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Li R, Zhou Q, Liu G, Zhu F, Liu Z, Bo H, Fan L. CSNK1G2-AS1 promotes metastasis, colony formation and serves as a biomarker in testicular germ cell tumor cells. J Cancer 2023; 14:2771-2783. [PMID: 37781070 PMCID: PMC10539554 DOI: 10.7150/jca.85640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/09/2023] [Indexed: 10/03/2023] Open
Abstract
Background/Aim: Some long non-coding RNAs (lncRNAs) have been found to significantly participate in the progression of TGCTs. In comparison to the normal testis, the TGCT tissues showed significantly decreased CSNK1G2-AS1 expression, however, its effect on TGCTs and its mechanism are still unclear. The aim of this study is to investigate the effect of CSNK1G2-AS1 on TGCTs and explore the mechanism underlying its effect on TGCTs. Materials and Methods: In this study, to evaluate the expression of CSNK1G2-AS1 in tissue samples from TGCTs, the UCSC and GEPIA databases were applied and qRT-PCR was conducted. The Kaplan-Meier Plotter was applied to analyze the correlation between CSNK1G2-AS1 methylation levels and the prognosis of TGCTs patients. The assays of MTS, clone formation, transwell, and flow cytometry were performed to investigate the effect of CSNK1G2-AS1 overexpression on the proliferation, metastasis, and apoptosis of TGCT cells, respectively. Finally, western blotting was conducted to determine the expressions of the proteins associated with EMT and AKT. Results: Our study first found that, compared to the normal testis, TGCTs tissue showed significantly decreased CSNK1G2-AS1 expression, and hypomethylation of CSNK1G2-AS1 was significantly correlated with a better prognosis with TGCTs patients. In vitro, we found that overexpression of CSNK1G2-AS1 dramatically promoted the clone formation, invasion, and migration of TGCT cells, but inhibited apoptosis. And CSNK1G2-AS1 overexpression significantly decreased the expression of EMT-associated proteins ZO-1 but increased the expression and phosphorylation of AKT. Conclusions: CSNK1G2-AS1 may play an essential role in the pathogenesis and metastasis of TGCTs through the EMT- and AKT-mediated signal pathways.
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Affiliation(s)
- Ruixue Li
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, 410078, People's Republic of China
| | - Qianyin Zhou
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, 410078, People's Republic of China
| | - Guangmin Liu
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, 410078, People's Republic of China
| | - Fang Zhu
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, 410078, People's Republic of China
| | - Zhizhong Liu
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, 410078, People's Republic of China
- Hunan Cancer Hospital, the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, People's Republic of China
| | - Hao Bo
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, 410078, People's Republic of China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410078, People's Republic of China
| | - Liqing Fan
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, 410078, People's Republic of China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410078, People's Republic of China
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Further insight into the global variability of the OCA2-HERC2 locus for human pigmentation from multiallelic markers. Sci Rep 2021; 11:22530. [PMID: 34795370 PMCID: PMC8602267 DOI: 10.1038/s41598-021-01940-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 11/02/2021] [Indexed: 11/20/2022] Open
Abstract
The OCA2-HERC2 locus is responsible for the greatest proportion of eye color variation in humans. Numerous studies extensively described both functional SNPs and associated patterns of variation over this region. The goal of our study is to examine how these haplotype structures and allelic associations vary when highly variable markers such as microsatellites are used. Eleven microsatellites spanning 357 Kb of OCA2-HERC2 genes are analyzed in 3029 individuals from worldwide populations. We found that several markers display large differences in allele frequency (10% to 35% difference) among Europeans, East Asians and Africans. In Europe, the alleles showing increased frequency can also discriminate individuals with (IrisPlex) predicted blue and brown eyes. Distinct haplotypes are identified around the variants C and T of the functional SNP rs12913832 (associated to blue eyes), with linkage disequilibrium r2 values significant up to 237 Kb. The haplotype carrying the allele rs12913832 C has high frequency (76%) in blue eye predicted individuals (30% in brown eye predicted individuals), while the haplotype associated to the allele rs12913832 T is restricted to brown eye predicted individuals. Finally, homozygosity values reach levels of 91% near rs12913832. Odds ratios show values of 4.2, 7.4 and 10.4 for four markers around rs12913832 and 7.1 for their core haplotype. Hence, this study provides an example on the informativeness of multiallelic markers that, despite their current limited potential contribution to forensic eye color prediction, supports the use of microsatellites for identifying causing variants showing similar genetic features and history.
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Xu Z, Chen Q, Zeng X, Li M, Liao J. lnc-NLC1-C inhibits migration, invasion and autophagy of glioma cells by targeting miR-383 and regulating PRDX-3 expression. Oncol Lett 2021; 22:640. [PMID: 34386062 PMCID: PMC8299021 DOI: 10.3892/ol.2021.12901] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 05/11/2021] [Indexed: 01/10/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) serve an important role in tumor progression, and their abnormal expression is associated with tumor development. The lncRNA narcolepsy candidate region 1 gene C (lnc-NLC1-C) is involved in numerous types of cancer, but its biological function in glioma remains unknown. In the present study, lnc-NLC1-C expression was detected using reverse transcription-quantitative (RT-q)PCR in U251, SHG44, U87MG and U118MG glioma cells. U87MG cells were transfected with lnc-NLC1-C overexpression or interference vectors. Cell proliferation was detected using a Cell Counting Kit-8 assay. Cell migration and invasion were examined using a Transwell assay, while apoptosis, cell cycle and reactive oxygen species production were evaluated using flow cytometry, and the expression levels of lnc-NLC1-C, microRNA (miR)-383 and peroxiredoxin 3 (PRDX-3) were measured using western blotting and RT-qPCR. Rescue experiments were performed to verify the function of the lnc-NLC1-C/miR-383/PRDX-3 axis. The highest expression levels of lnc-NLC1-C were identified in U87MG glioma cells. Overexpression of lnc-NLC1-C expression promoted cell proliferation, G1 phase blocking, migration and invasion, while inhibiting apoptosis and autophagy in U87MG cells. Mechanistically, miR-383 could bind to lnc-NLC1-C to regulate PRDX-3 expression and improve its oncogenic effect. Rescue experiments confirmed that the lnc-NLC1-C/miR-383/PRDX-3 axis was involved in the molecular mechanism of glioma progression. Therefore, lnc-NLC1-C may be a tumor promoter that affects multiple biological functions, such as migration, invasion and autophagy, in glioma cells.
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Affiliation(s)
- Zhou Xu
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Qianxue Chen
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Xingnuo Zeng
- Department of Nephrology and Rheumatology, The Central Hospital of Wuhan, Huazhong University of Science and Technology, Wuhan, Hubei 430014, P.R. China
| | - Mingchang Li
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Jianming Liao
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
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Bresesti C, Vezzoli V, Cangiano B, Bonomi M. Long Non-Coding RNAs: Role in Testicular Cancers. Front Oncol 2021; 11:605606. [PMID: 33767982 PMCID: PMC7986848 DOI: 10.3389/fonc.2021.605606] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 01/05/2021] [Indexed: 12/13/2022] Open
Abstract
In the last few years lncRNAs have gained increasing attention among the scientific community, thanks to the discovery of their implication in many physio-pathological processes. In particular, their contribution to tumor initiation, progression, and response to treatment has attracted the interest of experts in the oncologic field for their potential clinical application. Testicular cancer is one of the tumors in which lncRNAs role is emerging. Said malignancies already have very effective treatments, which although lead to the development of quite serious treatment-related conditions, such as secondary tumors, infertility, and cardiovascular diseases. It is therefore important to study the impact of lncRNAs in the tumorigenesis of testicular cancer in order to learn how to exploit them in a clinical setting and to substitute more toxic treatments. Eventually, the use of lncRNAs as biomarkers, drug targets, or therapeutics for testicular cancer may represent a valid alternative to that of conventional tools, leading to a better management of this malignancy and its related conditions, and possibly even to the treatment of poor prognosis cases.
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Affiliation(s)
- Chiara Bresesti
- Department of Endocrine and Metabolic Medicine, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Lab of Endocrine and Metabolic Researches, IRCCS Istituto Auxologico Italiano, Cusano Milanino, Italy
| | - Valeria Vezzoli
- Department of Endocrine and Metabolic Medicine, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Lab of Endocrine and Metabolic Researches, IRCCS Istituto Auxologico Italiano, Cusano Milanino, Italy
| | - Biagio Cangiano
- Department of Endocrine and Metabolic Medicine, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Lab of Endocrine and Metabolic Researches, IRCCS Istituto Auxologico Italiano, Cusano Milanino, Italy
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
| | - Marco Bonomi
- Department of Endocrine and Metabolic Medicine, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Lab of Endocrine and Metabolic Researches, IRCCS Istituto Auxologico Italiano, Cusano Milanino, Italy
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
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Obri A, Claret M. The role of epigenetics in hypothalamic energy balance control: implications for obesity. Cell Stress 2019; 3:208-220. [PMID: 31309172 PMCID: PMC6612891 DOI: 10.15698/cst2019.07.191] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Despite enormous social and scientific efforts, obesity rates continue to increase worldwide. While genetic factors contribute to obesity development, genetics alone cannot explain the current epidemic. Obesity is essentially the consequence of complex genetic-environmental interactions. Evidence suggests that contemporary lifestyles trigger epigenetic changes, which can dysregulate energy balance and thus contribute to obesity. The hypothalamus plays a pivotal role in the regulation of body weight, through a sophisticated network of neuronal systems. Alterations in the activity of these neuronal pathways have been implicated in the pathophysiology of obesity. Here, we review the current knowledge on the central control of energy balance with a focus on recent studies linking epigenetic mechanisms in the hypothalamus to the development of obesity and metabolic disorders.
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Affiliation(s)
- Arnaud Obri
- Neuronal Control of Metabolism Laboratory, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Marc Claret
- Neuronal Control of Metabolism Laboratory, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain.,Centro de Investigación Biomédica en Red (CIBER) de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), 08036 Barcelona, Spain
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Saito F, Kajii TS, Oka A, Ikuno K, Iida J. Genome-wide association study for mandibular prognathism using microsatellite and pooled DNA method. Am J Orthod Dentofacial Orthop 2017; 152:382-388. [PMID: 28863919 DOI: 10.1016/j.ajodo.2017.01.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 01/01/2017] [Accepted: 01/01/2017] [Indexed: 12/14/2022]
Abstract
INTRODUCTION The purpose of this study was to extend an association study from chromosome 1 to the whole genome (genome-wide association study) to find susceptibility loci of mandibular prognathism. METHODS Two hundred forty patients diagnosed with mandibular prognathism and 360 healthy controls of Japanese descent were recruited. The typing of microsatellites covering the whole genome was conducted using a pooled DNA method. Upon completion of the first and second screenings with pooled DNA, the positive microsatellite markers from both the first and second typings were retyped using individual-subject DNA samples to confirm the significance of allele frequency. RESULTS Six microsatellites (D1S0411i, D1S1358i, D3S0810i, D6S0827i, D7S0133i, and D15S0154i) showed differences between allele frequencies of the subjects and controls at P <0.001. D1S0411i, D1S1358i, D3S0810i, D6S0827i, D7S0133i, and D15S0154i were located on chromosomes 1p22.3, 1q32.2, 3q23, 6q23.2, 7q11.22, and 15q22.22, respectively. SSX2IP, PLXNA2, RASA2, TCF21, CALN1, and RORA were suggested as candidate genes. CONCLUSIONS The genome-wide association study using microsatellites suggested that 6 loci (1p22.3, 1q32.2, 3q23, 6q23.2, 7q11.22, and 15q22.22) were susceptibility regions of mandibular prognathism. The locus 1p22.3 was supported by a previous linkage analysis, and the other 5 were novel loci.
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Affiliation(s)
- Fumio Saito
- Department of Orthodontics, Division of Oral Functional Science, Graduate School of Dental Medicine, Hokkaido University, Sapporo, Japan
| | - Takashi S Kajii
- Section of Orthodontics, Department of Oral Growth and Development, Fukuoka Dental College, Fukuoka, Japan.
| | - Akira Oka
- Institute of Medical Science, Tokai University, Isehara, Japan
| | - Keiichiro Ikuno
- Department of Orthodontics, Division of Oral Functional Science, Graduate School of Dental Medicine, Hokkaido University, Sapporo, Japan
| | - Junichiro Iida
- Department of Orthodontics, Division of Oral Functional Science, Graduate School of Dental Medicine, Hokkaido University, Sapporo, Japan
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7
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Oberle D, Pavel J, Keller-Stanislawski B. Spontaneous reporting of suspected narcolepsy after vaccination against pandemic influenza A (H1N1) in Germany. Pharmacoepidemiol Drug Saf 2017; 26:1321-1327. [DOI: 10.1002/pds.4292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 07/17/2017] [Accepted: 07/19/2017] [Indexed: 12/24/2022]
Affiliation(s)
- Doris Oberle
- Department Safety of Medicinal Products and Medical Devices; Paul-Ehrlich-Institut, Federal Institute for Vaccines and Biomedicines; Langen Germany
| | - Jutta Pavel
- Department Safety of Medicinal Products and Medical Devices; Paul-Ehrlich-Institut, Federal Institute for Vaccines and Biomedicines; Langen Germany
| | - Brigitte Keller-Stanislawski
- Department Safety of Medicinal Products and Medical Devices; Paul-Ehrlich-Institut, Federal Institute for Vaccines and Biomedicines; Langen Germany
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8
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Oberle D, Pavel J, Mayer G, Geisler P, Keller-Stanislawski B. Retrospective multicenter matched case-control study on the risk factors for narcolepsy with special focus on vaccinations (including pandemic influenza vaccination) and infections in Germany. Sleep Med 2017; 34:71-83. [PMID: 28522102 DOI: 10.1016/j.sleep.2017.02.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 01/23/2017] [Accepted: 02/14/2017] [Indexed: 12/26/2022]
Abstract
OBJECTIVE Studies associate pandemic influenza vaccination with narcolepsy. In Germany, a retrospective, multicenter, matched case-control study was performed to identify risk factors for narcolepsy, particularly regarding vaccinations (seasonal and pandemic influenza vaccination) and infections (seasonal and pandemic influenza) and to quantify the detected risks. METHODS Patients with excessive daytime sleepiness who had been referred to a sleep center between April 2009 and December 2012 for multiple sleep latency test (MSLT) were eligible. Case report forms were validated according to the criteria for narcolepsy defined by the Brighton Collaboration (BC). Confirmed cases of narcolepsy (BC level of diagnostic certainty 1-4a) were matched with population-based controls by year of birth, gender, and place of residence. A second control group was established including patients in whom narcolepsy was definitely excluded (test-negative controls). RESULTS A total of 103 validated cases of narcolepsy were matched with 264 population-based controls. The second control group included 29 test-negative controls. A significantly increased odd ratio (OR) to develop narcolepsy (crude OR [cOR] = 3.9, 95% confidence interval [CI] = 1.8-8.5; adjusted OR [aOR] = 4.5, 95% CI = 2.0-9.9) was detected in individuals immunized with pandemic influenza A/H1N1/v vaccine prior to symptoms onset as compared to nonvaccinated individuals. Using test-negative controls, in individuals immunized with pandemic influenza A/H1N1/v vaccine prior to symptoms onset, a nonsignificantly increased OR of narcolepsy was detected when compared to nonvaccinated individuals (whole study population, BC levels 1-4a: cOR = 1.9, 95% CI = 0.5-6.9; aOR = 1.8, 95% CI = 0.3-10.1). CONCLUSIONS The findings of this study support an increased risk for narcolepsy after immunization with pandemic influenza A/H1N1/v vaccine.
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Affiliation(s)
- Doris Oberle
- Department Safety of Medicinal Products and Medical Devices, Paul-Ehrlich-Institut, Federal Institute for Vaccines and Biomedicines, Langen, Germany.
| | - Jutta Pavel
- Department Safety of Medicinal Products and Medical Devices, Paul-Ehrlich-Institut, Federal Institute for Vaccines and Biomedicines, Langen, Germany
| | - Geert Mayer
- Hephata-Klinik, Schlafzentrum, Schwalmstadt-Treysa, Germany
| | - Peter Geisler
- Sleep Disorders Center, Department of Psychiatry, University of Regensburg, Regensburg, Germany
| | - Brigitte Keller-Stanislawski
- Department Safety of Medicinal Products and Medical Devices, Paul-Ehrlich-Institut, Federal Institute for Vaccines and Biomedicines, Langen, Germany
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Jiang H, Good DJ. A molecular conundrum involving hypothalamic responses to and roles of long non-coding RNAs following food deprivation. Mol Cell Endocrinol 2016; 438:52-60. [PMID: 27555291 PMCID: PMC5116272 DOI: 10.1016/j.mce.2016.08.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 08/16/2016] [Accepted: 08/16/2016] [Indexed: 12/15/2022]
Abstract
Long non-coding RNAs (lncRNAs) are one of most poorly understood RNA classes in the mammalian transcriptome. However, they are emerging as important players in transcriptional regulation, especially within the complexity of the nervous system. This review summarizes the known information about lncRNAs, and their roles in endocrine processes, as well as the lesser-known information about lncRNAs in the brain, and in the neuroendocrine hypothalamus. A "call-to-action" is presented for researchers to use archival transcriptome data to characterize differentially expressed lncRNA species within the hypothalamus. In accordance, we analyze for differential-expression of lncRNA between normal mice and mice with a targeted deletion of the nescient helix-loop-helix 2 gene, and between C57Bl/6 and 129Sv/J mice. Finally, strategies and approaches for researchers to analyze their own datasets or those on the NCBI GEO datasets repository are provided, in hopes that future studies will reveal many new roles for lncRNAs in hypothalamic physiological responses, solving this so-called "molecular conundrum" once and for all.
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Affiliation(s)
- Hao Jiang
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Deborah J Good
- Department of Human Nutrition, Foods, and Exercise, Virginia Tech, Blacksburg, VA, 24061, USA.
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Piipponen M, Nissinen L, Farshchian M, Riihilä P, Kivisaari A, Kallajoki M, Peltonen J, Peltonen S, Kähäri VM. Long Noncoding RNA PICSAR Promotes Growth of Cutaneous Squamous Cell Carcinoma by Regulating ERK1/2 Activity. J Invest Dermatol 2016; 136:1701-1710. [DOI: 10.1016/j.jid.2016.03.028] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 02/26/2016] [Accepted: 03/10/2016] [Indexed: 01/08/2023]
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Lü M, Tian H, Cao YX, He X, Chen L, Song X, Ping P, Huang H, Sun F. Downregulation of miR-320a/383-sponge-like long non-coding RNA NLC1-C (narcolepsy candidate-region 1 genes) is associated with male infertility and promotes testicular embryonal carcinoma cell proliferation. Cell Death Dis 2015; 6:e1960. [PMID: 26539909 PMCID: PMC4670917 DOI: 10.1038/cddis.2015.267] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 08/21/2015] [Accepted: 08/25/2015] [Indexed: 01/09/2023]
Abstract
Long non-coding RNAs (lncRNAs), which are extensively transcribed from the genome, have been proposed to be key regulators of diverse biological processes. However, little is known about the role of lncRNAs in regulating spermatogenesis in human males. Here, using microarray technology, we show altered expression of lncRNAs in the testes of infertile men with maturation arrest (MA) or hypospermatogenesis (Hypo), with 757 and 2370 differentially down-regulated and 475 and 163 up-regulated lncRNAs in MA and Hypo, respectively. These findings were confirmed by quantitative real-time PCR (qRT-PCR) assays on select lncRNAs, including HOTTIP, imsrna320, imsrna292 and NLC1-C (narcolepsy candidate-region 1 genes). Interestingly, NLC1-C, also known as long intergenic non-protein-coding RNA162 (LINC00162), was down-regulated in the cytoplasm and accumulated in the nucleus of spermatogonia and primary spermatocytes in the testes of infertile men with mixed patterns of MA compared with normal control. The accumulation of NLC1-C in the nucleus repressed miR-320a and miR-383 transcript and promoted testicular embryonal carcinoma cell proliferation by binding to Nucleolin. Here, we define a novel mechanism by which lncRNAs modulate miRNA expression at the transcriptional level by binding to RNA-binding proteins to regulate human spermatogenesis.
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MESH Headings
- Adult
- Carcinoma, Embryonal/genetics
- Carcinoma, Embryonal/metabolism
- Carcinoma, Embryonal/pathology
- Case-Control Studies
- Cell Proliferation/genetics
- Down-Regulation
- Embryonal Carcinoma Stem Cells/metabolism
- Embryonal Carcinoma Stem Cells/physiology
- Humans
- Infertility, Male/genetics
- Infertility, Male/metabolism
- Infertility, Male/pathology
- Male
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Middle Aged
- Neoplasms, Germ Cell and Embryonal/genetics
- Neoplasms, Germ Cell and Embryonal/metabolism
- Neoplasms, Germ Cell and Embryonal/pathology
- Phosphoproteins/metabolism
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA-Binding Proteins/metabolism
- Testicular Neoplasms/genetics
- Testicular Neoplasms/metabolism
- Testicular Neoplasms/pathology
- Young Adult
- Nucleolin
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Affiliation(s)
- M Lü
- International Peace Maternity & Child Health Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
- Reproduction Medical Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Shanghai Key Laboratory for Reproductive Medicine, Shanghai, China
| | - H Tian
- International Peace Maternity & Child Health Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Y-x Cao
- Reproduction Medical Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - X He
- Reproduction Medical Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - L Chen
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - X Song
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - P Ping
- Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - H Huang
- International Peace Maternity & Child Health Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
- Shanghai Key Laboratory for Reproductive Medicine, Shanghai, China
| | - F Sun
- International Peace Maternity & Child Health Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
- Shanghai Key Laboratory for Reproductive Medicine, Shanghai, China
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Joshi PA, Poduri A, Kothare SV. Juvenile myoclonic epilepsy and narcolepsy: A series of three cases. Epilepsy Behav 2015; 51:163-5. [PMID: 26283305 DOI: 10.1016/j.yebeh.2015.07.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Revised: 07/20/2015] [Accepted: 07/22/2015] [Indexed: 10/23/2022]
Abstract
OBJECTIVE This paper sets out to demonstrate the coexistence of juvenile myoclonic epilepsy (JME) and narcolepsy that raises the possibility of a shared genetic predisposition to both conditions. METHODS The electronic medical records (EMRs) were searched for narcolepsy and JME over 10years. RESULTS We identified three young adult women diagnosed with JME in their teenage years, with myoclonic, generalized tonic-clonic, and absence seizure semiologies, along with psychiatric comorbidity, well managed on lamotrigine and/or levetiracetam. Our patients were also found to have disturbed sleep preceding the diagnosis of JME by many years, including excessive daytime sleepiness (EDS), fragmented nocturnal sleep, hypnagogic vivid hallucinations, and REM behavior disorder along with daytime cataplexy. They were ultimately diagnosed with coexisting narcolepsy, confirmed by sleep studies and multiple sleep latency testing, along with positive genetic testing for HLA-DQB1*0602 in all three patients. Stimulants, selective serotonin receptor inhibitors, and/or sodium oxybate were used to successfully treat their narcolepsy. SIGNIFICANCE The coexistence of JME and narcolepsy has not been well recognized and may be clinically relevant. In addition, it raises the possibility of a shared genetic predisposition to both conditions.
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Affiliation(s)
- Puja Aggarwal Joshi
- Department of Neurology, New York University Langone School of Medicine, New York, NY 10016, USA
| | - Annapurna Poduri
- Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Children's Hospital Boston and Harvard Medical School, Boston, MA 02115, USA
| | - Sanjeev V Kothare
- Comprehensive Epilepsy Center, Department of Neurology, New York University Langone Medical Center, New York, NY 10016, USA.
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Saka S, Hirawa N, Oka A, Yatsu K, Hirukawa T, Yamamoto R, Matsusaka T, Imai E, Narita I, Endoh M, Ichikawa I, Umemura S, Inoko H. Genome-wide association study of IgA nephropathy using 23 465 microsatellite markers in a Japanese population. J Hum Genet 2015. [PMID: 26202575 DOI: 10.1038/jhg.2015.88] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Immunoglobulin A nephropathy (IgAN) is the most common form of primary glomerulonephritis in many parts of the world. Although previous genome-wide association studies (GWAS) identified the major susceptibility loci for IgAN, the causal genes currently remain unknown. We performed a GWAS using 23 465 microsatellite (MS) markers to identify genes related to IgAN in a Japanese population. A pooled sample analysis was conducted in three-stage screenings of three independent case-control populations, and after the final step of individual typing, 11 markers survived. Of these, we focused on two regions on 6p21 and 12q21 because they (i) showed the strongest relationship with IgAN, and (ii) appeared to be highly relevant to IgAN in view of several previous studies. These regions contained the HLA, TSPAN8 and PTPRR genes. This study on GWAS, using >20 000 MS markers, provides a new approach regarding susceptible genes for IgAN for investigators seeking new tools for the prevention and treatment of IgAN.
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Affiliation(s)
- Sanae Saka
- Department of Medical Science and Cardiorenal Medicine, Yokohama City University, Graduate School of Medicine, Yokohama, Japan.,Department of Nephrology and Hypertension, Yokohama City University Medical Center, Yokohama, Japan
| | - Nobuhito Hirawa
- Department of Nephrology and Hypertension, Yokohama City University Medical Center, Yokohama, Japan
| | - Akira Oka
- The Institute of Medical Science, Tokai University, Isehara, Japan
| | - Keisuke Yatsu
- Department of Medical Science and Cardiorenal Medicine, Yokohama City University, Graduate School of Medicine, Yokohama, Japan
| | - Takeshi Hirukawa
- Division of Nephrology, Endocrinology and Metabolism, Department of Internal Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Ryohei Yamamoto
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Taiji Matsusaka
- Division of Nephrology, Endocrinology and Metabolism, Department of Internal Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Enyu Imai
- Nakayamadera Imai Clinic, Takarazuka, Japan.,Department of Nephrology, Fujita Health University, Toyoake, Japan
| | - Ichiei Narita
- Division of Clinical Nephrology and Rheumatology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Masayuki Endoh
- Division of Nephrology, Endocrinology and Metabolism, Department of Internal Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Iekuni Ichikawa
- Department of Ethics, Shinshu Univeristy, Nagano, Japan.,Departments of Pediatrics and Medicine, Vanderbilt University, Nashville, TN, USA
| | - Satoshi Umemura
- Department of Medical Science and Cardiorenal Medicine, Yokohama City University, Graduate School of Medicine, Yokohama, Japan
| | - Hidetoshi Inoko
- The Institute of Medical Science, Tokai University, Isehara, Japan
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Ikuno K, Kajii TS, Oka A, Inoko H, Ishikawa H, Iida J. Microsatellite genome-wide association study for mandibular prognathism. Am J Orthod Dentofacial Orthop 2014; 145:757-62. [PMID: 24880846 DOI: 10.1016/j.ajodo.2014.01.022] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 01/01/2014] [Accepted: 01/01/2014] [Indexed: 11/29/2022]
Abstract
INTRODUCTION Attempts have been made to identify susceptibility genes of mandibular prognathism by genome-wide linkage studies, but the results of susceptibility loci are inconsistent. There has been no genome-wide association study of mandibular prognathism. Our objective was to perform a genome-wide association study using 23,465 microsatellite markers to detect mandibular prognathism susceptibility regions. METHODS The study was based on the pooled DNA method, including 2 steps of screening on the whole genome and subsequent individual genotyping, with 240 experimental subjects and 360 control subjects from the Japanese population. RESULTS Two suggestive associations on chromosomes 1q32.2 (D1S1358i: P = 4.22 × 10(-4)) and 1p22.3 (D1S0411i: P = 6.66 × 10(-4)) were shown, and PLXNA2 and SSX2IP were suggested to be candidate genes; 1p22.3 flanked the region indicated by previous linkage analysis. CONCLUSIONS The results of the genome-wide association study showed that 2 loci (1q32.2 and 1p22.3) are likely to be susceptibility regions of mandibular prognathism: 1p32.2 is a novel locus, and identification of 1p22.3 supports the results of previous linkage analysis.
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Affiliation(s)
- Keiichiro Ikuno
- Postgraduate student, Division of Oral Functional Science, Department of Orthodontics, Graduate School of Dental Medicine, Hokkaido University, Hokkaido, Japan
| | - Takashi S Kajii
- Associate professor, Section of Orthodontics, Department of Oral Growth and Development, Fukuoka Dental College, Fukuoka, Japan.
| | - Akira Oka
- Lecturer, Institute of Medical Science, Tokai University, Kanagawa, Japan
| | - Hidetoshi Inoko
- Professor, Division of Basic Medical Science and Molecular Medicine, Department of Molecular Life Sciences, School of Medicine, Tokai University, Kanagawa, Japan
| | - Hiroyuki Ishikawa
- Professor, Section of Orthodontics, Department of Oral Growth and Development, Fukuoka Dental College, Fukuoka, Japan
| | - Junichiro Iida
- Professor, Division of Oral Functional Science, Department of Orthodontics, Graduate School of Dental Medicine, Hokkaido University, Hokkaido, Japan
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Hirukawa T, Wu Q, Sawada K, Matsusaka T, Saka S, Oka A, Hirawa N, Umemura S, Kakuta T, Endoh M, Inoko H, Ichikawa I, Fukagawa M. Kidney Diseases Enhance Expression of Tetraspanin-8: A Possible Protective Effect against Tubular Injury. NEPHRON EXTRA 2014; 4:70-81. [PMID: 24926311 PMCID: PMC4036207 DOI: 10.1159/000362451] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Background/Aims TSPAN8 encoding tetraspanin-8 was identified as a candidate gene for immunoglobulin A nephropathy (IgAN) by a genome-wide association study using microsatellites in the Japanese population. Tetraspanin-8 is a cell surface protein that contributes to the migration and invasion of epithelial cells. Methods We performed immunohistochemistry for tetraspanin-8 on human renal biopsy specimens associated with IgAN, antineutrophil cytoplasmic antibody-associated nephropathy and interstitial nephritis, as well as normal renal tissue. Furthermore, to study the potential function of tetraspanin-8, we performed cell migration and invasion assays using human renal tubule cells transfected with tetraspanin-8. Results Tetraspanin-8 was often expressed in vascular smooth muscle cells and occasionally in tubule cells in normal kidney. In the kidneys of all types of nephropathy, tetraspanin-8 staining in the arteries was unaffected, but that in the tubules was enhanced. The degree of tubular staining negatively correlated with the estimated glomerular filtration rate, independently of the type of nephropathy. Tetraspanin-8-expressing tubule cells were found predominantly in distal and collecting tubules, identified by cytokeratin 7 or aquaporin 2 staining. In vitro studies using cultured tubule cells revealed that tetraspanin-8 promoted migration by 2.7-fold without laminin, by 2.8-fold with laminin and invasion into Matrigel by 3.5-fold, suggesting that enhanced tetraspanin-8 may be involved in the repair of tubules. Conclusion The obtained findings indicate that tetraspanin-8 expression is enhanced in injured distal tubules, which may be involved in the repair of tubules by facilitating migration and invasion.
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Affiliation(s)
- Takashi Hirukawa
- Division of Nephrology, Endocrinology and Metabolism, Department of Internal Medicine, Yokohama, Japan
| | - Qiong Wu
- Division of Nephrology, Endocrinology and Metabolism, Department of Internal Medicine, Yokohama, Japan
| | - Kaichiro Sawada
- Division of Nephrology, Endocrinology and Metabolism, Department of Internal Medicine, Yokohama, Japan
| | - Taiji Matsusaka
- Division of Nephrology, Endocrinology and Metabolism, Department of Internal Medicine, Yokohama, Japan
| | - Sanae Saka
- Department of Medical Science and Cardiorenal Medicine, Yokohama City University, Graduate School of Medicine, Yokohama, Japan
| | - Akira Oka
- Department of Molecular Life Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Yokohama, Japan
| | - Nobuhito Hirawa
- Department of Medical Science and Cardiorenal Medicine, Yokohama City University, Graduate School of Medicine, Yokohama, Japan
| | - Satoshi Umemura
- Department of Medical Science and Cardiorenal Medicine, Yokohama City University, Graduate School of Medicine, Yokohama, Japan
| | - Takatoshi Kakuta
- Division of Nephrology, Endocrinology and Metabolism, Department of Internal Medicine, Yokohama, Japan
| | - Masayuki Endoh
- Division of Nephrology, Endocrinology and Metabolism, Department of Internal Medicine, Yokohama, Japan
| | - Hidetoshi Inoko
- Department of Molecular Life Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Yokohama, Japan
| | - Iekuni Ichikawa
- Division of Pediatric Nephrology, Vanderbilt University School of Medicine, Nashville, Tenn., USA
| | - Masafumi Fukagawa
- Division of Nephrology, Endocrinology and Metabolism, Department of Internal Medicine, Yokohama, Japan
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16
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Genome-wide association study of schizophrenia using microsatellite markers in the Japanese population. Psychiatr Genet 2013; 23:117-23. [PMID: 23474461 DOI: 10.1097/ypg.0b013e32835fe4f1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
OBJECTIVES To search for schizophrenia susceptibility loci, we carried out a case-control study using 28601 microsatellite markers distributed across the entire genome. MATERIALS AND METHODS To control the highly multiple testing, we designed three sequential steps of screening using three independent sets of pooled samples, followed by the confirmatory step using an independent sample set (>2200 case-control pairs). RESULTS The first screening using pooled samples of 157 case-control pairs showed 2966 markers to be significantly associated with the disorder (P<0.05). After the second and the third screening steps using pooled samples of 150 pairs each, 374 markers remained significantly associated with the disorder. We individually genotyped all screening samples using a total of 1536 tag single nucleotide polymorphisms (SNPs) located in the vicinity of ~200 kb from the 59 positive microsatellite markers. Of the 167 SNPs that replicated the significance, we selected 31 SNPs on the basis of the levels of P values for the confirmatory association test using an independent-sample set. The best association signal was observed in rs13404754, located in the upstream region of SLC23A3. We genotyped six additional SNPs in the vicinity of rs13404754. Significant associations were observed in rs13404754, rs6436122, and rs1043160 in the cumulative samples (2617 cases and 2698 controls) (P=0.005, 0.035, and 0.011, respectively). These SNPs are located in the linkage disequilibrium block of 20 kb in size containing SLC23A3, CNPPD1, and FAM134A genes. CONCLUSION Genome-wide association study using microsatellite markers suggested SLC23A3, CNPPD1, and FAM134A genes as candidates for schizophrenia susceptibility in the Japanese population.
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Harkensee C, Oka A, Onizuka M, Middleton PG, Inoko H, Nakaoka H, Gennery AR, Ando K, Morishima Y. Microsatellite scanning of the immunogenome associates MAPK14 and ELTD1 with graft-versus-host disease in hematopoietic stem cell transplantation. Immunogenetics 2013; 65:417-27. [PMID: 23474535 DOI: 10.1007/s00251-013-0691-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2012] [Accepted: 02/16/2013] [Indexed: 12/16/2022]
Abstract
Graft-versus-host disease (GVHD) is the main complication after hematopoietic stem cell transplantation (HSCT). Evidence for non-HLA gene polymorphisms as a cause of GVHD lacks consistency, which is, in part, due to methodological issues of previous candidate gene association studies and small effect size of their results, demanding for larger scale and more robust approaches. Here, non-HLA gene polymorphisms were studied on a large population (922 HSCT pairs) from a homogeneous ethnic background with selection/correction for important clinical confounders. A methodology was applied exploiting the strength of confirmatory typing in an independent study cohort. Targeting an immunogenome of 2,909 genes, an approach of pooled DNA typing of 4,321 microsatellite (MS) markers in two independent screening steps and confirmation of associated markers by further individual genotyping on combined screening cohorts was used to identify genetic susceptibility loci for moderate to severe GVHD (grades 2-4). Ten MS loci (D5S424, D6S0035i, D1S0818i, DXS0151i, D17S0219i, DXS0629i, DXS0324i, D17S0271i, D6S0330i, and D1S1335i) passed the two pooled DNA typing steps and confirmation by individual sample genotyping; two of these (D1S0818i-ELTD1 and D6S0035i-MAPK14) remain associated following application of Bonferroni's correction and multivariate analysis. The MAPK14 locus was exemplarily explored by typing of haplotype single nucleotide polymorphisms (SNP) confirming this association. This study identified several new MS susceptibility loci for GVHD that warrant further investigation. Immunogenome scanning using MS markers is a useful method for the identification of non-HLA gene loci associating with HSCT outcomes.
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Affiliation(s)
- Christian Harkensee
- Division of Molecular Life Sciences, Tokai University School of Medicine, Isehara, Kanagawa, Japan.
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18
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Fall-Kontroll-Studie zu Risikofaktoren von Narkolepsie in Deutschland. SOMNOLOGIE 2013. [DOI: 10.1007/s11818-013-0604-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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19
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Meguro A, Ideta H, Ota M, Ito N, Ideta R, Yonemoto J, Takeuchi M, Uemoto R, Nishide T, Iijima Y, Kawagoe T, Okada E, Shiota T, Hagihara Y, Oka A, Inoko H, Mizuki N. Common variants in the COL4A4 gene confer susceptibility to lattice degeneration of the retina. PLoS One 2012; 7:e39300. [PMID: 22723992 PMCID: PMC3378527 DOI: 10.1371/journal.pone.0039300] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Accepted: 05/17/2012] [Indexed: 11/18/2022] Open
Abstract
Lattice degeneration of the retina is a vitreoretinal disorder characterized by a visible fundus lesion predisposing the patient to retinal tears and detachment. The etiology of this degeneration is still uncertain, but it is likely that both genetic and environmental factors play important roles in its development. To identify genetic susceptibility regions for lattice degeneration of the retina, we performed a genome-wide association study (GWAS) using a dense panel of 23,465 microsatellite markers covering the entire human genome. This GWAS in a Japanese cohort (294 patients with lattice degeneration and 294 controls) led to the identification of one microsatellite locus, D2S0276i, in the collagen type IV alpha 4 (COL4A4) gene on chromosome 2q36.3. To validate the significance of this observation, we evaluated the D2S0276i region in the GWAS cohort and in an independent Japanese cohort (280 patients and 314 controls) using D2S0276i and 47 single nucleotide polymorphisms covering the region. The strong associations were observed in D2S0276i and rs7558081 in the COL4A4 gene (Pc = 5.8 × 10(-6), OR = 0.63 and Pc = 1.0 × 10(-5), OR = 0.69 in a total of 574 patients and 608 controls, respectively). Our findings suggest that variants in the COL4A4 gene may contribute to the development of lattice degeneration of the retina.
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Affiliation(s)
- Akira Meguro
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | | | - Masao Ota
- Department of Legal Medicine, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Norihiko Ito
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | | | - Junichi Yonemoto
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Masaki Takeuchi
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Riyo Uemoto
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Tadayuki Nishide
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Yasuhito Iijima
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Tatsukata Kawagoe
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | | | - Tomoko Shiota
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Yuta Hagihara
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Akira Oka
- Division of Molecular Life Science, Department of Genetic Information, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Hidetoshi Inoko
- Division of Molecular Life Science, Department of Genetic Information, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Nobuhisa Mizuki
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
- * E-mail:
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Wickboldt AT, Bowen AF, Kaye AJ, Kaye AM, Rivera Bueno F, Kaye AD. Sleep physiology, abnormal States, and therapeutic interventions. Ochsner J 2012; 12:122-34. [PMID: 22778676 PMCID: PMC3387837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023] Open
Abstract
Sleep is essential. Unfortunately, a significant portion of the population experiences altered sleep states that often result in a multitude of health-related issues. The regulation of sleep and sleep-wake cycles is an area of intense research, and many options for treatment are available. The following review summarizes the current understanding of normal and abnormal sleep-related conditions and the available treatment options. All clinicians managing patients must recommend appropriate therapeutic interventions for abnormal sleep states. Clinicians' solid understanding of sleep physiology, abnormal sleep states, and treatments will greatly benefit patients regardless of their disease process.
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Affiliation(s)
| | - Alex F. Bowen
- Louisiana State University School of Medicine, New Orleans, LA
| | - Aaron J. Kaye
- Louisiana State University School of Medicine, New Orleans, LA
- Stanford University, Palo Alto, CA
| | - Adam M. Kaye
- Thomas J. Long School of Pharmacy and Health Sciences, University of the Pacific, Stockton, CA
| | - Franklin Rivera Bueno
- Louisiana State University School of Medicine, New Orleans, LA
- Department of Pharmacology, Tulane School of Medicine, New Orleans, LA
| | - Alan D. Kaye
- Departments of Anesthesiology and Pharmacology, Louisiana State University Health Sciences Center, New Orleans, LA
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Bernardini C, Lattanzi W, Bosco P, Franceschini C, Plazzi G, Michetti F, Ferri R. Genome-wide gene expression profiling of human narcolepsy. Gene Expr 2012; 15:171-81. [PMID: 22783726 PMCID: PMC6043843 DOI: 10.3727/105221612x13372578119652] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The objective of this study was to perform global gene expression profiling of patients affected by narcolepsy with cataplexy (NRLCP). This enabled identifying new potential biomarkers and relevant molecules possibly involved in the disease pathogenesis. In this study 10 NRLCP patients and 10 healthy controls were compared. Total RNA isolated from blood specimens was analyzed using microarray technology followed by statistical data analysis to detect genome-wide differential gene expression between patients and controls. Functional analysis of the gene list was performed in order to interpret the biological significance of the data. One hundred and seventy-three genes showed significant (p < 0.01) differential expression between the two tested conditions. The biological interpretation allowed categorizing differentially expressed genes involved in neurite outgrowth/extension and brain development, which could be possibly regarded as peripheral markers of the disease. Moreover, the NRLCP-related gene expression profiles indicated a dysregulation of metabolic and immune-related mechanisms. In conclusion, the gene expression profile associated to NRLCP suggested that molecular markers of neurological impairment, dysmetabolic and immune-related mechanisms, can be detected in blood of NRLCP patients.
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Affiliation(s)
- Camilla Bernardini
- Institute of Anatomy and Cell Biology, Catholic University, Rome, Italy.
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Hiruma A, Ikeda S, Terui T, Ozawa M, Hashimoto T, Yasumoto S, Nakayama J, Kubota Y, Iijima M, Sueki H, Matsumoto Y, Kato M, Akasaka E, Ikoma N, Mabuchi T, Tamiya S, Matsuyama T, Ozawa A, Inoko H, Oka A. A novel splicing variant of CADM2 as a protective transcript of psoriasis. Biochem Biophys Res Commun 2011; 412:626-32. [DOI: 10.1016/j.bbrc.2011.08.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Accepted: 08/04/2011] [Indexed: 01/14/2023]
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Tiercy JM. Immunogenetics of hematopoietic stem cell transplantation: the contribution of microsatellite polymorphism studies. Int J Immunogenet 2011; 38:365-72. [PMID: 21816003 DOI: 10.1111/j.1744-313x.2011.01026.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polymorphisms of short tandem repeats of <10 nucleotides, or microsatellites (Msat), are largely used for post-transplant chimerism analyses in clinical hematopoietic stem cell transplantation (HSCT). Compared to single nucleotide polymorphisms (SNP), they have the advantage of a higher degree of allelic polymorphism and thus a potentially larger degree of informativity. Msat markers contribute to approximately 3% of the human genome and have been highly informative in disease association studies, population genetics, forensic medicine and organ and HSC transplantation. They allowed to expand our knowledge of the haplotypic structure of the HLA complex, including the noncoding sequences in the MHC, and to reach a better characterization of immunological phenotypes. Among the different immunogenetic studies in HSCT patients reviewed here, four Msat loci linked to cytokine genes have been analysed by a number of laboratories as potential candidates markers for HSCT outcome: IFNG, TNFd, IL-10(-1064) and IL-1RN. The low patient numbers and high diversity of clinical parameters account for some heterogeneity of the results. Among the trends starting to emerge from these studies, specific TNFd Msat alleles seem to be associated with acute graft-versus-host disease and mortality. Patient/donor Msat incompatibilities have also been used as surrogate markers to map biologically relevant polymorphisms, with a main focus on MHC-resident genetic variation. High throughput SNP typing and next-generation sequencing technologies will allow acquisition of large-scale genomic data and should allow refined analyses of clinically relevant genotypes in the transplantation settting, although the heterogeneity of the study cohorts will remain an issue. The analysis of Msat polymorphisms may still have a place in functional studies on the impact of Msat diversity in the control of immune response gene expression.
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Affiliation(s)
- J-M Tiercy
- National Reference Laboratory for Histocompatibility, Department of Internal Medicine, University Hospital Geneva, Geneva, Switzerland.
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Michikawa Y, Suga T, Ishikawa A, Hayashi H, Oka A, Inoko H, Iwakawa M, Imai T. Genome wide screen identifies microsatellite markers associated with acute adverse effects following radiotherapy in cancer patients. BMC MEDICAL GENETICS 2010; 11:123. [PMID: 20701746 PMCID: PMC2928773 DOI: 10.1186/1471-2350-11-123] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2009] [Accepted: 08/11/2010] [Indexed: 01/24/2023]
Abstract
Background The response of normal tissues in cancer patients undergoing radiotherapy varies, possibly due to genetic differences underlying variation in radiosensitivity. Methods Cancer patients (n = 360) were selected retrospectively from the RadGenomics project. Adverse effects within 3 months of radiotherapy completion were graded using the National Cancer Institute Common Toxicity Criteria; high grade group were grade 3 or more (n = 180), low grade group were grade 1 or less (n = 180). Pooled genomic DNA (gDNA) (n = 90 from each group) was screened using 23,244 microsatellites. Markers with different inter-group frequencies (Fisher exact test P < 0.05) were analyzed using the remaining pooled gDNA. Silencing RNA treatment was performed in cultured normal human skin fibroblasts. Results Forty-seven markers had positive association values; including one in the SEMA3A promoter region (P = 1.24 × 10-5). SEMA3A knockdown enhanced radiation resistance. Conclusions This study identified 47 putative radiosensitivity markers, and suggested a role for SEMA3A in radiosensitivity.
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Affiliation(s)
- Yuichi Michikawa
- RadGenomics Project, Research Center for Charged Particle Therapy, National Institute of Radiological Sciences, Chiba, Japan
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Hypocretin ligand deficiency in narcolepsy: recent basic and clinical insights. Curr Neurol Neurosci Rep 2010; 10:180-9. [PMID: 20425033 DOI: 10.1007/s11910-010-0100-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Narcolepsy is a chronic sleep disorder characterized by excessive daytime sleepiness, cataplexy, hypnagogic hallucinations, and sleep paralysis. Both sporadic and familial forms exist in humans. Recently, the major pathophysiology of human narcolepsy was indicated, based on discovery, through animal study, of narcolepsy genes involved in the pathology of hypocretin/orexin ligand and its receptor. Hypocretin ligand deficiency is found in most patients with narcolepsy with cataplexy. This deficiency likely is the result of postnatal cell death of hypocretin neurons, and involvement of autoimmune mechanisms is suggested. Hypocretin deficiency also is found in symptomatic narcolepsy and excessive daytime sleepiness with neurologic conditions, including immune-mediated neurologic disorders. These findings have significant clinical relevance and promote understanding of hypocretin cell death mechanisms. Already, discoveries in humans have led to a new diagnostic test for narcolepsy. Currently, hypocretin replacement therapy has emerged as a promising therapeutic option, and experiments using gene therapy and cell transplantation are in progress.
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Abstract
Narcolepsy with cataplexy is a rare but life-long and challenging disorder. Current insight into the pathophysiology of this condition seems to be autoimmune-mediated postnatal cell death of hypocretin neurons occurring by organ-specific autoimmune targeting with HLA-T-cell receptor interactions. The hypocretin system seems to have an influence on multiple organ systems beyond its wake-promoting mechanisms. The recent availability of cerebrospinal fluid hypocretin-1 analysis has led to definitive diagnostic criteria for narcolepsy with cataplexy. Pharmacologic first-line treatments for excessive daytime sleepiness and cataplexy is sodium oxybate, with modafinil for daytime sleepiness, in adults and children. Other investigative agents and treatment modalities hold promise in future directions for narcolepsy.
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Li Wang, Zeng Chan Wang, Cui Xie, Xiao Feng Liu, Mao Sheng Yang. Genome-wide screening for risk loci of idiopathic recurrent miscarriage in a Han Chinese population: a pilot study. Reprod Sci 2010; 17:578-584. [PMID: 20305137 DOI: 10.1177/1933719110364248] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
The etiology of recurrent miscarriage (RM) is extremely heterogeneous, including genetic, immunologic, anatomic, endocrinological, and infectious anomalies. About 50% of RM is unexplained or poorly understood, which is called idiopathic recurrent miscarriage (IRM). The primary aim of this study was to identify the genetic loci that might be susceptible to IRM. Forty-four Han Chinese patients with IRM during the first trimester of their pregnancies and 44 healthy sex- and ethnic-matched controls were enrolled in this study. A case-control and genome-wide study was performed and 430 polymorphic microsatellite markers were analyzed. Three loci, 6q27 (D6S446, P = .028), 9q33.1 (D9S1776, P = .037), and Xp22.11 (DXS1226, P = .008), significantly associated with IRM were found. This work identified 3 genetic regions that might harbor genes predisposed to IRM and provided new insights for future genetic and etiological study of IRM. Further study is required to confirm it.
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Affiliation(s)
- Li Wang
- Laboratory of Disorder Genes and Pharmacogenomics Research Center, Institute of Life Sciences, Chongqing University of Medical Sciences, Chongqing, People's Republic of China
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Serretti A, Gaspar-Barba E, Calati R, Cruz-Fuentes CS, Gomez-Sanchez A, Perez-Molina A, De Ronchi D. 3111T/C CLOCKGENE POLYMORPHISM IS NOT ASSOCIATED WITH SLEEP DISTURBANCES IN UNTREATED DEPRESSED PATIENTS. Chronobiol Int 2010; 27:265-77. [DOI: 10.3109/07420521003663785] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Nishino S, Okuro M, Kotorii N, Anegawa E, Ishimaru Y, Matsumura M, Kanbayashi T. Hypocretin/orexin and narcolepsy: new basic and clinical insights. Acta Physiol (Oxf) 2010; 198:209-22. [PMID: 19555382 DOI: 10.1111/j.1748-1716.2009.02012.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Narcolepsy is a chronic sleep disorder, characterized by excessive daytime sleepiness (EDS), cataplexy, sleep paralysis and hypnagogic hallucinations. Both sporadic (95%) and familial (5%) forms of narcolepsy exist in humans. The major pathophysiology of human narcolepsy has been recently discovered based on the discovery of narcolepsy genes in animals; the genes involved in the pathology of the hypocretin/orexin ligand and its receptor. Mutations in hypocretin-related genes are rare in humans, but hypocretin ligand deficiency is found in a large majority of narcolepsy with cataplexy. Hypocretin ligand deficiency in human narcolepsy is probably due to the post-natal cell death of hypocretin neurones. Although a close association between human leucocyte antigen (HLA) and human narcolepsy with cataplexy suggests an involvement of autoimmune mechanisms, this has not yet been proved. Hypocretin deficiency is also found in symptomatic cases of narcolepsy and EDS with various neurological conditions, including immune-mediated neurological disorders, such as Guillain-Barre syndrome, MA2-positive paraneoplastic syndrome and neuromyelitis optica (NMO)-related disorder. The findings in symptomatic narcoleptic cases may have significant clinical relevance to the understanding of the mechanisms of hypocretin cell death and choice of treatment option. The discoveries in human cases lead to the establishment of the new diagnostic test of narcolepsy (i.e. low cerebrospinal fluid hypocretin-1 levels for 'narcolepsy with cataplexy' and 'narcolepsy due to medical condition'). As a large majority of human narcolepsy patients are ligand deficient, hypocretin replacement therapy may be a promising new therapeutic option, and animal experiments using gene therapy and cell transplantations are in progress.
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Affiliation(s)
- S Nishino
- Stanford University, Sleep and Circadian Neurobiology Laboratory, Palo Alto, CA 94304-5489, USA.
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Caylak E. The genetics of sleep disorders in humans: narcolepsy, restless legs syndrome, and obstructive sleep apnea syndrome. Am J Med Genet A 2009; 149A:2612-26. [PMID: 19876894 DOI: 10.1002/ajmg.a.33087] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Sleep disorders are a group of neurological disorders known to cause public health problems associated with interference with daily activities including cognitive problems, poor job performance and reduced productivity. There is strong evidence emerging for the presence of genes influencing sleep disorders, such as narcolepsy (NRCLP), restless legs syndrome (RLS), and obstructive sleep apnea syndrome (OSAS). NRCLP is typically characterized by excessive daytime sleepiness, cataplexy, sleep paralysis and hallucinations. RLS is manifested by compelling need to move the legs and usually experienced when trying to sleep. OSAS is major sleep problem characterized by recurrent episodes of upper airway collapse and obstruction during sleep. In the recent years, many research groups have attempted to identify the susceptibility and candidate genes for NRCLP, RLS, and OSAS through the sequential analyses of genetic linkage and association. The purpose of this review is to summarize some of remarkable molecular advances in sleep and sleep disorders, thereby providing a greater understanding of the complex sleep processes, and a platform for future therapeutic interventions.
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Affiliation(s)
- Emrah Caylak
- Department of Biochemistry and Clinical Biochemistry, Firat University, School of Medicine, Elazig, Turkey.
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Detection of genomic variation by selection of a 9 mb DNA region and high throughput sequencing. PLoS One 2009; 4:e6659. [PMID: 19684856 PMCID: PMC2722027 DOI: 10.1371/journal.pone.0006659] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Accepted: 07/26/2009] [Indexed: 11/19/2022] Open
Abstract
Detection of the rare polymorphisms and causative mutations of genetic diseases in a targeted genomic area has become a major goal in order to understand genomic and phenotypic variability. We have interrogated repeat-masked regions of 8.9 Mb on human chromosomes 21 (7.8 Mb) and 7 (1.1 Mb) from an individual from the International HapMap Project (NA12872). We have optimized a method of genomic selection for high throughput sequencing. Microarray-based selection and sequencing resulted in 260-fold enrichment, with 41% of reads mapping to the target region. 83% of SNPs in the targeted region had at least 4-fold sequence coverage and 54% at least 15-fold. When assaying HapMap SNPs in NA12872, our sequence genotypes are 91.3% concordant in regions with coverage≥4-fold, and 97.9% concordant in regions with coverage≥15-fold. About 81% of the SNPs recovered with both thresholds are listed in dbSNP. We observed that regions with low sequence coverage occur in close proximity to low-complexity DNA. Validation experiments using Sanger sequencing were performed for 46 SNPs with 15-20 fold coverage, with a confirmation rate of 96%, suggesting that DNA selection provides an accurate and cost-effective method for identifying rare genomic variants.
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Tabeta K, Shimada Y, Tai H, Ishihara Y, Noguchi T, Soga Y, Takashiba S, Suzuki G, Kobayashi T, Oka A, Kobayashi T, Yamazaki K, Inoko H, Yoshie H. Assessment of chromosome 19 for genetic association in severe chronic periodontitis. J Periodontol 2009; 80:663-71. [PMID: 19335087 DOI: 10.1902/jop.2009.080516] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND A genome-association study is a powerful tool for analyzing small gene effects in complex diseases such as chronic periodontitis (CP), although the cost of analysis is prohibitive. We designed a study using the DNA pooling method, which could be a breakthrough in lowering such costs. This study was conducted to assess the genetic association in severe CP in a Japanese population. METHODS We adopted a DNA pooling method by genotyping 454 densely spaced microsatellite (MS) markers in chromosome 19 as a pilot study, with the possibility of future use in a whole-genome study. This can reduce the high cost and technical burden, which is generally unavoidable in a genomic association study. Pooled DNA samples from 300 case subjects, 300 control subjects, and 200 systemically healthy subjects were screened by genotyping MS markers. The case-control association in the candidate region was analyzed by individual typing of MS and single nucleotide polymorphisms (SNPs). RESULTS The single MS marker allele 17 of 1902G31 was isolated in association with severe CP (P = 0.0012 for 2 x 2; P <0.046 for 2 x m, where m refers to the number of polymorphic alleles observed in a population). No other SNP or MS polymorphism hypothesized to affect biologic functions in the critical region was found in the linkage disequilibrium block analysis. CONCLUSIONS We efficiently isolated the susceptible locus for severe CP in chromosome 19 and identified a useful marker to evaluate the risk for disease. This approach can be applied to a whole-genome study in severe CP.
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Affiliation(s)
- Koichi Tabeta
- Center for Transdisciplinary Research, Niigata University, Niigata, Japan.
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Megakaryoblastic leukemia factor-1 gene in the susceptibility to coronary artery disease. Hum Genet 2009; 126:539-47. [PMID: 19513752 DOI: 10.1007/s00439-009-0698-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Accepted: 05/30/2009] [Indexed: 01/18/2023]
Abstract
Coronary artery disease (CAD) is based on the atherosclerosis of coronary artery and may manifest with myocardial infarction or angina pectoris. Although it is widely accepted that genetic factors are linked to CAD and several disease-related genes have been reported, only a few could be replicated suggesting that there might be some other CAD-related genes. To identify novel susceptibility loci for CAD, we used microsatellite markers in the screening and found six different candidate CAD loci. Subsequent single nucleotide polymorphism (SNP) association studies revealed an association between CAD and megakaryoblastic leukemia factor-1 gene (MKL1). The association with a promoter SNP of MKL1, -184C > T, was found in a Japanese population and the association was replicated in another Japanese population and a Korean population. Functional analysis of the MKL1 promoter SNP suggested that the higher MKL1 expression was associated with CAD. These findings suggest that MKL1 is involved in the pathogenesis of CAD.
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Alaez C, Lin L, Flores-A H, Vazquez M, Munguia A, Mignot E, Haro R, Baker H, Gorodezky C. Association of narcolepsy-cataplexy with HLA-DRB1 and DQB1 in Mexican patients: a relationship between HLA and gender is suggested. BMC MEDICAL GENETICS 2008; 9:79. [PMID: 18706091 PMCID: PMC2533302 DOI: 10.1186/1471-2350-9-79] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/03/2008] [Accepted: 08/15/2008] [Indexed: 12/20/2022]
Abstract
Background Narcolepsy-cataplexy is characterized by excessive daytime sleepiness with recurrent episodes of irresistible sleep, cataplexy, hallucinations and sleep paralysis. Its aetiology is unknown, but it is positively associated with the human leukocyte antigens (HLA) in all studied populations. The purpose of the present study was to investigate the association of HLA class II DRB1/DQB1 alleles with narcolepsy-cataplexy in Mexican Mestizo patients. Methods This is a case-control study of consecutive patients and ethnically matched controls. We included 32 patients diagnosed with typical narcolepsy-cataplexy, of the National Institute of Neurology, of the Institute of Psychiatry and at the Center of Narcolepsy at Stanford University. As healthy controls, 203 Mexican Mestizos were included. DRB1 alleles were identified using sequence based typing. A PCR-SSOP reverse dot blot was used for DQB1 typing. Allele frequency was calculated by direct counting and the significance of the differences was assessed using the Yates Chi square. Odds ratio and confidence intervals were evaluated. Results HLA-DRB1*1501 (OR = 8.2; pc < 0.0001) and DQB1*0602 (OR = 8.4; pc < 0.0001) were found positively associated with narcolepsy. When deleting DQB1*0602+ patients from the analysis, DQB1*0301 was also found increased (OR = 2.7; p = 0.035; pc = NS). DQB1*0602/DQB1*0301 genotype was present in 15.6% of the cases (OR = 11.5; p = 0.00035), conferring a high risk. DRB1*0407 (OR = 0.2; p = 0.016 pc = NS) and DQB1*0302(OR = 0.4; p = 0.017, pc = NS) were found decreased in the patients. The gender stratification analysis showed a higher risk in females carrying DRB1*1501 (OR = 15.8, pc < 0.0001) and DQB1*0602 (OR = 19.8, pc < 0.0001) than in males (OR = 5.0 for both alleles; p = 0.012, pc = NS for DRB1 & p = 0.0012, pc = 0.017 for DQB1). The susceptibility alleles found in Mexicans with narcolepsy are also present in Japanese and Caucasians; DRB1*04 linked protection has also been shown in Koreans. A stronger HLA association is suggested in females, in accordance with the sexual dimorphism claimed previously. Conclusion This knowledge may contribute to a better understanding of the disease pathogenesis in different populations. The evaluation of the risk to develop narcolepsy-cataplexy in carriers of the described alleles/genotypes may also be possible. A larger sample should be analysed in Mexican and in other Hispanic patients to confirm these results.
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Affiliation(s)
- Carmen Alaez
- Department of Immunology and Immunogenetics, InDRE, Mexico City, Mexico.
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Kimura T, Kobayashi T, Munkhbat B, Oyungerel G, Bilegtsaikhan T, Anar D, Jambaldorj J, Munkhsaikhan S, Munkhtuvshin N, Hayashi H, Oka A, Inoue I, Inoko H. Genome-wide association analysis with selective genotyping identifies candidate loci for adult height at 8q21.13 and 15q22.33-q23 in Mongolians. Hum Genet 2008; 123:655-60. [PMID: 18491143 PMCID: PMC2440952 DOI: 10.1007/s00439-008-0512-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2008] [Accepted: 05/12/2008] [Indexed: 02/04/2023]
Abstract
We performed a genome-wide association study with 23,465 microsatellite markers to identify genes related to adult height. Selective genotyping was applied to extremely tall and extremely short individuals from the Khalkh-Mongolian population. Two loci, 8q21.13 and 15q22.33, which showed the strongest association with microsatellites were subjected to further analyses of SNPs in 782 tall and 773 short individuals. The most significant association was observed with SNP rs2220456 at 8q21.13 (P = 0.000016). In the LD block at 15q22.32, SNP rs8038652 located in intron 1 of IQCH was strongly associated (P = 0.0003), especially the AA genotype of the SNP under a recessive model was strongly associated with adult height (P = 0.000046).
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Affiliation(s)
- Tetsuaki Kimura
- Department of Molecular Life Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1193, Japan,
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Abstract
Narcolepsy with cataplexy is a debilitating sleep disorder with an estimated prevalence of about 0.05%. Narcolepsy is caused by a selective loss of hypocretin (orexin) producing neurons in the perifornical hypothalamus. Based on the very strong association with the HLA subtype DQB1*0602, it is currently hypothesized narcolepsy is caused by an autoimmune-mediated process directed at the hypocretin neurons. So far however, studies focusing on general markers of (auto)immune activation, as well as humoral immunity against the hypocretin system have not yielded consistent results supporting this hypothesis.
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Affiliation(s)
- Sebastiaan Overeem
- Department of Neurology, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands.
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Hui J, Oka A, James A, Palmer LJ, Musk AW, Beilby J, Inoko H. A genome-wide association scan for asthma in a general Australian population. Hum Genet 2008; 123:297-306. [PMID: 18253752 DOI: 10.1007/s00439-008-0477-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2007] [Accepted: 01/25/2008] [Indexed: 01/31/2023]
Abstract
To date, almost every chromosome has been implicated in genetic susceptibility to asthma to some degree. When compared with single nucleotide polymorphism, microsatellite markers exhibit high levels of heterozygosity and therefore provide higher statistical power in association. The objective of this study was to perform a genome-wide association study using 23,465 in-house microsatellite markers to detect asthma susceptibility regions in the Busselton population. In this study, three separate pooled DNA screenings yielded 18 markers with significantly different estimated frequencies in the three separate "case and control" pools: each pool consisting of 60 males and 60 females. These markers were evaluated by individual typing in 360 cases and 360 controls. Two markers showed significant differences between cases and controls (P = 0.001 and P = 0.003). Regions surrounding the two markers were subjected to high-density association mapping with a total of 14 additional markers. We were able to confirm and fine map the association in these two regions by typing 14 additional microsatellite markers (1805A09 (D18S0325i), P = 0.002; 1806D05 (D18S0181i), P = 0.001). Each region contains a predicted gene that showed strong associations with asthma. Further studies are underway to characterize the novel candidate asthma susceptibility genes identified in this genome-wide study.
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Affiliation(s)
- J Hui
- Western Australian Institute for Medical Research and UWA Centre for Medical Research, B Block, QEII Medical Centre, The University of Western Australia, Nedlands, WA, 6009, Australia.
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Hawkins GA, Meyers DA, Bleecker ER, Pack AI. Identification of coding polymorphisms in human circadian rhythm genes PER1, PER2, PER3, CLOCK, ARNTL, CRY1, CRY2 and TIMELESS in a multi-ethnic screening panel. DNA SEQUENCE : THE JOURNAL OF DNA SEQUENCING AND MAPPING 2008; 19:44-9. [PMID: 17852344 DOI: 10.1080/10425170701322197] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
STUDY OBJECTIVE In this study, the exonic regions of the circadian rhythm genes PER1, PER2, PER3, CLOCK, ARNTL, CRY1, CRY2 and TIMELESS were re-sequenced and coding changes identified in a panel of 95 individuals varying in ethnicity. STUDY PARTICIPANTS DNA screening panel consisting of 95 DNA samples (17 American Caucasians, 17 African Americans, 8 Ashkenazi Jews, 8 Chinese, 8 Japanese, 5 Mexican Indians, 8 Mexicans, 8 Northern Europeans, 8 Puerto Ricans, and 8 South Americans) selected from the Coriell Institute Human Variation Panel. RESULTS In addition to coding changes already identified in the database dbSNP, novel coding changes were identified, including PER1: Pro37Ser, Pro351Ser, Gln988Pro, Ala998Thr; PER2: Leu83Arg, Leu157Leu, Thre174Ile, Phe400Phe, Pro822Pro, Ala828Thr, Ala861Val, Phe876Leu, Val883Met, Val903Ile, Ala923Pro; PER3: Pro67Pro, Val90Ile, His638His, Ala820Ala, Leu929Leu; ARNTL: Arg166Gln, Ser459Phe; CLOCK: Ala34Ala, Ser208Cys, Phe233Phe, Ser632Thr, Ser816Ser; TIMELESS: Met870Val and CRY2: His35His. No coding polymorphisms were identified in CRY1. CONCLUSIONS Considerable genetic variation occurs within the coding region of the genes regulating circadian rhythm. Many of the non-synonymous coding polymorphisms could affect protein structure/function with the potential to affect molecular regulation of the sleep/wake cycle. Many of the potential functional effects could be ethnic group specific.
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Affiliation(s)
- Gregory A Hawkins
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA.
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Tanaka S, Honda Y, Honda M. Identification of differentially expressed genes in blood cells of narcolepsy patients. Sleep 2007; 30:974-9. [PMID: 17702266 PMCID: PMC1978392 DOI: 10.1093/sleep/30.8.974] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
STUDY OBJECTIVE A close association between the human leukocyte antigen (HLA)-DRB1*1501/DQB1*0602 and abnormalities in some inflammatory cytokines have been demonstrated in narcolepsy. Specific alterations in the immune system have been suggested to occur in this disorder. We attempted to identify alterations in gene expression underlying the abnormalities in the blood cells of narcoleptic patients. DESIGNS Total RNA from 12 narcolepsy-cataplexy patients and from 12 age- and sex-matched healthy controls were pooled. The pooled samples were initially screened for candidate genes for narcolepsy by differential display analysis using annealing control primers (ACP). The second screening of the samples was carried out by semiquantitative PCR using gene-specific primers. Finally, the expression levels of the candidate genes were further confirmed by quantitative real-time PCR using a new set of samples (20 narcolepsy-cataplexy patients and 20 healthy controls). RESULTS The second screening revealed differential expression of 4 candidate genes. Among them, MX2 was confirmed as a significantly down-regulated gene in the white blood cells of narcoleptic patients by quantitative real-time PCR. CONCLUSION We found the MX2 gene to be significantly less expressed in comparison with normal subjects in the white blood cells of narcoleptic patients. This gene is relevant to the immune system. Although differential display analysis using ACP technology has a limitation in that it does not help in determining the functional mechanism underlying sleep/wakefulness dysregulation, it is useful for identifying novel genetic factors related to narcolepsy, such as HLA molecules. Further studies are required to explore the functional relationship between the MX2 gene and narcolepsy pathophysiology.
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Affiliation(s)
- Susumu Tanaka
- The Sleep Disorders Project, Department of Sleep Disorders Research, Tokyo Institute of Psychiatry, Setagaya-ku, Tokyo, Japan.
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Tafti M, Dauvilliers Y, Overeem S. Narcolepsy and familial advanced sleep-phase syndrome: molecular genetics of sleep disorders. Curr Opin Genet Dev 2007; 17:222-7. [PMID: 17467264 DOI: 10.1016/j.gde.2007.04.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2007] [Accepted: 04/16/2007] [Indexed: 11/22/2022]
Abstract
Sleep disorders are very prevalent and represent an emerging worldwide epidemic. However, research into the molecular genetics of sleep disorders remains surprisingly one of the least active fields. Nevertheless, rapid progress is being made in several prototypical disorders, leading recently to the identification of the molecular pathways underlying narcolepsy and familial advanced sleep-phase syndrome. Since the first reports of spontaneous and induced loss-of-function mutations leading to hypocretin deficiency in human and animal models of narcolepsy, the role of this novel neurotransmission pathway in sleep and several other behaviors has gained extensive interest. Also, very recent studies using an animal model of familial advanced sleep-phase syndrome shed new light on the regulation of circadian rhythms.
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Affiliation(s)
- Mehdi Tafti
- Center for Integrative Genomics (CIG) and Center for Investigation and Research in Sleep (CIRS), University of Lausanne and Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland.
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