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Nguyen MC, Rostamian H, Raman A, Wei P, Becht DC, Erbse AH, Klein BJ, Gilbert TM, Zhang G, Blanco MA, Strahl BD, Taverna SD, Kutateladze TG. Molecular insight into interactions between the Taf14, Yng1 and Sas3 subunits of the NuA3 complex. Nat Commun 2024; 15:5335. [PMID: 38914563 PMCID: PMC11196586 DOI: 10.1038/s41467-024-49730-y] [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: 02/11/2024] [Accepted: 06/17/2024] [Indexed: 06/26/2024] Open
Abstract
The NuA3 complex is a major regulator of gene transcription and the cell cycle in yeast. Five core subunits are required for complex assembly and function, but it remains unclear how these subunits interact to form the complex. Here, we report that the Taf14 subunit of the NuA3 complex binds to two other subunits of the complex, Yng1 and Sas3, and describe the molecular mechanism by which the extra-terminal domain of Taf14 recognizes the conserved motif present in Yng1 and Sas3. Structural, biochemical, and mutational analyses show that two motifs are sandwiched between the two extra-terminal domains of Taf14. The head-to-toe dimeric complex enhances the DNA binding activity of Taf14, and the formation of the hetero-dimer involving the motifs of Yng1 and Sas3 is driven by sequence complementarity. In vivo assays in yeast demonstrate that the interactions of Taf14 with both Sas3 and Yng1 are required for proper function of the NuA3 complex in gene transcription and DNA repair. Our findings suggest a potential basis for the assembly of three core subunits of the NuA3 complex, Taf14, Yng1 and Sas3.
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Affiliation(s)
- Minh Chau Nguyen
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Hosein Rostamian
- Department of Biochemistry & Biophysics, The University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
- Curriculum in Genetics and Molecular Biology, The University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Ana Raman
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Pengcheng Wei
- Department of Biomedical Research, National Jewish Health, Denver, CO, 80206, USA
- Guangxi Key Laboratory of Special Biomedicine, School of Medicine, Guangxi University, Nanning, 530004, China
| | - Dustin C Becht
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Annette H Erbse
- Department of Biochemistry, University of Colorado, Boulder, CO, 80303, USA
| | - Brianna J Klein
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Tonya M Gilbert
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Gongyi Zhang
- Department of Biomedical Research, National Jewish Health, Denver, CO, 80206, USA
| | - M Andres Blanco
- Department of Biomedical Sciences, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA, 19104, USA
| | - Brian D Strahl
- Department of Biochemistry & Biophysics, The University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Sean D Taverna
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, 72202, USA
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
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2
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Ferreras-Gutiérrez M, Chaves-Arquero B, González-Magaña A, Merino N, Amusategui-Mateu I, Huecas S, Medrano FJ, Blanco FJ. Structural analysis of ING3 protein and histone H3 binding. Int J Biol Macromol 2023; 242:124724. [PMID: 37148949 DOI: 10.1016/j.ijbiomac.2023.124724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/21/2023] [Accepted: 04/30/2023] [Indexed: 05/08/2023]
Abstract
Proteins belonging to the ING family regulate the transcriptional state of chromatin by recruiting remodeling complexes to sites with histone H3 trimethylated at Lysine 4 (H3K4me3). This modification is recognized by the Plant HomeoDomain (PHD) present at the C-terminal region of the five ING proteins. ING3 facilitates acetylation of histones H2A and H4 by the NuA4-Tip60 MYST histone acetyl transferase complex, and it has been proposed to be an oncoprotein. The crystal structure of the N-terminal domain of ING3 shows that it forms homodimers with an antiparallel coiled-coil fold. The crystal structure of the PHD is similar to those of its four homologs. These structures explain the possible deleterious effects of ING3 mutations detected in tumors. The PHD binds histone H3K4me3 with low-micromolar, and binds the non-methylated histone with a 54-fold reduced affinity. Our structure explains the impact of site directed mutagenesis experiments on histone recognition. These structural features could not be confirmed for the full-length protein as solubility was insufficient for structural studies, but the structure of its folded domains suggest a conserved structural organization for the ING proteins as homodimers and bivalent readers of the histone H3K4me3 mark.
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Affiliation(s)
| | - Belén Chaves-Arquero
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid 28040, Spain
| | - Amaia González-Magaña
- Instituto Biofisika and Departamento de Bioquímica y Biología Molecular (CSIC, UPV/EHU), University of the Basque Country, 48940 Leioa, Spain
| | - Nekane Merino
- CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Spain
| | | | - Sonia Huecas
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid 28040, Spain
| | - Francisco J Medrano
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid 28040, Spain
| | - Francisco J Blanco
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid 28040, Spain.
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3
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Jaudal M, Mayo‐Smith M, Poulet A, Whibley A, Peng Y, Zhang L, Thomson G, Trimborn L, Jacob Y, van Wolfswinkel JC, Goldstone DC, Wen J, Mysore KS, Putterill J. MtING2 encodes an ING domain PHD finger protein which affects Medicago growth, flowering, global patterns of H3K4me3, and gene expression. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:1029-1050. [PMID: 36178149 PMCID: PMC9828230 DOI: 10.1111/tpj.15994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 09/04/2022] [Accepted: 09/24/2022] [Indexed: 06/16/2023]
Abstract
Flowering of the reference legume Medicago truncatula is promoted by winter cold (vernalization) followed by long-day photoperiods (VLD) similar to winter annual Arabidopsis. However, Medicago lacks FLC and CO, key regulators of Arabidopsis VLD flowering. Most plants have two INHIBITOR OF GROWTH (ING) genes (ING1 and ING2), encoding proteins with an ING domain with two anti-parallel alpha-helices and a plant homeodomain (PHD) finger, but their genetic role has not been previously described. In Medicago, Mting1 gene-edited mutants developed and flowered normally, but an Mting2-1 Tnt1 insertion mutant and gene-edited Mting2 mutants had developmental abnormalities including delayed flowering particularly in VLD, compact architecture, abnormal leaves with extra leaflets but no trichomes, and smaller seeds and barrels. Mting2 mutants had reduced expression of activators of flowering, including the FT-like gene MtFTa1, and increased expression of the candidate repressor MtTFL1c, consistent with the delayed flowering of the mutant. MtING2 overexpression complemented Mting2-1, but did not accelerate flowering in wild type. The MtING2 PHD finger bound H3K4me2/3 peptides weakly in vitro, but analysis of gene-edited mutants indicated that it was dispensable to MtING2 function in wild-type plants. RNA sequencing experiments indicated that >7000 genes are mis-expressed in the Mting2-1 mutant, consistent with its strong mutant phenotypes. Interestingly, ChIP-seq analysis identified >5000 novel H3K4me3 locations in the genome of Mting2-1 mutants compared to wild type R108. Overall, our mutant study has uncovered an important physiological role of a plant ING2 gene in development, flowering, and gene expression, which likely involves an epigenetic mechanism.
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Affiliation(s)
- Mauren Jaudal
- School of Biological SciencesUniversity of AucklandPrivate Bag 92019Auckland1142New Zealand
| | - Matthew Mayo‐Smith
- School of Biological SciencesUniversity of AucklandPrivate Bag 92019Auckland1142New Zealand
| | - Axel Poulet
- Yale UniversityDepartment of MolecularCellular and Developmental BiologyFaculty of Arts and Sciences260 Whitney AvenueNew HavenCT06511USA
| | - Annabel Whibley
- School of Biological SciencesUniversity of AucklandPrivate Bag 92019Auckland1142New Zealand
| | - Yongyan Peng
- School of Biological SciencesUniversity of AucklandPrivate Bag 92019Auckland1142New Zealand
| | - Lulu Zhang
- School of Biological SciencesUniversity of AucklandPrivate Bag 92019Auckland1142New Zealand
| | - Geoffrey Thomson
- School of Biological SciencesUniversity of AucklandPrivate Bag 92019Auckland1142New Zealand
- Yale UniversityDepartment of MolecularCellular and Developmental BiologyFaculty of Arts and Sciences260 Whitney AvenueNew HavenCT06511USA
| | - Laura Trimborn
- School of Biological SciencesUniversity of AucklandPrivate Bag 92019Auckland1142New Zealand
- Institute for Plant Sciences, BiocenterUniversity of CologneZülpicher Str. 47b50674CologneGermany
| | - Yannick Jacob
- Yale UniversityDepartment of MolecularCellular and Developmental BiologyFaculty of Arts and Sciences260 Whitney AvenueNew HavenCT06511USA
| | - Josien C. van Wolfswinkel
- Yale UniversityDepartment of MolecularCellular and Developmental BiologyFaculty of Arts and Sciences260 Whitney AvenueNew HavenCT06511USA
| | - David C. Goldstone
- School of Biological SciencesUniversity of AucklandPrivate Bag 92019Auckland1142New Zealand
| | - Jiangqi Wen
- Institute for Agricultural BiosciencesOklahoma State University3210 Sam Noble ParkwayArdmoreOK73401USA
| | - Kirankumar S. Mysore
- Institute for Agricultural BiosciencesOklahoma State University3210 Sam Noble ParkwayArdmoreOK73401USA
| | - Joanna Putterill
- School of Biological SciencesUniversity of AucklandPrivate Bag 92019Auckland1142New Zealand
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4
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Shatnawi A, Abu Rabe DI, Frigo DE. Roles of the tumor suppressor inhibitor of growth family member 4 (ING4) in cancer. Adv Cancer Res 2021; 152:225-262. [PMID: 34353439 DOI: 10.1016/bs.acr.2021.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Inhibitor of growth family member 4 (ING4) is best known as a tumor suppressor that is frequently downregulated, deleted, or mutated in many cancers. ING4 regulates a broad array of tumor-related processes including proliferation, apoptosis, migration, autophagy, invasion, angiogenesis, DNA repair and chromatin remodeling. ING4 alters local chromatin structure by functioning as an epigenetic reader of H3K4 trimethylation histone marks (H3K4Me3) and regulating gene transcription through directing histone acetyltransferase (HAT) and histone deacetylase (HDAC) protein complexes. ING4 may serve as a useful prognostic biomarker for many cancer types and help guide treatment decisions. This review provides an overview of ING4's central functions in gene expression and summarizes current literature on the role of ING4 in cancer and its possible use in therapy.
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Affiliation(s)
- Aymen Shatnawi
- Department of Pharmaceutical and Administrative Sciences, University of Charleston School of Pharmacy, Charleston, WV, United States.
| | - Dina I Abu Rabe
- Integrated Bioscience Program, North Carolina Central University, Durham, NC, United States
| | - Daniel E Frigo
- Department of Cancer Systems Imaging, University of Texas MD Anderson Cancer Center, Houston, TX, United States; Department of Genitourinary Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
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5
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Jacquet K, Binda O. ING Proteins: Tumour Suppressors or Oncoproteins. Cancers (Basel) 2021; 13:cancers13092110. [PMID: 33925563 PMCID: PMC8123807 DOI: 10.3390/cancers13092110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 03/25/2021] [Indexed: 02/06/2023] Open
Abstract
The INhibitor of Growth family was defined in the mid-1990s by the identification of a tumour suppressor, ING1, and subsequent expansion of the family based essentially on sequence similarities. However, later work and more recent investigations demonstrate that at least a few ING proteins are actually required for normal proliferation of eukaryotic cells, from yeast to human. ING proteins are also part of a larger family of chromatin-associated factors marked by a plant homeodomain (PHD), which mediates interactions with methylated lysine residues. Herein, we discuss the role of ING proteins and their various roles in chromatin signalling in the context of cancer development and progression.
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Affiliation(s)
- Karine Jacquet
- Institut NeuroMyoGène (INMG), Université Claude Bernard Lyon 1, Université de Lyon, CNRS UMR 5310, INSERM U 1217, 69008 Lyon, France;
| | - Olivier Binda
- Institut NeuroMyoGène (INMG), Université Claude Bernard Lyon 1, Université de Lyon, CNRS UMR 5310, INSERM U 1217, 69008 Lyon, France;
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Correspondence:
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6
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Macromolecular Crowding Increases the Affinity of the PHD of ING4 for the Histone H3K4me3 Mark. Biomolecules 2020; 10:biom10020234. [PMID: 32033221 PMCID: PMC7072245 DOI: 10.3390/biom10020234] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/27/2020] [Accepted: 01/30/2020] [Indexed: 12/29/2022] Open
Abstract
The five members of the family of tumor suppressors ING contain a Plant Homeodomain (PHD) that specifically recognizes histone H3 trimethylated at lysine 4 (H3K4me3) with an affinity in the low micromolar range. Here, we use NMR to show that in the presence of 15% Ficoll 70, an inert macromolecular crowding agent, the mode of binding does not change but the affinity increases by one order of magnitude. The affinity increases also for unmethylated histone H3 tail, but the difference with H3K4me3 is larger in the presence of Ficoll. These results indicate that in the cellular milieu, the affinity of the ING proteins for their chromatin target is larger than previously thought.
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7
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Archambeau J, Blondel A, Pedeux R. Focus-ING on DNA Integrity: Implication of ING Proteins in Cell Cycle Regulation and DNA Repair Modulation. Cancers (Basel) 2019; 12:cancers12010058. [PMID: 31878273 PMCID: PMC7017203 DOI: 10.3390/cancers12010058] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/20/2019] [Accepted: 12/21/2019] [Indexed: 12/16/2022] Open
Abstract
The ING family of tumor suppressor genes is composed of five members (ING1-5) involved in cell cycle regulation, DNA damage response, apoptosis and senescence. All ING proteins belong to various HAT or HDAC complexes and participate in chromatin remodeling that is essential for genomic stability and signaling pathways. The gatekeeper functions of the INGs are well described by their role in the negative regulation of the cell cycle, notably by modulating the stability of p53 or the p300 HAT activity. However, the caretaker functions are described only for ING1, ING2 and ING3. This is due to their involvement in DNA repair such as ING1 that participates not only in NERs after UV-induced damage, but also in DSB repair in which ING2 and ING3 are required for accumulation of ATM, 53BP1 and BRCA1 near the lesion and for the subsequent repair. This review summarizes evidence of the critical roles of ING proteins in cell cycle regulation and DNA repair to maintain genomic stability.
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8
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Ormaza G, Rodríguez JA, Ibáñez de Opakua A, Merino N, Villate M, Gorroño I, Rábano M, Palmero I, Vilaseca M, Kypta R, Vivanco MDM, Rojas AL, Blanco FJ. The Tumor Suppressor ING5 Is a Dimeric, Bivalent Recognition Molecule of the Histone H3K4me3 Mark. J Mol Biol 2019; 431:2298-2319. [PMID: 31026448 DOI: 10.1016/j.jmb.2019.04.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 04/10/2019] [Accepted: 04/10/2019] [Indexed: 10/26/2022]
Abstract
The INhibitor of Growth (ING) family of tumor suppressors regulates the transcriptional state of chromatin by recruiting remodeling complexes to sites with histone H3 trimethylated at lysine 4 (H3K4me3). This modification is recognized by the plant homeodomain (PHD) present at the C-terminus of the five ING proteins. ING5 facilitates histone H3 acetylation by the HBO1 complex, and also H4 acetylation by the MOZ/MORF complex. We show that ING5 forms homodimers through its N-terminal domain, which folds independently into an elongated coiled-coil structure. The central region of ING5, which contains the nuclear localization sequence, is flexible and disordered, but it binds dsDNA with micromolar affinity. NMR analysis of the full-length protein reveals that the two PHD fingers of the dimer are chemically equivalent and independent of the rest of the molecule, and they bind H3K4me3 in the same way as the isolated PHD. We have observed that ING5 can form heterodimers with the highly homologous ING4, and that two of three primary tumor-associated mutants in the N-terminal domain strongly destabilize the coiled-coil structure. They also affect cell proliferation and cell cycle phase distribution, suggesting a driver role in cancer progression.
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Affiliation(s)
- Georgina Ormaza
- CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Spain
| | | | | | - Nekane Merino
- CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Spain
| | - Maider Villate
- CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Spain
| | - Irantzu Gorroño
- CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Spain
| | - Miriam Rábano
- CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Spain
| | - Ignacio Palmero
- Instituto de Investigaciones Biomédicas "Alberto Sols", CSIC-UAM, 28029 Madrid, Spain
| | - Marta Vilaseca
- Institute for Research in Biomedicine, 08028 Barcelona, Spain
| | - Robert Kypta
- CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Spain; Department of Surgery and Cancer, Imperial College London, London, W12 0NN, UK
| | | | - Adriana L Rojas
- CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Spain
| | - Francisco J Blanco
- CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Spain; IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain.
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9
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The essential role of tumor suppressor gene ING4 in various human cancers and non-neoplastic disorders. Biosci Rep 2019; 39:BSR20180773. [PMID: 30643005 PMCID: PMC6356015 DOI: 10.1042/bsr20180773] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 12/19/2018] [Accepted: 01/13/2019] [Indexed: 12/21/2022] Open
Abstract
Inhibitor of growth 4 (ING4), a member of the ING family discovered in 2003, has been shown to act as a tumor suppressor and is frequently down-regulated in various human cancers. Numerous published in vivo and in vitro studies have shown that ING4 is responsible for important cancer hallmarks such as pathologic cell cycle arrest, apoptosis, autophagy, contact inhibition, and hypoxic adaptation, and also affects tumor angiogenesis, invasion, and metastasis. These characteristics are typically associated with regulation through chromatin acetylation by binding histone H3 trimethylated at lysine 4 (H3K4me3) and through transcriptional activity of transcription factor P53 and NF-κB. In addition, emerging evidence has indicated that abnormalities in ING4 expression and function play key roles in non-neoplastic disorders. Here, we provide an overview of ING4-modulated chromosome remodeling and transcriptional function, as well as the functional consequences of different genetic variants. We also present the current understanding concerning the role of ING4 in the development of neoplastic and non-neoplastic diseases. These studies offer inspiration for pursuing novel therapeutics for various cancers.
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10
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You Q, Li H, Liu Y, Xu Y, Miao S, Yao G, Xue Y, Geng J, Jin X, Meng H. MicroRNA-650 targets inhibitor of growth 4 to promote colorectal cancer progression via mitogen activated protein kinase signaling. Oncol Lett 2018; 16:2326-2334. [PMID: 30008936 PMCID: PMC6036455 DOI: 10.3892/ol.2018.8910] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 11/29/2017] [Indexed: 12/11/2022] Open
Abstract
Colorectal cancer (CRC) is the third most common malignant disease globally and causes numerous cancer-associated mortalities; however, the underlying molecular mechanisms remain unresolved. MicroRNAs (miRs) are endogenous noncoding RNAs that regulate post-transcriptional gene silencing by annealing to partially complementary sequences in the 3′-untranslated regions of target mRNAs. In the present study, expression of the tumor suppressor gene inhibitor of growth protein 4 (ING4) in cell lines was investigated using reverse transcription-quantitative polymerase chain reaction and western blotting. miR-650 overexpression promoted CRC cell proliferation and migration by targeting ING4 when the cells were transfected with the miR-650 mimics. Additionally, overexpression of miR-650 increased the epithelial-mesenchymal transition and activation of the Ras homolog gene family member A/Ras-related C3 botulinum toxin GTPase. Extracellular signal-regulated kinases and p38 mitogen-activated protein kinase signaling were markedly activated when miR-650 was increased in CRC cells. Combined, the results indicate the mechanism underlying the miR-650 promotion of CRC progression, and provide promising potential biomarkers for the prognosis and treatment of CRC.
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Affiliation(s)
- Qi You
- Department of Pathology, Basic Research College, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China.,Department of Gastroenterology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang 150081, P.R. China
| | - Huining Li
- Department of Pathology, Basic Research College, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China.,Department of Pathology, The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang 150081, P.R. China
| | - Yao Liu
- Department of Otolaryngology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang 150081, P.R. China
| | - Yangyang Xu
- Department of Urology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang 150081, P.R. China
| | - Susheng Miao
- Department of Otolaryngology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang 150081, P.R. China
| | - Guodong Yao
- Department of Pathology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang 150081, P.R. China
| | - Yingwei Xue
- Department of Gastroenterology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang 150081, P.R. China
| | - Jingshu Geng
- Department of Pathology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang 150081, P.R. China
| | - Xiaoming Jin
- Department of Pathology, Basic Research College, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Hongxue Meng
- Department of Pathology, Basic Research College, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China.,Department of Pathology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang 150081, P.R. China
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11
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Shao B, Liu E. Expression of ING4 is negatively correlated with cellular proliferation and microvessel density in human glioma. Oncol Lett 2017; 14:3663-3668. [PMID: 28927128 DOI: 10.3892/ol.2017.6618] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 12/06/2016] [Indexed: 12/11/2022] Open
Abstract
The present study aimed to investigate the associations of tumor inhibitor of growth 4 (ING4) with tumor cell proliferation and microvessel density (MVD) in human glioma. Semi-quantitative reverse transcription polymerase chain reaction, western blotting and immunohistochemistry (IHC) were used to detect the level of ING4 expression in normal brain tissues and glioma tissues of different pathological grades. The cell proliferation index (PI) and the level of MVD were detected using IHC, facilitating the analysis of the correlation between ING4 and cellular proliferation and MVD in human glioma. The expression levels of ING4 mRNA and protein were significantly lower in the glioma tissues compared with the normal brain tissues (P<0.05) and decreased as the pathological grade of the glioma tissue increased (P<0.05). PI was reduced in the ING4 protein positively expressed (ING4+) glioma tissues compared with the ING4 protein negatively expressed (ING4-) glioma tissues (P≤0.01). The level of MVD was significantly higher in the glioma tissues than that in the normal brain tissues (P≤0.01), while the level of MVD decreased in the ING4+ glioma tissue compared with the ING4- glioma tissue (P≤0.001). A Spearman's rank correlation test revealed that ING4 protein expression was negatively correlated with PI and MVD. ING4 might inhibit tumor proliferation and angiogenesis in human glioma. The expression of ING4 was also associated with the pathological grading of the glioma tissue and negatively correlated with cellular proliferation and MVD in human glioma.
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Affiliation(s)
- Bin Shao
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Enzhong Liu
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
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12
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Sica V, Bravo-San Pedro JM, Chen G, Mariño G, Lachkar S, Izzo V, Maiuri MC, Niso-Santano M, Kroemer G. Inhibitor of growth protein 4 interacts with Beclin 1 and represses autophagy. Oncotarget 2017; 8:89527-89538. [PMID: 29163768 PMCID: PMC5685689 DOI: 10.18632/oncotarget.19033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 04/17/2017] [Indexed: 12/14/2022] Open
Abstract
Beclin 1 (BECN1) is a multifunctional protein that activates the pro-autophagic class III phosphatidylinositol 3-kinase (PIK3C3, best known as VPS34), yet also interacts with multiple negative regulators. Here we report that BECN1 interacts with inhibitor of growth family member 4 (ING4), a tumor suppressor protein that is best known for its capacity to interact with the tumor suppressor protein p53 (TP53) and the acetyltransferase E1A binding protein p300 (EP300). Removal of TP53 or EP300 did not affect the BECN1/ING4 interaction, which however was lost upon culture of cells in autophagy-inducing, nutrient free conditions. Depletion of ING4 stimulated the enzymatic activity of PIK3C3, as visualized by means of a red fluorescent protein-tagged short peptide (FYVE) that specifically binds to phosphatidylinositol-3-phosphate (PI3P)-containing subcellular vesicles and enhanced autophagy, as indicated by an enhanced lipidation of microtubule-associated proteins 1A/1B light chain 3 beta (LC3B) and the redistribution of a green-fluorescent protein (GFP)-LC3B fusion protein to cytoplasmic puncta. The generation of GFP-LC3B puncta stimulated by ING4 depletion was reduced by simultaneous depletion, or pharmacological inhibition, of PIK3C3/VPS34. In conclusion, ING4 acts as a negative regulator of the lipid kinase activity of the BECN1 complex, and starvation-induced autophagy is accompanied by the dissociation of the ING4/BECN1 interaction.
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Affiliation(s)
- Valentina Sica
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Equipe 11 labellisée Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,Institut National de la Santé et de la Recherche Médicale, Paris, France.,Université Pierre et Marie Curie, Paris, France.,Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France
| | - José Manuel Bravo-San Pedro
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Equipe 11 labellisée Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,Institut National de la Santé et de la Recherche Médicale, Paris, France.,Université Pierre et Marie Curie, Paris, France.,Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France
| | - Guo Chen
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Equipe 11 labellisée Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,Institut National de la Santé et de la Recherche Médicale, Paris, France.,Université Pierre et Marie Curie, Paris, France.,Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France
| | - Guillermo Mariño
- Institut National de la Santé et de la Recherche Médicale, Paris, France.,Departamento de Biología Fundamental, Instituto de Investigación Sanitaria del Principado de Asturias, Universidad de Oviedo, Spain
| | - Sylvie Lachkar
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Equipe 11 labellisée Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,Institut National de la Santé et de la Recherche Médicale, Paris, France.,Université Pierre et Marie Curie, Paris, France.,Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France
| | - Valentina Izzo
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Equipe 11 labellisée Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,Institut National de la Santé et de la Recherche Médicale, Paris, France.,Université Pierre et Marie Curie, Paris, France.,Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France
| | - Maria Chiara Maiuri
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Equipe 11 labellisée Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,Institut National de la Santé et de la Recherche Médicale, Paris, France.,Université Pierre et Marie Curie, Paris, France.,Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France
| | - Mireia Niso-Santano
- Institut National de la Santé et de la Recherche Médicale, Paris, France.,Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas, Cáceres, Spain.,Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, C.P, Cáceres, Cáceres, Spain
| | - Guido Kroemer
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Equipe 11 labellisée Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,Institut National de la Santé et de la Recherche Médicale, Paris, France.,Université Pierre et Marie Curie, Paris, France.,Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France.,Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, France.,Department of Women's and Children's Health, Karolinska University Hospital, Stockholm, Sweden
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13
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Affiliation(s)
- Gesche Tallen
- Department of Paediatrics, Faculty of Medicine, University of Calgary, Canada.,Department of Paediatric Haematology and Oncology, University Medical Centre Hamburg-Eppendorf (UKE), Germany
| | - Karl Riabowol
- Departments of Biochemistry & Molecular Biology and Oncology, Cumming School of Medicine, University of Calgary, Canada
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14
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Berger PL, Winn ME, Miranti CK. Miz1, a Novel Target of ING4, Can Drive Prostate Luminal Epithelial Cell Differentiation. Prostate 2017; 77:49-59. [PMID: 27527891 PMCID: PMC6739073 DOI: 10.1002/pros.23249] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 08/03/2016] [Indexed: 01/28/2023]
Abstract
BACKGROUND How prostate epithelial cells differentiate and how dysregulation of this process contributes to prostate tumorigenesis remain unclear. We recently identified a Myc target and chromatin reader protein, ING4, as a necessary component of human prostate luminal epithelial cell differentiation, which is often lost in primary prostate tumors. Furthermore, loss of ING4 in the context of oncogenic mutations is required for prostate tumorigenesis. Identifying the gene targets of ING4 can provide insight into how its loss disrupts differentiation and leads to prostate cancer. METHODS Using a combination of RNA-Seq, a best candidate approach, and chromatin immunoprecipitation (ChIP), we identified Miz1 as a new ING4 target. ING4 or Miz1 overexpression, shRNA knock-down, and a Myc-binding mutant were used in a human in vitro differentiation assay to assess the role of Miz1 in luminal cell differentiation. RESULTS ING4 directly binds the Miz1 promoter and is required to induce Miz1 mRNA and protein expression during luminal cell differentiation. Miz1 mRNA was not induced in shING4 expressing cells or tumorigenic cells in which ING4 is not expressed. Miz1 dependency on ING4 was unique to differentiating luminal cells; Miz1 mRNA expression was not induced in basal cells. Although Miz1 is a direct target of ING4, and its overexpression can drive luminal cell differentiation, Miz1 was not required for differentiation. CONCLUSIONS Miz1 is a newly identified ING4-induced target gene which can drive prostate luminal epithelial cell differentiation although it is not absolutely required. Prostate 77:49-59, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Penny L. Berger
- laboratory of Integrin Signaling, Van Andel Research Institute, Grand Rapids, Michigan
| | - Mary E. Winn
- Bioinformatics and Biostatistics Core, Van Andel Research Institute, Grand Rapids, Michigan
| | - Cindy K. Miranti
- laboratory of Integrin Signaling, Van Andel Research Institute, Grand Rapids, Michigan
- Correspondence to: Cindy K. Miranti, Laboratory of Integrin Signaling, Van Andel Research Institute, 333 Bostwick Ave NE, Grand Rapids, MI 49503.
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15
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Ormaza G, Medagli B, Ibáñez de Opakua A, Rodríguez JA, Merino N, Villate M, Onesti S, Blanco FJ. The tumor suppressor inhibitor of growth 4 binds double-stranded DNA through its disordered central region. FEBS Lett 2016; 591:425-432. [DOI: 10.1002/1873-3468.12514] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 11/28/2016] [Accepted: 11/30/2016] [Indexed: 12/31/2022]
Affiliation(s)
| | | | | | | | | | | | | | - Francisco J. Blanco
- CIC bioGUNE; Derio Spain
- IKERBASQUE; Basque Foundation for Science; Bilbao Spain
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16
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Boyko A, Riabowol K. A minimal ING1b fragment that improves the efficacy of HDAC-based cancer cell killing. Cell Death Dis 2015; 6:e2027. [PMID: 26720336 PMCID: PMC4720907 DOI: 10.1038/cddis.2015.376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- A Boyko
- Departments of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
| | - K Riabowol
- Departments of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
- Department of Oncology, University of Calgary, Calgary, Alberta, Canada
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17
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Defining the minimal peptide sequence of the ING1b tumour suppressor capable of efficiently inducing apoptosis. Cell Death Discov 2015; 1:15048. [PMID: 27551477 PMCID: PMC4979497 DOI: 10.1038/cddiscovery.2015.48] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 09/08/2015] [Indexed: 02/07/2023] Open
Abstract
The ING1b protein is a type-II tumour suppressor and stoichiometric member of the Sin3 histone deacetylase (HDAC) protein complex in which it acts to target HDAC activity to regulate chromatin structure. Altering ING1 levels by ectopic expression of ING1b in cancer cells promotes apoptosis, whereas altering levels by knockout in normal murine fibroblasts alters sensitivity to doxorubicin-induced apoptosis. We have identified a minimal region of ING1b capable of inducing levels of apoptosis in targeted cells as effectively as full-length ING1b, using transient overexpression of ING1b fragments followed by the Annexin V assay. We observed high levels of apoptosis in 14 of 14 cancer cell lines tested. Infecting triple-negative tumorigenic MDA-MB-468 breast cancer, U2OS or Saos-2 cells at multiplicities of infection (MOIs) ranging from 10 to 20 rapidly triggered apoptosis in ~80% of infected cells within 48 h. This was not due to the effects of virus, as infection at the same MOI with a control adenovirus expressing GFP was not effective in inducing apoptosis. When used at low MOIs, the ING1b fragment showed a cell-killing efficacy that was higher than native, full-length ING1b. Using a doxycycline-regulated inducible p53 expression system demonstrated that apoptosis induced by the ING1b fragment was p53 independent. Given the growing importance of combination therapies, we evaluated whether there was synergism between the ING1b fragment and HDAC inhibitors. Combination treatments with TSA, LBH 589 and SAHA reduced cancer cell survival by 3.9–4.7-fold as compared with single-drug treatment, and resulted in ~90% reduction in cell survival. Normalized isobologram analysis confirmed strong synergism between the ING1b fragment and drugs tested. These findings provide support for using ING1b-derived therapeutics as adjuvant treatments in combination with existing epigenetic therapies.
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18
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Yao Y, Des Marais TL, Costa M. Chromatin Memory in the Development of Human Cancers. GENE TECHNOLOGY 2014; 3:114. [PMID: 25606572 PMCID: PMC4297643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Cancer is a complex disease with acquired genomic and epigenomic alterations that affect cell proliferation, viability and invasiveness. Almost all the epigenetic mechanisms including cytosine methylation and hydroxymethylation, chromatin remodeling and non-coding RNAs have been found associate with carcinogenesis and cancer specific expression profile. Altered histone modification as an epigenetic hallmark is frequently found in tumors. Understanding the epigenetic alterations induced by carcinogens or infectious agents may help us understand early epigenetic changes prior to the development of cancer. In this review, we focus on chromatin remodeling and the associated histone modifiers in the development of cancer; the application of these modifiers as a cancer therapy target in different clinical trial phases is also discussed.
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Affiliation(s)
- Yixin Yao
- Department of Environmental Medicine New York University, New York, USA,Corresponding author: Yixin Yao, Department of Environmental Medicine, New York University, New York, USA; Tel: 845-731-3517;
| | | | - Max Costa
- Department of Environmental Medicine New York University, New York, USA,Department of Biochemistry and Molecular Pharmacology, New York University Langone Medical Center, Tuxedo, New York, USA
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19
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Anantharajan J, Koski MK, Kursula P, Hieta R, Bergmann U, Myllyharju J, Wierenga RK. The structural motifs for substrate binding and dimerization of the α subunit of collagen prolyl 4-hydroxylase. Structure 2013; 21:2107-18. [PMID: 24207127 DOI: 10.1016/j.str.2013.09.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 09/09/2013] [Accepted: 09/11/2013] [Indexed: 11/16/2022]
Abstract
Collagen prolyl 4-hydroxylase (C-P4H) catalyzes the proline hydroxylation of procollagen, an essential modification in the maturation of collagens. C-P4H consists of two catalytic α subunits and two protein disulfide isomerase β subunits. The assembly of these subunits is unknown. The α subunit contains an N domain (1-143), a peptide-substrate-binding-domain (PSB, 144-244) and a catalytic domain (245-517). Here, we report the dimeric structure of the N-terminal region (1-244) of the α subunit. It is shown that the N domain has an important role in the assembly of the C-P4H tetramer, by forming an extended four-helix bundle that includes an antiparallel coiled-coil dimerization motif between the two α subunits. Complexes of this construct with a C-P4H inhibitor and substrate show the mode of peptide-binding to the PSB domain. Both peptides adopt a poly-(L)-proline-type-II helix conformation and bind in a curved, asymmetric groove lined by conserved tyrosines and an Arg-Asp salt bridge.
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Affiliation(s)
- Jothi Anantharajan
- Biocenter Oulu and Department of Biochemistry, University of Oulu, P.O. Box 3000, FIN-90014 Oulu, Finland
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20
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Guérillon C, Larrieu D, Pedeux R. ING1 and ING2: multifaceted tumor suppressor genes. Cell Mol Life Sci 2013; 70:3753-72. [PMID: 23412501 PMCID: PMC11113716 DOI: 10.1007/s00018-013-1270-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 01/14/2013] [Accepted: 01/17/2013] [Indexed: 01/27/2023]
Abstract
Inhibitor of Growth 1 (ING1) was identified and characterized as a "candidate" tumor suppressor gene in 1996. Subsequently, four more genes, also characterized as "candidate" tumor suppressor genes, were identified by homology search: ING2, ING3, ING4, and ING5. The ING proteins are characterized by a high homology in their C-terminal domain, which contains a Nuclear Localization Sequence and a Plant HomeoDomain (PHD), which has a high affinity to Histone 3 tri-methylated on lysine 4 (H3K4Me3). The ING proteins have been involved in the control of cell growth, senescence, apoptosis, chromatin remodeling, and DNA repair. Within the ING family, ING1 and ING2 form a subgroup since they are evolutionarily and functionally close. In yeast, only one gene, Pho23, is related to ING1 and ING2 and possesses also a PHD. Recently, the ING1 and ING2 tumor suppressor status has been fully established since several studies have described the loss of ING1 and ING2 protein expression in human tumors and both ING1 and ING2 knockout mice were reported to have spontaneously developed tumors, B cell lymphomas, and soft tissue sarcomas, respectively. In this review, we will describe for the first time what is known about the ING1 and ING2 genes, proteins, their regulations in both human and mice, and their status in human tumors. Furthermore, we explore the current knowledge about identified functions involving ING1 and ING2 in tumor suppression pathways especially in the control of cell cycle and in genome stability.
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Affiliation(s)
- Claire Guérillon
- INSERM U917, Faculté de Médecine de Rennes, Microenvironnement et Cancer, Building 2, Room 117, 2 avenue du Professeur Léon Bernard, 35043 Rennes, France
- Université de Rennes 1, Rennes, France
| | - Delphine Larrieu
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN UK
| | - Rémy Pedeux
- INSERM U917, Faculté de Médecine de Rennes, Microenvironnement et Cancer, Building 2, Room 117, 2 avenue du Professeur Léon Bernard, 35043 Rennes, France
- Université de Rennes 1, Rennes, France
- Etablissement Français du Sang, Rennes, France
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21
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ING4 inhibits the translation of proto-oncogene MYC by interacting with AUF1. FEBS Lett 2013; 587:1597-604. [DOI: 10.1016/j.febslet.2013.04.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 04/02/2013] [Accepted: 04/02/2013] [Indexed: 12/11/2022]
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