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Yeh CW, Hsu KL, Lin ST, Huang WC, Yeh KH, Liu CFJ, Wang LC, Li TT, Chen SC, Yu CH, Leu JY, Yeang CH, Yen HCS. Altered assembly paths mitigate interference among paralogous complexes. Nat Commun 2024; 15:7169. [PMID: 39169013 PMCID: PMC11339298 DOI: 10.1038/s41467-024-51286-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 08/05/2024] [Indexed: 08/23/2024] Open
Abstract
Protein complexes are fundamental to all cellular processes, so understanding their evolutionary history and assembly processes is important. Gene duplication followed by divergence is considered a primary mechanism for diversifying protein complexes. Nonetheless, to what extent assembly of present-day paralogous complexes has been constrained by their long evolutionary pathways and how cross-complex interference is avoided remain unanswered questions. Subunits of protein complexes are often stabilized upon complex formation, whereas unincorporated subunits are degraded. How such cooperative stability influences protein complex assembly also remains unclear. Here, we demonstrate that subcomplexes determined by cooperative stabilization interactions serve as building blocks for protein complex assembly. We further develop a protein stability-guided method to compare the assembly processes of paralogous complexes in cellulo. Our findings support that oligomeric state and the structural organization of paralogous complexes can be maintained even if their assembly processes are rearranged. Our results indicate that divergent assembly processes by paralogous complexes not only enable the complexes to evolve new functions, but also reinforce their segregation by establishing incompatibility against deleterious hybrid assemblies.
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Affiliation(s)
- Chi-Wei Yeh
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Kuan-Lun Hsu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Shu-Ting Lin
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Wei-Chieh Huang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Kun-Hai Yeh
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | | | - Li-Chin Wang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
| | - Ting-Ting Li
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Shu-Chuan Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Chen-Hsin Yu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Jun-Yi Leu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
| | - Chen-Hsiang Yeang
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Hsueh-Chi S Yen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan.
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2
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Shi J, Shiraishi K, Choi J, Matsuo K, Chen TY, Dai J, Hung RJ, Chen K, Shu XO, Kim YT, Landi MT, Lin D, Zheng W, Yin Z, Zhou B, Song B, Wang J, Seow WJ, Song L, Chang IS, Hu W, Chien LH, Cai Q, Hong YC, Kim HN, Wu YL, Wong MP, Richardson BD, Funderburk KM, Li S, Zhang T, Breeze C, Wang Z, Blechter B, Bassig BA, Kim JH, Albanes D, Wong JYY, Shin MH, Chung LP, Yang Y, An SJ, Zheng H, Yatabe Y, Zhang XC, Kim YC, Caporaso NE, Chang J, Ho JCM, Kubo M, Daigo Y, Song M, Momozawa Y, Kamatani Y, Kobayashi M, Okubo K, Honda T, Hosgood DH, Kunitoh H, Patel H, Watanabe SI, Miyagi Y, Nakayama H, Matsumoto S, Horinouchi H, Tsuboi M, Hamamoto R, Goto K, Ohe Y, Takahashi A, Goto A, Minamiya Y, Hara M, Nishida Y, Takeuchi K, Wakai K, Matsuda K, Murakami Y, Shimizu K, Suzuki H, Saito M, Ohtaki Y, Tanaka K, Wu T, Wei F, Dai H, Machiela MJ, Su J, Kim YH, Oh IJ, Lee VHF, Chang GC, Tsai YH, Chen KY, Huang MS, Su WC, Chen YM, Seow A, Park JY, Kweon SS, Chen KC, Gao YT, Qian B, Wu C, Lu D, Liu J, Schwartz AG, Houlston R, Spitz MR, Gorlov IP, Wu X, Yang P, Lam S, Tardon A, Chen C, Bojesen SE, Johansson M, Risch A, Bickeböller H, Ji BT, Wichmann HE, Christiani DC, Rennert G, Arnold S, Brennan P, McKay J, Field JK, Shete SS, Le Marchand L, Liu G, Andrew A, Kiemeney LA, Zienolddiny-Narui S, Grankvist K, Johansson M, Cox A, Taylor F, Yuan JM, Lazarus P, Schabath MB, Aldrich MC, Jeon HS, Jiang SS, Sung JS, Chen CH, Hsiao CF, Jung YJ, Guo H, Hu Z, Burdett L, Yeager M, Hutchinson A, Hicks B, Liu J, Zhu B, Berndt SI, Wu W, Wang J, Li Y, Choi JE, Park KH, Sung SW, Liu L, Kang CH, Wang WC, Xu J, Guan P, Tan W, Yu CJ, Yang G, Sihoe ADL, Chen Y, Choi YY, Kim JS, Yoon HI, Park IK, Xu P, He Q, Wang CL, Hung HH, Vermeulen RCH, Cheng I, Wu J, Lim WY, Tsai FY, Chan JKC, Li J, Chen H, Lin HC, Jin L, Liu J, Sawada N, Yamaji T, Wyatt K, Li SA, Ma H, Zhu M, Wang Z, Cheng S, Li X, Ren Y, Chao A, Iwasaki M, Zhu J, Jiang G, Fei K, Wu G, Chen CY, Chen CJ, Yang PC, Yu J, Stevens VL, Fraumeni JF, Chatterjee N, Gorlova OY, Hsiung CA, Amos CI, Shen H, Chanock SJ, Rothman N, Kohno T, Lan Q. Genome-wide association study of lung adenocarcinoma in East Asia and comparison with a European population. Nat Commun 2023; 14:3043. [PMID: 37236969 PMCID: PMC10220065 DOI: 10.1038/s41467-023-38196-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 04/19/2023] [Indexed: 05/28/2023] Open
Abstract
Lung adenocarcinoma is the most common type of lung cancer. Known risk variants explain only a small fraction of lung adenocarcinoma heritability. Here, we conducted a two-stage genome-wide association study of lung adenocarcinoma of East Asian ancestry (21,658 cases and 150,676 controls; 54.5% never-smokers) and identified 12 novel susceptibility variants, bringing the total number to 28 at 25 independent loci. Transcriptome-wide association analyses together with colocalization studies using a Taiwanese lung expression quantitative trait loci dataset (n = 115) identified novel candidate genes, including FADS1 at 11q12 and ELF5 at 11p13. In a multi-ancestry meta-analysis of East Asian and European studies, four loci were identified at 2p11, 4q32, 16q23, and 18q12. At the same time, most of our findings in East Asian populations showed no evidence of association in European populations. In our studies drawn from East Asian populations, a polygenic risk score based on the 25 loci had a stronger association in never-smokers vs. individuals with a history of smoking (Pinteraction = 0.0058). These findings provide new insights into the etiology of lung adenocarcinoma in individuals from East Asian populations, which could be important in developing translational applications.
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Affiliation(s)
- Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA.
| | - Kouya Shiraishi
- Division of Genome Biology, National Cancer Research Institute, Tokyo, Japan
| | - Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Keitaro Matsuo
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Tzu-Yu Chen
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Juncheng Dai
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Rayjean J Hung
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center and Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Young Tae Kim
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Dongxin Lin
- Department of Etiology & Carcinogenesis and State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center and Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Zhihua Yin
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | - Baosen Zhou
- Department of Clinical Epidemiology and Center of Evidence Based Medicine, The First Hospital of China Medical University, Shenyang, China
| | - Bao Song
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Jinan, China
| | - Jiucun Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Wei Jie Seow
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - I-Shou Chang
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | - Wei Hu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Li-Hsin Chien
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center and Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Yun-Chul Hong
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hee Nam Kim
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Yi-Long Wu
- Guangdong Lung Cancer Institute, Medical Research Center and Cancer Center of Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Maria Pik Wong
- Department of Pathology, Queen Mary Hospital, Hong Kong, Hong Kong
| | - Brian Douglas Richardson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Karen M Funderburk
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Shilan Li
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Department of Biostatistics, Bioinformatics & Biomathematics, Georgetown University Medical Center, Washington, DC, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Charles Breeze
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Zhaoming Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Batel Blechter
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Bryan A Bassig
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jin Hee Kim
- Department of Environmental Health, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jason Y Y Wong
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Min-Ho Shin
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Lap Ping Chung
- Department of Pathology, Queen Mary Hospital, Hong Kong, Hong Kong
| | - Yang Yang
- Shanghai Pulmonary Hospital, Shanghai, China
| | - She-Juan An
- Guangdong Lung Cancer Institute, Medical Research Center and Cancer Center of Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Hong Zheng
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Yasushi Yatabe
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo, Japan
| | - Xu-Chao Zhang
- Guangdong Lung Cancer Institute, Medical Research Center and Cancer Center of Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Young-Chul Kim
- Lung and Esophageal Cancer Clinic, Chonnam National University Hwasun Hospital, Hwasuneup, Republic of Korea
- Department of Internal Medicine, Chonnam National Univerisity Medical School, Gwangju, Republic of Korea
| | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jiang Chang
- Department of Etiology & Carcinogenesis, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - James Chung Man Ho
- Department of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, Hong Kong
| | - Michiaki Kubo
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yataro Daigo
- Center for Antibody and Vaccine Therapy, Research Hospital, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Medical Oncology and Cancer Center, and Center for Advanced Medicine against Cancer, Shiga University of Medical Science, Shiga, Japan
| | - Minsun Song
- Department of Statistics & Research Institute of Natural Sciences, Sookmyung Women's University, Seoul, Republic of Korea
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Masashi Kobayashi
- Department of Thoracic Surgery, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kenichi Okubo
- Department of Thoracic Surgery, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takayuki Honda
- Department of Respiratory Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Dean H Hosgood
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, New York, NY, USA
| | - Hideo Kunitoh
- Department of Medical Oncology, Japanese Red Cross Medical Center, Tokyo, Japan
| | - Harsh Patel
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Shun-Ichi Watanabe
- Department of Thoracic Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Yohei Miyagi
- Molecular Pathology and Genetics Division, Kanagawa Cancer Center Research Institute, Yokohama, Japan
| | - Haruhiko Nakayama
- Department of Thoracic Surgery, Kanagawa Cancer Center, Yokohama, Japan
| | - Shingo Matsumoto
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Hidehito Horinouchi
- Department of Thoracic Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Masahiro Tsuboi
- Department of Thoracic Surgery, National Cancer Center Hospital East, Kashiwa, Japan
| | - Ryuji Hamamoto
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Koichi Goto
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Yuichiro Ohe
- Department of Thoracic Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Atsushi Takahashi
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Akiteru Goto
- Department of Cellular and Organ Pathology, Graduate School of Medicine, Akita University, Akita, Japan
| | - Yoshihiro Minamiya
- Department of Thoracic Surgery, Graduate School of Medicine, Akita University, Akita, Japan
| | - Megumi Hara
- Department of Preventive Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Yuichiro Nishida
- Department of Preventive Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Kenji Takeuchi
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kenji Wakai
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Koichi Matsuda
- Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Science, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Yoshinori Murakami
- Division of Molecular Pathology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kimihiro Shimizu
- Department of Surgery, Division of General Thoracic Surgery, Shinshu University School of Medicine Asahi, Nagano, Japan
| | - Hiroyuki Suzuki
- Department of Chest Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Motonobu Saito
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Yoichi Ohtaki
- Department of Integrative center of General Surgery, Gunma University Hospital, Gunma, Japan
| | - Kazumi Tanaka
- Department of Integrative center of General Surgery, Gunma University Hospital, Gunma, Japan
| | - Tangchun Wu
- Institute of Occupational Medicine and Ministry of Education Key Lab for Environment and Health, School of Public Health, Huazhong University of Science and Technology, Wuhan, China
| | - Fusheng Wei
- China National Environmental Monitoring Center, Beijing, China
| | - Hongji Dai
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jian Su
- Guangdong Lung Cancer Institute, Medical Research Center and Cancer Center of Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yeul Hong Kim
- Department of Internal Medicine, Division of Oncology/Hematology, College of Medicine, Korea University Anam Hospital, Seoul, Republic of Korea
| | - In-Jae Oh
- Lung and Esophageal Cancer Clinic, Chonnam National University Hwasun Hospital, Hwasuneup, Republic of Korea
- Department of Internal Medicine, Chonnam National Univerisity Medical School, Gwangju, Republic of Korea
| | - Victor Ho Fun Lee
- Department of Clinical Oncology, The University of Hong Kong, Queen Mary Hospital, Hong Kong, Hong Kong
| | - Gee-Chen Chang
- School of Medicine and Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Department of Internal Medicine, Division of Pulmonary Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan
- Institute of Biomedical Sciences, National Chung Hsing University, Taichung, Taiwan
- Department of Internal Medicine, Division of Chest Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Ying-Huang Tsai
- Department of Respiratory Therapy, Chang Gung University, Taoyuan, Taiwan
- Department of Pulmonary and Critical Care, Xiamen Chang Gung Hospital, Xiamen, China
| | - Kuan-Yu Chen
- Department of Internal Medicine, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
| | - Ming-Shyan Huang
- Department of Internal Medicine, E-Da Cancer Hospital, I-Shou University and Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wu-Chou Su
- Department of Oncology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yuh-Min Chen
- Department of Chest Medicine, Taipei Veterans General Hospital, and school of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Adeline Seow
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Jae Yong Park
- Lung Cancer Center, Kyungpook National University Medical Center, Daegu, Republic of Korea
| | - Sun-Seog Kweon
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, Republic of Korea
- Jeonnam Regional Cancer Center, Chonnam National University, Hwasun, Republic of Korea
| | - Kun-Chieh Chen
- Department of Internal Medicine, Division of Pulmonary Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai, China
| | - Biyun Qian
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Chen Wu
- Department of Etiology & Carcinogenesis and State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Daru Lu
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Jianjun Liu
- Genome Institute of Singapore, Agency of Science, Technology and Research, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | | | - Richard Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Margaret R Spitz
- Department of Medicine, Section of Epidemiology and Population Science, Institute for Clinical and Translational Research, Houston, TX, USA
| | - Ivan P Gorlov
- Department of Medicine, Section of Epidemiology and Population Science, Institute for Clinical and Translational Research, Houston, TX, USA
| | - Xifeng Wu
- School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ping Yang
- Department of Health Sciences Research, Mayo Clinic, Scottsdale, AZ, USA
| | - Stephen Lam
- British Columbia Cancer Agency, Vancouver, BC, Canada
| | | | - Chu Chen
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Stig E Bojesen
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Mattias Johansson
- International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Angela Risch
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- University of Salzburg and Cancer Cluster Salzburg, Salzburg, Austria
| | | | - Bu-Tian Ji
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - H-Erich Wichmann
- Institute of Medical Informatics, Biometry and Epidemiology, Ludwig Maximilians University, Munich, Germany
- Helmholtz Center Munich, Institute of Epidemiology, Munich, Germany
- Institute of Medical Statistics and Epidemiology, Technical University Munich, Munich, Germany
| | | | | | | | - Paul Brennan
- International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - James McKay
- International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | | | - Sanjay S Shete
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Geoffrey Liu
- Princess Margaret Cancer Center, Toronto, ON, Canada
| | | | | | | | - Kjell Grankvist
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | | | | | | | - Jian-Min Yuan
- UPMC Hillman Cancer Center and Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Philip Lazarus
- Washington State University College of Pharmacy, Spokane, WA, USA
| | - Matthew B Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Melinda C Aldrich
- Department of Thoracic Surgery, Division of Epidemiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Hyo-Sung Jeon
- Cancer Research Center, Kyungpook National University Medical Center, Daegu, Republic of Korea
| | - Shih Sheng Jiang
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | - Jae Sook Sung
- Department of Internal Medicine, Division of Oncology/Hematology, College of Medicine, Korea University Anam Hospital, Seoul, Republic of Korea
| | - Chung-Hsing Chen
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | - Chin-Fu Hsiao
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Yoo Jin Jung
- Department of Thoracic and Cardiovascular Surgery, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Huan Guo
- Department of Occupational and Environmental Health and Ministry of Education Key Lab for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhibin Hu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Laurie Burdett
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Rockville, MD, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Rockville, MD, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Rockville, MD, USA
| | - Belynda Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Rockville, MD, USA
| | - Jia Liu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Rockville, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Rockville, MD, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Wei Wu
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | - Junwen Wang
- Department of Biochemistry, Li Ka Shing (LKS) Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Centre for Genomic Sciences, Li Ka Shing (LKS) Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Yuqing Li
- Department of Human Genetics, Genome Institute of Singapore, Singapore, Singapore
| | - Jin Eun Choi
- Cancer Research Center, Kyungpook National University Medical Center, Daegu, Republic of Korea
| | - Kyong Hwa Park
- Department of Internal Medicine, Division of Oncology/Hematology, College of Medicine, Korea University Anam Hospital, Seoul, Republic of Korea
| | - Sook Whan Sung
- Department of Thoracic and Cardiovascular Surgery, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Li Liu
- Department of Oncology, Cancer Center, Union Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Chang Hyun Kang
- Department of Thoracic and Cardiovascular Surgery, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Wen-Chang Wang
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Jun Xu
- School of Public Health, Li Ka Shing (LKS) Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Peng Guan
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
- Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang, China
| | - Wen Tan
- Department of Etiology & Carcinogenesis and State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chong-Jen Yu
- Department of Internal Medicine, National Taiwan University Hospital Hsin-Chu Branch, Hsinchu, Taiwan
| | - Gong Yang
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center and Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | | | - Ying Chen
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Yi Young Choi
- Cancer Research Center, Kyungpook National University Medical Center, Daegu, Republic of Korea
| | - Jun Suk Kim
- Department of Internal Medicine, Division of Medical Oncology, College of Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Ho-Il Yoon
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - In Kyu Park
- Department of Thoracic and Cardiovascular Surgery, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ping Xu
- Department of Oncology, Wuhan Iron and Steel (Group) Corporation Staff-Worker Hospital, Wuhan, China
| | - Qincheng He
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | - Chih-Liang Wang
- Department of Pulmonary and Critical Care, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Hsiao-Han Hung
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | - Roel C H Vermeulen
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
| | - Iona Cheng
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Junjie Wu
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Wei-Yen Lim
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Fang-Yu Tsai
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | - John K C Chan
- Department of Pathology, Queen Elizabeth Hospital, Hong Kong, China
| | - Jihua Li
- Qujing Center for Diseases Control and Prevention, Qujing, China
| | - Hongyan Chen
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Hsien-Chih Lin
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Li Jin
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Jie Liu
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Jinan, China
| | - Norie Sawada
- Division of Cohort Research, National Cancer Center Institute for Cancer Control, National Cancer Center, Tokyo, Japan
| | - Taiki Yamaji
- Division of Epidemiology, National Cancer Center Institute for Cancer Control, National Cancer Center, Tokyo, Japan
| | - Kathleen Wyatt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Rockville, MD, USA
| | - Shengchao A Li
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Rockville, MD, USA
| | - Hongxia Ma
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Meng Zhu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Zhehai Wang
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Jinan, China
| | - Sensen Cheng
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Jinan, China
| | - Xuelian Li
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
- Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang, China
| | - Yangwu Ren
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
- Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang, China
| | - Ann Chao
- Center for Global Health, National Cancer Institute, Bethesda, MD, USA
| | - Motoki Iwasaki
- Division of Cohort Research, National Cancer Center Institute for Cancer Control, National Cancer Center, Tokyo, Japan
- Division of Epidemiology, National Cancer Center Institute for Cancer Control, National Cancer Center, Tokyo, Japan
| | - Junjie Zhu
- Shanghai Pulmonary Hospital, Shanghai, China
| | | | - Ke Fei
- Shanghai Pulmonary Hospital, Shanghai, China
| | - Guoping Wu
- China National Environmental Monitoring Center, Beijing, China
| | - Chih-Yi Chen
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Division of Thoracic Surgery, Department of Surgery, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Chien-Jen Chen
- Genomic Research Center, Academia Sinica, Taipei, Taiwan
| | - Pan-Chyr Yang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Jinming Yu
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Jinan, China
| | | | - Joseph F Fraumeni
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Nilanjan Chatterjee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Olga Y Gorlova
- Department of Medicine, Section of Epidemiology and Population Science, Institute for Clinical and Translational Research, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Chao Agnes Hsiung
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Christopher I Amos
- Department of Medicine, Section of Epidemiology and Population Science, Institute for Clinical and Translational Research, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Hongbing Shen
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Research Institute, Tokyo, Japan
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA.
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3
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Li Y, Wang W, Lim HY. Drosophila transmembrane protein 214 (dTMEM214) regulates midgut glucose uptake and systemic glucose homeostasis. Dev Biol 2023; 495:92-103. [PMID: 36657508 PMCID: PMC9905329 DOI: 10.1016/j.ydbio.2023.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023]
Abstract
The availability of glucose transporter in the small intestine critically determines the capacity for glucose uptake and consequently systemic glucose homeostasis. Hence a better understanding of the physiological regulation of intestinal glucose transporter is pertinent. However, the molecular mechanisms that regulate sodium-glucose linked transporter 1 (SGLT1), the primary glucose transporter in the small intestine, remain incompletely understood. Recently, the Drosophila SLC5A5 (dSLC5A5) has been found to exhibit properties consistent with a dietary glucose transporter in the Drosophila midgut, the equivalence of the mammalian small intestine. Hence, the fly midgut could serve as a suitable model system for the study of the in vivo molecular underpinnings of SGLT1 function. Here, we report the identification, through a genetic screen, of Drosophila transmembrane protein 214 (dTMEM214) that acts in the midgut enterocytes to regulate systemic glucose homeostasis and glucose uptake. We show that dTMEM214 resides in the apical membrane and cytoplasm of the midgut enterocytes, and that the proper subcellular distribution of dTMEM214 in the enterocytes is regulated by the Rab4 GTPase. As a corollary, Rab4 loss-of-function phenocopies dTMEM214 loss-of-function in the midgut as shown by a decrease in enterocyte glucose uptake and an alteration in systemic glucose homeostasis. We further show that dTMEM214 regulates the apical membrane localization of dSLC5A5 in the enterocytes, thereby revealing dTMEM214 as a molecular regulator of glucose transporter in the midgut.
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Affiliation(s)
- Yue Li
- Department of Physiology, University of Oklahoma Health Science Center, Oklahoma City, OK, USA
| | - Weidong Wang
- Department of Medicine, Section of Endocrinology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Hui-Ying Lim
- Department of Physiology, University of Oklahoma Health Science Center, Oklahoma City, OK, USA.
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4
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Töpf A, Pyle A, Griffin H, Matalonga L, Schon K, Sickmann A, Schara-Schmidt U, Hentschel A, Chinnery PF, Kölbel H, Roos A, Horvath R. Exome reanalysis and proteomic profiling identified TRIP4 as a novel cause of cerebellar hypoplasia and spinal muscular atrophy (PCH1). Eur J Hum Genet 2021; 29:1348-1353. [PMID: 34075209 PMCID: PMC8440675 DOI: 10.1038/s41431-021-00851-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 02/12/2021] [Accepted: 02/26/2021] [Indexed: 01/26/2023] Open
Abstract
TRIP4 is one of the subunits of the transcriptional coregulator ASC-1, a ribonucleoprotein complex that participates in transcriptional coactivation and RNA processing events. Recessive variants in the TRIP4 gene have been associated with spinal muscular atrophy with bone fractures as well as a severe form of congenital muscular dystrophy. Here we present the diagnostic journey of a patient with cerebellar hypoplasia and spinal muscular atrophy (PCH1) and congenital bone fractures. Initial exome sequencing analysis revealed no candidate variants. Reanalysis of the exome data by inclusion in the Solve-RD project resulted in the identification of a homozygous stop-gain variant in the TRIP4 gene, previously reported as disease-causing. This highlights the importance of analysis reiteration and improved and updated bioinformatic pipelines. Proteomic profile of the patient's fibroblasts showed altered RNA-processing and impaired exosome activity supporting the pathogenicity of the detected variant. In addition, we identified a novel genetic form of PCH1, further strengthening the link of this characteristic phenotype with altered RNA metabolism.
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Affiliation(s)
- Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Angela Pyle
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Helen Griffin
- Primary Immunodeficiency Group, Newcastle University Translational and Clinical Research Institute, Newcastle upon Tyne, UK
| | - Leslie Matalonga
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Katherine Schon
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
- MRC Mitochondrial Biology Unit, Cambridge Biomedical Campus, Cambridge, UK
| | - Albert Sickmann
- Department of Bioanalytics, Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany
- Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, Scotland, UK
- Medizinische Proteom-Center (MPC), Medizinische Fakultät, Ruhr-Universität Bochum, Bochum, Germany
| | - Ulrike Schara-Schmidt
- Department of Pediatric Neurology, Developmental Neurology and Social Pediatrics, Children's Hospital University of Essen, Essen, Germany
| | - Andreas Hentschel
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
- MRC Mitochondrial Biology Unit, Cambridge Biomedical Campus, Cambridge, UK
| | - Heike Kölbel
- Department of Pediatric Neurology, Developmental Neurology and Social Pediatrics, Children's Hospital University of Essen, Essen, Germany
| | - Andreas Roos
- Department of Pediatric Neurology, Developmental Neurology and Social Pediatrics, Children's Hospital University of Essen, Essen, Germany.
| | - Rita Horvath
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK.
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5
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Privitera F, Calonaci A, Doddato G, Papa FT, Baldassarri M, Pinto AM, Mari F, Longo I, Caini M, Galimberti D, Hadjistilianou T, De Francesco S, Renieri A, Ariani F. 13q Deletion Syndrome Involving RB1: Characterization of a New Minimal Critical Region for Psychomotor Delay. Genes (Basel) 2021; 12:1318. [PMID: 34573300 PMCID: PMC8471443 DOI: 10.3390/genes12091318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/24/2021] [Accepted: 08/24/2021] [Indexed: 11/17/2022] Open
Abstract
Retinoblastoma (RB) is an ocular tumor of the pediatric age caused by biallelic inactivation of the RB1 gene (13q14). About 10% of cases are due to gross-sized molecular deletions. The deletions can involve the surrounding genes delineating a contiguous gene syndrome characterized by RB, developmental anomalies, and peculiar facial dysmorphisms. Overlapping deletions previously found by traditional and/or molecular cytogenetic analysis allowed to define some critical regions for intellectual disability (ID) and multiple congenital anomalies, with key candidate genes. In the present study, using array-CGH, we characterized seven new patients with interstitial 13q deletion involving RB1. Among these cases, three patients with medium or large 13q deletions did not present psychomotor delay. This allowed defining a minimal critical region for ID that excludes the previously suggested candidate genes (HTR2A, NUFIP1, PCDH8, and PCDH17). The region contains 36 genes including NBEA, which emerged as the candidate gene associated with developmental delay. In addition, MAB21L1, DCLK1, EXOSC8, and SPART haploinsufficiency might contribute to the observed impaired neurodevelopmental phenotype. In conclusion, this study adds important novelties to the 13q deletion syndrome, although further studies are needed to better characterize the contribution of different genes and to understand how the haploinsufficiency of this region can determine ID.
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Affiliation(s)
- Flavia Privitera
- Medical Genetics, University of Siena, 53100 Siena, Italy; (F.P.); (G.D.); (F.T.P.); (M.B.); (F.M.); (A.R.)
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Arianna Calonaci
- Unit of Pediatrics, Department of Maternal, Newborn and Child Health, Azienda Ospedaliera Universitaria Senese, Policlinico ‘Santa Maria alle Scotte’, 53100 Siena, Italy; (A.C.); (M.C.); (D.G.)
| | - Gabriella Doddato
- Medical Genetics, University of Siena, 53100 Siena, Italy; (F.P.); (G.D.); (F.T.P.); (M.B.); (F.M.); (A.R.)
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Filomena Tiziana Papa
- Medical Genetics, University of Siena, 53100 Siena, Italy; (F.P.); (G.D.); (F.T.P.); (M.B.); (F.M.); (A.R.)
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Margherita Baldassarri
- Medical Genetics, University of Siena, 53100 Siena, Italy; (F.P.); (G.D.); (F.T.P.); (M.B.); (F.M.); (A.R.)
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Anna Maria Pinto
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy; (A.M.P.); (I.L.)
| | - Francesca Mari
- Medical Genetics, University of Siena, 53100 Siena, Italy; (F.P.); (G.D.); (F.T.P.); (M.B.); (F.M.); (A.R.)
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy; (A.M.P.); (I.L.)
| | - Ilaria Longo
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy; (A.M.P.); (I.L.)
| | - Mauro Caini
- Unit of Pediatrics, Department of Maternal, Newborn and Child Health, Azienda Ospedaliera Universitaria Senese, Policlinico ‘Santa Maria alle Scotte’, 53100 Siena, Italy; (A.C.); (M.C.); (D.G.)
| | - Daniela Galimberti
- Unit of Pediatrics, Department of Maternal, Newborn and Child Health, Azienda Ospedaliera Universitaria Senese, Policlinico ‘Santa Maria alle Scotte’, 53100 Siena, Italy; (A.C.); (M.C.); (D.G.)
| | - Theodora Hadjistilianou
- Unit of Ophthalmology and Retinoblastoma Referral Center, Department of Surgery, University of Siena, Policlinico ‘Santa Maria alle Scotte’, 53100 Siena, Italy; (T.H.); (S.D.F.)
| | - Sonia De Francesco
- Unit of Ophthalmology and Retinoblastoma Referral Center, Department of Surgery, University of Siena, Policlinico ‘Santa Maria alle Scotte’, 53100 Siena, Italy; (T.H.); (S.D.F.)
| | - Alessandra Renieri
- Medical Genetics, University of Siena, 53100 Siena, Italy; (F.P.); (G.D.); (F.T.P.); (M.B.); (F.M.); (A.R.)
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy; (A.M.P.); (I.L.)
| | - Francesca Ariani
- Medical Genetics, University of Siena, 53100 Siena, Italy; (F.P.); (G.D.); (F.T.P.); (M.B.); (F.M.); (A.R.)
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy; (A.M.P.); (I.L.)
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6
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Zhang W, Zhu J, He X, Liu X, Li J, Li W, Yang P, Wang J, Hu K, Zhang X, Li X, Jing H. Exosome complex genes mediate RNA degradation and predict survival in mantle cell lymphoma. Oncol Lett 2019; 18:5119-5128. [PMID: 31612023 PMCID: PMC6781731 DOI: 10.3892/ol.2019.10850] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 07/26/2019] [Indexed: 11/06/2022] Open
Abstract
Exosome complex (EXOSC) genes, which encode a multi-protein intracellular complex, mediate the degradation of various types of RNA molecules. EXOSCs, also known as polymyositis/scleroderma complexes, exist in eukaryotic cells and archaea, and primarily mediate 3′ to 5′mRNA degradation. However, how EXOSC genes are implicated in processes of B-cell immune-associated pathways and B-cell tumorigenesis remains unclear. The present bioinformatics study indicated that 6 of 10 EXOSC genes, particularly the EXO.index, were able to predict the survival of patients with mantle cell lymphoma (MCL), by analyzing gene expression profiles of 123 patients with MCL from the Gene Expression Omnibus database. The results suggested that EXOSC gene expression may be a molecular marker for MCL. Compared with the whole transcript profile, patients with MCL with a high EXO.index exhibited poorer survival and decreased RNA levels, which was also verified in a second dataset. The EXOSC genes may be associated with DNA repair and B-cell activation pathways, which may be the cause of poorer survival of patients with MCL.
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Affiliation(s)
- Weilong Zhang
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, Beijing 100191, P.R. China
| | - Junyong Zhu
- Department of General Surgery, Chinese People's Liberation Army General Hospital, Beijing 100853, P.R. China
| | - Xue He
- Department of Pathology, Beijing Tiantan Hospital Affiliated with Capital Medical University, Beijing 100050, P.R. China
| | - Xiaoni Liu
- Department of Respiratory Medicine, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Guangdong 341000, P.R. China
| | - Jinhang Li
- Department of Pathology, Chinese People's Liberation Army General Hospital, Beijing 100853, P.R. China
| | - Wei Li
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, Beijing 100191, P.R. China
| | - Ping Yang
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, Beijing 100191, P.R. China
| | - Jing Wang
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, Beijing 100191, P.R. China
| | - Kai Hu
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, Beijing 100191, P.R. China
| | - Xiuru Zhang
- Department of Pathology, Beijing Tiantan Hospital Affiliated with Capital Medical University, Beijing 100050, P.R. China
| | - Xiru Li
- Department of General Surgery, Chinese People's Liberation Army General Hospital, Beijing 100853, P.R. China
| | - Hongmei Jing
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, Beijing 100191, P.R. China
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7
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Xu Y, Chen L, Liu M, Lu Y, Yue Y, Liu Y, Chen H, Xie F, Zhang C. High-throughput transcriptome sequencing reveals extremely high doses of ionizing radiation-response genes in Caenorhabditis elegans. Toxicol Res (Camb) 2019; 8:754-766. [PMID: 31588352 PMCID: PMC6762013 DOI: 10.1039/c9tx00101h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 08/06/2019] [Indexed: 12/27/2022] Open
Abstract
This study sought novel ionizing radiation-response (IR-response) genes in Caenorhabditis elegans (C. elegans). C. elegans was divided into three groups and exposed to different high doses of IR: 0 gray (Gy), 200 Gy, and 400 Gy. Total RNA was extracted from each group and sequenced. When the transcriptomes were compared among these groups, many genes were shown to be differentially expressed, and these genes were significantly enriched in IR-related biological processes and pathways, including gene ontology (GO) terms related to cellular behaviours, cellular growth and purine metabolism and kyoto encyclopedia of genes and genomes (KEGG) pathways related to ATP binding, GTPase regulator activity, and RNA degradation. Quantitative reverse-transcription PCR (qRT-PCR) confirmed that these genes displayed differential expression across the treatments. Further gene network analysis showed a cluster of novel gene families, such as the guanylate cyclase (GCY), Sm-like protein (LSM), diacylglycerol kinase (DGK), skp1-related protein (SKR), and glutathione S-transferase (GST) gene families which were upregulated. Thus, these genes likely play important roles in IR response. Meanwhile, some important genes that are well known to be involved in key signalling pathways, such as phosphoinositide-specific phospholipase C-3 (PLC-3), phosphatidylinositol 3-kinase age-1 (AGE-1), Raf homolog serine/threonine-protein kinase (LIN-45) and protein cbp-1 (CBP-1), also showed differential expression during IR response, suggesting that IR response might perturb these key signalling pathways. Our study revealed a series of novel IR-response genes in Caenorhabditis elegans that might act as regulators of IR response and represent promising markers of IR exposure.
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Affiliation(s)
- Youqin Xu
- Department of Biochemistry and Molecular Biology , School of Basic Medical Science , Southern Medical University and Guangdong Provincial Key Laboratory of Single Cell Technology and Application , Guangzhou , Guangdong Province , China . ; Tel: +86-13824447151
- Department of Medical Oncology , Taishan People's Hospital , Guangdong Province , China
| | - Lina Chen
- Basic Medical College , Xiangnan University , Chenzhou , China
| | - Mengyi Liu
- Department of Biochemistry and Molecular Biology , School of Basic Medical Science , Southern Medical University and Guangdong Provincial Key Laboratory of Single Cell Technology and Application , Guangzhou , Guangdong Province , China . ; Tel: +86-13824447151
| | - Yanfang Lu
- Department of Biochemistry and Molecular Biology , School of Basic Medical Science , Southern Medical University and Guangdong Provincial Key Laboratory of Single Cell Technology and Application , Guangzhou , Guangdong Province , China . ; Tel: +86-13824447151
| | - Yanwei Yue
- Blood Transfusion Department , The First Affiliated Hospital of Xi'an Jiaotong University , Xi'an , China
| | - Yue Liu
- Department of Biochemistry and Molecular Biology , School of Basic Medical Science , Southern Medical University and Guangdong Provincial Key Laboratory of Single Cell Technology and Application , Guangzhou , Guangdong Province , China . ; Tel: +86-13824447151
| | - Honghao Chen
- Department of Biochemistry and Molecular Biology , School of Basic Medical Science , Southern Medical University and Guangdong Provincial Key Laboratory of Single Cell Technology and Application , Guangzhou , Guangdong Province , China . ; Tel: +86-13824447151
| | - Fuliang Xie
- Department of Biochemistry and Molecular Biology , School of Basic Medical Science , Southern Medical University and Guangdong Provincial Key Laboratory of Single Cell Technology and Application , Guangzhou , Guangdong Province , China . ; Tel: +86-13824447151
- Department of Biology , East Carolina University , Greenville , NC , USA
| | - Chao Zhang
- Department of Biochemistry and Molecular Biology , School of Basic Medical Science , Southern Medical University and Guangdong Provincial Key Laboratory of Single Cell Technology and Application , Guangzhou , Guangdong Province , China . ; Tel: +86-13824447151
- Department of Medical Oncology , Taishan People's Hospital , Guangdong Province , China
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8
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Ramos-Alonso L, Romero AM, Soler MÀ, Perea-García A, Alepuz P, Puig S, Martínez-Pastor MT. Yeast Cth2 protein represses the translation of ARE-containing mRNAs in response to iron deficiency. PLoS Genet 2018; 14:e1007476. [PMID: 29912874 PMCID: PMC6023232 DOI: 10.1371/journal.pgen.1007476] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 06/28/2018] [Accepted: 06/07/2018] [Indexed: 11/29/2022] Open
Abstract
In response to iron deficiency, the budding yeast Saccharomyces cerevisiae undergoes a metabolic remodeling in order to optimize iron utilization. The tandem zinc finger (TZF)-containing protein Cth2 plays a critical role in this adaptation by binding and promoting the degradation of multiple mRNAs that contain AU-rich elements (AREs). Here, we demonstrate that Cth2 also functions as a translational repressor of its target mRNAs. By complementary approaches, we demonstrate that Cth2 protein inhibits the translation of SDH4, which encodes a subunit of succinate dehydrogenase, and CTH2 mRNAs in response to iron depletion. Both the AREs within SDH4 and CTH2 transcripts, and the Cth2 TZF are essential for translational repression. We show that the role played by Cth2 as a negative translational regulator extends to other mRNA targets such as WTM1, CCP1 and HEM15. A structure-function analysis of Cth2 protein suggests that the Cth2 amino-terminal domain (NTD) is important for both mRNA turnover and translation inhibition, while its carboxy-terminal domain (CTD) only participates in the regulation of translation, but is dispensable for mRNA degradation. Finally, we demonstrate that the Cth2 CTD is physiologically relevant for adaptation to iron deficiency. Iron is essential for eukaryotes because it is required for many fundamental processes such as DNA replication, protein translation or respiration, but it is very insoluble and can, therefore, easily go scarce. For this reason, eukaryotic cells have developed adaptive responses to iron deficiency. Under iron limitation conditions, the yeast Saccharomyces cerevisiae induces the expression of Cth2, a protein with tandem zinc fingers that binds to adenine and uracil-rich sequences in the 3’-UTR of specific mRNAs related to iron metabolism, promoting their degradation. Here we show that Cth2 inhibits the translation of ARE-containing mRNAs, including SDH4, WTM1, HEM15 and CCP1, which encode proteins that contain iron or participate in iron-dependent pathways, and CTH2 itself, which is subjected to an autoregulatory loop that controls its expression. We also dissected different domains of Cth2 that are differentially involved in mRNA decay and translational inhibition. The involvement of Cth2 in translational control reinforces the importance of this ARE-binding protein as a post-transcriptional regulator of the iron response in yeast. By acting at different steps in the life of specific mRNA targets, Cth2 action ensures yeast cells a proper distribution of iron by optimizing its utilization in essential processes.
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Affiliation(s)
- Lucía Ramos-Alonso
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
| | - Antonia María Romero
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
| | - Maria Àngel Soler
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Valencia, Spain
| | - Ana Perea-García
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
| | - Paula Alepuz
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Valencia, Spain
- ERI Biotecmed, Universitat de València, Burjassot, Valencia, Spain
| | - Sergi Puig
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
- * E-mail: (MTMP); (SP)
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9
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Burns DT, Donkervoort S, Müller JS, Knierim E, Bharucha-Goebel D, Faqeih EA, Bell SK, AlFaifi AY, Monies D, Millan F, Retterer K, Dyack S, MacKay S, Morales-Gonzalez S, Giunta M, Munro B, Hudson G, Scavina M, Baker L, Massini TC, Lek M, Hu Y, Ezzo D, AlKuraya FS, Kang PB, Griffin H, Foley AR, Schuelke M, Horvath R, Bönnemann CG. Variants in EXOSC9 Disrupt the RNA Exosome and Result in Cerebellar Atrophy with Spinal Motor Neuronopathy. Am J Hum Genet 2018; 102:858-873. [PMID: 29727687 PMCID: PMC5986733 DOI: 10.1016/j.ajhg.2018.03.011] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/06/2018] [Indexed: 12/30/2022] Open
Abstract
The exosome is a conserved multi-protein complex that is essential for correct RNA processing. Recessive variants in exosome components EXOSC3, EXOSC8, and RBM7 cause various constellations of pontocerebellar hypoplasia (PCH), spinal muscular atrophy (SMA), and central nervous system demyelination. Here, we report on four unrelated affected individuals with recessive variants in EXOSC9 and the effect of the variants on the function of the RNA exosome in vitro in affected individuals' fibroblasts and skeletal muscle and in vivo in zebrafish. The clinical presentation was severe, early-onset, progressive SMA-like motor neuronopathy, cerebellar atrophy, and in one affected individual, congenital fractures of the long bones. Three affected individuals of different ethnicity carried the homozygous c.41T>C (p.Leu14Pro) variant, whereas one affected individual was compound heterozygous for c.41T>C (p.Leu14Pro) and c.481C>T (p.Arg161∗). We detected reduced EXOSC9 in fibroblasts and skeletal muscle and observed a reduction of the whole multi-subunit exosome complex on blue-native polyacrylamide gel electrophoresis. RNA sequencing of fibroblasts and skeletal muscle detected significant >2-fold changes in genes involved in neuronal development and cerebellar and motor neuron degeneration, demonstrating the widespread effect of the variants. Morpholino oligonucleotide knockdown and CRISPR/Cas9-mediated mutagenesis of exosc9 in zebrafish recapitulated aspects of the human phenotype, as they have in other zebrafish models of exosomal disease. Specifically, portions of the cerebellum and hindbrain were absent, and motor neurons failed to develop and migrate properly. In summary, we show that variants in EXOSC9 result in a neurological syndrome combining cerebellar atrophy and spinal motoneuronopathy, thus expanding the list of human exosomopathies.
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10
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Lee H, Patschull AOM, Bagnéris C, Ryan H, Sanderson CM, Ebrahimi B, Nobeli I, Barrett TE. KSHV SOX mediated host shutoff: the molecular mechanism underlying mRNA transcript processing. Nucleic Acids Res 2017; 45:4756-4767. [PMID: 28132029 PMCID: PMC5416870 DOI: 10.1093/nar/gkw1340] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 12/22/2016] [Indexed: 11/18/2022] Open
Abstract
Onset of the lytic phase in the KSHV life cycle is accompanied by the rapid, global degradation of host (and viral) mRNA transcripts in a process termed host shutoff. Key to this destruction is the virally encoded alkaline exonuclease SOX. While SOX has been shown to possess an intrinsic RNase activity and a potential consensus sequence for endonucleolytic cleavage identified, the structures of the RNA substrates targeted remained unclear. Based on an analysis of three reported target transcripts, we were able to identify common structures and confirm that these are indeed degraded by SOX in vitro as well as predict the presence of such elements in the KSHV pre-microRNA transcript K12-2. From these studies, we were able to determine the crystal structure of SOX productively bound to a 31 nucleotide K12-2 fragment. This complex not only reveals the structural determinants required for RNA recognition and degradation but, together with biochemical and biophysical studies, reveals distinct roles for residues implicated in host shutoff. Our results further confirm that SOX and the host exoribonuclease Xrn1 act in concert to elicit the rapid degradation of mRNA substrates observed in vivo, and that the activities of the two ribonucleases are co-ordinated.
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Affiliation(s)
- Hyunah Lee
- Institute for Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London WC1E 7HX, UK.,Department of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Anathe O M Patschull
- Institute for Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London WC1E 7HX, UK
| | - Claire Bagnéris
- Institute for Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London WC1E 7HX, UK
| | - Hannah Ryan
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Christopher M Sanderson
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Crown Street, Liverpool, L69 3BX, UK
| | - Bahram Ebrahimi
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Irene Nobeli
- Institute for Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London WC1E 7HX, UK
| | - Tracey E Barrett
- Institute for Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London WC1E 7HX, UK
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11
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Schottmann G, Picker-Minh S, Schwarz JM, Gill E, Rodenburg RJT, Stenzel W, Kaindl AM, Schuelke M. Recessive mutation in EXOSC3 associates with mitochondrial dysfunction and pontocerebellar hypoplasia. Mitochondrion 2017; 37:46-54. [PMID: 28687512 DOI: 10.1016/j.mito.2017.06.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Revised: 06/06/2017] [Accepted: 06/21/2017] [Indexed: 12/13/2022]
Abstract
Recessive mutations in EXOSC3, encoding a subunit of the human RNA exosome complex, cause pontocerebellar hypoplasia type 1b (PCH1B). We report a boy with severe muscular hypotonia, psychomotor retardation, progressive microcephaly, and cerebellar atrophy. Biochemical abnormalities comprised mitochondrial complex I and pyruvate dehydrogenase complex (PDHc) deficiency. Whole exome sequencing uncovered a known EXOSC3 mutation p.(D132A) as the underlying cause. In patient fibroblasts, a large portion of the EXOSC3 protein was trapped in the cytosol. MtDNA copy numbers in muscle were reduced to 35%, but mutations in the mtDNA and in nuclear mitochondrial genes were ruled out. RNA-Seq of patient muscle showed highly increased mRNA copy numbers, especially for genes encoding structural subunits of OXPHOS complexes I, III, and IV, possibly due to reduced degradation by a dysfunctional exosome complex. This is the first case of mitochondrial dysfunction associated with an EXOSC3 mutation, which expands the phenotypic spectrum of PCH1B. We discuss the links between exosome and mitochondrial dysfunction.
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Affiliation(s)
- Gudrun Schottmann
- NeuroCure Clinical Research Center (NCRC), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Germany; Department of Neuropediatrics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Germany
| | - Sylvie Picker-Minh
- Department of Neuropediatrics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Germany; Center for Chronically Sick Children, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Germany; Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Germany; Berlin Institute of Health (BIH), Berlin, Germany
| | - Jana Marie Schwarz
- NeuroCure Clinical Research Center (NCRC), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Germany
| | - Esther Gill
- NeuroCure Clinical Research Center (NCRC), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Germany
| | - Richard J T Rodenburg
- Radboud Center for Mitochondrial Disorders, Department of Pediatrics, Translational Metabolic Laboratory, Radboudumc, Nijmegen, The Netherlands
| | - Werner Stenzel
- Institute of Neuropathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Germany
| | - Angela M Kaindl
- Department of Neuropediatrics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Germany; Center for Chronically Sick Children, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Germany; Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Germany; Berlin Institute of Health (BIH), Berlin, Germany.
| | - Markus Schuelke
- NeuroCure Clinical Research Center (NCRC), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Germany; Department of Neuropediatrics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Germany.
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12
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Chintalapudi SR, Jablonski MM. Systems Genetics Analysis to Identify the Genetic Modulation of a Glaucoma-Associated Gene. Methods Mol Biol 2017; 1488:391-417. [PMID: 27933535 DOI: 10.1007/978-1-4939-6427-7_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Loss of retinal ganglion cells (RGCs) is one of the hallmarks of retinal neurodegenerative diseases, glaucoma being one of the most common. Recently, γ-synuclein (SNCG) was shown to be highly expressed in the somas and axons of RGCs. In various mouse models of glaucoma, downregulation of Sncg gene expression correlates with RGC loss. To investigate the regulation of Sncg in RGCs, we used a systems genetics approach to identify a gene that modulates the expression of Sncg, followed by confirmatory studies in both healthy and diseased retinas. We found that chromosome 1 harbors an eQTL that modulates the expression of Sncg in the mouse retina and identified Pfdn2 as the candidate upstream modulator of Sncg expression. Downregulation of Pfdn2 in enriched RGCs causes a concomitant reduction in Sncg. In this chapter, we describe our strategy and methods for identifying and confirming a genetic modulation of a glaucoma-associated gene. A similar method can be applied to other genes expressed in other tissues.
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Affiliation(s)
- Sumana R Chintalapudi
- Department of Anatomy and Neurobiology, Hamilton Eye Institute, The University of Tennessee Health Science Center, 930 Madison Ave., Suite 710, Memphis, TN, 38163, USA
| | - Monica M Jablonski
- Department of Ophthalmology, Hamilton Eye Institute, The University of Tennessee Health Science Center, 930 Madison Ave., Suite 710, Memphis, TN, 38163, USA. .,Department of Anatomy and Neurobiology, Hamilton Eye Institute, The University of Tennessee Health Science Center, 930 Madison Ave., Suite 710, Memphis, TN, 38163, USA. .,Department of Pharmaceutical Sciences, Hamilton Eye Institute, The University of Tennessee Health Science Center, 930 Madison Ave., Suite 710, Memphis, TN, 38163, USA.
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13
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Emerging Roles for Ciz1 in Cell Cycle Regulation and as a Driver of Tumorigenesis. Biomolecules 2016; 7:biom7010001. [PMID: 28036012 PMCID: PMC5372713 DOI: 10.3390/biom7010001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/12/2016] [Accepted: 12/14/2016] [Indexed: 12/19/2022] Open
Abstract
Precise duplication of the genome is a prerequisite for the health and longevity of multicellular organisms. The temporal regulation of origin specification, replication licensing, and firing at replication origins is mediated by the cyclin-dependent kinases. Here the role of Cip1 interacting Zinc finger protein 1 (Ciz1) in regulation of cell cycle progression is discussed. Ciz1 contributes to regulation of the G1/S transition in mammalian cells. Ciz1 contacts the pre-replication complex (pre-RC) through cell division cycle 6 (Cdc6) interactions and aids localization of cyclin A- cyclin-dependent kinase 2 (CDK2) activity to chromatin and the nuclear matrix during initiation of DNA replication. We discuss evidence that Ciz1 serves as a kinase sensor that regulates both initiation of DNA replication and prevention of re-replication. Finally, the emerging role for Ciz1 in cancer biology is discussed. Ciz1 is overexpressed in common tumors and tumor growth is dependent on Ciz1 expression, suggesting that Ciz1 is a driver of tumor growth. We present evidence that Ciz1 may contribute to deregulation of the cell cycle due to its ability to alter the CDK activity thresholds that are permissive for initiation of DNA replication. We propose that Ciz1 may contribute to oncogenesis by induction of DNA replication stress and that Ciz1 may be a multifaceted target in cancer therapy.
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14
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Kim K, Heo DH, Kim I, Suh JY, Kim M. Exosome Cofactors Connect Transcription Termination to RNA Processing by Guiding Terminated Transcripts to the Appropriate Exonuclease within the Nuclear Exosome. J Biol Chem 2016; 291:13229-42. [PMID: 27076633 DOI: 10.1074/jbc.m116.715771] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Indexed: 12/11/2022] Open
Abstract
The yeast Nrd1 interacts with the C-terminal domain (CTD) of RNA polymerase II (RNApII) through its CTD-interacting domain (CID) and also associates with the nuclear exosome, thereby acting as both a transcription termination and RNA processing factor. Previously, we found that the Nrd1 CID is required to recruit the nuclear exosome to the Nrd1 complex, but it was not clear which exosome subunits were contacted. Here, we show that two nuclear exosome cofactors, Mpp6 and Trf4, directly and competitively interact with the Nrd1 CID and differentially regulate the association of Nrd1 with two catalytic subunits of the exosome. Importantly, Mpp6 promotes the processing of Nrd1-terminated transcripts preferentially by Dis3, whereas Trf4 leads to Rrp6-dependent processing. This suggests that Mpp6 and Trf4 may play a role in choosing a particular RNA processing route for Nrd1-terminated transcripts within the exosome by guiding the transcripts to the appropriate exonuclease.
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Affiliation(s)
- Kyumin Kim
- From the Department of Cellular and Molecular Pharmacology, University of California and California Institute for Quantitative Biosciences, San Francisco, California 94158
| | - Dong-Hyuk Heo
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
| | - Iktae Kim
- Department of Agricultural Biotechnology, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul 08826, Korea, and
| | - Jeong-Yong Suh
- Department of Agricultural Biotechnology, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul 08826, Korea, and Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Matsumoto, Nagano 390-8621, Japan
| | - Minkyu Kim
- From the Department of Cellular and Molecular Pharmacology, University of California and California Institute for Quantitative Biosciences, San Francisco, California 94158,
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15
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Smiley S, Nickerson PE, Comanita L, Daftarian N, El-Sehemy A, Tsai ELS, Matan-Lithwick S, Yan K, Thurig S, Touahri Y, Dixit R, Aavani T, De Repentingy Y, Baker A, Tsilfidis C, Biernaskie J, Sauvé Y, Schuurmans C, Kothary R, Mears AJ, Wallace VA. Establishment of a cone photoreceptor transplantation platform based on a novel cone-GFP reporter mouse line. Sci Rep 2016; 6:22867. [PMID: 26965927 PMCID: PMC4786810 DOI: 10.1038/srep22867] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 02/23/2016] [Indexed: 12/18/2022] Open
Abstract
We report successful retinal cone enrichment and transplantation using a novel cone-GFP reporter mouse line. Using the putative cone photoreceptor-enriched transcript Coiled-Coil Domain Containing 136 (Ccdc136) GFP-trapped allele, we monitored developmental reporter expression, facilitated the enrichment of cones, and evaluated transplanted GFP-labeled cones in wildtype and retinal degeneration mutant retinas. GFP reporter and endogenous Ccdc136 transcripts exhibit overlapping temporal and spatial expression patterns, both initiated in cone precursors of the embryonic retina and persisting to the adult stage in S and S/M opsin(+) cones as well as rod bipolar cells. The trapped allele does not affect cone function or survival in the adult mutant retina. When comparing the integration of GFP(+) embryonic cones and postnatal Nrl(-/-) 'cods' into retinas of adult wildtype and blind mice, both cell types integrated and exhibited a degree of morphological maturation that was dependent on donor age. These results demonstrate the amenability of the adult retina to cone transplantation using a novel transgenic resource that can advance therapeutic cone transplantation in models of age-related macular degeneration.
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Affiliation(s)
- Sheila Smiley
- Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, Ontario, K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Division of Vision Science, Department of Ophthalmology and Vision Science, Krembil Research Institute, University Health Network, Toronto, ON M5T 2S8, Canada
| | - Philip E. Nickerson
- Division of Vision Science, Department of Ophthalmology and Vision Science, Krembil Research Institute, University Health Network, Toronto, ON M5T 2S8, Canada
| | - Lacrimioara Comanita
- Division of Vision Science, Department of Ophthalmology and Vision Science, Krembil Research Institute, University Health Network, Toronto, ON M5T 2S8, Canada
| | - Narsis Daftarian
- Department of Biochemistry and Molecular Biology, Hotchkiss Brain Institute and Alberta Children’s Hospital Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary, T2N 4N1, Canada
- Ocular Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences (SBMU), Tehran, Iran
| | - Ahmed El-Sehemy
- Division of Vision Science, Department of Ophthalmology and Vision Science, Krembil Research Institute, University Health Network, Toronto, ON M5T 2S8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 2J4, Canada
| | - En Leh Samuel Tsai
- Division of Vision Science, Department of Ophthalmology and Vision Science, Krembil Research Institute, University Health Network, Toronto, ON M5T 2S8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 2J4, Canada
| | - Stuart Matan-Lithwick
- Division of Vision Science, Department of Ophthalmology and Vision Science, Krembil Research Institute, University Health Network, Toronto, ON M5T 2S8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 2J4, Canada
| | - Keqin Yan
- Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, Ontario, K1H 8L6, Canada
| | - Sherry Thurig
- Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, Ontario, K1H 8L6, Canada
| | - Yacine Touahri
- Department of Biochemistry and Molecular Biology, Hotchkiss Brain Institute and Alberta Children’s Hospital Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary, T2N 4N1, Canada
| | - Rajiv Dixit
- Department of Biochemistry and Molecular Biology, Hotchkiss Brain Institute and Alberta Children’s Hospital Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary, T2N 4N1, Canada
| | - Tooka Aavani
- Department of Biochemistry and Molecular Biology, Hotchkiss Brain Institute and Alberta Children’s Hospital Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary, T2N 4N1, Canada
| | - Yves De Repentingy
- Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, Ontario, K1H 8L6, Canada
| | - Adam Baker
- Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, Ontario, K1H 8L6, Canada
| | - Catherine Tsilfidis
- Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, Ontario, K1H 8L6, Canada
- Department of Ophthalmology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Jeff Biernaskie
- Department of Comparative Biology and Experimental Medicine, Hotchkiss Brain Institute and Alberta Children’s Hospital Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary, T2N 4N1, Canada
| | - Yves Sauvé
- Department of Ophthalmology and Visual Sciences, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Carol Schuurmans
- Department of Biochemistry and Molecular Biology, Hotchkiss Brain Institute and Alberta Children’s Hospital Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary, T2N 4N1, Canada
| | - Rashmi Kothary
- Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, Ontario, K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Department of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Alan J. Mears
- Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, Ontario, K1H 8L6, Canada
- Departments of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Valerie A. Wallace
- Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, Ontario, K1H 8L6, Canada
- Department of Ophthalmology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Departments of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Division of Vision Science, Department of Ophthalmology and Vision Science, Krembil Research Institute, University Health Network, Toronto, ON M5T 2S8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 2J4, Canada
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16
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Fu R, Olsen MT, Webb K, Bennett EJ, Lykke-Andersen J. Recruitment of the 4EHP-GYF2 cap-binding complex to tetraproline motifs of tristetraprolin promotes repression and degradation of mRNAs with AU-rich elements. RNA (NEW YORK, N.Y.) 2016; 22:373-382. [PMID: 26763119 PMCID: PMC4748815 DOI: 10.1261/rna.054833.115] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 11/30/2015] [Indexed: 06/05/2023]
Abstract
The zinc finger protein tristetraprolin (TTP) promotes translation repression and degradation of mRNAs containing AU-rich elements (AREs). Although much attention has been directed toward understanding the decay process and machinery involved, the translation repression role of TTP has remained poorly understood. Here we identify the cap-binding translation repression 4EHP-GYF2 complex as a cofactor of TTP. Immunoprecipitation and in vitro pull-down assays demonstrate that TTP associates with the 4EHP-GYF2 complex via direct interaction with GYF2, and mutational analyses show that this interaction occurs via conserved tetraproline motifs of TTP. Mutant TTP with diminished 4EHP-GYF2 binding is impaired in its ability to repress a luciferase reporter ARE-mRNA. 4EHP knockout mouse embryonic fibroblasts (MEFs) display increased induction and slower turnover of TTP-target mRNAs as compared to wild-type MEFs. Our work highlights the function of the conserved tetraproline motifs of TTP and identifies 4EHP-GYF2 as a cofactor in translational repression and mRNA decay by TTP.
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Affiliation(s)
- Rui Fu
- Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA
| | - Myanna T Olsen
- Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA
| | - Kristofor Webb
- Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA
| | - Eric J Bennett
- Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA
| | - Jens Lykke-Andersen
- Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA
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17
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Polledo JM, Cervini G, Romaniuk MA, Cassola A. Interactions between RNA-binding proteins and P32 homologues in trypanosomes and human cells. Curr Genet 2015; 62:203-12. [PMID: 26385742 DOI: 10.1007/s00294-015-0519-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 09/09/2015] [Accepted: 09/10/2015] [Indexed: 12/25/2022]
Abstract
RNA-binding proteins (RBPs) are involved in many aspects of mRNA metabolism such as splicing, nuclear export, translation, silencing, and decay. To cope with these tasks, these proteins use specialized domains such as the RNA recognition motif (RRM), the most abundant and widely spread RNA-binding domain. Although this domain was first described as a dedicated RNA-binding moiety, current evidence indicates these motifs can also engage in direct protein-protein interactions. Here, we discuss recent evidence describing the interaction between the RRM of the trypanosomatid RBP UBP1 and P22, the homolog of the human multifunctional protein P32/C1QBP. Human P32 was also identified while performing a similar interaction screening using both RRMs of TDP-43, an RBP involved in splicing regulation and Amyotrophic Lateral Sclerosis. Furthermore, we show that this interaction is mediated by RRM1. The relevance of this interaction is discussed in the context of recent TDP-43 interactomic approaches that identified P32, and the numerous evidences supporting interactions between P32 and RBPs. Finally, we discuss the vast universe of interactions involving P32, supporting its role as a molecular chaperone regulating the function of its ligands.
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Affiliation(s)
- Juan Manuel Polledo
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús, UNSAM-CONICET, Buenos Aires, Argentina
| | - Gabriela Cervini
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús, UNSAM-CONICET, Buenos Aires, Argentina
| | - María Albertina Romaniuk
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús, UNSAM-CONICET, Buenos Aires, Argentina
| | - Alejandro Cassola
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús, UNSAM-CONICET, Buenos Aires, Argentina.
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18
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Müller JS, Giunta M, Horvath R. Exosomal Protein Deficiencies: How Abnormal RNA Metabolism Results in Childhood-Onset Neurological Diseases. J Neuromuscul Dis 2015; 2:S31-S37. [PMID: 27127732 PMCID: PMC4845884 DOI: 10.3233/jnd-150086] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Defects of RNA metabolism have been increasingly identified in various forms of inherited neurological diseases. Recently, abnormal RNA degradation due to mutations in human exosome subunit genes has been shown to cause complex childhood onset neurological presentations including spinal muscular atrophy, pontocerebellar hypoplasia and myelination deficiencies. This paper summarizes our current knowledge about the exosome in human neurological disease and provides some important insights into potential disease mechanisms.
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Affiliation(s)
- Juliane S. Müller
- Institute of Genetic Medicine, The John Walton Muscular Dystrophy Research Centre, Wellcome Trust Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Michele Giunta
- Institute of Genetic Medicine, The John Walton Muscular Dystrophy Research Centre, Wellcome Trust Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Rita Horvath
- Institute of Genetic Medicine, The John Walton Muscular Dystrophy Research Centre, Wellcome Trust Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
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19
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NVL2, a nucleolar AAA-ATPase, is associated with the nuclear exosome and is involved in pre-rRNA processing. Biochem Biophys Res Commun 2015; 464:780-6. [PMID: 26166824 DOI: 10.1016/j.bbrc.2015.07.032] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 07/07/2015] [Indexed: 11/22/2022]
Abstract
Nuclear VCP-like 2 (NVL2) is a member of the chaperone-like AAA-ATPase family and is involved in the biosynthesis of 60S ribosomal subunits in mammalian cells. We previously showed the interaction of NVL2 with a DExD/H-box RNA helicase MTR4/DOB1, which is a known cofactor for an exoribonuclease complex, the exosome. This finding implicated NVL2 in RNA metabolic processes during ribosome biogenesis. In the present study, we found that a series of mutations within the ATPase domain of NVL2 causes a defect in pre-rRNA processing into mature 28S and 5.8S rRNAs. Co-immunoprecipitation analysis showed that NVL2 was associated with the nuclear exosome complex, which includes RRP6 as a nucleus-specific catalytic subunit. This interaction was prevented by depleting either MTR4 or RRP6, indicating their essential role in mediating this interaction with NVL2. Additionally, knockdown of MPP6, another cofactor for the nuclear exosome, also prevented the interaction by causing MTR4 to dissociate from the nuclear exosome. These results suggest that NVL2 is involved in pre-rRNA processing by associating with the nuclear exosome complex and that MPP6 is required for maintaining the integrity of this rRNA processing complex.
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20
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Boczonadi V, Müller JS, Pyle A, Munkley J, Dor T, Quartararo J, Ferrero I, Karcagi V, Giunta M, Polvikoski T, Birchall D, Princzinger A, Cinnamon Y, Lützkendorf S, Piko H, Reza M, Florez L, Santibanez-Koref M, Griffin H, Schuelke M, Elpeleg O, Kalaydjieva L, Lochmüller H, Elliott DJ, Chinnery PF, Edvardson S, Horvath R. EXOSC8 mutations alter mRNA metabolism and cause hypomyelination with spinal muscular atrophy and cerebellar hypoplasia. Nat Commun 2014; 5:4287. [PMID: 24989451 PMCID: PMC4102769 DOI: 10.1038/ncomms5287] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 06/03/2014] [Indexed: 12/21/2022] Open
Abstract
The exosome is a multi-protein complex, required for the degradation of AU-rich element (ARE) containing messenger RNAs (mRNAs). EXOSC8 is an essential protein of the exosome core, as its depletion causes a severe growth defect in yeast. Here we show that homozygous missense mutations in EXOSC8 cause progressive and lethal neurological disease in 22 infants from three independent pedigrees. Affected individuals have cerebellar and corpus callosum hypoplasia, abnormal myelination of the central nervous system or spinal motor neuron disease. Experimental downregulation of EXOSC8 in human oligodendroglia cells and in zebrafish induce a specific increase in ARE mRNAs encoding myelin proteins, showing that the imbalanced supply of myelin proteins causes the disruption of myelin, and explaining the clinical presentation. These findings show the central role of the exosomal pathway in neurodegenerative disease. The exosome is responsible for mRNA degradation, which is an important step in the regulation of gene expression. Here the authors report that homozygous missense mutations in the exosome subunit, EXOSC8, may cause neurodegenerative disease in infants through the dysregulation of myelin expression.
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Affiliation(s)
- Veronika Boczonadi
- 1] Institute of Genetic Medicine, Wellcome Trust Centre for Mitochondrial Research, Newcastle University, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK [2]
| | - Juliane S Müller
- 1] Institute of Genetic Medicine, Wellcome Trust Centre for Mitochondrial Research, Newcastle University, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK [2]
| | - Angela Pyle
- 1] Institute of Genetic Medicine, Wellcome Trust Centre for Mitochondrial Research, Newcastle University, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK [2]
| | - Jennifer Munkley
- 1] Institute of Genetic Medicine, Wellcome Trust Centre for Mitochondrial Research, Newcastle University, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK [2]
| | - Talya Dor
- The Monique and Jacques Roboh Department of Genetic Research, Hadassah- Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Jade Quartararo
- Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, Parma 43124, Italy
| | - Ileana Ferrero
- Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, Parma 43124, Italy
| | - Veronika Karcagi
- Department of Molecular Genetics and Diagnostics, NIEH, Albert Florian ut 2-6, Budapest 1097, Hungary
| | - Michele Giunta
- Institute of Genetic Medicine, Wellcome Trust Centre for Mitochondrial Research, Newcastle University, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK
| | - Tuomo Polvikoski
- Department of Pathology, Institute for Ageing and Health, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne NE4 5PL, UK
| | - Daniel Birchall
- Neuroradiology Department, Regional Neurosciences Centre, Queen Victoria Road, Newcastle upon Tyne NE1 4PL, UK
| | - Agota Princzinger
- Department of Paediatrics, Josa Andras Hospital, Szent Istvan utca 6, Nyiregyhaza 4400, Hungary
| | - Yuval Cinnamon
- 1] The Monique and Jacques Roboh Department of Genetic Research, Hadassah- Hebrew University Medical Center, Jerusalem 91120, Israel [2] Department of Poultry and Aquaculture Sciences, Institute of Animal Science, Agricultural Research Organization, The Volcani Center, P.O.Box 6, Bet Dagan 50250, Israel
| | - Susanne Lützkendorf
- Department of Neuropediatrics and NeuroCure Clinical Research Center, Charité-Universitätsmedizin, Charité-Platz 1, 10117 Berlin, Germany
| | - Henriett Piko
- Department of Molecular Genetics and Diagnostics, NIEH, Albert Florian ut 2-6, Budapest 1097, Hungary
| | - Mojgan Reza
- Institute of Genetic Medicine, Wellcome Trust Centre for Mitochondrial Research, Newcastle University, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK
| | - Laura Florez
- Western Australian Institute for Medical Research/Centre for Medical Research, The University of Western Australia, 35 Stirling Highway Crawley, Western Australia 6009 Perth, Australia
| | - Mauro Santibanez-Koref
- Institute of Genetic Medicine, Wellcome Trust Centre for Mitochondrial Research, Newcastle University, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK
| | - Helen Griffin
- Institute of Genetic Medicine, Wellcome Trust Centre for Mitochondrial Research, Newcastle University, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK
| | - Markus Schuelke
- Department of Neuropediatrics and NeuroCure Clinical Research Center, Charité-Universitätsmedizin, Charité-Platz 1, 10117 Berlin, Germany
| | - Orly Elpeleg
- The Monique and Jacques Roboh Department of Genetic Research, Hadassah- Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Luba Kalaydjieva
- Western Australian Institute for Medical Research/Centre for Medical Research, The University of Western Australia, 35 Stirling Highway Crawley, Western Australia 6009 Perth, Australia
| | - Hanns Lochmüller
- Institute of Genetic Medicine, Wellcome Trust Centre for Mitochondrial Research, Newcastle University, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK
| | - David J Elliott
- Institute of Genetic Medicine, Wellcome Trust Centre for Mitochondrial Research, Newcastle University, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK
| | - Patrick F Chinnery
- Institute of Genetic Medicine, Wellcome Trust Centre for Mitochondrial Research, Newcastle University, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK
| | - Shimon Edvardson
- The Monique and Jacques Roboh Department of Genetic Research, Hadassah- Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Rita Horvath
- Institute of Genetic Medicine, Wellcome Trust Centre for Mitochondrial Research, Newcastle University, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK
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21
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Clayton CE. Networks of gene expression regulation in Trypanosoma brucei. Mol Biochem Parasitol 2014; 195:96-106. [PMID: 24995711 DOI: 10.1016/j.molbiopara.2014.06.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 06/19/2014] [Accepted: 06/23/2014] [Indexed: 10/25/2022]
Abstract
Regulation of gene expression in Kinetoplastids relies mainly on post-transcriptional mechanisms. Recent high-throughput analyses, combined with mathematical modelling, have demonstrated possibilities for transcript-specific regulation at every stage: trans splicing, polyadenylation, translation, and degradation of both the precursor and the mature mRNA. Different mRNA degradation pathways result in different types of degradation kinetics. The original idea that the fate of an mRNA - or even just its degradation kinetics - can be defined by a single "regulatory element" is an over-simplification. It is now clear that every mRNA can bind many different proteins, some of which may compete with each other. Superimposed upon this complexity are the interactions of those proteins with effectors of gene expression. The amount of protein that is made from a gene is therefore determined by a complex network of interactions.
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Affiliation(s)
- C E Clayton
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.
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22
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Quality control of mRNP biogenesis: networking at the transcription site. Semin Cell Dev Biol 2014; 32:37-46. [PMID: 24713468 DOI: 10.1016/j.semcdb.2014.03.033] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 03/28/2014] [Indexed: 11/20/2022]
Abstract
Eukaryotic cells carry out quality control (QC) over the processes of RNA biogenesis to inactivate or eliminate defective transcripts, and to avoid their production. In the case of protein-coding transcripts, the quality controls can sense defects in the assembly of mRNA-protein complexes, in the processing of the precursor mRNAs, and in the sequence of open reading frames. Different types of defect are monitored by different specialized mechanisms. Some of them involve dedicated factors whose function is to identify faulty molecules and target them for degradation. Others are the result of a more subtle balance in the kinetics of opposing activities in the mRNA biogenesis pathway. One way or another, all such mechanisms hinder the expression of the defective mRNAs through processes as diverse as rapid degradation, nuclear retention and transcriptional silencing. Three major degradation systems are responsible for the destruction of the defective transcripts: the exosome, the 5'-3' exoribonucleases, and the nonsense-mediated mRNA decay (NMD) machinery. This review summarizes recent findings on the cotranscriptional quality control of mRNA biogenesis, and speculates that a protein-protein interaction network integrates multiple mRNA degradation systems with the transcription machinery.
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23
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Pastrello C, Pasini E, Kotlyar M, Otasek D, Wong S, Sangrar W, Rahmati S, Jurisica I. Integration, visualization and analysis of human interactome. Biochem Biophys Res Commun 2014; 445:757-73. [DOI: 10.1016/j.bbrc.2014.01.151] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 01/24/2014] [Indexed: 02/06/2023]
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24
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Romano M, Buratti E, Romano G, Klima R, Del Bel Belluz L, Stuani C, Baralle F, Feiguin F. Evolutionarily conserved heterogeneous nuclear ribonucleoprotein (hnRNP) A/B proteins functionally interact with human and Drosophila TAR DNA-binding protein 43 (TDP-43). J Biol Chem 2014; 289:7121-7130. [PMID: 24492607 DOI: 10.1074/jbc.m114.548859] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human TDP-43 represents the main component of neuronal inclusions found in patients with neurodegenerative diseases, especially frontotemporal lobar degeneration and amyotrophic lateral sclerosis. In vitro and in vivo studies have shown that the TAR DNA-binding protein 43 (TDP-43) Drosophila ortholog (TBPH) can biochemically and functionally overlap the properties of the human factor. The recent direct implication of the human heterogeneous nuclear ribonucleoproteins (hnRNPs) A2B1 and A1, known TDP-43 partners, in the pathogenesis of multisystem proteinopathy and amyotrophic lateral sclerosis supports the hypothesis that the physical and functional interplay between TDP-43 and hnRNP A/B orthologs might play a crucial role in the pathogenesis of neurodegenerative diseases. To test this hypothesis and further validate the fly system as a useful model to study this type of diseases, we have now characterized human TDP-43 and Drosophila TBPH similarity in terms of protein-protein interaction pathways. In this work we show that TDP-43 and TBPH share the ability to associate in vitro with Hrp38/Hrb98DE/CG9983, the fruit fly ortholog of the human hnRNP A1/A2 factors. Interestingly, the protein regions of TDP-43 and Hrp38 responsible for reciprocal interactions are conserved through evolution. Functionally, experiments in HeLa cells demonstrate that TDP-43 is necessary for the inhibitory activity of Hrp38 on splicing. Finally, Drosophila in vivo studies show that Hrp38 deficiency produces locomotive defects and life span shortening in TDP-43 with and without animals. These results suggest that hnRNP protein levels can play a modulatory role on TDP-43 functions.
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Affiliation(s)
- Maurizio Romano
- Department of Life Sciences, University of Trieste, Via A. Valerio 28, 34127 Trieste, Italy.
| | - Emanuele Buratti
- International Centre for Genetic Engineering an Biotechnology, Padriciano 99, I-34149 Trieste, Italy
| | - Giulia Romano
- International Centre for Genetic Engineering an Biotechnology, Padriciano 99, I-34149 Trieste, Italy
| | - Raffaella Klima
- International Centre for Genetic Engineering an Biotechnology, Padriciano 99, I-34149 Trieste, Italy
| | - Lisa Del Bel Belluz
- Department of Life Sciences, University of Trieste, Via A. Valerio 28, 34127 Trieste, Italy
| | - Cristiana Stuani
- International Centre for Genetic Engineering an Biotechnology, Padriciano 99, I-34149 Trieste, Italy
| | - Francisco Baralle
- International Centre for Genetic Engineering an Biotechnology, Padriciano 99, I-34149 Trieste, Italy
| | - Fabian Feiguin
- International Centre for Genetic Engineering an Biotechnology, Padriciano 99, I-34149 Trieste, Italy
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25
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Abstract
Messenger RNA deadenylation is a process that allows rapid regulation of gene expression in response to different cellular conditions. The change of the mRNA poly(A) tail length by the activation of deadenylation might regulate gene expression by affecting mRNA stability, mRNA transport, or translation initiation. Activation of deadenylation processes are highly regulated and associated with different cellular conditions such as cancer, development, mRNA surveillance, DNA damage response, and cell differentiation. In the last few years, new technologies for studying deadenylation have been developed. Here we overview concepts related to deadenylation and its regulation in eukaryotic cells. We also describe some of the most commonly used protocols to study deadenylation in eukaryotic cells.
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Affiliation(s)
- Xiaokan Zhang
- Department of Chemistry, Hunter College and Graduate Center, City University of New York, 10065, New York, NY, USA
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26
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Lubin A, Zhang L, Chen H, White VM, Gong F. A human XPC protein interactome--a resource. Int J Mol Sci 2013; 15:141-58. [PMID: 24366067 PMCID: PMC3907802 DOI: 10.3390/ijms15010141] [Citation(s) in RCA: 26] [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: 11/06/2013] [Revised: 12/12/2013] [Accepted: 12/17/2013] [Indexed: 12/13/2022] Open
Abstract
Global genome nucleotide excision repair (GG-NER) is responsible for identifying and removing bulky adducts from non-transcribed DNA that result from damaging agents such as UV radiation and cisplatin. Xeroderma pigmentosum complementation group C (XPC) is one of the essential damage recognition proteins of the GG-NER pathway and its dysfunction results in xeroderma pigmentosum (XP), a disorder involving photosensitivity and a predisposition to cancer. To better understand the identification of DNA damage by XPC in the context of chromatin and the role of XPC in the pathogenesis of XP, we characterized the interactome of XPC using a high throughput yeast two-hybrid screening. Our screening showed 49 novel interactors of XPC involved in DNA repair and replication, proteolysis and post-translational modifications, transcription regulation, signal transduction, and metabolism. Importantly, we validated the XPC-OTUD4 interaction by co-IP and provided evidence that OTUD4 knockdown in human cells indeed affects the levels of ubiquitinated XPC, supporting a hypothesis that the OTUD4 deubiquitinase is involved in XPC recycling by cleaving the ubiquitin moiety. This high-throughput characterization of the XPC interactome provides a resource for future exploration and suggests that XPC may have many uncharacterized cellular functions.
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Affiliation(s)
- Abigail Lubin
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33156, USA; E-Mails: (A.L.); (L.Z.); (H.C.); (V.M.W.)
| | - Ling Zhang
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33156, USA; E-Mails: (A.L.); (L.Z.); (H.C.); (V.M.W.)
| | - Hua Chen
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33156, USA; E-Mails: (A.L.); (L.Z.); (H.C.); (V.M.W.)
| | - Victoria M. White
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33156, USA; E-Mails: (A.L.); (L.Z.); (H.C.); (V.M.W.)
| | - Feng Gong
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33156, USA; E-Mails: (A.L.); (L.Z.); (H.C.); (V.M.W.)
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27
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Fu X, Sun Y, Wang J, Xing Q, Zou J, Li R, Wang Z, Wang S, Hu X, Zhang L, Bao Z. Sequencing-based gene network analysis provides a core set of gene resource for understanding thermal adaptation in Zhikong scallop Chlamys farreri. Mol Ecol Resour 2013; 14:184-98. [PMID: 24128079 DOI: 10.1111/1755-0998.12169] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 08/28/2013] [Accepted: 09/07/2013] [Indexed: 12/14/2022]
Abstract
Marine organisms are commonly exposed to variable environmental conditions, and many of them are under threat from increased sea temperatures caused by global climate change. Generating transcriptomic resources under different stress conditions are crucial for understanding molecular mechanisms underlying thermal adaptation. In this study, we conducted transcriptome-wide gene expression profiling of the scallop Chlamys farreri challenged by acute and chronic heat stress. Of the 13 953 unique tags, more than 850 were significantly differentially expressed at each time point after acute heat stress, which was more than the number of tags differentially expressed (320-350) under chronic heat stress. To obtain a systemic view of gene expression alterations during thermal stress, a weighted gene coexpression network was constructed. Six modules were identified as acute heat stress-responsive modules. Among them, four modules involved in apoptosis regulation, mRNA binding, mitochondrial envelope formation and oxidation reduction were downregulated. The remaining two modules were upregulated. One was enriched with chaperone and the other with microsatellite sequences, whose coexpression may originate from a transcription factor binding site. These results indicated that C. farreri triggered several cellular processes to acclimate to elevated temperature. No modules responded to chronic heat stress, suggesting that the scallops might have acclimated to elevated temperature within 3 days. This study represents the first sequencing-based gene network analysis in a nonmodel aquatic species and provides valuable gene resources for the study of thermal adaptation, which should assist in the development of heat-tolerant scallop lines for aquaculture.
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Affiliation(s)
- X Fu
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
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28
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Lin W, Li XM, Zhang J, Huang Y, Wang J, Zhang J, Jiang XF, Fei Z. Increased expression of the 58-kD microspherule protein (MSP58) is correlated with poor prognosis in glioma patients. Med Oncol 2013; 30:677. [PMID: 23996240 DOI: 10.1007/s12032-013-0677-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 07/21/2013] [Indexed: 10/26/2022]
Abstract
The pathological grading system for human gliomas is usually used to evaluate the prognosis of glioma patients. However, some glioma patients with similar grades have obvious discrepancies in survival. It is therefore necessary to identify some new certain tumor biomarkers that are more suitable for the prognostic assessment of gliomas than the grading system. The 58-kD microspherule protein (MSP58) is an evolutionarily conserved nuclear protein and plays an important role in the regulation of cell proliferation and malignant transformation. However, whether MSP58 can be used as a biomarker to evaluate the malignancy and the prognosis of glioma patients is unknown. In the present study, we performed immunohistochemical analysis to evaluate MSP58 protein expression in 158 specimens of human gliomas and 34 normal control brain tissues. Compared with the control tissues, MSP58 expression was not only significantly higher in the glioma tissues (P < 0.05), but also increased with the increasing pathological grade (P < 0.001). Furthermore, the Kaplan-Meier analysis showed that high expression of MSP58 could predict poor survival in glioma patients (P < 0.001). In the multivariate analysis, high expression of MSP58 was also an independent unfavorable prognostic factor for the overall survival in glioma patients (P < 0.001, hazard ratio, 8.177, 95% CI 2.571-26.008). In conclusion, the increased expression of MSP58 is correlated with a higher malignant grade and poor prognosis in glioma patients. MSP58 is valuable both as an indicator of the malignancy of gliomas and as a prognostic factor for the clinical outcome of glioma patients.
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Affiliation(s)
- Wei Lin
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, China
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29
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Zanni G, Scotton C, Passarelli C, Fang M, Barresi S, Dallapiccola B, Wu B, Gualandi F, Ferlini A, Bertini E, Wei W. Exome sequencing in a family with intellectual disability, early onset spasticity, and cerebellar atrophy detects a novel mutation in EXOSC3. Neurogenetics 2013; 14:247-50. [PMID: 23975261 DOI: 10.1007/s10048-013-0371-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 08/07/2013] [Indexed: 01/03/2023]
Abstract
Whole exome sequencing in two-generational kindred from Bangladesh with early onset spasticity, mild intellectual disability, distal amyotrophy, and cerebellar atrophy transmitted as an autosomal recessive trait identified the following two missense mutations in the EXOSC3 gene: a novel p.V80F mutation and a known p.D132A change previously associated with mild variants of pontocerebellar hypoplasia type 1. This study confirms the involvement of RNA processing proteins in disorders with motor neuron and cerebellar degeneration overlapping with spinocerebellar ataxia 36 and rare forms of hereditary spastic paraplegia with cerebellar features.
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Affiliation(s)
- Ginevra Zanni
- Department of Neurosciences, Unit of Molecular Medicine for Neuromuscular and Neurodegenerative disorders, Rome, Italy
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30
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Abstract
Dysfunctions at the level of RNA processing have recently been shown to play a fundamental role in the pathogenesis of many neurodegenerative diseases. Several proteins responsible for these dysfunctions (TDP-43, FUS/TLS, and hnRNP A/Bs) belong to the nuclear class of heterogeneous ribonucleoproteins (hnRNPs) that predominantly function as general regulators of both coding and noncoding RNA metabolism. The discovery of the importance of these factors in mediating neuronal death has represented a major paradigmatic shift in our understanding of neurodegenerative processes. As a result, these discoveries have also opened the way toward novel biomolecular screening approaches in our search for therapeutic options. One of the major hurdles in this search is represented by the correct identification of the most promising targets to be prioritized. These may include aberrant aggregation processes, protein-protein interactions, RNA-protein interactions, or specific cellular pathways altered by disease. In this review, we discuss these four major options together with their various advantages and drawbacks.
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Affiliation(s)
- Maurizio Romano
- 1Department of Life Sciences, University of Trieste, Trieste, Italy
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31
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Li C, Wei J, Li Y, He X, Zhou Q, Yan J, Zhang J, Liu Y, Liu Y, Shu HB. Transmembrane Protein 214 (TMEM214) mediates endoplasmic reticulum stress-induced caspase 4 enzyme activation and apoptosis. J Biol Chem 2013; 288:17908-17. [PMID: 23661706 PMCID: PMC3682588 DOI: 10.1074/jbc.m113.458836] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 05/01/2013] [Indexed: 11/06/2022] Open
Abstract
Endoplasmic reticulum (ER) stress caused by excessive aggregation of misfolded proteins induces apoptosis. Although ER stress-induced apoptosis has been implicated in many diseases, the detailed mechanisms are not well understood. Here, we identified human transmembrane protein 214 (TMEM214) as a critical mediator of ER stress-induced apoptosis. Overexpression of TMEM214 induced apoptosis, whereas knockdown of TMEM214 inhibited ER stress-induced apoptosis. TMEM214 was localized on the outer membrane of the ER and constitutively associated with procaspase 4, which was also critical for ER stress-induced apoptosis. TMEM214-induced apoptosis was abolished by a dominant negative mutant of procaspase 4, whereas caspase 4-induced apoptosis was inhibited by knockdown of TMEM214. Furthermore, knockdown of TMEM214 inhibited the activation and cleavage of procaspase 4 by impairing its recruitment to the ER. Our findings suggest that TMEM214 is essential for ER stress-induced apoptosis by acting as an anchor for recruitment of procaspase 4 to the ER and its subsequent activation.
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Affiliation(s)
- Chao Li
- From the College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jin Wei
- From the College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Ying Li
- From the College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiao He
- From the College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Qian Zhou
- From the College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jie Yan
- From the College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jing Zhang
- From the College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Ying Liu
- From the College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yu Liu
- From the College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Hong-Bing Shu
- From the College of Life Sciences, Wuhan University, Wuhan 430072, China
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Brooks SA, Blackshear PJ. Tristetraprolin (TTP): interactions with mRNA and proteins, and current thoughts on mechanisms of action. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1829:666-79. [PMID: 23428348 PMCID: PMC3752887 DOI: 10.1016/j.bbagrm.2013.02.003] [Citation(s) in RCA: 296] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 01/25/2013] [Accepted: 02/04/2013] [Indexed: 12/14/2022]
Abstract
Changes in mRNA stability and translation are critical control points in the regulation of gene expression, particularly genes encoding growth factors, inflammatory mediators, and proto-oncogenes. Adenosine and uridine (AU)-rich elements (ARE), often located in the 3' untranslated regions (3'UTR) of mRNAs, are known to target transcripts for rapid decay. They are also involved in the regulation of mRNA stability and translation in response to extracellular cues. This review focuses on one of the best characterized ARE binding proteins, tristetraprolin (TTP), the founding member of a small family of CCCH tandem zinc finger proteins. In this survey, we have reviewed the current status of TTP interactions with mRNA and proteins, and discussed current thinking about TTP's mechanism of action to promote mRNA decay. We also review the proposed regulation of TTP's functions by phosphorylation. Finally, we have discussed emerging evidence for TTP operating as a translational regulator. This article is part of a Special Issue entitled: RNA Decay mechanisms.
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Affiliation(s)
- Seth A. Brooks
- Veterans Affairs Medical Center, White River Junction, Vermont, USA
- Department of Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
| | - Perry J. Blackshear
- The Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
- Departments of Medicine and Biochemistry, Duke University Medical Center, Durham, North Carolina USA
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Biancheri R, Cassandrini D, Pinto F, Trovato R, Di Rocco M, Mirabelli-Badenier M, Pedemonte M, Panicucci C, Trucks H, Sander T, Zara F, Rossi A, Striano P, Minetti C, Santorelli FM. EXOSC3 mutations in isolated cerebellar hypoplasia and spinal anterior horn involvement. J Neurol 2013; 260:1866-70. [DOI: 10.1007/s00415-013-6896-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 03/05/2013] [Accepted: 03/14/2013] [Indexed: 10/27/2022]
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Hsp27 and F-box protein β-TrCP promote degradation of mRNA decay factor AUF1. Mol Cell Biol 2013; 33:2315-26. [PMID: 23530064 DOI: 10.1128/mcb.00931-12] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Activation of the mitogen-activated protein (MAP) pathway kinases p38 and MK2 induces phosphorylation of the chaperone Hsp27 and stabilization of mRNAs containing AU-rich elements (AREs) (ARE-mRNAs). Likewise, expression of phosphomimetic mutant forms of Hsp27 also stabilizes ARE-mRNAs. It appears to perform this function by promoting degradation of the ARE-mRNA decay factor AUF1 by proteasomes. In this study, we examined the molecular mechanism linking Hsp27 phosphorylation to AUF1 degradation by proteasomes. AUF1 is a target of β-TrCP, the substrate recognition subunit of the E3 ubiquitin ligase Skp1-cullin-F-box protein complex, SCF(β-TrCP). Depletion of β-TrCP stabilized AUF1. In contrast, overexpression of β-TrCP enhanced ubiquitination and degradation of AUF1 and led to stabilization of reporter mRNAs containing cytokine AREs. Enhanced AUF1 degradation required expression of phosphomimetic mutant forms of both Hsp27 and AUF1. Our results suggest that a signaling axis composed of p38 MAP kinase-MK2-Hsp27-β-TrCP may promote AUF1 degradation by proteasomes and stabilization of cytokine ARE-mRNAs.
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Yang M, Zhang B, Jia J, Yan C, Habaike A, Han Y. RRP41L, a putative core subunit of the exosome, plays an important role in seed germination and early seedling growth in Arabidopsis. PLANT PHYSIOLOGY 2013; 161:165-78. [PMID: 23132787 PMCID: PMC3532249 DOI: 10.1104/pp.112.206706] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Accepted: 11/01/2012] [Indexed: 05/18/2023]
Abstract
In prokaryotic and eukaryotic cells, the 3'-5'-exonucleolytic decay and processing of RNAs are essential for RNA metabolism. However, the understanding of the mechanism of 3'-5'-exonucleolytic decay in plants is very limited. Here, we report the characterization of an Arabidopsis (Arabidopsis thaliana) transfer DNA insertional mutant that shows severe growth defects in early seedling growth, including delayed germination and cotyledon expansion, thinner yellow/pale-green leaves, and a slower growth rate. High-efficiency thermal asymmetric interlaced polymerase chain reaction analysis showed that the insertional locus was in the sixth exon of AT4G27490, encoding a predicted 3'-5'-exonuclease, that contained a conserved RNase phosphorolytic domain with high similarity to RRP41, designated RRP41L. Interestingly, we detected highly accumulated messenger RNAs (mRNAs) that encode seed storage protein and abscisic acid (ABA) biosynthesis and signaling pathway-related protein during the early growth stage in rrp41l mutants. The mRNA decay kinetics analysis for seed storage proteins, 9-cis-epoxycarotenoid dioxygenases, and ABA INSENSITIVEs revealed that RRP41L catalyzed the decay of these mRNAs in the cytoplasm. Consistent with these results, the rrp41l mutant was more sensitive to ABA in germination and root growth than wild-type plants, whereas overexpression lines of RRP41L were more resistant to ABA in germination and root growth than wild-type plants. RRP41L was localized to both the cytoplasm and nucleus, and RRP41L was preferentially expressed in seedlings. Altogether, our results showed that RRP41L plays an important role in seed germination and early seedling growth by mediating specific cytoplasmic mRNA decay in Arabidopsis.
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Abstract
Most RNAs in eukaryotic cells are produced as precursors that undergo processing at the 3' and/or 5' end to generate the mature transcript. In addition, many transcripts are degraded not only as part of normal recycling, but also when recognized as aberrant by the RNA surveillance machinery. The exosome, a conserved multiprotein complex containing two nucleases, is involved in both the 3' processing and the turnover of many RNAs in the cell. A series of factors, including the TRAMP (Trf4-Air2-Mtr4 polyadenylation) complex, Mpp6 and Rrp47, help to define the targets to be processed and/or degraded and assist in exosome function. The majority of the data on the exosome and RNA maturation/decay have been derived from work performed in the yeast Saccharomyces cerevisiae. In the present paper, we provide an overview of the exosome and its role in RNA processing/degradation and discuss important new insights into exosome composition and function in human cells.
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Abstract
UPF1 (up-frameshift 1) is a protein conserved in all eukaryotes that is necessary for NMD (nonsense-mediated mRNA decay). UPF1 mainly localizes to the cytoplasm and, via mechanisms that are linked to translation termination but not yet well understood, stimulates rapid destruction of mRNAs carrying a PTC (premature translation termination codon). However, some studies have indicated that in human cells UPF1 has additional roles, possibly unrelated to NMD, which are carried out in the nucleus. These might involve telomere maintenance, cell cycle progression and DNA replication. In the present paper, we review the available experimental evidence implicating UPF1 in nuclear functions. The unexpected view that emerges from this literature is that the nuclear functions primarily stem from UPF1 having an important role in DNA replication, rather than NMD affecting the expression of proteins involved in these processes. Our bioinformatics survey of the interaction network of UPF1 with other human proteins, however, highlights that UPF1 also interacts with proteins associated with nuclear RNA degradation and transcription termination; therefore suggesting involvement in processes that could also impinge on DNA replication indirectly.
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38
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Hayes SD, Liu H, MacDonald E, Sanderson CM, Coulson JM, Clague MJ, Urbé S. Direct and indirect control of mitogen-activated protein kinase pathway-associated components, BRAP/IMP E3 ubiquitin ligase and CRAF/RAF1 kinase, by the deubiquitylating enzyme USP15. J Biol Chem 2012; 287:43007-18. [PMID: 23105109 PMCID: PMC3522295 DOI: 10.1074/jbc.m112.386938] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The opposing regulators of ubiquitylation status, E3 ligases and deubiquitylases, are often found to be associated in complexes. Here we report on a novel interaction between the E3 ligase BRAP (also referred to as IMP), a negative regulator of the MAPK scaffold protein KSR, and two closely related deubiquitylases, USP15 and USP4. We map the interaction to the N-terminal DUSP-UBL domain of USP15 and the coiled coil region of BRAP. USP15 as well as USP4 oppose the autoubiquitylation of BRAP, whereas BRAP promotes the ubiquitylation of USP15. Importantly, USP15 but not USP4 depletion destabilizes BRAP by promoting its proteasomal degradation, and BRAP-protein levels can be rescued by reintroducing catalytically active but not inactive mutant USP15. Unexpectedly, USP15 depletion results in a decrease in amplitude of MAPK signaling in response to EGF and PDGF. We provide evidence for a model in which the dominant effect of prolonged USP15 depletion upon signal amplitude is due to a decrease in CRAF levels while allowing for the possibility that USP15 may also function to dampen MAPK signaling through direct stabilization of a negative regulator, the E3 ligase BRAP.
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Affiliation(s)
- Sebastian D Hayes
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Crown Street, Liverpool L69 3BX, United Kingdom
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Zhou J, Qiu L, Jiang S, Zhou F, Huang J, Yang L, Su T, Zhang D. Molecular cloning and mRNA expression of M-phase phosphoprotein 6 gene in black tiger shrimp (Penaeus monodon). Mol Biol Rep 2012; 40:1301-6. [PMID: 23065290 DOI: 10.1007/s11033-012-2173-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Accepted: 10/08/2012] [Indexed: 11/29/2022]
Abstract
It is widely accepted that protein phosphorylation is a major control event in regulating cell cycle. In the present study, a novel M-phase phosphoprotein 6 (MPP6) was identified from black tiger shrimp Penaeus monodon (designated as PmMPP6) by cDNA library and RACE approaches. The full-length cDNA of PmMPP6 was of 690 bp, including a 5'-terminal un-translated region (5'UTR) of 68 bp, a 3'UTR of 172 bp with a poly (A) tail, and an open reading frame (ORF) of 450 bp encoding a polypeptide of 149 amino acids with a predicted molecular weight of 17.01 kDa. Blastx and phylogenetic analysis together supported that PmMPP6 was a novel member of shrimp MPP6. The mRNA expression of PmMPP6 in thirteen tissues was examined by real-time PCR, and mRNA transcript of PmMPP6 was predominantly detectable in tissues of lymphoid and muscle, to a lesser degree in the tissues of gill, ovary and hepatopancreas, and mainly detected in haemocytes, heart and gonad. The temporal expression of PmMPP6 in different developmental stages of ovary was investigated by real-time PCR. During the six stages of ovary development, two peaks expression of PmMPP6 was detected in stage II with 3.78-fold increase and stage V with 3.48-fold increase compared to that in stage I. All these results indicated that PmMPP6 might be involved in regulating shrimp cell cycle and ovary development.
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Affiliation(s)
- Jun Zhou
- Biotechnology and Aquiculture Laboratory, The South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingangxi Road, Guangzhou, 510300, People's Republic of China
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40
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Diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system. Microbiol Mol Biol Rev 2012; 76:331-82. [PMID: 22688816 DOI: 10.1128/mmbr.05021-11] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The yeast two-hybrid system pioneered the field of in vivo protein-protein interaction methods and undisputedly gave rise to a palette of ingenious techniques that are constantly pushing further the limits of the original method. Sensitivity and selectivity have improved because of various technical tricks and experimental designs. Here we present an exhaustive overview of the genetic approaches available to study in vivo binary protein interactions, based on two-hybrid and protein fragment complementation assays. These methods have been engineered and employed successfully in microorganisms such as Saccharomyces cerevisiae and Escherichia coli, but also in higher eukaryotes. From single binary pairwise interactions to whole-genome interactome mapping, the self-reassembly concept has been employed widely. Innovative studies report the use of proteins such as ubiquitin, dihydrofolate reductase, and adenylate cyclase as reconstituted reporters. Protein fragment complementation assays have extended the possibilities in protein-protein interaction studies, with technologies that enable spatial and temporal analyses of protein complexes. In addition, one-hybrid and three-hybrid systems have broadened the types of interactions that can be studied and the findings that can be obtained. Applications of these technologies are discussed, together with the advantages and limitations of the available assays.
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41
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Abstract
The composition of the multisubunit eukaryotic RNA exosome was described more than a decade ago, and structural studies conducted since that time have contributed to our mechanistic understanding of factors that are required for 3'-to-5' RNA processing and decay. This chapter describes the organization of the eukaryotic RNA exosome with a focus on presenting results related to the noncatalytic nine-subunit exosome core as well as the hydrolytic exo- and endoribonuclease Rrp44 (Dis3) and the exoribonuclease Rrp6. This is achieved in large part by describing crystal structures of Rrp44, Rrp6, and the nine-subunit exosome core with an emphasis on how these molecules interact to endow the RNA exosome with its catalytic activities.
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Affiliation(s)
- Elizabeth V Wasmuth
- Structural Biology Program, Sloan-Kettering Institute, New York, USA; Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, USA
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42
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Abstract
Messenger RNAs transcribed by RNA polymerase II are modified at their 5'-end by the cotranscriptional addition of a 7-methylguanosine (m(7)G) cap. The cap is an important modulator of gene expression and the mechanism and components involved in its removal have been extensively studied. At least two decapping enzymes, Dcp2 and Nudt16, and an array of decapping regulatory proteins remove the m(7)G cap from an mRNA exposing the 5'-end to exonucleolytic decay. In contrast, relatively less is known about the decay of mRNAs that may be aberrantly capped. The recent demonstration that the Saccharomyces cerevisiae Rai1 protein selectively hydrolyzes aberrantly capped mRNAs provides new insights into the modulation of mRNA that lack a canonical m(7)G cap 5'-end. Whether an mRNA is uncapped or capped but missing the N7 methyl moiety, Rai1 hydrolyzes its 5'-end to generate an mRNA with a 5' monophosphate. Interestingly, Rai1 heterodimerizes with the Rat1 5'-3' exoribonuclease, which subsequently degrades the 5'-end monophosphorylated mRNA. Importantly, Rat1 stimulates the 5'-end hydrolysis activities of Rai1 to generate a 5'-end unprotected mRNA substrate for Rat1 and, in turn, Rai1 stimulates the activity of Rat1. The Rai1-Rat1 heterodimer functions as a molecular motor to detect and degrade mRNAs with aberrant caps and defines a novel quality control mechanism that ensures mRNA 5'-end integrity. The increase in aberrantly capped mRNA population following nutritional stress in S. cerevisiae demonstrates the presence of aberrantly capped mRNAs in cells and further reinforces the functional significance of the Rai1 in ensuring mRNA 5'-end integrity.
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Affiliation(s)
- Megerditch Kiledjian
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey, USA.
| | - Mi Zhou
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey, USA
| | - Xinfu Jiao
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey, USA
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43
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Hegele A, Kamburov A, Grossmann A, Sourlis C, Wowro S, Weimann M, Will CL, Pena V, Lührmann R, Stelzl U. Dynamic protein-protein interaction wiring of the human spliceosome. Mol Cell 2012; 45:567-80. [PMID: 22365833 DOI: 10.1016/j.molcel.2011.12.034] [Citation(s) in RCA: 293] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Revised: 11/01/2011] [Accepted: 12/12/2011] [Indexed: 12/12/2022]
Abstract
More than 200 proteins copurify with spliceosomes, the compositionally dynamic RNPs catalyzing pre-mRNA splicing. To better understand protein - protein interactions governing splicing, we systematically investigated interactions between human spliceosomal proteins. A comprehensive Y2H interaction matrix screen generated a protein interaction map comprising 632 interactions between 196 proteins. Among these, 242 interactions were found between spliceosomal core proteins and largely validated by coimmunoprecipitation. To reveal dynamic changes in protein interactions, we integrated spliceosomal complex purification information with our interaction data and performed link clustering. These data, together with interaction competition experiments, suggest that during step 1 of splicing, hPRP8 interactions with SF3b proteins are replaced by hSLU7, positioning this second step factor close to the active site, and that the DEAH-box helicases hPRP2 and hPRP16 cooperate through ordered interactions with GPKOW. Our data provide extensive information about the spliceosomal protein interaction network and its dynamics.
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Affiliation(s)
- Anna Hegele
- Otto-Warburg Laboratory, Max-Planck Institute for Molecular Genetics, 14195 Berlin, Germany
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44
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Koh GCKW, Porras P, Aranda B, Hermjakob H, Orchard SE. Analyzing protein-protein interaction networks. J Proteome Res 2012; 11:2014-31. [PMID: 22385417 DOI: 10.1021/pr201211w] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The advent of the "omics" era in biology research has brought new challenges and requires the development of novel strategies to answer previously intractable questions. Molecular interaction networks provide a framework to visualize cellular processes, but their complexity often makes their interpretation an overwhelming task. The inherently artificial nature of interaction detection methods and the incompleteness of currently available interaction maps call for a careful and well-informed utilization of this valuable data. In this tutorial, we aim to give an overview of the key aspects that any researcher needs to consider when working with molecular interaction data sets and we outline an example for interactome analysis. Using the molecular interaction database IntAct, the software platform Cytoscape, and its plugins BiNGO and clusterMaker, and taking as a starting point a list of proteins identified in a mass spectrometry-based proteomics experiment, we show how to build, visualize, and analyze a protein-protein interaction network.
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Affiliation(s)
- Gavin C K W Koh
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
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45
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Nag A, Steitz JA. Tri-snRNP-associated proteins interact with subunits of the TRAMP and nuclear exosome complexes, linking RNA decay and pre-mRNA splicing. RNA Biol 2012; 9:334-42. [PMID: 22336707 PMCID: PMC3384585 DOI: 10.4161/rna.19431] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Nuclear RNA decay factors are involved in many different pathways including rRNA processing, snRNA and snoRNA biogenesis, pre-mRNA processing, and the rapid decay of cryptic intergenic transcripts. In contrast to its yeast counterpart, the mammalian nuclear decay machinery is largely uncharacterized. Here we report interactions of several putative components of the human nuclear RNA decay machinery, including the TRAMP complex protein Mtr4 and the nuclear exosome constituents PM/Scl-100 and PM/Scl-75, with components of the U4/U6.U5 tri-snRNP complex required for pre-mRNA splicing. The tri-snRNP component Prp31 interacts indirectly with Mtr4 and PM/Scl-100 in a manner that is dependent on the phosphorylation sites in the middle of the protein, while Prp3 and Prp4 interact with the nuclear decay complex independent of Prp31. Together our results suggest recruitment of the nuclear decay machinery to the spliceosome to ensure production of properly spliced mRNA.
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Affiliation(s)
- Anita Nag
- Department of Molecular Biophysics and Biochemistry-MB&B, Howard Hughes Medical Institute-HHMI, Yale University School of Medicine, Boyer Center for Molecular Medicine, New Haven, CT, USA
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46
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Schaefer MH, Fontaine JF, Vinayagam A, Porras P, Wanker EE, Andrade-Navarro MA. HIPPIE: Integrating protein interaction networks with experiment based quality scores. PLoS One 2012; 7:e31826. [PMID: 22348130 PMCID: PMC3279424 DOI: 10.1371/journal.pone.0031826] [Citation(s) in RCA: 232] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Accepted: 01/12/2012] [Indexed: 01/03/2023] Open
Abstract
Protein function is often modulated by protein-protein interactions (PPIs) and therefore defining the partners of a protein helps to understand its activity. PPIs can be detected through different experimental approaches and are collected in several expert curated databases. These databases are used by researchers interested in examining detailed information on particular proteins. In many analyses the reliability of the characterization of the interactions becomes important and it might be necessary to select sets of PPIs of different confidence levels. To this goal, we generated HIPPIE (Human Integrated Protein-Protein Interaction rEference), a human PPI dataset with a normalized scoring scheme that integrates multiple experimental PPI datasets. HIPPIE's scoring scheme has been optimized by human experts and a computer algorithm to reflect the amount and quality of evidence for a given PPI and we show that these scores correlate to the quality of the experimental characterization. The HIPPIE web tool (available at http://cbdm.mdc-berlin.de/tools/hippie) allows researchers to do network analyses focused on likely true PPI sets by generating subnetworks around proteins of interest at a specified confidence level.
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Affiliation(s)
| | | | - Arunachalam Vinayagam
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Pablo Porras
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
- IntAct Scientific Curator, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
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47
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Miroci H, Schob C, Kindler S, Ölschläger-Schütt J, Fehr S, Jungenitz T, Schwarzacher SW, Bagni C, Mohr E. Makorin ring zinc finger protein 1 (MKRN1), a novel poly(A)-binding protein-interacting protein, stimulates translation in nerve cells. J Biol Chem 2011; 287:1322-34. [PMID: 22128154 DOI: 10.1074/jbc.m111.315291] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The poly(A)-binding protein (PABP), a key component of different ribonucleoprotein complexes, plays a crucial role in the control of mRNA translation rates, stability, and subcellular targeting. In this study we identify RING zinc finger protein Makorin 1 (MKRN1), a bona fide RNA-binding protein, as a binding partner of PABP that interacts with PABP in an RNA-independent manner. In rat brain, a so far uncharacterized short MKRN1 isoform, MKRN1-short, predominates and is detected in forebrain nerve cells. In neuronal dendrites, MKRN1-short co-localizes with PABP in granule-like structures, which are morphological correlates of sites of mRNA metabolism. Moreover, in primary rat neurons MKRN1-short associates with dendritically localized mRNAs. When tethered to a reporter mRNA, MKRN1-short significantly enhances reporter protein synthesis. Furthermore, after induction of synaptic plasticity via electrical stimulation of the perforant path in vivo, MKRN1-short specifically accumulates in the activated dendritic lamina, the middle molecular layer of the hippocampal dentate gyrus. Collectively, these data indicate that in mammalian neurons MKRN1-short interacts with PABP to locally control the translation of dendritic mRNAs at synapses.
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Affiliation(s)
- Hatmone Miroci
- Institute of Neuroanatomy, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
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48
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Giritharan G, Ilic D, Gormley M, Krtolica A. Human embryonic stem cells derived from embryos at different stages of development share similar transcription profiles. PLoS One 2011; 6:e26570. [PMID: 22039509 PMCID: PMC3198782 DOI: 10.1371/journal.pone.0026570] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 09/29/2011] [Indexed: 11/18/2022] Open
Abstract
We have derived hESC from biopsied blastomeres of cleavage stage embryos under virtually the same conditions we used for the derivation of hESC lines from inner cell mass of blastocyst stage embryos. Blastomere-derived hESC lines exhibited all the standard characteristics of hESC including undifferentiated proliferation, genomic stability, expression of pluripotency markers and the ability to differentiate into the cells of all three germ layers both in vitro and in vivo. To examine whether hESC lines derived from two developmental stages of the embryo differ in gene expression, we have subjected three blastomere-derived hESC lines and two ICM-derived hESC lines grown under identical culture conditions to transcriptome analysis using gene expression arrays. Unlike previously reported comparisons of hESC lines which demonstrated, apart from core hESC-associated pluripotency signature, significant variations in gene expression profiles of different lines, our data show that hESC lines derived and grown under well-controlled defined culture conditions adopt nearly identical gene expression profiles. Moreover, blastomere-derived and ICM-derived hESC exhibited very similar transcriptional profiles independent of the developmental stage of the embryo from which they originated. Furthermore, this profile was evident in very early passages of the cells and did not appear to be affected by extensive passaging. These results suggest that during derivation process cells which give rise to hESC acquire virtually identical stable phenotype and are not affected by the developmental stage of the starting cell population.
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Affiliation(s)
| | - Dusko Ilic
- SLL Sciences, StemLifeLine, Inc., San Carlos, California, United States of America
| | - Matthew Gormley
- University of California San Francisco, San Francisco, California, United States of America
| | - Ana Krtolica
- SLL Sciences, StemLifeLine, Inc., San Carlos, California, United States of America
- * E-mail:
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Ternette N, Wright C, Kramer HB, Altun M, Kessler BM. Label-free quantitative proteomics reveals regulation of interferon-induced protein with tetratricopeptide repeats 3 (IFIT3) and 5'-3'-exoribonuclease 2 (XRN2) during respiratory syncytial virus infection. Virol J 2011; 8:442. [PMID: 21933386 PMCID: PMC3190389 DOI: 10.1186/1743-422x-8-442] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2011] [Accepted: 09/20/2011] [Indexed: 01/06/2023] Open
Abstract
ABSTRACT: A large quantitative study was carried out to compare the proteome of respiratory syncytial virus (RSV) infected versus uninfected cells in order to determine novel pathways regulated during viral infection. RSV infected and mock-infected HEp2 cells were lysed and proteins separated by preparative isoelectric focussing using offgel fractionation. Following tryptic digestion, purified peptides were characterized using label-free quantitative expression profiling by nano-ultra performance liquid chromatography coupled to electrospray ionisation mass spectrometry with collision energy ramping for all-ion fragmentation (UPLC-MSE). A total of 1352 unique cellular proteins were identified and their abundance compared between infected and non-infected cells. Ingenuity pathway analysis revealed regulation of several central cellular metabolic and signalling pathways during infection. Selected proteins that were found regulated in RSV infected cells were screened by quantitative real-time PCR for their regulation on the transcriptional level. Synthesis of interferon-induced protein with tetratricopeptide repeats 3 (IFIT3) and 5'-3'-exoribonuclease 2 (XRN2) mRNAs were found to be highly induced upon RSV infection in a time dependent manner. Accordingly, IFIT3 protein levels accumulated during the time course of infection. In contrast, little variation was observed in XRN2 protein levels, but different forms were present in infected versus non-infected cells. This suggests a role of these proteins in viral infection, and analysis of their function will shed further light on mechanisms of RNA virus replication and the host cell defence machinery.
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Affiliation(s)
- Nicola Ternette
- Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK.
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Fiesel FC, Kahle PJ. TDP-43 and FUS/TLS: cellular functions and implications for neurodegeneration. FEBS J 2011; 278:3550-68. [PMID: 21777389 DOI: 10.1111/j.1742-4658.2011.08258.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
TDP-43 (transactive response binding protein of 43 kDa) and FUS (fused in sarcoma) comprise the neuropathological protein aggregates of distinct subtypes of the neurodegenerative diseases frontotemporal lobar degeneration and amyotrophic lateral sclerosis. Moreover, the genes encoding TDP-43 and FUS are linked to these diseases. Both TDP-43 and FUS contain RNA binding motifs, and specific targets are being identified. Potential actions of TDP-43 and FUS include transcriptional regulation, mRNA processing and micro RNA biogenesis. These activities are probably modulated by interacting proteins in cell type specific manners as well as distinctly within the nucleus and cytosol, as both proteins shuttle between these compartments. In this minireview the specific functions of TDP-43 and FUS are described and discussed in the context of how TDP-43 and FUS may contribute to the pathogenesis of frontotemporal lobar degeneration and amyotrophic lateral sclerosis.
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Affiliation(s)
- Fabienne C Fiesel
- Department of Neurodegeneration, Faculty of Medicine, University of Tuebingen, Tuebingen, Germany.
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