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Roy S, Adhikary H, D’Amours D. The SMC5/6 complex: folding chromosomes back into shape when genomes take a break. Nucleic Acids Res 2024; 52:2112-2129. [PMID: 38375830 PMCID: PMC10954462 DOI: 10.1093/nar/gkae103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/28/2024] [Accepted: 02/01/2024] [Indexed: 02/21/2024] Open
Abstract
High-level folding of chromatin is a key determinant of the shape and functional state of chromosomes. During cell division, structural maintenance of chromosome (SMC) complexes such as condensin and cohesin ensure large-scale folding of chromatin into visible chromosomes. In contrast, the SMC5/6 complex plays more local and context-specific roles in the structural organization of interphase chromosomes with important implications for health and disease. Recent advances in single-molecule biophysics and cryo-electron microscopy revealed key insights into the architecture of the SMC5/6 complex and how interactions connecting the complex to chromatin components give rise to its unique repertoire of interphase functions. In this review, we provide an integrative view of the features that differentiates the SMC5/6 complex from other SMC enzymes and how these enable dramatic reorganization of DNA folding in space during DNA repair reactions and other genome transactions. Finally, we explore the mechanistic basis for the dynamic targeting of the SMC5/6 complex to damaged chromatin and its crucial role in human health.
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Affiliation(s)
- Shamayita Roy
- Ottawa Institute of Systems Biology, Department of Cellular and Molecular Medicine, University of Ottawa, Roger Guindon Hall, 451 Smyth Rd, Ottawa, ON K1H 8M5, Canada
| | - Hemanta Adhikary
- Ottawa Institute of Systems Biology, Department of Cellular and Molecular Medicine, University of Ottawa, Roger Guindon Hall, 451 Smyth Rd, Ottawa, ON K1H 8M5, Canada
| | - Damien D’Amours
- Ottawa Institute of Systems Biology, Department of Cellular and Molecular Medicine, University of Ottawa, Roger Guindon Hall, 451 Smyth Rd, Ottawa, ON K1H 8M5, Canada
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Odiba AS, Liao G, Ezechukwu CS, Zhang L, Hong Y, Fang W, Jin C, Gartner A, Wang B. Caenorhabditis elegans NSE3 homolog (MAGE-1) is involved in genome stability and acts in inter-sister recombination during meiosis. Genetics 2023; 225:iyad149. [PMID: 37579186 PMCID: PMC10691751 DOI: 10.1093/genetics/iyad149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/17/2023] [Accepted: 07/17/2023] [Indexed: 08/16/2023] Open
Abstract
Melanoma antigen (MAGE) genes encode for a family of proteins that share a common MAGE homology domain. These genes are conserved in eukaryotes and have been linked to a variety of cellular and developmental processes including ubiquitination and oncogenesis in cancer. Current knowledge on the MAGE family of proteins mainly comes from the analysis of yeast and human cell lines, and their functions have not been reported at an organismal level in animals. Caenorhabditis elegans only encodes 1 known MAGE gene member, mage-1 (NSE3 in yeast), forming part of the SMC-5/6 complex. Here, we characterize the role of mage-1/nse-3 in mitosis and meiosis in C. elegans. mage-1/nse-3 has a role in inter-sister recombination repair during meiotic recombination and for preserving chromosomal integrity upon treatment with a variety of DNA-damaging agents. MAGE-1 directly interacts with NSE-1 and NSE-4. In contrast to smc-5, smc-6, and nse-4 mutants which cause the loss of NSE-1 nuclear localization and strong cytoplasmic accumulation, mage-1/nse-3 mutants have a reduced level of NSE-1::GFP, remnant NSE-1::GFP being partially nuclear but largely cytoplasmic. Our data suggest that MAGE-1 is essential for NSE-1 stability and the proper functioning of the SMC-5/6 complex.
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Affiliation(s)
- Arome Solomon Odiba
- State Key Laboratory of Non-food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Guiyan Liao
- State Key Laboratory of Non-food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China
| | - Chiemekam Samuel Ezechukwu
- State Key Laboratory of Non-food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China
| | - Lanlan Zhang
- State Key Laboratory of Non-food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China
- College of Life Sciences, Hebei University, Baoding 071002, China
| | - Ye Hong
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Wenxia Fang
- State Key Laboratory of Non-food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China
| | - Cheng Jin
- State Key Laboratory of Non-food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Anton Gartner
- IBS Center for Genomic Integrity, Department for Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 689-798, Republic of Korea
| | - Bin Wang
- State Key Laboratory of Non-food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China
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3
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Lin J, Huang N, Li M, Zheng M, Wang Z, Zhang X, Gao H, Lao Y, Zhang J, Ding B. Dendritic Cell-Derived Exosomes Driven Drug Co-Delivery Biomimetic Nanosystem for Effective Combination of Malignant Melanoma Immunotherapy and Gene Therapy. Drug Des Devel Ther 2023; 17:2087-2106. [PMID: 37489176 PMCID: PMC10363389 DOI: 10.2147/dddt.s414758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 07/04/2023] [Indexed: 07/26/2023] Open
Abstract
Purpose Malignant melanoma (MM), the most lethal skin cancer, is highly invasive and metastatic. These qualities are related to not only genetic mutations in MM itself but also the interaction of MM cells with the immune system and microenvironment. This study aimed to construct a combined immunotherapy and gene therapy drug delivery system for the effective treatment of MM. Methods Mature dendritic cell (mDC) exosomes (mDexos) with immune induction functions were used as carriers. BRAF siRNA (siBRAF) with the ability to silence mutated BRAF in MM was encapsulated in mDexos by electroporation to construct a biomimetic nanosystem for the codelivery of immunotherapy and gene therapy drugs (siBRAF-mDexos) to the MM microenvironment. Then, we investigated the nanosystem's serum stability and biocompatibility, uptake efficiency in mouse melanoma cells (B16-F10 cells), cytotoxicity against B16-F10 cells and inhibitory effect on BRAF expression. Furthermore, we evaluated its antimelanoma activity and safety in vivo. Results SiBRAF-mDexos were nanosized. Compared to siBRAF, siBRAF-mDexos displayed significantly increased serum stability, biocompatibility, uptake efficiency in B16-F10 cells, and cytotoxicity to B16-F10 melanoma cells; they also had a significantly greater inhibitory effect on BRAF expression and induced T-lymphocyte proliferation. Moreover, compared with siBRAF, siBRAF-mDexos showed significantly enhanced anti-MM activity and a high level of safety in vivo. Conclusion The study suggests that the siBRAF-mDexo biomimetic drug codelivery system can be used to effectively treat MM, which provides a new strategy for combined gene therapy and immunotherapy for MM.
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Affiliation(s)
- Jiecheng Lin
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 214122, People’s Republic of China
- Department of Pharmaceutics, Jiaxing Key Laboratory for Photonanomedicine and Experimental Therapeutics, College of Medicine, Jiaxing University, Jiaxing, 314001, People’s Republic of China
| | - Na Huang
- Department of Pharmaceutics, Jiaxing Key Laboratory for Photonanomedicine and Experimental Therapeutics, College of Medicine, Jiaxing University, Jiaxing, 314001, People’s Republic of China
| | - Mingjuan Li
- Department of Pharmaceutics, Jiaxing Key Laboratory for Photonanomedicine and Experimental Therapeutics, College of Medicine, Jiaxing University, Jiaxing, 314001, People’s Republic of China
| | - Mengyuan Zheng
- Department of Pharmaceutics, Jiaxing Key Laboratory for Photonanomedicine and Experimental Therapeutics, College of Medicine, Jiaxing University, Jiaxing, 314001, People’s Republic of China
| | - Zhuoxiang Wang
- Department of Pharmaceutics, Jiaxing Key Laboratory for Photonanomedicine and Experimental Therapeutics, College of Medicine, Jiaxing University, Jiaxing, 314001, People’s Republic of China
| | - Xiaojuan Zhang
- Department of Pharmaceutics, Jiaxing Key Laboratory for Photonanomedicine and Experimental Therapeutics, College of Medicine, Jiaxing University, Jiaxing, 314001, People’s Republic of China
| | - Huan Gao
- Department of Pharmaceutics, Jiaxing Key Laboratory for Photonanomedicine and Experimental Therapeutics, College of Medicine, Jiaxing University, Jiaxing, 314001, People’s Republic of China
| | - Yunzhe Lao
- Department of Pharmaceutics, Jiaxing Key Laboratory for Photonanomedicine and Experimental Therapeutics, College of Medicine, Jiaxing University, Jiaxing, 314001, People’s Republic of China
| | - Jie Zhang
- Department of Pharmaceutics, Jiaxing Key Laboratory for Photonanomedicine and Experimental Therapeutics, College of Medicine, Jiaxing University, Jiaxing, 314001, People’s Republic of China
| | - Baoyue Ding
- Department of Pharmaceutics, Jiaxing Key Laboratory for Photonanomedicine and Experimental Therapeutics, College of Medicine, Jiaxing University, Jiaxing, 314001, People’s Republic of China
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4
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Ibars E, Codina-Fabra J, Bellí G, Casas C, Tarrés M, Solé-Soler R, Lorite NP, Ximénez-Embún P, Muñoz J, Colomina N, Torres-Rosell J. Ubiquitin proteomics identifies RNA polymerase I as a target of the Smc5/6 complex. Cell Rep 2023; 42:112463. [PMID: 37141096 DOI: 10.1016/j.celrep.2023.112463] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 12/29/2022] [Accepted: 04/18/2023] [Indexed: 05/05/2023] Open
Abstract
Ubiquitination controls numerous cellular processes, and its deregulation is associated with many pathologies. The Nse1 subunit in the Smc5/6 complex contains a RING domain with ubiquitin E3 ligase activity and essential functions in genome integrity. However, Nse1-dependent ubiquitin targets remain elusive. Here, we use label-free quantitative proteomics to analyze the nuclear ubiquitinome of nse1-C274A RING mutant cells. Our results show that Nse1 impacts the ubiquitination of several proteins involved in ribosome biogenesis and metabolism that, importantly, extend beyond canonical functions of Smc5/6. In addition, our analysis suggests a connection between Nse1 and RNA polymerase I (RNA Pol I) ubiquitination. Specifically, Nse1 and the Smc5/6 complex promote ubiquitination of K408 and K410 in the clamp domain of Rpa190, a modification that induces its degradation in response to blocks in transcriptional elongation. We propose that this mechanism contributes to Smc5/6-dependent segregation of the rDNA array, the locus transcribed by RNA Pol I.
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Affiliation(s)
- Eva Ibars
- Departament de Ciencies Mediques Basiques, Institut de Recerca Biomedica de Lleida, Universitat de Lleida, 25198 Lleida, Spain
| | - Joan Codina-Fabra
- Departament de Ciencies Mediques Basiques, Institut de Recerca Biomedica de Lleida, Universitat de Lleida, 25198 Lleida, Spain
| | - Gemma Bellí
- Departament de Ciencies Mediques Basiques, Institut de Recerca Biomedica de Lleida, Universitat de Lleida, 25198 Lleida, Spain
| | - Celia Casas
- Departament de Ciencies Mediques Basiques, Institut de Recerca Biomedica de Lleida, Universitat de Lleida, 25198 Lleida, Spain
| | - Marc Tarrés
- Departament de Ciencies Mediques Basiques, Institut de Recerca Biomedica de Lleida, Universitat de Lleida, 25198 Lleida, Spain
| | - Roger Solé-Soler
- Departament de Ciencies Mediques Basiques, Institut de Recerca Biomedica de Lleida, Universitat de Lleida, 25198 Lleida, Spain
| | - Neus P Lorite
- Departament de Ciencies Mediques Basiques, Institut de Recerca Biomedica de Lleida, Universitat de Lleida, 25198 Lleida, Spain
| | - Pilar Ximénez-Embún
- Proteomics Unit, Spanish National Cancer Research Center (CNIO), Madrid, Spain; ProteoRed-ISCIII, Madrid, Spain
| | - Javier Muñoz
- Proteomics Unit, Spanish National Cancer Research Center (CNIO), Madrid, Spain; ProteoRed-ISCIII, Madrid, Spain
| | - Neus Colomina
- Departament de Ciencies Mediques Basiques, Institut de Recerca Biomedica de Lleida, Universitat de Lleida, 25198 Lleida, Spain
| | - Jordi Torres-Rosell
- Departament de Ciencies Mediques Basiques, Institut de Recerca Biomedica de Lleida, Universitat de Lleida, 25198 Lleida, Spain.
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Preimplantation Genetic Testing (PGT) and Prenatal Diagnosis of Schaaf-Yang Syndrome: A Report of Three Families and a Research on Genotype-Phenotype Correlations. J Clin Med 2023; 12:jcm12041688. [PMID: 36836222 PMCID: PMC9962152 DOI: 10.3390/jcm12041688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/10/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
Schaaf-Yang Syndrome (SYS) is a genetic disorder caused by truncating pathogenic variants in the paternal allele of the maternally imprinted, paternally expressed gene MAGEL2 and is characterized by genital hypoplasia, neonatal hypotonia, developmental delay, intellectual disability, autism spectrum disorder (ASD), and other features. In this study, eleven SYS patients from three families were enrolled and comprehensive clinical features were gathered regarding each family. Whole-exome sequencing (WES) was performed for the definitive molecular diagnosis of the disease. Identified variants were validated using Sanger sequencing. Three couples underwent PGT for monogenic diseases (PGT-M) and/or a prenatal diagnosis. Haplotype analysis was performed to deduce the embryo's genotype by using the short tandem repeats (STRs) identified in each sample. The prenatal diagnosis results showed that the fetus in each case did not carry pathogenic variants, and all the babies of the three families were born at full term and were healthy. We also performed a review of SYS cases. In addition to the 11 patients in our study, a total of 127 SYS patients were included in 11 papers. We summarized all variant sites and clinical symptoms thus far, and conducted a genotype-phenotype correlation analysis. Our results also indicated that the variation in phenotypic severity may depend on the specific location of the truncating variant, suggestive of a genotype-phenotype association.
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Liu C, Liu J, Shao J, Huang C, Dai X, Shen Y, Hou W, Shen Y, Yu Y. MAGED4B Promotes Glioma Progression via Inactivation of the TNF-α-induced Apoptotic Pathway by Down-regulating TRIM27 Expression. Neurosci Bull 2023; 39:273-291. [PMID: 35986882 PMCID: PMC9905453 DOI: 10.1007/s12264-022-00926-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/09/2022] [Indexed: 10/15/2022] Open
Abstract
MAGED4B belongs to the melanoma-associated antigen family; originally found in melanoma, it is expressed in various types of cancer, and is especially enriched in glioblastoma. However, the functional role and molecular mechanisms of MAGED4B in glioma are still unclear. In this study, we found that the MAGED4B level was higher in glioma tissue than that in non-cancer tissue, and the level was positively correlated with glioma grade, tumor diameter, Ki-67 level, and patient age. The patients with higher levels had a worse prognosis than those with lower MAGED4B levels. In glioma cells, MAGED4B overexpression promoted proliferation, invasion, and migration, as well as decreasing apoptosis and the chemosensitivity to cisplatin and temozolomide. On the contrary, MAGED4B knockdown in glioma cells inhibited proliferation, invasion, and migration, as well as increasing apoptosis and the chemosensitivity to cisplatin and temozolomide. MAGED4B knockdown also inhibited the growth of gliomas implanted into the rat brain. The interaction between MAGED4B and tripartite motif-containing 27 (TRIM27) in glioma cells was detected by co-immunoprecipitation assay, which showed that MAGED4B was co-localized with TRIM27. In addition, MAGED4B overexpression down-regulated the TRIM27 protein level, and this was blocked by carbobenzoxyl-L-leucyl-L-leucyl-L-leucine (MG132), an inhibitor of the proteasome. On the contrary, MAGED4B knockdown up-regulated the TRIM27 level. Furthermore, MAGED4B overexpression increased TRIM27 ubiquitination in the presence of MG132. Accordingly, MAGED4B down-regulated the protein levels of genes downstream of ubiquitin-specific protease 7 (USP7) involved in the tumor necrosis factor-alpha (TNF-α)-induced apoptotic pathway. These findings indicate that MAGED4B promotes glioma growth via a TRIM27/USP7/receptor-interacting serine/threonine-protein kinase 1 (RIP1)-dependent TNF-α-induced apoptotic pathway, which suggests that MAGED4B is a potential target for glioma diagnosis and treatment.
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Affiliation(s)
- Can Liu
- Department of Radiology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
- Biopharmaceutical Research Institute, Anhui Medical University, Hefei, 230032, China
| | - Jun Liu
- Biopharmaceutical Research Institute, Anhui Medical University, Hefei, 230032, China
- School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, China
| | - Juntang Shao
- Biopharmaceutical Research Institute, Anhui Medical University, Hefei, 230032, China
- School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, China
| | - Cheng Huang
- Department of Pathology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Xingliang Dai
- Department of Neurosurgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Yujun Shen
- Biopharmaceutical Research Institute, Anhui Medical University, Hefei, 230032, China
- School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, China
| | - Weishu Hou
- Department of Radiology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Yuxian Shen
- Biopharmaceutical Research Institute, Anhui Medical University, Hefei, 230032, China.
- School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, China.
| | - Yongqiang Yu
- Department of Radiology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China.
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Guenette RG, Yang SW, Min J, Pei B, Potts PR. Target and tissue selectivity of PROTAC degraders. Chem Soc Rev 2022; 51:5740-5756. [PMID: 35587208 DOI: 10.1039/d2cs00200k] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Targeted protein degradation (TPD) strategies have revolutionized how scientists tackle challenging protein targets deemed undruggable with traditional small molecule inhibitors. Many promising campaigns to inhibit proteins have failed due to factors surrounding inhibition selectivity and targeting of compounds to specific tissues and cell types. One of the major improvements that PROTAC (proteolysis targeting chimera) and molecular glue technology can exert is highly selective control of target inhibition. Multiple studies have shown that PROTACs can gain selectivity for their protein targets beyond that of their parent ligands via optimization of linker length and stabilization of ternary complexes. Due to the bifunctional nature of PROTACs, the tissue selective nature of E3 ligases can be exploited to uncover novel targeting mechanisms. In this review, we provide critical analysis of the recent progress towards making selective PROTAC molecules and new PROTAC technologies that will continue to push the boundaries of achieving selectivity. These efforts have wide implications in the future of treating disease as they will broaden the possible targets that can be addressed by small molecules, like undruggable proteins or broadly active targets that would benefit from degradation in specific tissue types.
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Affiliation(s)
| | - Seung Wook Yang
- Induced Proximity Platform, Amgen, Thousand Oaks, CA 91320, USA.
| | - Jaeki Min
- Induced Proximity Platform, Amgen, Thousand Oaks, CA 91320, USA.
| | - Baikang Pei
- Genome Analysis Unit, Amgen, Thousand Oaks, CA 91320, USA
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Xu F, Song H, Xiao Q, Wei Q, Pang X, Gao Y, Tan G. Type-III interferon stimulated gene TRIM31 mutation in an HBV patient blocks its ability in promoting HBx degradation. Virus Res 2022; 308:198650. [PMID: 34863820 DOI: 10.1016/j.virusres.2021.198650] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/29/2021] [Accepted: 11/29/2021] [Indexed: 10/19/2022]
Abstract
TRIM5γ, together with TRIM31, has been shown to promote HBx ubiquitination and degradation. This study aimed to explore whether a patient with HCC (hepatic cell carcinoma) having a small nucleotide inserted into the TRIM31 gene, which made a shorter transcript stop at 768 bp, would result in blocking the activity of TRIM31 in promoting HBx degradation. Besides, this study aimed to determine the binding region of the TRIM31-TRIM5γ-HBx complex. HBV (Hepatitis B virus) infection was reported to induce type-III IFN but not type-I or type-II IFNs, here TRIM31 was found to be a type III rather than a type I stimulated gene, which was indispensable in inhibiting the hepatitis B virus replication by the interferon families. Thus, this study further identified the critical role of TRIM31 in the host-hepatitis B virus interaction.
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Affiliation(s)
- Fengchao Xu
- Department of Immunology, Institute of Translational Medicine, the First Hospital of Jilin University, Changchun, Jilin 130061, China
| | - Hongxiao Song
- Department of Immunology, Institute of Translational Medicine, the First Hospital of Jilin University, Changchun, Jilin 130061, China
| | - Qingfei Xiao
- Department of Nephrology, the First Hospital of Jilin University, Changchun, 130031, Jilin, China
| | - Qi Wei
- Department of Anesthesia, the First Hospital, Jilin University, Changchun, 130021, Jilin, China
| | - Xiaoli Pang
- Department of Pediatric Gastroenterology, the First Hospital, Jilin University, Changchun 130021, Jilin, China
| | - Yanli Gao
- Department of Pediatrics, the First Hospital, Jilin University, Changchun 130021, Jilin, China.
| | - Guangyun Tan
- Department of Immunology, Institute of Translational Medicine, the First Hospital of Jilin University, Changchun, Jilin 130061, China.
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Kolesar P, Stejskal K, Potesil D, Murray JM, Palecek JJ. Role of Nse1 Subunit of SMC5/6 Complex as a Ubiquitin Ligase. Cells 2022; 11:165. [PMID: 35011726 PMCID: PMC8750328 DOI: 10.3390/cells11010165] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/15/2021] [Accepted: 01/01/2022] [Indexed: 11/16/2022] Open
Abstract
Structural Maintenance of Chromosomes (SMC) complexes are important for many aspects of the chromosomal organization. Unlike cohesin and condensin, the SMC5/6 complex contains a variant RING domain carried by its Nse1 subunit. RING domains are characteristic for ubiquitin ligases, and human NSE1 has been shown to possess ubiquitin-ligase activity in vitro. However, other studies were unable to show such activity. Here, we confirm Nse1 ubiquitin-ligase activity using purified Schizosaccharomyces pombe proteins. We demonstrate that the Nse1 ligase activity is stimulated by Nse3 and Nse4. We show that Nse1 specifically utilizes Ubc13/Mms2 E2 enzyme and interacts directly with ubiquitin. We identify the Nse1 mutation (R188E) that specifically disrupts its E3 activity and demonstrate that the Nse1-dependent ubiquitination is particularly important under replication stress. Moreover, we determine Nse4 (lysine K181) as the first known SMC5/6-associated Nse1 substrate. Interestingly, abolition of Nse4 modification at K181 leads to suppression of DNA-damage sensitivity of other SMC5/6 mutants. Altogether, this study brings new evidence for Nse1 ubiquitin ligase activity, significantly advancing our understanding of this enigmatic SMC5/6 function.
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Affiliation(s)
- Peter Kolesar
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Karel Stejskal
- Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (K.S.); (D.P.)
| | - David Potesil
- Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (K.S.); (D.P.)
| | - Johanne M. Murray
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RH, UK;
| | - Jan J. Palecek
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (K.S.); (D.P.)
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Li S, Shi X, Li J, Zhou X. Pathogenicity of the MAGE family. Oncol Lett 2021; 22:844. [PMID: 34733362 PMCID: PMC8561213 DOI: 10.3892/ol.2021.13105] [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] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/07/2021] [Indexed: 12/12/2022] Open
Abstract
The melanoma antigen gene (MAGE) protein family is a group of highly conserved proteins that share a common homology domain. Under normal circumstances, numerous MAGE proteins are only expressed in reproduction-related tissues; however, abnormal expression levels are observed in a variety of tumor tissues. The MAGE family consists of type I and II proteins, several of which are cancer-testis antigens that are highly expressed in cancer and serve a critical role in tumorigenesis. Therefore, this review will use the relationship between MAGEs and tumors as a starting point, focusing on the latest developments regarding the function of MAGEs as oncogenes, and preliminarily reveal their possible mechanisms.
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Affiliation(s)
- Sanyan Li
- Department of Pathology, Qianjiang Central Hospital, Qianjiang, Hubei 433100, P.R. China
| | - Xiang Shi
- Department of Pathology, Qianjiang Central Hospital, Qianjiang, Hubei 433100, P.R. China
| | - Jingping Li
- Department of Respiratory Medicine, Qianjiang Central Hospital, Qianjiang, Hubei 433100, P.R. China
| | - Xianrong Zhou
- Department of Pathology, Qianjiang Central Hospital, Qianjiang, Hubei 433100, P.R. China
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Poojary M, Jishnu PV, Kabekkodu SP. Prognostic Value of Melanoma-Associated Antigen-A (MAGE-A) Gene Expression in Various Human Cancers: A Systematic Review and Meta-analysis of 7428 Patients and 44 Studies. Mol Diagn Ther 2021; 24:537-555. [PMID: 32548799 PMCID: PMC7497308 DOI: 10.1007/s40291-020-00476-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Background Members of the melanoma-associated antigen-A (MAGE-A) subfamily are overexpressed in many cancers and can drive cancer progression, metastasis, and therapeutic recurrence. Objective This study is the first comprehensive meta-analysis evaluating the prognostic utility of MAGE-A members in different cancers. Methods A systematic literature search was conducted in PubMed, Google Scholar, Science Direct, and Web of Science. The pooled hazard ratios with 95% confidence intervals were estimated to evaluate the prognostic significance of MAGE-A expression in various cancers. Results In total, 44 eligible studies consisting of 7428 patients from 11 countries were analysed. Univariate and multivariate analysis for overall survival, progression-free survival, and disease-free survival showed a significant association between high MAGE-A expression and various cancers (P < 0.00001). Additionally, subgroup analysis demonstrated that high MAGE-A expression was significantly associated with poor prognosis for lung, gastrointestinal, breast, and ovarian cancer in both univariate and multivariate analysis for overall survival. Conclusion Overexpression of MAGE-A subfamily members is linked to poor prognosis in multiple cancers. Therefore, it could serve as a potential prognostic marker of poor prognosis in cancers. Electronic supplementary material The online version of this article (10.1007/s40291-020-00476-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Manish Poojary
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
| | - Padacherri Vethil Jishnu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India.
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12
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Sanderson MR, Fahlman RP, Wevrick R. The N-terminal domain of the Schaaf-Yang syndrome protein MAGEL2 likely has a role in RNA metabolism. J Biol Chem 2021; 297:100959. [PMID: 34265304 PMCID: PMC8350409 DOI: 10.1016/j.jbc.2021.100959] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 06/22/2021] [Accepted: 07/11/2021] [Indexed: 02/08/2023] Open
Abstract
MAGEL2 encodes the L2 member of the melanoma-associated antigen gene (MAGE) protein family, truncating mutations of which can cause Schaaf-Yang syndrome, an autism spectrum disorder. MAGEL2 is also inactivated in Prader-Willi syndrome, which overlaps clinically and mechanistically with Schaaf-Yang syndrome. Studies to date have only investigated the C-terminal portion of the MAGEL2 protein, containing the MAGE homology domain that interacts with RING-E3 ubiquitin ligases and deubiquitinases to form protein complexes that modify protein ubiquitination. In contrast, the N-terminal portion of the MAGEL2 protein has never been studied. Here, we find that MAGEL2 has a low-complexity intrinsically disordered N-terminus rich in Pro-Xn-Gly motifs that is predicted to mediate liquid-liquid phase separation to form biomolecular condensates. We used proximity-dependent biotin identification (BioID) and liquid chromatography-tandem mass spectrometry to identify MAGEL2-proximal proteins, then clustered these proteins into functional networks. We determined that coding mutations analogous to disruptive mutations in other MAGE proteins alter these networks in biologically relevant ways. Proteins identified as proximal to the N-terminal portion of MAGEL2 are primarily involved in mRNA metabolic processes and include three mRNA N 6-methyladenosine (m6A)-binding YTHDF proteins and two RNA interference-mediating TNRC6 proteins. We found that YTHDF2 coimmunoprecipitates with MAGEL2, and coexpression of MAGEL2 reduces the nuclear accumulation of YTHDF2 after heat shock. We suggest that the N-terminal region of MAGEL2 may have a role in RNA metabolism and in particular the regulation of mRNAs modified by m6A methylation. These results provide mechanistic insight into pathogenic MAGEL2 mutations associated with Schaaf-Yang syndrome and related disorders.
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Affiliation(s)
- Matthea R Sanderson
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Richard P Fahlman
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada; Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - Rachel Wevrick
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada.
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13
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Tsimberidou AM, Van Morris K, Vo HH, Eck S, Lin YF, Rivas JM, Andersson BS. T-cell receptor-based therapy: an innovative therapeutic approach for solid tumors. J Hematol Oncol 2021; 14:102. [PMID: 34193217 PMCID: PMC8243554 DOI: 10.1186/s13045-021-01115-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/18/2021] [Indexed: 02/06/2023] Open
Abstract
T-cell receptor (TCR)-based adoptive therapy employs genetically modified lymphocytes that are directed against specific tumor markers. This therapeutic modality requires a structured and integrated process that involves patient screening (e.g., for HLA-A*02:01 and specific tumor targets), leukapheresis, generation of transduced TCR product, lymphodepletion, and infusion of the TCR-based adoptive therapy. In this review, we summarize the current technology and early clinical development of TCR-based therapy in patients with solid tumors. The challenges of TCR-based therapy include those associated with TCR product manufacturing, patient selection, and preparation with lymphodepletion. Overcoming these challenges, and those posed by the immunosuppressive microenvironment, as well as developing next-generation strategies is essential to improving the efficacy and safety of TCR-based therapies. Optimization of technology to generate TCR product, treatment administration, and patient monitoring for adverse events is needed. The implementation of novel TCR strategies will require expansion of the TCR approach to patients with HLA haplotypes beyond HLA-A*02:01 and the discovery of novel tumor markers that are expressed in more patients and tumor types. Ongoing clinical trials will determine the ultimate role of TCR-based therapy in patients with solid tumors.
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Affiliation(s)
- Apostolia-Maria Tsimberidou
- Department of Investigational Cancer Therapeutics, Unit 455, Phase I Clinical Trials Program, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA.
| | - Karlyle Van Morris
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA
| | - Henry Hiep Vo
- Department of Investigational Cancer Therapeutics, Unit 455, Phase I Clinical Trials Program, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA
| | - Stephen Eck
- MacroGenics, Inc., 9704 Medical Center Drive, Rockville, MD, 20850, USA
| | - Yu-Feng Lin
- Immatics US, Inc., 2201 Holcombe Blvd., Suite 205, Houston, TX, 77030, USA
| | | | - Borje S Andersson
- Department of Stem Cell Transplantation, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA
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14
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Hong J, Won M, Ro H. The Molecular and Pathophysiological Functions of Members of the LNX/PDZRN E3 Ubiquitin Ligase Family. Molecules 2020; 25:E5938. [PMID: 33333989 PMCID: PMC7765395 DOI: 10.3390/molecules25245938] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/10/2020] [Accepted: 12/10/2020] [Indexed: 12/27/2022] Open
Abstract
The ligand of Numb protein-X (LNX) family, also known as the PDZRN family, is composed of four discrete RING-type E3 ubiquitin ligases (LNX1, LNX2, LNX3, and LNX4), and LNX5 which may not act as an E3 ubiquitin ligase owing to the lack of the RING domain. As the name implies, LNX1 and LNX2 were initially studied for exerting E3 ubiquitin ligase activity on their substrate Numb protein, whose stability was negatively regulated by LNX1 and LNX2 via the ubiquitin-proteasome pathway. LNX proteins may have versatile molecular, cellular, and developmental functions, considering the fact that besides these proteins, none of the E3 ubiquitin ligases have multiple PDZ (PSD95, DLGA, ZO-1) domains, which are regarded as important protein-interacting modules. Thus far, various proteins have been isolated as LNX-interacting proteins. Evidence from studies performed over the last two decades have suggested that members of the LNX family play various pathophysiological roles primarily by modulating the function of substrate proteins involved in several different intracellular or intercellular signaling cascades. As the binding partners of RING-type E3s, a large number of substrates of LNX proteins undergo degradation through ubiquitin-proteasome system (UPS) dependent or lysosomal pathways, potentially altering key signaling pathways. In this review, we highlight recent and relevant findings on the molecular and cellular functions of the members of the LNX family and discuss the role of the erroneous regulation of these proteins in disease progression.
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Affiliation(s)
- Jeongkwan Hong
- Department of Biological Sciences, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 305-764, Korea;
| | - Minho Won
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 30 Yeongudanji-ro, Cheongwon-gu, Cheongju 28116, Korea
| | - Hyunju Ro
- Department of Biological Sciences, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 305-764, Korea;
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15
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Florke Gee RR, Chen H, Lee AK, Daly CA, Wilander BA, Fon Tacer K, Potts PR. Emerging roles of the MAGE protein family in stress response pathways. J Biol Chem 2020; 295:16121-16155. [PMID: 32921631 PMCID: PMC7681028 DOI: 10.1074/jbc.rev120.008029] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 09/08/2020] [Indexed: 12/21/2022] Open
Abstract
The melanoma antigen (MAGE) proteins all contain a MAGE homology domain. MAGE genes are conserved in all eukaryotes and have expanded from a single gene in lower eukaryotes to ∼40 genes in humans and mice. Whereas some MAGEs are ubiquitously expressed in tissues, others are expressed in only germ cells with aberrant reactivation in multiple cancers. Much of the initial research on MAGEs focused on exploiting their antigenicity and restricted expression pattern to target them with cancer immunotherapy. Beyond their potential clinical application and role in tumorigenesis, recent studies have shown that MAGE proteins regulate diverse cellular and developmental pathways, implicating them in many diseases besides cancer, including lung, renal, and neurodevelopmental disorders. At the molecular level, many MAGEs bind to E3 RING ubiquitin ligases and, thus, regulate their substrate specificity, ligase activity, and subcellular localization. On a broader scale, the MAGE genes likely expanded in eutherian mammals to protect the germline from environmental stress and aid in stress adaptation, and this stress tolerance may explain why many cancers aberrantly express MAGEs Here, we present an updated, comprehensive review on the MAGE family that highlights general characteristics, emphasizes recent comparative studies in mice, and describes the diverse functions exerted by individual MAGEs.
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Affiliation(s)
- Rebecca R Florke Gee
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Helen Chen
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Anna K Lee
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Christina A Daly
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Benjamin A Wilander
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Klementina Fon Tacer
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; School of Veterinary Medicine, Texas Tech University, Amarillo, Texas, USA.
| | - Patrick Ryan Potts
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
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16
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Yang SW, Huang X, Lin W, Min J, Miller DJ, Mayasundari A, Rodrigues P, Griffith EC, Gee CT, Li L, Li W, Lee RE, Rankovic Z, Chen T, Potts PR. Structural basis for substrate recognition and chemical inhibition of oncogenic MAGE ubiquitin ligases. Nat Commun 2020; 11:4931. [PMID: 33004795 PMCID: PMC7529893 DOI: 10.1038/s41467-020-18708-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 09/08/2020] [Indexed: 12/17/2022] Open
Abstract
Testis-restricted melanoma antigen (MAGE) proteins are frequently hijacked in cancer and play a critical role in tumorigenesis. MAGEs assemble with E3 ubiquitin ligases and function as substrate adaptors that direct the ubiquitination of novel targets, including key tumor suppressors. However, how MAGEs recognize their targets is unknown and has impeded the development of MAGE-directed therapeutics. Here, we report the structural basis for substrate recognition by MAGE ubiquitin ligases. Biochemical analysis of the degron motif recognized by MAGE-A11 and the crystal structure of MAGE-A11 bound to the PCF11 substrate uncovered a conserved substrate binding cleft (SBC) in MAGEs. Mutation of the SBC disrupted substrate recognition by MAGEs and blocked MAGE-A11 oncogenic activity. A chemical screen for inhibitors of MAGE-A11:substrate interaction identified 4-Aminoquinolines as potent inhibitors of MAGE-A11 that show selective cytotoxicity. These findings provide important insights into the large family of MAGE ubiquitin ligases and identify approaches for developing cancer-specific therapeutics.
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Affiliation(s)
- Seung Wook Yang
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA
| | - Xin Huang
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA
| | - Wenwei Lin
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA
| | - Jaeki Min
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA
| | - Darcie J Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA
| | - Anand Mayasundari
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA
| | - Patrick Rodrigues
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA
| | - Elizabeth C Griffith
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA
| | - Clifford T Gee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA
| | - Lei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California Irvine, 5270 California Ave, Irvine, CA, 92617, USA
| | - Wei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California Irvine, 5270 California Ave, Irvine, CA, 92617, USA
| | - Richard E Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA
| | - Zoran Rankovic
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA
| | - Patrick Ryan Potts
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA.
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17
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Sanderson MR, Badior KE, Fahlman RP, Wevrick R. The necdin interactome: evaluating the effects of amino acid substitutions and cell stress using proximity-dependent biotinylation (BioID) and mass spectrometry. Hum Genet 2020; 139:1513-1529. [PMID: 32529326 DOI: 10.1007/s00439-020-02193-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 06/03/2020] [Indexed: 02/07/2023]
Abstract
Prader-Willi syndrome (PWS) is a neurodevelopmental disorder caused by the loss of function of a set of imprinted genes on chromosome 15q11-15q13. One of these genes, NDN, encodes necdin, a protein that is important for neuronal differentiation and survival. Loss of Ndn in mice causes defects in the formation and function of the nervous system. Necdin is a member of the melanoma-associated antigen gene (MAGE) protein family. The functions of MAGE proteins depend highly on their interactions with other proteins, and in particular MAGE proteins interact with E3 ubiquitin ligases and deubiquitinases to form MAGE-RING E3 ligase-deubiquitinase complexes. Here, we used proximity-dependent biotin identification (BioID) and mass spectrometry (MS) to determine the network of protein-protein interactions (interactome) of the necdin protein. This process yielded novel as well as known necdin-proximate proteins that cluster into a protein network. Next, we used BioID-MS to define the interactomes of necdin proteins carrying coding variants. Variant necdin proteins had interactomes that were distinct from wildtype necdin. BioID-MS is not only a useful tool to identify protein-protein interactions, but also to analyze the effects of variants of unknown significance on the interactomes of proteins involved in genetic disease.
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Affiliation(s)
| | - Katherine E Badior
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.,Membrane Protein Disease Research Group, University of Alberta, Edmonton, AB, Canada
| | - Richard P Fahlman
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.,Department of Oncology, University of Alberta, Edmonton, AB, Canada
| | - Rachel Wevrick
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada.
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18
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Tan G, Yi Z, Song H, Xu F, Li F, Aliyari R, Zhang H, Du P, Ding Y, Niu J, Wang X, Su L, Qin FXF, Cheng G. Type-I-IFN-Stimulated Gene TRIM5γ Inhibits HBV Replication by Promoting HBx Degradation. Cell Rep 2019; 29:3551-3563.e3. [PMID: 31825835 PMCID: PMC6996557 DOI: 10.1016/j.celrep.2019.11.041] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 09/08/2019] [Accepted: 11/08/2019] [Indexed: 02/06/2023] Open
Abstract
To understand the molecular mechanisms that mediate the anti-hepatitis B virus (HBV) effect of interferon (IFN) therapy, we conduct high-throughput bimolecular fluorescence complementation screening to identify potential physical interactions between the HBx protein and 145 IFN-stimulated genes (ISGs). Seven HBx-interacting ISGs have consistent and significant inhibitory effects on HBV replication, among which TRIM5γ suppresses HBV replication by promoting K48-linked ubiquitination and degradation of the HBx protein on the K95 ubiquitin site. The B-Box domain of TRIM5γ under overexpression conditions is sufficient to trigger HBx degradation and is responsible both for interacting with HBx and recruiting TRIM31, which is an ubiquitin ligase that triggers HBx ubiquitination. High expression levels of TRIM5γ in IFN-α-treated HBV patients might indicate a better therapeutic effect. Thus, our studies identify a crucial role for TRIM5γ and TRIM31 in promoting HBx degradation, which may facilitate the development of therapeutic agents for the treatment of patients with IFN-resistant HBV infection.
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Affiliation(s)
- Guangyun Tan
- Department of Immunology, Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, Jilin 130061, China.
| | - Zhaohong Yi
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Hongxiao Song
- Department of Immunology, Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, Jilin 130061, China
| | - Fengchao Xu
- Department of Immunology, Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, Jilin 130061, China
| | - Feng Li
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Roghiyh Aliyari
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Hong Zhang
- Phase I Clinical Research Center, The First Hospital of Jilin University, Jilin 130021, China
| | - Peishuang Du
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Yanhua Ding
- Phase I Clinical Research Center, The First Hospital of Jilin University, Jilin 130021, China
| | - Junqi Niu
- Department of Hepatology, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Xiaosong Wang
- Department of Immunology, Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, Jilin 130061, China
| | - Lishan Su
- Department of Immunology, Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, Jilin 130061, China; CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, China; Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - F Xiao-Feng Qin
- Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China; Suzhou Institute of Systems Medicine, Suzhou, Jiangsu 215123, China.
| | - Genhong Cheng
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA.
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19
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Zelkowski M, Zelkowska K, Conrad U, Hesse S, Lermontova I, Marzec M, Meister A, Houben A, Schubert V. Arabidopsis NSE4 Proteins Act in Somatic Nuclei and Meiosis to Ensure Plant Viability and Fertility. FRONTIERS IN PLANT SCIENCE 2019; 10:774. [PMID: 31281325 PMCID: PMC6596448 DOI: 10.3389/fpls.2019.00774] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/28/2019] [Indexed: 05/02/2023]
Abstract
The SMC 5/6 complex together with cohesin and condensin is a member of the structural maintenance of chromosome (SMC) protein family. In non-plant organisms SMC5/6 is engaged in DNA repair, meiotic synapsis, genome organization and stability. In plants, the function of SMC5/6 is still enigmatic. Therefore, we analyzed the crucial δ-kleisin component NSE4 of the SMC5/6 complex in the model plant Arabidopsis thaliana. Two functional conserved Nse4 paralogs (Nse4A and Nse4B) are present in A. thaliana, which may have evolved via gene subfunctionalization. Due to its high expression level, Nse4A seems to be the more essential gene, whereas Nse4B appears to be involved mainly in seed development. The morphological characterization of A. thaliana T-DNA mutants suggests that the NSE4 proteins are essential for plant growth and fertility. Detailed investigations in wild-type and the mutants based on live cell imaging of transgenic GFP lines, fluorescence in situ hybridization (FISH), immunolabeling and super-resolution microscopy suggest that NSE4A acts in several processes during plant development, such as mitosis, meiosis and chromatin organization of differentiated nuclei, and that NSE4A operates in a cell cycle-dependent manner. Differential response of NSE4A and NSE4B mutants after induced DNA double strand breaks (DSBs) suggests their involvement in DNA repair processes.
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Affiliation(s)
- Mateusz Zelkowski
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Katarzyna Zelkowska
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Udo Conrad
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Susann Hesse
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Inna Lermontova
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
- Plant Cytogenomics Research Group, Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Marek Marzec
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Armin Meister
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
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20
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Paleček JJ, Vondrová L, Zábrady K, Otočka J. Multicomponent Yeast Two-Hybrid System: Applications to Study Protein-Protein Interactions in SMC Complexes. Methods Mol Biol 2019; 2004:79-90. [PMID: 31147911 DOI: 10.1007/978-1-4939-9520-2_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Analysis of protein-protein interactions (PPI) is key for the understanding of most protein assemblies including structural maintenance of chromosomes (SMC) complexes. SMC complexes are composed of SMC proteins, kleisin, and kleisin-interacting subunits. These subunits interact in specific ways to constitute and regulate the closed structure of the complexes. Specifically, kleisin molecules bridge the SMC dimers and the kleisin-interacting subunits modulate stability of the bridge. Here we describe a multicomponent version of a yeast two-hybrid (Y2H) method and its application for analysis of the bridging role of the Nse4 kleisin in the SMC5/6 complex. Using this technique, we also show a stabilizing effect of KITE (kleisin-interacting tandem winged-helix element) proteins on SMC5/6.
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Affiliation(s)
- Jan Josef Paleček
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic. .,Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
| | - Lucie Vondrová
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Kateřina Zábrady
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Jakub Otočka
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
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21
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Palecek JJ. SMC5/6: Multifunctional Player in Replication. Genes (Basel) 2018; 10:genes10010007. [PMID: 30583551 PMCID: PMC6356406 DOI: 10.3390/genes10010007] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 12/18/2018] [Accepted: 12/19/2018] [Indexed: 12/13/2022] Open
Abstract
The genome replication process is challenged at many levels. Replication must proceed through different problematic sites and obstacles, some of which can pause or even reverse the replication fork (RF). In addition, replication of DNA within chromosomes must deal with their topological constraints and spatial organization. One of the most important factors organizing DNA into higher-order structures are Structural Maintenance of Chromosome (SMC) complexes. In prokaryotes, SMC complexes ensure proper chromosomal partitioning during replication. In eukaryotes, cohesin and SMC5/6 complexes assist in replication. Interestingly, the SMC5/6 complexes seem to be involved in replication in many ways. They stabilize stalled RFs, restrain RF regression, participate in the restart of collapsed RFs, and buffer topological constraints during RF progression. In this (mini) review, I present an overview of these replication-related functions of SMC5/6.
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Affiliation(s)
- Jan J Palecek
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, 61137 Brno, Czech Republic.
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic.
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Hwang G, Verver DE, Handel MA, Hamer G, Jordan PW. Depletion of SMC5/6 sensitizes male germ cells to DNA damage. Mol Biol Cell 2018; 29:3003-3016. [PMID: 30281394 PMCID: PMC6333175 DOI: 10.1091/mbc.e18-07-0459] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The structural maintenance of chromosomes complex SMC5/6 is thought to be essential for DNA repair and chromosome segregation during mitosis and meiosis. To determine the requirements of the SMC5/6 complex during mouse spermatogenesis we combined a conditional knockout allele for Smc5, with four germ cell–specific Cre-recombinase transgenes, Ddx4-Cre, Stra8-Cre, Spo11-Cre, and Hspa2-Cre, to mutate Smc5 in spermatogonia, in spermatocytes before meiotic entry, during early meiotic stages, and during midmeiotic stages, respectively. Conditional mutation of Smc5 resulted in destabilization of the SMC5/6 complex. Despite this, we observed only mild defects in spermatogenesis. Mutation of Smc5 mediated by Ddx4-Cre and Stra8-Cre resulted in partial loss of preleptotene spermatocytes; however, spermatogenesis progresses and mice are fertile. Mutation of Smc5 via Spo11-Cre or Hspa2-Cre did not result in detectable defects of spermatogenesis. Upon exposure to gamma irradiation or etoposide treatment, each conditional Smc5 mutant demonstrated an increase in the number of enlarged round spermatids with multiple acrosomes and supernumerary chromosome content. We propose that the SMC5/6 complex is not acutely required for premeiotic DNA replication and meiotic progression during mouse spermatogenesis; however, when germ cells are challenged by exogenous DNA damage, the SMC5/6 complex ensures genome integrity, and thus, fertility.
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Affiliation(s)
- G Hwang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205
| | - D E Verver
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Academic Medical Center, 1105 AZ Amsterdam, the Netherlands
| | - M A Handel
- The Jackson Laboratory, Bar Harbor, ME 04609
| | - G Hamer
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Academic Medical Center, 1105 AZ Amsterdam, the Netherlands
| | - P W Jordan
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205
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23
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TRIM8 regulated autophagy modulates the level of cleaved Caspase-3 subunit to inhibit genotoxic stress induced cell death. Cell Signal 2018; 48:1-12. [DOI: 10.1016/j.cellsig.2018.04.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 04/08/2018] [Accepted: 04/13/2018] [Indexed: 01/07/2023]
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Furmanová K, Byška J, Gröller EM, Viola I, Paleček JJ, Kozlíková B. COZOID: contact zone identifier for visual analysis of protein-protein interactions. BMC Bioinformatics 2018; 19:125. [PMID: 29625561 PMCID: PMC5889581 DOI: 10.1186/s12859-018-2113-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 03/12/2018] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Studying the patterns of protein-protein interactions (PPIs) is fundamental for understanding the structure and function of protein complexes. The exploration of the vast space of possible mutual configurations of interacting proteins and their contact zones is very time consuming and requires the proteomic expert knowledge. RESULTS In this paper, we propose a novel tool containing a set of visual abstraction techniques for the guided exploration of PPI configuration space. It helps proteomic experts to select the most relevant configurations and explore their contact zones at different levels of detail. The system integrates a set of methods that follow and support the workflow of proteomics experts. The first visual abstraction method, the Matrix view, is based on customized interactive heat maps and provides the users with an overview of all possible residue-residue contacts in all PPI configurations and their interactive filtering. In this step, the user can traverse all input PPI configurations and obtain an overview of their interacting amino acids. Then, the models containing a particular pair of interacting amino acids can be selectively picked and traversed. Detailed information on the individual amino acids in the contact zones and their properties is presented in the Contact-Zone list-view. The list-view provides a comparative tool to rank the best models based on the similarity of their contacts to the template-structure contacts. All these techniques are interactively linked with other proposed methods, the Exploded view and the Open-Book view, which represent individual configurations in three-dimensional space. These representations solve the high overlap problem associated with many configurations. Using these views, the structural alignment of the best models can also be visually confirmed. CONCLUSIONS We developed a system for the exploration of large sets of protein-protein complexes in a fast and intuitive way. The usefulness of our system has been tested and verified on several docking structures covering the three major types of PPIs, including coiled-coil, pocket-string, and surface-surface interactions. Our case studies prove that our tool helps to analyse and filter protein-protein complexes in a fraction of the time compared to using previously available techniques.
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Affiliation(s)
| | - Jan Byška
- Department of Informatics, University of Bergen, Bergen, Norway
| | - Eduard M Gröller
- Institute of Visual Computing & Human-Centered Technology, TU Wien, Wien, Austria
| | - Ivan Viola
- Institute of Visual Computing & Human-Centered Technology, TU Wien, Wien, Austria
| | - Jan J Paleček
- National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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25
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Wijesuriya TM, De Ceuninck L, Masschaele D, Sanderson MR, Carias KV, Tavernier J, Wevrick R. The Prader-Willi syndrome proteins MAGEL2 and necdin regulate leptin receptor cell surface abundance through ubiquitination pathways. Hum Mol Genet 2018; 26:4215-4230. [PMID: 28973533 DOI: 10.1093/hmg/ddx311] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 08/01/2017] [Indexed: 12/13/2022] Open
Abstract
In Prader-Willi syndrome (PWS), obesity is caused by the disruption of appetite-controlling pathways in the brain. Two PWS candidate genes encode MAGEL2 and necdin, related melanoma antigen proteins that assemble into ubiquitination complexes. Mice lacking Magel2 are obese and lack leptin sensitivity in hypothalamic pro-opiomelanocortin neurons, suggesting dysregulation of leptin receptor (LepR) activity. Hypothalamus from Magel2-null mice had less LepR and altered levels of ubiquitin pathway proteins that regulate LepR processing (Rnf41, Usp8, and Stam1). MAGEL2 increased the cell surface abundance of LepR and decreased their degradation. LepR interacts with necdin, which interacts with MAGEL2, which complexes with RNF41 and USP8. Mutations in the MAGE homology domain of MAGEL2 suppress RNF41 stabilization and prevent the MAGEL2-mediated increase of cell surface LepR. Thus, MAGEL2 and necdin together control LepR sorting and degradation through a dynamic ubiquitin-dependent pathway. Loss of MAGEL2 and necdin may uncouple LepR from ubiquitination pathways, providing a cellular mechanism for obesity in PWS.
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Affiliation(s)
| | - Leentje De Ceuninck
- Department of Biochemistry, VIB Center for Medical Biotechnology and Faculty of Medicine and Health Sciences, Ghent University, B-9000 Ghent, Belgium
| | - Delphine Masschaele
- Department of Biochemistry, VIB Center for Medical Biotechnology and Faculty of Medicine and Health Sciences, Ghent University, B-9000 Ghent, Belgium
| | - Matthea R Sanderson
- Department of Medical Genetics, University of Alberta, Edmonton T6G 2H7, Canada
| | | | - Jan Tavernier
- Department of Biochemistry, VIB Center for Medical Biotechnology and Faculty of Medicine and Health Sciences, Ghent University, B-9000 Ghent, Belgium
| | - Rachel Wevrick
- Department of Medical Genetics, University of Alberta, Edmonton T6G 2H7, Canada
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Guo P, Ma X, Zhao W, Huai W, Li T, Qiu Y, Zhang Y, Han L. TRIM31 is upregulated in hepatocellular carcinoma and promotes disease progression by inducing ubiquitination of TSC1–TSC2 complex. Oncogene 2017; 37:478-488. [DOI: 10.1038/onc.2017.349] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 08/16/2017] [Accepted: 08/21/2017] [Indexed: 12/20/2022]
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Zhang X, Sun F, Qiao Y, Zheng W, Liu Y, Chen Y, Wu Q, Liu X, Zhu G, Chen Y, Yu Y, Pan Q, Wang J. TFCP2 Is Required for YAP-Dependent Transcription to Stimulate Liver Malignancy. Cell Rep 2017; 21:1227-1239. [DOI: 10.1016/j.celrep.2017.10.017] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 08/30/2017] [Accepted: 10/03/2017] [Indexed: 12/26/2022] Open
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Abstract
Melanoma antigen L2 (MAGEL2 or MAGE-L2) is a member of the MAGE family of ubiquitin ligase regulators. It is maternally imprinted and often paternally deleted or mutated in the related neurodevelopmental syndromes, Prader-Willi Syndrome (PWS) and Schaaf-Yang Syndrome (SHFYNG). MAGEL2 is highly expressed in the hypothalamus and plays an important role in a fundamental cellular process that recycles membrane proteins from endosomes through the retromer sorting pathway. MAGEL2 is part of a multi-subunit protein complex consisting of MAGEL2, the TRIM27 E3 ubiquitin ligase, and the USP7 deubiquitinating enzyme. The MAGEL2-USP7-TRIM27 (or MUST) complex facilitates the retromer recycling pathway through ubiquitination and activation of the WASH actin nucleation promoting factor. This review provides an overview of the MAGE protein family of ubiquitin ligases regulators and details the molecular and cellular role of MAGEL2 in ubiquitination, actin regulation and endosomal sorting processes, as well as MAGEL2 implications in PWS and SHFYNG disorders. The physiological functions of MAGEL2, elucidated through the study of Magel2 knockout mouse models, are also discussed.
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29
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RNF41 interacts with the VPS52 subunit of the GARP and EARP complexes. PLoS One 2017; 12:e0178132. [PMID: 28542518 PMCID: PMC5439944 DOI: 10.1371/journal.pone.0178132] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 04/12/2017] [Indexed: 11/19/2022] Open
Abstract
RNF41 (Ring Finger Protein 41) is an E3 ubiquitin ligase involved in the intracellular sorting and function of a diverse set of substrates. Next to BRUCE and Parkin, RNF41 can directly ubiquitinate ErbB3, IL-3, EPO and RARα receptors or downstream signaling molecules such as Myd88, TBK1 and USP8. In this way it can regulate receptor signaling and routing. To further elucidate the molecular mechanism behind the role of RNF41 in intracellular transport we performed an Array MAPPIT (Mammalian Protein-Protein Interaction Trap) screen using an extensive set of proteins derived from the human ORFeome collection. This paper describes the identification of VPS52, a subunit of the GARP (Golgi-Associated Retrograde Protein) and the EARP (Endosome-Associated Recycling Protein) complexes, as a novel interaction partner of RNF41. Through interaction via their coiled coil domains, RNF41 ubiquitinates and relocates VPS52 away from VPS53, a common subunit of the GARP and EARP complexes, towards RNF41 bodies.
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Zhao J, Wang Y, Mu C, Xu Y, Sang J. MAGEA1 interacts with FBXW7 and regulates ubiquitin ligase-mediated turnover of NICD1 in breast and ovarian cancer cells. Oncogene 2017; 36:5023-5034. [DOI: 10.1038/onc.2017.131] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 03/22/2017] [Accepted: 03/27/2017] [Indexed: 12/17/2022]
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31
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Lee AK, Potts PR. A Comprehensive Guide to the MAGE Family of Ubiquitin Ligases. J Mol Biol 2017; 429:1114-1142. [PMID: 28300603 DOI: 10.1016/j.jmb.2017.03.005] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 03/07/2017] [Accepted: 03/07/2017] [Indexed: 12/28/2022]
Abstract
Melanoma antigen (MAGE) genes are conserved in all eukaryotes and encode for proteins sharing a common MAGE homology domain. Although only a single MAGE gene exists in lower eukaryotes, the MAGE family rapidly expanded in eutherians and consists of more than 50 highly conserved genes in humans. A subset of MAGEs initially garnered interest as cancer biomarkers and immunotherapeutic targets due to their antigenic properties and unique expression pattern that is primary restricted to germ cells and aberrantly reactivated in various cancers. However, further investigation revealed that MAGEs not only drive tumorigenesis but also regulate pathways essential for diverse cellular and developmental processes. Therefore, MAGEs are implicated in a broad range of diseases including neurodevelopmental, renal, and lung disorders, and cancer. Recent biochemical and biophysical studies indicate that MAGEs assemble with E3 RING ubiquitin ligases to form MAGE-RING ligases (MRLs) and act as regulators of ubiquitination by modulating ligase activity, substrate specification, and subcellular localization. Here, we present a comprehensive guide to MAGEs highlighting the molecular mechanisms of MRLs and their physiological roles in germ cell and neural development, oncogenic functions in cancer, and potential as therapeutic targets in disease.
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Affiliation(s)
- Anna K Lee
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
| | - Patrick Ryan Potts
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, USA.
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Li G, Zou W, Jian L, Qian J, Deng Y, Zhao J. Non-SMC elements 1 and 3 are required for early embryo and seedling development in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1039-1054. [PMID: 28207059 PMCID: PMC5441860 DOI: 10.1093/jxb/erx016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Early embryo development from the zygote is an essential stage in the formation of the seed, while seedling development is the beginning of the formation of an individual plant. AtNSE1 and AtNSE3 are subunits of the structural maintenance of chromosomes (SMC) 5/6 complex and have been identified as non-SMC elements, but their functions in Arabidopsis growth and development remain as yet unknown. In this study, we found that loss of function of AtNSE1 and AtNSE3 led to severe defects in early embryo development. Partially complemented mutants showed that the development of mutant seedlings was inhibited, that chromosome fragments occurred during anaphase, and that the cell cycle was delayed at G2/M, which led to the occurrence of endoreduplication. Further, a large number of DNA double-strand breaks (DSBs) occurred in the nse1 and nse3 mutants, and the expression of AtNSE1 and AtNSE3 was up-regulated following treatment of the plants with DSB inducer compounds, suggesting that AtNSE1 and AtNSE3 have a role in DNA damage repair. Therefore, we conclude that AtNSE1 and AtNSE3 facilitate DSB repair and contribute to maintaining genome stability and cell division in mitotic cells. Thus, we think that AtNSE1 and AtNSE3 may be crucial factors for maintaining proper early embryonic and post-embryonic development.
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Affiliation(s)
- Gang Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Wenxuan Zou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Liufang Jian
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jie Qian
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yingtian Deng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jie Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
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van der Crabben SN, Hennus MP, McGregor GA, Ritter DI, Nagamani SC, Wells OS, Harakalova M, Chinn IK, Alt A, Vondrova L, Hochstenbach R, van Montfrans JM, Terheggen-Lagro SW, van Lieshout S, van Roosmalen MJ, Renkens I, Duran K, Nijman IJ, Kloosterman WP, Hennekam E, Orange JS, van Hasselt PM, Wheeler DA, Palecek JJ, Lehmann AR, Oliver AW, Pearl LH, Plon SE, Murray JM, van Haaften G. Destabilized SMC5/6 complex leads to chromosome breakage syndrome with severe lung disease. J Clin Invest 2016; 126:2881-92. [PMID: 27427983 PMCID: PMC4966312 DOI: 10.1172/jci82890] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 05/12/2016] [Indexed: 11/27/2022] Open
Abstract
The structural maintenance of chromosomes (SMC) family of proteins supports mitotic proliferation, meiosis, and DNA repair to control genomic stability. Impairments in chromosome maintenance are linked to rare chromosome breakage disorders. Here, we have identified a chromosome breakage syndrome associated with severe lung disease in early childhood. Four children from two unrelated kindreds died of severe pulmonary disease during infancy following viral pneumonia with evidence of combined T and B cell immunodeficiency. Whole exome sequencing revealed biallelic missense mutations in the NSMCE3 (also known as NDNL2) gene, which encodes a subunit of the SMC5/6 complex that is essential for DNA damage response and chromosome segregation. The NSMCE3 mutations disrupted interactions within the SMC5/6 complex, leading to destabilization of the complex. Patient cells showed chromosome rearrangements, micronuclei, sensitivity to replication stress and DNA damage, and defective homologous recombination. This work associates missense mutations in NSMCE3 with an autosomal recessive chromosome breakage syndrome that leads to defective T and B cell function and acute respiratory distress syndrome in early childhood.
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Affiliation(s)
| | - Marije P. Hennus
- Department of Pediatric Intensive Care, Wilhelmina Children’s Hospital, University Medical Center Utrecht (UMCU), Utrecht, Netherlands
| | - Grant A. McGregor
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, United Kingdom
| | | | | | - Owen S. Wells
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, United Kingdom
| | | | - Ivan K. Chinn
- Texas Children’s Hospital, and
- Department of Pediatrics, Baylor College of Medicine, Houston Texas, USA
| | - Aaron Alt
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, United Kingdom
| | - Lucie Vondrova
- Central European Institute of Technology and Faculty of Science, Masaryk University, Brno, Czech Republic
| | | | | | | | | | | | - Ivo Renkens
- Department of Genetics (Center for Molecular Medicine) and
| | - Karen Duran
- Department of Genetics (Center for Molecular Medicine) and
| | | | | | - Eric Hennekam
- Department of Genetics (Center for Molecular Medicine) and
| | - Jordan S. Orange
- Texas Children’s Hospital, and
- Department of Pediatrics, Baylor College of Medicine, Houston Texas, USA
| | - Peter M. van Hasselt
- Department of Metabolic Diseases, Wilhelmina Children’s Hospital, UMCU, Utrecht, Netherlands
| | - David A. Wheeler
- Human Genome Sequencing Center
- Department of Molecular and Human Genetics
| | - Jan J. Palecek
- Central European Institute of Technology and Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Alan R. Lehmann
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, United Kingdom
| | - Antony W. Oliver
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, United Kingdom
| | - Laurence H. Pearl
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, United Kingdom
| | - Sharon E. Plon
- Human Genome Sequencing Center
- Department of Molecular and Human Genetics
- Texas Children’s Hospital, and
- Department of Pediatrics, Baylor College of Medicine, Houston Texas, USA
| | - Johanne M. Murray
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, United Kingdom
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Sang M, Gu L, Liu F, Lian Y, Yin D, Fan X, Ding C, Huang W, Liu S, Shan B. Prognostic Significance of MAGE-A11 in Esophageal Squamous Cell Carcinoma and Identification of Related Genes Based on DNA Microarray. Arch Med Res 2016; 47:151-61. [PMID: 27362547 DOI: 10.1016/j.arcmed.2016.06.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 06/08/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND AND AIMS This study aims to investigate the expression pattern of melanoma-associated antigen-A11 (MAGE-A11) in esophageal squamous cell carcinoma (ESCC) specimens and analyze its prognostic significance for ESCC patients. In addition, the purpose of our study was also to explore the biological function of MAGE-A11 in ESCC cells based on DNA microarray. METHODS Immunohistochemistry was used to detect the expression of MAGE-A11 in ESCC specimens, and its prognostic significance was analyzed by statistical analysis. DNA microarray and quantitative RT-PCR were used to explore the different expression of MAGE-A11 downstream genes in ESCC cells. Cell invasion assay and MTT assay were used to detect the effect of MAGE-A11 cDNA on the invasion and proliferation of ESCC cells. RESULTS Of the ESCC specimens, 59.3% showed positive MAGE-A11 expression. MAGE-A11 expression in ESCC specimens was positively associated with distant lymph node metastasis. Overall survival of ESCC patients with positive MAGE-A11 expression was shorter than in patients with negative MAGE-A11 expression. Multivariate Cox regression analysis showed MAGE-A11 expression is an independent poor prognostic factor for ESCC patients. Overexpression of MAGE-A11 changed a variety of gene expressions, which was associated with various cell functions such as protein ubiquitination, cell proliferation and apoptosis, tumor invasion and metastasis. Overexpression of MAGE-A11 directly increased the invasion and proliferation of ESCC cells. CONCLUSIONS MAGE-A11 is an independent poor prognostic marker for ESCC patients. MAGE-A11 regulates various cell functions and directly increases the invasion and proliferation of ESCC cells.
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Affiliation(s)
- Meixiang Sang
- Research Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, People's Republic of China; Tumor Research Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, People's Republic of China
| | - Lina Gu
- Research Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, People's Republic of China
| | - Fei Liu
- Research Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, People's Republic of China
| | - Yishui Lian
- Research Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, People's Republic of China
| | - Danjing Yin
- Research Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, People's Republic of China
| | - Xiaojie Fan
- Research Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, People's Republic of China
| | - Chunyan Ding
- Research Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, People's Republic of China
| | - Weina Huang
- Research Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, People's Republic of China
| | - Shina Liu
- Research Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, People's Republic of China
| | - Baoen Shan
- Research Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, People's Republic of China; Tumor Research Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, People's Republic of China.
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35
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Zabrady K, Adamus M, Vondrova L, Liao C, Skoupilova H, Novakova M, Jurcisinova L, Alt A, Oliver AW, Lehmann AR, Palecek JJ. Chromatin association of the SMC5/6 complex is dependent on binding of its NSE3 subunit to DNA. Nucleic Acids Res 2016; 44:1064-79. [PMID: 26446992 PMCID: PMC4756808 DOI: 10.1093/nar/gkv1021] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 09/23/2015] [Accepted: 09/26/2015] [Indexed: 11/13/2022] Open
Abstract
SMC5/6 is a highly conserved protein complex related to cohesin and condensin, which are the key components of higher-order chromatin structures. The SMC5/6 complex is essential for proliferation in yeast and is involved in replication fork stability and processing. However, the precise mechanism of action of SMC5/6 is not known. Here we present evidence that the NSE1/NSE3/NSE4 sub-complex of SMC5/6 binds to double-stranded DNA without any preference for DNA-replication/recombination intermediates. Mutations of key basic residues within the NSE1/NSE3/NSE4 DNA-binding surface reduce binding to DNA in vitro. Their introduction into the Schizosaccharomyces pombe genome results in cell death or hypersensitivity to DNA damaging agents. Chromatin immunoprecipitation analysis of the hypomorphic nse3 DNA-binding mutant shows a reduced association of fission yeast SMC5/6 with chromatin. Based on our results, we propose a model for loading of the SMC5/6 complex onto the chromatin.
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Affiliation(s)
- Katerina Zabrady
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, Brno, 61137, Czech Republic
| | - Marek Adamus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic
| | - Lucie Vondrova
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, Brno, 61137, Czech Republic
| | - Chunyan Liao
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, United Kingdom
| | - Hana Skoupilova
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, Brno, 61137, Czech Republic
| | - Marketa Novakova
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, Brno, 61137, Czech Republic
| | - Lenka Jurcisinova
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, Brno, 61137, Czech Republic
| | - Aaron Alt
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, United Kingdom
| | - Antony W Oliver
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, United Kingdom
| | - Alan R Lehmann
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, United Kingdom
| | - Jan J Palecek
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, Brno, 61137, Czech Republic
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Zhang C, Li X, Adelmant G, Dobbins J, Geisen C, Oser MG, Wucherpfenning KW, Marto JA, Kaelin WG. Peptidic degron in EID1 is recognized by an SCF E3 ligase complex containing the orphan F-box protein FBXO21. Proc Natl Acad Sci U S A 2015; 112:15372-7. [PMID: 26631746 PMCID: PMC4687553 DOI: 10.1073/pnas.1522006112] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
EP300-interacting inhibitor of differentiation 1 (EID1) belongs to a protein family implicated in the control of transcription, differentiation, DNA repair, and chromosomal maintenance. EID1 has a very short half-life, especially in G0 cells. We discovered that EID1 contains a peptidic, modular degron that is necessary and sufficient for its polyubiquitylation and proteasomal degradation. We found that this degron is recognized by an Skp1, Cullin, and F-box (SCF)-containing ubiquitin ligase complex that uses the F-box Only Protein 21 (FBXO21) as its substrate recognition subunit. SCF(FBXO21) polyubiquitylates EID1 both in vitro and in vivo and is required for the efficient degradation of EID1 in both cycling and quiescent cells. The EID1 degron partially overlaps with its retinoblastoma tumor suppressor protein-binding domain and is congruent with a previously defined melanoma-associated antigen-binding motif shared by EID family members, suggesting that binding to retinoblastoma tumor suppressor and melanoma-associated antigen family proteins could affect the polyubiquitylation and turnover of EID family members in cells.
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Affiliation(s)
- Cuiyan Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215
| | - Xiaotong Li
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Guillaume Adelmant
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02215; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215
| | - Jessica Dobbins
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02215
| | - Christoph Geisen
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215; Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - Matthew G Oser
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215
| | - Kai W Wucherpfenning
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02215
| | - Jarrod A Marto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02215; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215
| | - William G Kaelin
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215; Howard Hughes Medical Institute, Chevy Chase, MD 20815
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Palecek JJ, Gruber S. Kite Proteins: a Superfamily of SMC/Kleisin Partners Conserved Across Bacteria, Archaea, and Eukaryotes. Structure 2015; 23:2183-2190. [DOI: 10.1016/j.str.2015.10.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 09/23/2015] [Accepted: 10/01/2015] [Indexed: 10/22/2022]
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Weon JL, Potts PR. The MAGE protein family and cancer. Curr Opin Cell Biol 2015; 37:1-8. [PMID: 26342994 DOI: 10.1016/j.ceb.2015.08.002] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Accepted: 08/17/2015] [Indexed: 12/21/2022]
Abstract
The Melanoma Antigen Gene (MAGE) protein family is a large, highly conserved group of proteins that share a common MAGE homology domain. Intriguingly, many MAGE proteins are restricted in expression to reproductive tissues, but are aberrantly expressed in a wide variety of cancer types. Originally discovered as antigens on tumor cells and developed as cancer immunotherapy targets, recent literature suggests a more prominent role for MAGEs in driving tumorigenesis. This review will highlight recent developments into the function of MAGEs as oncogenes, their mechanisms of action in regulation of ubiquitin ligases, and outstanding questions in the field.
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Affiliation(s)
- Jenny L Weon
- Departments of Physiology, Pharmacology, and Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, United States
| | - Patrick Ryan Potts
- Departments of Physiology, Pharmacology, and Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, United States.
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Affiliation(s)
- Melania E Zanchetta
- Cluster in Biomedicine; Trieste, Italy
- Dipartimento di Scienze della Vita; Università degli Studi di Trieste; Trieste, Italy
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