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Kaisinger LR, Kentistou KA, Stankovic S, Gardner EJ, Day FR, Zhao Y, Mörseburg A, Carnie CJ, Zagnoli-Vieira G, Puddu F, Jackson SP, O’Rahilly S, Farooqi IS, Dearden L, Pantaleão LC, Ozanne SE, Ong KK, Perry JR. Large-scale exome sequence analysis identifies sex- and age-specific determinants of obesity. CELL GENOMICS 2023; 3:100362. [PMID: 37601970 PMCID: PMC10435378 DOI: 10.1016/j.xgen.2023.100362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 03/15/2023] [Accepted: 07/03/2023] [Indexed: 08/22/2023]
Abstract
Obesity contributes substantially to the global burden of disease and has a significant heritable component. Recent large-scale exome sequencing studies identified several genes in which rare, protein-coding variants have large effects on adult body mass index (BMI). Here we extended such work by performing sex-stratified associations in the UK Biobank study (N∼420,000). We identified genes in which rare heterozygous loss-of-function increases adult BMI in women (DIDO1, PTPRG, and SLC12A5) and in men (SLTM), with effect sizes up to ∼8 kg/m2. This is complemented by analyses implicating rare variants in OBSCN and MADD for recalled childhood adiposity. The known functions of these genes, as well as findings of common variant genome-wide pathway enrichment analyses, suggest a role for neuron death, apoptosis, and DNA damage response mechanisms in the susceptibility to obesity across the life-course. These findings highlight the importance of considering sex-specific and life-course effects in the genetic regulation of obesity.
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Affiliation(s)
- Lena R. Kaisinger
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Katherine A. Kentistou
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Stasa Stankovic
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Eugene J. Gardner
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Felix R. Day
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Yajie Zhao
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Alexander Mörseburg
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
- MRC Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Christopher J. Carnie
- Wellcome Trust/Cancer Research UK Gurdon Institute, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
- Cancer Research UK Cambridge Institute, Li Ka Shing Building, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Guido Zagnoli-Vieira
- Wellcome Trust/Cancer Research UK Gurdon Institute, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Fabio Puddu
- Wellcome Trust/Cancer Research UK Gurdon Institute, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Stephen P. Jackson
- Wellcome Trust/Cancer Research UK Gurdon Institute, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
- Cancer Research UK Cambridge Institute, Li Ka Shing Building, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Stephen O’Rahilly
- MRC Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - I. Sadaf Farooqi
- MRC Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Laura Dearden
- MRC Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Lucas C. Pantaleão
- MRC Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Susan E. Ozanne
- MRC Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Ken K. Ong
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - John R.B. Perry
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
- MRC Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
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Appel LM, Benedum J, Engl M, Platzer S, Schleiffer A, Strobl X, Slade D. SPOC domain proteins in health and disease. Genes Dev 2023; 37:140-170. [PMID: 36927757 PMCID: PMC10111866 DOI: 10.1101/gad.350314.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Since it was first described >20 yr ago, the SPOC domain (Spen paralog and ortholog C-terminal domain) has been identified in many proteins all across eukaryotic species. SPOC-containing proteins regulate gene expression on various levels ranging from transcription to RNA processing, modification, export, and stability, as well as X-chromosome inactivation. Their manifold roles in controlling transcriptional output implicate them in a plethora of developmental processes, and their misregulation is often associated with cancer. Here, we provide an overview of the biophysical properties of the SPOC domain and its interaction with phosphorylated binding partners, the phylogenetic origin of SPOC domain proteins, the diverse functions of mammalian SPOC proteins and their homologs, the mechanisms by which they regulate differentiation and development, and their roles in cancer.
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Affiliation(s)
- Lisa-Marie Appel
- Department of Radiation Oncology, Medical University of Vienna, 1090 Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
| | - Johannes Benedum
- Department of Radiation Oncology, Medical University of Vienna, 1090 Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Magdalena Engl
- Department of Radiation Oncology, Medical University of Vienna, 1090 Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Sebastian Platzer
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology (IMP), 1030 Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Xué Strobl
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Dea Slade
- Department of Radiation Oncology, Medical University of Vienna, 1090 Vienna, Austria;
- Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
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3
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Geiger-Schuller K, Eraslan B, Kuksenko O, Dey KK, Jagadeesh KA, Thakore PI, Karayel O, Yung AR, Rajagopalan A, Meireles AM, Yang KD, Amir-Zilberstein L, Delorey T, Phillips D, Raychowdhury R, Moussion C, Price AL, Hacohen N, Doench JG, Uhler C, Rozenblatt-Rosen O, Regev A. Systematically characterizing the roles of E3-ligase family members in inflammatory responses with massively parallel Perturb-seq. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.23.525198. [PMID: 36747789 PMCID: PMC9900845 DOI: 10.1101/2023.01.23.525198] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
E3 ligases regulate key processes, but many of their roles remain unknown. Using Perturb-seq, we interrogated the function of 1,130 E3 ligases, partners and substrates in the inflammatory response in primary dendritic cells (DCs). Dozens impacted the balance of DC1, DC2, migratory DC and macrophage states and a gradient of DC maturation. Family members grouped into co-functional modules that were enriched for physical interactions and impacted specific programs through substrate transcription factors. E3s and their adaptors co-regulated the same processes, but partnered with different substrate recognition adaptors to impact distinct aspects of the DC life cycle. Genetic interactions were more prevalent within than between modules, and a deep learning model, comβVAE, predicts the outcome of new combinations by leveraging modularity. The E3 regulatory network was associated with heritable variation and aberrant gene expression in immune cells in human inflammatory diseases. Our study provides a general approach to dissect gene function.
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The Dengue Virus Nonstructural Protein 1 (NS1) Interacts with the Putative Epigenetic Regulator DIDO1 to Promote Flavivirus Replication in Mosquito Cells. J Virol 2022; 96:e0070422. [PMID: 35652656 DOI: 10.1128/jvi.00704-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Dengue virus (DENV) NS1 is a multifunctional protein essential for viral replication. To gain insights into NS1 functions in mosquito cells, the protein interactome of DENV NS1 in C6/36 cells was investigated using a proximity biotinylation system and mass spectrometry. A total of 817 mosquito targets were identified as protein-protein interacting with DENV NS1. Approximately 14% of them coincide with interactomes previously obtained in vertebrate cells, including the oligosaccharide transferase complex, the chaperonin containing TCP-1, vesicle localization, and ribosomal proteins. Notably, other protein pathways not previously reported in vertebrate cells, such as epigenetic regulation and RNA silencing, were also found in the NS1 interactome in mosquito cells. Due to the novel and strong interactions observed for NS1 and the epigenetic regulator DIDO1 (Death-Inducer Obliterator 1), the role of DIDO1 in viral replication was further explored. Interactions between NS1 and DIDO1 were corroborated in infected mosquito cells, by colocalization and proximity ligation assays. Silencing DIDO1 expression results in a significant reduction in DENV and ZIKV replication and progeny production. Comparison of transcription analysis of mock or DENV infected cells silenced for DIDO1 revealed variations in multiple gene expression pathways, including pathways associated with DENV infection such as RNA surveillance, IMD, and Toll. These results suggest that DIDO1 is a host factor involved in the negative modulation of the antiviral response necessary for flavivirus replication in mosquito cells. Our findings uncover novel mechanisms of NS1 to promote DENV and ZIKV replication, and add to the understanding of NS1 as a multifunctional protein. IMPORTANCE Dengue is the most important mosquito-borne viral disease to humans. Dengue virus NS1 is a multifunctional protein essential for replication and modulation of innate immunity. To gain insights into NS1 functions, the protein interactome of dengue virus NS1 in Aedes albopictus cells was investigated using a proximity biotinylation system and mass spectrometry. Several protein pathways, not previously observed in vertebrate cells, such as transcription and epigenetic regulation, were found as part of the NS1 interactome in mosquito cells. Among those, DIDO1 was found to be a necessary host factor for dengue and Zika virus replication in mosquito cells. Transcription analysis of infected mosquito cells silenced for DIDO1 revealed alterations of the IMD and Toll pathways, part of the antiviral response in mosquitoes. The results suggest that DIDO1 is a host factor involved in modulation of the antiviral response and necessary for flavivirus replication.
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Zhang Y, Jiang J, Zhang J, Shen H, Wang M, Guo Z, Zang X, Shi H, Gao J, Cai H, Fang X, Qian H, Xu W, Zhang X. CircDIDO1 inhibits gastric cancer progression by encoding a novel DIDO1-529aa protein and regulating PRDX2 protein stability. Mol Cancer 2021; 20:101. [PMID: 34384442 PMCID: PMC8359101 DOI: 10.1186/s12943-021-01390-y] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 07/02/2021] [Indexed: 12/19/2022] Open
Abstract
Background Circular RNAs (circRNAs) play important roles in cancer development and progression. The purpose of this study is to identify aberrantly expressed circRNAs in gastric cancer (GC), unravel their roles in GC progression, and provide new targets for GC diagnosis and therapy. Methods Bioinformatic analyses were performed to identify the aberrantly expression of hsa_circ_0061137 (termed as circDIDO1) in GC. Gain- and loss-of-function studies were performed to examine the biological roles of circDIDO1 in GC progression. Tagged RNA affinity purification, mass spectrometry, immunofluorescence, co-immunoprecipitation, and Western blot were used to identify circRNA-interacting and circRNA-encoded proteins. RNA sequencing, qRT-PCR, and Western blot were performed to analyze circRNA-regulated downstream target genes and signaling pathways. Mouse tumor models were used to analyze the effects of circDIDO1 on GC growth and metastasis. Results CircDIDO1 was transcribed from human DIDO1 (death-inducer obliterator 1) gene and formed by back-splicing of exons 2–6 of the linear transcript. circDIDO1 was down-regulated in GC tissues and its low levels were associated with larger tumor size, distal metastasis, and poor prognosis. CircDIDO1 overexpression inhibited while knockdown promoted GC cell proliferation, migration and invasion. CircDIDO1 overexpression suppressed GC growth and metastasis in mouse tumor models. Mechanistically, circDIDO1 encoded a novel 529aa protein that directly interacted with poly ADP-ribose polymerase 1 (PARP1) and inhibited its activity. CircDIDO1 also specifically bound to peroxiredoxin 2 (PRDX2) and promoted RBX1-mediated ubiquitination and degradation of PRDX2, which led to the inactivation of its downstream signaling pathways. Conclusions CircDIDO1 is a new circRNA that has tumor suppressor function in GC and it may serve as a potential prognostic biomarker and therapeutic target for GC. Supplementary Information The online version contains supplementary material available at 10.1186/s12943-021-01390-y.
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Affiliation(s)
- Yu Zhang
- Aoyang Cancer Institute, Affiliated Aoyang Hospital of Jiangsu University, Zhangjiagang, 215600, Jiangsu, China.,Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.,Department of Laboratory Medicine, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, 210009, Jiangsu, China
| | - Jiajia Jiang
- Aoyang Cancer Institute, Affiliated Aoyang Hospital of Jiangsu University, Zhangjiagang, 215600, Jiangsu, China.,Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jiayin Zhang
- Aoyang Cancer Institute, Affiliated Aoyang Hospital of Jiangsu University, Zhangjiagang, 215600, Jiangsu, China.,Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Han Shen
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.,Department of Laboratory Medicine, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, 210009, Jiangsu, China
| | - Maoye Wang
- Aoyang Cancer Institute, Affiliated Aoyang Hospital of Jiangsu University, Zhangjiagang, 215600, Jiangsu, China.,Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Zhen Guo
- Aoyang Cancer Institute, Affiliated Aoyang Hospital of Jiangsu University, Zhangjiagang, 215600, Jiangsu, China.,Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Xueyan Zang
- Aoyang Cancer Institute, Affiliated Aoyang Hospital of Jiangsu University, Zhangjiagang, 215600, Jiangsu, China.,Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Hui Shi
- Aoyang Cancer Institute, Affiliated Aoyang Hospital of Jiangsu University, Zhangjiagang, 215600, Jiangsu, China.,Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.,Department of Oncology, Lianyungang Hospital Affiliated To Jiangsu University, Lianyungang, 222000, Jiangsu, China.,Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province, Gansu Hospital of Jiangsu University, Lanzhou, 730000, Gansu, China
| | - Jiayan Gao
- Aoyang Cancer Institute, Affiliated Aoyang Hospital of Jiangsu University, Zhangjiagang, 215600, Jiangsu, China
| | - Hui Cai
- Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province, Gansu Hospital of Jiangsu University, Lanzhou, 730000, Gansu, China
| | - Xinjian Fang
- Department of Oncology, Lianyungang Hospital Affiliated To Jiangsu University, Lianyungang, 222000, Jiangsu, China
| | - Hui Qian
- Aoyang Cancer Institute, Affiliated Aoyang Hospital of Jiangsu University, Zhangjiagang, 215600, Jiangsu, China.,Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Wenrong Xu
- Aoyang Cancer Institute, Affiliated Aoyang Hospital of Jiangsu University, Zhangjiagang, 215600, Jiangsu, China. .,Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
| | - Xu Zhang
- Aoyang Cancer Institute, Affiliated Aoyang Hospital of Jiangsu University, Zhangjiagang, 215600, Jiangsu, China. .,Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China. .,Department of Laboratory Medicine, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, 210009, Jiangsu, China. .,Department of Oncology, Lianyungang Hospital Affiliated To Jiangsu University, Lianyungang, 222000, Jiangsu, China. .,Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province, Gansu Hospital of Jiangsu University, Lanzhou, 730000, Gansu, China.
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Phosphorylation of H3-Thr3 by Haspin Is Required for Primary Cilia Regulation. Int J Mol Sci 2021; 22:ijms22147753. [PMID: 34299370 PMCID: PMC8307231 DOI: 10.3390/ijms22147753] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/13/2021] [Accepted: 07/16/2021] [Indexed: 01/19/2023] Open
Abstract
Primary cilia are commonly found on most quiescent, terminally differentiated cells and play a major role in the regulation of the cell cycle, cell motility, sensing, and cell–cell communication. Alterations in ciliogenesis and cilia maintenance are causative of several human diseases, collectively known as ciliopathies. A key determinant of primary cilia is the histone deacetylase HDAC6, which regulates their length and resorption and whose distribution is regulated by the death inducer-obliterator 3 (Dido3). Here, we report that the atypical protein kinase Haspin is a key regulator of cilia dynamics. Cells defective in Haspin activity exhibit longer primary cilia and a strong delay in cilia resorption upon cell cycle reentry. We show that Haspin is active in quiescent cells, where it phosphorylates threonine 3 of histone H3, a known mitotic Haspin substrate. Forcing Dido3 detachment from the chromatin prevents Haspin inhibition from impacting cilia dynamics, suggesting that Haspin activity is required for the relocalization of Dido3–HDAC6 to the basal body. Exploiting the zebrafish model, we confirmed the physiological relevance of this mechanism. Our observations shed light on a novel player, Haspin, in the mechanisms that govern the determination of cilia length and the homeostasis of mature cilia.
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Albanese KI, Waters ML. Contributions of methionine to recognition of trimethyllysine in aromatic cage of PHD domains: implications of polarizability, hydrophobicity, and charge on binding. Chem Sci 2021; 12:8900-8908. [PMID: 34257891 PMCID: PMC8246079 DOI: 10.1039/d1sc02175c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 05/27/2021] [Indexed: 11/21/2022] Open
Abstract
Recognition of trimethyllysine (Kme3) by reader proteins is an important regulator of gene expression. This recognition event is mediated by an aromatic cage made up of 2-4 aromatic residues in the reader proteins that bind Kme3 via cation-π interactions. A small subset of reader proteins contain a methionine (Met) residue in place of an aromatic sidechain in the binding pocket. The unique role of sulfur in molecular recognition has been demonstrated in a number of noncovalent interactions recently, including interactions of thiols, thioethers, and sulfoxides with aromatic rings. However, the interaction of a thioether with an ammonium ion has not previously been investigated and the role of Met in binding Kme3 has not yet been explored. Herein, we systematically vary the Met in two reader proteins, DIDO1 and TAF3, and the ligand, Kme3 or its neutral analog tert-butyl norleucine (tBuNle), to determine the role of Met in the recognition of the cationic Kme3. Our studies demonstrate that Met contributes to binding via dispersion forces, with about an equal contribution to binding Kme3 and tBuNle, indicating that electrostatic interactions do not play a role. During the course of these studies, we also discovered that DIDO1 exhibits equivalent binding to tBuNle and Kme3 through a change in the mechanism of binding.
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Affiliation(s)
- Katherine I Albanese
- Department of Chemistry, University of North Carolina at Chapel Hill CB 3290 Chapel Hill NC 27599 USA
| | - Marcey L Waters
- Department of Chemistry, University of North Carolina at Chapel Hill CB 3290 Chapel Hill NC 27599 USA
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8
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Hiwasa T, Wang H, Goto KI, Mine S, Machida T, Kobayashi E, Yoshida Y, Adachi A, Matsutani T, Sata M, Yamagishi K, Iso H, Sawada N, Tsugane S, Kunimatsu M, Kamitsukasa I, Mori M, Sugimoto K, Uzawa A, Muto M, Kuwabara S, Kobayashi Y, Ohno M, Nishi E, Hattori A, Yamamoto M, Maezawa Y, Kobayashi K, Ishibashi R, Takemoto M, Yokote K, Takizawa H, Kishimoto T, Matsushita K, Kobayashi S, Nomura F, Arasawa T, Kagaya A, Maruyama T, Matsubara H, Tomiita M, Hamanaka S, Imai Y, Nakagawa T, Kato N, Terada J, Matsumura T, Katsumata Y, Naito A, Tanabe N, Sakao S, Tatsumi K, Ito M, Shiratori F, Sumazaki M, Yajima S, Shimada H, Shirouzu M, Yokoyama S, Kudo T, Doi H, Iwase K, Ashino H, Li SY, Kubota M, Tomiyoshi G, Shinmen N, Nakamura R, Kuroda H, Iwadate Y. Serum anti-DIDO1, anti-CPSF2, and anti-FOXJ2 antibodies as predictive risk markers for acute ischemic stroke. BMC Med 2021; 19:131. [PMID: 34103026 PMCID: PMC8188684 DOI: 10.1186/s12916-021-02001-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 04/30/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Acute ischemic stroke (AIS) is a serious cause of mortality and disability. AIS is a serious cause of mortality and disability. Early diagnosis of atherosclerosis, which is the major cause of AIS, allows therapeutic intervention before the onset, leading to prevention of AIS. METHODS Serological identification by cDNA expression cDNA libraries and the protein array method were used for the screening of antigens recognized by serum IgG antibodies in patients with atherosclerosis. Recombinant proteins or synthetic peptides derived from candidate antigens were used as antigens to compare serum IgG levels between healthy donors (HDs) and patients with atherosclerosis-related disease using the amplified luminescent proximity homogeneous assay-linked immunosorbent assay. RESULTS The first screening using the protein array method identified death-inducer obliterator 1 (DIDO1), forkhead box J2 (FOXJ2), and cleavage and polyadenylation specificity factor (CPSF2) as the target antigens of serum IgG antibodies in patients with AIS. Then, we prepared various antigens including glutathione S-transferase-fused DIDO1 protein as well as peptides of the amino acids 297-311 of DIDO1, 426-440 of FOXJ2, and 607-621 of CPSF2 to examine serum antibody levels. Compared with HDs, a significant increase in antibody levels of the DIDO1 protein and peptide in patients with AIS, transient ischemic attack (TIA), and chronic kidney disease (CKD) but not in those with acute myocardial infarction and diabetes mellitus (DM). Serum anti-FOXJ2 antibody levels were elevated in most patients with atherosclerosis-related diseases, whereas serum anti-CPSF2 antibody levels were associated with AIS, TIA, and DM. Receiver operating characteristic curves showed that serum DIDO1 antibody levels were highly associated with CKD, and correlation analysis revealed that serum anti-FOXJ2 antibody levels were associated with hypertension. A prospective case-control study on ischemic stroke verified that the serum antibody levels of the DIDO1 protein and DIDO1, FOXJ2, and CPSF2 peptides showed significantly higher odds ratios with a risk of AIS in patients with the highest quartile than in those with the lowest quartile, indicating that these antibody markers are useful as risk factors for AIS. CONCLUSIONS Serum antibody levels of DIDO1, FOXJ2, and CPSF2 are useful in predicting the onset of atherosclerosis-related AIS caused by kidney failure, hypertension, and DM, respectively.
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Affiliation(s)
- Takaki Hiwasa
- Department of Neurological Surgery, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan. .,Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan. .,Comprehensive Stroke Center, Chiba University Hospital, Chiba, 260-8677, Japan.
| | - Hao Wang
- Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan.,Department of Anesthesia, The First Affiliated Hospital, Jinan University, Guanzhou, 510632, P. R. China
| | - Ken-Ichiro Goto
- Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Seiichiro Mine
- Department of Neurological Surgery, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan.,Department of Neurological Surgery, Chiba Prefectural Sawara Hospital, Chiba, 287-0003, Japan.,Department of Neurological Surgery, Chiba Cerebral and Cardiovascular Center, Chiba, 290-0512, Japan
| | - Toshio Machida
- Department of Neurological Surgery, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan.,Department of Neurological Surgery, Chiba Cerebral and Cardiovascular Center, Chiba, 290-0512, Japan.,Department of Neurosurgery, Eastern Chiba Medical Center, Chiba, 283-8686, Japan
| | - Eiichi Kobayashi
- Department of Neurological Surgery, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan.,Comprehensive Stroke Center, Chiba University Hospital, Chiba, 260-8677, Japan
| | - Yoichi Yoshida
- Department of Neurological Surgery, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan.,Comprehensive Stroke Center, Chiba University Hospital, Chiba, 260-8677, Japan
| | - Akihiko Adachi
- Department of Neurological Surgery, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan.,Comprehensive Stroke Center, Chiba University Hospital, Chiba, 260-8677, Japan
| | - Tomoo Matsutani
- Department of Neurological Surgery, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan.,Comprehensive Stroke Center, Chiba University Hospital, Chiba, 260-8677, Japan
| | - Mizuki Sata
- Department of Public Health Medicine, Faculty of Medicine, and Health Services Research and Development Center, University of Tsukuba, Tsukuba, 305-8575, Japan.,Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Kazumasa Yamagishi
- Department of Public Health Medicine, Faculty of Medicine, and Health Services Research and Development Center, University of Tsukuba, Tsukuba, 305-8575, Japan
| | - Hiroyasu Iso
- Public Health, Department of Social Medicine, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan
| | - Norie Sawada
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Tokyo, 104-0045, Japan
| | - Shoichiro Tsugane
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Tokyo, 104-0045, Japan
| | - Mitoshi Kunimatsu
- Department of Home Economics, Nagoya Women's University, Nagoya, 467-8610, Japan
| | - Ikuo Kamitsukasa
- Department of Neurology, Chiba Rosai Hospital, Chiba, 290-0003, Japan.,Department of Neurology, Chibaken Saiseikai Narashino Hospital, Chiba, 275-8580, Japan
| | - Masahiro Mori
- Department of Neurology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Kazuo Sugimoto
- Department of Neurological Surgery, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan.,Department of Neurology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Akiyuki Uzawa
- Comprehensive Stroke Center, Chiba University Hospital, Chiba, 260-8677, Japan.,Department of Neurology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Mayumi Muto
- Department of Neurology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Satoshi Kuwabara
- Comprehensive Stroke Center, Chiba University Hospital, Chiba, 260-8677, Japan.,Department of Neurology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Yoshio Kobayashi
- Department of Cardiovascular Medicine, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Mikiko Ohno
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan.,Department of Pharmacology, Shiga University of Medical Science, Shiga, 520-2192, Japan
| | - Eiichiro Nishi
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan.,Department of Pharmacology, Shiga University of Medical Science, Shiga, 520-2192, Japan
| | - Akiko Hattori
- Department of Endocrinology, Hematology and Gerontology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Masashi Yamamoto
- Department of Endocrinology, Hematology and Gerontology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Yoshiro Maezawa
- Department of Endocrinology, Hematology and Gerontology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Kazuki Kobayashi
- Department of Endocrinology, Hematology and Gerontology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Ryoichi Ishibashi
- Department of Endocrinology, Hematology and Gerontology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Minoru Takemoto
- Department of Endocrinology, Hematology and Gerontology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan.,Department of Diabetes, Metabolism and Endocrinology, School of Medicine, International University of Health and Welfare, Chiba, 286-8686, Japan
| | - Koutaro Yokote
- Department of Endocrinology, Hematology and Gerontology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Hirotaka Takizawa
- Port Square Kashiwado Clinic, Kashiwado Memorial Foundation, Chiba, 260-0025, Japan
| | - Takashi Kishimoto
- Department of Molecular Pathology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Kazuyuki Matsushita
- Department of Laboratory Medicine & Division of Clinical Genetics, Chiba University Hospital, Chiba, 260-8677, Japan
| | - Sohei Kobayashi
- Department of Laboratory Medicine & Division of Clinical Genetics, Chiba University Hospital, Chiba, 260-8677, Japan.,Department of Medical Technology and Sciences, School of Health Sciences at Narita, International University of Health and Welfare, Chiba, 286-8686, Japan
| | - Fumio Nomura
- Division of Clinical Genetics, Chiba Foundation for Health Promotion and Disease Prevention, Chiba, 261-0002, Japan
| | - Takahiro Arasawa
- Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan.,Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Akiko Kagaya
- Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Tetsuro Maruyama
- Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Hisahiro Matsubara
- Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Minako Tomiita
- Department of Allergy and Rheumatology, Chiba Children's Hospital, Chiba, 266-0007, Japan
| | - Shinsaku Hamanaka
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Yushi Imai
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Tomoo Nakagawa
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Naoya Kato
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Jiro Terada
- Department of Respirology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Takuma Matsumura
- Department of Respirology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Yusuke Katsumata
- Department of Respirology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Akira Naito
- Department of Respirology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Nobuhiro Tanabe
- Department of Respirology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan.,Department of Advanced Medicine in Pulmonary Hypertension, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Seiichiro Sakao
- Department of Respirology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Koichiro Tatsumi
- Department of Respirology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Masaaki Ito
- Department of Gastroenterological Surgery and Clinical Oncology, Toho University Graduate School of Medicine, Tokyo, 143-8541, Japan
| | - Fumiaki Shiratori
- Department of Gastroenterological Surgery and Clinical Oncology, Toho University Graduate School of Medicine, Tokyo, 143-8541, Japan
| | - Makoto Sumazaki
- Department of Gastroenterological Surgery and Clinical Oncology, Toho University Graduate School of Medicine, Tokyo, 143-8541, Japan
| | - Satoshi Yajima
- Department of Gastroenterological Surgery and Clinical Oncology, Toho University Graduate School of Medicine, Tokyo, 143-8541, Japan
| | - Hideaki Shimada
- Department of Gastroenterological Surgery and Clinical Oncology, Toho University Graduate School of Medicine, Tokyo, 143-8541, Japan
| | - Mikako Shirouzu
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Shigeyuki Yokoyama
- RIKEN Structural Biology Laboratory, Yokohama, Kanagawa, 230-0045, Japan
| | | | | | - Katsuro Iwase
- Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Hiromi Ashino
- Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Shu-Yang Li
- Department of Neurological Surgery, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan.,Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Masaaki Kubota
- Department of Neurological Surgery, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Go Tomiyoshi
- Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan.,Medical Project Division, Research Development Center, Fujikura Kasei Co., Saitama, 340-0203, Japan
| | - Natsuko Shinmen
- Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan.,Medical Project Division, Research Development Center, Fujikura Kasei Co., Saitama, 340-0203, Japan
| | - Rika Nakamura
- Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan.,Medical Project Division, Research Development Center, Fujikura Kasei Co., Saitama, 340-0203, Japan
| | - Hideyuki Kuroda
- Medical Project Division, Research Development Center, Fujikura Kasei Co., Saitama, 340-0203, Japan
| | - Yasuo Iwadate
- Department of Neurological Surgery, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan.,Comprehensive Stroke Center, Chiba University Hospital, Chiba, 260-8677, Japan
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9
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Bone Morphogenic Protein Signaling and Melanoma. Curr Treat Options Oncol 2021; 22:48. [PMID: 33866453 DOI: 10.1007/s11864-021-00849-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/16/2021] [Indexed: 10/21/2022]
Abstract
OPINION STATEMENT Malignant melanoma is a deadly form of skin cancer caused by neoplastic transformation of melanocytic cells. Despite recent progress in melanoma therapy, by inhibition of activated oncogenes or immunotherapy, survival rate for metastatic melanoma patients remains low. The remarkable phenotypic plasticity of melanoma cells allows for rapid development of invasive properties and metastatic tumors, the main cause of mortality in melanoma patients. Phenotypic and molecular analyses of developing tumors revealed that epithelial-mesenchymal transition (EMT), a cellular and molecular mechanism, controls transition from mature melanocyte to less differentiated melanocyte lineage progenitor cells forming melanoma tumors. This transition is facilitated by persistence of transcriptional regulatory circuit characteristic of embryonic stage in mature melanocytes. Switching of the developmental program of mature melanocyte to EMT is induced by accumulated mutations, especially targeting BRAF, N-RAS, or MEK1/2 signaling pathways, and further promoted by dynamic stimuli from local environment including hypoxia, interactions with extracellular matrix and growth factors or cytokines. Recent reports demonstrate that signaling mediated by transforming growth factor-β (TGF-β) and bone morphogenic proteins (BMPs) play critical roles in inducing EMT by controlling expression of critical transcription factors. BMPs are essential modulators of differentiation, proliferation, apoptosis, invasiveness, and metastases in developing melanoma tumors. They control transcription and epigenetic landscape of melanoma cells. Better understanding of the role of BMPs may lead to new strategies to control EMT processes in melanocyte cell lineage and to achieve clinical benefits for the patients.
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10
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Leal-Gutiérrez JD, Elzo MA, Carr C, Mateescu RG. RNA-seq analysis identifies cytoskeletal structural genes and pathways for meat quality in beef. PLoS One 2020; 15:e0240895. [PMID: 33175867 PMCID: PMC7657496 DOI: 10.1371/journal.pone.0240895] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 10/05/2020] [Indexed: 01/03/2023] Open
Abstract
RNA sequencing (RNA-seq) has allowed for transcriptional profiling of biological systems through the identification of differentially expressed (DE) genes and pathways. A total of 80 steers with extreme phenotypes were selected from the University of Florida multibreed Angus-Brahman herd. The average slaughter age was 12.91±8.69 months. Tenderness, juiciness and connective tissue assessed by sensory panel, along with marbling, Warner-Bratzler Shear Force (WBSF) and cooking loss, were measured in longissimus dorsi muscle. Total RNA was extracted from muscle and one RNA-seq library per sample was constructed, multiplexed, and sequenced based on protocols by Illumina HiSeq-3000 platform to generate 2×101 bp paired-end reads. The overall read mapping rate using the Btau_4.6.1 reference genome was 63%. A total of 8,799 genes were analyzed using two different methodologies, an expression association and a DE analysis. A gene and exon expression association analysis was carried out using a meat quality index on all 80 samples as a continuous response variable. The expression of 208 genes and 3,280 exons from 1,565 genes was associated with the meat quality index (p-value ≤ 0.05). A gene and isoform DE evaluation was performed analyzing two groups with extreme WBSF, tenderness and marbling. A total of 676 (adjusted p-value≤0.05), 70 (adjusted p-value≤0.1) and 198 (adjusted p-value≤0.1) genes were DE for WBSF, tenderness and marbling, respectively. A total of 106 isoforms from 98 genes for WBSF, 13 isoforms from 13 genes for tenderness and 43 isoforms from 42 genes for marbling (FDR≤0.1) were DE. Cytoskeletal and transmembrane anchoring genes and pathways were identified in the expression association, DE and the gene enrichment analyses; these proteins can have a direct effect on meat quality. Cytoskeletal proteins and transmembrane anchoring molecules can influence meat quality by allowing cytoskeletal interaction with myocyte and organelle membranes, contributing to cytoskeletal structure and architecture maintenance postmortem.
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Affiliation(s)
- Joel D. Leal-Gutiérrez
- Department of Animal Sciences, University of Florida, Gainesville, Florida, United States of America
| | - Mauricio A. Elzo
- Department of Animal Sciences, University of Florida, Gainesville, Florida, United States of America
| | - Chad Carr
- Department of Animal Sciences, University of Florida, Gainesville, Florida, United States of America
| | - Raluca G. Mateescu
- Department of Animal Sciences, University of Florida, Gainesville, Florida, United States of America
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11
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Cardon T, Franck J, Coyaud E, Laurent EMN, Damato M, Maffia M, Vergara D, Fournier I, Salzet M. Alternative proteins are functional regulators in cell reprogramming by PKA activation. Nucleic Acids Res 2020; 48:7864-7882. [PMID: 32324228 PMCID: PMC7641301 DOI: 10.1093/nar/gkaa277] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 04/06/2020] [Accepted: 04/21/2020] [Indexed: 12/28/2022] Open
Abstract
It has been recently shown that many proteins are lacking from reference databases used in mass spectrometry analysis, due to their translation templated on alternative open reading frames. This questions our current understanding of gene annotation and drastically expands the theoretical proteome complexity. The functions of these alternative proteins (AltProts) still remain largely unknown. We have developed a large-scale and unsupervised approach based on cross-linking mass spectrometry (XL-MS) followed by shotgun proteomics to gather information on the functional role of AltProts by mapping them back into known signalling pathways through the identification of their reference protein (RefProt) interactors. We have identified and profiled AltProts in a cancer cell reprogramming system: NCH82 human glioma cells after 0, 16, 24 and 48 h Forskolin stimulation. Forskolin is a protein kinase A activator inducing cell differentiation and epithelial–mesenchymal transition. Our data show that AltMAP2, AltTRNAU1AP and AltEPHA5 interactions with tropomyosin 4 are downregulated under Forskolin treatment. In a wider perspective, Gene Ontology and pathway enrichment analysis (STRING) revealed that RefProts associated with AltProts are enriched in cellular mobility and transfer RNA regulation. This study strongly suggests novel roles of AltProts in multiple essential cellular functions and supports the importance of considering them in future biological studies.
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Affiliation(s)
- Tristan Cardon
- Univ. Lille, Inserm, CHU Lille, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Julien Franck
- Univ. Lille, Inserm, CHU Lille, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Etienne Coyaud
- Univ. Lille, Inserm, CHU Lille, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Estelle M N Laurent
- Univ. Lille, Inserm, CHU Lille, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Marina Damato
- Univ. Lille, Inserm, CHU Lille, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse (PRISM), F-59000 Lille, France.,Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy
| | - Michele Maffia
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy
| | - Daniele Vergara
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy
| | - Isabelle Fournier
- Univ. Lille, Inserm, CHU Lille, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse (PRISM), F-59000 Lille, France.,Institut Universitaire de France (IUF),75005 Paris, France
| | - Michel Salzet
- Univ. Lille, Inserm, CHU Lille, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse (PRISM), F-59000 Lille, France.,Institut Universitaire de France (IUF),75005 Paris, France
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12
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Xiao J, Zhang R, Peng J, Yang Z. BAP1 maintains chromosome stability by stabilizing DIDO1 in renal cell carcinoma. Am J Cancer Res 2020; 10:1455-1466. [PMID: 32509391 PMCID: PMC7269789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 04/04/2020] [Indexed: 06/11/2023] Open
Abstract
BRCA1-associated protein 1 (BAP1) is a member of the ubiquitin C-terminal hydrolase family of deubiquitinating enzymes and is implicated in transcriptional regulation. The BAP1 gene is mutated in 5%-15% of patients with clear cell renal cell carcinoma (ccRCC), the most common form of renal cancer, which suggests that BAP1 is a tumor suppressor. However, whether BAP1 influences the progression of ccRCC tumors expressing wildtype (WT) BAP1 is unclear. Here, we identified DIDO1 as a bona fide substrate for BAP1. DIDO1 is a component of the centrosome proteins and plays an essential role in spindle assembly. BAP1 binds to DIDO1 and stabilizes DIDO1 through de-ubiquitination. BAP1 contributes to chromosome stability partially via DIDO1. A positive correlation was identified between BAP1 and DIDO1 expression in ccRCC tissues. Downregulation of both BAP1-loss and DIDO1 protein expression in ccRCC was associated with adverse clinicopathological features. This study revealed a novel mechanism involving BAP1 in the regulation of DIDO1 stability, and the results also provide insight into the relationship between BAP1 mutations and chromosome instability in ccRCC.
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Affiliation(s)
- Jiantao Xiao
- Department of Urology, Zhongnan Hospital of Wuhan UniversityWuhan, China
| | - Ruhan Zhang
- Department of Nursing, Zhongnan Hospital of Wuhan UniversityWuhan, China
| | - Jingtao Peng
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan, China
| | - Zhonghua Yang
- Department of Urology, Zhongnan Hospital of Wuhan UniversityWuhan, China
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13
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Petell CJ, Pham AT, Skela J, Strahl BD. Improved methods for the detection of histone interactions with peptide microarrays. Sci Rep 2019; 9:6265. [PMID: 31000785 PMCID: PMC6472351 DOI: 10.1038/s41598-019-42711-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 04/05/2019] [Indexed: 02/07/2023] Open
Abstract
Histone post-translational modifications contribute to chromatin function largely through the recruitment of effector proteins that contain specialized "reader" domains. While a significant number of reader domains have been characterized for their histone binding specificities, many of these domains remain poorly characterized. Peptide microarrays have been widely employed for the characterization of histone readers, as well as modifying enzymes and histone antibodies. While powerful, this platform has limitations in terms of its sensitivity and they frequently miss low affinity reader domain interactions. Here, we provide several technical changes that improve reader domain detection of low-affinity interactions. We show that 1% non-fat milk in 1X PBST as the blocking reagent during incubation improved reader-domain interaction results. Further, coupling this with post-binding high-salt washes and a brief, low-percentage formaldehyde cross-linking step prior to the high-salt washes provided the optimal balance between resolving specific low-affinity interactions and minimizing background or spurious signals. We expect this improved methodology will lead to the elucidation of previously unreported reader-histone interactions that will be important for chromatin function.
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Affiliation(s)
- Christopher J Petell
- Department of Biochemistry and Biophysics, 120 Mason Farm Rd, University of North Carolina at Chapel Hill, NC, Chapel Hill, 27599, USA
- UNC Lineberger Comprehensive Cancer Center, 450 West Drive, University of North Carolina at Chapel Hill, NC, Chapel Hill, 27599, USA
| | - Andrea T Pham
- Department of Biochemistry and Biophysics, 120 Mason Farm Rd, University of North Carolina at Chapel Hill, NC, Chapel Hill, 27599, USA
| | - Jessica Skela
- Department of Biochemistry and Biophysics, 120 Mason Farm Rd, University of North Carolina at Chapel Hill, NC, Chapel Hill, 27599, USA
| | - Brian D Strahl
- Department of Biochemistry and Biophysics, 120 Mason Farm Rd, University of North Carolina at Chapel Hill, NC, Chapel Hill, 27599, USA.
- UNC Lineberger Comprehensive Cancer Center, 450 West Drive, University of North Carolina at Chapel Hill, NC, Chapel Hill, 27599, USA.
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14
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Thutkawkorapin J, Lindblom A, Tham E. Exome sequencing in 51 early onset non-familial CRC cases. Mol Genet Genomic Med 2019; 7:e605. [PMID: 30809968 PMCID: PMC6503031 DOI: 10.1002/mgg3.605] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 12/22/2018] [Accepted: 01/16/2019] [Indexed: 12/12/2022] Open
Abstract
Background Colorectal cancer (CRC) cases with an age of onset <40 years suggests a germline genetic cause. In total, 51 simplex cases were included to test the hypothesis of CRC as a mendelian trait caused by either heterozygous autosomal dominant or bi‐allelic autosomal recessive pathogenic variants. Methods The cohort was whole exome sequenced (WES) at 100× coverage. Both a dominant‐ and recessive model were used for searching predisposing genetic factors. In addition, we assayed recessive variants of potential moderate risk that were enriched in our young‐onset CRC cohort. Variants were filtered using a candidate cancer gene list or by selecting variants more likely to be pathogenic based on variant type (e.g., loss‐of‐function) or allele frequency. Results We identified one pathogenic variant in PTEN in a patient subsequently confirmed to have a hereditary hamartoma tumor syndrome (Cowden syndrome) and one patient with a pathogenic heterozygous variant in PMS2 that was originally not identified by WES due to low quality reads resulting from pseudogenes. In addition, we identified three heterozygous candidate missense variants in known cancer susceptibility genes (BMPR1A,BRIP1, and SRC), three truncating variants in possibly novel cancer genes (CLSPN,SEC24B, SSH2) and four candidate missense variants in ACACA, NR2C2, INPP4A, and DIDO1. We also identify five possible autosomal recessive candidate genes: ATP10B,PKHD1,UGGT2,MYH13,TFF3. Conclusion Two clear pathogenic variants were identified in patients that had not been identified clinically. Thus, the chance of detecting a hereditary cancer syndrome in patients with CRC at young age but without family history is 2/51 (4%) and therefore the clinical benefit of genetic testing in this patient group is low. Of note, using stringent filtering, we have identified a total of ten candidate heterozygous variants and five possibly biallelic autosomal recessive candidate genes that warrant further study.
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Affiliation(s)
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet and Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Emma Tham
- Department of Molecular Medicine and Surgery, Karolinska Institutet and Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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15
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DNA methylation in a sea lamprey vasotocin receptor gene promoter correlates with tissue- and life-stage-specific mRNA expression. Comp Biochem Physiol B Biochem Mol Biol 2016; 202:56-66. [PMID: 27497665 DOI: 10.1016/j.cbpb.2016.07.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 07/28/2016] [Accepted: 07/30/2016] [Indexed: 11/23/2022]
Abstract
The jawless vertebrate sea lamprey (Petromyzon marinus) genome has a different structure from both invertebrates and jawed vertebrates featuring high guanine-cytosine (GC) content. This raises the question of whether DNA methylation of cytosine-guanine (CpG) dinucleotides could function to regulate lamprey gene transcription. We previously characterized a lamprey arginine vasotocin (AVT) receptor gene (Pm807) possessing characteristics of both arginine vasopressin (AVP) V1A and oxytocin (OXT) receptor genes of jawed vertebrates. Lamprey Pm807 mRNA is highly expressed in adult heart and larval liver but not expressed in adult liver. Using high-resolution melt (HRM) PCR on bisulfite-converted DNA, we pinpointed a region with tissue-specific differences in DNA melt characteristics, indicating differences in methylation level. Sequencing revealed a pattern of methylation at specific CpGs at consistently higher levels in adult heart and larval liver than adult liver. These CpGs are associated with putative transcription factor binding sequences organized similarly to functional OXTR promoters in mammals, suggesting functional similarity in lamprey gene transcription regulation.
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16
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Lu W, Fang L, Ouyang B, Zhang X, Zhan S, Feng X, Bai Y, Han X, Kim H, He Q, Wan M, Shi FT, Feng XH, Liu D, Huang J, Songyang Z. Actl6a protects embryonic stem cells from differentiating into primitive endoderm. Stem Cells 2016; 33:1782-93. [PMID: 25802002 DOI: 10.1002/stem.2000] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 01/30/2015] [Accepted: 02/18/2015] [Indexed: 02/06/2023]
Abstract
Actl6a (actin-like protein 6A, also known as Baf53a or Arp4) is a subunit shared by multiple complexes including esBAF, INO80, and Tip60-p400, whose main components (Brg1, Ino80, and p400, respectively) are crucial for the maintenance of embryonic stem cells (ESCs). However, whether and how Actl6a functions in ESCs has not been investigated. ESCs originate from the epiblast (EPI) that is derived from the inner cell mass (ICM) in blastocysts, which also give rise to primitive endoderm (PrE). The molecular mechanisms for EPI/PrE specification remain unclear. In this study, we provide the first evidence that Actl6a can protect mouse ESCs (mESCs) from differentiating into PrE. While RNAi knockdown of Actl6a, which appeared highly expressed in mESCs and downregulated during differentiation, induced mESCs to differentiate towards the PrE lineage, ectopic expression of Actl6a was able to repress PrE differentiation. Our work also revealed that Actl6a could interact with Nanog and Sox2 and promote Nanog binding to pluripotency genes such as Oct4 and Sox2. Interestingly, cells depleted of p400, but not of Brg1 or Ino80, displayed similar PrE differentiation patterns. Mutant Actl6a with impaired ability to bind Tip60 and p400 failed to block PrE differentiation induced by Actl6a dysfunction. Finally, we showed that Actl6a could target to the promoters of key PrE regulators (e.g., Sall4 and Fgf4), repressing their expression and inhibiting PrE differentiation. Our findings uncover a novel function of Actl6a in mESCs, where it acts as a gatekeeper to prevent mESCs from entering into the PrE lineage through a Yin/Yang regulating pattern.
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Affiliation(s)
- Weisi Lu
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Reproductive Medicine of Guangdong Province, School of Life Sciences and the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Lekun Fang
- Guangdong Gastroenterology Institute, Department of Gastrointestinal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Bin Ouyang
- Department of Urology, The First People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Xiya Zhang
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Reproductive Medicine of Guangdong Province, School of Life Sciences and the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shaoquan Zhan
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Reproductive Medicine of Guangdong Province, School of Life Sciences and the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xuyang Feng
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Reproductive Medicine of Guangdong Province, School of Life Sciences and the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yaofu Bai
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Reproductive Medicine of Guangdong Province, School of Life Sciences and the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xin Han
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Reproductive Medicine of Guangdong Province, School of Life Sciences and the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Hyeung Kim
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Quanyuan He
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Ma Wan
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Feng-Tao Shi
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xin-Hua Feng
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Dan Liu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Junjiu Huang
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Reproductive Medicine of Guangdong Province, School of Life Sciences and the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhou Songyang
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Reproductive Medicine of Guangdong Province, School of Life Sciences and the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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17
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Cecchi F, Lih CJ, Lee YH, Walsh W, Rabe DC, Williams PM, Bottaro DP. Expression array analysis of the hepatocyte growth factor invasive program. Clin Exp Metastasis 2015; 32:659-76. [PMID: 26231668 DOI: 10.1007/s10585-015-9735-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 07/13/2015] [Indexed: 02/17/2023]
Abstract
Signaling by human hepatocyte growth factor (hHGF) via its cell surface receptor (MET) drives mitogenesis, motogenesis and morphogenesis in a wide spectrum of target cell types and embryologic, developmental and homeostatic contexts. Oncogenic pathway activation also contributes to tumorigenesis and cancer progression, including tumor angiogenesis and metastasis, in several prevalent malignancies. The HGF gene encodes full-length hHGF and two truncated isoforms known as NK1 and NK2. NK1 induces all three HGF activities at modestly reduced potency, whereas NK2 stimulates only motogenesis and enhances HGF-driven tumor metastasis in transgenic mice. Prior studies have shown that mouse HGF (mHGF) also binds with high affinity to human MET. Here we show that, like NK2, mHGF stimulates cell motility, invasion and spontaneous metastasis of PC3M human prostate adenocarcinoma cells in mice through human MET. To identify target genes and signaling pathways associated with motogenic and metastatic HGF signaling, i.e., the HGF invasive program, gene expression profiling was performed using PC3M cells treated with hHGF, NK2 or mHGF. Results obtained using Ingenuity Pathway Analysis software showed significant overlap with networks and pathways involved in cell movement and metastasis. Interrogating The Cancer Genome Atlas project also identified a subset of 23 gene expression changes in PC3M with a strong tendency for co-occurrence in prostate cancer patients that were associated with significantly decreased disease-free survival.
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Affiliation(s)
- Fabiola Cecchi
- Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892-1501, USA
| | - Chih-Jian Lih
- Molecular Characterization and Clinical Assay Development Laboratory, Leidos Biomedical Research, Inc. and Frederick National Laboratory for Cancer Research, Frederick, MD, 21702-1201, USA
| | - Young H Lee
- Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892-1501, USA
| | - William Walsh
- Molecular Characterization and Clinical Assay Development Laboratory, Leidos Biomedical Research, Inc. and Frederick National Laboratory for Cancer Research, Frederick, MD, 21702-1201, USA
| | - Daniel C Rabe
- Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892-1501, USA
| | - Paul M Williams
- Molecular Characterization and Clinical Assay Development Laboratory, Leidos Biomedical Research, Inc. and Frederick National Laboratory for Cancer Research, Frederick, MD, 21702-1201, USA
| | - Donald P Bottaro
- Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892-1501, USA. .,Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bldg 10 CRC Rm 2-3952, 10 Center Drive MSC 1107, Bethesda, MD, 20892-1107, USA.
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