1
|
Jankowski K, Jagana V, Bisserier M, Hadri L. Switch-Independent 3A: An Epigenetic Regulator in Cancer with New Implications for Pulmonary Arterial Hypertension. Biomedicines 2023; 12:10. [PMID: 38275371 PMCID: PMC10813728 DOI: 10.3390/biomedicines12010010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/03/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024] Open
Abstract
Epigenetic mechanisms, including DNA methylation, histone modifications, and non-coding RNA, play a crucial role in the regulation of gene expression and are pivotal in biological processes like apoptosis, cell proliferation, and differentiation. SIN3a serves as a scaffold protein and facilitates interactions with transcriptional epigenetic partners and specific DNA-binding transcription factors to modulate gene expression by adding or removing epigenetic marks. However, the activation or repression of gene expression depends on the factors that interact with SIN3a, as it can recruit both transcriptional activators and repressors. The role of SIN3a has been extensively investigated in the context of cancer, including melanoma, lung, and breast cancer. Our group is interested in defining the roles of SIN3a and its partners in pulmonary vascular disease. Pulmonary arterial hypertension (PAH) is a multifactorial disease often described as a cancer-like disease and characterized by disrupted cellular metabolism, sustained vascular cell proliferation, and resistance to apoptosis. Molecularly, PAH shares many common signaling pathways with cancer cells, offering the opportunity to further consider therapeutic strategies used for cancer. As a result, many signaling pathways observed in cancer were studied in PAH and have encouraged new research studying SIN3a's role in PAH due to its impact on cancer growth. This comparison offers new therapeutic options. In this review, we delineate the SIN3a-associated epigenetic mechanisms in cancer and PAH cells and highlight their impact on cell survival and proliferation. Furthermore, we explore in detail the role of SIN3a in cancer to provide new insights into its emerging role in PAH pathogenesis.
Collapse
Affiliation(s)
- Katherine Jankowski
- Center for Translational Medicine and Pharmacology, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Vineeta Jagana
- Department of Cell Biology and Anatomy & Physiology, New York Medical College, 15 Dana Road, BSB 131A, Valhalla, NY 10595, USA; (V.J.); (M.B.)
| | - Malik Bisserier
- Department of Cell Biology and Anatomy & Physiology, New York Medical College, 15 Dana Road, BSB 131A, Valhalla, NY 10595, USA; (V.J.); (M.B.)
| | - Lahouaria Hadri
- Center for Translational Medicine and Pharmacology, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| |
Collapse
|
2
|
Mitra A, Vo L, Soukar I, Chaubal A, Greenberg ML, Pile LA. Isoforms of the transcriptional cofactor SIN3 differentially regulate genes necessary for energy metabolism and cell survival. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119322. [PMID: 35820484 PMCID: PMC10557476 DOI: 10.1016/j.bbamcr.2022.119322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 11/24/2022]
Abstract
The SIN3 scaffolding protein is a conserved transcriptional regulator known to fine-tune gene expression. In Drosophila, there are two major isoforms of SIN3, SIN3 220 and SIN3 187, which each assemble into multi-subunit histone modifying complexes. The isoforms have distinct developmental expression patterns and non-redundant functions. Gene regulatory network analyses indicate that both isoforms affect genes encoding proteins in pathways such as the cell cycle and cell morphogenesis. Interestingly, the SIN3 187 isoform uniquely regulates a subset of pathways including post-embryonic development, phosphate metabolism and apoptosis. Target genes in the phosphate metabolism pathway include nuclear-encoded mitochondrial genes coding for proteins responsible for oxidative phosphorylation. Here, we investigate the physiological effects of SIN3 isoforms on energy metabolism and cell survival. We find that ectopic expression of SIN3 187 represses expression of several nuclear-encoded mitochondrial genes affecting production of ATP and generation of reactive oxygen species (ROS). Forced expression of SIN3 187 also activates several pro-apoptotic and represses a few anti-apoptotic genes. In the SIN3 187 expressing cells, these gene expression patterns are accompanied with an increased sensitivity to paraquat-mediated oxidative stress. These findings indicate that SIN3 187 influences the regulation of mitochondrial function, apoptosis and oxidative stress response in ways that are dissimilar from SIN3 220. The data suggest that the distinct SIN3 histone modifying complexes are deployed in different cellular contexts to maintain cellular homeostasis.
Collapse
Affiliation(s)
- Anindita Mitra
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, United States of America
| | - Linh Vo
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, United States of America
| | - Imad Soukar
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, United States of America
| | - Ashlesha Chaubal
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, United States of America; Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, United States of America
| | - Miriam L Greenberg
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, United States of America
| | - Lori A Pile
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, United States of America.
| |
Collapse
|
3
|
Kadamb R, Leibovitch BA, Farias EF, Dahiya N, Suryawanshi H, Bansal N, Waxman S. Invasive phenotype in triple negative breast cancer is inhibited by blocking SIN3A-PF1 interaction through KLF9 mediated repression of ITGA6 and ITGB1. Transl Oncol 2021; 16:101320. [PMID: 34968869 PMCID: PMC8718897 DOI: 10.1016/j.tranon.2021.101320] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 12/15/2021] [Indexed: 12/17/2022] Open
Abstract
We show that the PAH2 domain of SIN3A is a target when it is inhibited from binding to PF1 results in inhibition of invasive phenotype in TNBC. Epigenetic repression of integrins expression and downstream pathways results from enhanced binding of KLF9 /SIN3A repressor complex to their promoters. Genome wide transcriptomic analysis showed downregulation of multiple invasion related genes. Tumor growth and lung metastasis were markedly decreased in vivo. Our studies highlight that PF1 might serve as a gatekeeper for trafficking SID protein binding to PAH2 of SIN3A and has functional role in presentation of different regulatory complexes. Blocking the function of PAH2 offers a promising targeted therapy approach for inhibiting the invasive phenotype in TNBC.
SIN3A, a scaffold protein has regulatory functions in tumor biology. Through its Paired amphipathic helix (PAH2) domain, SIN3A interacts with PHF12 (PF1), a protein with SIN3 interaction domain (SID) that forms a complex with MRG15 and KDM5A/B. These components are often overexpressed in cancer. In the present study, we evaluated the role of SIN3A and its interacting partner PF1 in mediating inhibition of tumor growth and invasion in triple negative breast cancer (TNBC). We found profound inhibition of invasion, migration, and induction of cellular senescence by specific disruption of the PF1/SIN3A PAH2 domain interaction in TNBC cells expressing PF1-SID transcript or peptide treatment. Genome-wide transcriptomic analysis by RNA-seq revealed that PF1-SID downregulates several gene sets and pathways linked to invasion and migration. Integrin α6 (ITGA6) and integrin ß1 (ITGB1) and their downstream target proteins were downregulated in PF1-SID cells. We further determined increased presence of SIN3A and transcriptional repressor, KLF9, on promoters of ITGA6 and ITGB1 in PF1-SID cells. Knockdown of KLF9 leads to re-expression of ITGA6 and ITGB1 and restoration of the invasive phenotype, functionally linking KLF9 to this process. Overall, these data demonstrate that specific disruption of PF1/SIN3A, inhibits tumor growth, migration, and invasion. Also, PF1-SID not only inhibits tumor growth by senescence induction and reduced proliferation, but it also targets cancer stem cell gene expression and blocks mammosphere formation. Overall, these data demonstrate a mechanism whereby invasion and metastasis of TNBC can be suppressed by inhibiting SIN3A-PF1 interaction and enhancing KLF9 mediated suppression of ITGA6 and ITGB1.
Collapse
Affiliation(s)
- Rama Kadamb
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Boris A Leibovitch
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eduardo F Farias
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nisha Dahiya
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Nidhi Bansal
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Samuel Waxman
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| |
Collapse
|
4
|
Luna-Maldonado F, Andonegui-Elguera MA, Díaz-Chávez J, Herrera LA. Mitotic and DNA Damage Response Proteins: Maintaining the Genome Stability and Working for the Common Good. Front Cell Dev Biol 2021; 9:700162. [PMID: 34966733 PMCID: PMC8710681 DOI: 10.3389/fcell.2021.700162] [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: 04/25/2021] [Accepted: 11/22/2021] [Indexed: 12/14/2022] Open
Abstract
Cellular function is highly dependent on genomic stability, which is mainly ensured by two cellular mechanisms: the DNA damage response (DDR) and the Spindle Assembly Checkpoint (SAC). The former provides the repair of damaged DNA, and the latter ensures correct chromosome segregation. This review focuses on recently emerging data indicating that the SAC and the DDR proteins function together throughout the cell cycle, suggesting crosstalk between both checkpoints to maintain genome stability.
Collapse
Affiliation(s)
- Fernando Luna-Maldonado
- Unidad de Investigación Biomédica en Cáncer, Instituto de Investigaciones Biomédicas–Universidad Nacional Autónoma de México, Instituto Nacional de Cancerología, México City, Mexico
| | - Marco A. Andonegui-Elguera
- Unidad de Investigación Biomédica en Cáncer, Instituto de Investigaciones Biomédicas–Universidad Nacional Autónoma de México, Instituto Nacional de Cancerología, México City, Mexico
| | - José Díaz-Chávez
- Unidad de Investigación Biomédica en Cáncer, Instituto de Investigaciones Biomédicas–Universidad Nacional Autónoma de México, Instituto Nacional de Cancerología, México City, Mexico
| | - Luis A. Herrera
- Unidad de Investigación Biomédica en Cáncer, Instituto de Investigaciones Biomédicas–Universidad Nacional Autónoma de México, Instituto Nacional de Cancerología, México City, Mexico
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| |
Collapse
|
5
|
Huang S, Lu Y, Li S, Zhou T, Wang J, Xia J, Zhang X, Zhou Z. Key proteins of proteome underlying sperm malformation of rats exposed to low fenvalerate doses are highly related to P53. ENVIRONMENTAL TOXICOLOGY 2021; 36:1181-1194. [PMID: 33656234 DOI: 10.1002/tox.23117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 02/19/2021] [Indexed: 06/12/2023]
Abstract
Fenvalerate (Fen) is an endocrine disruptor, capable of interfering with the activity of estrogen and androgen. Our objective was to explore the molecular mechanisms of Fen on sperm in vivo. Adult male Sprague-Dawley rats were orally exposed to 0, 0.00625, 0.125, 2.5, 30 mg/kg/day Fen for 8 weeks. Sperm morphology, differential proteomics of sperm and testes, bioinformatic analysis, western blotting (WB), and RT-PCR were used to explore the mechanism of Fen on sperm. Data showed that low Fen doses significantly induced sperm malformations. In sperm proteomics, 47 differentially expressed (DE) proteins were enriched in biological processes (BPs) related to energy metabolism, response to estrogen, spermatogenesis; and enriched in cellular components (CCs) relating to energy-metabolism, sperm fibrous sheath and their outer dense fibers. In testicular proteomics, 56 DE proteins were highly associated with mRNA splicing, energy metabolism; and enriched in CCs relating to vesicles, myelin sheath, microtubules, mitochondria. WB showed that the expression of selected proteins was identical to their tendency in 2D gels. Literature indicates that key DE proteins in proteomic profiles (such as Trap1, Hnrnpa2b1, Hnrnpk, Hspa8, and Gapdh) are involved in P53-related processes or morphogenesis or spermatogenesis. Also, P53 mRNA and protein levels were significantly increased by Fen; bioinformatic re-analysis showed that 88.5% DE proteins and P53 formed a complex interacting network, and the key DE proteins were coenriched with P53-related BPs. Results indicate that key DE proteins of proteome underlying sperm malformations of rats exposed to low Fen doses are highly related to P53.
Collapse
Affiliation(s)
- Shaoping Huang
- Department of Histology and Embryology, Medical School, Southeast University, Nanjing, China
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Ying Lu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
- Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Suying Li
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
- Reproductive Center of Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Tao Zhou
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
- Central Laboratory, Wuxi Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Wuxi, China
| | - Jing Wang
- Zhong Da Hospital, Southeast University, Nanjing, China
| | - Jiangyan Xia
- Zhong Da Hospital, Southeast University, Nanjing, China
| | - Xinxin Zhang
- Department of Histology and Embryology, Medical School, Southeast University, Nanjing, China
| | - Zuomin Zhou
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| |
Collapse
|
6
|
Activation of farnesoid X receptor (FXR) induces crystallin zeta expression in mouse medullary collecting duct cells. Pflugers Arch 2020; 472:1631-1641. [PMID: 32914211 DOI: 10.1007/s00424-020-02456-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 08/24/2020] [Accepted: 08/28/2020] [Indexed: 02/05/2023]
Abstract
Crystallin zeta (CRYZ) is a phylogenetically restricted water-soluble protein and provides cytoprotection against oxidative stress via multiple mechanisms. Increasing evidence suggests that CRYZ is high abundantly expressed in the kidney where it acts as a transacting factor in increasing glutaminolysis and the Na+/K+/2Cl- cotransporter (BSC1/NKCC2) expression to help maintain acid-base balance and medullary hyperosmotic gradient. However, the mechanism by which CRYZ is regulated in the kidney remains largely uncharacterized. Here, we show that CRYZ is a direct target of farnesoid X receptor (FXR), a nuclear receptor important for renal physiology. We found that CRYZ was ubiquitously expressed in mouse kidney and constitutively expressed in the cytoplasm of medullary collecting duct cells (MCDs). In primary cultured mouse MCDs, CRYZ expression was significantly upregulated by the activation and overexpression of FXR. FXR-induced CRYZ expression was almost completely abolished in the MCD cells with siRNA-mediated FXR knockdown. Consistently, treatment with FXR agonists failed to induce CRYZ expression in the MCDs isolated from mice with global and collecting duct-specific FXR deficiency. We identified a putative FXR response element (FXRE) on the CRYZ gene promoter. The luciferase reporter and ChIP assays revealed that FXR can bind directly to the FXRE site, which was further markedly enhanced by FXR activation. Furthermore, we found CRYZ overexpression in MCDs significantly attenuated hypertonicity-induced cell death possibly via increasing Bcl-2 expression. Collectively, our findings demonstrate that CRYZ is constitutively expressed in renal medullary collecting duct cells, where it is transcriptionally controlled by FXR. Given a critical role of FXR in MCDs, CRYZ may be responsible for protective effect of FXR on the survival of MCDs under hypertonic condition during dehydration.
Collapse
|
7
|
Lulli M, Nencioni D, Papucci L, Schiavone N. Zeta-crystallin: a moonlighting player in cancer. Cell Mol Life Sci 2020; 77:965-976. [PMID: 31563996 PMCID: PMC11104887 DOI: 10.1007/s00018-019-03301-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 09/10/2019] [Accepted: 09/16/2019] [Indexed: 12/13/2022]
Abstract
Crystallins were firstly found as structural proteins of the eye lens. To this family belong proteins, such as ζ-crystallin, expressed ubiquitously, and endowed with enzyme activity. ζ-crystallin is a moonlighting protein endowed with two main different functions: (1) mRNA binding with stabilizing activity; (2) NADPH:quinone oxidoreductase. ζ-crystallin has been clearly demonstrated to stabilize mRNAs encoding proteins involved in renal glutamine catabolism during metabolic acidosis resulting in ammoniagenesis and bicarbonate ion production that concur to compensate such condition. ζ-crystallin binds also mRNAs encoding for antiapoptotic proteins, such as Bcl-2 in leukemia cells. On the other hand, the physiological role of its enzymatic activity is still elusive. Gathering research evidences and data mined from public databases, we provide a framework where all the known ζ-crystallin properties are called into question, making it a hypothetical pivotal player in cancer, allowing cells to hijack or subjugate the acidity response mechanism to increase their ability to resist oxidative stress and apoptosis, while fueling their glutamine addicted metabolism.
Collapse
Affiliation(s)
- Matteo Lulli
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", Università Degli Studi di Firenze, Viale G.B. Morgagni, 50, Firenze, 50134, Italy.
| | - Daniele Nencioni
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", Università Degli Studi di Firenze, Viale G.B. Morgagni, 50, Firenze, 50134, Italy
| | - Laura Papucci
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", Università Degli Studi di Firenze, Viale G.B. Morgagni, 50, Firenze, 50134, Italy
| | - Nicola Schiavone
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", Università Degli Studi di Firenze, Viale G.B. Morgagni, 50, Firenze, 50134, Italy.
| |
Collapse
|
8
|
John SP, Sun J, Carlson RJ, Cao B, Bradfield CJ, Song J, Smelkinson M, Fraser IDC. IFIT1 Exerts Opposing Regulatory Effects on the Inflammatory and Interferon Gene Programs in LPS-Activated Human Macrophages. Cell Rep 2020; 25:95-106.e6. [PMID: 30282041 PMCID: PMC6492923 DOI: 10.1016/j.celrep.2018.09.002] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 07/06/2018] [Accepted: 08/30/2018] [Indexed: 12/15/2022] Open
Abstract
Activation of the TLR4 signaling pathway by lipopolysaccharide (LPS) leads to induction of both inflammatory and interferon-stimulated genes, but the mechanisms through which these coordinately activated transcriptional programs are balanced to promote an optimal innate immune response remain poorly understood. In a genome-wide small interfering RNA (siRNA) screen of the LPS-induced tumor necrosis factor α (TNF-α) response in macrophages, we identify the interferon-stimulated protein IFIT1 as a negative regulator of the inflammatory gene program. Transcriptional profiling further identifies a positive regulatory role for IFIT1 in type I interferon expression, implicating IFIT1 as a reciprocal modulator of LPS-induced gene classes. We demonstrate that these effects of IFIT1 are mediated through modulation of a Sin3A-HDAC2 transcriptional regulatory complex at LPS-induced gene loci. Beyond the well-studied role of cytosolic IFIT1 in restricting viral replication, our data demonstrate a function for nuclear IFIT1 in differential transcriptional regulation of separate branches of the LPS-induced gene program.
Collapse
Affiliation(s)
- Sinu P John
- Signaling Systems Section, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA.
| | - Jing Sun
- Signaling Systems Section, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Rebecca J Carlson
- Signaling Systems Section, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Binh Cao
- Signaling Systems Section, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Clinton J Bradfield
- Signaling Systems Section, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Jian Song
- Bioinformatics Group, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Margery Smelkinson
- Biological Imaging Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Iain D C Fraser
- Signaling Systems Section, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA.
| |
Collapse
|
9
|
Vandemoortele G, De Sutter D, Moliere A, Pauwels J, Gevaert K, Eyckerman S. A Well-Controlled BioID Design for Endogenous Bait Proteins. J Proteome Res 2018; 18:95-106. [PMID: 30525648 DOI: 10.1021/acs.jproteome.8b00367] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The CRISPR/Cas9 revolution is profoundly changing the way life sciences technologies are used. Many assays now rely on engineered clonal cell lines to eliminate the overexpression of bait proteins. Control cell lines are typically nonengineered cells or engineered clones, implying a considerable risk for artifacts because of clonal variation. Genome engineering can also transform BioID, a proximity labeling method that relies on fusing a bait protein to a promiscuous biotin ligase, BirA*, resulting in the tagging of vicinal proteins. We here propose an innovative design to enable BioID for endogenous proteins wherein we introduce a T2A-BirA* module at the C-terminus of endogenous p53 by genome engineering, leading to bicistronic expression of both p53 and BirA* under control of the endogenous promoter. By targeting a Cas9-cytidine deaminase base editor to the T2A autocleavage site, we can efficiently derive an isogenic population expressing a functional p53-BirA* fusion protein. Using quantitative proteomics we show significant benefits over the classical ectopic expression of p53-BirA*, and we provide a first well-controlled view of the proximal proteins of endogenous p53 in colon carcinoma cells. This novel application for base editors expands the CRISPR/Cas9 toolbox and can be a valuable addition for synthetic biology.
Collapse
Affiliation(s)
- Giel Vandemoortele
- VIB Center for Medical Biotechnology, VIB , B-9000 Ghent , Belgium.,Department of Biomolecular Medicine , Ghent University , B-9000 Ghent , Belgium
| | - Delphine De Sutter
- VIB Center for Medical Biotechnology, VIB , B-9000 Ghent , Belgium.,Department of Biomolecular Medicine , Ghent University , B-9000 Ghent , Belgium
| | - Aline Moliere
- VIB Center for Medical Biotechnology, VIB , B-9000 Ghent , Belgium.,Department of Biomolecular Medicine , Ghent University , B-9000 Ghent , Belgium
| | - Jarne Pauwels
- VIB Center for Medical Biotechnology, VIB , B-9000 Ghent , Belgium.,Department of Biomolecular Medicine , Ghent University , B-9000 Ghent , Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, VIB , B-9000 Ghent , Belgium.,Department of Biomolecular Medicine , Ghent University , B-9000 Ghent , Belgium
| | - Sven Eyckerman
- VIB Center for Medical Biotechnology, VIB , B-9000 Ghent , Belgium.,Department of Biomolecular Medicine , Ghent University , B-9000 Ghent , Belgium
| |
Collapse
|
10
|
Snezhkina AV, Nyushko KM, Zaretsky AR, Shagin DA, Sadritdinova AF, Fedorova MS, Guvatova ZG, Abramov IS, Pudova EA, Alekseev BY, Dmitriev AA, Kudryavtseva AV. Transcription Factor SAP30 Is Involved in the Activation of NETO2 Gene Expression in Clear Cell Renal Cell Carcinoma. Mol Biol 2018. [DOI: 10.1134/s0026893318020152] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
11
|
Moravec CE, Yousef H, Kinney BA, Salerno-Eichenholz R, Monestime CM, Martin BL, Sirotkin HI. Zebrafish sin3b mutants are viable but have size, skeletal, and locomotor defects. Dev Dyn 2017; 246:946-955. [PMID: 28850761 DOI: 10.1002/dvdy.24581] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 07/12/2017] [Accepted: 08/01/2017] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The transcriptional co-repressor Sin3 is highly conserved from yeast to vertebrates and has multiple roles controlling cell fate, cell cycle progression, and senescence programming. Sin3 proteins recruit histone deacetylases and other chromatin modifying factors to specific loci through interactions with transcription factors including Myc, Rest, p53 and E2F. Most vertebrates have two Sin3 family members (sin3a and sin3b), but zebrafish have a second sin3a paralogue. In mice, sin3a and sin3b are essential for embryonic development. Sin3b knockout mice show defects in growth as well as bone and blood differentiation. RESULTS To study the requirement for Sin3b during development, we disrupted zebrafish sin3b using CRISPR-Cas9, and studied the effects on early development and locomotor behavior. CONCLUSIONS Surprisingly, Sin3b is not essential in zebrafish. sin3b mutants show a decrease in fitness, small size, changes to locomotor behavior, and delayed bone development. We did not detect a role for Sin3b in cell proliferation. Our analysis of the sin3b mutant revealed a more nuanced requirement for zebrafish Sin3b than would be predicted from analysis of mutants in other species. Developmental Dynamics 246:946-955, 2017. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Cara E Moravec
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, New York.,Genetics Gradate Program Stony Brook University, Stony Brook, New York
| | - Hakeem Yousef
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, New York
| | - Brian A Kinney
- Genetics Gradate Program Stony Brook University, Stony Brook, New York.,Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York
| | - Ryan Salerno-Eichenholz
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, New York.,Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York
| | - Camillia M Monestime
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, New York
| | - Benjamin L Martin
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York
| | - Howard I Sirotkin
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, New York.,Genetics Gradate Program Stony Brook University, Stony Brook, New York
| |
Collapse
|
12
|
Fischer M. Census and evaluation of p53 target genes. Oncogene 2017; 36:3943-3956. [PMID: 28288132 PMCID: PMC5511239 DOI: 10.1038/onc.2016.502] [Citation(s) in RCA: 592] [Impact Index Per Article: 84.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 11/23/2016] [Accepted: 11/29/2016] [Indexed: 12/17/2022]
Abstract
The tumor suppressor p53 functions primarily as a transcription factor. Mutation of the TP53 gene alters its response pathway, and is central to the development of many cancers. The discovery of a large number of p53 target genes, which confer p53's tumor suppressor function, has led to increasingly complex models of p53 function. Recent meta-analysis approaches, however, are simplifying our understanding of how p53 functions as a transcription factor. In the survey presented here, a total set of 3661 direct p53 target genes is identified that comprise 3509 potential targets from 13 high-throughput studies, and 346 target genes from individual gene analyses. Comparison of the p53 target genes reported in individual studies with those identified in 13 high-throughput studies reveals limited consistency. Here, p53 target genes have been evaluated based on the meta-analysis data, and the results show that high-confidence p53 target genes are involved in multiple cellular responses, including cell cycle arrest, DNA repair, apoptosis, metabolism, autophagy, mRNA translation and feedback mechanisms. However, many p53 target genes are identified only in a small number of studies and have a higher likelihood of being false positives. While numerous mechanisms have been proposed for mediating gene regulation in response to p53, recent advances in our understanding of p53 function show that p53 itself is solely an activator of transcription, and gene downregulation by p53 is indirect and requires p21. Taking into account the function of p53 as an activator of transcription, recent results point to an unsophisticated means of regulation.
Collapse
Affiliation(s)
- M Fischer
- Molecular Oncology, Medical School, University of Leipzig, Leipzig, Germany
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
13
|
Zhang RX, Li Y, Tian DD, Liu Y, Nian W, Zou X, Chen QZ, Zhou LY, Deng ZL, He BC. Ursolic acid inhibits proliferation and induces apoptosis by inactivating Wnt/β-catenin signaling in human osteosarcoma cells. Int J Oncol 2016; 49:1973-1982. [PMID: 27665868 DOI: 10.3892/ijo.2016.3701] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 09/01/2016] [Indexed: 11/06/2022] Open
Abstract
Although multiple chemotherapeutic agents have been used for osteosarcoma (OS) treatment, their mechanisms need further study. Ursolic acid (UA), a pentacyclic triterpenoid, can reduce cell proliferation and induce apoptosis in various cancer cells, such as OS. However, the exact mechanism underlying this function remains unclear. In this study, we investigated the anti‑proliferative effect of UA in human OS 143B cells and dissected the possible molecular mechanism underlying this effect. We demonstrated that UA can reduce cell proliferation, induce apoptosis and arrest cell cycle in 143B cells, as well as inhibit OS tumor growth in a mouse xenograft model. Using a luciferase reporter assay, we found that the Wnt/β‑catenin signaling is inhibited by UA in 143B cells. Correspondingly, the expression level and nuclear translocation of β‑catenin are both decreased by UA. Exogenous expression of β‑catenin attenuates the anticancer effect of UA in 143B cells, while knockdown of β‑catenin enhances this effect. UA increases the expression level of p53 in a concentration‑dependent manner, and inhibition of p53 reduces the anticancer effect of UA in 143B cells. Moreover, inhibition of p53 partly reverses the UA‑induced downregulation of β‑catenin, as do the targets of Wnt/β‑catenin signaling, such as c‑Myc and cyclin D1. Our findings indicated that UA can inhibit the proliferation of 143B OS cells through inactivation of Wnt/β-catenin signaling, which may be mediated partly by upregulating the expression of p53.
Collapse
Affiliation(s)
- Ran-Xi Zhang
- Chongqing Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing Medical University, Chongqing, P.R. China
| | - Yang Li
- Chongqing Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing Medical University, Chongqing, P.R. China
| | - Dong-Dong Tian
- Chongqing Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing Medical University, Chongqing, P.R. China
| | - Yang Liu
- Department of Orthopaedics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, P.R. China
| | - Wu Nian
- Chongqing Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing Medical University, Chongqing, P.R. China
| | - Xiang Zou
- Chongqing Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing Medical University, Chongqing, P.R. China
| | - Qian-Zhao Chen
- Chongqing Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing Medical University, Chongqing, P.R. China
| | - Lin-Yun Zhou
- Chongqing Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing Medical University, Chongqing, P.R. China
| | - Zhong-Liang Deng
- Department of Orthopaedics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, P.R. China
| | - Bai-Cheng He
- Chongqing Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing Medical University, Chongqing, P.R. China
| |
Collapse
|
14
|
Bansal N, Petrie K, Christova R, Chung CY, Leibovitch BA, Howell L, Gil V, Sbirkov Y, Lee E, Wexler J, Ariztia EV, Sharma R, Zhu J, Bernstein E, Zhou MM, Zelent A, Farias E, Waxman S. Targeting the SIN3A-PF1 interaction inhibits epithelial to mesenchymal transition and maintenance of a stem cell phenotype in triple negative breast cancer. Oncotarget 2016; 6:34087-105. [PMID: 26460951 PMCID: PMC4741438 DOI: 10.18632/oncotarget.6048] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 09/24/2015] [Indexed: 12/15/2022] Open
Abstract
Triple negative breast cancer (TNBC) is characterized by a poorly differentiated phenotype and limited treatment options. Aberrant epigenetics in this subtype represent a potential therapeutic opportunity, but a better understanding of the mechanisms contributing to the TNBC pathogenesis is required. The SIN3 molecular scaffold performs a critical role in multiple cellular processes, including epigenetic regulation, and has been identified as a potential therapeutic target. Using a competitive peptide corresponding to the SIN3 interaction domain of MAD (Tat-SID), we investigated the functional consequences of selectively blocking the paired amphipathic α-helix (PAH2) domain of SIN3. Here, we report the identification of the SID-containing adaptor PF1 as a factor required for maintenance of the TNBC stem cell phenotype and epithelial-to-mesenchymal transition (EMT). Tat-SID peptide blocked the interaction between SIN3A and PF1, leading to epigenetic modulation and transcriptional downregulation of TNBC stem cell and EMT markers. Importantly, Tat-SID treatment also led to a reduction in primary tumor growth and disseminated metastatic disease in vivo. In support of these findings, knockdown of PF1 expression phenocopied treatment with Tat-SID both in vitro and in vivo. These results demonstrate a critical role for a complex containing SIN3A and PF1 in TNBC and provide a rational for its therapeutic targeting.
Collapse
Affiliation(s)
- Nidhi Bansal
- Division of Hematology and Oncology, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kevin Petrie
- Division of Clinical Studies, Institute of Cancer Research, Sutton, United Kingdom
| | - Rossitza Christova
- Division of Clinical Studies, Institute of Cancer Research, Sutton, United Kingdom
| | - Chi-Yeh Chung
- Department of Oncological Sciences, Department of Genetics and Genomic Sciences, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Boris A Leibovitch
- Division of Hematology and Oncology, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Louise Howell
- Division of Clinical Studies, Institute of Cancer Research, Sutton, United Kingdom
| | - Veronica Gil
- Division of Clinical Studies, Institute of Cancer Research, Sutton, United Kingdom
| | - Yordan Sbirkov
- Division of Clinical Studies, Institute of Cancer Research, Sutton, United Kingdom
| | - EunJee Lee
- Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joanna Wexler
- Division of Hematology and Oncology, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edgardo V Ariztia
- Division of Hematology and Oncology, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rajal Sharma
- Division of Hematology and Oncology, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jun Zhu
- Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emily Bernstein
- Department of Oncological Sciences, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ming-Ming Zhou
- Division of Hematology and Oncology, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Arthur Zelent
- Division of Hemato-Oncology, Department of Medicine, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Eduardo Farias
- Division of Hematology and Oncology, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Samuel Waxman
- Division of Hematology and Oncology, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| |
Collapse
|
15
|
Bansal N, David G, Farias E, Waxman S. Emerging Roles of Epigenetic Regulator Sin3 in Cancer. Adv Cancer Res 2016; 130:113-35. [PMID: 27037752 DOI: 10.1016/bs.acr.2016.01.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Revolutionizing treatment strategies is an urgent clinical need in the fight against cancer. Recently the scientific community has recognized chromatin-associated proteins as promising therapeutic candidates. However, there is a need to develop more targeted epigenetic inhibitors with less toxicity. Sin3 family is one such target which consists of evolutionary conserved proteins with two paralogues Sin3A and Sin3B. Sin3A/B are global transcription regulators that provide a versatile platform for diverse chromatin-modifying activities. Sin3 proteins regulate key cellular functions that include cell cycle, proliferation, and differentiation, and have recently been implicated in cancer pathogenesis. In this chapter, we summarize the key concepts of Sin3 biology and elaborate the recent advancements in the role of Sin3 proteins in cancer with specific examples in multiple endocrine neoplasia type 2, pancreatic ductal adenocarcinoma, and triple negative breast cancer. Finally, a program to create an integrative approach for screening antitumor agents that target chromatin-associated factors like Sin3 is presented.
Collapse
Affiliation(s)
- N Bansal
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - G David
- New York University School of Medicine, New York, NY, United States
| | - E Farias
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - S Waxman
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States.
| |
Collapse
|
16
|
Chang J, Lu Y, Boswell WT, Boswell M, Caballero KL, Walter RB. Molecular genetic response to varied wavelengths of light in Xiphophorus maculatus skin. Comp Biochem Physiol C Toxicol Pharmacol 2015; 178:104-115. [PMID: 26460196 PMCID: PMC4662885 DOI: 10.1016/j.cbpc.2015.10.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 10/01/2015] [Accepted: 10/05/2015] [Indexed: 12/14/2022]
Abstract
Xiphophorus fishes represent a model often utilized to study UVB induced tumorigenesis. Recently, varied genetic responses to UVB exposure have been documented in the skin of female and male Xiphophorus, as have differences in UVB response in the skin of different parental species and for interspecies hybrids produced from crossing them. Additionally, it has been shown that exposure to "cool white" fluorescent light induces a shift in the genetic profiles of Xiphophorus skin that is nearly as robust as the UVB response, but involves a fundamentally different set of genes. Given these results and the use of Xiphophorus interspecies hybrids as an experimental model for UVB inducible melanoma, it is of interest to characterize genes that may be transcriptionally modulated in a wavelength specific manner. The global molecular genetic response of skin upon exposure of the intact animal to specific wavelengths of light has not been investigated. Herein, we report results of RNA-Seq experiments from the skin of male Xiphophorus maculatus Jp 163 B following exposure to varied 50nm wavelengths of light ranging from 300-600nm. We identify two specific wavelength regions, 350-400nm (88 genes) and 500-550nm (276 genes), that exhibit transcriptional modulation of a significantly greater number of transcripts than any of the other 50nm regions in the 300-600nm range. Observed functional sets of genes modulated within these two transcriptionally active light regions suggest different mechanisms of gene modulation.
Collapse
Affiliation(s)
- Jordan Chang
- Molecular Bioscience Research Group and Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA.
| | - Yuan Lu
- Molecular Bioscience Research Group and Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA.
| | - William T Boswell
- Molecular Bioscience Research Group and Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA.
| | - Mikki Boswell
- Molecular Bioscience Research Group and Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA.
| | - Kaela L Caballero
- Molecular Bioscience Research Group and Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA.
| | - Ronald B Walter
- Molecular Bioscience Research Group and Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA.
| |
Collapse
|
17
|
Li M, Zhang F, Wang X, Wu X, Zhang B, Zhang N, Wu W, Wang Z, Weng H, Liu S, Gao G, Mu J, Shu Y, Bao R, Cao Y, Lu J, Gu J, Zhu J, Liu Y. Magnolol inhibits growth of gallbladder cancer cells through the p53 pathway. Cancer Sci 2015; 106:1341-50. [PMID: 26250568 PMCID: PMC4638010 DOI: 10.1111/cas.12762] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 07/29/2015] [Accepted: 08/02/2015] [Indexed: 12/24/2022] Open
Abstract
Magnolol, the major active compound found in Magnolia officinalis has a wide range of clinical applications due to its anti-inflammation and anti-oxidation effects. This study investigated the effects of magnolol on the growth of human gallbladder carcinoma (GBC) cell lines. The results indicated that magnolol could significantly inhibit the growth of GBC cell lines in a dose- and time-dependent manner. Magnolol also blocked cell cycle progression at G0 /G1 phase and induced mitochondrial-related apoptosis by upregulating p53 and p21 protein levels and by downregulating cyclin D1, CDC25A, and Cdk2 protein levels. When cells were pretreated with a p53 inhibitor (pifithrin-a), followed by magnolol treatment, pifithrin-a blocked magnolol-induced apoptosis and G0 /G1 arrest. In vivo, magnolol suppressed tumor growth and activated the same mechanisms as were activated in vitro. In conclusion, our study is the first to report that magnolol has an inhibitory effect on the growth of GBC cells and that this compound may have potential as a novel therapeutic agent for the treatment of GBC.
Collapse
Affiliation(s)
- Maolan Li
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong, University School of MedicineShanghai, China
- Laboratory of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong, University School of MedicineShanghai, China
- Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Fei Zhang
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong, University School of MedicineShanghai, China
- Laboratory of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong, University School of MedicineShanghai, China
- Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Xu’an Wang
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong, University School of MedicineShanghai, China
- Laboratory of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong, University School of MedicineShanghai, China
- Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Xiangsong Wu
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong, University School of MedicineShanghai, China
- Laboratory of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong, University School of MedicineShanghai, China
- Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Bingtai Zhang
- Department of General Surgery, Shanxi Medical University Second HospitalTaiyuan, China
| | - Ning Zhang
- Department of General Surgery, Shanxi Medical University Second HospitalTaiyuan, China
| | - Wenguang Wu
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong, University School of MedicineShanghai, China
- Laboratory of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong, University School of MedicineShanghai, China
- Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Zheng Wang
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong, University School of MedicineShanghai, China
- Laboratory of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong, University School of MedicineShanghai, China
- Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Hao Weng
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong, University School of MedicineShanghai, China
- Laboratory of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong, University School of MedicineShanghai, China
- Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Shibo Liu
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong, University School of MedicineShanghai, China
- Laboratory of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong, University School of MedicineShanghai, China
- Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Guofeng Gao
- Department of General Surgery, Shanxi Medical University Second HospitalTaiyuan, China
| | - Jiasheng Mu
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong, University School of MedicineShanghai, China
- Laboratory of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong, University School of MedicineShanghai, China
- Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Yijun Shu
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong, University School of MedicineShanghai, China
- Laboratory of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong, University School of MedicineShanghai, China
- Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Runfa Bao
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong, University School of MedicineShanghai, China
- Laboratory of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong, University School of MedicineShanghai, China
- Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Yang Cao
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong, University School of MedicineShanghai, China
- Laboratory of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong, University School of MedicineShanghai, China
- Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Jianhua Lu
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong, University School of MedicineShanghai, China
- Laboratory of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong, University School of MedicineShanghai, China
- Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Jun Gu
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong, University School of MedicineShanghai, China
- Laboratory of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong, University School of MedicineShanghai, China
- Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Jian Zhu
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong, University School of MedicineShanghai, China
- Laboratory of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong, University School of MedicineShanghai, China
- Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Yingbin Liu
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong, University School of MedicineShanghai, China
- Laboratory of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong, University School of MedicineShanghai, China
- Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of MedicineShanghai, China
| |
Collapse
|
18
|
Chen M, Zhu A, Storey KB. Comparative phosphoproteomic analysis of intestinal phosphorylated proteins in active versus aestivating sea cucumbers. J Proteomics 2015; 135:141-150. [PMID: 26385000 DOI: 10.1016/j.jprot.2015.09.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 08/27/2015] [Accepted: 09/09/2015] [Indexed: 01/18/2023]
Abstract
UNLABELLED The sea cucumber Apostichopus japonicus is becoming an excellent model marine invertebrate for studies of environmentally-induced aestivation. Reversible protein phosphorylation as a regulatory mechanism in aestivation is known for some terrestrial aestivators but has never before been documented in sea cucumbers. The present study provides a global quantitative analysis of the role of reversible phosphorylation in sea cucumber aestivation by using tandem mass tag (TMT) labeling followed by an IMAC enrichment strategy to map aestivation-responsive changes in the phosphoproteome of sea cucumber intestine. We identified 2295 unique phosphosites derived from 1283 phosphoproteins and, of these, 211 hyperphosphorylated and 65 hypophosphorylated phosphoproteins were identified in intestine during deep aestivation compared with the active state based on the following criterion: quantitative ratios over 1.5 or less than 0.67 with corrected p-value <0.05. Six major functional classes of proteins exhibited changes in their phosphorylation status during aestivation: (1) protein synthesis, (2) transcriptional regulators, (3) kinases, (4) signaling, (5) transporter, (6) DNA binding. These data on the global involvement of phosphorylation in sea cucumber aestivation significantly improve our understanding of the regulatory mechanisms involved in metabolic arrest when marine invertebrates face environmental stress and provide substantial candidate phosphorylated proteins that could be important for identifying functionally adaptive variation in marine invertebrates. SIGNIFICANCE Sea cucumber Apostichopus japonicus is an excellent model organism for studies of environmentally-induced aestivation by a marine invertebrate. The present study provides the first quantitative phosphoproteomic analysis of sea cucumber aestivation using isobaric tag based TMT labeling followed by an IMAC enrichment strategy. These data on the global involvement of phosphorylation in sea cucumber aestivation significantly improve our understanding of the regulatory mechanism involved in metabolic arrest when marine invertebrates face environmental stress and provide substantial candidate phosphorylated proteins that could be important for identifying functionally adaptive variation in marine invertebrates. This study also demonstrates the usefulness of the TMT-based quantitative phosphoproteomics approach to explore the survival responses of a non-model marine invertebrate species to seasonal changes in its environment.
Collapse
Affiliation(s)
- Muyan Chen
- Fisheries College, Ocean University of China, Qingdao, PR China.
| | - Aijun Zhu
- Fisheries College, Ocean University of China, Qingdao, PR China
| | - Kenneth B Storey
- Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, Canada, K1S 5B6
| |
Collapse
|
19
|
Abstract
The predominant function of the tumor suppressor p53 is transcriptional regulation. It is generally accepted that p53-dependent transcriptional activation occurs by binding to a specific recognition site in promoters of target genes. Additionally, several models for p53-dependent transcriptional repression have been postulated. Here, we evaluate these models based on a computational meta-analysis of genome-wide data. Surprisingly, several major models of p53-dependent gene regulation are implausible. Meta-analysis of large-scale data is unable to confirm reports on directly repressed p53 target genes and falsifies models of direct repression. This notion is supported by experimental re-analysis of representative genes reported as directly repressed by p53. Therefore, p53 is not a direct repressor of transcription, but solely activates its target genes. Moreover, models based on interference of p53 with activating transcription factors as well as models based on the function of ncRNAs are also not supported by the meta-analysis. As an alternative to models of direct repression, the meta-analysis leads to the conclusion that p53 represses transcription indirectly by activation of the p53-p21-DREAM/RB pathway.
Collapse
Key Words
- CDE, cell cycle-dependent element
- CDKN1A
- CHR, cell cycle genes homology region
- ChIP, chromatin immunoprecipitation
- DREAM complex
- DREAM, DP, RB-like, E2F4, and MuvB complex
- E2F/RB complex
- HPV, human papilloma virus
- NF-Y, Nuclear factor Y
- cdk, cyclin-dependent kinase
- genome-wide meta-analysis
- p53
Collapse
Affiliation(s)
- Martin Fischer
- a Molecular Oncology; Medical School ; University of Leipzig ; Leipzig , Germany
| | | | | |
Collapse
|
20
|
Kadamb R, Mittal S, Bansal N, Saluja D. Stress-mediated Sin3B activation leads to negative regulation of subset of p53 target genes. Biosci Rep 2015; 35:e00234. [PMID: 26181367 PMCID: PMC4613689 DOI: 10.1042/bsr20150122] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 06/03/2015] [Accepted: 06/19/2015] [Indexed: 11/28/2022] Open
Abstract
The multiprotein SWI-independent 3 (Sin3)-HDAC (histone deacetylase) corepressor complex mediates gene repression through its interaction with DNA-binding factors and recruitment of chromatin-modifying proteins on to the promoters of target gene. Previously, an increased expression of Sin3B and tumour suppressor protein, p53 has been established upon adriamycin treatment. We, now provide evidence that Sin3B expression is significantly up-regulated under variety of stress conditions and this response is not stress-type specific. We observed that Sin3B expression is significantly up-regulated both at transcript and at protein level upon DNA damage induced by bleomycin drug, a radiomimetic agent. This increase in Sin3B expression upon stress is found to be p53-dependent and is associated with enhanced interaction of Sin3B with Ser(15) phosphorylated p53. Binding of Sin3-HDAC repressor complex on to the promoters of p53 target genes influences gene regulation by altering histone modifications (H3K9me3 and H3K27me3) at target genes. Furthermore, knockdown of Sin3B by shRNA severely compromises p53-mediated gene repression under stress conditions. Taken together, these results suggest that stress-induced Sin3B activation is p53-dependent and is essential for p53-mediated repression of its selective target genes. The present study has an implication in understanding the transrepression mechanism of p53 under DNA damaging conditions.
Collapse
Affiliation(s)
- Rama Kadamb
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi-110007, India
| | - Shilpi Mittal
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi-110007, India
| | - Nidhi Bansal
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi-110007, India
| | - Daman Saluja
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi-110007, India
| |
Collapse
|
21
|
Cilli D, Mirasole C, Pennisi R, Pallotta V, D'Alessandro A, Antoccia A, Zolla L, Ascenzi P, di Masi A. Identification of the interactors of human nibrin (NBN) and of its 26 kDa and 70 kDa fragments arising from the NBN 657del5 founder mutation. PLoS One 2014; 9:e114651. [PMID: 25485873 PMCID: PMC4259352 DOI: 10.1371/journal.pone.0114651] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 11/12/2014] [Indexed: 01/17/2023] Open
Abstract
Nibrin (also named NBN or NBS1) is a component of the MRE11/RAD50/NBN complex, which is involved in early steps of DNA double strand breaks sensing and repair. Mutations within the NBN gene are responsible for the Nijmegen breakage syndrome (NBS). The 90% of NBS patients are homozygous for the 657del5 mutation, which determines the synthesis of two truncated proteins of 26 kDa (p26) and 70 kDa (p70). Here, HEK293 cells have been exploited to transiently express either the full-length NBN protein or the p26 or p70 fragments, followed by affinity chromatography enrichment of the eluates. The application of an unsupervised proteomics approach, based upon SDS-PAGE separation and shotgun digestion of protein bands followed by MS/MS protein identification, indicates the occurrence of previously unreported protein interacting partners of the full-length NBN protein and the p26 fragment containing the FHA/BRCT1 domains, especially after cell irradiation. In particular, results obtained shed light on new possible roles of NBN and of the p26 fragment in ROS scavenging, in the DNA damage response, and in protein folding and degradation. In particular, here we show that p26 interacts with PARP1 after irradiation, and this interaction exerts an inhibitory effect on PARP1 activity as measured by NAD+ levels. Furthermore, the p26-PARP1 interaction seems to be responsible for the persistence of ROS, and in turn of DSBs, at 24 h from IR. Since some of the newly identified interactors of the p26 and p70 fragments have not been found to interact with the full-length NBN, these interactions may somehow contribute to the key biological phenomena underpinning NBS.
Collapse
Affiliation(s)
| | - Cristiana Mirasole
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Rosa Pennisi
- Department of Science, Roma Tre University, Rome, Italy
| | - Valeria Pallotta
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Angelo D'Alessandro
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Antonio Antoccia
- Department of Science, Roma Tre University, Rome, Italy
- Istituto Nazionale Biostrutture e Biosistemi – Consorzio Interuniversitario, Rome, Italy
| | - Lello Zolla
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Paolo Ascenzi
- Istituto Nazionale Biostrutture e Biosistemi – Consorzio Interuniversitario, Rome, Italy
- Interdepartmental Laboratory for Electron Microscopy, Roma Tre University, Rome, Italy
| | - Alessandra di Masi
- Department of Science, Roma Tre University, Rome, Italy
- Istituto Nazionale Biostrutture e Biosistemi – Consorzio Interuniversitario, Rome, Italy
- * E-mail:
| |
Collapse
|
22
|
Noh HJ, Kim KA, Kim KC. p53 down-regulates SETDB1 gene expression during paclitaxel induced-cell death. Biochem Biophys Res Commun 2014; 446:43-8. [PMID: 24565839 DOI: 10.1016/j.bbrc.2014.02.053] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Accepted: 02/11/2014] [Indexed: 10/25/2022]
Abstract
Paclitaxel (PTX) is a chemotherapeutic drug which induces tubulin stability and regulates expression of death related genes in human cancer cells. Its anticancer mechanism is well known, however its effects on chromatin remodeling factors are poorly understood. In this study, we examine if PTX affects expression of SETDB1 HMTase during cell death. PTX induces cell death via G2/M arrest in human lung cancer cells. PTX treatment induces the p53 protein, but down-regulates expression of SETDB1 at the transcriptional level as well as the protein level. SETDB1 promoter activity is increased to approximately 30-fold in normal condition, but the activity is significantly inhibited in the PTX treated group. In addition, p53 transfection inhibits SETDB1 promoter activity. The p53 protein directly binds to proximal region of the SETDB1 promoter, and H3K9me3 occupancy in this region also increased in the presence of p53. Immunoprecipitation experiment showed interaction of p53 and SUV39H1, suggesting that association of p53 and SUV39H1 is responsible for increased H3K9me3 occupancy and transcription repression of SETDB1. This result demonstrates that PTX down-regulates SETDB1 gene expression in a p53 dependent manner, and p53 might participate in heterochromatic repression on the promoter regions of SETDB1.
Collapse
Affiliation(s)
- Hee-Jung Noh
- Medical & Bio-Material Research Center, Department of Biological Sciences, College of Natural Sciences, Kangwon National University, Chuncheon 200-701, Republic of Korea
| | - Kyeong-Ah Kim
- Medical & Bio-Material Research Center, Department of Biological Sciences, College of Natural Sciences, Kangwon National University, Chuncheon 200-701, Republic of Korea
| | - Keun-Cheol Kim
- Medical & Bio-Material Research Center, Department of Biological Sciences, College of Natural Sciences, Kangwon National University, Chuncheon 200-701, Republic of Korea.
| |
Collapse
|
23
|
Kadamb R, Mittal S, Bansal N, Batra H, Saluja D. Sin3: insight into its transcription regulatory functions. Eur J Cell Biol 2013; 92:237-46. [PMID: 24189169 DOI: 10.1016/j.ejcb.2013.09.001] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 08/27/2013] [Accepted: 09/11/2013] [Indexed: 10/26/2022] Open
Abstract
Sin3, a large acidic protein, shares structural similarity with the helix-loop-helix dimerization domain of proteins of the Myc family of transcription factors. Sin3/HDAC corepressor complex functions in transcriptional regulation of several genes and is therefore implicated in the regulation of key biological processes. Knockdown studies have confirmed the role of Sin3 in cellular proliferation, differentiation, apoptosis and cell cycle regulation, emphasizing Sin3 as an essential regulator of critical cellular events in normal and pathological processes. The present review covers the diverse functions of this master transcriptional regulator as well as illustrates the redundant and distinct functions of its two mammalian isoforms.
Collapse
Affiliation(s)
- Rama Kadamb
- Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110007, India.
| | | | | | | | | |
Collapse
|
24
|
The Justy mutant mouse strain produces a spontaneous murine model of salivary gland cancer with myoepithelial and basal cell differentiation. J Transl Med 2013; 93:711-9. [PMID: 23608756 PMCID: PMC3669254 DOI: 10.1038/labinvest.2013.62] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We previously identified a novel mutant mouse strain on the C3HeB/FeJ background named Justy. This strain bears a recessive mutation in the Gon4l gene that greatly reduces expression of the encoded protein, a nuclear factor implicated in transcriptional regulation. Here, we report that Justy mutant mice aged 6 months or older spontaneously developed carcinomas with myoepithelial and basaloid differentiation in salivary glands with an incidence of ∼25%. Tumors developed proximate to submandibular glands and to a lesser extent in the sublingual and parotid glands. Histologically, tumors often had central cavitary lesions filled with necrotic debris that were lined by tumor cells, and had spindle and epithelioid cell differentiation with lesser basaloid to clear cell features. Tumor tissue often had variable evidence of a high mitotic rate, pleomorphism, and invasion into adjacent salivary glands. Neoplastic cells had diffuse immunoreactivity for pancytokeratin (AE1/AE3) and p63. Although CK5/6 immunostaining was seen in the much of the tumor cells, it was often lacking in pleomorphic areas. Tumor cells lacked immunoreactivity for alpha-smooth muscle actin, S100, c-Kit, and glial fibrillary acid protein. In addition, tumors had immunoreactivity for phosphorylated and total epidermal growth factor receptor, suggesting that EGFR signaling may participate in growth regulation of these tumors. These findings indicate that the salivary gland carcinomas occur spontaneously in Justy mice, and that these tumors may offer a valuable model for study of EGFR regulation. In combination, our data suggest that Justy mice warrant further investigation for use as a mouse model for human salivary gland neoplasia.
Collapse
|
25
|
Huang Y, Kesselman D, Kizub D, Guerrero-Preston R, Ratovitski EA. Phospho-ΔNp63α/microRNA feedback regulation in squamous carcinoma cells upon cisplatin exposure. Cell Cycle 2013; 12:684-97. [PMID: 23343772 DOI: 10.4161/cc.23598] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Our previous reports showed that the cisplatin exposure induced the ATM-dependent phosphorylation of ΔNp63a, which is subsequently involved in transcriptional regulation of gene promoters encoding mRNAs and microRNAs in squamous cell carcinoma (SCC) cells upon cisplatin-induced cell death. We showed that phosphorylated (p)-ΔNp63a plays a role in upregulation of pro-apoptotic proteins, while non-p-ΔNp63a is implicated in pro-survival signaling. In contrast to non-p-ΔNp63a, p-ΔNp63a modulated expression of specific microRNAs in SCC cells exposed to cisplatin. These microRNAs were shown to attenuate the expression of several proteins involved in cell death/survival, suggesting the critical role for p-ΔNp63a in regulation of tumor cell resistance to cisplatin. Here, we studied the function of ΔNp63a in transcriptional activation and repression of the specific microRNA promoters whose expression is affected by cisplatin treatment of SCC cells. We quantitatively studied chromatin-associated proteins bound to tumor protein (TP) p63-responsive element, we found that p-ΔNp63a along with certain transcription coactivators (e.g., CARM1, KAT2B, TFAP2A, etc.) necessary to induce gene promoters for microRNAs (630 and 885-3p) or with transcription corepressors (e.g., EZH2, CTBP1, HDACs, etc.) needed to repress promoters for microRNAs (181a-5p, 374a-5p and 519a-3p) in SCC cells exposed to cisplatin.
Collapse
Affiliation(s)
- Yiping Huang
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | | | | | | |
Collapse
|
26
|
Qu Y, Yang Y, Ma D, He L, Xiao W. Expression level of histone deacetylase 2 correlates with occurring of chronic obstructive pulmonary diseases. Mol Biol Rep 2012; 40:3995-4000. [DOI: 10.1007/s11033-012-2477-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 12/18/2012] [Indexed: 02/01/2023]
|
27
|
Global effect of inauhzin on human p53-responsive transcriptome. PLoS One 2012; 7:e52172. [PMID: 23284922 PMCID: PMC3528779 DOI: 10.1371/journal.pone.0052172] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 11/15/2012] [Indexed: 12/19/2022] Open
Abstract
Background Previously, we reported that Inauhzin (INZ) induces p53 activity and suppresses tumor growth by inhibiting Sirt1. However, it remains unknown whether INZ may globally affect p53-dependent gene expression or not. Herein, we have conducted microarray and real-time PCR analyses of gene expression to determine the global effect of INZ on human p53-responsive transcriptome. Methodology/Principal Findings In this study, we conducted microarray analysis followed by PCR validation of general gene expression in HCT116p53+/+ and HCT116p53−/− cells treated with or without INZ. Microarray data showed that 324 genes were up-regulated by ≥2.3-fold and 266 genes were down-regulated by ≥2-fold in response to INZ treatment in a p53-dependent manner. GO analysis for these genes further revealed that INZ affects several biological processes, including apoptosis (GO:0006915), cell cycle (GO:0007049), immune system process (GO:0002376), and cell adhesion (GO:0007155), which are in line with p53 functions in cells. Also, pathway and STRING analyses of these genes indicated that the p53-signaling pathway is the most significant pathway responsive to INZ treatment as predicted, since a number of these p53 target genes have been previously reported and some of them were validated by RT-qPCR. Finally, among the 9 tested and highly expressed genes, ACBD4, APOBEC3C, and FLJ14327 could be novel p53 target genes, for they were up-regulated by INZ in HCT116p53+/+ cells, but not in HCT116p53−/− cells. Conclusions/Significance From our whole genome microarray analysis followed by validation with RT-qPCR, we found that INZ can indeed induce the expression of p53 target genes at a larger scale or globally. Our findings not only verify that INZ indeed activates the p53 signaling pathway, but also provide useful information for identifying novel INZ and/or p53 targets. The global effect of INZ on human p53-responsive transcriptome could also be instrumental to the future design of INZ clinical trials.
Collapse
|
28
|
Liu D, Zhou P, Zhang L, Zheng Y, He F. HPV16 activates the promoter of Oct4 gene by sequestering HDAC1 from repressor complex to target it to proteasomal degradation. Med Hypotheses 2012; 79:531-4. [PMID: 22867868 DOI: 10.1016/j.mehy.2012.07.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Revised: 05/25/2012] [Accepted: 07/10/2012] [Indexed: 10/28/2022]
Abstract
Human papillomavirus 16 (HPV16) is the key factor to initiate cervical carcinogenesis and development. Octamer-binding transcription factor 4 (Oct4) is an important transcriptional factor which is up-regulated in some cancer cells. Our study showed that the expression of Oct4 might be activated by HPV16 infection. Both the levels of histone deacetylase 1 (HDAC1) and DNA methyltransferase 3A (DNMT3A) were negatively correlated with the level of Oct4 in cervical cancer cells. Moreover, HDAC1 and DNMT3A proteins were in the same complex, the level of which was higher in the presence of HPV16. The treatment with HDAC1 inhibitor reduced the level of this complex, followed by the upregulation of Oct4 expression. Based on these findings and previous reports, we hypothesize that a repressor complex containing methyl CpG-binding domain protein 2 (MBD2), DNMT3A and HDAC1 binds to the hyper-methylated regulatory regions of Oct4 gene to facilitate forming a close chromatin which results in the suppression of Oct4 transcription in cervical cells. The oncoproteins of HPV16 synergistically sequester HDAC1 protein from repressor complex, and target it to ubiquitin mediated proteasome degradation. The repressor complex is thus destroyed and the close chromatin is relaxed, which eventually lead to the upregulation of Oct4 expression.
Collapse
Affiliation(s)
- Dongbo Liu
- Department of Biochemistry and Molecular Biology, Third Military Medical University, 30 Gaotanyan Street, Shapingba, Chongqing 400038, China
| | | | | | | | | |
Collapse
|
29
|
Huang JG, Gao XJ, Li QZ, Lu LM, Liu R, Luo CC, Wang JL, Bin Q, Jin X. Proteomic analysis of the nuclear phosphorylated proteins in dairy cow mammary epithelial cells treated with estrogen. In Vitro Cell Dev Biol Anim 2012; 48:449-57. [PMID: 22806971 DOI: 10.1007/s11626-012-9531-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 06/21/2012] [Indexed: 01/27/2023]
Abstract
Estrogen regulates a variety of physiological processes, including mammary gland growth, morphogenesis of the mammary gland, proliferation and differentiation, and elevating the expression of milk proteins. Many nuclear phosphorylated proteins such as pStat5 and mTOR regulate milk protein synthesis. But the detail of milk protein synthesis controlled at the transcript level and posttranslational level is not well-known. To contribute to the understanding of the molecular mechanism underlying estrogen action on the dairy cow mammary epithelial cells (DCMECs), nuclear phosphorylated proteins regulated by estrogen in DCMECs were identified. Two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization/time of flight mass spectrometry were used to identify the changes of nuclear phosphorylated proteins in DCMECs treated with estrogen. Seven proteins were identified differentially up-expressed in DCMECs after 24-h estrogen exposure: including glycyl-tRNA synthetase, previously reported in milk protein synthesis of DCMECs, belonging to the class-II aminoacyl-tRNA synthetase family; proteins involved in other cellular functions, such as translation initiation factors, GTP-binding nuclear proteins, heat-shock proteins, and proteins belonging to ubiquitin-proteasome system. This screening reveals that estrogen influences the levels of nuclear phosphorylated proteins of DCMECs which opens new avenue for the study of the molecular mechanism linking to milk synthesis.
Collapse
Affiliation(s)
- Jian-Guo Huang
- The Key Laboratory of Dairy Science of Education Ministry, Northeast Agricultural University, Xiangfang District, Harbin, Heilongjiang Province, China
| | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Botchkarev VA, Gdula MR, Mardaryev AN, Sharov AA, Fessing MY. Epigenetic regulation of gene expression in keratinocytes. J Invest Dermatol 2012; 132:2505-21. [PMID: 22763788 PMCID: PMC3650472 DOI: 10.1038/jid.2012.182] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Nucleus is a complex and highly compartmentalized organelle, which organization undergoes major changes during cell differentiation allowing cells to become specialized and fulfill their functions.During terminal differentiation of the epidermal keratinocytes, nucleus undergoes programmed transformation from active status, associated with execution of the genetic programs of cornification and epidermal barrier formation, to fully inactive condition and becomes a part of the keratinized cells of the cornified layer. Tremendous progress achieved within the last two decades in understanding the biology of the nucleus and epigenetic mechanisms controlling gene expression allowed defining several levels in the regulation of cell differentiation-associated gene expression programs, including an accessibility of the gene regulatory regions to DNA-protein interactions, covalent DNA and histone modifications and ATP-dependent chromatin remodeling, as well as higher-order chromatin remodeling and nuclear compartmentalization of the genes and transcription machinery. Here, we integrate our current knowledge of the mechanisms controlling gene expression during terminal keratinocyte differentiation with distinct levels of chromatin organization and remodeling. We also propose the directions to further explore the role of epigenetic mechanisms and their interactions with other regulatory systems in the control of keratinocyte differentiation in normal and diseased skin.
Collapse
|
31
|
Differentiated embryo-chondrocyte expressed gene 1 regulates p53-dependent cell survival versus cell death through macrophage inhibitory cytokine-1. Proc Natl Acad Sci U S A 2012; 109:11300-5. [PMID: 22723347 DOI: 10.1073/pnas.1203185109] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Activation of p53 upon DNA damage induces an array of target genes, leading to cell cycle arrest and/or apoptosis. However, the mechanism by which the cell fate is controlled by p53 remains to be clarified. Previously, we showed that DEC1, a basic helix-loop-helix transcription factor and a target of p53, is capable of inducing cell cycle arrest and mediating DNA damage-induced premature senescence. Here, we found that ectopic expression of DEC1 inhibits, whereas knockdown of DEC1 enhances, DNA damage-induced cell death. Surprisingly, we showed that the anti-cell-death activity of DEC1 is p53 dependent, but DEC1 does not directly modulate p53 expression. Instead, we showed that DEC1 inhibits the ability of p53 to induce macrophage inhibitory cytokine-1 (MIC-1), but not other prosurvival/proapoptotic targets, including p21 and Puma. Importantly, we showed that upon binding to their respective response elements on the MIC-1 promoter, DEC1 and p53 physically interact on the MIC-1 promoter via the basic helix-loop-helix domain in DEC1 and the tetramerization domain in p53, which likely weakens the DNA-binding activity of p53 to the MIC-1 promoter. Finally, we found that depletion of MIC-1 abrogates the ability of DEC1 to attenuate DNA damage-induced cell death. Together, we hypothesize that DEC1 controls the response of p53-dependent cell survival vs. cell death to a stress signal through MIC-1.
Collapse
|