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Vorreiter C, Robaa D, Sippl W. Exploring Aromatic Cage Flexibility Using Cosolvent Molecular Dynamics Simulations─An In-Silico Case Study of Tudor Domains. J Chem Inf Model 2024; 64:4553-4569. [PMID: 38771194 PMCID: PMC11167732 DOI: 10.1021/acs.jcim.4c00298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/02/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024]
Abstract
Cosolvent molecular dynamics (MD) simulations have proven to be powerful in silico tools to predict hotspots for binding regions on protein surfaces. In the current study, the method was adapted and applied to two Tudor domain-containing proteins, namely Spindlin1 (SPIN1) and survival motor neuron protein (SMN). Tudor domains are characterized by so-called aromatic cages that recognize methylated lysine residues of protein targets. In the study, the conformational transitions from closed to open aromatic cage conformations were investigated by performing MD simulations with cosolvents using six different probe molecules. It is shown that a trajectory clustering approach in combination with volume and atomic distance tracking allows a reasonable discrimination between open and closed aromatic cage conformations and the docking of inhibitors yields very good reproducibility with crystal structures. Cosolvent MDs are suitable to capture the flexibility of aromatic cages and thus represent a promising tool for the optimization of inhibitors.
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Affiliation(s)
- Christopher Vorreiter
- Department of Medicinal Chemistry,
Institute of Pharmacy, Martin-Luther-University
of Halle-Wittenberg, 06120 Halle, Saale, Germany
| | - Dina Robaa
- Department of Medicinal Chemistry,
Institute of Pharmacy, Martin-Luther-University
of Halle-Wittenberg, 06120 Halle, Saale, Germany
| | - Wolfgang Sippl
- Department of Medicinal Chemistry,
Institute of Pharmacy, Martin-Luther-University
of Halle-Wittenberg, 06120 Halle, Saale, Germany
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2
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Zhu QC, Sun JH, Liang MJ, Zhang ZY, Xia Y. PHF20L1 mediates PAX2 expression to promote angiogenesis and liver metastasis in colorectal cancer through regulating HIC1. Biol Chem 2022; 403:917-928. [PMID: 35357096 DOI: 10.1515/hsz-2022-0103] [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: 01/14/2022] [Accepted: 03/10/2022] [Indexed: 11/15/2022]
Abstract
Colorectal cancer (CRC) is a common cancer with poor prognosis. The research was designed to explore the role of PHF20L1 in angiogenesis and liver metastasis in CRC and discuss its molecular mechanism. Expression levels of PHF20L1, HIC1 and PAX2 in CRC tissues collected from CRC patients were detected using qRT-PCR, WB and immunohistochemical staining. CRC cells were transfected with PHF20L1, HIC1 and PAX2 overexpression or knockdown vectors and the proliferation, apoptosis, EMT and angiogenesis of the cells were determined. WB was utilized to assess protein levels of PHF20L1, HIC1, PAX2 and angiogenesis factor (ANGPT2, FGF1, PDGFA and VEGFA). The role of PHF20L1 regulating tumor formation and liver metastasis in vivo was detected as well. PHF20L1 was observed to express at a high level of CRC tissues. PHF20L1 promoted CRC cell growth, EMT and angiogenesis, and inhibited cell apoptosis. Knockdown of PHF20L1 had opposite effects on CRC cells. PHF20L1 negatively regulated HIC1 expression to promote PAX2 expression, thus promoting CRC cell progression. The in vivo results showed that PHF20L1 contributed to tumor formation and liver metastasis. PHF20L1 increases PAX2 expression to promote angiogenesis in CRC by inhibiting HIC1, therefore facilitating CRC cell EMT and liver metastasis. Our finding may provide a novel insight for CRC pathogenesis.
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Affiliation(s)
- Qing-Chao Zhu
- Department of Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Jian-Hua Sun
- Department of Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Ming-Jun Liang
- Department of Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Zheng-Yun Zhang
- Department of Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Yang Xia
- Department of Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
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3
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Alberto-Aguilar DR, Hernández-Ramírez VI, Osorio-Trujillo JC, Gallardo-Rincón D, Toledo-Leyva A, Talamás-Rohana P. PHD finger protein 20-like protein 1 (PHF20L1) in ovarian cancer: from its overexpression in tissue to its upregulation by the ascites microenvironment. Cancer Cell Int 2022; 22:6. [PMID: 34991589 PMCID: PMC8740351 DOI: 10.1186/s12935-021-02425-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 12/23/2021] [Indexed: 02/08/2023] Open
Abstract
Background Ovarian cancer is the most aggressive gynecological malignancy. Transcriptional regulators impact the tumor phenotype and, consequently, clinical progression and response to therapy. PHD finger protein 20-like protein 1 (PHF20L1) is a transcriptional regulator with several isoforms, and studies on its role in ovarian cancer are limited. We previously reported that PHF20L1 is expressed as a fucosylated protein in SKOV-3 cells stimulated with ascites from patients with ovarian cancer. Methods We decided to analyze the expression of PHF20L1 in ovarian cancer tissues, determine whether a correlation exists between PHF20L1 expression and patient clinical data, and analyze whether ascites can modulate the different isoforms of this protein. Ovarian cancer biopsies from 29 different patients were analyzed by immunohistochemistry, and the expression of the isoforms in ovarian cancer cells with or without exposure to the tumor microenvironment, i.e., the ascitic fluid, was determined by western blotting assays. Results Immunohistochemical results suggest that PHF20L1 exhibits increased expression in sections of tumor tissues from patients with ovarian cancer and that higher PHF20L1 expression correlates with shorter progression-free survival and shorter overall survival. Furthermore, western blotting assays determined that protein isoforms are differentially regulated in SKOV-3 cells in response to stimulation with ascites from patients with epithelial ovarian cancer. Conclusion The results suggest that PHF20L1 could play a relevant role in ovarian cancer given that higher PHF20L1 protein expression is associated with lower overall patient survival. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02425-6.
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Affiliation(s)
- Dulce Rosario Alberto-Aguilar
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Delegación Gustavo A. Madero, 07360, Mexico City, Mexico
| | - Verónica Ivonne Hernández-Ramírez
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Delegación Gustavo A. Madero, 07360, Mexico City, Mexico
| | - Juan Carlos Osorio-Trujillo
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Delegación Gustavo A. Madero, 07360, Mexico City, Mexico
| | - Dolores Gallardo-Rincón
- Instituto Nacional de Cancerología, Av. San Fernando No. 22, Col. Sección XVI, Delegación Tlalpan, 07360, Mexico City, Mexico
| | - Alfredo Toledo-Leyva
- Instituto Nacional de Cancerología, Av. San Fernando No. 22, Col. Sección XVI, Delegación Tlalpan, 07360, Mexico City, Mexico
| | - Patricia Talamás-Rohana
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Delegación Gustavo A. Madero, 07360, Mexico City, Mexico.
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4
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Ayati M, Chance MR, Koyutürk M. Co-phosphorylation networks reveal subtype-specific signaling modules in breast cancer. Bioinformatics 2021; 37:221-228. [PMID: 32730576 DOI: 10.1093/bioinformatics/btaa678] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 07/10/2020] [Accepted: 07/22/2020] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Protein phosphorylation is a ubiquitous mechanism of post-translational modification that plays a central role in cellular signaling. Phosphorylation is particularly important in the context of cancer, as downregulation of tumor suppressors and upregulation of oncogenes by the dysregulation of associated kinase and phosphatase networks are shown to have key roles in tumor growth and progression. Despite recent advances that enable large-scale monitoring of protein phosphorylation, these data are not fully incorporated into such computational tasks as phenotyping and subtyping of cancers. RESULTS We develop a network-based algorithm, CoPPNet, to enable unsupervised subtyping of cancers using phosphorylation data. For this purpose, we integrate prior knowledge on evolutionary, structural and functional association of phosphosites, kinase-substrate associations and protein-protein interactions with the correlation of phosphorylation of phosphosites across different tumor samples (a.k.a co-phosphorylation) to construct a context-specific-weighted network of phosphosites. We then mine these networks to identify subnetworks with correlated phosphorylation patterns. We apply the proposed framework to two mass-spectrometry-based phosphorylation datasets for breast cancer (BC), and observe that (i) the phosphorylation pattern of the identified subnetworks are highly correlated with clinically identified subtypes, and (ii) the identified subnetworks are highly reproducible across datasets that are derived from different studies. Our results show that integration of quantitative phosphorylation data with network frameworks can provide mechanistic insights into the differences between the signaling mechanisms that drive BC subtypes. Furthermore, the reproducibility of the identified subnetworks suggests that phosphorylation can provide robust classification of disease response and markers. AVAILABILITY AND IMPLEMENTATION CoPPNet is available at http://compbio.case.edu/coppnet/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Marzieh Ayati
- Department of Computer Science, University of Texas Rio Grande Valley, Edinburg, TX 78539, USA
| | - Mark R Chance
- Department of Nutrition, Case Western Reserve University, Cleveland, OH 44106, USA.,Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH 44106, USA.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Mehmet Koyutürk
- Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH 44106, USA.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA.,Department of Computer and Data Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
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5
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Park IG, Jeon M, Kim H, Lee JM. Coordinated methyl readers: Functional communications in cancer. Semin Cancer Biol 2021; 83:88-99. [PMID: 33753223 DOI: 10.1016/j.semcancer.2021.03.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 02/18/2021] [Accepted: 03/16/2021] [Indexed: 01/28/2023]
Abstract
Methylation is a major post-translational modification (PTM) generated by methyltransferase on target proteins; it is recognized by the epigenetic reader to expand the functional diversity of proteins. Methylation can occur on specific lysine or arginine residues localized within regulatory domains in both histone and nonhistone proteins, thereby allowing distinguished properties of the targeted protein. Methylated residues are recognized by chromodomain, malignant brain tumor (MBT), Tudor, plant homeodomain (PHD), PWWP, WD-40, ADD, and ankyrin repeats by an induced-fit mechanism. Methylation-dependent activities regulate distinct aspects of target protein function and are largely reliant on methyl readers of histone and nonhistone proteins in various diseases. Methylation of nonhistone proteins that are recognized by methyl readers facilitates the degradation of unwanted proteins, as well as the stabilization of necessary proteins. Unlike nonhistone substrates, which are mainly monomethylated by methyltransferase, histones are di- or trimethylated by the same methyltransferases and then connected to other critical regulators by methyl readers. These fine-tuned controls by methyl readers are significant for the progression or inhibition of diseases, including cancers. Here, current knowledge and our perspectives about regulating protein function by methyl readers are summarized. We also propose that expanded research on the strong crosstalk mechanisms between methylation and other PTMs via methyl readers would augment therapeutic research in cancer.
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Affiliation(s)
- Il-Geun Park
- Department of Molecular Bioscience, College of Biomedical Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Minsol Jeon
- Department of Biochemistry and Molecular Biology, Korea University College of Medicine, Seoul 02841, Republic of Korea; BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Hyunkyung Kim
- Department of Biochemistry and Molecular Biology, Korea University College of Medicine, Seoul 02841, Republic of Korea; BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea.
| | - Ji Min Lee
- Department of Molecular Bioscience, College of Biomedical Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea.
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Lv M, Gao J, Li M, Ma R, Li F, Liu Y, Liu M, Zhang J, Yao X, Wu J, Shi Y, Tang Y, Pan Y, Zhang Z, Ruan K. Conformational Selection in Ligand Recognition by the First Tudor Domain of PHF20L1. J Phys Chem Lett 2020; 11:7932-7938. [PMID: 32885980 DOI: 10.1021/acs.jpclett.0c02039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The first Tudor domain (Tudor1) of PHF20L1 recognizes (non)histone methylation to play versatile roles. However, the underlying ligand-recognition mechanism remains unknown as a closed state revealed in the free-form structure. NMR relaxation dispersion and molecular dynamics simulations suggest a pre-existing low-population conformation with a remarkable rearrangement of aromatic cage residues of PHF20L1 Tudor1. Such an open-form conformation is utilized to recognize lysine 142 methylated DNMT1, a cosolvent, and an NMR fragment screening hit, as revealed by the complex crystal structures. Intriguingly, the ligand binding capacity was enhanced by mutation that tunes up the open-state population only. The recognition of DNMT1 by PHF20L1 was further validated in cancer cells. This conformational selection mechanism will enable the discovery of small molecule inhibitors against the seemingly "undruggable" PHF20L1 Tudor1.
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Affiliation(s)
- Mengqi Lv
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Jia Gao
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Mingwei Li
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Rongsheng Ma
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Fudong Li
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Yaqian Liu
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Mingqing Liu
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Jiahai Zhang
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Xuebiao Yao
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Jihui Wu
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Yunyu Shi
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Yajun Tang
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Yueyin Pan
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Zhiyong Zhang
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Ke Ruan
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, the First Affiliated Hospital & School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
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7
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Fan X, Liu L, Shi Y, Guo F, Wang H, Zhao X, Zhong D, Li G. Integrated analysis of RNA-binding proteins in human colorectal cancer. World J Surg Oncol 2020; 18:222. [PMID: 32828126 PMCID: PMC7443297 DOI: 10.1186/s12957-020-01995-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 08/09/2020] [Indexed: 12/15/2022] Open
Abstract
Background Although RNA-binding proteins play an essential role in a variety of different tumours, there are still limited efforts made to systematically analyse the role of RNA-binding proteins (RBPs) in the survival of colorectal cancer (CRC) patients. Methods Analysis of CRC transcriptome data collected from the TCGA database was conducted, and RBPs were extracted from CRC. R software was applied to analyse the differentially expressed genes (DEGs) of RBPs. To identify related pathways and perform functional annotation of RBP DEGs, Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were carried out using the database for annotation, visualization and integrated discovery. Protein-protein interactions (PPIs) of these DEGs were analysed based on the Search Tool for the Retrieval of Interacting Genes (STRING) database and visualized by Cytoscape software. Based on the Cox regression analysis of the prognostic value of RBPs (from the PPI network) with survival time, the RBPs related to survival were identified, and a prognostic model was constructed. To verify the model, the data stored in the TCGA database were designated as the training set, while the chip data obtained from the GEO database were treated as the test set. Then, both survival analysis and ROC curve verification were conducted. Finally, the risk curves and nomograms of the two groups were generated to predict the survival period. Results Among RBP DEGs, 314 genes were upregulated while 155 were downregulated, of which twelve RBPs (NOP14, MRPS23, MAK16, TDRD6, POP1, TDRD5, TDRD7, PPARGC1A, LIN28B, CELF4, LRRFIP2, MSI2) with prognostic value were obtained. Conclusions The twelve identified genes may be promising predictors of CRC and play an essential role in the pathogenesis of CRC. However, further investigation of the underlying mechanism is needed.
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Affiliation(s)
- Xuehui Fan
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, 23 You Zheng Street, Harbin, 150001, Heilongjiang Province, People's Republic of China
| | - Lili Liu
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, 23 You Zheng Street, Harbin, 150001, Heilongjiang Province, People's Republic of China
| | - Yue Shi
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, 23 You Zheng Street, Harbin, 150001, Heilongjiang Province, People's Republic of China
| | - Fanghan Guo
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, 23 You Zheng Street, Harbin, 150001, Heilongjiang Province, People's Republic of China
| | - Haining Wang
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, 23 You Zheng Street, Harbin, 150001, Heilongjiang Province, People's Republic of China
| | - Xiuli Zhao
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, 23 You Zheng Street, Harbin, 150001, Heilongjiang Province, People's Republic of China
| | - Di Zhong
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, 23 You Zheng Street, Harbin, 150001, Heilongjiang Province, People's Republic of China
| | - Guozhong Li
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, 23 You Zheng Street, Harbin, 150001, Heilongjiang Province, People's Republic of China.
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8
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Heat Stress Affects H3K9me3 Level at Human Alpha Satellite DNA Repeats. Genes (Basel) 2020; 11:genes11060663. [PMID: 32570830 PMCID: PMC7348797 DOI: 10.3390/genes11060663] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/10/2020] [Accepted: 06/16/2020] [Indexed: 12/19/2022] Open
Abstract
Satellite DNAs are tandemly repeated sequences preferentially assembled into large arrays within constitutive heterochromatin and their transcription is often activated by stress conditions, particularly by heat stress. Bioinformatic analyses of sequenced genomes however reveal single repeats or short arrays of satellite DNAs dispersed in the vicinity of genes within euchromatin. Here, we analyze transcription of a major human alpha satellite DNA upon heat stress and follow the dynamics of “silent” H3K9me3 and “active” H3K4me2/3 histone marks at dispersed euchromatic and tandemly arranged heterochromatic alpha repeats. The results show H3K9me3 enrichment at alpha repeats upon heat stress, which correlates with the dynamics of alpha satellite DNA transcription activation, while no change in H3K4me2/3 level is detected. Spreading of H3K9me3 up to 1–2 kb from the insertion sites of the euchromatic alpha repeats is detected, revealing the alpha repeats as modulators of local chromatin structure. In addition, expression of genes containing alpha repeats within introns as well as of genes closest to the intergenic alpha repeats is downregulated upon heat stress. Further studies are necessary to reveal the possible contribution of H3K9me3 enriched alpha repeats, in particular those located within introns, to the silencing of their associated genes.
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9
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Jiang Y, Guo X, Liu L, Rode S, Wang R, Liu H, Yang ZQ. Metagenomic characterization of lysine acetyltransferases in human cancer and their association with clinicopathologic features. Cancer Sci 2020; 111:1829-1839. [PMID: 32162442 PMCID: PMC7226209 DOI: 10.1111/cas.14385] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 03/05/2020] [Accepted: 03/07/2020] [Indexed: 12/19/2022] Open
Abstract
Lysine acetyltransferases (KATs) are a highly diverse group of epigenetic enzymes that play important roles in various cellular processes including transcription, signal transduction, and cellular metabolism. However, our knowledge of the genomic and transcriptomic alterations of KAT genes and their clinical significance in human cancer remains incomplete. We undertook a metagenomic analysis of 37 KATs in more than 10 000 cancer samples across 33 tumor types, focusing on breast cancer. We identified associations among recurrent genetic alteration, gene expression, clinicopathologic features, and patient survival. Loss‐of‐function analysis was carried out to examine which KAT has important roles in growth and viability of breast cancer cells. We identified that a subset of KAT genes, including NAA10, KAT6A, and CREBBP, have high frequencies of genomic amplification or mutation in a spectrum of human cancers. Importantly, we found that 3 KATs, NAA10, ACAT2, and BRD4, were highly expressed in the aggressive basal‐like subtype, and their expression was significantly associated with disease‐free survival. Furthermore, we showed that depletion of NAA10 inhibits basal‐like breast cancer growth in vitro. Our findings provide a strong foundation for further mechanistic research and for developing therapies that target NAA10 or other KATs in human cancer.
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Affiliation(s)
- Yuanyuan Jiang
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Xuhui Guo
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA.,Department of Breast Surgery, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, China
| | - Lanxin Liu
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Shomita Rode
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Rui Wang
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA.,Department of Diagnostics of Chinese Medicine, Hebei University of Chinese Medicine, Hebei, China
| | - Hui Liu
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA.,The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, China
| | - Zeng-Quan Yang
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA.,Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Detroit, MI, USA
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10
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Hou Y, Liu W, Yi X, Yang Y, Su D, Huang W, Yu H, Teng X, Yang Y, Feng W, Zhang T, Gao J, Zhang K, Qiu R, Wang Y. PHF20L1 as a H3K27me2 reader coordinates with transcriptional repressors to promote breast tumorigenesis. SCIENCE ADVANCES 2020; 6:eaaz0356. [PMID: 32494608 PMCID: PMC7159910 DOI: 10.1126/sciadv.aaz0356] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 01/22/2020] [Indexed: 05/12/2023]
Abstract
TUDOR domain-containing proteins (TDRDs) are chiefly responsible for recognizing methyl-lysine/arginine residue. However, how TDRD dysregulation contributes to breast tumorigenesis is poorly understood. Here, we report that TUDOR domain-containing PHF20L1 as a H3K27me2 reader exerts transcriptional repression by recruiting polycomb repressive complex 2 (PRC2) and Mi-2/nucleosome remodeling and deacetylase (NuRD) complex, linking PRC2-mediated methylation and NuRD-mediated deacetylation of H3K27. Furthermore, PHF20L1 was found to serve as a potential MYC and hypoxia-driven oncogene, promoting glycolysis, proliferation, and metastasis of breast cancer cells by directly inhibiting tumor suppressors such as HIC1, KISS1, and BRCA1. PHF20L1 expression was also strongly correlated with higher histologic grades of breast cancer and markedly up-regulated in several cancers. Meanwhile, Phf20l1 deletion not only induces growth retardation and mammary ductal outgrowth delay but also inhibits tumorigenesis in vivo. Our data indicate that PHF20L1 promotes tumorigenesis, supporting the pursuit of PHF20L1 as a target for cancer therapy.
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Affiliation(s)
- Yongqiang Hou
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Wei Liu
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Xianfu Yi
- School of Biomedical Engineering, Tianjin Medical University, Tianjin 300070, China
| | - Yang Yang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Dongxue Su
- Beijing Key Laboratory for Tumor Invasion and Metastasis, Advanced Innovation Center for Human Brain Protection, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Wei Huang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Hefen Yu
- Beijing Key Laboratory for Tumor Invasion and Metastasis, Advanced Innovation Center for Human Brain Protection, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Xu Teng
- Beijing Key Laboratory for Tumor Invasion and Metastasis, Advanced Innovation Center for Human Brain Protection, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Ying Yang
- Beijing Key Laboratory for Tumor Invasion and Metastasis, Advanced Innovation Center for Human Brain Protection, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Wei Feng
- School of Biomedical Engineering, Tianjin Medical University, Tianjin 300070, China
| | - Tao Zhang
- School of Biomedical Engineering, Tianjin Medical University, Tianjin 300070, China
| | - Jie Gao
- School of Biomedical Engineering, Tianjin Medical University, Tianjin 300070, China
| | - Kai Zhang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Rongfang Qiu
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Yan Wang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
- Beijing Key Laboratory for Tumor Invasion and Metastasis, Advanced Innovation Center for Human Brain Protection, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
- Corresponding author.
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11
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Mo HY, Choi EJ, Yoo NJ, Lee SH. Mutational alterations of TDRD 1, 4 and 9 genes in colorectal cancers. Pathol Oncol Res 2020; 26:2007-2008. [PMID: 32036563 DOI: 10.1007/s12253-020-00798-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 01/23/2020] [Indexed: 01/09/2023]
Affiliation(s)
- Ha Yoon Mo
- Department of Pathology, College of Medicine, The CatholicUniversity of Korea, 505 Banpo-dong, Socho-gu, 137-701, Seoul, Korea
| | - Eun Ji Choi
- Department of Pathology, College of Medicine, The CatholicUniversity of Korea, 505 Banpo-dong, Socho-gu, 137-701, Seoul, Korea
| | - Nam Jin Yoo
- Department of Pathology, College of Medicine, The CatholicUniversity of Korea, 505 Banpo-dong, Socho-gu, 137-701, Seoul, Korea
| | - Sug Hyung Lee
- Department of Pathology, College of Medicine, The CatholicUniversity of Korea, 505 Banpo-dong, Socho-gu, 137-701, Seoul, Korea. .,Cancer Research Institute, College of Medicine, The Catholic University of Korea, 137-701, Seoul, Korea.
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12
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Manning M, Jiang Y, Wang R, Liu L, Rode S, Bonahoom M, Kim S, Yang ZQ. Pan-cancer analysis of RNA methyltransferases identifies FTSJ3 as a potential regulator of breast cancer progression. RNA Biol 2020; 17:474-486. [PMID: 31957540 PMCID: PMC7237164 DOI: 10.1080/15476286.2019.1708549] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
RNA methylation, catalysed by a set of RNA methyltransferases (RNMTs), modulates RNA structures, properties, and biological functions. RNMTs are increasingly documented to be dysregulated in various human diseases, particularly developmental disorders and cancer. However, the genomic and transcriptomic alterations of RNMTs, as well as their functional roles in human cancer, are limited. In this study, we utilized an unbiased approach to examine copy number alterations and mutation rates of 58 RNMTs in more than 10,000 clinical samples across 32 human cancer types. We also investigated these alterations and RNMT expression level as they related to clinical features such as tumour subtype, grade, and survival in a large cohort of tumour samples, focusing on breast cancer. Loss-of-function analysis was performed to examine RNMT candidates with important roles in growth and viability of breast cancer cells. We identified a subset of RNMTs, notably TRMT12, NSUN2, TARBP1, and FTSJ3, that were amplified or mutated in a subset of human cancers. Several RNMTs were significantly associated with breast cancer aggressiveness and poor prognosis. Loss-of-function analysis indicated FTSJ3, a 2'-O-Me methyltransferase, as a candidate RNMT with functional roles in promoting cancer growth and survival. A subset of RNMTs, like FTSJ3, represents promising novel targets for anticancer drug discovery. Our findings provide a framework for further study of the functional consequences of RNMT alterations in human cancer and for developing therapies that target cancer-promoting RNMTs in the future.
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Affiliation(s)
- Morenci Manning
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Yuanyuan Jiang
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Rui Wang
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA.,Department of Diagnostics of Chinese Medicine, Hebei University of Chinese Medicine, Hebei, China
| | - Lanxin Liu
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Shomita Rode
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Madison Bonahoom
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Seongho Kim
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA.,Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Detroit, MI, USA
| | - Zeng-Quan Yang
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA.,Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Detroit, MI, USA
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13
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de Almeida BP, Apolónio JD, Binnie A, Castelo-Branco P. Roadmap of DNA methylation in breast cancer identifies novel prognostic biomarkers. BMC Cancer 2019; 19:219. [PMID: 30866861 PMCID: PMC6416975 DOI: 10.1186/s12885-019-5403-0] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 02/25/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Breast cancer is a highly heterogeneous disease resulting in diverse clinical behaviours and therapeutic responses. DNA methylation is a major epigenetic alteration that is commonly perturbed in cancers. The aim of this study is to characterize the relationship between DNA methylation and aberrant gene expression in breast cancer. METHODS We analysed DNA methylation and gene expression profiles from breast cancer tissue and matched normal tissue in The Cancer Genome Atlas (TCGA). Genome-wide differential methylation analysis and methylation-gene expression correlation was performed. Gene expression changes were subsequently validated in the METABRIC dataset. The Oncoscore tool was used to identify genes that had previously been associated with cancer in the literature. A subset of genes that had not previously been studied in cancer was chosen for further analysis. RESULTS We identified 368 CpGs that were differentially methylated between tumor and normal breast tissue (∆β > 0.4). Hypermethylated CpGs were overrepresented in tumor tissue and were found predominantly (56%) in upstream promoter regions. Conversely, hypomethylated CpG sites were found primarily in the gene body (66%). Expression analysis revealed that 209 of the differentially-methylated CpGs were located in 169 genes that were differently expressed between normal and breast tumor tissue. Methylation-expression correlations were predominantly negative (70%) for promoter CpG sites and positive (74%) for gene body CpG sites. Among these differentially-methylated and differentially-expressed genes, we identified 7 that had not previously been studied in any form of cancer. Three of these, TDRD10, PRAC2 and TMEM132C, contained CpG sites that showed diagnostic and prognostic value in breast cancer, particularly in estrogen-receptor (ER)-positive samples. A pan-cancer analysis confirmed differential expression of these genes together with diagnostic and prognostic value of their respective CpG sites in multiple cancer types. CONCLUSION We have identified 368 DNA methylation changes that characterize breast cancer tumor tissue, of which 209 are associated with genes that are differentially-expressed in the same samples. Novel DNA methylation markers were identified, of which cg12374721 (PRAC2), cg18081940 (TDRD10) and cg04475027 (TMEM132C) show promise as diagnostic and prognostic markers in breast cancer as well as other cancer types.
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Affiliation(s)
- Bernardo P. de Almeida
- Institute of Molecular Medicine, Faculty of Medicine, University of Lisbon, 1649-028 Lisbon, Portugal
- Department of Biomedical Sciences and Medicine, University of Algarve, Campus Gambelas, Bld. 2 - Ala Norte, 8005-139 Faro, Portugal
- Present address: Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Joana Dias Apolónio
- Department of Biomedical Sciences and Medicine, University of Algarve, Campus Gambelas, Bld. 2 - Ala Norte, 8005-139 Faro, Portugal
- Centre for Biomedical Research (CBMR), University of Algarve, 8005-139 Faro, Portugal
- Algarve Biomedical Center, Campus Gambelas, 8005-139 Faro, Portugal
| | - Alexandra Binnie
- Department of Biomedical Sciences and Medicine, University of Algarve, Campus Gambelas, Bld. 2 - Ala Norte, 8005-139 Faro, Portugal
- Centre for Biomedical Research (CBMR), University of Algarve, 8005-139 Faro, Portugal
- Algarve Biomedical Center, Campus Gambelas, 8005-139 Faro, Portugal
- William Osler Health System, Brampton, ON Canada
| | - Pedro Castelo-Branco
- Department of Biomedical Sciences and Medicine, University of Algarve, Campus Gambelas, Bld. 2 - Ala Norte, 8005-139 Faro, Portugal
- Centre for Biomedical Research (CBMR), University of Algarve, 8005-139 Faro, Portugal
- Algarve Biomedical Center, Campus Gambelas, 8005-139 Faro, Portugal
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14
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Mio C, Bulotta S, Russo D, Damante G. Reading Cancer: Chromatin Readers as Druggable Targets for Cancer Treatment. Cancers (Basel) 2019; 11:cancers11010061. [PMID: 30634442 PMCID: PMC6356452 DOI: 10.3390/cancers11010061] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 12/30/2018] [Accepted: 01/03/2019] [Indexed: 02/07/2023] Open
Abstract
The epigenetic machinery deputed to control histone post-translational modifications is frequently dysregulated in cancer cells. With epigenetics being naturally reversible, it represents a good target for therapies directed to restore normal gene expression. Since the discovery of Bromodomain and Extra Terminal (BET) inhibitors, a great effort has been spent investigating the effects of chromatin readers’ inhibition, specifically the class of proteins assigned to bind acetylated and methylated residues. So far, focused studies have been produced on epigenetic regulation, dissecting a specific class of epigenetic-related proteins or investigating epigenetic therapy in a specific tumor type. In this review, recent steps toward drug discovery on the different classes of chromatin readers have been outlined, highlighting the pros and cons of current therapeutic approaches.
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Affiliation(s)
- Catia Mio
- Department of Medical Area, University of Udine, 33100 Udine, Italy.
| | - Stefania Bulotta
- Department of Health Sciences, "Magna Graecia" University of Catanzaro, 88100 Catanzaro, Italy.
| | - Diego Russo
- Department of Health Sciences, "Magna Graecia" University of Catanzaro, 88100 Catanzaro, Italy.
| | - Giuseppe Damante
- Department of Medical Area, University of Udine, 33100 Udine, Italy.
- Medical Genetics Institute, University Hospital of Udine, 33100 Udine, Italy.
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15
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PHF20L1 antagonizes SOX2 proteolysis triggered by the MLL1/WDR5 complexes. J Transl Med 2018; 98:1627-1641. [PMID: 30089852 DOI: 10.1038/s41374-018-0106-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 05/25/2018] [Accepted: 06/13/2018] [Indexed: 01/02/2023] Open
Abstract
Transcriptional factor SOX2 regulates stem cell pluripotency, cell differentiation and tumorigenesis. As a key factor, the expression of SOX2 is tightly regulated at transcriptional and post-translational levels. However, the underlying mechanism of SOX2 protein stability remains to be elucidated. Here we show that the histone-lysine N-methyltransferase MLL1/WDR5 complexes physically interact with SOX2 and evoke SOX2 proteolysis, possibly through methylation on a potential site lysine 42 (K42). Small interfering RNA (siRNA)-mediated gene silencing of the components of the MLL1/WDR5 complexes WDR5, MLL1, RBBP5, and ASH2L lead to the accumulation of SOX2, while forced expression of WDR5 promotes SOX2 ubiquitination and proteolysis. Conversely, PHD finger protein 20-like protein 1 (PHF20L1) associates with SOX2, antagonizes SOX2 ubiquitination and the sequential degradation induced by the MLL1/WDR5 complexes. RNA interferences of PHF20L1 promote the degradation of SOX2, while forced expression of PHF20L1 stabilizes SOX2. Co-silencing of MLL1/WDR5 components and PHF20L1 preclude degradation of SOX2 induced by knockdown of PHF20L1. Moreover, co-expression of PHF20L1 and WDR5 prevent ubiquitination of SOX2 triggered by WDR5 over-expression. However, SOX2 mutant K42R is non-sensitive to the MLL1/WDR5 complexes or PHF20L1. In addition, PHF20L1 may regulate the stability of SOX2 through its malignant brain tumor (MBT) domain, since the degradation of SOX2 is accelerated by UNC1215 and UNC669, inhibitors that bind to the MBT domain. Furthermore, abundant expression of SOX2 is highly correlated to immature ovarian teratoma. Loss of PHF20L1 weakened the tumor initiation ability of PA-1 cells while ablation of MLL1 promoted the growth of tumors. Thus, our studies reveal an antagonistic mechanism by which the protein stability of SOX2 is regulated by the MLL1/WDR5 complexes and PHF20L1, possibly through methylation of SOX2 protein, and provide a novel perspective on SOX2-positive cancer treatment.
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16
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Zhang C, Leng F, Saxena L, Hoang N, Yu J, Alejo S, Lee L, Qi D, Lu F, Sun H, Zhang H. Proteolysis of methylated SOX2 protein is regulated by L3MBTL3 and CRL4 DCAF5 ubiquitin ligase. J Biol Chem 2018; 294:476-489. [PMID: 30442713 DOI: 10.1074/jbc.ra118.005336] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 10/22/2018] [Indexed: 01/23/2023] Open
Abstract
SOX2 is a dose-dependent master stem cell protein that controls the self-renewal and pluripotency or multipotency of embryonic stem (ES) cells and many adult stem cells. We have previously found that SOX2 protein is monomethylated at lysine residues 42 and 117 by SET7 methyltransferase to promote SOX2 proteolysis, whereas LSD1 and PHF20L1 act on both methylated Lys-42 and Lys-117 to prevent SOX2 proteolysis. However, the mechanism by which the methylated SOX2 protein is degraded remains unclear. Here, we report that L3MBTL3, a protein with the malignant-brain-tumor (MBT) methylation-binding domain, is required for SOX2 proteolysis. Our studies showed that L3MBTL3 preferentially binds to the methylated Lys-42 in SOX2, although mutation of Lys-117 also partially reduces the interaction between SOX2 and L3MBTL3. The direct binding of L3MBTL3 to the methylated SOX2 protein leads to the recruitment of the CRL4DCAF5 ubiquitin E3 ligase to target SOX2 protein for ubiquitin-dependent proteolysis. Whereas loss of either LSD1 or PHF20L1 destabilizes SOX2 protein and impairs the self-renewal and pluripotency of mouse ES cells, knockdown of L3MBTL3 or DCAF5 is sufficient to restore the protein levels of SOX2 and rescue the defects of mouse ES cells caused by LSD1 or PHF20L1 deficiency. We also found that retinoic acid-induced differentiation of mouse ES cells is accompanied by the enhanced degradation of the methylated SOX2 protein at both Lys-42 and Lys-117. Our studies provide novel insights into the mechanism by which the methylation-dependent degradation of SOX2 protein is controlled by the L3MBTL3-CRL4DCAF5 ubiquitin ligase complex.
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Affiliation(s)
- Chunxiao Zhang
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and.,the School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, Guangdong, China
| | - Feng Leng
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and
| | - Lovely Saxena
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and
| | - Nam Hoang
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and
| | - Jiekai Yu
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and
| | - Salvador Alejo
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and
| | - Logan Lee
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and
| | - Dandan Qi
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and
| | - Fei Lu
- the School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, Guangdong, China
| | - Hong Sun
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and
| | - Hui Zhang
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and
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17
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Methylated DNMT1 and E2F1 are targeted for proteolysis by L3MBTL3 and CRL4 DCAF5 ubiquitin ligase. Nat Commun 2018; 9:1641. [PMID: 29691401 PMCID: PMC5915600 DOI: 10.1038/s41467-018-04019-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 03/27/2018] [Indexed: 01/29/2023] Open
Abstract
Many non-histone proteins are lysine methylated and a novel function of this modification is to trigger the proteolysis of methylated proteins. Here, we report that the methylated lysine 142 of DNMT1, a major DNA methyltransferase that preserves epigenetic inheritance of DNA methylation patterns during DNA replication, is demethylated by LSD1. A novel methyl-binding protein, L3MBTL3, binds the K142-methylated DNMT1 and recruits a novel CRL4DCAF5 ubiquitin ligase to degrade DNMT1. Both LSD1 and PHF20L1 act primarily in S phase to prevent DNMT1 degradation by L3MBTL3-CRL4DCAF5. Mouse L3MBTL3/MBT-1 deletion causes accumulation of DNMT1 protein, increased genomic DNA methylation, and late embryonic lethality. DNMT1 contains a consensus methylation motif shared by many non-histone proteins including E2F1, a key transcription factor for S phase. We show that the methylation-dependent E2F1 degradation is also controlled by L3MBTL3-CRL4DCAF5. Our studies elucidate for the first time a novel mechanism by which the stability of many methylated non-histone proteins are regulated.
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18
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Zhang C, Hoang N, Leng F, Saxena L, Lee L, Alejo S, Qi D, Khal A, Sun H, Lu F, Zhang H. LSD1 demethylase and the methyl-binding protein PHF20L1 prevent SET7 methyltransferase-dependent proteolysis of the stem-cell protein SOX2. J Biol Chem 2018; 293:3663-3674. [PMID: 29358331 DOI: 10.1074/jbc.ra117.000342] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 01/12/2018] [Indexed: 11/06/2022] Open
Abstract
The pluripotency-controlling stem-cell protein SRY-box 2 (SOX2) plays a pivotal role in maintaining the self-renewal and pluripotency of embryonic stem cells and also of teratocarcinoma or embryonic carcinoma cells. SOX2 is monomethylated at lysine 119 (Lys-119) in mouse embryonic stem cells by the SET7 methyltransferase, and this methylation triggers ubiquitin-dependent SOX2 proteolysis. However, the molecular regulators and mechanisms controlling SET7-induced SOX2 proteolysis are unknown. Here, we report that in human ovarian teratocarcinoma PA-1 cells, methylation-dependent SOX2 proteolysis is dynamically regulated by the LSD1 lysine demethylase and a methyl-binding protein, PHD finger protein 20-like 1 (PHF20L1). We found that LSD1 not only removes the methyl group from monomethylated Lys-117 (equivalent to Lys-119 in mouse SOX2), but it also demethylates monomethylated Lys-42 in SOX2, a reaction that SET7 also regulated and that also triggered SOX2 proteolysis. Our studies further revealed that PHF20L1 binds both monomethylated Lys-42 and Lys-117 in SOX2 and thereby prevents SOX2 proteolysis. Down-regulation of either LSD1 or PHF20L1 promoted SOX2 proteolysis, which was prevented by SET7 inactivation in both PA-1 and mouse embryonic stem cells. Our studies also disclosed that LSD1 and PHF20L1 normally regulate the growth of pluripotent mouse embryonic stem cells and PA-1 cells by preventing methylation-dependent SOX2 proteolysis. In conclusion, our findings reveal an important mechanism by which the stability of the pluripotency-controlling stem-cell protein SOX2 is dynamically regulated by the activities of SET7, LSD1, and PHF20L1 in pluripotent stem cells.
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Affiliation(s)
- Chunxiao Zhang
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and.,the Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Nam Hoang
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and
| | - Feng Leng
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and.,the Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Lovely Saxena
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and
| | - Logan Lee
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and
| | - Salvador Alejo
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and
| | - Dandan Qi
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and.,the Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Anthony Khal
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and
| | - Hong Sun
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and
| | - Fei Lu
- the Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Hui Zhang
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and
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19
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Carr SM, Munro S, Sagum CA, Fedorov O, Bedford MT, La Thangue NB. Tudor-domain protein PHF20L1 reads lysine methylated retinoblastoma tumour suppressor protein. Cell Death Differ 2017; 24:2139-2149. [PMID: 28841214 PMCID: PMC5686351 DOI: 10.1038/cdd.2017.135] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 07/12/2017] [Accepted: 07/14/2017] [Indexed: 12/30/2022] Open
Abstract
The retinoblastoma tumour suppressor protein (pRb) classically functions to regulate early cell cycle progression where it acts to enforce a number of checkpoints in response to cellular stress and DNA damage. Methylation at lysine (K) 810, which occurs within a critical CDK phosphorylation site and antagonises a CDK-dependent phosphorylation event at the neighbouring S807 residue, acts to hold pRb in the hypo-phosphorylated growth-suppressing state. This is mediated in part by the recruitment of the reader protein 53BP1 to di-methylated K810, which allows pRb activity to be effectively integrated with the DNA damage response. Here, we report the surprising observation that an additional methylation-dependent interaction occurs at K810, but rather than the di-methyl mark, it is selective for the mono-methyl K810 mark. Binding of the mono-methyl PHF20L1 reader to methylated pRb occurs on E2F target genes, where it acts to mediate an additional level of control by recruiting the MOF acetyltransferase complex to E2F target genes. Significantly, we find that the interplay between PHF20L1 and mono-methyl pRb is important for maintaining the integrity of a pRb-dependent G1-S-phase checkpoint. Our results highlight the distinct roles that methyl-lysine readers have in regulating the biological activity of pRb.
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Affiliation(s)
- Simon M Carr
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Old Road Campus, Roosevelt Drive, Headington, Oxford OX3 7DQ, UK
| | - Shonagh Munro
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Old Road Campus, Roosevelt Drive, Headington, Oxford OX3 7DQ, UK
| | - Cari A Sagum
- Department of Molecular Carcinogenesis, The University of Texas, MD Anderson Cancer Center, Smithville, TX 77030, USA
| | - Oleg Fedorov
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium Oxford, University of Oxford, Old Road Campus Research Building, Old Road Campus, Roosevelt Drive, Headington, Oxford OX3 7DQ, UK
| | - Mark T Bedford
- Department of Molecular Carcinogenesis, The University of Texas, MD Anderson Cancer Center, Smithville, TX 77030, USA
| | - Nicholas B La Thangue
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Old Road Campus, Roosevelt Drive, Headington, Oxford OX3 7DQ, UK
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20
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Chu X, Guo X, Jiang Y, Yu H, Liu L, Shan W, Yang Z. Genotranscriptomic meta-analysis of the CHD family chromatin remodelers in human cancers - initial evidence of an oncogenic role for CHD7. Mol Oncol 2017; 11:1348-1360. [PMID: 28649742 PMCID: PMC5623824 DOI: 10.1002/1878-0261.12104] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 05/27/2017] [Accepted: 06/10/2017] [Indexed: 12/14/2022] Open
Abstract
Chromodomain helicase DNA binding proteins (CHDs) are characterized by N-terminal tandem chromodomains and a central adenosine triphosphate-dependent helicase domain. CHDs govern the cellular machinery's access to DNA, thereby playing critical roles in various cellular processes including transcription, proliferation, and DNA damage repair. Accumulating evidence demonstrates that mutation and dysregulation of CHDs are implicated in the pathogenesis of developmental disorders and cancer. However, we know little about genomic and transcriptomic alterations and the clinical significance of most CHDs in human cancer. We used TCGA and METABRIC datasets to perform integrated genomic and transcriptomic analyses of nine CHD genes in more than 10 000 primary cancer specimens from 32 tumor types, focusing on breast cancers. We identified associations among recurrent copy number alteration, gene expression, clinicopathological features, and patient survival. We found that CHD7 was the most commonly gained/amplified and mutated, whereas CHD3 was the most deleted across the majority of tumor types, including breast cancer. Overexpression of CHD7 was more prevalent in aggressive subtypes of breast cancer and was significantly correlated with high tumor grade and poor prognosis. CHD7 is required to maintain open, accessible chromatin, thus providing fine-tuning of transcriptional regulation of certain classes of genes. We found that CHD7 expression was positively correlated with a small subset of classical oncogenes, notably NRAS, in breast cancer. Knockdown of CHD7 inhibits cell proliferation and decreases gene expression of several CHD7 targets, including NRAS, in breast cancer cell lines. Thus, our results demonstrate the oncogenic potential of CHD7 and its association with poor prognostic parameters in human cancer.
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Affiliation(s)
- Xiaofang Chu
- Department of OncologyWayne State University School of MedicineDetroitMIUSA
| | - Xuhui Guo
- Department of OncologyWayne State University School of MedicineDetroitMIUSA
- Department of Breast SurgeryAffiliated Cancer Hospital of Zhengzhou UniversityHenanChina
| | - Yuanyuan Jiang
- Department of OncologyWayne State University School of MedicineDetroitMIUSA
| | - Huimei Yu
- Department of OncologyWayne State University School of MedicineDetroitMIUSA
- College of Basic MedicineJilin UniversityChangchunChina
| | - Lanxin Liu
- Department of OncologyWayne State University School of MedicineDetroitMIUSA
| | - Wenqi Shan
- Department of OncologyWayne State University School of MedicineDetroitMIUSA
| | - Zeng‐Quan Yang
- Department of OncologyWayne State University School of MedicineDetroitMIUSA
- Molecular Therapeutics ProgramBarbara Ann Karmanos Cancer InstituteDetroitMIUSA
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21
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Yu H, Jiang Y, Liu L, Shan W, Chu X, Yang Z, Yang ZQ. Integrative genomic and transcriptomic analysis for pinpointing recurrent alterations of plant homeodomain genes and their clinical significance in breast cancer. Oncotarget 2017; 8:13099-13115. [PMID: 28055972 PMCID: PMC5355080 DOI: 10.18632/oncotarget.14402] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 12/05/2016] [Indexed: 11/29/2022] Open
Abstract
A wide range of the epigenetic effectors that regulate chromatin modification, gene expression, genomic stability, and DNA repair contain structurally conserved domains called plant homeodomain (PHD) fingers. Alternations of several PHD finger-containing proteins (PHFs) due to genomic amplification, mutations, deletions, and translocations have been linked directly to various types of cancer. However, little is known about the genomic landscape and the clinical significance of PHFs in breast cancer. Hence, we performed a large-scale genomic and transcriptomic analysis of 98 PHF genes in breast cancer using TCGA and METABRIC datasets and correlated the recurrent alterations with clinicopathological features and survival of patients. Different subtypes of breast cancer had different patterns of copy number and expression for each PHF. We identified a subset of PHF genes that was recurrently altered with high prevalence, including PYGO2 (pygopus family PHD finger 2), ZMYND8 (zinc finger, MYND-type containing 8), ASXL1 (additional sex combs like 1) and CHD3 (chromodomain helicase DNA binding protein 3). Copy number increase and overexpression of ZMYND8 were more prevalent in Luminal B subtypes and were significantly associated with shorter survival of breast cancer patients. ZMYND8 was also involved in a positive feedback circuit of the estrogen receptor (ER) pathway, and the expression of ZMYND8 was repressed by the bromodomain and extra terminal (BET) inhibitor in breast cancer. Our findings suggest a promising avenue for future research-to focus on a subset of PHFs to better understand the molecular mechanisms and to identify therapeutic targets in breast cancer.
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Affiliation(s)
- Huimei Yu
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA
- College of Basic Medicine, Jilin University, Changchun, China
| | - Yuanyuan Jiang
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Lanxin Liu
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Wenqi Shan
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Xiaofang Chu
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Zhe Yang
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Zeng-Quan Yang
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Detroit, MI 48201, USA
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22
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An integrated genomic analysis of Tudor domain-containing proteins identifies PHD finger protein 20-like 1 (PHF20L1) as a candidate oncogene in breast cancer. Mol Oncol 2015; 10:292-302. [PMID: 26588862 DOI: 10.1016/j.molonc.2015.10.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 10/15/2015] [Accepted: 10/16/2015] [Indexed: 12/18/2022] Open
Abstract
Tudor domain-containing proteins (TDRDs), which recognize and bind to methyl-lysine/arginine residues on histones and non-histone proteins, play critical roles in regulating chromatin architecture, transcription, genomic stability, and RNA metabolism. Dysregulation of several TDRDs have been observed in various types of cancer. However, neither the genomic landscape nor clinical significance of TDRDs in breast cancer has been explored comprehensively. Here, we performed an integrated genomic and transcriptomic analysis of 41 TDRD genes in breast cancer (TCGA and METABRIC datasets) and identified associations among recurrent copy number alterations, gene expressions, clinicopathological features, and survival of patients. Among seven TDRDs that had the highest frequency (>10%) of gene amplification, the plant homeodomain finger protein 20-like 1 (PHF20L1) was the most commonly amplified (17.62%) TDRD gene in TCGA breast cancers. Different subtypes of breast cancer had different patterns of copy number and expression for each TDRD. Notably, amplification and overexpression of PHF20L1 were more prevalent in aggressive basal-like and Luminal B subtypes and were significantly associated with shorter survival of breast cancer patients. Furthermore, knockdown of PHF20L1 inhibited cell proliferation in PHF20L1-amplified breast cancer cell lines. PHF20L1 protein contains N-terminal Tudor and C-terminal plant homeodomain domains. Detailed characterization of PHF20L1 in breast cancer revealed that the Tudor domain likely plays a critical role in promoting cancer. Mechanistically, PHF20L1 might participate in regulating DNA methylation by stabilizing DNA methyltransferase 1 (DNMT1) protein in breast cancer. Thus, our results demonstrated the oncogenic potential of PHF20L1 and its association with poor prognostic parameters in breast cancer.
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