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Ma X, Guan L, Wu W, Zhang Y, Zheng W, Gao YT, Long J, Wu N, Wu L, Xiang Y, Xu B, Shen M, Chen Y, Wang Y, Yin Y, Li Y, Xu H, Xu X, Li Y. Whole-exome sequencing identifies OR2W3 mutation as a cause of autosomal dominant retinitis pigmentosa. Sci Rep 2015; 5:9236. [PMID: 25783483 PMCID: PMC4363838 DOI: 10.1038/srep09236] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 02/24/2015] [Indexed: 11/09/2022] Open
Abstract
Retinitis pigmentosa (RP), a heterogeneous group of inherited ocular diseases, is a genetic condition that causes retinal degeneration and eventual vision loss. Though some genes have been identified to be associated with RP, still a large part of the clinical cases could not be explained. Here we reported a four-generation Chinese family with RP, during which 6 from 9 members of the second generation affected the disease. To identify the genetic defect in this family, whole-exome sequencing together with validation analysis by Sanger sequencing were performed to find possible pathogenic mutations. After a pipeline of database filtering, including public databases and in-house databases, a novel missense mutation, c. 424 C > T transition (p.R142W) in OR2W3 gene, was identified as a potentially causative mutation for autosomal dominant RP. The mutation co-segregated with the disease phenotype over four generations. This mutation was validated in another independent three-generation family. RT-PCR analysis also identified that OR2W3 gene was expressed in HESC-RPE cell line. The results will not only enhance our current understanding of the genetic basis of RP, but also provide helpful clues for designing future studies to further investigate genetic factors for familial RP.
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Affiliation(s)
- Xiangyu Ma
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Liping Guan
- BGI-Shenzhen, Shenzhen, People's Republic of China
| | - Wei Wu
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University, Chongqing, People's Republic of China
| | - Yao Zhang
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai, People's Republic of China
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Na Wu
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Long Wu
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Ying Xiang
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Bin Xu
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | | | - Yanhua Chen
- BGI-Shenzhen, Shenzhen, People's Republic of China
| | - Yuewen Wang
- BGI-Shenzhen, Shenzhen, People's Republic of China
| | - Ye Yin
- BGI-Shenzhen, Shenzhen, People's Republic of China
| | - Yingrui Li
- 1] BGI-Shenzhen, Shenzhen, People's Republic of China [2] BGI-Tech, Shenzhen, People's Republic of China
| | - Haiwei Xu
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University, Chongqing, People's Republic of China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, People's Republic of China
| | - Yafei Li
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China
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Flegel C, Manteniotis S, Osthold S, Hatt H, Gisselmann G. Expression profile of ectopic olfactory receptors determined by deep sequencing. PLoS One 2013; 8:e55368. [PMID: 23405139 PMCID: PMC3566163 DOI: 10.1371/journal.pone.0055368] [Citation(s) in RCA: 195] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 12/21/2012] [Indexed: 02/03/2023] Open
Abstract
Olfactory receptors (ORs) provide the molecular basis for the detection of volatile odorant molecules by olfactory sensory neurons. The OR supergene family encodes G-protein coupled proteins that belong to the seven-transmembrane-domain receptor family. It was initially postulated that ORs are exclusively expressed in the olfactory epithelium. However, recent studies have demonstrated ectopic expression of some ORs in a variety of other tissues. In the present study, we conducted a comprehensive expression analysis of ORs using an extended panel of human tissues. This analysis made use of recent dramatic technical developments of the so-called Next Generation Sequencing (NGS) technique, which encouraged us to use open access data for the first comprehensive RNA-Seq expression analysis of ectopically expressed ORs in multiple human tissues. We analyzed mRNA-Seq data obtained by Illumina sequencing of 16 human tissues available from Illumina Body Map project 2.0 and from an additional study of OR expression in testis. At least some ORs were expressed in all the tissues analyzed. In several tissues, we could detect broadly expressed ORs such as OR2W3 and OR51E1. We also identified ORs that showed exclusive expression in one investigated tissue, such as OR4N4 in testis. For some ORs, the coding exon was found to be part of a transcript of upstream genes. In total, 111 of 400 OR genes were expressed with an FPKM (fragments per kilobase of exon per million fragments mapped) higher than 0.1 in at least one tissue. For several ORs, mRNA expression was verified by RT-PCR. Our results support the idea that ORs are broadly expressed in a variety of tissues and provide the basis for further functional studies.
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Affiliation(s)
- Caroline Flegel
- Department of Cell Physiology, Ruhr-University Bochum, Bochum, Germany
| | | | - Sandra Osthold
- Department of Cell Physiology, Ruhr-University Bochum, Bochum, Germany
| | - Hanns Hatt
- Department of Cell Physiology, Ruhr-University Bochum, Bochum, Germany
| | - Günter Gisselmann
- Department of Cell Physiology, Ruhr-University Bochum, Bochum, Germany
- * E-mail:
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Sakharov DA, Maltseva DV, Riabenko EA, Shkurnikov MU, Northoff H, Tonevitsky AG, Grigoriev AI. Passing the anaerobic threshold is associated with substantial changes in the gene expression profile in white blood cells. Eur J Appl Physiol 2011; 112:963-72. [PMID: 21717121 DOI: 10.1007/s00421-011-2048-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Accepted: 06/09/2011] [Indexed: 12/16/2022]
Abstract
High and moderate intensity endurance exercise alters gene expression in human white blood cells (WBCs), but the understanding of how this effect occurs is limited. To increase our knowledge of the nature of this process, we investigated the effects of passing the anaerobic threshold (AnT) on the gene expression profile in WBCs of athletes. Nineteen highly trained skiers participated in a treadmill test with an incremental step protocol until exhaustion (ramp test to exhaustion, RTE). The average total time to exhaustion was 14:40 min and time after AnT was 4:50 min. Two weeks later, seven of these skiers participated in a moderate treadmill test (MT) at 80% peak O(2) uptake for 30 min, which was slightly below their AnTs. Blood samples were obtained before and immediately after both tests. RTE was associated with substantially greater leukocytosis and acidosis than MT. Gene expression in WBCs was measured using whole genome microarray expression analysis before and immediately after each test. A total of 310 upregulated genes were found after RTE, and 69 genes after MT of which 64 were identical to RTE. Both tests influenced a variety of known gene pathways related to inflammation, stress response, signal transduction and apoptosis. A large group of differentially expressed previously unknown small nucleolar RNA and small Cajal body RNA was found. In conclusion, a 15-min test to exhaustion was associated with substantially greater changes of gene expression than a 30-min test just below the AnT.
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Affiliation(s)
- Dmitry A Sakharov
- Department of Molecular Physiology, Russian Research Institute of Physical Education and Sport, Elizavetinsky lane 10, Moscow, Russia.
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