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Zhang T, Xie P, Dong Y, Liu Z, Zhou F, Pan D, Huang Z, Zhai Q, Gu Y, Wu Q, Tanaka N, Obata Y, Bradley A, Lelliott CJ, Nutter LMJ, McKerlie C, Flenniken AM, Champy MF, Sorg T, Herault Y, Angelis MHD, Durner VG, Mallon AM, Brown SDM, Meehan T, Parkinson HE, Smedley D, Lloyd KCK, Yan J, Gao X, Seong JK, Wang CKL, Sedlacek R, Liu Y, Rozman J, Yang L, Xu Y. High-throughput discovery of genetic determinants of circadian misalignment. PLoS Genet 2020; 16:e1008577. [PMID: 31929527 PMCID: PMC6980734 DOI: 10.1371/journal.pgen.1008577] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 01/24/2020] [Accepted: 12/19/2019] [Indexed: 12/31/2022] Open
Abstract
Circadian systems provide a fitness advantage to organisms by allowing them to adapt to daily changes of environmental cues, such as light/dark cycles. The molecular mechanism underlying the circadian clock has been well characterized. However, how internal circadian clocks are entrained with regular daily light/dark cycles remains unclear. By collecting and analyzing indirect calorimetry (IC) data from more than 2000 wild-type mice available from the International Mouse Phenotyping Consortium (IMPC), we show that the onset time and peak phase of activity and food intake rhythms are reliable parameters for screening defects of circadian misalignment. We developed a machine learning algorithm to quantify these two parameters in our misalignment screen (SyncScreener) with existing datasets and used it to screen 750 mutant mouse lines from five IMPC phenotyping centres. Mutants of five genes (Slc7a11, Rhbdl1, Spop, Ctc1 and Oxtr) were found to be associated with altered patterns of activity or food intake. By further studying the Slc7a11tm1a/tm1a mice, we confirmed its advanced activity phase phenotype in response to a simulated jetlag and skeleton photoperiod stimuli. Disruption of Slc7a11 affected the intercellular communication in the suprachiasmatic nucleus, suggesting a defect in synchronization of clock neurons. Our study has established a systematic phenotype analysis approach that can be used to uncover the mechanism of circadian entrainment in mice. Synchronization to environmental changes such as day and night cycles and seasonal cycles is critical for survival. Organisms have therefore evolved a specialized circadian system to anticipate and adapt to daily changes in the environment. Loss of synchrony between the internal circadian clock and environment day and night changes is responsible for jet lag, but may also promote sleep disorders, metabolic disorders and many diseases. The availability of large amounts of mouse data from the International Mouse Phenotype Consortium provides new opportunities to identify novel genetic components of mouse behaviour and metabolism. In this study, we performed a high-throughput identification of genetic components of circadian misalignment by developing a machine learning-based algorithm. By analyzing the indirect calorimetry parameters from more than 2000 C57BL/6N mice and mice from 750 mutant lines, we identified 5 genes involved in circadian misalignment of activity and feeding behaviour. Further analyzing genetic knock-out mice for one of these genes, we were able to validate our screening method by functional studies. Our systemic analysis thus paves the way for searching the genetic determinants for circadian misalignment.
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Affiliation(s)
- Tao Zhang
- Cambridge-Suda Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases, Medical college of Soochow University, Suzhou, Jiangsu, China
| | - Pancheng Xie
- Cambridge-Suda Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases, Medical college of Soochow University, Suzhou, Jiangsu, China
| | - Yingying Dong
- Cambridge-Suda Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases, Medical college of Soochow University, Suzhou, Jiangsu, China
| | - Zhiwei Liu
- Cambridge-Suda Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases, Medical college of Soochow University, Suzhou, Jiangsu, China
| | - Fei Zhou
- Cambridge-Suda Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases, Medical college of Soochow University, Suzhou, Jiangsu, China
| | - Dejing Pan
- Cambridge-Suda Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases, Medical college of Soochow University, Suzhou, Jiangsu, China
| | - Zhengyun Huang
- Cambridge-Suda Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases, Medical college of Soochow University, Suzhou, Jiangsu, China
| | - Qiaocheng Zhai
- Cambridge-Suda Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases, Medical college of Soochow University, Suzhou, Jiangsu, China
| | - Yue Gu
- Cambridge-Suda Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases, Medical college of Soochow University, Suzhou, Jiangsu, China
| | - Qingyu Wu
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
- State Key Laboratory of Radiation Medicine and Prevention, Medical college of Soochow University, Suzhou, China
| | | | | | - Allan Bradley
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | | | | | | | | | | | | | - Tania Sorg
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), Illkirch, France
| | - Yann Herault
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), Illkirch, France
| | - Martin Hrabe De Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Valerie Gailus Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | - Ann-Marie Mallon
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, United Kingdom
| | - Steve D. M. Brown
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, United Kingdom
| | - Terry Meehan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Helen E. Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Damian Smedley
- School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - K. C. Kent Lloyd
- School of Medicine and Mouse Biology Program, University of California, Davis, California, United States of America
| | - Jun Yan
- SKL of Pharmaceutical Biotechnology and Model Animal Research Center, Collaborative Innovation Center for Genetics and Development, Nanjing Biomedical Research Institute, Nanjing University, Nanjing, China
| | - Xiang Gao
- SKL of Pharmaceutical Biotechnology and Model Animal Research Center, Collaborative Innovation Center for Genetics and Development, Nanjing Biomedical Research Institute, Nanjing University, Nanjing, China
| | - Je Kyung Seong
- College of Veterinary Medicine, Seoul National University, and Korea Mouse Phenotyping Center, Seoul, Republic of Korea
| | - Chi-Kuang Leo Wang
- National Laboratory Animal Center, National Applied Research Laboratories (NARLabs), Taipei, Taiwan
| | - Radislav Sedlacek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Yi Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Jan Rozman
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- * E-mail: (JR); (LY); (YX)
| | - Ling Yang
- Cambridge-Suda Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases, Medical college of Soochow University, Suzhou, Jiangsu, China
- * E-mail: (JR); (LY); (YX)
| | - Ying Xu
- Cambridge-Suda Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases, Medical college of Soochow University, Suzhou, Jiangsu, China
- State Key Laboratory of Radiation Medicine and Prevention, Medical college of Soochow University, Suzhou, China
- * E-mail: (JR); (LY); (YX)
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