1
|
Jiang L, Mei JP, Zhao YW, Zhang R, Pan HX, Yang Y, Sun QY, Xu Q, Yan XX, Tan JQ, Li JC, Tang BS, Guo JF. Low-frequency and rare coding variants of NUS1 contribute to susceptibility and phenotype of Parkinson's disease. Neurobiol Aging 2021; 110:106-112. [PMID: 34635350 DOI: 10.1016/j.neurobiolaging.2021.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 08/18/2021] [Accepted: 09/02/2021] [Indexed: 01/13/2023]
Abstract
NUS1 has been recently identified as a candidate gene for Parkinson's disease (PD). Few studies have examined the association of NUS1 variants with PD susceptibility and phenotypes. In the first cohort, whole-exome sequencing was performed to identify variants in NUS1 exon-coding and exon-intron regions in 1542 cases and 1625 controls. 13 variants were totally detected, of which 10 rare variants and 3 low-frequency variants. Burden analysis showed that rare NUS1 variants significantly enriched in PD (p=0.016). We also performed a meta-analysis based on previous and our studies to correlate NUS1 mutations with PD susceptibility. Integrating our previous cohort (3210 cases and 2807 controls) and the first cohort identified the significant association of rs539668656 with PD risk (odds ratio (OR) = 2.82, p = 0.016). The genotype-phenotype association analysis showed that patients carrying rare variants, or rs539668656 were significantly associated with earlier onset age, depression, emotional impairment and severe disease condition. Our results support the role of NUS1 rare variants and rs539668656 towards PD susceptibility and phenotype.
Collapse
Affiliation(s)
- Li Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jun-Pu Mei
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yu-Wen Zhao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Rui Zhang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hong-Xu Pan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yang Yang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qi-Ying Sun
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qian Xu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xin-Xiang Yan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jie-Qiong Tan
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Jin-Chen Li
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Bei-Sha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ji-Feng Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.
| |
Collapse
|
2
|
Pan HX, Zhao YW, Mei JP, Fang ZH, Wang Y, Zhou X, Zhou YJ, Zhang R, Zhang KL, Jiang L, Zeng Q, He Y, Wang Z, Liu ZH, Xu Q, Sun QY, Yang Y, Hu YC, Chen YS, Du J, Lei LF, Zhang HN, Wang CY, Yan XX, Shen L, Jiang H, Tan JQ, Li JC, Tang BS, Guo JF. GCH1 variants contribute to the risk and earlier age-at-onset of Parkinson's disease: a two-cohort case-control study. Transl Neurodegener 2020; 9:31. [PMID: 32746945 PMCID: PMC7401216 DOI: 10.1186/s40035-020-00212-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 07/21/2020] [Indexed: 12/26/2022] Open
Abstract
Background Common and rare variants of guanosine triphosphate cyclohydrolase 1 (GCH1) gene may play important roles in Parkinson’s disease (PD). However, there is a lack of comprehensive analysis of GCH1 genotypes, especially in non-coding regions. The aim of this study was to explore the genetic characteristics of GCH1, including rare and common variants in coding and non-coding regions, in a large population of PD patients in Chinese mainland, as well as the phenotypic characteristics of GCH1 variant carriers. Methods In the first cohort of this case-control study, we performed whole-exome sequencing in 1555 patients with early-onset or familial PD and 2234 healthy controls; then in the second cohort, whole-genome sequencing was performed in sporadic late-onset PD samples (1962 patients), as well as 1279 controls. Variants at target GCH1 regions were extracted, and then genetic and detailed phenotypic data were analyzed using regression models and the sequence kernel association test. We also performed a meta-analysis to correlate deleterious GCH1 variants with age at onset (AAO) in PD patients. Results For coding variants, we identified a significant burden of GCH1 deleterious variants in early-onset or familial PD cases compared to controls (1.2% vs 0.1%, P < 0.0001). In the analysis of possible regulatory variants in GCH1 non-coding regions, rs12323905 (P = 0.001, odds ratio = 1.19, 95%CI 1.07–1.32) was significantly associated with PD, and variant sets in untranslated regions and intron regions, GCH1 brain-specific expression quantitative trait loci, and two possible promoter/enhancer (GH14J054857 and GH14J054880) were suggestively associated with PD. Genotype-phenotype correlation analysis revealed that the carriers of GCH1 deleterious variants manifested younger AAO (P < 0.0001), and had milder motor symptoms, milder fatigue symptoms and more autonomic nervous dysfunctions. Meta-analysis of six studies demonstrated 6.4-year earlier onset in GCH1 deleterious variant carriers (P = 0.0009). Conclusions The results highlight the importance of deleterious variants and non-coding variants of GCH1 in PD in Chinese mainland and suggest that GCH1 mutation can influence the PD phenotype, which may help design experimental studies to elucidate the mechanisms of GCH1 in the pathogenesis of PD.
Collapse
Affiliation(s)
- Hong-Xu Pan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Yu-Wen Zhao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Jun-Pu Mei
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Zheng-Huan Fang
- Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410008, China
| | - Yige Wang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Xun Zhou
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Yang-Jie Zhou
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Rui Zhang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Kai-Lin Zhang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Li Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Qian Zeng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Yan He
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Zheng Wang
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Zhen-Hua Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Qian Xu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Qi-Ying Sun
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Yang Yang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Ya-Cen Hu
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Ya-Se Chen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Juan Du
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Li-Fang Lei
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, 410013, China
| | - Hai-Nan Zhang
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Chun-Yu Wang
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Xin-Xiang Yan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Lu Shen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, 410008, China
| | - Hong Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, 410008, China
| | - Jie-Qiong Tan
- Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410008, China
| | - Jin-Chen Li
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China.,Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410008, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, 410008, China
| | - Bei-Sha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China. .,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China. .,Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410008, China. .,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, 410008, China.
| | - Ji-Feng Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China. .,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China. .,Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410008, China. .,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, 410008, China.
| |
Collapse
|
3
|
Liu L, Zhang L, Li HM, Wang ZR, Xie XF, Mei JP, Jin JL, Shi J, Sun L, Li SC, Tan YL, Yang L, Wang J, Yang HM, Qian QJ, Wang YF. The SNP-set based association study identifies ITGA1 as a susceptibility gene of attention-deficit/hyperactivity disorder in Han Chinese. Transl Psychiatry 2017; 7:e1201. [PMID: 28809852 PMCID: PMC5611725 DOI: 10.1038/tp.2017.156] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 05/20/2017] [Accepted: 06/07/2017] [Indexed: 01/02/2023] Open
Abstract
Genome-wide association studies, which detect the association between single-nucleotide polymorphisms (SNPs) and disease susceptibility, have been extensively applied to study attention-deficit/hyperactivity disorder (ADHD), but genome-wide significant associations have not been found yet. Genetic heterogeneity and insufficient genomic coverage may account for the missing heritability. We performed a two-stage association study for ADHD in the Han Chinese population. In the discovery stage, 1033 ADHD patients and 950 healthy controls were genotyped using both the Affymetrix Genome-Wide Human SNP Array 6.0 and the Illumina Infinium HumanExome BeadChip. The genotyped SNPs were combined to generate a powerful SNP set with better genomic coverage especially for the nonsynonymous variants. In addition to the association of single SNPs, we collected adjacent SNPs as SNP sets, which were determined by either genes or successive sliding windows, to evaluate their synergetic effect. The candidate susceptibility SNPs were further replicated in an independent cohort of 1441 ADHD patients and 1447 healthy controls. No genome-wide significant SNPs or gene-based SNP sets were found to be associated with ADHD. However, two continuous sliding windows located in ITGA1 (P-value=8.33E-7 and P-value=8.43E-7) were genome-wide significant. The quantitative trait analyses also demonstrated their association with ADHD core symptoms and executive functions. The association was further validated by follow-up replications for four selected SNPs: rs1979398 (P-value=2.64E-6), rs16880453 (P-value=3.58E-4), rs1531545 (P-value=7.62E-4) and rs4074793 (P-value=2.03E-4). Our results suggest that genetic variants in ITGA1 may be involved in the etiology of ADHD and the SNP-set based analysis is a promising strategy for the detection of underlying genetic risk factors.
Collapse
Affiliation(s)
- L Liu
- Department of Child Psychiatry, Peking University Sixth Hospital/Institute of Mental Health, Beijing, China,National Clinical Research Center for Mental Disorders & Key Laboratory of Mental Health, Ministry of Health (Peking University), Beijing, China
| | - L Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China,Department of Computer Science, City University of Hong Kong, Hong Kong, China,Department of Computer Science, Stanford University, Stanford, CA, USA
| | - H M Li
- Department of Child Psychiatry, Peking University Sixth Hospital/Institute of Mental Health, Beijing, China,National Clinical Research Center for Mental Disorders & Key Laboratory of Mental Health, Ministry of Health (Peking University), Beijing, China
| | - Z R Wang
- Psychiatry Research Center, Beijing HuiLongGuan Hospital, Peking University, Beijing, China
| | - X F Xie
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - J P Mei
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - J L Jin
- Department of Child Psychiatry, Peking University Sixth Hospital/Institute of Mental Health, Beijing, China,National Clinical Research Center for Mental Disorders & Key Laboratory of Mental Health, Ministry of Health (Peking University), Beijing, China
| | - J Shi
- Psychiatry Research Center, Beijing HuiLongGuan Hospital, Peking University, Beijing, China
| | - L Sun
- Department of Child Psychiatry, Peking University Sixth Hospital/Institute of Mental Health, Beijing, China,National Clinical Research Center for Mental Disorders & Key Laboratory of Mental Health, Ministry of Health (Peking University), Beijing, China
| | - S C Li
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Y L Tan
- Psychiatry Research Center, Beijing HuiLongGuan Hospital, Peking University, Beijing, China
| | - L Yang
- Department of Child Psychiatry, Peking University Sixth Hospital/Institute of Mental Health, Beijing, China,National Clinical Research Center for Mental Disorders & Key Laboratory of Mental Health, Ministry of Health (Peking University), Beijing, China
| | - J Wang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China,James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - H M Yang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China,James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Q J Qian
- Department of Child Psychiatry, Peking University Sixth Hospital/Institute of Mental Health, Beijing, China,National Clinical Research Center for Mental Disorders & Key Laboratory of Mental Health, Ministry of Health (Peking University), Beijing, China,Peking University Sixth Hospital/Institute of Mental Health, No. 51, Hua Yuan Bei Lu, Haidian Disrtrict, Beijing 100191, China. E-mail: or
| | - Y F Wang
- Department of Child Psychiatry, Peking University Sixth Hospital/Institute of Mental Health, Beijing, China,National Clinical Research Center for Mental Disorders & Key Laboratory of Mental Health, Ministry of Health (Peking University), Beijing, China,Peking University Sixth Hospital/Institute of Mental Health, No. 51, Hua Yuan Bei Lu, Haidian Disrtrict, Beijing 100191, China. E-mail: or
| |
Collapse
|