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Chen K, Dai J, Klöting N, Cao X, Jin S, Chen L, Wang Y, Liu S, Hu Y, Jiang L, Liew CW, Blüher M, Wang X. Serum scEMC10 Levels are Negatively Associated With Resting Metabolic Rate and age in Humans. J Clin Endocrinol Metab 2023; 108:e1074-e1081. [PMID: 37071730 DOI: 10.1210/clinem/dgad214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/05/2023] [Indexed: 04/20/2023]
Abstract
CONTEXT We have recently shown that the secreted isoform of endoplasmic reticulum membrane complex subunit 10 (scEMC10) is upregulated in human obesity and that overexpression of scEMC10 promotes, whereas antibody neutralization of circulating scEMC10 prevents diet-induced obesity in mice. OBJECTIVE To explore associations of serum scEMC10 with body mass index (BMI), resting metabolism rate (RMR), and age in humans. DESIGN A cross-sectional study. SETTING AND PATIENTS A total of 833 participants from a Chinese physical examination cohort and 191 participants from the Leipzig Obesity Biobank cohort. MAIN OUTCOME MEASURES Serum scEMC10 concentrations are measured using chemiluminescent immunoassay. RMR is calculated based on measurements from indirect calorimetry with an open-circuit ventilated-hood system. RESULTS In the Chinese physical examination cohort, a J-shaped nonlinear correlation between BMI and serum scEMC10 was identified in participants where underweight, overweight, and obese people all presented higher serum scEMC10 levels than normal weight people. Participants younger than age 30 years old exhibited significantly higher serum scEMC10 levels than those older than 50 years of age. In addition, participants aged 30 to 40 years also had significantly higher serum scEMC10 levels than those aged 50 to 60 years. In the Leipzig Obesity Biobank cohort, we observed a significantly negative correlation between serum scEMC10 and resting energy expenditure after adjusting for BMI. Participants in the highest quartile of serum scEMC10 levels had significantly lower RMR than those in the first quartile. RMR had an independently inverse association with serum scEMC10. CONCLUSIONS Serum scEMC10 levels are negatively associated with age and RMR in humans.
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Affiliation(s)
- Kuangyang Chen
- Department of Endocrinology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China
| | - Jiarong Dai
- Department of Endocrinology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China
| | - Nora Klöting
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig 04103, Germany
| | - Xinyi Cao
- Department of Endocrinology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China
| | - Shuoshuo Jin
- Department of Endocrinology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China
| | - Lijiao Chen
- Department of Endocrinology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China
| | - Yahao Wang
- Department of Endocrinology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China
| | - Shan Liu
- Department of Endocrinology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China
| | - Yao Hu
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China
| | - Lin Jiang
- Healthcare center of Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Chong Wee Liew
- Department of Physiology & Biophysics, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Matthias Blüher
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig 04103, Germany
- Medical Department III-Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig 04103, Germany
| | - Xuanchun Wang
- Department of Endocrinology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China
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2
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Nie T, Lu J, Zhang H, Mao L. Latest advances in the regulatory genes of adipocyte thermogenesis. Front Endocrinol (Lausanne) 2023; 14:1250487. [PMID: 37680891 PMCID: PMC10482227 DOI: 10.3389/fendo.2023.1250487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/07/2023] [Indexed: 09/09/2023] Open
Abstract
An energy imbalance cause obesity: more energy intake or less energy expenditure, or both. Obesity could be the origin of many metabolic disorders, such as type 2 diabetes and cardiovascular disease. UCP1 (uncoupling protein1), which is highly and exclusively expressed in the thermogenic adipocytes, including beige and brown adipocytes, can dissipate proton motive force into heat without producing ATP to increase energy expenditure. It is an attractive strategy to combat obesity and its related metabolic disorders by increasing non-shivering adipocyte thermogenesis. Adipocyte thermogenesis has recently been reported to be regulated by several new genes. This work provided novel and potential targets to activate adipocyte thermogenesis and resist obesity, such as secreted proteins ADISSP and EMC10, enzyme SSU72, etc. In this review, we have summarized the latest research on adipocyte thermogenesis regulation to shed more light on this topic.
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Affiliation(s)
- Tao Nie
- School of Basic Medicine, Hubei University of Arts and Science, Xiangyang, China
| | - Jinli Lu
- Scientific Research Center, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Hua Zhang
- Department of Medical Iconography, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Liufeng Mao
- Scientific Research Center, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
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3
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Wang X, Li Y, Qiang G, Wang K, Dai J, McCann M, Munoz MD, Gil V, Yu Y, Li S, Yang Z, Xu S, Cordoba-Chacon J, De Jesus DF, Sun B, Chen K, Wang Y, Liu X, Miao Q, Zhou L, Hu R, Ding Q, Kulkarni RN, Gao D, Blüher M, Liew CW. Secreted EMC10 is upregulated in human obesity and its neutralizing antibody prevents diet-induced obesity in mice. Nat Commun 2022; 13:7323. [PMID: 36443308 PMCID: PMC9705309 DOI: 10.1038/s41467-022-34259-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 10/17/2022] [Indexed: 11/29/2022] Open
Abstract
Secreted isoform of endoplasmic reticulum membrane complex subunit 10 (scEMC10) is a poorly characterized secreted protein of largely unknown physiological function. Here we demonstrate that scEMC10 is upregulated in people with obesity and is positively associated with insulin resistance. Consistent with a causal role for scEMC10 in obesity, Emc10-/- mice are resistant to diet-induced obesity due to an increase in energy expenditure, while scEMC10 overexpression decreases energy expenditure, thus promoting obesity in mouse. Furthermore, neutralization of circulating scEMC10 using a monoclonal antibody reduces body weight and enhances insulin sensitivity in obese mice. Mechanistically, we provide evidence that scEMC10 can be transported into cells where it binds to the catalytic subunit of PKA and inhibits its stimulatory action on CREB while ablation of EMC10 promotes thermogenesis in adipocytes via activation of the PKA signalling pathway and its downstream targets. Taken together, our data identify scEMC10 as a circulating inhibitor of thermogenesis and a potential therapeutic target for obesity and its cardiometabolic complications.
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Affiliation(s)
- Xuanchun Wang
- Department of Endocrinology, Huashan Hospital, Fudan University, Shanghai, China.
| | - Yanliang Li
- Department of Endocrinology, Huashan Hospital, Fudan University, Shanghai, China
- Department of Physiology & Biophysics, University of Illinois at Chicago, Chicago, IL, USA
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, USA
| | - Guifen Qiang
- Department of Physiology & Biophysics, University of Illinois at Chicago, Chicago, IL, USA
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Kaihua Wang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiarong Dai
- Department of Endocrinology, Huashan Hospital, Fudan University, Shanghai, China
| | - Maximilian McCann
- Department of Physiology & Biophysics, University of Illinois at Chicago, Chicago, IL, USA
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, USA
| | - Marcos D Munoz
- Department of Physiology & Biophysics, University of Illinois at Chicago, Chicago, IL, USA
| | - Victoria Gil
- Department of Physiology & Biophysics, University of Illinois at Chicago, Chicago, IL, USA
| | - Yifei Yu
- Department of Endocrinology, Huashan Hospital, Fudan University, Shanghai, China
| | - Shengxian Li
- Department of Physiology & Biophysics, University of Illinois at Chicago, Chicago, IL, USA
- Department of Endocrinology and Metabolism, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhihong Yang
- Research Division, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA
- Department of Transplant Surgery, Mass General Hospital, Harvard Medical School, Boston, MA, USA
| | - Shanshan Xu
- Department of Physiology & Biophysics, University of Illinois at Chicago, Chicago, IL, USA
| | - Jose Cordoba-Chacon
- Department of Medicine, Section of Endocrinology, Diabetes and Metabolism, University of Illinois at Chicago, Chicago, IL, USA
| | - Dario F De Jesus
- Research Division, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA
| | - Bei Sun
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin, China
| | - Kuangyang Chen
- Department of Endocrinology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yahao Wang
- Department of Endocrinology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiaoxia Liu
- Department of Endocrinology, Huashan Hospital, Fudan University, Shanghai, China
| | - Qing Miao
- Department of Endocrinology, Huashan Hospital, Fudan University, Shanghai, China
| | - Linuo Zhou
- Department of Endocrinology, Huashan Hospital, Fudan University, Shanghai, China
| | - Renming Hu
- Department of Endocrinology, Huashan Hospital, Fudan University, Shanghai, China
| | - Qiang Ding
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Rohit N Kulkarni
- Research Division, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA
| | - Daming Gao
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Matthias Blüher
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Chong Wee Liew
- Department of Physiology & Biophysics, University of Illinois at Chicago, Chicago, IL, USA.
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4
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Liu L, Mao S, Chen K, Dai J, Jin S, Chen L, Wang Y, Guo L, Yang Y, Zhan C, Xiong Z, Diao H, Zhou Y, Ding Q, Wang X. Membrane-Bound EMC10 Is Required for Sperm Motility via Maintaining the Homeostasis of Cytoplasm Sodium in Sperm. Int J Mol Sci 2022; 23:ijms231710069. [PMID: 36077468 PMCID: PMC9456234 DOI: 10.3390/ijms231710069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022] Open
Abstract
Endoplasmic reticulum membrane protein complex subunit 10 (EMC10) is an evolutionarily conserved and multifunctional factor across species. We previously reported that Emc10 knockout (KO) leads to mouse male infertility. Emc10-null spermatozoa exhibit multiple aspects of dysfunction, including reduced sperm motility. Two subunits of a Na/K-ATPase, ATP1A4 and ATP1B3, are nearly absent in Emc10 KO spermatozoa. Here, two isoforms of EMC10 were characterized in the mouse testis and epididymis: the membrane-bound (mEMC10) and secreted (scEMC10) isoforms. We present evidence that mEMC10, rather than scEMC10, is required for cytoplasm sodium homeostasis by positively regulating ATP1B3 expression in germ cells. Intra-testis mEMC10 overexpression rescued the sperm motility defect caused by Emc10 KO, while exogenous recombinant scEMC10 protein could not improve the motility of spermatozoa from either Emc10 KO mouse or asthenospermic subjects. Clinically, there is a positive association between ATP1B3 and EMC10 protein levels in human spermatozoa, whereas no correlation was proven between seminal plasma scEMC10 levels and sperm motility. These results highlight the important role of the membrane-bound EMC10 isoform in maintaining cytoplasm sodium homeostasis and sperm motility. Based on the present results, the mEMC10-Na, K/ATPase α4β3 axis is proposed as a novel mechanism underlying the regulation of cytoplasmic sodium and sperm motility, and its components seem to have therapeutic potential for asthenospermia.
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Affiliation(s)
- Lijie Liu
- Department of Urology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Shanhua Mao
- Department of Urology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Kuangyang Chen
- Department of Endocrinology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Jiarong Dai
- Department of Endocrinology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Shuoshuo Jin
- Department of Endocrinology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Lijiao Chen
- Department of Endocrinology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Yahao Wang
- Department of Endocrinology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Lina Guo
- NHC Key Laboratory of Reproduction Regulation (Shanghai Institute for Biomedical and Pharmaceutical Technologies), School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yiting Yang
- NHC Key Laboratory of Reproduction Regulation (Shanghai Institute for Biomedical and Pharmaceutical Technologies), School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Chongwen Zhan
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Zuquan Xiong
- Department of Urology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Hua Diao
- NHC Key Laboratory of Reproduction Regulation (Shanghai Institute for Biomedical and Pharmaceutical Technologies), School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yuchuan Zhou
- Shanghai Key Laboratory of Embryo Original Diseases, The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Qiang Ding
- Department of Urology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Xuanchun Wang
- Department of Endocrinology, Huashan Hospital, Fudan University, Shanghai 200040, China
- Correspondence: ; Tel.: +86-21-5288-8286
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5
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Tirincsi A, Sicking M, Hadzibeganovic D, Haßdenteufel S, Lang S. The Molecular Biodiversity of Protein Targeting and Protein Transport Related to the Endoplasmic Reticulum. Int J Mol Sci 2021; 23:143. [PMID: 35008565 PMCID: PMC8745461 DOI: 10.3390/ijms23010143] [Citation(s) in RCA: 12] [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: 10/27/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 12/15/2022] Open
Abstract
Looking at the variety of the thousands of different polypeptides that have been focused on in the research on the endoplasmic reticulum from the last five decades taught us one humble lesson: no one size fits all. Cells use an impressive array of components to enable the safe transport of protein cargo from the cytosolic ribosomes to the endoplasmic reticulum. Safety during the transit is warranted by the interplay of cytosolic chaperones, membrane receptors, and protein translocases that together form functional networks and serve as protein targeting and translocation routes. While two targeting routes to the endoplasmic reticulum, SRP (signal recognition particle) and GET (guided entry of tail-anchored proteins), prefer targeting determinants at the N- and C-terminus of the cargo polypeptide, respectively, the recently discovered SND (SRP-independent) route seems to preferentially cater for cargos with non-generic targeting signals that are less hydrophobic or more distant from the termini. With an emphasis on targeting routes and protein translocases, we will discuss those functional networks that drive efficient protein topogenesis and shed light on their redundant and dynamic nature in health and disease.
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Affiliation(s)
- Andrea Tirincsi
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
| | - Mark Sicking
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
| | - Drazena Hadzibeganovic
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
| | - Sarah Haßdenteufel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sven Lang
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
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6
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Miller-Vedam LE, Bräuning B, Popova KD, Schirle Oakdale NT, Bonnar JL, Prabu JR, Boydston EA, Sevillano N, Shurtleff MJ, Stroud RM, Craik CS, Schulman BA, Frost A, Weissman JS. Structural and mechanistic basis of the EMC-dependent biogenesis of distinct transmembrane clients. eLife 2020; 9:e62611. [PMID: 33236988 PMCID: PMC7785296 DOI: 10.7554/elife.62611] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 11/17/2020] [Indexed: 12/11/2022] Open
Abstract
Membrane protein biogenesis in the endoplasmic reticulum (ER) is complex and failure-prone. The ER membrane protein complex (EMC), comprising eight conserved subunits, has emerged as a central player in this process. Yet, we have limited understanding of how EMC enables insertion and integrity of diverse clients, from tail-anchored to polytopic transmembrane proteins. Here, yeast and human EMC cryo-EM structures reveal conserved intricate assemblies and human-specific features associated with pathologies. Structure-based functional studies distinguish between two separable EMC activities, as an insertase regulating tail-anchored protein levels and a broader role in polytopic membrane protein biogenesis. These depend on mechanistically coupled yet spatially distinct regions including two lipid-accessible membrane cavities which confer client-specific regulation, and a non-insertase EMC function mediated by the EMC lumenal domain. Our studies illuminate the structural and mechanistic basis of EMC's multifunctionality and point to its role in differentially regulating the biogenesis of distinct client protein classes.
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Affiliation(s)
- Lakshmi E Miller-Vedam
- Molecular, Cellular, and Computational Biophysics Graduate Program, University of California, San FranciscoSan FranciscoUnited States
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Department of Biology, Whitehead Institute, MITCambridgeUnited States
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
| | - Bastian Bräuning
- Department of Molecular Machines and Signaling, Max Planck Institute of BiochemistryMartinsriedGermany
| | - Katerina D Popova
- Department of Biology, Whitehead Institute, MITCambridgeUnited States
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
- Biomedical Sciences Graduate Program, University of California, San FranciscoSan FranciscoUnited States
| | - Nicole T Schirle Oakdale
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
| | - Jessica L Bonnar
- Department of Biology, Whitehead Institute, MITCambridgeUnited States
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
| | - Jesuraj R Prabu
- Department of Molecular Machines and Signaling, Max Planck Institute of BiochemistryMartinsriedGermany
| | - Elizabeth A Boydston
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
| | - Natalia Sevillano
- Department of Pharmaceutical Chemistry, University of California, San FranciscoSan FranciscoUnited States
| | - Matthew J Shurtleff
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
| | - Robert M Stroud
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San FranciscoSan FranciscoUnited States
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of BiochemistryMartinsriedGermany
| | - Adam Frost
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Jonathan S Weissman
- Department of Biology, Whitehead Institute, MITCambridgeUnited States
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
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7
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Umair M, Ballow M, Asiri A, Alyafee Y, Al Tuwaijri A, Alhamoudi KM, Aloraini T, Abdelhakim M, Althagafi AT, Kafkas S, Alsubaie L, Alrifai MT, Hoehndorf R, Alfares A, Alfadhel M. EMC10 homozygous variant identified in a family with global developmental delay, mild intellectual disability, and speech delay. Clin Genet 2020; 98:555-561. [PMID: 32869858 PMCID: PMC7756316 DOI: 10.1111/cge.13842] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 12/27/2022]
Abstract
In recent years, several genes have been implicated in the variable disease presentation of global developmental delay (GDD) and intellectual disability (ID). The endoplasmic reticulum membrane protein complex (EMC) family is known to be involved in GDD and ID. Homozygous variants of EMC1 are associated with GDD, scoliosis, and cerebellar atrophy, indicating the relevance of this pathway for neurogenetic disorders. EMC10 is a bone marrow‐derived angiogenic growth factor that plays an important role in infarct vascularization and promoting tissue repair. However, this gene has not been previously associated with human disease. Herein, we describe a Saudi family with two individuals segregating a recessive neurodevelopmental disorder. Both of the affected individuals showed mild ID, speech delay, and GDD. Whole‐exome sequencing (WES) and Sanger sequencing were performed to identify candidate genes. Further, to elucidate the functional effects of the variant, quantitative real‐time PCR (RT‐qPCR)‐based expression analysis was performed. WES revealed a homozygous splice acceptor site variant (c.679‐1G>A) in EMC10 (chromosome 19q13.33) that segregated perfectly within the family. RT‐qPCR showed a substantial decrease in the relative EMC10 gene expression in the patients, indicating the pathogenicity of the identified variant. For the first time in the literature, the EMC10 gene variant was associated with mild ID, speech delay, and GDD. Thus, this gene plays a key role in developmental milestones, with the potential to cause neurodevelopmental disorders in humans.
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Affiliation(s)
- Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia
| | - Mariam Ballow
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia
| | - Abdulaziz Asiri
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia
| | - Yusra Alyafee
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia
| | - Abeer Al Tuwaijri
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia
| | - Kheloud M Alhamoudi
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia
| | - Taghrid Aloraini
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Marwa Abdelhakim
- Computer, Electrical and Mathematical Sciences & Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Azza Thamer Althagafi
- Computer, Electrical and Mathematical Sciences & Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,College of Computers and Information Technology, Taif University, Taif, Saudi Arabia
| | - Senay Kafkas
- Computer, Electrical and Mathematical Sciences & Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Lamia Alsubaie
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Muhammad Talal Alrifai
- Department of Pediatrics, Division of Neurology, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia
| | - Robert Hoehndorf
- Computer, Electrical and Mathematical Sciences & Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Ahmed Alfares
- Department of Pediatrics, College of Medicine, Qassim University, Saudi Arabia
| | - Majid Alfadhel
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia.,Division of Genetics, Department of Pediatrics, King Abdullah Specialized Children's Hospital, King Abdulaziz Medical City, Riyadh, Saudi Arabia
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8
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Volkmar N, Christianson JC. Squaring the EMC - how promoting membrane protein biogenesis impacts cellular functions and organismal homeostasis. J Cell Sci 2020; 133:133/8/jcs243519. [PMID: 32332093 PMCID: PMC7188443 DOI: 10.1242/jcs.243519] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Integral membrane proteins play key functional roles at organelles and the plasma membrane, necessitating their efficient and accurate biogenesis to ensure appropriate targeting and activity. The endoplasmic reticulum membrane protein complex (EMC) has recently emerged as an important eukaryotic complex for biogenesis of integral membrane proteins by promoting insertion and stability of atypical and sub-optimal transmembrane domains (TMDs). Although confirmed as a bona fide complex almost a decade ago, light is just now being shed on the mechanism and selectivity underlying the cellular responsibilities of the EMC. In this Review, we revisit the myriad of functions attributed the EMC through the lens of these new mechanistic insights, to address questions of the cellular and organismal roles the EMC has evolved to undertake. Summary: The EMC is an important factor facilitating membrane protein biogenesis. Here we discuss the broad cellular and organismal responsibilities overseen by client proteins requiring the EMC for maturation.
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Affiliation(s)
- Norbert Volkmar
- Jeffrey Cheah Biomedical Centre, Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - John C Christianson
- Oxford Centre for Translational Myeloma Research, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Botnar Research Centre, Headington, Oxford OX3 7LD, UK
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Zhou Y, Wu F, Zhang M, Xiong Z, Yin Q, Ru Y, Shi H, Li J, Mao S, Li Y, Cao X, Hu R, Liew CW, Ding Q, Wang X, Zhang Y. EMC10 governs male fertility via maintaining sperm ion balance. J Mol Cell Biol 2019; 10:503-514. [PMID: 29659949 DOI: 10.1093/jmcb/mjy024] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 04/05/2018] [Indexed: 02/01/2023] Open
Abstract
Infertility is a severe public health problem worldwide that prevails up to 15% in reproductive-age couples, and male infertility accounts for half of total infertility. Studies on genetically modified animal models have identified lots of genes involved in the pathogenesis of male infertility. The underlying causes, however, remain largely unclear. In this study, we provide evidence that EMC10, one subunit of endoplasmic reticulum (ER) membrane protein complex (EMC), is required for male fertility. EMC10 is significantly decreased in spermatozoa from patients with asthenozoospermia and positively associated with human sperm motility. Male mice lacking Emc10 gene are completely sterile. Emc10-null spermatozoa exhibit multiple defects including abnormal morphology, decreased motility, impaired capacitation, and impotency of acrosome reaction, thereby which are incapable of fertilizing intact or ZP-free oocytes. However, intracytoplasmic sperm injection could rescue this defect caused by EMC10 deletion. Mechanistically, EMC10 deficiency leads to inactivation of Na/K-ATPase, in turn giving rise to an increased level of intracellular Na+ in spermatozoa, which contributes to decreased sperm motility and abnormal morphology. Other mechanistic investigations demonstrate that the absence of EMC10 results in a reduction of HCO3- entry and subsequent decreases of both cAMP-dependent protein kinase A substrate phosphorylation and protein tyrosine phosphorylation. These data demonstrate that EMC10 is indispensable to male fertility via maintaining sperm ion balance of Na+ and HCO3-, and also suggest that EMC10 is a promising biomarker for male fertility and a potential pharmaceutical target to treat male infertility.
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Affiliation(s)
- Yuchuan Zhou
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Fei Wu
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Man Zhang
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Zuquan Xiong
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Qianqian Yin
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yanfei Ru
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Huijuan Shi
- China National Population and Family Planning Key Laboratory of Contraceptive Drugs and Devices, Shanghai Institute of Planned Parenthood Research, Shanghai, China
| | - Jinsong Li
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Shanhua Mao
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yanliang Li
- Department of Endocrinology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xinyi Cao
- Department of Endocrinology, Huashan Hospital, Fudan University, Shanghai, China
| | - Renming Hu
- Department of Endocrinology, Huashan Hospital, Fudan University, Shanghai, China
| | - Chong Wee Liew
- Department of Physiology & Biophysics, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Qiang Ding
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xuanchun Wang
- Department of Endocrinology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yonglian Zhang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
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10
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Reboll MR, Korf-Klingebiel M, Klede S, Polten F, Brinkmann E, Reimann I, Schönfeld HJ, Bobadilla M, Faix J, Kensah G, Gruh I, Klintschar M, Gaestel M, Niessen HW, Pich A, Bauersachs J, Gogos JA, Wang Y, Wollert KC. EMC10 (Endoplasmic Reticulum Membrane Protein Complex Subunit 10) Is a Bone Marrow-Derived Angiogenic Growth Factor Promoting Tissue Repair After Myocardial Infarction. Circulation 2017; 136:1809-1823. [PMID: 28931551 DOI: 10.1161/circulationaha.117.029980] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 08/31/2017] [Indexed: 01/05/2023]
Abstract
BACKGROUND Clinical trials of bone marrow cell-based therapies after acute myocardial infarction (MI) have produced mostly neutral results. Treatment with specific bone marrow cell-derived secreted proteins may provide an alternative biological approach to improving tissue repair and heart function after MI. We recently performed a bioinformatic secretome analysis in bone marrow cells from patients with acute MI and discovered a poorly characterized secreted protein, EMC10 (endoplasmic reticulum membrane protein complex subunit 10), showing activity in an angiogenic screen. METHODS We investigated the angiogenic potential of EMC10 and its mouse homolog (Emc10) in cultured endothelial cells and infarcted heart explants. We defined the cellular sources and function of Emc10 after MI using wild-type, Emc10-deficient, and Emc10 bone marrow-chimeric mice subjected to transient coronary artery ligation. Furthermore, we explored the therapeutic potential of recombinant Emc10 delivered by osmotic minipumps after MI in heart failure-prone FVB/N mice. RESULTS Emc10 signaled through small GTPases, p21-activated kinase, and the p38 mitogen-activated protein kinase (MAPK)-MAPK-activated protein kinase 2 (MK2) pathway to promote actin polymerization and endothelial cell migration. Confirming the importance of these signaling events in the context of acute MI, Emc10 stimulated endothelial cell outgrowth from infarcted mouse heart explants via p38 MAPK-MK2. Emc10 protein abundance was increased in the infarcted region of the left ventricle and in the circulation of wild-type mice after MI. Emc10 expression was also increased in left ventricular tissue samples from patients with acute MI. Bone marrow-derived monocytes and macrophages were the predominant sources of Emc10 in the infarcted murine heart. Emc10 KO mice showed no cardiovascular phenotype at baseline. After MI, however, capillarization of the infarct border zone was impaired in KO mice, and the animals developed larger infarct scars and more pronounced left ventricular remodeling compared with wild-type mice. Transplanting KO mice with wild-type bone marrow cells rescued the angiogenic defect and ameliorated left ventricular remodeling. Treating FVB/N mice with recombinant Emc10 enhanced infarct border-zone capillarization and exerted a sustained beneficial effect on left ventricular remodeling. CONCLUSIONS We have identified Emc10 as a previously unknown angiogenic growth factor that is produced by bone marrow-derived monocytes and macrophages as part of an endogenous adaptive response that can be enhanced therapeutically to repair the heart after MI.
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Affiliation(s)
- Marc R Reboll
- From Division of Molecular and Translational Cardiology, Department of Cardiology and Angiology (M.R.R., M.K.-K., S.K., E.B., I.R., Y.W., K.C.W.), Core Unit Proteomics, Institute of Toxicology (F.P., A.P.), Department of Biophysical Chemistry (J.F.), Leibniz Research Laboratories for Biotechnology and Artificial Organs, Department of Cardiothoracic, Transplantation, and Vascular Surgery (G.K., I.G.), Institute of Legal Medicine (M.K.), Institute of Physiological Chemistry (M.G.), and Department of Cardiology and Angiology (J.B.), Hannover Medical School, Germany; F. Hoffmann-La Roche, Pharma Research and Early Development, Basel, Switzerland (H.-J.S., M.B.); Department of Pathology and Department of Cardiac Surgery, Institute for Cardiovascular Research, Vrije Universiteit University Medical Center, Amsterdam, The Netherlands (H.W.N.); and Department of Physiology and Cellular Biophysics and Department of Neuroscience, College of Physicians and Surgeons, Columbia University, New York, NY (J.A.G.)
| | - Mortimer Korf-Klingebiel
- From Division of Molecular and Translational Cardiology, Department of Cardiology and Angiology (M.R.R., M.K.-K., S.K., E.B., I.R., Y.W., K.C.W.), Core Unit Proteomics, Institute of Toxicology (F.P., A.P.), Department of Biophysical Chemistry (J.F.), Leibniz Research Laboratories for Biotechnology and Artificial Organs, Department of Cardiothoracic, Transplantation, and Vascular Surgery (G.K., I.G.), Institute of Legal Medicine (M.K.), Institute of Physiological Chemistry (M.G.), and Department of Cardiology and Angiology (J.B.), Hannover Medical School, Germany; F. Hoffmann-La Roche, Pharma Research and Early Development, Basel, Switzerland (H.-J.S., M.B.); Department of Pathology and Department of Cardiac Surgery, Institute for Cardiovascular Research, Vrije Universiteit University Medical Center, Amsterdam, The Netherlands (H.W.N.); and Department of Physiology and Cellular Biophysics and Department of Neuroscience, College of Physicians and Surgeons, Columbia University, New York, NY (J.A.G.)
| | - Stefanie Klede
- From Division of Molecular and Translational Cardiology, Department of Cardiology and Angiology (M.R.R., M.K.-K., S.K., E.B., I.R., Y.W., K.C.W.), Core Unit Proteomics, Institute of Toxicology (F.P., A.P.), Department of Biophysical Chemistry (J.F.), Leibniz Research Laboratories for Biotechnology and Artificial Organs, Department of Cardiothoracic, Transplantation, and Vascular Surgery (G.K., I.G.), Institute of Legal Medicine (M.K.), Institute of Physiological Chemistry (M.G.), and Department of Cardiology and Angiology (J.B.), Hannover Medical School, Germany; F. Hoffmann-La Roche, Pharma Research and Early Development, Basel, Switzerland (H.-J.S., M.B.); Department of Pathology and Department of Cardiac Surgery, Institute for Cardiovascular Research, Vrije Universiteit University Medical Center, Amsterdam, The Netherlands (H.W.N.); and Department of Physiology and Cellular Biophysics and Department of Neuroscience, College of Physicians and Surgeons, Columbia University, New York, NY (J.A.G.)
| | - Felix Polten
- From Division of Molecular and Translational Cardiology, Department of Cardiology and Angiology (M.R.R., M.K.-K., S.K., E.B., I.R., Y.W., K.C.W.), Core Unit Proteomics, Institute of Toxicology (F.P., A.P.), Department of Biophysical Chemistry (J.F.), Leibniz Research Laboratories for Biotechnology and Artificial Organs, Department of Cardiothoracic, Transplantation, and Vascular Surgery (G.K., I.G.), Institute of Legal Medicine (M.K.), Institute of Physiological Chemistry (M.G.), and Department of Cardiology and Angiology (J.B.), Hannover Medical School, Germany; F. Hoffmann-La Roche, Pharma Research and Early Development, Basel, Switzerland (H.-J.S., M.B.); Department of Pathology and Department of Cardiac Surgery, Institute for Cardiovascular Research, Vrije Universiteit University Medical Center, Amsterdam, The Netherlands (H.W.N.); and Department of Physiology and Cellular Biophysics and Department of Neuroscience, College of Physicians and Surgeons, Columbia University, New York, NY (J.A.G.)
| | - Eva Brinkmann
- From Division of Molecular and Translational Cardiology, Department of Cardiology and Angiology (M.R.R., M.K.-K., S.K., E.B., I.R., Y.W., K.C.W.), Core Unit Proteomics, Institute of Toxicology (F.P., A.P.), Department of Biophysical Chemistry (J.F.), Leibniz Research Laboratories for Biotechnology and Artificial Organs, Department of Cardiothoracic, Transplantation, and Vascular Surgery (G.K., I.G.), Institute of Legal Medicine (M.K.), Institute of Physiological Chemistry (M.G.), and Department of Cardiology and Angiology (J.B.), Hannover Medical School, Germany; F. Hoffmann-La Roche, Pharma Research and Early Development, Basel, Switzerland (H.-J.S., M.B.); Department of Pathology and Department of Cardiac Surgery, Institute for Cardiovascular Research, Vrije Universiteit University Medical Center, Amsterdam, The Netherlands (H.W.N.); and Department of Physiology and Cellular Biophysics and Department of Neuroscience, College of Physicians and Surgeons, Columbia University, New York, NY (J.A.G.)
| | - Ines Reimann
- From Division of Molecular and Translational Cardiology, Department of Cardiology and Angiology (M.R.R., M.K.-K., S.K., E.B., I.R., Y.W., K.C.W.), Core Unit Proteomics, Institute of Toxicology (F.P., A.P.), Department of Biophysical Chemistry (J.F.), Leibniz Research Laboratories for Biotechnology and Artificial Organs, Department of Cardiothoracic, Transplantation, and Vascular Surgery (G.K., I.G.), Institute of Legal Medicine (M.K.), Institute of Physiological Chemistry (M.G.), and Department of Cardiology and Angiology (J.B.), Hannover Medical School, Germany; F. Hoffmann-La Roche, Pharma Research and Early Development, Basel, Switzerland (H.-J.S., M.B.); Department of Pathology and Department of Cardiac Surgery, Institute for Cardiovascular Research, Vrije Universiteit University Medical Center, Amsterdam, The Netherlands (H.W.N.); and Department of Physiology and Cellular Biophysics and Department of Neuroscience, College of Physicians and Surgeons, Columbia University, New York, NY (J.A.G.)
| | - Hans-Joachim Schönfeld
- From Division of Molecular and Translational Cardiology, Department of Cardiology and Angiology (M.R.R., M.K.-K., S.K., E.B., I.R., Y.W., K.C.W.), Core Unit Proteomics, Institute of Toxicology (F.P., A.P.), Department of Biophysical Chemistry (J.F.), Leibniz Research Laboratories for Biotechnology and Artificial Organs, Department of Cardiothoracic, Transplantation, and Vascular Surgery (G.K., I.G.), Institute of Legal Medicine (M.K.), Institute of Physiological Chemistry (M.G.), and Department of Cardiology and Angiology (J.B.), Hannover Medical School, Germany; F. Hoffmann-La Roche, Pharma Research and Early Development, Basel, Switzerland (H.-J.S., M.B.); Department of Pathology and Department of Cardiac Surgery, Institute for Cardiovascular Research, Vrije Universiteit University Medical Center, Amsterdam, The Netherlands (H.W.N.); and Department of Physiology and Cellular Biophysics and Department of Neuroscience, College of Physicians and Surgeons, Columbia University, New York, NY (J.A.G.)
| | - Maria Bobadilla
- From Division of Molecular and Translational Cardiology, Department of Cardiology and Angiology (M.R.R., M.K.-K., S.K., E.B., I.R., Y.W., K.C.W.), Core Unit Proteomics, Institute of Toxicology (F.P., A.P.), Department of Biophysical Chemistry (J.F.), Leibniz Research Laboratories for Biotechnology and Artificial Organs, Department of Cardiothoracic, Transplantation, and Vascular Surgery (G.K., I.G.), Institute of Legal Medicine (M.K.), Institute of Physiological Chemistry (M.G.), and Department of Cardiology and Angiology (J.B.), Hannover Medical School, Germany; F. Hoffmann-La Roche, Pharma Research and Early Development, Basel, Switzerland (H.-J.S., M.B.); Department of Pathology and Department of Cardiac Surgery, Institute for Cardiovascular Research, Vrije Universiteit University Medical Center, Amsterdam, The Netherlands (H.W.N.); and Department of Physiology and Cellular Biophysics and Department of Neuroscience, College of Physicians and Surgeons, Columbia University, New York, NY (J.A.G.)
| | - Jan Faix
- From Division of Molecular and Translational Cardiology, Department of Cardiology and Angiology (M.R.R., M.K.-K., S.K., E.B., I.R., Y.W., K.C.W.), Core Unit Proteomics, Institute of Toxicology (F.P., A.P.), Department of Biophysical Chemistry (J.F.), Leibniz Research Laboratories for Biotechnology and Artificial Organs, Department of Cardiothoracic, Transplantation, and Vascular Surgery (G.K., I.G.), Institute of Legal Medicine (M.K.), Institute of Physiological Chemistry (M.G.), and Department of Cardiology and Angiology (J.B.), Hannover Medical School, Germany; F. Hoffmann-La Roche, Pharma Research and Early Development, Basel, Switzerland (H.-J.S., M.B.); Department of Pathology and Department of Cardiac Surgery, Institute for Cardiovascular Research, Vrije Universiteit University Medical Center, Amsterdam, The Netherlands (H.W.N.); and Department of Physiology and Cellular Biophysics and Department of Neuroscience, College of Physicians and Surgeons, Columbia University, New York, NY (J.A.G.)
| | - George Kensah
- From Division of Molecular and Translational Cardiology, Department of Cardiology and Angiology (M.R.R., M.K.-K., S.K., E.B., I.R., Y.W., K.C.W.), Core Unit Proteomics, Institute of Toxicology (F.P., A.P.), Department of Biophysical Chemistry (J.F.), Leibniz Research Laboratories for Biotechnology and Artificial Organs, Department of Cardiothoracic, Transplantation, and Vascular Surgery (G.K., I.G.), Institute of Legal Medicine (M.K.), Institute of Physiological Chemistry (M.G.), and Department of Cardiology and Angiology (J.B.), Hannover Medical School, Germany; F. Hoffmann-La Roche, Pharma Research and Early Development, Basel, Switzerland (H.-J.S., M.B.); Department of Pathology and Department of Cardiac Surgery, Institute for Cardiovascular Research, Vrije Universiteit University Medical Center, Amsterdam, The Netherlands (H.W.N.); and Department of Physiology and Cellular Biophysics and Department of Neuroscience, College of Physicians and Surgeons, Columbia University, New York, NY (J.A.G.)
| | - Ina Gruh
- From Division of Molecular and Translational Cardiology, Department of Cardiology and Angiology (M.R.R., M.K.-K., S.K., E.B., I.R., Y.W., K.C.W.), Core Unit Proteomics, Institute of Toxicology (F.P., A.P.), Department of Biophysical Chemistry (J.F.), Leibniz Research Laboratories for Biotechnology and Artificial Organs, Department of Cardiothoracic, Transplantation, and Vascular Surgery (G.K., I.G.), Institute of Legal Medicine (M.K.), Institute of Physiological Chemistry (M.G.), and Department of Cardiology and Angiology (J.B.), Hannover Medical School, Germany; F. Hoffmann-La Roche, Pharma Research and Early Development, Basel, Switzerland (H.-J.S., M.B.); Department of Pathology and Department of Cardiac Surgery, Institute for Cardiovascular Research, Vrije Universiteit University Medical Center, Amsterdam, The Netherlands (H.W.N.); and Department of Physiology and Cellular Biophysics and Department of Neuroscience, College of Physicians and Surgeons, Columbia University, New York, NY (J.A.G.)
| | - Michael Klintschar
- From Division of Molecular and Translational Cardiology, Department of Cardiology and Angiology (M.R.R., M.K.-K., S.K., E.B., I.R., Y.W., K.C.W.), Core Unit Proteomics, Institute of Toxicology (F.P., A.P.), Department of Biophysical Chemistry (J.F.), Leibniz Research Laboratories for Biotechnology and Artificial Organs, Department of Cardiothoracic, Transplantation, and Vascular Surgery (G.K., I.G.), Institute of Legal Medicine (M.K.), Institute of Physiological Chemistry (M.G.), and Department of Cardiology and Angiology (J.B.), Hannover Medical School, Germany; F. Hoffmann-La Roche, Pharma Research and Early Development, Basel, Switzerland (H.-J.S., M.B.); Department of Pathology and Department of Cardiac Surgery, Institute for Cardiovascular Research, Vrije Universiteit University Medical Center, Amsterdam, The Netherlands (H.W.N.); and Department of Physiology and Cellular Biophysics and Department of Neuroscience, College of Physicians and Surgeons, Columbia University, New York, NY (J.A.G.)
| | - Matthias Gaestel
- From Division of Molecular and Translational Cardiology, Department of Cardiology and Angiology (M.R.R., M.K.-K., S.K., E.B., I.R., Y.W., K.C.W.), Core Unit Proteomics, Institute of Toxicology (F.P., A.P.), Department of Biophysical Chemistry (J.F.), Leibniz Research Laboratories for Biotechnology and Artificial Organs, Department of Cardiothoracic, Transplantation, and Vascular Surgery (G.K., I.G.), Institute of Legal Medicine (M.K.), Institute of Physiological Chemistry (M.G.), and Department of Cardiology and Angiology (J.B.), Hannover Medical School, Germany; F. Hoffmann-La Roche, Pharma Research and Early Development, Basel, Switzerland (H.-J.S., M.B.); Department of Pathology and Department of Cardiac Surgery, Institute for Cardiovascular Research, Vrije Universiteit University Medical Center, Amsterdam, The Netherlands (H.W.N.); and Department of Physiology and Cellular Biophysics and Department of Neuroscience, College of Physicians and Surgeons, Columbia University, New York, NY (J.A.G.)
| | - Hans W Niessen
- From Division of Molecular and Translational Cardiology, Department of Cardiology and Angiology (M.R.R., M.K.-K., S.K., E.B., I.R., Y.W., K.C.W.), Core Unit Proteomics, Institute of Toxicology (F.P., A.P.), Department of Biophysical Chemistry (J.F.), Leibniz Research Laboratories for Biotechnology and Artificial Organs, Department of Cardiothoracic, Transplantation, and Vascular Surgery (G.K., I.G.), Institute of Legal Medicine (M.K.), Institute of Physiological Chemistry (M.G.), and Department of Cardiology and Angiology (J.B.), Hannover Medical School, Germany; F. Hoffmann-La Roche, Pharma Research and Early Development, Basel, Switzerland (H.-J.S., M.B.); Department of Pathology and Department of Cardiac Surgery, Institute for Cardiovascular Research, Vrije Universiteit University Medical Center, Amsterdam, The Netherlands (H.W.N.); and Department of Physiology and Cellular Biophysics and Department of Neuroscience, College of Physicians and Surgeons, Columbia University, New York, NY (J.A.G.)
| | - Andreas Pich
- From Division of Molecular and Translational Cardiology, Department of Cardiology and Angiology (M.R.R., M.K.-K., S.K., E.B., I.R., Y.W., K.C.W.), Core Unit Proteomics, Institute of Toxicology (F.P., A.P.), Department of Biophysical Chemistry (J.F.), Leibniz Research Laboratories for Biotechnology and Artificial Organs, Department of Cardiothoracic, Transplantation, and Vascular Surgery (G.K., I.G.), Institute of Legal Medicine (M.K.), Institute of Physiological Chemistry (M.G.), and Department of Cardiology and Angiology (J.B.), Hannover Medical School, Germany; F. Hoffmann-La Roche, Pharma Research and Early Development, Basel, Switzerland (H.-J.S., M.B.); Department of Pathology and Department of Cardiac Surgery, Institute for Cardiovascular Research, Vrije Universiteit University Medical Center, Amsterdam, The Netherlands (H.W.N.); and Department of Physiology and Cellular Biophysics and Department of Neuroscience, College of Physicians and Surgeons, Columbia University, New York, NY (J.A.G.)
| | - Johann Bauersachs
- From Division of Molecular and Translational Cardiology, Department of Cardiology and Angiology (M.R.R., M.K.-K., S.K., E.B., I.R., Y.W., K.C.W.), Core Unit Proteomics, Institute of Toxicology (F.P., A.P.), Department of Biophysical Chemistry (J.F.), Leibniz Research Laboratories for Biotechnology and Artificial Organs, Department of Cardiothoracic, Transplantation, and Vascular Surgery (G.K., I.G.), Institute of Legal Medicine (M.K.), Institute of Physiological Chemistry (M.G.), and Department of Cardiology and Angiology (J.B.), Hannover Medical School, Germany; F. Hoffmann-La Roche, Pharma Research and Early Development, Basel, Switzerland (H.-J.S., M.B.); Department of Pathology and Department of Cardiac Surgery, Institute for Cardiovascular Research, Vrije Universiteit University Medical Center, Amsterdam, The Netherlands (H.W.N.); and Department of Physiology and Cellular Biophysics and Department of Neuroscience, College of Physicians and Surgeons, Columbia University, New York, NY (J.A.G.)
| | - Joseph A Gogos
- From Division of Molecular and Translational Cardiology, Department of Cardiology and Angiology (M.R.R., M.K.-K., S.K., E.B., I.R., Y.W., K.C.W.), Core Unit Proteomics, Institute of Toxicology (F.P., A.P.), Department of Biophysical Chemistry (J.F.), Leibniz Research Laboratories for Biotechnology and Artificial Organs, Department of Cardiothoracic, Transplantation, and Vascular Surgery (G.K., I.G.), Institute of Legal Medicine (M.K.), Institute of Physiological Chemistry (M.G.), and Department of Cardiology and Angiology (J.B.), Hannover Medical School, Germany; F. Hoffmann-La Roche, Pharma Research and Early Development, Basel, Switzerland (H.-J.S., M.B.); Department of Pathology and Department of Cardiac Surgery, Institute for Cardiovascular Research, Vrije Universiteit University Medical Center, Amsterdam, The Netherlands (H.W.N.); and Department of Physiology and Cellular Biophysics and Department of Neuroscience, College of Physicians and Surgeons, Columbia University, New York, NY (J.A.G.)
| | - Yong Wang
- From Division of Molecular and Translational Cardiology, Department of Cardiology and Angiology (M.R.R., M.K.-K., S.K., E.B., I.R., Y.W., K.C.W.), Core Unit Proteomics, Institute of Toxicology (F.P., A.P.), Department of Biophysical Chemistry (J.F.), Leibniz Research Laboratories for Biotechnology and Artificial Organs, Department of Cardiothoracic, Transplantation, and Vascular Surgery (G.K., I.G.), Institute of Legal Medicine (M.K.), Institute of Physiological Chemistry (M.G.), and Department of Cardiology and Angiology (J.B.), Hannover Medical School, Germany; F. Hoffmann-La Roche, Pharma Research and Early Development, Basel, Switzerland (H.-J.S., M.B.); Department of Pathology and Department of Cardiac Surgery, Institute for Cardiovascular Research, Vrije Universiteit University Medical Center, Amsterdam, The Netherlands (H.W.N.); and Department of Physiology and Cellular Biophysics and Department of Neuroscience, College of Physicians and Surgeons, Columbia University, New York, NY (J.A.G.)
| | - Kai C Wollert
- From Division of Molecular and Translational Cardiology, Department of Cardiology and Angiology (M.R.R., M.K.-K., S.K., E.B., I.R., Y.W., K.C.W.), Core Unit Proteomics, Institute of Toxicology (F.P., A.P.), Department of Biophysical Chemistry (J.F.), Leibniz Research Laboratories for Biotechnology and Artificial Organs, Department of Cardiothoracic, Transplantation, and Vascular Surgery (G.K., I.G.), Institute of Legal Medicine (M.K.), Institute of Physiological Chemistry (M.G.), and Department of Cardiology and Angiology (J.B.), Hannover Medical School, Germany; F. Hoffmann-La Roche, Pharma Research and Early Development, Basel, Switzerland (H.-J.S., M.B.); Department of Pathology and Department of Cardiac Surgery, Institute for Cardiovascular Research, Vrije Universiteit University Medical Center, Amsterdam, The Netherlands (H.W.N.); and Department of Physiology and Cellular Biophysics and Department of Neuroscience, College of Physicians and Surgeons, Columbia University, New York, NY (J.A.G.).
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Loss-of-function mutation in Mirta22/Emc10 rescues specific schizophrenia-related phenotypes in a mouse model of the 22q11.2 deletion. Proc Natl Acad Sci U S A 2017; 114:E6127-E6136. [PMID: 28696314 DOI: 10.1073/pnas.1615719114] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Identification of protective loss-of-function (LoF) mutations holds great promise for devising novel therapeutic interventions, although it faces challenges due to the scarcity of protective LoF alleles in the human genome. Exploiting the detailed mechanistic characterization of animal models of validated disease mutations offers an alternative. Here, we provide insights into protective-variant biology based on our characterization of a model of the 22q11.2 deletion, a strong genetic risk factor for schizophrenia (SCZ). Postnatal brain up-regulation of Mirta22/Emc10, an inhibitor of neuronal maturation, represents the major transcriptional effect of the 22q11.2-associated microRNA dysregulation. Here, we demonstrate that mice in which the Df(16)A deficiency is combined with a LoF Mirta22 allele show rescue of key SCZ-related deficits, namely prepulse inhibition decrease, working memory impairment, and social memory deficits, as well as synaptic and structural plasticity abnormalities in the prefrontal cortex. Additional analysis of homozygous Mirta22 knockout mice, in which no alteration is observed in the above-mentioned SCZ-related phenotypes, highlights the deleterious effects of Mirta22 up-regulation. Our results support a causal link between dysregulation of a miRNA target and SCZ-related deficits and provide key insights into beneficial LoF mutations and potential new treatments.
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Stepanenko AA, Heng HH. Transient and stable vector transfection: Pitfalls, off-target effects, artifacts. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2017; 773:91-103. [DOI: 10.1016/j.mrrev.2017.05.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 05/09/2017] [Accepted: 05/13/2017] [Indexed: 12/15/2022]
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13
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Lin B, Lee H, Yoon JG, Madan A, Wayner E, Tonning S, Hothi P, Schroeder B, Ulasov I, Foltz G, Hood L, Cobbs C. Global analysis of H3K4me3 and H3K27me3 profiles in glioblastoma stem cells and identification of SLC17A7 as a bivalent tumor suppressor gene. Oncotarget 2016; 6:5369-81. [PMID: 25749033 PMCID: PMC4467155 DOI: 10.18632/oncotarget.3030] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 01/01/2015] [Indexed: 01/21/2023] Open
Abstract
Epigenetic changes, including H3K4me3 and H3K27me3 histone modification, play an important role in carcinogenesis. However, no genome-wide histone modification map has been generated for gliomas. Here, we report a genome-wide map of H3K4me3 and H3K27me3 histone modifications for 8 glioma stem cell (GSC) lines, together with the associated gene activation or repression patterns. In addition, we compared the genome-wide histone modification maps of GSC lines to those of astrocytes to identify unique gene activation or repression profiles in GSCs and astrocytes. We also identified a set of bivalent genes, which are genes that are associated with both H3K4me3 and H3K27me3 marks and are poised for action in embryonic stem cells. These bivalent genes are potential targets for inducing differentiation in glioblastoma (GBM) as a therapeutic approach. Finally, we identified SLC17A7 as a bivalent tumor suppressor gene in GBM, as it is down-regulated at both the protein and RNA levels in GBM tissues compared with normal brain tissues, and it inhibits GBM cell proliferation, migration and invasion.
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Affiliation(s)
- Biaoyang Lin
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China.,Dept. of Urology, University of Washington, Seattle, WA 98195, USA.,System Biology Division, Zhejiang-California International Nanosystem Institute (ZCNI), Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hwahyung Lee
- Swedish Neuroscience Institute, Swedish Medical Center, Seattle, WA 98122, USA
| | - Jae-Geun Yoon
- Swedish Neuroscience Institute, Swedish Medical Center, Seattle, WA 98122, USA
| | - Anup Madan
- Swedish Neuroscience Institute, Swedish Medical Center, Seattle, WA 98122, USA.,LabCorp Clinical Trials (Genomics Laboratory), Seattle, WA 98109, USA
| | - Elizabeth Wayner
- Swedish Neuroscience Institute, Swedish Medical Center, Seattle, WA 98122, USA
| | - Sanja Tonning
- Swedish Neuroscience Institute, Swedish Medical Center, Seattle, WA 98122, USA
| | - Parvinder Hothi
- Swedish Neuroscience Institute, Swedish Medical Center, Seattle, WA 98122, USA
| | - Brett Schroeder
- Swedish Neuroscience Institute, Swedish Medical Center, Seattle, WA 98122, USA
| | - Ilya Ulasov
- Swedish Neuroscience Institute, Swedish Medical Center, Seattle, WA 98122, USA
| | - Gregory Foltz
- Swedish Neuroscience Institute, Swedish Medical Center, Seattle, WA 98122, USA
| | - Leroy Hood
- The Institute for Systems Biology, Seattle, WA 98109, USA
| | - Charles Cobbs
- Swedish Neuroscience Institute, Swedish Medical Center, Seattle, WA 98122, USA
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14
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Junes-Gill KS, Lawrence CE, Wheeler CJ, Cordner R, Gill TG, Mar V, Shiri L, Basile LA. Human Hematopoietic Signal peptide-containing Secreted 1 (hHSS1) modulates genes and pathways in glioma: implications for the regulation of tumorigenicity and angiogenesis. BMC Cancer 2014; 14:920. [PMID: 25481245 PMCID: PMC4295481 DOI: 10.1186/1471-2407-14-920] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 11/27/2014] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Human Hematopoietic Signal peptide-containing Secreted 1 (hHSS1) is a truly novel protein, defining a new class of secreted factors. We have previously reported that ectopic overexpression of hHSS1 has a negative modulatory effect on cell proliferation and tumorigenesis in glioblastoma model systems. Here we have used microarray analysis, screened glioblastoma samples in The Cancer Genome Atlas (TCGA), and studied the effects of hHSS1 on glioma-derived cells and endothelial cells to elucidate the molecular mechanisms underlying the anti-tumorigenic effects of hHSS1. METHODS Gene expression profiling of human glioma U87 and A172 cells overexpressing hHSS1 was performed. Ingenuity® iReport™ and Ingenuity Pathway Analysis (IPA) were used to analyze the gene expression in the glioma cells. DNA content and cell cycle analysis were performed by FACS, while cell migration, cell invasion, and effects of hHSS1 on HUVEC tube formation were determined by transwell and matrigel assays. Correlation was made between hHSS1 expression and specific genes in glioblastoma samples in the TCGA database. RESULTS We have clarified the signaling and metabolic pathways (i.e. role of BRCA1 in DNA damage response), networks (i.e. cell cycle) and biological processes (i.e. cell division process of chromosomes) that result from hHSS1effects upon glioblastoma growth. U87-overexpressing hHSS1 significantly decreased the number of cells in the G0/G1 cell cycle phase, and significantly increased cells in the S and G2/M phases (P < 0.05). U87-overexpressing hHSS1 significantly lost their ability to migrate (P < 0.001) and to invade (P < 0.01) through matrigel matrix. hHSS1-overexpression significantly decreased migration of A172 cells (P < 0.001), inhibited A172 tumor-induced migration and invasion of HUVECs (P < 0.001), and significantly inhibited U87 tumor-induced invasion of HUVECs (P < 0.001). Purified hHSS1 protein inhibited HUVEC tube formation. TCGA database revealed significant correlation between hHSS1 and BRCA2 (r = -0.224, P < 0.0005), ADAMTS1 (r = -0.132, P <0.01) and endostatin (r = 0.141, P < 0.005). CONCLUSIONS hHSS1-overexpression modulates signaling pathways involved in tumorigenesis. hHSS1 inhibits glioma-induced cell cycle progression, cell migration, invasion and angiogenesis. Our data suggest that hHSS1 is a potential therapeutic for malignant glioblastoma possessing significant antitumor and anti-angiogenic activity.
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Affiliation(s)
| | - Chris E Lawrence
- />Neumedicines Inc., 133 N Altadena Dr. #310, Pasadena, CA 91107 USA
| | - Christopher J Wheeler
- />Department of Neurosurgery, Maxine Dunitz Neurosurgical Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd., Davis Rm. 2097, Los Angeles, CA 90048 USA
| | - Ryan Cordner
- />Department of Neurosurgery, Maxine Dunitz Neurosurgical Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd., Davis Rm. 2097, Los Angeles, CA 90048 USA
| | - Tristan G Gill
- />Ingenuity Systems, 1700 Seaport Blvd, 3rd Floor, Redwood City, CA 94063 USA
| | - Vernon Mar
- />Neumedicines Inc., 133 N Altadena Dr. #310, Pasadena, CA 91107 USA
| | - Liron Shiri
- />Neumedicines Inc., 133 N Altadena Dr. #310, Pasadena, CA 91107 USA
| | - Lena A Basile
- />Neumedicines Inc., 133 N Altadena Dr. #310, Pasadena, CA 91107 USA
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15
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Xu B, Hsu PK, Stark KL, Karayiorgou M, Gogos JA. Derepression of a neuronal inhibitor due to miRNA dysregulation in a schizophrenia-related microdeletion. Cell 2013; 152:262-75. [PMID: 23332760 PMCID: PMC3556818 DOI: 10.1016/j.cell.2012.11.052] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Revised: 08/23/2012] [Accepted: 11/26/2012] [Indexed: 02/04/2023]
Abstract
22q11.2 microdeletions result in specific cognitive deficits and schizophrenia. Analysis of Df(16)A(+/-) mice, which model this microdeletion, revealed abnormalities in the formation of neuronal dendrites and spines, as well as altered brain microRNAs. Here, we show a drastic reduction of miR-185, which resides within the 22q11.2 locus, to levels more than expected by a hemizygous deletion, and we demonstrate that this reduction alters dendritic and spine development. miR-185 represses, through an evolutionarily conserved target site, a previously unknown inhibitor of these processes that resides in the Golgi apparatus and shows higher prenatal brain expression. Sustained derepression of this inhibitor after birth represents the most robust transcriptional disturbance in the brains of Df(16)A(+/-) mice and results in structural alterations in the hippocampus. Reduction of miR-185 also has milder age- and region-specific effects on the expression of some Golgi-related genes. Our findings illuminate the contribution of microRNAs in psychiatric disorders and cognitive dysfunction.
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Affiliation(s)
- Bin Xu
- Department of Psychiatry, College of Physicians and Surgeons, Columbia University, 1051 Riverside Drive, New York, NY 10032, USA
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16
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Comparative analysis of methods for identifying recurrent copy number alterations in cancer. PLoS One 2012; 7:e52516. [PMID: 23285074 PMCID: PMC3527554 DOI: 10.1371/journal.pone.0052516] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 11/14/2012] [Indexed: 11/19/2022] Open
Abstract
Recurrent copy number alterations (CNAs) play an important role in cancer genesis. While a number of computational methods have been proposed for identifying such CNAs, their relative merits remain largely unknown in practice since very few efforts have been focused on comparative analysis of the methods. To facilitate studies of recurrent CNA identification in cancer genome, it is imperative to conduct a comprehensive comparison of performance and limitations among existing methods. In this paper, six representative methods proposed in the latest six years are compared. These include one-stage and two-stage approaches, working with raw intensity ratio data and discretized data respectively. They are based on various techniques such as kernel regression, correlation matrix diagonal segmentation, semi-parametric permutation and cyclic permutation schemes. We explore multiple criteria including type I error rate, detection power, Receiver Operating Characteristics (ROC) curve and the area under curve (AUC), and computational complexity, to evaluate performance of the methods under multiple simulation scenarios. We also characterize their abilities on applications to two real datasets obtained from cancers with lung adenocarcinoma and glioblastoma. This comparison study reveals general characteristics of the existing methods for identifying recurrent CNAs, and further provides new insights into their strengths and weaknesses. It is believed helpful to accelerate the development of novel and improved methods.
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