS. Their validation was obtained by TFBS mutagenesis and TF overexpression experiments. In conclusion, we experimentally demonstrated the involvement of both NRF-1 and HIF-1α in the regulation of VDAC1 promoter activation at basal level and in some peculiar cell stress conditions.
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Affiliation(s)
- Francesca Guarino
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 64, 95123 Catania, Italy.
| | - Federica Zinghirino
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 64, 95123 Catania, Italy
| | - Lia Mela
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 64, 95123 Catania, Italy
| | - Xena Giada Pappalardo
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 64, 95123 Catania, Italy
| | - François Ichas
- CNRS, Institut des Maladies Neurodégénératives, UMR 5293, Université de Bordeaux, Bordeaux, France; INSERM, Laboratoire de Neurosciences Expérimentales et Cliniques, U-1084, Université de Poitiers, Poitiers, France
| | - Vito De Pinto
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 64, 95123 Catania, Italy; National Institute for Biostructures and Biosystems, Section of Catania, Rome, Italy.
| | - Angela Messina
- Department of Biological, Geological and Environmental Sciences, Section of Molecular Biology, University of Catania, Viale A. Doria 6, 95125 Catania, Italy; National Institute for Biostructures and Biosystems, Section of Catania, Rome, Italy
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10
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Koutelou E, Farria AT, Dent SYR. Complex functions of Gcn5 and Pcaf in development and disease. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194609. [PMID: 32730897 DOI: 10.1016/j.bbagrm.2020.194609] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 12/12/2022]
Abstract
A wealth of biochemical and cellular data, accumulated over several years by multiple groups, has provided a great degree of insight into the molecular mechanisms of actions of GCN5 and PCAF in gene activation. Studies of these lysine acetyltransferases (KATs) in vitro, in cultured cells, have revealed general mechanisms for their recruitment by sequence-specific binding factors and their molecular functions as transcriptional co-activators. Genetic studies indicate that GCN5 and PCAF are involved in multiple developmental processes in vertebrates, yet our understanding of their molecular functions in these contexts remains somewhat rudimentary. Understanding the functions of GCN5/PCAF in developmental processes provides clues to the roles of these KATs in disease states. Here we will review what is currently known about the developmental roles of GCN5 and PCAF, as well as emerging role of these KATs in oncogenesis.
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Affiliation(s)
- Evangelia Koutelou
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park, Smithville, TX 78957, United States of America; Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States of America
| | - Aimee T Farria
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park, Smithville, TX 78957, United States of America; Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States of America
| | - Sharon Y R Dent
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park, Smithville, TX 78957, United States of America; Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States of America.
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11
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Sibon D, Coman T, Rossignol J, Lamarque M, Kosmider O, Bayard E, Fouquet G, Rignault R, Topçu S, Bonneau P, Bernex F, Dussiot M, Deroy K, Laurent L, Callebert J, Launay JM, Georgin-Lavialle S, Courtois G, Maroteaux L, Vaillancourt C, Fontenay M, Hermine O, Côté F. Enhanced Renewal of Erythroid Progenitors in Myelodysplastic Anemia by Peripheral Serotonin. Cell Rep 2020; 26:3246-3256.e4. [PMID: 30893598 DOI: 10.1016/j.celrep.2019.02.071] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 12/30/2018] [Accepted: 02/20/2019] [Indexed: 10/27/2022] Open
Abstract
Tryptophan as the precursor of several active compounds, including kynurenine and serotonin, is critical for numerous important metabolic functions. Enhanced tryptophan metabolism toward the kynurenine pathway has been associated with myelodysplastic syndromes (MDSs), which are preleukemic clonal diseases characterized by dysplastic bone marrow and cytopenias. Here, we reveal a fundamental role for tryptophan metabolized along the serotonin pathway in normal erythropoiesis and in the physiopathology of MDS-related anemia. We identify, both in human and murine erythroid progenitors, a functional cell-autonomous serotonergic network with pro-survival and proliferative functions. In vivo studies demonstrate that pharmacological increase of serotonin levels using fluoxetine, a common antidepressant, has the potential to become an important therapeutic strategy in low-risk MDS anemia refractory to erythropoietin.
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Affiliation(s)
- David Sibon
- Institut Imagine, INSERM U1163, CNRS ERL 8254, Université Paris Descartes, Sorbonne Paris-Cité, Laboratoire d'Excellence GR-Ex, Paris, France
| | - Tereza Coman
- Institut Imagine, INSERM U1163, CNRS ERL 8254, Université Paris Descartes, Sorbonne Paris-Cité, Laboratoire d'Excellence GR-Ex, Paris, France; Département d'Hématologie, Gustave Roussy Cancer Campus Grand Paris, 94800 Villejuif, France
| | - Julien Rossignol
- Institut Imagine, INSERM U1163, CNRS ERL 8254, Université Paris Descartes, Sorbonne Paris-Cité, Laboratoire d'Excellence GR-Ex, Paris, France; Département d'Hématologie, Gustave Roussy Cancer Campus Grand Paris, 94800 Villejuif, France
| | - Mathilde Lamarque
- Institut Imagine, INSERM U1163, CNRS ERL 8254, Université Paris Descartes, Sorbonne Paris-Cité, Laboratoire d'Excellence GR-Ex, Paris, France
| | - Olivier Kosmider
- Institut Cochin, INSERM U1016, CNRS UMR 8104, Université Paris Descartes, Paris, APHP, Service d'Hématologie Biologique, Hôpitaux Universitaires Paris Centre-Cochin, Paris 75014, France
| | - Elisa Bayard
- Institut Imagine, INSERM U1163, CNRS ERL 8254, Université Paris Descartes, Sorbonne Paris-Cité, Laboratoire d'Excellence GR-Ex, Paris, France
| | - Guillemette Fouquet
- Institut Imagine, INSERM U1163, CNRS ERL 8254, Université Paris Descartes, Sorbonne Paris-Cité, Laboratoire d'Excellence GR-Ex, Paris, France
| | - Rachel Rignault
- Institut Imagine, INSERM U1163, CNRS ERL 8254, Université Paris Descartes, Sorbonne Paris-Cité, Laboratoire d'Excellence GR-Ex, Paris, France
| | - Selin Topçu
- Institut Imagine, INSERM U1163, CNRS ERL 8254, Université Paris Descartes, Sorbonne Paris-Cité, Laboratoire d'Excellence GR-Ex, Paris, France
| | - Pierre Bonneau
- Institut Imagine, INSERM U1163, CNRS ERL 8254, Université Paris Descartes, Sorbonne Paris-Cité, Laboratoire d'Excellence GR-Ex, Paris, France
| | - Florence Bernex
- Institut de Recherche en Cancérologie de Montpellier, Montpellier 34298, France; INSERM, U1194, Network of Experimental Histology, BioCampus, CNRS, UMS3426, Montpellier 34094, France
| | - Michael Dussiot
- Institut Imagine, INSERM U1163, CNRS ERL 8254, Université Paris Descartes, Sorbonne Paris-Cité, Laboratoire d'Excellence GR-Ex, Paris, France
| | - Kathy Deroy
- INRS-Institut Armand-Frappier and Center for Interdisciplinary Research on Well-Being, Health, Society and Environment, Montreal, QC H7V 1B7, Canada
| | - Laetitia Laurent
- INRS-Institut Armand-Frappier and Center for Interdisciplinary Research on Well-Being, Health, Society and Environment, Montreal, QC H7V 1B7, Canada
| | - Jacques Callebert
- Service de Biochimie, INSERM U942, Hôpital Lariboisière, 75010 Paris, France
| | - Jean-Marie Launay
- Service de Biochimie, INSERM U942, Hôpital Lariboisière, 75010 Paris, France
| | - Sophie Georgin-Lavialle
- Département de Médecine Interne, Hôpital Tenon, Université Pierre et Marie Curie, AP-HP, 4 rue de la Chine, 75020 Paris, France
| | - Geneviève Courtois
- Institut Imagine, INSERM U1163, CNRS ERL 8254, Université Paris Descartes, Sorbonne Paris-Cité, Laboratoire d'Excellence GR-Ex, Paris, France
| | - Luc Maroteaux
- INSERM UMR-S1270, Sorbonne Universités, Université Pierre et Marie Curie, Institut du Fer à Moulin, 75005 Paris, France
| | - Cathy Vaillancourt
- INRS-Institut Armand-Frappier and Center for Interdisciplinary Research on Well-Being, Health, Society and Environment, Montreal, QC H7V 1B7, Canada
| | - Michaela Fontenay
- Institut Cochin, INSERM U1016, CNRS UMR 8104, Université Paris Descartes, Paris, APHP, Service d'Hématologie Biologique, Hôpitaux Universitaires Paris Centre-Cochin, Paris 75014, France
| | - Olivier Hermine
- Institut Imagine, INSERM U1163, CNRS ERL 8254, Université Paris Descartes, Sorbonne Paris-Cité, Laboratoire d'Excellence GR-Ex, Paris, France; Department of Hematology, Hôpital Necker AP-HP, 75015 Paris, France
| | - Francine Côté
- Institut Imagine, INSERM U1163, CNRS ERL 8254, Université Paris Descartes, Sorbonne Paris-Cité, Laboratoire d'Excellence GR-Ex, Paris, France.
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12
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Woo AJ, Patry CAA, Ghamari A, Pregernig G, Yuan D, Zheng K, Piers T, Hibbs M, Li J, Fidalgo M, Wang JY, Lee JH, Leedman PJ, Wang J, Fraenkel E, Cantor AB. Zfp281 (ZBP-99) plays a functionally redundant role with Zfp148 (ZBP-89) during erythroid development. Blood Adv 2019; 3:2499-2511. [PMID: 31455666 PMCID: PMC6712527 DOI: 10.1182/bloodadvances.2018030551] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 06/11/2019] [Indexed: 12/17/2022] Open
Abstract
Erythroid maturation requires the concerted action of a core set of transcription factors. We previously identified the Krüppel-type zinc finger transcription factor Zfp148 (also called ZBP-89) as an interacting partner of the master erythroid transcription factor GATA1. Here we report the conditional knockout of Zfp148 in mice. Global loss of Zfp148 results in perinatal lethality from nonhematologic causes. Selective Zfp148 loss within the hematopoietic system results in a mild microcytic and hypochromic anemia, mildly impaired erythroid maturation, and delayed recovery from phenylhydrazine-induced hemolysis. Based on the mild erythroid phenotype of these mice compared with GATA1-deficient mice, we hypothesized that additional factor(s) may complement Zfp148 function during erythropoiesis. We show that Zfp281 (also called ZBP-99), another member of the Zfp148 transcription factor family, is highly expressed in murine and human erythroid cells. Zfp281 knockdown by itself results in partial erythroid defects. However, combined deficiency of Zfp148 and Zfp281 causes a marked erythroid maturation block. Zfp281 physically associates with GATA1, occupies many common chromatin sites with GATA1 and Zfp148, and regulates a common set of genes required for erythroid cell differentiation. These findings uncover a previously unknown role for Zfp281 in erythroid development and suggest that it functionally overlaps with that of Zfp148 during erythropoiesis.
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Affiliation(s)
- Andrew J Woo
- Division of Pediatric Hematology-Oncology, Boston Children's Hospital/Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, University of Western Australia, Perth, WA, Australia
| | - Chelsea-Ann A Patry
- Division of Pediatric Hematology-Oncology, Boston Children's Hospital/Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Alireza Ghamari
- Division of Pediatric Hematology-Oncology, Boston Children's Hospital/Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Gabriela Pregernig
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA
| | - Daniel Yuan
- Division of Pediatric Hematology-Oncology, Boston Children's Hospital/Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Kangni Zheng
- Division of Pediatric Hematology-Oncology, Boston Children's Hospital/Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Taylor Piers
- Division of Pediatric Hematology-Oncology, Boston Children's Hospital/Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Moira Hibbs
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, University of Western Australia, Perth, WA, Australia
| | - Ji Li
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, University of Western Australia, Perth, WA, Australia
| | - Miguel Fidalgo
- Department of Cell, Developmental and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY
- Center for Research in Molecular Medicine and Chronic Diseases, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Jenny Y Wang
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Joo-Hyeon Lee
- Wellcome Trust/Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom; and
| | - Peter J Leedman
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, University of Western Australia, Perth, WA, Australia
| | - Jianlong Wang
- Department of Cell, Developmental and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Ernest Fraenkel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA
| | - Alan B Cantor
- Division of Pediatric Hematology-Oncology, Boston Children's Hospital/Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA
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13
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Limi S, Senecal A, Coleman R, Lopez-Jones M, Guo P, Polumbo C, Singer RH, Skoultchi AI, Cvekl A. Transcriptional burst fraction and size dynamics during lens fiber cell differentiation and detailed insights into the denucleation process. J Biol Chem 2018; 293:13176-13190. [PMID: 29959226 DOI: 10.1074/jbc.ra118.001927] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 06/11/2018] [Indexed: 01/05/2023] Open
Abstract
Genes are transcribed in irregular pulses of activity termed transcriptional bursts. Cellular differentiation requires coordinated gene expression; however, it is unknown whether the burst fraction (i.e. the number of active phases of transcription) or size/intensity (the number of RNA molecules produced within a burst) changes during cell differentiation. In the ocular lens, the positions of lens fiber cells correlate precisely with their differentiation status, and the most advanced cells degrade their nuclei. Here, we examined the transcriptional parameters of the β-actin and lens differentiation-specific α-, β-, and γ-crystallin genes by RNA fluorescent in situ hybridization (FISH) in the lenses of embryonic day (E) E12.5, E14.5, and E16.5 mouse embryos and newborns. We found that cellular differentiation dramatically alters the burst fraction in synchronized waves across the lens fiber cell compartment with less dramatic changes in burst intensity. Surprisingly, we observed nascent transcription of multiple genes in nuclei just before nuclear destruction. Nuclear condensation was accompanied by transfer of nuclear proteins, including histone and nonhistone proteins, to the cytoplasm. Although lens-specific deletion of the chromatin remodeler SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 (Smarca5/Snf2h) interfered with denucleation, persisting nuclei remained transcriptionally competent and exhibited changes in both burst intensity and fraction depending on the gene examined. Our results uncover the mechanisms of nascent transcriptional control during differentiation and chromatin remodeling, confirm the burst fraction as the major factor adjusting gene expression levels, and reveal transcriptional competence of fiber cell nuclei even as they approach disintegration.
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Affiliation(s)
| | | | | | | | | | | | - Robert H Singer
- Anatomy and Structural Biology.,Cell Biology.,Neuroscience, and
| | | | - Ales Cvekl
- From the Departments of Genetics, .,Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, New York 10461
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14
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Zhang YC, Ye H, Zeng Z, Chin YE, Huang YN, Fu GH. The NF-κB p65/miR-23a-27a-24 cluster is a target for leukemia treatment. Oncotarget 2016; 6:33554-67. [PMID: 26378023 PMCID: PMC4741785 DOI: 10.18632/oncotarget.5591] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 08/23/2015] [Indexed: 11/25/2022] Open
Abstract
p65 is a transcription factor that is involved in many physiological and pathologic processes. Here we report that p65 strongly binds to the miR-23a-27a-24 cluster promoter to up-regulate its expression. As bone marrow-derived cells differentiate into red blood cells in vitro, p65/miR-23a-27a-24 cluster expression increases sharply and then declines before the appearance of red blood cells, suggesting that this cluster is negatively related to erythroid terminal differentiation. Bioinformatic and molecular biology experiments confirmed that the miR-23a-27a-24 cluster inhibited the expression of the erythroid proteome and contributed to erythroleukemia progression. In addition, high level of the p65/miR-23a-27a-24 cluster was found in APL and AML cell lines and in nucleated peripheral blood cells from leukemia patients. Furthermore, anti-leukemia drugs significantly inhibited the expression of the p65/miR-23a-27a-24 cluster in leukemia cells. Administration of the p65 inhibitor parthenolide significantly improved hematology and myelogram indices while prolonging the life span of erythroleukemia mice. Meanwhile, stable overexpression of these three miRNAs in mouse erythroleukemia cells enhanced cell malignancy. Our findings thus connect a novel regulation pathway of the p65/miR-23a-27a-24 cluster with the erythroid proteome and provide an applicable approach for treating leukemia.
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Affiliation(s)
- Yong-Chang Zhang
- Pathology Center, Shanghai General Hospital/Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hui Ye
- Pathology Center, Shanghai General Hospital/Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhi Zeng
- Pathology Center, Shanghai General Hospital/Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Y Eugene Chin
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS) and Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, China
| | - Yu-Ning Huang
- Pathology Center, Shanghai General Hospital/Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guo-Hui Fu
- Pathology Center, Shanghai General Hospital/Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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15
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Loss of One Copy of Zfp148 Reduces Lesional Macrophage Proliferation and Atherosclerosis in Mice by Activating p53. Circ Res 2014; 115:781-9. [DOI: 10.1161/circresaha.115.304992] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Rationale:
Cell proliferation and cell cycle control mechanisms are thought to play central roles in the pathogenesis of atherosclerosis. The transcription factor Zinc finger protein 148 (Zfp148) was shown recently to maintain cell proliferation under oxidative conditions by suppressing p53, a checkpoint protein that arrests proliferation in response to various stressors. It is established that inactivation of p53 accelerates atherosclerosis, but whether increased p53 activation confers protection against the disease remains to be determined.
Objective:
We aimed to test the hypothesis that
Zfp148
deficiency reduces atherosclerosis by unleashing p53 activity.
Methods and Results:
Mice harboring a gene-trap mutation in the
Zfp148
locus (
Zfp148
gt/+
) were bred onto the apolipoprotein E (
Apoe
)
–/–
genetic background and fed a high-fat or chow diet. Loss of 1 copy of
Zfp148
markedly reduced atherosclerosis without affecting lipid metabolism. Bone marrow transplantation experiments revealed that the effector cell is of hematopoietic origin. Peritoneal macrophages and atherosclerotic lesions from
Zfp148
gt/+
Apoe
–/–
mice showed increased levels of phosphorylated p53 compared with controls, and atherosclerotic lesions contained fewer proliferating macrophages.
Zfp148
gt/+
Apoe
–/–
mice were further crossed with p53-null mice (
Trp53
–/–
[the gene encoding p53]). There was no difference in atherosclerosis between
Zfp148
gt/+
Apoe
–/–
mice and controls on a
Trp53
+/–
genetic background, and there was no difference in levels of phosphorylated p53 or cell proliferation.
Conclusions:
Zfp148
deficiency increases p53 activity and protects against atherosclerosis by causing proliferation arrest of lesional macrophages, suggesting that drugs targeting macrophage proliferation may be useful in the treatment of atherosclerosis.
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16
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Ju J, Wang Y, Liu R, Zhang Y, Xu Z, Wang Y, Wu Y, Liu M, Cerruti L, Zou F, Ma C, Fang M, Tan R, Jane SM, Zhao Q. Human fetal globin gene expression is regulated by LYAR. Nucleic Acids Res 2014; 42:9740-52. [PMID: 25092918 PMCID: PMC4150809 DOI: 10.1093/nar/gku718] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Human globin gene expression during development is modulated by transcription factors in a stage-dependent manner. However, the mechanisms controlling the process are still largely unknown. In this study, we found that a nuclear protein, LYAR (human homologue of mouse Ly-1 antibody reactive clone) directly interacted with the methyltransferase PRMT5 which triggers the histone H4 Arg3 symmetric dimethylation (H4R3me2s) mark. We found that PRMT5 binding on the proximal γ-promoter was LYAR-dependent. The LYAR DNA-binding motif (GGTTAT) was identified by performing CASTing (cyclic amplification and selection of targets) experiments. Results of EMSA and ChIP assays confirmed that LYAR bound to a DNA region corresponding to the 5′-untranslated region of the γ-globin gene. We also found that LYAR repressed human fetal globin gene expression in both K562 cells and primary human adult erythroid progenitor cells. Thus, these data indicate that LYAR acts as a novel transcription factor that binds the γ-globin gene, and is essential for silencing the γ-globin gene.
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Affiliation(s)
- Junyi Ju
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Ying Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Ronghua Liu
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Yichong Zhang
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Zhen Xu
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Yadong Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Yupeng Wu
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Ming Liu
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Loretta Cerruti
- Department of Medicine, Monash University Central Clinical School, Prahran, VIC 3181, Australia
| | - Fengwei Zou
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Chi Ma
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Ming Fang
- Institute of Life Sciences, Southeast University, Nanjing 210096, China
| | - Renxiang Tan
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Stephen M Jane
- Department of Medicine, Monash University Central Clinical School, Prahran, VIC 3181, Australia
| | - Quan Zhao
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
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17
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Liu J, Samuel K, Turner ML, Gallagher RCJ. Use of IL3 and chromatin-modifying reagents valproic acid and 5-aza-2′-deoxycytidine to affect mobilized peripheral blood CD34+cell fate decisions. Vox Sang 2014; 107:83-9. [DOI: 10.1111/vox.12124] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 11/08/2013] [Accepted: 11/14/2013] [Indexed: 01/13/2023]
Affiliation(s)
- J. Liu
- Scottish National Blood Transfusion Service (SNBTS) Cell Therapy Group; MRC Centre for Regenerative Medicine; Edinburgh UK
| | - K. Samuel
- Scottish National Blood Transfusion Service (SNBTS) Cell Therapy Group; MRC Centre for Regenerative Medicine; Edinburgh UK
| | - M. L. Turner
- Scottish National Blood Transfusion Service (SNBTS) Cell Therapy Group; MRC Centre for Regenerative Medicine; Edinburgh UK
| | - R. C. J. Gallagher
- Scottish National Blood Transfusion Service (SNBTS) Cell Therapy Group; MRC Centre for Regenerative Medicine; Edinburgh UK
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18
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Ye CG, Chen GG, Ho RLK, Merchant JL, He ML, Lai PBS. Epigenetic upregulation of Bak by ZBP-89 inhibits the growth of hepatocellular carcinoma. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:2970-2979. [PMID: 23954442 DOI: 10.1016/j.bbamcr.2013.08.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 07/12/2013] [Accepted: 08/02/2013] [Indexed: 12/20/2022]
Abstract
Zinc-binding protein-89 regulates Bak to facilitate apoptosis in cancer cells. This study examined if zinc-binding protein-89 regulates Bak through an epigenetic mechanism in hepatocellular carcinoma. We first demonstrated that the expression of Bak was reduced but the levels of deoxyribonucleic acid methyltransferase 1 and histone deacetylase 3 were increased in hepatocellular carcinoma cancer tissues compared to the corresponding non-cancer tissues. Moreover, there was a negative correlation between Bak expression and deoxyribonucleic acid methyltransferase 1 levels in hepatocellular carcinoma. Administration of zinc-binding protein-89 downregulated histone deacetylase 3 expression and suppressed the activities of histone deacetylase and deoxyribonucleic acid methyltransferase, which led to maintenance of histone acetylation status, inhibited the binding of methyl-CpG-binding protein 2 to genomic deoxyribonucleic acid and demethylated CpG islands in the Bak promoter in hepatocellular carcinoma cells. Using the xenograft mouse tumor model, we demonstrated that zinc-binding protein-89 or inhibitors of either epigenetic enzymes could stimulate Bak expression, induce apoptosis, and arrest tumor growth and that the maximal effort was achieved when zinc-binding protein-89 and the enzyme inhibitors were used in combination. Conclusively, zinc-binding protein-89 upregulates the expression of Bak by targeting multiple components of the epigenetic pathway in hepatocellular carcinoma.
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Affiliation(s)
- Cai Guo Ye
- Department of Surgery, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong; China-America Cancer Research Institute, Guangdong Medical College, Dongguan 523808, PR China
| | - George G Chen
- Department of Surgery, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
| | - Rocky L K Ho
- Department of Surgery, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Juanita L Merchant
- Internal Medicine-Gastroenterology, University of Michigan, Ann Arbor, MI 48109, USA; Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ming-Liang He
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong; School of Public Health and Primary Care, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Paul B S Lai
- Department of Surgery, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
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Pourfarzad F, Aghajanirefah A, de Boer E, Ten Have S, Bryn van Dijk T, Kheradmandkia S, Stadhouders R, Thongjuea S, Soler E, Gillemans N, von Lindern M, Demmers J, Philipsen S, Grosveld F. Locus-specific proteomics by TChP: targeted chromatin purification. Cell Rep 2013; 4:589-600. [PMID: 23911284 DOI: 10.1016/j.celrep.2013.07.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 07/01/2013] [Accepted: 07/07/2013] [Indexed: 12/20/2022] Open
Abstract
Here, we show that transcription factors bound to regulatory sequences can be identified by purifying these unique sequences directly from mammalian cells in vivo. Using targeted chromatin purification (TChP), a double-pull-down strategy with a tetracycline-sensitive "hook" bound to a specific promoter, we identify transcription factors bound to the repressed γ-globin gene-associated regulatory regions. After validation of the binding, we show that, in human primary erythroid cells, knockdown of a number of these transcription factors induces γ-globin gene expression. Reactivation of γ-globin gene expression ameliorates the symptoms of β-thalassemia and sickle cell disease, and these factors provide potential targets for the development of therapeutics for treating these patients.
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Affiliation(s)
- Farzin Pourfarzad
- Department of Cell Biology, Erasmus MC, Dr. Molewaterplein 50, 3015GE Rotterdam, the Netherlands; Center for Biomedical Genetics, Erasmus MC, Dr. Molewaterplein 50, 3015GE Rotterdam, the Netherlands
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20
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Zinc finger protein 148 is dispensable for primitive and definitive hematopoiesis in mice. PLoS One 2013; 8:e70022. [PMID: 23936136 PMCID: PMC3729454 DOI: 10.1371/journal.pone.0070022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 06/19/2013] [Indexed: 11/19/2022] Open
Abstract
Hematopoiesis is regulated by transcription factors that induce cell fate and differentiation in hematopoietic stem cells into fully differentiated hematopoietic cell types. The transcription factor zinc finger protein 148 (Zfp148) interacts with the hematopoietic transcription factor Gata1 and has been implicated to play an important role in primitive and definitive hematopoiesis in zebra fish and mouse chimeras. We have recently created a gene-trap knockout mouse model deficient for Zfp148, opening up for analyses of hematopoiesis in a conventional loss-of-function model in vivo. Here, we show that Zfp148-deficient neonatal and adult mice have normal or slightly increased levels of hemoglobin, hematocrit, platelets and white blood cells, compared to wild type controls. Hematopoietic lineages in bone marrow, thymus and spleen from Zfp148gt/gt mice were further investigated by flow cytometry. There were no differences in T-cells (CD4 and CD8 single positive cells, CD4 and CD8 double negative/positive cells) in either organ. However, the fraction of CD69- and B220-positive cells among lymphocytes in spleen was slightly lower at postnatal day 14 in Zfp148gt/gt mice compared to wild type mice. Our results demonstrate that Zfp148-deficient mice generate normal mature hematopoietic populations thus challenging earlier studies indicating that Zfp148 plays a critical role during hematopoietic development.
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Vecchio L, Seke Etet PF, Kipanyula MJ, Krampera M, Nwabo Kamdje AH. Importance of epigenetic changes in cancer etiology, pathogenesis, clinical profiling, and treatment: what can be learned from hematologic malignancies? Biochim Biophys Acta Rev Cancer 2013; 1836:90-104. [PMID: 23603458 DOI: 10.1016/j.bbcan.2013.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 01/25/2013] [Accepted: 04/10/2013] [Indexed: 02/06/2023]
Abstract
Epigenetic alterations represent a key cancer hallmark, even in hematologic malignancies (HMs) or blood cancers, whose clinical features display a high inter-individual variability. Evidence accumulated in recent years indicates that inactivating DNA hypermethylation preferentially targets the subset of polycomb group (PcG) genes that are regulators of developmental processes. Conversely, activating DNA hypomethylation targets oncogenic signaling pathway genes, but outcomes of both events lead in the overexpression of oncogenic signaling pathways that contribute to the stem-like state of cancer cells. On the basis of recent evidence from population-based, clinical and experimental studies, we hypothesize that factors associated with risk for developing a HM, such as metabolic syndrome and chronic inflammation, trigger epigenetic mechanisms to increase the transcriptional expression of oncogenes and activate oncogenic signaling pathways. Among others, signaling pathways associated with such risk factors include pro-inflammatory nuclear factor κB (NF-κB), and mitogenic, growth, and survival Janus kinase (JAK) intracellular non-receptor tyrosine kinase-triggered pathways, which include signaling pathways such as transducer and activator of transcription (STAT), Ras GTPases/mitogen-activated protein kinases (MAPKs)/extracellular signal-related kinases (ERKs), phosphatidylinositol 3-kinase (PI3K)/Akt/mammalian target of rapamycin (mTOR), and β-catenin pathways. Recent findings on epigenetic mechanisms at work in HMs and their importance in the etiology and pathogenesis of these diseases are herein summarized and discussed. Furthermore, the role of epigenetic processes in the determination of biological identity, the consequences for interindividual variability in disease clinical profile, and the potential of epigenetic drugs in HMs are also considered.
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Affiliation(s)
- Lorella Vecchio
- Laboratory of Cytometry, Institute of Molecular Genetics, CNR, University of Pavia, 27100 Pavia, Italy
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The small MAF transcription factors MAFF, MAFG and MAFK: current knowledge and perspectives. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1823:1841-6. [PMID: 22721719 DOI: 10.1016/j.bbamcr.2012.06.012] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 06/11/2012] [Accepted: 06/12/2012] [Indexed: 12/13/2022]
Abstract
The small MAFs, MAFF, MAFG and MAFK have emerged as crucial regulators of mammalian gene expression. Previous studies have linked small MAF function, by virtue of their heterodimerization with the Cap 'n' Collar (CNC) family of transcription factors, to the stress response and detoxification pathways. Recent analyses have revealed a complex regulatory network involving small MAF transcription factors and other cellular proteins. The expression and activity of small MAFs are tightly regulated at multiple levels. With regard to their clinical importance, small MAFs have been linked to various diseases, such as diabetes, neuronal disorders, thrombocytopenia and carcinogenesis. A better understanding of the molecular mechanisms governing the activity of small MAFs will provide novel insights into the control of mammalian transcription and may lead to the development of novel therapeutic strategies to treat common human disorders.
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