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Yang Y, Li Y, Sears RC, Sun XX, Dai MS. SUMOylation regulation of ribosome biogenesis: Emerging roles for USP36. FRONTIERS IN RNA RESEARCH 2024; 2:1389104. [PMID: 38764604 PMCID: PMC11101209 DOI: 10.3389/frnar.2024.1389104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2024]
Abstract
Ribosome biogenesis is essential for cell growth, proliferation, and animal development. Its deregulation leads to various human disorders such as ribosomopathies and cancer. Thus, tight regulation of ribosome biogenesis is crucial for normal cell homeostasis. Emerging evidence suggests that posttranslational modifications such as ubiquitination and SUMOylation play a crucial role in regulating ribosome biogenesis. Our recent studies reveal that USP36, a nucleolar deubiquitinating enzyme (DUB), acts also as a SUMO ligase to regulate nucleolar protein group SUMOylation, thereby being essential for ribosome biogenesis. Here, we provide an overview of the current understanding of the SUMOylation regulation of ribosome biogenesis and discuss the role of USP36 in nucleolar SUMOylation.
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Affiliation(s)
- Yunhan Yang
- Department of Molecular & Medical Genetics, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Yanping Li
- Department of Molecular & Medical Genetics, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Rosalie C. Sears
- Department of Molecular & Medical Genetics, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Xiao-Xin Sun
- Department of Molecular & Medical Genetics, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Mu-Shui Dai
- Department of Molecular & Medical Genetics, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
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2
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Ma X, Zhao C, Xu Y, Zhang H. Roles of host SUMOylation in bacterial pathogenesis. Infect Immun 2023; 91:e0028323. [PMID: 37725062 PMCID: PMC10580907 DOI: 10.1128/iai.00283-23] [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] [Indexed: 09/21/2023] Open
Abstract
Bacteria frequently interfere with the post-translational modifications of host cells to facilitate their survival and growth after invasion. SUMOylation, a reversible post-translational modification process, plays an important role in biological life activities. In addition to being critical to host cell metabolism and survival, SUMOylation also regulates gene expression and cell signal transmission. Moreover, SUMOylation in eukaryotic cells can be used by a variety of bacterial pathogens to advance bacterial invasion. In this minireview, we focused on the role and mechanism of host SUMOylation in the pathogenesis of six important clinical bacterial pathogens (Listeria monocytogenes, Shigella flexneri, Salmonella Typhimurium, Klebsiella pneumoniae, Staphylococcus aureus, and Escherichia coli). Taken together, this review provided new insights for understanding the unique pathogen-host interaction based on host SUMOylation and provided a novel perspective on the development of new strategies to combat bacterial infections in the future.
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Affiliation(s)
- Xin Ma
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Chenhao Zhao
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Yuyao Xu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
- Department of Clinical Laboratory, Zhangjiagang Traditional Chinese Medicine Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, Jiangsu, China
| | - Haifang Zhang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
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3
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Arenas V, Castaño JL, Domínguez-García JJ, Yáñez L, Pipaón C. A Different View for an Old Disease: NEDDylation and Other Ubiquitin-Like Post-Translational Modifications in Chronic Lymphocytic Leukemia. Front Oncol 2021; 11:729550. [PMID: 34631557 PMCID: PMC8495217 DOI: 10.3389/fonc.2021.729550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/07/2021] [Indexed: 12/03/2022] Open
Abstract
Despite the enormous amount of molecular data obtained over the years, the molecular etiology of chronic lymphocytic leukemia (CLL) is still largely unknown. All that information has enabled the development of new therapeutic approaches that have improved life expectancy of the patients but are still not curative. We must increase our knowledge of the molecular alterations responsible for the characteristics common to all CLL patients. One of such characteristics is the poor correlation between mRNA and protein expression, that suggests a role of post-translational mechanisms in CLL physiopathology. Drugs targeting these processes have indeed demonstrated an effect either alone or in combination with other aimed at specific pathways. A recent article unveiled an increment in ubiquitin-like modifications in CLL, with many protein members of relevant pathways affected. Interestingly, the inhibition of the NEDD8-activating protein NAE reverted a substantial number of those modifications. The present review gets the scarce data published about the role of NEDDylation in CLL together and establishes connections to what is known from other neoplasias, thus providing a new perspective to the underlying mechanisms in CLL.
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Affiliation(s)
- Víctor Arenas
- Laboratorio de Hematología Molecular, Servicio de Hematología, Hospital Universitario Marqués de Valdecilla-Instituto de Investigación Marqués de Valdecilla (IDIVAL), Santander, Spain
| | - Jose Luis Castaño
- Laboratorio de Hematología Molecular, Servicio de Hematología, Hospital Universitario Marqués de Valdecilla-Instituto de Investigación Marqués de Valdecilla (IDIVAL), Santander, Spain
| | - Juan José Domínguez-García
- Laboratorio de Hematología Molecular, Servicio de Hematología, Hospital Universitario Marqués de Valdecilla-Instituto de Investigación Marqués de Valdecilla (IDIVAL), Santander, Spain
| | - Lucrecia Yáñez
- Laboratorio de Hematología Molecular, Servicio de Hematología, Hospital Universitario Marqués de Valdecilla-Instituto de Investigación Marqués de Valdecilla (IDIVAL), Santander, Spain
| | - Carlos Pipaón
- Laboratorio de Hematología Molecular, Servicio de Hematología, Hospital Universitario Marqués de Valdecilla-Instituto de Investigación Marqués de Valdecilla (IDIVAL), Santander, Spain
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4
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Ryu H, Sun XX, Chen Y, Li Y, Wang X, Dai RS, Zhu HM, Klimek J, David L, Fedorov LM, Azuma Y, Sears RC, Dai MS. The deubiquitinase USP36 promotes snoRNP group SUMOylation and is essential for ribosome biogenesis. EMBO Rep 2021; 22:e50684. [PMID: 33852194 DOI: 10.15252/embr.202050684] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 03/05/2021] [Accepted: 03/09/2021] [Indexed: 12/21/2022] Open
Abstract
SUMOylation plays a crucial role in regulating diverse cellular processes including ribosome biogenesis. Proteomic analyses and experimental evidence showed that a number of nucleolar proteins involved in ribosome biogenesis are modified by SUMO. However, how these proteins are SUMOylated in cells is less understood. Here, we report that USP36, a nucleolar deubiquitinating enzyme (DUB), promotes nucleolar SUMOylation. Overexpression of USP36 enhances nucleolar SUMOylation, whereas its knockdown or genetic deletion reduces the levels of SUMOylation. USP36 interacts with SUMO2 and Ubc9 and directly mediates SUMOylation in cells and in vitro. We show that USP36 promotes the SUMOylation of the small nucleolar ribonucleoprotein (snoRNP) components Nop58 and Nhp2 in cells and in vitro and their binding to snoRNAs. It also promotes the SUMOylation of snoRNP components Nop56 and DKC1. Functionally, we show that knockdown of USP36 markedly impairs rRNA processing and translation. Thus, USP36 promotes snoRNP group SUMOylation and is critical for ribosome biogenesis and protein translation.
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Affiliation(s)
- Hyunju Ryu
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Xiao-Xin Sun
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Yingxiao Chen
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Yanping Li
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Xiaoyan Wang
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Roselyn S Dai
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Hong-Ming Zhu
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - John Klimek
- Department of Chemical Physiology & Biochemistry, School of Medicine, Oregon Health & Science University, Portland, OR, USA.,OHSU Proteomics Shared Resource, Oregon Health & Science University, Portland, OR, USA
| | - Larry David
- Department of Chemical Physiology & Biochemistry, School of Medicine, Oregon Health & Science University, Portland, OR, USA.,OHSU Proteomics Shared Resource, Oregon Health & Science University, Portland, OR, USA
| | - Lev M Fedorov
- OHSU Transgenic Mouse Models Shared Resource, Oregon Health & Science University, Portland, OR, USA
| | - Yoshiaki Azuma
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
| | - Rosalie C Sears
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Mu-Shui Dai
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
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5
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Sheng Z, Wang X, Ma Y, Zhang D, Yang Y, Zhang P, Zhu H, Xu N, Liang S. MS-based strategies for identification of protein SUMOylation modification. Electrophoresis 2019; 40:2877-2887. [PMID: 31216068 PMCID: PMC6899701 DOI: 10.1002/elps.201900100] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 06/06/2019] [Accepted: 06/12/2019] [Indexed: 02/05/2023]
Abstract
Protein SUMOylation modification conjugated with small ubiquitin-like modifiers (SUMOs) is one kind of PTMs, which exerts comprehensive roles in cellular functions, including gene expression regulation, DNA repair, intracellular transport, stress responses, and tumorigenesis. With the development of the peptide enrichment approaches and MS technology, more than 6000 SUMOylated proteins and about 40 000 SUMO acceptor sites have been identified. In this review, we summarize several popular approaches that have been developed for the identification of SUMOylated proteins in human cells, and further compare their technical advantages and disadvantages. And we also introduce identification approaches of target proteins which are co-modified by both SUMOylation and ubiquitylation. We highlight the emerging trends in the SUMOylation field as well. Especially, the advent of the clustered regularly interspaced short palindromic repeats/ Cas9 technique will facilitate the development of MS for SUMOylation identification.
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Affiliation(s)
- Zenghua Sheng
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalCollaborative Innovation Center for BiotherapySichuan UniversityChengduP. R. China
| | - Xixi Wang
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalCollaborative Innovation Center for BiotherapySichuan UniversityChengduP. R. China
| | - Yanni Ma
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalCollaborative Innovation Center for BiotherapySichuan UniversityChengduP. R. China
| | - Dan Zhang
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalCollaborative Innovation Center for BiotherapySichuan UniversityChengduP. R. China
| | - Yanfang Yang
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalCollaborative Innovation Center for BiotherapySichuan UniversityChengduP. R. China
| | - Peng Zhang
- Department of Urinary SurgeryWest China HospitalSichuan UniversityChengduSichuanP. R. China
| | - Hongxia Zhu
- Laboratory of Cell and Molecular Biology & State Key Laboratory of Molecular OncologyCancer Institute & Cancer HospitalChinese Academy of Medical SciencesBeijingP. R. China
| | - Ningzhi Xu
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalCollaborative Innovation Center for BiotherapySichuan UniversityChengduP. R. China
- Laboratory of Cell and Molecular Biology & State Key Laboratory of Molecular OncologyCancer Institute & Cancer HospitalChinese Academy of Medical SciencesBeijingP. R. China
| | - Shufang Liang
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalCollaborative Innovation Center for BiotherapySichuan UniversityChengduP. R. China
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6
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Chen Y, Sun XX, Sears RC, Dai MS. Writing and erasing MYC ubiquitination and SUMOylation. Genes Dis 2019; 6:359-371. [PMID: 31832515 PMCID: PMC6889025 DOI: 10.1016/j.gendis.2019.05.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 05/23/2019] [Accepted: 05/29/2019] [Indexed: 12/22/2022] Open
Abstract
The transcription factor c-MYC (MYC thereafter) controls diverse transcription programs and plays a key role in the development of many human cancers. Cells develop multiple mechanisms to ensure that MYC levels and activity are precisely controlled in normal physiological context. As a short half-lived protein, MYC protein levels are tightly regulated by the ubiquitin proteasome system. Over a dozen of ubiquitin ligases have been found to ubiquitinate MYC whereas a number of deubiquitinating enzymes counteract this process. Recent studies show that SUMOylation and deSUMOylation can also regulate MYC protein stability and activity. Interestingly, evidence suggests an intriguing crosstalk between MYC ubiquitination and SUMOylation. Deregulation of the MYC ubiquitination-SUMOylation regulatory network may contribute to tumorigenesis. This review is intended to provide the current understanding of the complex regulation of the MYC biology by dynamic ubiquitination and SUMOylation and their crosstalk.
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Affiliation(s)
- Yingxiao Chen
- Departments of Molecular & Medical Genetics, School of Medicine, OHSU Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Xiao-Xin Sun
- Departments of Molecular & Medical Genetics, School of Medicine, OHSU Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Rosalie C Sears
- Departments of Molecular & Medical Genetics, School of Medicine, OHSU Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Mu-Shui Dai
- Departments of Molecular & Medical Genetics, School of Medicine, OHSU Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
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7
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Liu F, Li L, Li Y, Ma X, Bian X, Liu X, Wang G, Zhang D. Overexpression of SENP1 reduces the stemness capacity of osteosarcoma stem cells and increases their sensitivity to HSVtk/GCV. Int J Oncol 2018; 53:2010-2020. [PMID: 30226577 PMCID: PMC6192779 DOI: 10.3892/ijo.2018.4537] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 07/17/2018] [Indexed: 12/14/2022] Open
Abstract
Osteosarcoma stem cells are able to escape treatment with conventional chemotherapeutic drugs, as the majority of them are in a quiescent state. Recent reports have suggested that small ubiquitin-like modifiers (SUMOs) serve important roles in the maintenance of cancer stem cell stemness. Therefore, a potential strategy to increase the effectiveness of chemotherapeutic agents is to interfere with SUMO modification of proteins associated with the maintenance of stemness in osteosarcoma stem cells. The present study revealed a significant decrease in the expression of SUMO1 specific peptidase 1 (SENP1) in osteosarcoma tissues and osteosarcoma cell lines, and SENP1 expression was much lower in osteosarcoma stem cells than in non-cancer stem cells. Further experiments indicated that the low levels of SENP1 were essential for maintenance of stemness in osteosarcoma stem cells. Overexpression of SENP1 resulted in a marked decrease in the maintenance of stemness, but only slightly induced apoptosis of osteosarcoma cells, which is crucial to reduce the side effects of drugs on normal precursor cells. Finally, SENP1 overexpression led to a significant increase in the sensitivity of osteosarcoma stem cells to the herpes simplex virus 1 thymidine kinase gene in combination with ganciclovir in vitro and in vivo. In conclusion, the present study described a novel method to increase the sensitivity of osteosarcoma stem cells to chemotherapeutic drugs. Notably, this approach may significantly reduce the required dose of conventional chemotherapeutic drugs and reduce side effects.
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Affiliation(s)
- Fengting Liu
- Department of Bone and Soft Tissue Tumors, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, P.R. China
| | - Lili Li
- Department of Bone and Soft Tissue Tumors, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, P.R. China
| | - Yanxia Li
- Central Laboratory, The Fifth Central Hospital of Tianjin, Tianjin 300450, P.R. China
| | - Xiaofang Ma
- Central Laboratory, The Fifth Central Hospital of Tianjin, Tianjin 300450, P.R. China
| | - Xiyun Bian
- Central Laboratory, The Fifth Central Hospital of Tianjin, Tianjin 300450, P.R. China
| | - Xiaozhi Liu
- Central Laboratory, The Fifth Central Hospital of Tianjin, Tianjin 300450, P.R. China
| | - Guowen Wang
- Department of Bone and Soft Tissue Tumors, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, P.R. China
| | - Dianying Zhang
- Department of Trauma and Orthopedics, Peking University People's Hospital, Beijing 100044, P.R. China
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8
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Ubc9 overexpression and SUMO1 deficiency blunt inflammation after intestinal ischemia/reperfusion. J Transl Med 2018; 98:799-813. [PMID: 29472640 PMCID: PMC6397426 DOI: 10.1038/s41374-018-0035-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/27/2017] [Accepted: 01/10/2018] [Indexed: 11/08/2022] Open
Abstract
The intestinal epithelium constitutes a crucial defense to the potentially life-threatening effects of gut microbiota. However, due to a complex underlying vasculature, hypoperfusion and resultant tissue ischemia pose a particular risk to function and integrity of the epithelium. The small ubiquitin-like modifier (SUMO) conjugation pathway critically regulates adaptive responses to metabolic stress and is of particular significance in the gut, as inducible knockout of the SUMO-conjugating enzyme Ubc9 results in rapid intestinal epithelial disintegration. Here we analyzed the pattern of individual SUMO isoforms in intestinal epithelium and investigated their roles in intestinal ischemia/reperfusion (I/R) damage. Immunostaining revealed that epithelial SUMO2/3 expression was almost exclusively limited to crypt epithelial nuclei in unchallenged mice. However, intestinal I/R or overexpression of Ubc9 caused a remarkable enhancement of epithelial SUMO2/3 staining along the crypt-villus axis. Unexpectedly, a similar pattern was found in SUMO1 knockout mice. Ubc9 transgenic mice, but also SUMO1 knockout mice were protected from I/R injury as evidenced by better preserved barrier function and blunted inflammatory responses. PCR array analysis of microdissected villus-tip epithelia revealed a specific epithelial contribution to reduced inflammatory responses in Ubc9 transgenic mice, as key chemotactic signaling molecules such as IL17A were significantly downregulated. Together, our data indicate a critical role particularly of the SUMO2/3 isoforms in modulating responses to I/R and provide the first evidence that SUMO1 deletion activates a compensatory process that protects from ischemic damage.
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9
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He X, Riceberg J, Soucy T, Koenig E, Minissale J, Gallery M, Bernard H, Yang X, Liao H, Rabino C, Shah P, Xega K, Yan ZH, Sintchak M, Bradley J, Xu H, Duffey M, England D, Mizutani H, Hu Z, Guo J, Chau R, Dick LR, Brownell JE, Newcomb J, Langston S, Lightcap ES, Bence N, Pulukuri SM. Probing the roles of SUMOylation in cancer cell biology by using a selective SAE inhibitor. Nat Chem Biol 2017; 13:1164-1171. [PMID: 28892090 DOI: 10.1038/nchembio.2463] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 07/21/2017] [Indexed: 01/29/2023]
Abstract
Small ubiquitin-like modifier (SUMO) family proteins regulate target-protein functions by post-translational modification. However, a potent and selective inhibitor targeting the SUMO pathway has been lacking. Here we describe ML-792, a mechanism-based SUMO-activating enzyme (SAE) inhibitor with nanomolar potency in cellular assays. ML-792 selectively blocks SAE enzyme activity and total SUMOylation, thus decreasing cancer cell proliferation. Moreover, we found that induction of the MYC oncogene increased the ML-792-mediated viability effect in cancer cells, thus indicating a potential application of SAE inhibitors in treating MYC-amplified tumors. Using ML-792, we further explored the critical roles of SUMOylation in mitotic progression and chromosome segregation. Furthermore, expression of an SAE catalytic-subunit (UBA2) S95N M97T mutant rescued SUMOylation loss and the mitotic defect induced by ML-792, thus confirming the selectivity of ML-792. As a potent and selective SAE inhibitor, ML-792 provides rapid loss of endogenously SUMOylated proteins, thereby facilitating novel insights into SUMO biology.
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Affiliation(s)
- Xingyue He
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts, USA
| | - Jessica Riceberg
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts, USA
| | - Teresa Soucy
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts, USA
| | - Erik Koenig
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts, USA
| | - James Minissale
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts, USA
| | - Melissa Gallery
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts, USA
| | - Hugues Bernard
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts, USA
| | - Xiaofeng Yang
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts, USA
| | - Hua Liao
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts, USA
| | - Claudia Rabino
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts, USA
| | - Pooja Shah
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts, USA
| | - Kristina Xega
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts, USA
| | - Zhong-Hua Yan
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts, USA
| | - Mike Sintchak
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts, USA
| | - John Bradley
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts, USA
| | - He Xu
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts, USA
| | - Matt Duffey
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts, USA
| | - Dylan England
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts, USA
| | - Hirotake Mizutani
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts, USA
| | - Zhigen Hu
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts, USA
| | - Jianping Guo
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts, USA
| | - Ryan Chau
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts, USA
| | - Lawrence R Dick
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts, USA
| | - James E Brownell
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts, USA
| | - John Newcomb
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts, USA
| | - Steve Langston
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts, USA
| | - Eric S Lightcap
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts, USA
| | - Neil Bence
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts, USA
| | - Sai M Pulukuri
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts, USA
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10
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Mateescu B, Kowal EJK, van Balkom BWM, Bartel S, Bhattacharyya SN, Buzás EI, Buck AH, de Candia P, Chow FWN, Das S, Driedonks TAP, Fernández-Messina L, Haderk F, Hill AF, Jones JC, Van Keuren-Jensen KR, Lai CP, Lässer C, Liegro ID, Lunavat TR, Lorenowicz MJ, Maas SLN, Mäger I, Mittelbrunn M, Momma S, Mukherjee K, Nawaz M, Pegtel DM, Pfaffl MW, Schiffelers RM, Tahara H, Théry C, Tosar JP, Wauben MHM, Witwer KW, Nolte-'t Hoen ENM. Obstacles and opportunities in the functional analysis of extracellular vesicle RNA - an ISEV position paper. J Extracell Vesicles 2017; 6:1286095. [PMID: 28326170 PMCID: PMC5345583 DOI: 10.1080/20013078.2017.1286095] [Citation(s) in RCA: 519] [Impact Index Per Article: 74.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 12/25/2016] [Indexed: 02/07/2023] Open
Abstract
The release of RNA-containing extracellular vesicles (EV) into the extracellular milieu has been demonstrated in a multitude of different in vitro cell systems and in a variety of body fluids. RNA-containing EV are in the limelight for their capacity to communicate genetically encoded messages to other cells, their suitability as candidate biomarkers for diseases, and their use as therapeutic agents. Although EV-RNA has attracted enormous interest from basic researchers, clinicians, and industry, we currently have limited knowledge on which mechanisms drive and regulate RNA incorporation into EV and on how RNA-encoded messages affect signalling processes in EV-targeted cells. Moreover, EV-RNA research faces various technical challenges, such as standardisation of EV isolation methods, optimisation of methodologies to isolate and characterise minute quantities of RNA found in EV, and development of approaches to demonstrate functional transfer of EV-RNA in vivo. These topics were discussed at the 2015 EV-RNA workshop of the International Society for Extracellular Vesicles. This position paper was written by the participants of the workshop not only to give an overview of the current state of knowledge in the field, but also to clarify that our incomplete knowledge – of the nature of EV(-RNA)s and of how to effectively and reliably study them – currently prohibits the implementation of gold standards in EV-RNA research. In addition, this paper creates awareness of possibilities and limitations of currently used strategies to investigate EV-RNA and calls for caution in interpretation of the obtained data.
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Affiliation(s)
- Bogdan Mateescu
- Department of Biology, Swiss Federal Institute of Technology Zurich (ETH Zürich) , Zurich , Switzerland
| | - Emma J K Kowal
- Department of Biology, Massachusetts Institute of Technology , Cambridge , MA , USA
| | - Bas W M van Balkom
- Department of Nephrology and Hypertension, UMC Utrecht , Utrecht , the Netherlands
| | - Sabine Bartel
- Experimental Asthma Research, Priority Area Asthma & Allergy, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL) , Borstel , Germany
| | - Suvendra N Bhattacharyya
- Department of Science and Technology, CSIR-Indian Institute of Chemical Biology , Kolkata , India
| | - Edit I Buzás
- Department of Genetics, Cell- and Immunobiology, Semmelweis University , Budapest , Hungary
| | - Amy H Buck
- Institute of Immunology and Infection Research, Centre for Immunity, Infection and Evolution, School of Biological Sciences, University of Edinburgh , Edinburgh , UK
| | | | - Franklin W N Chow
- Institute of Immunology and Infection Research, Centre for Immunity, Infection and Evolution, School of Biological Sciences, University of Edinburgh , Edinburgh , UK
| | - Saumya Das
- Cardiovascular Research Institute, Massachusetts General Hospital , Boston , MA , USA
| | - Tom A P Driedonks
- Department of Biochemistry & Cell Biology, Faculty of Veterinary Medicine, Utrecht University , Utrecht , the Netherlands
| | | | - Franziska Haderk
- Department of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Medicine, Helen Diller Family Comprehensive Cancer Center, UC San Francisco, San Francisco, CA, USA
| | - Andrew F Hill
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University , Bundoora , Australia
| | - Jennifer C Jones
- Molecular Immunogenetics & Vaccine Research Section, Vaccine Branch, CCR, NCI , Bethesda , MD , USA
| | | | - Charles P Lai
- Institute of Biomedical Engineering, National Tsing Hua University , Hsinchu , Taiwan
| | - Cecilia Lässer
- Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and NeuroDiscovery Center, Harvard Medical School, Boston, MA, USA; Krefting Research Centre, Department of Internal Medicine and Clinical Nutrition, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Italia di Liegro
- Department of Experimental Biomedicine and Clinical Neurosciences (BIONEC), University of Palermo , Palermo , Italy
| | - Taral R Lunavat
- Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and NeuroDiscovery Center, Harvard Medical School, Boston, MA, USA; Krefting Research Centre, Department of Internal Medicine and Clinical Nutrition, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Magdalena J Lorenowicz
- Center for Molecular Medicine, University Medical Center Utrecht & Regenerative Medicine Center , Utrecht , the Netherlands
| | - Sybren L N Maas
- Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and NeuroDiscovery Center, Harvard Medical School , Boston , MA , USA
| | - Imre Mäger
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK; Institute of Technology, University of Tartu, Tartu, Estonia
| | - Maria Mittelbrunn
- Instituto de Investigación del Hospital 12 de Octubre , Madrid , Spain
| | - Stefan Momma
- Institute of Neurology (Edinger Institute), Frankfurt University Medical School , Frankfurt am Main , Germany
| | - Kamalika Mukherjee
- Department of Science and Technology, CSIR-Indian Institute of Chemical Biology , Kolkata , India
| | - Muhammed Nawaz
- Department of Pathology and Forensic Medicine, Ribeirão Preto School of Medicine, University of Sao Paulo , Sao Paulo , Brazil
| | - D Michiel Pegtel
- Department of Pathology, Exosomes Research Group, VU University Medical Center , Amsterdam , the Netherlands
| | - Michael W Pfaffl
- Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich (TUM) Weihenstephan , Freising , Germany
| | - Raymond M Schiffelers
- Laboratory Clinical Chemistry & Haematology, University Medical Center Utrecht , Utrecht , the Netherlands
| | - Hidetoshi Tahara
- Department of Cellular and Molecular Biology, Institute of Biomedical & Health Sciences, Hiroshima University , Hiroshima , Japan
| | - Clotilde Théry
- Institut Curie, PSL Research University, INSERM U932 , Paris , France
| | - Juan Pablo Tosar
- Functional Genomics Unit, Institut Pasteur de Montevideo, Nuclear Research Center, Faculty of Science, Universidad de la República , Montevideo , Uruguay
| | - Marca H M Wauben
- Department of Biochemistry & Cell Biology, Faculty of Veterinary Medicine, Utrecht University , Utrecht , the Netherlands
| | - Kenneth W Witwer
- Department of Molecular and Comparative Pathobiology and Department of Neurology, The Johns Hopkins University School of Medicine , Baltimore , MD , USA
| | - Esther N M Nolte-'t Hoen
- Department of Biochemistry & Cell Biology, Faculty of Veterinary Medicine, Utrecht University , Utrecht , the Netherlands
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11
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Mateo Sánchez S, Freeman SD, Delacroix L, Malgrange B. The role of post-translational modifications in hearing and deafness. Cell Mol Life Sci 2016; 73:3521-33. [PMID: 27147466 PMCID: PMC11108544 DOI: 10.1007/s00018-016-2257-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 04/21/2016] [Accepted: 04/26/2016] [Indexed: 12/20/2022]
Abstract
Post-translational modifications (PTMs) are key molecular events that modify proteins after their synthesis and modulate their ultimate functional properties by affecting their stability, localisation, interaction potential or activity. These chemical changes expand the size of the proteome adding diversity to the molecular pathways governing the biological outcome of cells. PTMs are, thus, crucial in regulating a variety of cellular processes such as apoptosis, proliferation and differentiation and have been shown to be instrumental during embryonic development. In addition, alterations in protein PTMs have been implicated in the pathogenesis of many human diseases, including deafness. In this review, we summarize the recent progress made in understanding the roles of PTMs during cochlear development, with particular emphasis on the enzymes driving protein phosphorylation, acetylation, methylation, glycosylation, ubiquitination and SUMOylation. We also discuss how these enzymes may contribute to hearing impairment and deafness.
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Affiliation(s)
- Susana Mateo Sánchez
- Developmental Neurobiology Unit, GIGA-Neurosciences, University of Liège, Quartier Hôpital (CHU), Avenue Hippocrate 15, Tour 4, 1er étage, Bât. B36, 4000, Liège, Belgium
| | - Stephen D Freeman
- Developmental Neurobiology Unit, GIGA-Neurosciences, University of Liège, Quartier Hôpital (CHU), Avenue Hippocrate 15, Tour 4, 1er étage, Bât. B36, 4000, Liège, Belgium
| | - Laurence Delacroix
- Developmental Neurobiology Unit, GIGA-Neurosciences, University of Liège, Quartier Hôpital (CHU), Avenue Hippocrate 15, Tour 4, 1er étage, Bât. B36, 4000, Liège, Belgium
| | - Brigitte Malgrange
- Developmental Neurobiology Unit, GIGA-Neurosciences, University of Liège, Quartier Hôpital (CHU), Avenue Hippocrate 15, Tour 4, 1er étage, Bât. B36, 4000, Liège, Belgium.
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12
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Kota V, Sommer G, Durette C, Thibault P, van Niekerk EA, Twiss JL, Heise T. SUMO-Modification of the La Protein Facilitates Binding to mRNA In Vitro and in Cells. PLoS One 2016; 11:e0156365. [PMID: 27224031 PMCID: PMC4880191 DOI: 10.1371/journal.pone.0156365] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 05/12/2016] [Indexed: 02/05/2023] Open
Abstract
The RNA-binding protein La is involved in several aspects of RNA metabolism including the translational regulation of mRNAs and processing of pre-tRNAs. Besides its well-described phosphorylation by Casein kinase 2, the La protein is also posttranslationally modified by the Small Ubiquitin-like MOdifier (SUMO), but the functional outcome of this modification has not been defined. The objective of this study was to test whether sumoylation changes the RNA-binding activity of La. Therefore, we established an in vitro sumoylation assay for recombinant human La and analyzed its RNA-binding activity by electrophoretic mobility shift assays. We identified two novel SUMO-acceptor sites within the La protein located between the RNA recognition motif 1 and 2 and we demonstrate for the first time that sumoylation facilitates the RNA-binding of La to small RNA oligonucleotides representing the oligopyrimidine tract (TOP) elements from the 5' untranslated regions (UTR) of mRNAs encoding ribosomal protein L22 and L37 and to a longer RNA element from the 5' UTR of cyclin D1 (CCND1) mRNA in vitro. Furthermore, we show by RNA immunoprecipitation experiments that a La mutant deficient in sumoylation has impaired RNA-binding activity in cells. These data suggest that modulating the RNA-binding activity of La by sumoylation has important consequences on its functionality.
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Affiliation(s)
- Venkatesh Kota
- Medical University of South Carolina, Department of Biochemistry & Molecular Biology, Charleston, South Carolina, United States of America
| | - Gunhild Sommer
- Medical University of South Carolina, Department of Biochemistry & Molecular Biology, Charleston, South Carolina, United States of America
| | - Chantal Durette
- Institute of Research in Immunology and Cancer University de Montreal, Station Centre-ville, Montreal, Canada
| | - Pierre Thibault
- Institute of Research in Immunology and Cancer University de Montreal, Station Centre-ville, Montreal, Canada
| | - Erna A. van Niekerk
- Department of Neurosciences-0626, University of California, San Diego, La Jolla, California, United States of America
| | - Jeffery L. Twiss
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, United States of America
| | - Tilman Heise
- Medical University of South Carolina, Department of Biochemistry & Molecular Biology, Charleston, South Carolina, United States of America
- * E-mail:
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