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Lv CX, Zhou LP, Yang YB, Shi J, Dong FH, Wei HR, Shan YQ. The relationship between innate/adaptive immunity and gastrointestinal cancer : a multi-omics Mendelian randomization study. BMC Gastroenterol 2024; 24:197. [PMID: 38877387 PMCID: PMC11177483 DOI: 10.1186/s12876-024-03284-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 06/07/2024] [Indexed: 06/16/2024] Open
Abstract
BACKGROUND Innate/adaptive immunity is the key to anti-tumor therapy. However, its causal relationship to Gastrointestinal (GI) cancer remains unclear. METHODS Immunity genes were extracted from the MSigDB database. The Genome-wide association studies (GWAS) summary data of GI cancer were integrated with expression quantitative trait loci (eQTL) and DNA methylation quantitative trait loci (mQTL) associated with genes. Summary-data-based Mendelian randomization (SMR) and co-localization analysis were used to reveal causal relationships between genes and GI cancer. Two-sample MR analysis was used for sensitivity analysis. Single cell analysis clarified the enrichment of genes. RESULTS Three-step SMR analysis showed that a putative mechanism, cg17294865 CpG site regulating HLA-DRA expression was negatively associated with gastric cancer risk. HLA-DRA was significantly differentially expressed in monocyte/macrophage and myeloid cells in gastric cancer. CONCLUSION This study provides evidence that upregulating the expression level of HLA-DRA can reduce the risk of gastric cancer.
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Affiliation(s)
- Chen-Xi Lv
- The Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310053, China
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Westlake University, Hangzhou, Zhejiang, 310006, China
- Department of General Surgery, Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, 310006, China
| | - Lin-Po Zhou
- The Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310053, China
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Westlake University, Hangzhou, Zhejiang, 310006, China
- Department of General Surgery, Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, 310006, China
| | - Ye-Bing Yang
- The Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310053, China
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Westlake University, Hangzhou, Zhejiang, 310006, China
- Department of General Surgery, Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, 310006, China
| | - Jing Shi
- The Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310053, China
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Westlake University, Hangzhou, Zhejiang, 310006, China
- Department of General Surgery, Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, 310006, China
| | - Fan-He Dong
- The Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310053, China
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Westlake University, Hangzhou, Zhejiang, 310006, China
- Department of General Surgery, Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, 310006, China
| | - Hao-Ran Wei
- The Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310053, China
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Westlake University, Hangzhou, Zhejiang, 310006, China
- Department of General Surgery, Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, 310006, China
| | - Yu-Qiang Shan
- The Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310053, China.
- Department of General Surgery, Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, 310006, China.
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2
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Danaeifar M, Najafi A. Artificial Intelligence and Computational Biology in Gene Therapy: A Review. Biochem Genet 2024:10.1007/s10528-024-10799-1. [PMID: 38635012 DOI: 10.1007/s10528-024-10799-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 04/02/2024] [Indexed: 04/19/2024]
Abstract
One of the trending fields in almost all areas of science and technology is artificial intelligence. Computational biology and artificial intelligence can help gene therapy in many steps including: gene identification, gene editing, vector design, development of new macromolecules and modeling of gene delivery. There are various tools used by computational biology and artificial intelligence in this field, such as genomics, transcriptomic and proteomics data analysis, machine learning algorithms and molecular interaction studies. These tools can introduce new gene targets, novel vectors, optimized experiment conditions, predict the outcomes and suggest the best solutions to avoid undesired immune responses following gene therapy treatment.
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Affiliation(s)
- Mohsen Danaeifar
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Science, P.O. Box 19395-5487, Tehran, Iran
| | - Ali Najafi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Science, P.O. Box 19395-5487, Tehran, Iran.
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3
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Wang Y, Huang X, Zhang Q, Cheng C, Qin Z, Lu L, Huang Q. The osteoporosis susceptibility SNP rs188303909 at 2q14.2 regulates EN1 expression by modulating DNA methylation and E2F6 binding. J Mol Med (Berl) 2024; 102:273-284. [PMID: 38153509 DOI: 10.1007/s00109-023-02412-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 12/11/2023] [Accepted: 12/19/2023] [Indexed: 12/29/2023]
Abstract
EN1 encodes a homeodomain-containing transcription factor and is a determinant of bone density and fracture. Previous powerful genome-wide association studies (GWASs) have identified multiple single-nucleotide polymorphisms (SNPs) near EN1 at 2q14.2 locus for osteoporosis, but the causal SNPs and functional mechanisms underlying these associations are poorly understood. The target genes regulated by the transcription factor EN1 are also unclear. In this study, we identified rs188303909, a functional CpG-SNP, as a causal SNP for osteoporosis at 2q14.2 through the integration of functional and epigenomic analyses. Functional experiments demonstrated that unmethylated rs188303909 acted as a strong allele-specific distal enhancer to regulate EN1 expression by modifying the binding of transcription factor E2F6, but rs188303909 methylation attenuated the active effect of E2F6 on EN1 expression. Importantly, transcription factor EN1 could differentially bind osteoporosis GWAS lead SNPs rs4869739-T and rs4355801-G to upregulate CCDC170 and COLEC10 expression, thus promoting bone formation. Our study provided a mechanistic insight into expression regulation of the osteoporosis susceptibility gene EN1, which could be a potential therapeutic target for osteoporosis precision medicine. KEY MESSAGES: CpG-SNP rs188303909 is a causal SNP at the osteoporosis susceptibility locus 2q14.2. Rs188303909 distally regulates EN1 expression by modulating DNA methylation and E2F6 binding. EN1 upregulates CCDC170 and COLEC10 expression through osteoporosis GWAS lead SNPs rs4869739 and rs4355801.
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Affiliation(s)
- Ya Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Xinyao Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Qiongdan Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Chen Cheng
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Zixuan Qin
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Li Lu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Qingyang Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China.
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4
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Qiu M, Lin Q, Liu Y, Chen P, Zhou Y, Jiang Y, Zhou Z, Wen Q, Zhou X, Liang X, Gan H, Yu H. Potentially functional genetic variants in RPS6KA4 and MAP2K5 in the MAPK signaling pathway predict HBV-related hepatocellular carcinoma survival. Mol Carcinog 2023; 62:1378-1387. [PMID: 37278562 DOI: 10.1002/mc.23583] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/09/2023] [Accepted: 05/22/2023] [Indexed: 06/07/2023]
Abstract
Hepatocellular carcinoma (HCC) ranks the third leading cause of cancer deaths with a dismal 5-year survival rate. The mitogen-activated protein kinase (MAPK) signaling pathway is abnormally activated in HCC to promote growth and aggressive metastatic potential of cancer cells. Therefore, genetic variants in the MAPK signaling pathway may serve as potential predictors of Hepatitis B virus (HBV)-related HCC survival. In the present study, we performed a two-stage survival analysis to evaluate the associations between 10,912 single nucleotide polymorphisms (SNPs) in 79 MAPK signaling pathway genes and the overall survival (OS) of 866 HBV-related HCC patients, followed by functional annotation. In combined datasets, we identified two novel and potential functional SNPs (RPS6KA4 rs600377 T>G and MAP2K5 rs17300363 A>C) as prognostic factors for HBV-related HCC, with adjusted allelic hazards ratios of 1.24 (95% confidence interval [CI] = 1.05-1.46, p = 0.010) and 1.48 (1.15-1.91, p = 0.001), respectively. Furthermore, their combined risk genotypes also predicted a poor survival in a dose-response manner in the combined data set (Ptrend < 0.001). Additional functional analysis showed that RPS6KA4 rs600377 G and MAP2K5 rs17300363 C alleles were associated with elevated mRNA expression levels of the corresponding genes in normal tissues. These results provide new insights into the role of genetic variants in the MAPK signaling pathway genes in HBV-related HCC survival.
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Affiliation(s)
- Moqin Qiu
- Department of Respiratory Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Qiuling Lin
- Drug Clinical Trial Institution, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Yingchun Liu
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Peiqin Chen
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Yunxiang Zhou
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Yanji Jiang
- Department of Research Service, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Zihan Zhou
- Department of Tumor Prevention and Control, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Qiuping Wen
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Xianguo Zhou
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Xiumei Liang
- Department of Disease Process Management, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Haijie Gan
- Department of Respiratory Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Hongping Yu
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning, China
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5
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Lin Q, Qiu M, Wei X, Xiang Z, Zhou Z, Ji I, Liang X, Zhou X, Wen Q, Liu Y, Yu H. Genetic variants of SOS2, MAP2K1 and RASGRF2 in the RAS pathway genes predict survival of HBV-related hepatocellular carcinoma patients. Arch Toxicol 2023; 97:1599-1611. [PMID: 37029817 DOI: 10.1007/s00204-023-03469-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 02/16/2023] [Indexed: 04/09/2023]
Abstract
The RAS pathway participates in the cascade of proliferation and cell division process, and the activated RAS pathway can lead to tumorigenesis including hepatocellular carcinoma (HCC). However, few studies have explored the effects of genetic variants in the RAS pathway-related genes on the survival of patients with HBV-related HCC. In the present study, we assessed the associations between 11,658 single-nucleotide polymorphisms (SNPs) in 62 RAS pathway genes and the overall survival (OS) of 866 HBV-related HCC individuals, which were randomly split (1:1) into discovery and validation datasets. As a result, three potentially functional SNPs were identified, based on multivariable cox proportional hazards regression analyses, in SOS Ras/Rho guanine nucleotide exchange factor 2 (SOS2, rs4632055 A > G), Ras protein-specific guanine nucleotide releasing factor 2 (RASGRF2, rs26418A > G) and mitogen-activated protein kinase 1 (MAP2K1,rs57120695 C > T), which were significantly and independently associated with OS of HBV-related HCC patients [adjusted hazards ratios (HRs) of 1.42, 1.32 and 1.50, respectively; 95% confidence intervals (CI), 1.14 to 1.76, 1.15 to 1.53 and 1.15 to 1.97, respectively; P = 0.001, < 0.001 and 0.003, respectively]. Additionally, the joint effects as the unfavorable genotypes of these three SNPs showed a significant association with the poor survival of HCC (trend test P < 0.001). The expression quantitative trait loci (eQTL) analysis further revealed that the rs4632055 G allele and the rs26418 A allele were associated with lower mRNA expression levels of SOS2 and RASGRF2, respectively. Collectively, these potentially functional SNPs of RASGRF2, SOS2 and M2PAK1 may become potential prognostic biomarkers for HBV-related HCC after hepatectomy.
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Affiliation(s)
- Qiuling Lin
- Department of Clinical Research, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
| | - Moqin Qiu
- Department of Respiratory Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Xueyan Wei
- School of Public Health, Guangxi Medical University, Nanning, China
| | - Zhouyun Xiang
- School of Public Health, Guangxi Medical University, Nanning, China
| | - Zihan Zhou
- Department of Cancer Prevention and Control, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Iiangyan Ji
- Department of Scientific Research Dept, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Xiumei Liang
- Department of Disease Process Management, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Xianguo Zhou
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
| | - Qiuping Wen
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
| | - Yingchun Liu
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China.
- Key Cultivated Laboratory of Cancer Molecular Medicine, Health Commission of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China.
| | - Hongping Yu
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China.
- Key Cultivated Laboratory of Cancer Molecular Medicine, Health Commission of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China.
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Guangxi Medical University, Ministry of Education, Nanning, China.
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6
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Wang Y, Li L, Li P. Novel single nucleotide polymorphisms in gestational diabetes mellitus. Clin Chim Acta 2023; 538:60-64. [PMID: 36375523 DOI: 10.1016/j.cca.2022.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 11/06/2022] [Accepted: 11/07/2022] [Indexed: 11/13/2022]
Abstract
The association between gestational diabetes mellitus (GDM) and single nucleotide polymorphisms (SNPs) has attracted global research attention. Exploring SNPs can help us further understand the pathogenesis of GDM, predict the risk of GDM, and guide the management of GDM patients. In this review, we summarized the studies on the association between SNPs and GDM, focusing on novel SNPs published in the last 10 years. The SNPs identified to be associated with GDM included HMG20A (rs7178572), CDKAL1 (rs7756992, rs7754840, and rs7747752), ADIPOQ (rs266729 and rs17300539), MTHFR (rs1801133), IL10 (rs3021094), CDKN2B (rs1063192), and TRPM5 (rs35197079). However, the role of SNPs in the prediction, diagnosis, treatment, and prognosis of GDM, as a polygenic disease, needs to be further explored in multiple ethnic populations.
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Affiliation(s)
- Yuqi Wang
- Department of Endocrinology, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province, People's Republic of China
| | - Ling Li
- Department of Endocrinology, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province, People's Republic of China
| | - Ping Li
- Department of Endocrinology, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province, People's Republic of China.
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SNPs in 3'UTR miRNA Target Sequences Associated with Individual Drug Susceptibility. Int J Mol Sci 2022; 23:ijms232213725. [PMID: 36430200 PMCID: PMC9692299 DOI: 10.3390/ijms232213725] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
The complementary interaction of microRNAs (miRNAs) with their binding sites in the 3'untranslated regions (3'UTRs) of target gene mRNAs represses translation, playing a leading role in gene expression control. MiRNA recognition elements (MREs) in the 3'UTRs of genes often contain single nucleotide polymorphisms (SNPs), which can change the binding affinity for target miRNAs leading to dysregulated gene expression. Accumulated data suggest that these SNPs can be associated with various human pathologies (cancer, diabetes, neuropsychiatric disorders, and cardiovascular diseases) by disturbing the interaction of miRNAs with their MREs located in mRNA 3'UTRs. Numerous data show the role of SNPs in 3'UTR MREs in individual drug susceptibility and drug resistance mechanisms. In this review, we brief the data on such SNPs focusing on the most rigorously proven cases. Some SNPs belong to conventional genes from the drug-metabolizing system (in particular, the genes coding for cytochromes P450 (CYP 450), phase II enzymes (SULT1A1 and UGT1A), and ABCB3 transporter and their expression regulators (PXR and GATA4)). Other examples of SNPs are related to the genes involved in DNA repair, RNA editing, and specific drug metabolisms. We discuss the gene-by-gene studies and genome-wide approaches utilized or potentially utilizable to detect the MRE SNPs associated with individual response to drugs.
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Kocheril PA, Moore SC, Lenz KD, Mukundan H, Lilley LM. Progress Toward a Multiomic Understanding of Traumatic Brain Injury: A Review. Biomark Insights 2022; 17:11772719221105145. [PMID: 35719705 PMCID: PMC9201320 DOI: 10.1177/11772719221105145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 05/17/2022] [Indexed: 12/11/2022] Open
Abstract
Traumatic brain injury (TBI) is not a single disease state but describes an array
of conditions associated with insult or injury to the brain. While some
individuals with TBI recover within a few days or months, others present with
persistent symptoms that can cause disability, neuropsychological trauma, and
even death. Understanding, diagnosing, and treating TBI is extremely complex for
many reasons, including the variable biomechanics of head impact, differences in
severity and location of injury, and individual patient characteristics. Because
of these confounding factors, the development of reliable diagnostics and
targeted treatments for brain injury remains elusive. We argue that the
development of effective diagnostic and therapeutic strategies for TBI requires
a deep understanding of human neurophysiology at the molecular level and that
the framework of multiomics may provide some effective solutions for the
diagnosis and treatment of this challenging condition. To this end, we present
here a comprehensive review of TBI biomarker candidates from across the
multiomic disciplines and compare them with known signatures associated with
other neuropsychological conditions, including Alzheimer’s disease and
Parkinson’s disease. We believe that this integrated view will facilitate a
deeper understanding of the pathophysiology of TBI and its potential links to
other neurological diseases.
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Affiliation(s)
- Philip A Kocheril
- Physical Chemistry and Applied Spectroscopy Group, Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Shepard C Moore
- Physical Chemistry and Applied Spectroscopy Group, Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Kiersten D Lenz
- Physical Chemistry and Applied Spectroscopy Group, Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Harshini Mukundan
- Physical Chemistry and Applied Spectroscopy Group, Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Laura M Lilley
- Physical Chemistry and Applied Spectroscopy Group, Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM, USA
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Genetic screening in patients of Meige syndrome and blepharospasm. Neurol Sci 2022; 43:3683-3694. [PMID: 35044558 DOI: 10.1007/s10072-022-05900-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 01/13/2022] [Indexed: 12/27/2022]
Abstract
OBJECTIVE Meige syndrome (MS) is cranial dystonia, including bilateral eyelid spasms (blepharospasm; BSP) and involuntary movements of the jaw muscles (oromandibular dystonia; OMD). Up to now, the pathogenic genes of MS and BSP are still unclear. METHODS We performed Sanger sequencing of GNAL, TOR1A, TOR2A, THAP1, and REEP4 exons on 78 patients, including 53 BSP and 25 MS and 96 healthy controls. RESULTS c.845G > C[R282P] of TOR1A, c.629delC[p.Gly210AlafsTer60] of TOR2A, c.1322A > G[N441S] of GNAL, c.446G > A[R149Q], and c.649C > T[R217C] of REEP4 were identified and predicated as deleterious probably damaging variants. Three potential alterations of splicing variants of TOR1A and TOR2A were identified in patients. The frequencies of TOR1A rs1435566780 and THAP1 rs545930392 were higher in patients than in controls. CONCLUSIONS TOR1A rs1435566780 (c.*16G > C(G > A)) and THAP1 rs545930392 (c.192G > A[K64K]) may contribute to the etiology of MS and BSP. Other identified rare mutations predicted as deleterious probably damaging need further confirmation. Larger MS and BSP cohorts and functional studies will need to be performed further to elucidate the association between these genes and the diseases.
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Wang Y, Lu L, Niu Y, Zhang Q, Cheng C, Huang H, Huang X, Huang Q. The osteoporosis risk variant rs9820407 at 3p22.1 acts as an allele-specific enhancer to regulate CTNNB1 expression by long-range chromatin loop formation. Bone 2021; 153:116165. [PMID: 34461284 DOI: 10.1016/j.bone.2021.116165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/25/2021] [Accepted: 08/25/2021] [Indexed: 11/26/2022]
Abstract
Previous powerful genome-wide association studies (GWASs) and whole-genome sequencing have identified multiple single-nucleotide polymorphisms (SNPs) located over 69 kb upstream of CTNNB1 at 3p22.1 locus associated with osteoporosis. The CTNNB1 gene encodes β-catenin that is an integral part of adherens junctions and the primary mediator of the canonical Wnt signaling pathway. The causal variants and underlying molecular mechanisms of the osteoporosis susceptibility locus 3p22.1 remains unknown. Through comprehensive computational analyses, including expression quantitative trait locus (eQTL), high-throughput chromatin interaction (Hi-C), epigenomic and functional annotation, four enhancer SNPs (rs9820407, rs9878224, rs454690 and rs9832204) were prioritized as potential causal SNPs at 3p22.1 for osteoporosis. Rs9820407 displayed the strongest enhancer activity in dual-luciferase assays. Specifically, the minor rs9820407-A can preferentially bind transcription factor FOXC1, elevate the enhancer activity and increase CTNNB1 expression. The architectural protein CTCF was presumably involved in long-range chromatin interaction between rs9820407 and CTNNB1. Our study provided a mechanistic insight into how noncoding enhancer SNP rs9820407 distally regulates CTNNB1 expression and modulates osteoporosis risk.
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Affiliation(s)
- Ya Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Li Lu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Yajing Niu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Qiongdan Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Chen Cheng
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Han Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Xinyao Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Qingyang Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China.
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11
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Twelve years of GWAS discoveries for osteoporosis and related traits: advances, challenges and applications. Bone Res 2021; 9:23. [PMID: 33927194 PMCID: PMC8085014 DOI: 10.1038/s41413-021-00143-3] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 12/21/2020] [Indexed: 02/03/2023] Open
Abstract
Osteoporosis is a common skeletal disease, affecting ~200 million people around the world. As a complex disease, osteoporosis is influenced by many factors, including diet (e.g. calcium and protein intake), physical activity, endocrine status, coexisting diseases and genetic factors. In this review, we first summarize the discovery from genome-wide association studies (GWASs) in the bone field in the last 12 years. To date, GWASs and meta-analyses have discovered hundreds of loci that are associated with bone mineral density (BMD), osteoporosis, and osteoporotic fractures. However, the GWAS approach has sometimes been criticized because of the small effect size of the discovered variants and the mystery of missing heritability, these two questions could be partially explained by the newly raised conceptual models, such as omnigenic model and natural selection. Finally, we introduce the clinical use of GWAS findings in the bone field, such as the identification of causal clinical risk factors, the development of drug targets and disease prediction. Despite the fruitful GWAS discoveries in the bone field, most of these GWAS participants were of European descent, and more genetic studies should be carried out in other ethnic populations to benefit disease prediction in the corresponding population.
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12
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Okoro PC, Schubert R, Guo X, Johnson WC, Rotter JI, Hoeschele I, Liu Y, Im HK, Luke A, Dugas LR, Wheeler HE. Transcriptome prediction performance across machine learning models and diverse ancestries. HGG ADVANCES 2021; 2:100019. [PMID: 33937878 PMCID: PMC8087249 DOI: 10.1016/j.xhgg.2020.100019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transcriptome prediction methods such as PrediXcan and FUSION have become popular in complex trait mapping. Most transcriptome prediction models have been trained in European populations using methods that make parametric linear assumptions like the elastic net (EN). To potentially further optimize imputation performance of gene expression across global populations, we built transcriptome prediction models using both linear and non-linear machine learning (ML) algorithms and evaluated their performance in comparison to EN. We trained models using genotype and blood monocyte transcriptome data from the Multi-Ethnic Study of Atherosclerosis (MESA) comprising individuals of African, Hispanic, and European ancestries and tested them using genotype and whole-blood transcriptome data from the Modeling the Epidemiology Transition Study (METS) comprising individuals of African ancestries. We show that the prediction performance is highest when the training and the testing population share similar ancestries regardless of the prediction algorithm used. While EN generally outperformed random forest (RF), support vector regression (SVR), and K nearest neighbor (KNN), we found that RF outperformed EN for some genes, particularly between disparate ancestries, suggesting potential robustness and reduced variability of RF imputation performance across global populations. When applied to a high-density lipoprotein (HDL) phenotype, we show including RF prediction models in PrediXcan revealed potential gene associations missed by EN models. Therefore, by integrating other ML modeling into PrediXcan and diversifying our training populations to include more global ancestries, we may uncover new genes associated with complex traits.
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Affiliation(s)
- Paul C Okoro
- Program in Bioinformatics, Loyola University Chicago, Chicago, IL, USA
| | - Ryan Schubert
- Department of Mathematics and Statistics, Loyola University Chicago, Chicago, IL, USA
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences, The Lundquist Institute and Department of Pediatrics at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - W Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, The Lundquist Institute and Department of Pediatrics at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Ina Hoeschele
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, USA.,Department of Statistics, Virginia Tech, Blacksburg, VA, USA.,Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Yongmei Liu
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Hae Kyung Im
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Amy Luke
- Department of Public Health Sciences, Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, IL, USA
| | - Lara R Dugas
- Department of Public Health Sciences, Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, IL, USA.,Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Heather E Wheeler
- Program in Bioinformatics, Loyola University Chicago, Chicago, IL, USA.,Department of Biology, Loyola University Chicago, Chicago, IL, USA.,Department of Computer Science, Loyola University Chicago, Chicago, IL, USA
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13
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Tsai DJ, Fang WH, Wu LW, Tai MC, Kao CC, Huang SM, Chen WT, Hsiao PJ, Chiu CC, Su W, Wu CC, Su SL. The Polymorphism at PLCB4 Promoter (rs6086746) Changes the Binding Affinity of RUNX2 and Affects Osteoporosis Susceptibility: An Analysis of Bioinformatics-Based Case-Control Study and Functional Validation. Front Endocrinol (Lausanne) 2021; 12:730686. [PMID: 34899595 PMCID: PMC8657146 DOI: 10.3389/fendo.2021.730686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 11/09/2021] [Indexed: 12/13/2022] Open
Abstract
PURPOSE Genome-wide association studies have identified numerous genetic variants that are associated with osteoporosis risk; however, most of them are present in the non-coding regions of the genome and the functional mechanisms are unknown. In this study, we aimed to investigate the potential variation in runt domain transcription factor 2 (RUNX2), which is an osteoblast-specific transcription factor that normally stimulates bone formation and osteoblast differentiation, regarding variants within RUNX2 binding sites and risk of osteoporosis in postmenopausal osteoporosis (PMOP). METHODS We performed bioinformatics-based prediction by combining whole genome sequencing and chromatin immunoprecipitation sequencing to screen functional SNPs in the RUNX2 binding site using data from the database of Taiwan Biobank; Case-control studies with 651 postmenopausal women comprising 107 osteoporosis patients, 290 osteopenia patients, and 254 controls at Tri-Service General Hospital between 2015 and 2019 were included. The subjects were examined for bone mass density and classified into normal and those with osteopenia or osteoporosis by T-scoring with dual-energy X-ray absorptiometry. Furthermore, mRNA expression and luciferase reporter assay were used to provide additional evidence regarding the associations identified in the association analyses. Chi-square tests and logistic regression were mainly used for statistical assessment. RESULTS Through candidate gene approaches, 3 SNPs in the RUNX2 binding site were selected. A novel SNP rs6086746 in the PLCB4 promoter was identified to be associated with osteoporosis in Chinese populations. Patients with AA allele had higher risk of osteoporosis than those with GG+AG (adjusted OR = 6.89; 95% confidence intervals: 2.23-21.31, p = 0.001). Moreover, the AA genotype exhibited lower bone mass density (p < 0.05). Regarding mRNA expression, there were large differences in the correlation between PLCB4 and different RUNX2 alleles (Cohen's q = 0.91). Functionally, the rs6086746 A allele reduces the RUNX2 binding affinity, thus enhancing the suppression of PLCB4 expression (p < 0.05). CONCLUSIONS Our results provide further evidence to support the important role of the SNP rs6086746 in the etiology of osteopenia/osteoporosis, thereby enhancing the current understanding of the susceptibility to osteoporosis. We further studied the mechanism underlying osteoporosis regulation by PLCB4.
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Affiliation(s)
- Dung-Jang Tsai
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
- School of Public Health, National Defense Medical Center, Taipei, Taiwan
| | - Wen-Hui Fang
- Department of Family and Community Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Li-Wei Wu
- Department of Family and Community Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Ming-Cheng Tai
- Department of Ophthalmology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Chung-Cheng Kao
- Superintendent’s Office, Tri-Service General Hospital Songshan Branch, National Defense Medical Center, Taipei, Taiwan
| | - Shih-Ming Huang
- Department of Biochemistry, National Defense Medical Center, Taipei, Taiwan
| | - Wei-Teing Chen
- Division of Thoracic Medicine, Department of Medicine, Cheng Hsin General Hospital, Taipei, Taiwan
- Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, ROC, Taiwan
| | - Po-Jen Hsiao
- Department of Internal Medicine, Taoyuan Armed Forces General Hospital, Taoyuan, Taiwan
- Division of Nephrology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Chih-Chien Chiu
- Division of Infectious Diseases, Department of Internal Medicine, Taoyuan Armed Forces General Hospital, National Defense Medical Center, Taoyuan, Taiwan
| | - Wen Su
- Graduate Institute of Aerospace and Undersea Medicine, National Defense Medical Center, Taipei, Taiwan
| | - Chia-Chun Wu
- Department of Orthopedics, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Sui-Lung Su
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
- School of Public Health, National Defense Medical Center, Taipei, Taiwan
- *Correspondence: Sui-Lung Su,
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14
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Wen Y, Zhou Y, Jiao B, Shen L. Genetics of Progressive Supranuclear Palsy: A Review. JOURNAL OF PARKINSON'S DISEASE 2021; 11:93-105. [PMID: 33104043 PMCID: PMC7990399 DOI: 10.3233/jpd-202302] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 09/26/2020] [Indexed: 02/06/2023]
Abstract
Progressive supranuclear palsy (PSP) is an atypical parkinsonism with prominent 4R-tau neuropathology, and the classical clinical phenotype is characterized by vertical supranuclear gaze palsy, unprovoked falls, akinetic-rigid syndrome and cognitive decline. Though PSP is generally regarded as sporadic, there is increasing evidence suggesting that a series of common and rare genetic variants impact on sporadic and familial forms of PSP. To date, more than 10 genes have been reported to show a potential association with PSP. Among these genes, the microtubule-associated protein tau (MAPT) is the risk locus with the strongest effect size on sporadic PSP in the case-control genome-wide association studies (GWAS). Additionally, MAPT mutations are the most common cause of familial PSP while the leucine-rich repeat kinase 2 (LRRK2) is a rare monogenic cause of PSP, and several other gene mutations may mimic the PSP phenotype, like the dynactin subunit 1 (DCTN1). In total, 15 MAPT mutations have been identified in cases with PSP, and the mean age at onset is much earlier than in cases carrying LRRK2 or DCTN1 mutations. GWAS have further identified several risk loci of PSP, proposing molecular pathways related to PSP. The present review focused on genetic studies on PSP and summarized genetic factors of PSP, which may help to elucidate the underlying pathogenesis and provide new perspectives for therapeutic strategies.
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Affiliation(s)
- Yafei Wen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
| | - Yafang Zhou
- Department of Geriatrics Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
| | - Bin Jiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
- National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, Hunan, PR China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, PR China
| | - Lu Shen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
- National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, Hunan, PR China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, PR China
- Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Changsha, Hunan, PR China
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Ye W, Wang Y, Hou S, Mei B, Liu X, Huang H, Zhou Q, Niu Y, Chen Y, Zhang M, Huang Q. USF3 modulates osteoporosis risk by targeting WNT16, RANKL, RUNX2, and two GWAS lead SNPs rs2908007 and rs4531631. Hum Mutat 2020; 42:37-49. [PMID: 33058301 DOI: 10.1002/humu.24126] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/09/2020] [Accepted: 10/05/2020] [Indexed: 01/15/2023]
Abstract
Osteoporotic fractures cause major morbidity and mortality in the aging population. Genome-wide association studies (GWAS) have identified USF3 as the novel susceptibility gene of osteoporosis. However, the functional role in bone metabolism and the target gene of the basic helix-loop-helix transcription factor USF3 are unclear. Here, we show that USF3 enhances osteoblast differentiation and suppresses osteoclastogenesis in cultured human osteoblast-like U-2OS cells. Mechanistic studies revealed that transcription factor USF3 antagonistically interacts with anti-osteogenic TWIST1/TCF12 heterodimer in the WNT16 and RUNX2 promoter, and counteracts CREB1 and JUN/FOS in the RANKL promoter. Importantly, the osteoporosis GWAS variant g.1744A>G (rs2908007A>G) located in the WNT16 promoter confers G-allele-specific transcriptional modulation by USF3, TWIST1/TCF12 and TBX5/TBX15, and USF3 transactivates the osteoclastogenesis suppressor WNT16 promoter activity and antagonizes the repression of WNT16 by TWIST1 and TCF12. The risk G allele of osteoporosis GWAS variant g.3260A>G (rs4531631A>G) in the RANKL promoter facilitates the binding of CREB1 and JUN/FOS and enhances transactivation of the osteoclastogenesis contributor RANKL that is inhibited by USF3. Our findings uncovered the functional mechanisms of osteoporosis novel GWAS-associated gene USF3 and lead single nucleotide polymorphisms rs2908007 and rs4531631 in the regulation of bone formation and resorption.
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Affiliation(s)
- Weiyuan Ye
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Ya Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Sasa Hou
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Bing Mei
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Xinhong Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Han Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Qian Zhou
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Yajing Niu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Yuanyuan Chen
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Manling Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Qingyang Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
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16
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Lin A, Zhou M, Hua RX, Zhang J, Zhou H, Li S, Cheng J, Xia H, Fu W, He J. METTL3 polymorphisms and Wilms tumor susceptibility in Chinese children: A five-center case-control study. J Gene Med 2020; 22:e3255. [PMID: 32716082 DOI: 10.1002/jgm.3255] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/21/2020] [Accepted: 07/21/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Wilms tumor is a common pediatric tumor worldwide. Methyltransferase like 3 (METTL3) is a core gene of the N6 -methyladenosine (m6 A) modification that widely affects the transcription of tumor-related genes in eukaryotes. METTL3 has been extensively investigated in various tumors but not Wilms tumor. METHODS We describe a five-center case-control study with 414 patients and 1199 controls aiming to explore the associations between METTL3 polymorphisms (rs1061026 T>G, rs1061027 C>A, rs1139130 A>G and rs1263801 G>C) and Wilms tumor susceptibility. A TaqMan real-time polymerase chain reaction was performed for genotyping. Odds ratios (ORs) and 95% confidence intervals (CIs) were reported as evaluation indicators to determine any associations. RESULTS Referring to the preliminary analysis results, protective genotypes were identified as rs1061026 TG/GG, rs1061027 CA/AA, rs1139130 GG and rs1263801 GC/CC. The children with three protective genotypes were less likely to develop Wilms tumor than children without protective genotypes (adjusted OR = 0.68, 95% CI = 0.46-0.999, p = 0.0496). Similarly, stratified analysis of the subgroup aged > 18 months, carrying 3 or 4 protective genotypes, was a protective factor for Wilms tumor compared to carrying 0-2 protective genotypes (adjusted OR = 0.59 95% CI = 0.39-0.91, p = 0.016). However, we did not observe any other significant results. CONCLUSIONS The combined effect of METTL3 polymorphisms reduce Wilms tumor susceptibility in Chinese children. This conclusion requires further verification.
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Affiliation(s)
- Ao Lin
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Mingming Zhou
- Department of Clinical Laboratory, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Zhejiang, Hangzhou, China
| | - Rui-Xi Hua
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
- Department of Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jiao Zhang
- Department of Pediatric Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Haixia Zhou
- Department of Hematology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Suhong Li
- Department of Pathology, Children Hospital and Women Health Center of Shanxi, Taiyuan, Shannxi, China
| | - Jiwen Cheng
- Department of Pediatric Surgery, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Huimin Xia
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Wen Fu
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jing He
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
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17
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Peat G, Jones W, Nuhn M, Marugán JC, Newell W, Dunham I, Zerbino D. The open targets post-GWAS analysis pipeline. Bioinformatics 2020; 36:2936-2937. [PMID: 31930349 PMCID: PMC7203748 DOI: 10.1093/bioinformatics/btaa020] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 12/19/2019] [Accepted: 01/09/2020] [Indexed: 11/17/2022] Open
Abstract
Motivation Genome-wide association studies (GWAS) are a powerful method to detect even weak associations between variants and phenotypes; however, many of the identified associated variants are in non-coding regions, and presumably influence gene expression regulation. Identifying potential drug targets, i.e. causal protein-coding genes, therefore, requires crossing the genetics results with functional data. Results We present a novel data integration pipeline that analyses GWAS results in the light of experimental epigenetic and cis-regulatory datasets, such as ChIP-Seq, Promoter-Capture Hi-C or eQTL, and presents them in a single report, which can be used for inferring likely causal genes. This pipeline was then fed into an interactive data resource. Availability and implementation The analysis code is available at www.github.com/Ensembl/postgap and the interactive data browser at postgwas.opentargets.io.
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Affiliation(s)
- Gareth Peat
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.,Open Targets, EBI South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - William Jones
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Michael Nuhn
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.,Open Targets, EBI South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - José Carlos Marugán
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.,Open Targets, EBI South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - William Newell
- Open Targets, EBI South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.,GSK, Medicines Research Center, Stevenage SG1 2NY, UK
| | - Ian Dunham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.,Open Targets, EBI South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.,Open Targets, EBI South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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18
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Xia X, Ding M, Xuan JF, Xing JX, Yao J, Wu X, Wang BJ. Functional polymorphisms and transcriptional analysis in the 5' region of the human serotonin receptor 1B gene (HTR1B) and their associations with psychiatric disorders. BMC Psychiatry 2020; 20:499. [PMID: 33036580 PMCID: PMC7545834 DOI: 10.1186/s12888-020-02906-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 09/30/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The 5-hydroxytryptamine 1B receptor (5-HT1B) plays an essential role in the serotonin (5-HT) system and is widely involved in a variety of brain activities. HTR1B is the gene encoding 5-HT1B. Genome-wide association studies have shown that HTR1B polymorphisms are closely related to multiple mental and behavioral disorders; however, the functional mechanisms underlying these associations are unknown. This study investigated the effect of several HTR1B haplotypes on regulation of gene expression in vitro and the functional sequences in the 5' regulatory region of HTR1B to determine their potential association with mental and behavioral disorders. METHODS Six haplotypes consisting of rs4140535, rs1778258, rs17273700, rs1228814, rs11568817, and rs130058 and several truncated fragments of the 5' regulatory region of HTR1B were transfected into SK-N-SH and HEK-293 cells. The relative fluorescence intensities of the different haplotypes and truncated fragments were detected using a dual-luciferase reporter assay system. RESULTS Compared to the major haplotype T-G-T-C-T-A, the relative fluorescence intensities of haplotypes C-A-T-C-T-A, C-G-T-C-T-A, C-G-C-A-G-T, and C-G-T-A-T-A were significantly lower, and that of haplotype C-G-C-A-G-A was significantly higher. Furthermore, the effects of the rs4140535T allele, the rs17273700C-rs11568817G linkage combination, and the rs1228814A allele made their relative fluorescence intensities significantly higher than their counterparts at each locus. Conversely, the rs1778258A and rs130058T alleles decreased the relative fluorescence intensities. In addition, we found that regions from - 1587 to - 1371 bp (TSS, + 1), - 1149 to - 894 bp, - 39 to + 130 bp, + 130 to + 341 bp, and + 341 to + 505 bp upregulated gene expression. In contrast, regions - 603 to - 316 bp and + 130 to + 341 bp downregulated gene expression. Region + 341 to + 505 bp played a decisive role in gene transcription. CONCLUSIONS HTR1B 5' regulatory region polymorphisms have regulatory effects on gene expression and potential correlate with several pathology and physiology conditions. This study suggests that a crucial sequence for transcription is located in region + 341 ~ + 505 bp. Regions - 1587 to - 1371 bp, - 1149 to - 894 bp, - 603 to - 316 bp, - 39 to + 130 bp, and + 130 to + 341 bp contain functional sequences that can promote or suppress the HTR1B gene expression.
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Affiliation(s)
- Xi Xia
- grid.412449.e0000 0000 9678 1884School of Forensic Medicine, China Medical University, No. 77 Puhe Road, Shenbei New District, Shenyang, 110122 China
| | - Mei Ding
- grid.412449.e0000 0000 9678 1884School of Forensic Medicine, China Medical University, No. 77 Puhe Road, Shenbei New District, Shenyang, 110122 China
| | - Jin-feng Xuan
- grid.412449.e0000 0000 9678 1884School of Forensic Medicine, China Medical University, No. 77 Puhe Road, Shenbei New District, Shenyang, 110122 China
| | - Jia-xin Xing
- grid.412449.e0000 0000 9678 1884School of Forensic Medicine, China Medical University, No. 77 Puhe Road, Shenbei New District, Shenyang, 110122 China
| | - Jun Yao
- grid.412449.e0000 0000 9678 1884School of Forensic Medicine, China Medical University, No. 77 Puhe Road, Shenbei New District, Shenyang, 110122 China
| | - Xue Wu
- grid.412449.e0000 0000 9678 1884School of Forensic Medicine, China Medical University, No. 77 Puhe Road, Shenbei New District, Shenyang, 110122 China
| | - Bao-jie Wang
- grid.412449.e0000 0000 9678 1884School of Forensic Medicine, China Medical University, No. 77 Puhe Road, Shenbei New District, Shenyang, 110122 China
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19
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Luningham JM, Chen J, Tang S, De Jager PL, Bennett DA, Buchman AS, Yang J. Bayesian Genome-wide TWAS Method to Leverage both cis- and trans-eQTL Information through Summary Statistics. Am J Hum Genet 2020; 107:714-726. [PMID: 32961112 PMCID: PMC7536614 DOI: 10.1016/j.ajhg.2020.08.022] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 08/24/2020] [Indexed: 12/17/2022] Open
Abstract
Transcriptome-wide association studies (TWASs) have been widely used to integrate gene expression and genetic data for studying complex traits. Due to the computational burden, existing TWAS methods do not assess distant trans-expression quantitative trait loci (eQTL) that are known to explain important expression variation for most genes. We propose a Bayesian genome-wide TWAS (BGW-TWAS) method that leverages both cis- and trans-eQTL information for a TWAS. Our BGW-TWAS method is based on Bayesian variable selection regression, which not only accounts for cis- and trans-eQTL of the target gene but also enables efficient computation by using summary statistics from standard eQTL analyses. Our simulation studies illustrated that BGW-TWASs achieved higher power compared to existing TWAS methods that do not assess trans-eQTL information. We further applied BWG-TWAS to individual-level GWAS data (N = ∼3.3K), which identified significant associations between the genetically regulated gene expression (GReX) of ZC3H12B and Alzheimer dementia (AD) (p value = 5.42 × 10-13), neurofibrillary tangle density (p value = 1.89 × 10-6), and global measure of AD pathology (p value = 9.59 × 10-7). These associations for ZC3H12B were completely driven by trans-eQTL. Additionally, the GReX of KCTD12 was found to be significantly associated with β-amyloid (p value = 3.44 × 10-8) which was driven by both cis- and trans-eQTL. Four of the top driven trans-eQTL of ZC3H12B are located within APOC1, a known major risk gene of AD and blood lipids. Additionally, by applying BGW-TWAS with summary-level GWAS data of AD (N = ∼54K), we identified 13 significant genes including known GWAS risk genes HLA-DRB1 and APOC1, as well as ZC3H12B.
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Affiliation(s)
- Justin M Luningham
- Department of Population Health Sciences, Georgia State University School of Public Health, Atlanta, GA 30303, USA; Center for Computational and Quantitative Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Junyu Chen
- Center for Computational and Quantitative Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Shizhen Tang
- Department of Biostatistics and Bioinformatics, Emory University School of Public Health, Atlanta, GA 30322, USA; Center for Computational and Quantitative Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology and Taub Institute for Research on Alzheimer disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - David A Bennett
- Rush Alzheimer disease Center, Rush University Medical Center, Chicago, IL 60612, USA
| | - Aron S Buchman
- Rush Alzheimer disease Center, Rush University Medical Center, Chicago, IL 60612, USA
| | - Jingjing Yang
- Center for Computational and Quantitative Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA.
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Wang D, Yang J, Fan J, Chen W, Nikolic‐Paterson DJ, Li J. Omics technologies for kidney disease research. Anat Rec (Hoboken) 2020; 303:2729-2742. [PMID: 32592293 DOI: 10.1002/ar.24413] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 12/31/2019] [Accepted: 02/17/2020] [Indexed: 12/24/2022]
Affiliation(s)
- Dan Wang
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen University Guangzhou China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province Guangzhou China
| | - Jiayi Yang
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen University Guangzhou China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province Guangzhou China
| | - Jinjin Fan
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen University Guangzhou China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province Guangzhou China
| | - Wei Chen
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen University Guangzhou China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province Guangzhou China
| | | | - Jinhua Li
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen University Guangzhou China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province Guangzhou China
- Shunde Women and Children Hospital, Guangdong Medical University Shunde Guangdong China
- The Second Clinical College, Guangdong Medical University Dongguan Guangdong China
- Department of Anatomy and Developmental BiologyMonash Biomedicine Discovery Institute, Monash University Clayton Victoria Australia
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21
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Wang P, Deng Y, Yan X, Zhu J, Yin Y, Shu Y, Bai D, Zhang S, Xu H, Lu X. The Role of ARID5B in Acute Lymphoblastic Leukemia and Beyond. Front Genet 2020; 11:598. [PMID: 32595701 PMCID: PMC7303299 DOI: 10.3389/fgene.2020.00598] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 05/18/2020] [Indexed: 02/05/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common malignancy in children with distinct characteristics among different subtypes. Although the etiology of ALL has not been fully unveiled, initiation of ALL has been demonstrated to partly depend on genetic factors. As indicated by several genome wide association studies (GWASs) and candidate gene analyses, ARID5B, a member of AT-rich interactive domain (ARID) protein family, is associated with the occurrence and prognosis of ALL. However, the mechanisms by which ARID5B genotype impact on the susceptibility and treatment outcome remain vague. In this review, we outline developments in the understanding of ARID5B in the susceptibility of ALL and its therapeutic perspectives, and summarize the underlying mechanisms based on the limited functional studies, hoping to illustrate the possible mechanisms of ARID5B impact and highlight the potential treatment regimens.
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Affiliation(s)
- Peiqi Wang
- Department of Pediatric Hematology/Oncology, West China Second University Hospital, Sichuan University, Chengdu, China.,State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yun Deng
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Xinyu Yan
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jianhui Zhu
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yuanyuan Yin
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yang Shu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Ding Bai
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Shouyue Zhang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Heng Xu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China.,Department of Laboratory Medicine/Research Center of Clinical Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China.,Precision Medicine Center, State Key Laboratory of Biotherapy and Precision Medicine, Key Laboratory of Sichuan Province, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Xiaoxi Lu
- Department of Pediatric Hematology/Oncology, West China Second University Hospital, Sichuan University, Chengdu, China
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22
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Mousavi-Nasab FS, Colagar AH. Investigation of the association of endothelial nitric oxide synthase (eNOS)-T786C gene polymorphism with the risk of male infertility in an Iranian population. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:22434-22440. [PMID: 32314287 DOI: 10.1007/s11356-020-08860-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/13/2020] [Indexed: 06/11/2023]
Abstract
Recent studies have demonstrated that making the sorts of oxygen reactive, such as nitric oxide, can cause oxidative lipid damage, protein damage, and damage to the DNA of cells. Sperm DNA damage effect on the reduction of sperm mobility and damage of acrosome membrane lead to the inability of sperm to fertilize the oocyte. Increasing expression of endothelial nitric oxide synthase (eNOS) gene is seen in various diseases such as cardiovascular and infertility diseases. This study aimed to assess the association between eNOS gene single nucleotide polymorphism/SNP (rs2070744, T786C) and risk of male infertility and the quality of sperm parameters in an Iranian population. In this case-control study, 100 infertile men were enrolled as a patient group. Control groups consisted of 100 fertile men. T786C genotypes were determined using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Results showed that T786C SNP, contained frequent genotype TC (p = 0.000; OR = 0.000; 95% CI = 0.000-0.015), TC + CC genotypes (p = 0.000; OR = 0.000; 95% CI = 0.000-0.015), and C allele (p = 0.000; OR = 0.00; 95% CI = 0.000-0.007), revealed a significant with male infertility. Based on the findings of this study suggested that although T786C SNP could not be applied as an appropriate genetic risk factor for male infertility, it probably may be considered a protective marker for other researchers. However, more comprehensive studies in different populations are required to confirm our data.
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Affiliation(s)
- Faezeh Sadat Mousavi-Nasab
- Department of Molecular and Cell Biology, Faculty of Basic Sciences, University of Mazandaran, Babolsar, Mazandaran, CP: 47416-95447, Iran
- Department of Molecular and Cell Biology, Faculty of Basic Sciences, Islamic Azad University-Tonekabon Branch, Tonekabon, Iran
| | - Abasalt Hosseinzadeh Colagar
- Department of Molecular and Cell Biology, Faculty of Basic Sciences, University of Mazandaran, Babolsar, Mazandaran, CP: 47416-95447, Iran.
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Atypical chemokine receptor ACKR2-V41A has decreased CCL2 binding, scavenging, and activation, supporting sustained inflammation and increased Alzheimer's disease risk. Sci Rep 2020; 10:8019. [PMID: 32415244 PMCID: PMC7229167 DOI: 10.1038/s41598-020-64755-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 03/23/2020] [Indexed: 01/21/2023] Open
Abstract
A recent genome-wide association study (GWAS) of 59 cerebrospinal fluid (CSF) proteins with a connection to Alzheimer's disease (AD) demonstrated an association between increased levels of chemokine ligand 2 (CCL2) with an atypical chemokine receptor chemokine-binding protein 2 variant V41A (ACKR2-V41A; rs2228467). High levels of CCL2 are associated with increased risk of AD development as well as other inflammatory diseases. In this study we characterized the biological function of the ACKR2-V41A receptor compared to the wild type allele by measuring its ligand binding affinity, CCL2 scavenging efficiency, and cell activation sensitivity. We transfected Chinese hamster ovary cells with plasmids carrying wild type ACKR2 (ACKR2-WT) or the mutant ACKR2-V41A receptor. Binding affinity assays showed that ACKR2-V41A has a lower binding affinity for CCL2 and CCL4 than ACKR2-WT. CCL2 scavenging results aligned with binding affinity assays, with ACKR2-V41A cells scavenging CCL2 with a lower efficiency than ACKR2-WT. Cell activation assays also showed that ACKR2-V41A cells had significantly lower receptor upregulation (β-Arrestin-dependent signaling pathway) upon stimulation compared to ACKR2-WT cells. These findings provide molecular and biological mechanistic insights into the GWAS association of ACKR2-V41A with increased levels of CCL2 in CSF and possibly other chemokine ligands. Increased CCL2 levels are associated with accelerated cognitive decline and increased risk of AD. Understanding how this atypical chemokine receptor allele increases serum markers of inflammation could lead to novel therapeutic solutions for AD.
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24
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Cheng M, Huang X, Zhang M, Huang Q. Computational and functional analyses of T2D GWAS SNPs for transcription factor binding. Biochem Biophys Res Commun 2020; 523:658-665. [PMID: 31948755 DOI: 10.1016/j.bbrc.2019.12.086] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 12/30/2019] [Indexed: 12/31/2022]
Abstract
Genome-wide association studies (GWASs) have successfully identified numerous non-coding genetic variants for type 2 diabetes (T2D), but the functional roles underlying these non-coding variants remain largely unknown. The effects of T2D GWAS lead SNPs on transcriptional factors binding motifs were firstly analyzed via JASPAR, followed by functional validations including dual-luciferase reporter assays, biotin-based DNA pull-down assays, real-time quantitative PCR, and western blotting. The results showed that GWAS SNP rs4430796 conferred T allele specific transcriptional enhancer activity via a PAX6 binding element, and upregulated the expression of HNF1B. GWAS SNP rs4607103 showed a bidirectional modulation of ADAMTS9-AS2 and ADAMTS9 by TCF7L2 in a T allele-specific manner. GWAS SNP rs849135 conferred C allele-specific bidirectional transcriptional enhancer activity via a CREB1 binding element. Our findings have uncovered the functional mechanisms of three T2D GWAS SNPs via affecting the binding of transcription factors, providing new insights into the genetics and molecular pathogenesis of T2D.
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Affiliation(s)
- Mengrong Cheng
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, PR China; College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, Hubei, PR China
| | - Xinyao Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, PR China
| | - Manling Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, PR China
| | - Qingyang Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, PR China.
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25
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Wang Y, Ye W, Liu Y, Mei B, Liu X, Huang Q. Osteoporosis genome-wide association study variant c.3781 C>A is regulated by a novel anti-osteogenic factor miR-345-5p. Hum Mutat 2020; 41:709-718. [PMID: 31883164 DOI: 10.1002/humu.23959] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 11/11/2019] [Accepted: 11/18/2019] [Indexed: 12/21/2022]
Abstract
Upstream transcription factor family member 3 (USF3) c.3781C>A (rs1026364) in the 3'-untranslated region (3'-UTR) has been firmly associated with bone mineral density (BMD) in genome-wide association study (GWAS). However, the molecular mechanism by which it influences BMD and osteoporosis is unknown. Bioinformatics analyses suggested that the risk c.3781A allele creates a target site for hsa-miR-345-5p binding. Luciferase assay validated that the c.3781A allele displayed significantly lower luciferase activities than the c.3781C allele in the human osteoblast cell line hFOB1.19, osteosarcoma cell lines U-2OS and Saos-2, and embryonic kidney cell line 293T. Furthermore, hsa-miR-345-5p regulated USF3 expression on both messenger RNA and protein levels in hFOB1.19 and U937 cells with heterozygous A/C genotype. Transfection of hsa-miR-345-5p antagomiR in heterozygous hFOB1.19 cells significantly increased the expression of osteogenic marker genes RUNX2, OSTERIX, COL1A1, ALP, OPN, OCN, and alkaline phosphatase activity and matrix mineralization level. Importantly, we found that hsa-miR-345-5p also inhibits osteoblast maturation in cell lines U-2OS with hsa-miR-345-5p nonbinding C/C genotype by targeting RUNX3 and SMAD1. Our findings uncovered a novel pathogenetic mechanism of osteoporosis by GWAS variant c.3781C>A-mediated disruption of hsa-miR-345-5p binding at the 3'-UTR of USF3 and the functional role of hsa-miR-345-5p in osteogenic differentiation.
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Affiliation(s)
- Ya Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Weiyuan Ye
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Yuyong Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Bing Mei
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Xinhong Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Qingyang Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
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26
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van Reij RR, Joosten EA, van den Hoogen NJ. Dopaminergic neurotransmission and genetic variation in chronification of post-surgical pain. Br J Anaesth 2019; 123:853-864. [DOI: 10.1016/j.bja.2019.07.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 07/10/2019] [Accepted: 07/26/2019] [Indexed: 01/30/2023] Open
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27
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Zhong R, Tian J, Fu M, Ma S, Liu L, Li J, Shen N, Ke J, Yang Y, Gong Y, Zhu Y, Wang Y, Gong J, Chang J, Lei P, Cheng X, Huang K, Shen G, Miao X. LINC01149 variant modulates MICA expression that facilitates hepatitis B virus spontaneous recovery but increases hepatocellular carcinoma risk. Oncogene 2019; 39:1944-1956. [PMID: 31754211 DOI: 10.1038/s41388-019-1117-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 11/04/2019] [Accepted: 11/11/2019] [Indexed: 02/06/2023]
Abstract
Interpreting disease-causing variants, especially in noncoding regions by genome-wide association studies (GWAS), has become one of the most challenging and demanding tasks. We hypothesized that functional lncRNAs variants in GWAS-identified loci might alter expression level of genes associated with persistent HBV infection and hepatocellular carcinoma (HCC). Integrated bioinformatics approaches were used to prioritize potentially functional variants and a two-stage case-control study (2473 HBV positive HCC patients, 2248 persistent HBV carriers and 2294 spontaneously recovered subjects) was performed to assess the roles of these variants. The rs2844512 G > C variant in LINC01149 was identified to facilitate HBV spontaneous recovery (OR = 0.84, 95% CI = 0.77-0.92) but increase the risk of HCC (OR = 1.21, 95% CI = 1.11-1.32) in combined samples. Subsequent biological assays indicated this variant created a binding site for miR-128-3p and upregulated MICA expression by serving as a miRNA sponge, which might recruit NK-cells to lyse infected cells, but release highly soluble MICA by shedding to induce NK-cells exhaustion and tumor immune evasion. These findings highlight a regulatory circuit between LINC01149 and MICA, mediating by miR-128-3p, and the important role of upregulated MICA in conferring susceptibility to persistent HBV infection and HCC.
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Affiliation(s)
- Rong Zhong
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianbo Tian
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mingpeng Fu
- Department of Immunology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Simin Ma
- Department of Immunology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Li Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Jiaoyuan Li
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Na Shen
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Juntao Ke
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Yang
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yajie Gong
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ying Zhu
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ying Wang
- Department of Virology, Wuhan Centers for Disease Prevention and Control, Wuhan, China
| | - Jing Gong
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiang Chang
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ping Lei
- Department of Immunology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiang Cheng
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kun Huang
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Guanxin Shen
- Department of Immunology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoping Miao
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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28
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Nagpal S, Meng X, Epstein MP, Tsoi LC, Patrick M, Gibson G, De Jager PL, Bennett DA, Wingo AP, Wingo TS, Yang J. TIGAR: An Improved Bayesian Tool for Transcriptomic Data Imputation Enhances Gene Mapping of Complex Traits. Am J Hum Genet 2019; 105:258-266. [PMID: 31230719 PMCID: PMC6698804 DOI: 10.1016/j.ajhg.2019.05.018] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 05/23/2019] [Indexed: 12/22/2022] Open
Abstract
The transcriptome-wide association studies (TWASs) that test for association between the study trait and the imputed gene expression levels from cis-acting expression quantitative trait loci (cis-eQTL) genotypes have successfully enhanced the discovery of genetic risk loci for complex traits. By using the gene expression imputation models fitted from reference datasets that have both genetic and transcriptomic data, TWASs facilitate gene-based tests with GWAS data while accounting for the reference transcriptomic data. The existing TWAS tools like PrediXcan and FUSION use parametric imputation models that have limitations for modeling the complex genetic architecture of transcriptomic data. Therefore, to improve on this, we employ a nonparametric Bayesian method that was originally proposed for genetic prediction of complex traits, which assumes a data-driven nonparametric prior for cis-eQTL effect sizes. The nonparametric Bayesian method is flexible and general because it includes both of the parametric imputation models used by PrediXcan and FUSION as special cases. Our simulation studies showed that the nonparametric Bayesian model improved both imputation R2 for transcriptomic data and the TWAS power over PrediXcan when ≥1% cis-SNPs co-regulate gene expression and gene expression heritability ≤0.2. In real applications, the nonparametric Bayesian method fitted transcriptomic imputation models for 57.8% more genes over PrediXcan, thus improving the power of follow-up TWASs. We implement both parametric PrediXcan and nonparametric Bayesian methods in a convenient software tool "TIGAR" (Transcriptome-Integrated Genetic Association Resource), which imputes transcriptomic data and performs subsequent TWASs using individual-level or summary-level GWAS data.
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Affiliation(s)
- Sini Nagpal
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Xiaoran Meng
- Department of Biostatistics and Bioinformatics, Emory University School of Public Health, Atlanta, GA 30322, USA; Center for Computational and Quantitative Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Michael P Epstein
- Department of Biostatistics and Bioinformatics, Emory University School of Public Health, Atlanta, GA 30322, USA; Center for Computational and Quantitative Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Lam C Tsoi
- Department of Dermatology; Department of Computational Medicine & Bioinformatics; Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Matthew Patrick
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Greg Gibson
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Philip L De Jager
- Medical Center Neurological Institute, Columbia University, New York, NY 10032, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL 60612, USA
| | - Aliza P Wingo
- Division of Mental Health, Atlanta VA Medical Center, Decatur, GA, USA; Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Thomas S Wingo
- Center for Computational and Quantitative Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jingjing Yang
- Center for Computational and Quantitative Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA.
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29
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Zeiler FA, McFadyen C, Newcombe VFJ, Synnot A, Donoghue EL, Ripatti S, Steyerberg EW, Gruen RL, McAllister TW, Rosand J, Palotie A, Maas AIR, Menon DK. Genetic Influences on Patient-Oriented Outcomes in Traumatic Brain Injury: A Living Systematic Review of Non-Apolipoprotein E Single-Nucleotide Polymorphisms. J Neurotrauma 2019; 38:1107-1123. [PMID: 29799308 PMCID: PMC8054522 DOI: 10.1089/neu.2017.5583] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
There is a growing literature on the impact of genetic variation on outcome in traumatic brain injury (TBI). Whereas a substantial proportion of these publications have focused on the apolipoprotein E (APOE) gene, several have explored the influence of other polymorphisms. We undertook a systematic review of the impact of single-nucleotide polymorphisms (SNPs) in non–apolipoprotein E (non-APOE) genes associated with patient outcomes in adult TBI). We searched EMBASE, MEDLINE, CINAHL, and gray literature from inception to the beginning of August 2017 for studies of genetic variance in relation to patient outcomes in adult TBI. Sixty-eight articles were deemed eligible for inclusion into the systematic review. The SNPs described were in the following categories: neurotransmitter (NT) in 23, cytokine in nine, brain-derived neurotrophic factor (BDNF) in 12, mitochondrial genes in three, and miscellaneous SNPs in 21. All studies were based on small patient cohorts and suffered from potential bias. A range of SNPs associated with genes coding for monoamine NTs, BDNF, cytokines, and mitochondrial proteins have been reported to be associated with variation in global, neuropsychiatric, and behavioral outcomes. An analysis of the tissue, cellular, and subcellular location of the genes that harbored the SNPs studied showed that they could be clustered into blood–brain barrier associated, neuroprotective/regulatory, and neuropsychiatric/degenerative groups. Several small studies report that various NT, cytokine, and BDNF-related SNPs are associated with variations in global outcome at 6–12 months post-TBI. The association of these SNPs with neuropsychiatric and behavioral outcomes is less clear. A definitive assessment of role and effect size of genetic variation in these genes on outcome remains uncertain, but could be clarified by an adequately powered genome-wide association study with appropriate recording of outcomes.
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Affiliation(s)
- Frederick A Zeiler
- Division of Anaesthesia, University of Cambridge, Cambridge, United Kingdom.,Section of Neurosurgery, Department of Surgery, University of Manitoba, Winnipeg, Manitoba, Canada.,Clinician Investigator Program, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Charles McFadyen
- Division of Anaesthesia, University of Cambridge, Cambridge, United Kingdom
| | | | - Anneliese Synnot
- Centre for Excellence in Traumatic Brain Injury Research, National Trauma Research Institute, Monash University, The Alfred Hospital, Melbourne, Australia and Cochrane Consumers and Communication Review Group, Centre for Health Communication and Participation, School of Psychology and Public Health, La Trobe University, Melbourne, Australia
| | - Emma L Donoghue
- Australian and New Zealand Intensive Care Research Centre, School of Public Health and Preventive Medicine and Cochrane Australia, Monash University, Melbourne, Australia
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM) and Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ewout W Steyerberg
- Department of Public Health, Erasmus MC-University Medical Center Rotterdam, Rotterdam, the Netherlands and Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
| | - Russel L Gruen
- Central Clinical School, Monash University, Melbourne, Australia and Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Thomas W McAllister
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, Indiana
| | - Jonathan Rosand
- Division of Neurocritical Care and Emergency Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, and Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Aarno Palotie
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland; Psychiatric and Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts; Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts
| | - Andrew I R Maas
- Department of Neurosurgery, Antwerp University Hospital and University of Antwerp, Edegem, Belgium
| | - David K Menon
- Division of Anaesthesia, University of Cambridge, Cambridge, United Kingdom
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30
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Laarman MD, Geeven G, Barnett P, Rinkel GJE, de Laat W, Ruigrok YM, Bakkers J. Chromatin Conformation Links Putative Enhancers in Intracranial Aneurysm-Associated Regions to Potential Candidate Genes. J Am Heart Assoc 2019; 8:e011201. [PMID: 30994044 PMCID: PMC6512097 DOI: 10.1161/jaha.118.011201] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background We previously showed that intracranial aneurysm (IA)–associated single‐nucleotide polymorphisms are enriched in promoters and putative enhancers identified in the human circle of Willis, on which IAs develop, suggesting a role for promoters and enhancers in IAs. We further investigated the role of putative enhancers in the pathogenesis of IA by identifying their potential target genes and validating their regulatory activity. Methods and Results Using our previously published circle of Willis chromatin immunoprecipitation and sequencing data, we selected 34 putative enhancers in IA‐associated regions from genome‐wide association studies. We then used a chromatin conformation capture technique to prioritize target genes and found that 15 putative enhancers interact with the promoters of 6 target genes: SOX17,CDKN2B,MTAP,CNNM2,RPEL1, and GATA6. Subsequently, we assessed the activity of these putative enhancers in vivo in zebrafish embryos and confirmed activity for 8 putative enhancers. Last, we found that all 6 target genes are expressed in the circle of Willis, on the basis of RNA sequencing data and in situ hybridization. Furthermore, in situ hybridization showed that these genes are expressed in multiple cell types in the circle of Willis. Conclusions In 4 of 6 IA‐associated genome‐wide association study regions, we identified 8 putative enhancers that are active in vivo and interact with 6 nearby genes, suggesting that these genes are regulated by the identified putative enhancers. These genes, SOX17,CDKN2B,MTAP,CNNM2,RPEL1, and GATA6, are therefore potential candidate genes involved in IA pathogenesis and should be studied using animal models in the future.
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Affiliation(s)
- Melanie D Laarman
- 1 Department of Neurology and Neurosurgery Brain Center Rudolf Magnus University Medical Center, Utrecht the Netherlands.,2 Hubrecht Institute (Royal Netherlands Academy of Arts and Sciences (KNAW)) University Medical Center, Utrecht the Netherlands
| | - Geert Geeven
- 2 Hubrecht Institute (Royal Netherlands Academy of Arts and Sciences (KNAW)) University Medical Center, Utrecht the Netherlands
| | - Phil Barnett
- 4 Department of Medical Biology Academic Medical Center University of Amsterdam the Netherlands
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- 5 Netherlands Institute for Neuroscience Amsterdam the Netherlands
| | - Gabriël J E Rinkel
- 1 Department of Neurology and Neurosurgery Brain Center Rudolf Magnus University Medical Center, Utrecht the Netherlands
| | - Wouter de Laat
- 2 Hubrecht Institute (Royal Netherlands Academy of Arts and Sciences (KNAW)) University Medical Center, Utrecht the Netherlands
| | - Ynte M Ruigrok
- 1 Department of Neurology and Neurosurgery Brain Center Rudolf Magnus University Medical Center, Utrecht the Netherlands
| | - Jeroen Bakkers
- 2 Hubrecht Institute (Royal Netherlands Academy of Arts and Sciences (KNAW)) University Medical Center, Utrecht the Netherlands.,3 Division of Heart and Lungs Department of Medical Physiology University Medical Center, Utrecht the Netherlands
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Zhuang H, Han J, Cheng L, Liu SL. A Positive Causal Influence of IL-18 Levels on the Risk of T2DM: A Mendelian Randomization Study. Front Genet 2019; 10:295. [PMID: 31024619 PMCID: PMC6459887 DOI: 10.3389/fgene.2019.00295] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 03/19/2019] [Indexed: 12/21/2022] Open
Abstract
A large number of clinical studies have shown that interleukin-18 (IL-18) plasma levels are positively correlated with the pathogenesis and development of type 2 diabetes mellitus (T2DM), but it remains unclear whether IL-18 causes T2DM, primarily due to the influence of reverse causality and residual confounding factors. Genome-wide association studies have led to the discovery of numerous common variants associated with IL-18 and T2DM and opened unprecedented opportunities for investigating possible associations between genetic traits and diseases. In this study, we employed a two-sample Mendelian randomization (MR) method to analyze the causal relationships between IL-18 plasma levels and T2DM using IL18-related SNPs as genetic instrumental variables (IVs). We first selected eight SNPs that were significantly associated with IL-18 but independent of T2DM. We then used these SNPs as IVs to evaluate their effects on T2DM using the inverse-variance weighted (IVW) method. Finally, we conducted sensitivity analysis and MR-Egger regression analysis to evaluate the heterogeneity and pleiotropic effects of each variant. The results based on the IVW method demonstrate that high IL-18 plasma levels significantly increase the risk of T2DM, and no heterogeneity or pleiotropic effects appeared after the sensitivity and MR-Egger analyses.
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Affiliation(s)
- He Zhuang
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China
| | - Junwei Han
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Liang Cheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Shu-Lin Liu
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China.,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
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32
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Cai X, Xu Q, Zhou C, Zhou L, Dai W, Ji G. The association of nucleotide-binding oligomerization domain 2 gene polymorphisms with the risk of asthma in the Chinese Han population. Mol Genet Genomic Med 2019; 7:e00675. [PMID: 30950247 PMCID: PMC6565575 DOI: 10.1002/mgg3.675] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 02/17/2019] [Accepted: 03/14/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Genetic background is one of the important risk factors for development of asthma. The nucleotide-binding oligomerization domain 2 (NOD2) has been involved in the pathogenesis of asthma. The purpose of this study was to explore the relationship between NOD2 gene polymorphisms and asthma susceptibility in the Chinese Han population. METHODS Children with asthma (n = 309) and Healthy children (n = 163) were recruited from Yancheng Third People's Hospital, Yancheng, China, between January 2016 and December 2017. The NOD2 gene polymorphisms were measured by the Snapshot SNP genotyping assays. Genotyping was performed for 4 tag SNPs of NOD2. Serum IFN-β levels were measured by ELISA. RESULTS The serum IFN-β levels were significantly lower in Asthmatic children than those in the controls (p < 0.001). Low levels of IFN-β may be related to the susceptibility to severe asthma. The rs3135499 C allele was associated with a significantly increased risk of asthma as compared with the rs3135499 A allele. CONCLUSION The rs3135499 polymorphism of NOD2 gene and IFN-β may play a role in the pathogenesis of asthma.
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Affiliation(s)
- Xulong Cai
- Department of Pediatrics, Yancheng Third People's Hospital, Yancheng, China
| | - Qiaolan Xu
- Department of Pediatrics, Yancheng Third People's Hospital, Yancheng, China
| | - Chenrong Zhou
- Department of Pediatrics, Yancheng Third People's Hospital, Yancheng, China
| | - Li Zhou
- Department of Pediatrics, Yancheng Third People's Hospital, Yancheng, China
| | - Weihua Dai
- Department of Pediatrics, Yancheng Third People's Hospital, Yancheng, China
| | - Guanchi Ji
- Department of Pediatrics, Yancheng Third People's Hospital, Yancheng, China
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Svishcheva GR. A generalized model for combining dependent SNP-level summary statistics and its extensions to statistics of other levels. Sci Rep 2019; 9:5461. [PMID: 30940856 PMCID: PMC6445108 DOI: 10.1038/s41598-019-41827-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 03/06/2019] [Indexed: 11/12/2022] Open
Abstract
Here I propose a fundamentally new flexible model to reveal the association between a trait and a set of genetic variants in a genomic region/gene. This model was developed for the situation when original individual-level phenotype and genotype data are not available, but the researcher possesses the results of statistical analyses conducted on these data (namely, SNP-level summary Z score statistics and SNP-by-SNP correlations). The new model was analytically derived from the classical multiple linear regression model applied for the region-based association analysis of individual-level phenotype and genotype data by using the linear compression of data, where the SNP-by-SNP correlations are among the explanatory variables, and the summary Z score statistics are categorized as the response variables. I analytically show that the regional association analysis methods developed within the framework of the classical multiple linear regression model with additive effects of genetic variants can be reformulated in terms of the new model without the loss of information. The results obtained from the regional association analysis utilizing the classical model and those derived using the proposed model are identical when SNP-by-SNP correlations and SNP-level statistics are estimated from the same genetic data.
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Affiliation(s)
- Gulnara R Svishcheva
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia. .,Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia.
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Papanikolaou IG, Giannelou P, Anagnostou E, Mavrogianni D, Drakakis P, Loutradis D. Combined study on the single nucleotide polymorphisms in the follicle-stimulating hormone receptor (Ser680Asn) and anti-Müllerian hormone receptor type II (-482A>G) as genetic markers in assisted reproduction. Horm Mol Biol Clin Investig 2019; 38:hmbci-2018-0077. [PMID: 30904901 DOI: 10.1515/hmbci-2018-0077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 02/10/2019] [Indexed: 12/30/2022]
Abstract
Background Infertile women may have underlying genetic abnormalities. There is, at present, a significant number of studies on the relation between the follicle stimulating hormone receptor (FSHR) or anti-Müllerian hormone type II receptor (AMHRII) polymorphisms and response to in-vitro fertilisation (IVF) treatment. However, it is not yet clear which genotype or combination of genotypes is favourable towards a better ovarian stimulation and pregnancy outcome. Materials and methods In this study we assessed the distribution of the genotypes of FSHR Ser680Asn and of AMHRII -482A>G gene polymorphisms in a group of 126 infertile women and a control group of 100 fertile women by using real-time polymerase chain reaction (RT-PCR). Results Statistical analysis showed that the frequency of the genotypes is similar in both control and IVF/ intracytoplasmic sperm injection (ICSI) groups. Further investigation of the frequency of the nine possible combinations of these polymorphisms in the groups revealed no correlation between infertility and combination of the polymorphisms. Women with one polymorphism have on average 5.5 units higher levels of AMH compared to women carrying no polymorphism. In women with no polymorphisms, for each unit of FSH increase, the average concentration of blood AMH is expected to be 72% lower. Conclusion The distribution of the FSHR Ser680Asn and of the AMHRII -482A>G gene polymorphisms, in the Greek population is similar in fertile and infertile women. The study showed that FSH and AMH correlated levels in certain cases could be used to estimate a patient's ovarian reserve.
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MESH Headings
- Adult
- Female
- Humans
- Infertility, Female/genetics
- Infertility, Female/therapy
- Ovarian Reserve
- Polymorphism, Single Nucleotide
- Receptors, FSH/blood
- Receptors, FSH/genetics
- Receptors, Peptide/blood
- Receptors, Peptide/genetics
- Receptors, Transforming Growth Factor beta/blood
- Receptors, Transforming Growth Factor beta/genetics
- Sperm Injections, Intracytoplasmic/statistics & numerical data
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Affiliation(s)
- Ioannis G Papanikolaou
- 1st Department of Obstetrics and Gynecology, Alexandra Hospital, Division of Human Reproduction, IVF Unit National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Polina Giannelou
- 1st Department of Obstetrics and Gynecology, Alexandra Hospital, Division of Human Reproduction, IVF Unit National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Elli Anagnostou
- 1st Department of Obstetrics and Gynecology, Alexandra Hospital, Division of Human Reproduction, IVF Unit National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Despoina Mavrogianni
- 1st Department of Obstetrics and Gynecology, Alexandra Hospital, Division of Human Reproduction, IVF Unit National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Petros Drakakis
- 1st Department of Obstetrics and Gynecology, Alexandra Hospital, Division of Human Reproduction, IVF Unit National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Dimitrios Loutradis
- 1st Department of Obstetrics and Gynecology, Alexandra Hospital, Division of Human Reproduction, IVF Unit National and Kapodistrian University of Athens, Medical School, 62 Sirinon Street, P. Faliro, 175 61 Athens, Greece, Phone: +30 6932421747, Fax: +30 210 6454902
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Abstract
Treatment outcomes for acute lymphoblastic leukemia (ALL), especially pediatric ALL, have greatly improved due to the risk-adapted therapy. Combination of drug development, clinical practice, as well as basic genetic researches has brought the survival rate of ALL from less than 10% to more than 90% today, not only increasing the treatment efficacy but also limiting adverse drug reactions (ADRs). In this review, we summarized the landscape identification of ALL genetic alterations, which provided the opportunity to increase the survival rate and especially minimize the relapse risk of ALL, and highlighted the importance of the development of new technologies of genomic investigation for translational medicine.
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Merkulov VM, Leberfarb EY, Merkulova TI. Regulatory SNPs and their widespread effects on the transcriptome. J Biosci 2018. [DOI: 10.1007/s12038-018-9817-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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37
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Timing during translation matters: synonymous mutations in human pathologies influence protein folding and function. Biochem Soc Trans 2018; 46:937-944. [PMID: 30065107 DOI: 10.1042/bst20170422] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 05/18/2018] [Accepted: 06/25/2018] [Indexed: 12/11/2022]
Abstract
Ribosomes translate mRNAs with non-uniform speed. Translation velocity patterns are a conserved feature of mRNA and have evolved to fine-tune protein folding, expression and function. Synonymous single-nucleotide polymorphisms (sSNPs) that alter programmed translational speed affect expression and function of the encoded protein. Synergistic advances in next-generation sequencing have led to the identification of sSNPs associated with disease penetrance. Here, we draw on studies with disease-related proteins to enhance our understanding of mechanistic contributions of sSNPs to functional alterations of the encoded protein. We emphasize the importance of identification of sSNPs along with disease-causing mutations to understand genotype-phenotype relationships.
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TrioMDR: Detecting SNP interactions in trio families with model-based multifactor dimensionality reduction. Genomics 2018; 111:1176-1182. [PMID: 30055230 DOI: 10.1016/j.ygeno.2018.07.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 07/11/2018] [Accepted: 07/15/2018] [Indexed: 12/18/2022]
Abstract
Single nucleotide polymorphism (SNP) interactions can explain the missing heritability of common complex diseases. Many interaction detection methods have been proposed in genome-wide association studies, and they can be divided into two types: population-based and family-based. Compared with population-based methods, family-based methods are robust vs. population stratification. Several family-based methods have been proposed, among which Multifactor Dimensionality Reduction (MDR)-based methods are popular and powerful. However, current MDR-based methods suffer from heavy computational burden. Furthermore, they do not allow for main effect adjustment. In this work we develop a two-stage model-based MDR approach (TrioMDR) to detect multi-locus interaction in trio families (i.e., two parents and one affected child). TrioMDR combines the MDR framework with logistic regression models to check interactions, so TrioMDR can adjust main effects. In addition, unlike consuming permutation procedures used in traditional MDR-based methods, TrioMDR utilizes a simple semi-parameter P-values correction procedure to control type I error rate, this procedure only uses a few permutations to achieve the significance of a multi-locus model and significantly speeds up TrioMDR. We performed extensive experiments on simulated data to compare the type I error and power of TrioMDR under different scenarios. The results demonstrate that TrioMDR is fast and more powerful in general than some recently proposed methods for interaction detection in trios. The R codes of TrioMDR are available at: https://github.com/TrioMDR/TrioMDR.
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van der Laan SW, Harshfield EL, Hemerich D, Stacey D, Wood AM, Asselbergs FW. From lipid locus to drug target through human genomics. Cardiovasc Res 2018; 114:1258-1270. [PMID: 29800275 DOI: 10.1093/cvr/cvy120] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 05/16/2018] [Indexed: 12/14/2022] Open
Abstract
In the last decade, over 175 genetic loci have robustly been associated to levels of major circulating blood lipids. Most loci are specific to one or two lipids, whereas some (SUGP1, ZPR1, TRIB1, HERPUD1, and FADS1) are associated to all. While exposing the polygenic architecture of circulating lipids and the underpinnings of dyslipidaemia, these genome-wide association studies (GWAS) have provided further evidence of the critical role that lipids play in coronary heart disease (CHD) risk, as indicated by the 2.7-fold enrichment for macrophage gene expression in atherosclerotic plaques and the association of 25 loci (such as PCSK9, APOB, ABCG5-G8, KCNK5, LPL, HMGCR, NPC1L1, CETP, TRIB1, ABO, PMAIP1-MC4R, and LDLR) with CHD. These GWAS also confirmed known and commonly used therapeutic targets, including HMGCR (statins), PCSK9 (antibodies), and NPC1L1 (ezetimibe). As we head into the post-GWAS era, we offer suggestions for how to move forward beyond genetic risk loci, towards refining the biology behind the associations and identifying causal genes and therapeutic targets. Deep phenotyping through lipidomics and metabolomics will refine and increase the resolution to find causal and druggable targets, and studies aimed at demonstrating gene transcriptional and regulatory effects of lipid associated loci will further aid in identifying these targets. Thus, we argue the need for deeply phenotyped, large genetic association studies to reduce costs and failures and increase the efficiency of the drug discovery pipeline. We conjecture that in the next decade a paradigm shift will tip the balance towards a data-driven approach to therapeutic target development and the application of precision medicine where human genomics takes centre stage.
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Affiliation(s)
- Sander W van der Laan
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands
| | - Eric L Harshfield
- Department of Public Health and Primary Care, University of Cambridge, 2 Worts Causeway, Cambridge CB1 8RN, UK
- Department of Clinical Neurosciences, University of Cambridge, R3, Box 83, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Daiane Hemerich
- Department of Cardiology, University Medical Center Utrecht, University of Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
- CAPES Foundation, Ministry of Education of Brazil, Brasília, Brazil
| | - David Stacey
- Department of Public Health and Primary Care, University of Cambridge, 2 Worts Causeway, Cambridge CB1 8RN, UK
| | - Angela M Wood
- Department of Public Health and Primary Care, University of Cambridge, 2 Worts Causeway, Cambridge CB1 8RN, UK
| | - Folkert W Asselbergs
- Department of Cardiology, University Medical Center Utrecht, University of Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
- Durrer Center for Cardiovascular Research, Netherlands Heart Institute, Utrecht, the Netherlands
- Faculty of Population Health Sciences, Institute of Cardiovascular Science, University College London, London, UK
- Farr Institute of Health Informatics Research, Institute of Health Informatics, University College London, London, UK
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Cheng M, Mei B, Zhou Q, Zhang M, Huang H, Han L, Huang Q. Computational analyses of obesity associated loci generated by genome-wide association studies. PLoS One 2018; 13:e0199987. [PMID: 29966015 PMCID: PMC6028139 DOI: 10.1371/journal.pone.0199987] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 06/17/2018] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES Genome-wide association studies (GWASs) have discovered associations of numerous SNPs and genes with obesity. However, the underlying molecular mechanisms through which these SNPs and genes affect the predisposition to obesity remain not fully understood. Aims of our study are to comprehensively characterize obesity GWAS SNPs and genes through computational approaches. METHODS For obesity GWAS identified SNPs, functional annotation, effects on miRNAs binding and impact on protein phosphorylation were performed via RegulomeDB and 3DSNP, miRNASNP, and the PhosSNP 1.0 database, respectively. For obesity associated genes, protein-protein interaction network construction, gene ontology and pathway enrichment analyses were performed by STRING, PANTHER and STRING, respectively. RESULTS A total of 445 SNPs are significantly associated with obesity related phenotypes at threshold P < 5×10-8. A number of SNPs were eQTLs for obesity associated genes, some SNPs located at binding sites of obesity related transcription factors. SNPs that might affect miRNAs binding and protein phosphorylation were identified. Protein-protein interaction network analysis identified the highly-interconnected "hub" genes. Obesity associated genes mainly involved in metabolic process and catalytic activity, and significantly enriched in 15 signal pathways. CONCLUSIONS Our results provided the targets for follow-up experimental testing and further shed new light on obesity pathophysiology.
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Affiliation(s)
- Mengrong Cheng
- College of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Bing Mei
- College of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Qian Zhou
- College of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Manling Zhang
- College of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Han Huang
- College of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Lanchun Han
- College of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Qingyang Huang
- College of Life Sciences, Central China Normal University, Wuhan, Hubei, China
- * E-mail:
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Ye W, Wang Y, Mei B, Hou S, Liu X, Wu G, Qin L, Zhao K, Huang Q. Computational and functional characterization of four SNPs in the SOST locus associated with osteoporosis. Bone 2018; 108:132-144. [PMID: 29307778 DOI: 10.1016/j.bone.2018.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/29/2017] [Accepted: 01/02/2018] [Indexed: 01/19/2023]
Abstract
The SOST gene encodes sclerostin, a C-terminal cysteine knot-like domain containing key negative regulator of osteoblastic bone formation that inhibits LRP5/6-mediated canonical Wnt signaling. Numerous single nucleotide polymorphisms (SNPs) in the SOST locus are firmly associated with bone mineral density (BMD) and fracture in genome-wide association studies (GWAS) and candidate gene association studies. However, the validation and mechanistic elucidation of causal genetic variants, especially for SNPs located beyond the promoter-proximal region, remain largely unresolved. By employing computational and experimental approaches, here we identify four SNPs rs1230399, rs7220711, rs1107748 and rs75901553 as functional variants which display allelic variation in SOST gene expression. The osteoporosis associated SNP rs1230399 in the SOST distal upstream regulatory region shows FOXA1 binding activity with subsequent transinactivation in a T allele-specific manner. The BMD GWAS lead SNPs rs7220711 and rs1107748 both reside in the 52-kb regulatory element deletion 35-kb downstream of the SOST gene which leads to Van Buchem disease. The rs7220711-A has a higher affinity for the transcriptional repressors MAFF or MAFK homodimers than rs7220711-G, while rs1107748 confers C allele specific transcriptional enhancer activity via a CTCF binding element. The variant rs75901553 C>T located in a conserved site of the SOST 3' UTR abolishes a target binding site for miR-98-5p which is negatively responsive to parathyroid hormone or 17β-estradiol in osteoblastic cell lines. Our findings uncover the biological consequences of four independent genetic variants in the SOST region and their important roles in SOST expression via diverse mechanisms, providing new insights into the genetics and molecular pathogenesis of osteoporosis.
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Affiliation(s)
- Weiyuan Ye
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Ya Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Bing Mei
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Sasa Hou
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Xinhong Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Guiju Wu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Longjuan Qin
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Kehui Zhao
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Qingyang Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China.
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Abstract
Atrial septal defect is one of the most common CHD. The pathogenesis of atrial septal defect still remains unknown. Cx43 is the most prevalent connexin in the mammalian heart during development. Its genetic variants can cause several CHD. The aim of our study was to investigate the association of genetic variations of the Cx43 with sporadic atrial septal defect. A total of 450 paediatric patients were recruited, including 150 cases with atrial septal defect and 300 healthy controls. The promoter region of Cx43 was analysed by sequencing after polymerase chain reaction. All data were analysed by using the Statistic Package for Social Science 19.0 software. The frequency of the single nucleotide polymorphism rs2071166 was significantly higher in atrial septal defect cases than in healthy controls. The CC genotype at rs2071166 site in Cx43 was correlated with an increased risk for atrial septal defect (p<0.0001, odds ratio=3.891, 95% confidence interval 1.948-7.772) and the C allele was positively correlated with atrial septal defect (p=0.007, odds ratio=1.567, 95% confidence interval 1.129-2.175). In conclusion, our results confirmed that rs2071166 in Cx43 may be relevant with an increased atrial septal defect risk.
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43
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Nedeljkovic I, Lahousse L, Carnero-Montoro E, Faiz A, Vonk JM, de Jong K, van der Plaat DA, van Diemen CC, van den Berge M, Obeidat M, Bossé Y, Nickle DC, Consortium BIOS, Uitterlinden AG, van Meurs JBJ, Stricker BHC, Brusselle GG, Postma DS, Boezen HM, van Duijn CM, Amin N. COPD GWAS variant at 19q13.2 in relation with DNA methylation and gene expression. Hum Mol Genet 2018; 27:396-405. [PMID: 29092026 PMCID: PMC5886099 DOI: 10.1093/hmg/ddx390] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 10/06/2017] [Accepted: 10/25/2017] [Indexed: 11/14/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is among the major health burdens in adults. While cigarette smoking is the leading risk factor, a growing number of genetic variations have been discovered to influence disease susceptibility. Epigenetic modifications may mediate the response of the genome to smoking and regulate gene expression. Chromosome 19q13.2 region is associated with both smoking and COPD, yet its functional role is unclear. Our study aimed to determine whether rs7937 (RAB4B, EGLN2), a top genetic variant in 19q13.2 region identified in genome-wide association studies of COPD, is associated with differential DNA methylation in blood (N = 1490) and gene expression in blood (N = 721) and lungs (N = 1087). We combined genetic and epigenetic data from the Rotterdam Study (RS) to perform the epigenome-wide association analysis of rs7937. Further, we used genetic and transcriptomic data from blood (RS) and from lung tissue (Lung expression quantitative trait loci mapping study), to perform the transcriptome-wide association study of rs7937. Rs7937 was significantly (FDR < 0.05) and consistently associated with differential DNA methylation in blood at 4 CpG sites in cis, independent of smoking. One methylation site (cg11298343-EGLN2) was also associated with COPD (P = 0.001). Additionally, rs7937 was associated with gene expression levels in blood in cis (EGLN2), 42% mediated through cg11298343, and in lung tissue, in cis and trans (NUMBL, EGLN2, DNMT3A, LOC101929709 and PAK2). Our results suggest that changes of DNA methylation and gene expression may be intermediate steps between genetic variants and COPD, but further causal studies in lung tissue should confirm this hypothesis.
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Affiliation(s)
- Ivana Nedeljkovic
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Lies Lahousse
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Bioanalysis, Pharmaceutical Care Unit, Ghent University Hospital, Ghent, Belgium
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Elena Carnero-Montoro
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- GENYO Center for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Region Government, Granada, Spain
| | - Alen Faiz
- University of Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - Judith M Vonk
- University of Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Kim de Jong
- University of Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Diana A van der Plaat
- University of Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Cleo C van Diemen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Maarten van den Berge
- University of Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
- Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ma’en Obeidat
- Center for Heart Lung Innovation, University of British Columbia, Vancouver, BC, Canada
| | - Yohan Bossé
- Department of Molecular Medicine, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Quebec, QC, Canada
| | - David C Nickle
- Merck Research Laboratories, Genetics and Pharmacogenomics (GpGx), Seattle, WA, USA
| | | | - Andre G Uitterlinden
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Joyce B J van Meurs
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Bruno H C Stricker
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Guy G Brusselle
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
- Department of Respiratory Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Dirkje S Postma
- University of Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
- Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - H Marike Boezen
- University of Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Najaf Amin
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
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The role of histone modification and a regulatory single-nucleotide polymorphism (rs2071166) in the Cx43 promoter in patients with TOF. Sci Rep 2017; 7:10435. [PMID: 28874875 PMCID: PMC5585261 DOI: 10.1038/s41598-017-10756-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 08/14/2017] [Indexed: 12/21/2022] Open
Abstract
Abnormal level of Cx43 expression could result in CHD. Epigenetic modification and disease-associated, non-coding SNPs might influence gene transcription and expression. Our study aimed to determine the role of histone modification and an rSNP (rs2071166) in the Cx43 promoter in patients with TOF. Our results indicate that H3K18ac bind to Cx43 promoter and that their levels are reduced in TOF patients relative to controls. The relationship between the non-coding SNP in the Cx43 gene and TOF patients was evaluated in 158 patients and 300 controls. The C allele of rs2071166 was confirmed to result in an increased risk of TOF (OR = 1.586, 95%CI 1.149–2.189). Individuals with the CC genotype at rs2071166 also showed a significant susceptibility to TOF (OR = 2.961, 95%CI 1.452–6.038). The mRNA level in TOF who were CC genotype was lower than that in patients with the AA/AC genotype. Functional analysis in cells and transgenic zebrafish models showed that rs2071166 decreased the activity of the promoter and could block the interaction between RXRα and RARE. This is the first study to illustrate that epigenetic modification and an rSNP in the Cx43 promoter region play a critical role in TOF by impacting the transcriptional activity and expression level of Cx43.
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Gupta R, Qaiser B, He L, Hiekkalinna TS, Zheutlin AB, Therman S, Ollikainen M, Ripatti S, Perola M, Salomaa V, Milani L, Cannon TD, Madden PAF, Korhonen T, Kaprio J, Loukola A. Neuregulin signaling pathway in smoking behavior. Transl Psychiatry 2017; 7:e1212. [PMID: 28892072 PMCID: PMC5611747 DOI: 10.1038/tp.2017.183] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 06/26/2017] [Accepted: 07/06/2017] [Indexed: 12/23/2022] Open
Abstract
Understanding molecular processes that link comorbid traits such as addictions and mental disorders can provide novel therapeutic targets. Neuregulin signaling pathway (NSP) has previously been implicated in schizophrenia, a neurodevelopmental disorder with high comorbidity to smoking. Using a Finnish twin family sample, we have previously detected association between nicotine dependence and ERBB4 (a neuregulin receptor), and linkage for smoking initiation at the ERBB4 locus on 2q33. Further, Neuregulin3 has recently been shown to associate with nicotine withdrawal in a behavioral mouse model. In this study, we scrutinized association and linkage between 15 036 common, low frequency and rare genetic variants in 10 NSP genes and phenotypes encompassing smoking and alcohol use. Using the Finnish twin family sample (N=1998 from 740 families), we detected 66 variants (representing 23 LD blocks) significantly associated (false discovery rate P<0.05) with smoking initiation, nicotine dependence and nicotine withdrawal. We comprehensively annotated the associated variants using expression (eQTL) and methylation quantitative trait loci (meQTL) analyses in a Finnish population sample. Among the 66 variants, we identified 25 eQTLs (in NRG1 and ERBB4), 22 meQTLs (in NRG3, ERBB4 and PSENEN), a missense variant in NRG1 (rs113317778) and a splicing disruption variant in ERBB4 (rs13385826). Majority of the QTLs in blood were replicated in silico using publicly available databases, with additional QTLs observed in brain. In conclusion, our results support the involvement of NSP in smoking behavior but not in alcohol use and abuse, and disclose functional potential for 56 of the 66 associated single-nucleotide polymorphism.
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Affiliation(s)
- R Gupta
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - B Qaiser
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - L He
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA
| | - T S Hiekkalinna
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- National Institute for Health and Welfare, Helsinki, Finland
| | - A B Zheutlin
- Department of Psychology, Yale University, New Haven, CT, USA
| | - S Therman
- National Institute for Health and Welfare, Helsinki, Finland
| | - M Ollikainen
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - S Ripatti
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - M Perola
- National Institute for Health and Welfare, Helsinki, Finland
| | - V Salomaa
- National Institute for Health and Welfare, Helsinki, Finland
| | - L Milani
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - T D Cannon
- Department of Psychology, Yale University, New Haven, CT, USA
| | - P A F Madden
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - T Korhonen
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- National Institute for Health and Welfare, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - J Kaprio
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - A Loukola
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
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46
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Elkon R, Agami R. Characterization of noncoding regulatory DNA in the human genome. Nat Biotechnol 2017; 35:732-746. [DOI: 10.1038/nbt.3863] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 03/31/2017] [Indexed: 12/22/2022]
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Diversity and inclusion in genomic research: why the uneven progress? J Community Genet 2017; 8:255-266. [PMID: 28770442 PMCID: PMC5614884 DOI: 10.1007/s12687-017-0316-6] [Citation(s) in RCA: 168] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/29/2017] [Indexed: 12/15/2022] Open
Abstract
Conducting genomic research in diverse populations has led to numerous advances in our understanding of human history, biology, and health disparities, in addition to discoveries of vital clinical significance. Conducting genomic research in diverse populations is also important in ensuring that the genomic revolution does not exacerbate health disparities by facilitating discoveries that will disproportionately benefit well-represented populations. Despite the general agreement on the need for genomic research in diverse populations in terms of equity and scientific progress, genomic research remains largely focused on populations of European descent. In this article, we describe the rationale for conducting genomic research in diverse populations by reviewing examples of advances facilitated by their inclusion. We also explore some of the factors that perpetuate the disproportionate attention on well-represented populations. Finally, we discuss ongoing efforts to ameliorate this continuing bias. Collaborative and intensive efforts at all levels of research, from the funding of studies to the publication of their findings, will be necessary to ensure that genomic research does not conserve historical inequalities or curtail the contribution that genomics could make to the health of all humanity.
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Association of regulatory TPH2 polymorphisms with higher reduction in depressive symptoms in children and adolescents treated with fluoxetine. Prog Neuropsychopharmacol Biol Psychiatry 2017; 77:236-240. [PMID: 28456685 DOI: 10.1016/j.pnpbp.2017.04.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 04/25/2017] [Indexed: 12/12/2022]
Abstract
Genetic variability related to the brain serotonergic system has a significant impact on both the susceptibility to psychiatric disorders, such as major depressive disorder (MDD), and the response to antidepressant drugs, such as fluoxetine. TPH2 is one of the most important serotonergic candidate genes in selective serotonin reuptake inhibitors (SSRIs) pharmacogenetic studies. The aim of the present study was to evaluate the influence of regulatory polymorphisms that are specifically located in human TPH2 transcription factor binding sites (TFBSs), and therefore could be functional by altering gene expression, on clinical improvement in children and adolescents treated with fluoxetine. The selection of SNPs was also based on their linkage disequilibrium with TPH2 rs4570625, a genetic variant with questionable functionality, which was previously associated with clinical response in our pediatric population. A total of 83 children and adolescents were clinically evaluated 12weeks after initiating antidepressant treatment with fluoxetine for the first time. Clinical improvement was assessed by reductions in depressive symptoms measured using the Children's Depression Inventory (CDI) scale. The polymorphisms rs11179002, rs60032326 and rs34517220 were, for the first time in the literature, significantly associated with higher clinical improvement. The strongest association was found for rs34517220. In particular, minor allele homozygotes showed higher score reductions on the CDI scale compared with the major allele carriers. Interestingly, this polymorphism is located in a human TPH2 TFBS for two relevant transcription factors in the serotoninergic neurons, Foxa1 and Foxa2, which together with the high level of significance found for this SNP, could indicate that rs34517220 is in fact the crucial functional genetic variant related to the fluoxetine response. These results provide new evidence for the role of regulatory genetic variants that could modulate human TPH2 expression in the SSRI antidepressant response.
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49
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Abstract
Genome-wide association studies (GWASs) discovered a number of SNPs and genes associated with Alzheimer's disease (AD). However, how these SNPs and genes influence the liability to AD is not fully understood. We deployed computational approaches to explore the function and action mechanisms of AD -related SNPs and genes identified by GWASs, including the effects of 195 GWAS lead SNPs and 338 proxy SNPs on miRNAs binding and protein phosphorylation, their RegulomeDB and 3DSNP scores, and gene ontology, pathway enrichment and protein-protein interaction network of 126 AD-associated genes. Our computational analysis identified 6 lead SNPs (rs10119, rs1048699, rs148763909, rs610932, rs6857 and rs714948) and 2 proxy SNPs (rs12539172 and rs2847655) that potentially impacted the miRNA binding. Lead SNP rs2296160 and proxy SNPs rs679620 and rs2228145 were identified as PhosSNPs potentially influencing protein phosphorylation. AD-associated genes showed enrichment of “regulation of beta-amyloid formation”, “regulation of neurofibrillary tangle assembly”, “leukocyte mediated immunity” and “protein-lipid complex assembly” signaling pathway. Protein-protein interaction network and functional module analyses identified highly-interconnected “hub” genes (APOE, PICALM, BIN1, ABCA7, CD2AP, CLU, CR1, MS4A4E and MS4A6A) and bottleneck genes (APOE, TOMM40, NME8, PICALM, CD2AP, ZCWPW1, FAM180B, GAB2 and PTK2B) that created three tight subnetworks. Our results provided the targets for further experimental assessment and further insight on AD pathophysiology.
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Affiliation(s)
- Zengpeng Han
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - Han Huang
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - Yue Gao
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - Qingyang Huang
- School of Life Sciences, Central China Normal University, Wuhan, China
- * E-mail:
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50
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Tang J, Fan Y, Li H, Xiang Q, Zhang DF, Li Z, He Y, Liao Y, Wang Y, He F, Zhang F, Shugart YY, Liu C, Tang Y, Chan RCK, Wang CY, Yao YG, Chen X. Whole-genome sequencing of monozygotic twins discordant for schizophrenia indicates multiple genetic risk factors for schizophrenia. J Genet Genomics 2017. [PMID: 28645778 DOI: 10.1016/j.jgg.2017.05.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Schizophrenia is a common disorder with a high heritability, but its genetic architecture is still elusive. We implemented whole-genome sequencing (WGS) analysis of 8 families with monozygotic (MZ) twin pairs discordant for schizophrenia to assess potential association of de novo mutations (DNMs) or inherited variants with susceptibility to schizophrenia. Eight non-synonymous DNMs (including one splicing site) were identified and shared by twins, which were either located in previously reported schizophrenia risk genes (p.V24689I mutation in TTN, p.S2506T mutation in GCN1L1, IVS3+1G > T in DOCK1) or had a benign to damaging effect according to in silico prediction analysis. By searching the inherited rare damaging or loss-of-function (LOF) variants and common susceptible alleles from three classes of schizophrenia candidate genes, we were able to distill genetic alterations in several schizophrenia risk genes, including GAD1, PLXNA2, RELN and FEZ1. Four inherited copy number variations (CNVs; including a large deletion at 16p13.11) implicated for schizophrenia were identified in four families, respectively. Most of families carried both missense DNMs and inherited risk variants, which might suggest that DNMs, inherited rare damaging variants and common risk alleles together conferred to schizophrenia susceptibility. Our results support that schizophrenia is caused by a combination of multiple genetic factors, with each DNM/variant showing a relatively small effect size.
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Affiliation(s)
- Jinsong Tang
- Institute of Mental Health, National Clinical Research Center for Mental Health Disorders and National Technology Institute of Psychiatry, and Key Laboratory of Psychiatry and Mental Health of Hunan Province, The Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Yu Fan
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming 650223, China
| | - Hong Li
- Institute of Mental Health, National Clinical Research Center for Mental Health Disorders and National Technology Institute of Psychiatry, and Key Laboratory of Psychiatry and Mental Health of Hunan Province, The Second Xiangya Hospital, Central South University, Changsha 410011, China; Department of Psychiatry, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Qun Xiang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Deng-Feng Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming 650223, China
| | - Zongchang Li
- Institute of Mental Health, National Clinical Research Center for Mental Health Disorders and National Technology Institute of Psychiatry, and Key Laboratory of Psychiatry and Mental Health of Hunan Province, The Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Ying He
- Institute of Mental Health, National Clinical Research Center for Mental Health Disorders and National Technology Institute of Psychiatry, and Key Laboratory of Psychiatry and Mental Health of Hunan Province, The Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Yanhui Liao
- Institute of Mental Health, National Clinical Research Center for Mental Health Disorders and National Technology Institute of Psychiatry, and Key Laboratory of Psychiatry and Mental Health of Hunan Province, The Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Ya Wang
- Neuropsychology and Applied Cognitive Neuroscience Laboratory, and CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing 100101, China
| | - Fan He
- Beijing Key Laboratory of Mental Disorders, Department of Psychiatry, Beijing Anding Hospital, and Center of Schizophrenia, Beijing Institute for Brain Disorders and Laboratory of Brain Disorders of the Ministry of Science and Technology, Capital Medical University, Beijing 100088, China
| | - Fengyu Zhang
- Institute of Mental Health, National Clinical Research Center for Mental Health Disorders and National Technology Institute of Psychiatry, and Key Laboratory of Psychiatry and Mental Health of Hunan Province, The Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Yin Yao Shugart
- Unit on Statistical Genomics, Intramural Research Programs, National Institute of Mental Health, NIH, Bethesda 20892, USA
| | - Chunyu Liu
- Institute of Human Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Yanqing Tang
- Department of Psychiatry, The First Affiliated Hospital of China Medical University, Shenyang 110122, China.
| | - Raymond C K Chan
- Neuropsychology and Applied Cognitive Neuroscience Laboratory, and CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Chuan-Yue Wang
- Beijing Key Laboratory of Mental Disorders, Department of Psychiatry, Beijing Anding Hospital, and Center of Schizophrenia, Beijing Institute for Brain Disorders and Laboratory of Brain Disorders of the Ministry of Science and Technology, Capital Medical University, Beijing 100088, China.
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China; CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Xiaogang Chen
- Institute of Mental Health, National Clinical Research Center for Mental Health Disorders and National Technology Institute of Psychiatry, and Key Laboratory of Psychiatry and Mental Health of Hunan Province, The Second Xiangya Hospital, Central South University, Changsha 410011, China.
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