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Li RY, Huang Y, Zhao Z, Qin ZS. Comprehensive 100-bp resolution genome-wide epigenomic profiling data for the hg38 human reference genome. Data Brief 2022; 46:108827. [PMID: 36582986 PMCID: PMC9792340 DOI: 10.1016/j.dib.2022.108827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 11/21/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
This manuscript presents a comprehensive collection of diverse epigenomic profiling data for the human genome in 100-bp resolution with full genome-wide coverage. The datasets are processed from raw read count data collected from five types of sequencing-based assays collected by the Encyclopedia of DNA Elements consortium (ENCODE, http://www.encodeproject.org). Data from high-throughput sequencing assays were processed and crystallized into a total of 6,305 genome-wide profiles. To ensure the quality of the features, we filtered out assays with low read depth, inconsistent read counts, and poor data quality. The types of sequencing-based experiment assays include DNase-seq, histone and TF ChIP-seq, ATAC-seq, and Poly(A) RNA-seq. Merging of processed data was done by averaging read counts across technical replicates to obtain signals in about 30 million predefined 100-bp bins that tile the entire genome. We provide an example of fetching read counts using disease-related risk variants from the GWAS Catalog. Additionally, we have created a tabix index enabling fast user retrieval of read counts given coordinates in the human genome. The data processing pipeline is replicable for users' own purposes and for other experimental assays. The processed data can be found on Zenodo at https://zenodo.org/record/7015783. These data can be used as features for statistical and machine learning models to predict or infer a wide range of variables of biological interest. They can also be applied to generate novel insights into gene expression, chromatin accessibility, and epigenetic modifications across the human genome. Finally, the processing pipeline can be easily applied to data from any other genome-wide profiling assays, expanding the amount of available data.
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Affiliation(s)
- Ronnie Y. Li
- Graduate program in Neuroscience, Emory University, United States
| | - Yanting Huang
- Department of Computer Science, Emory University, United States
| | - Zhiyue Zhao
- Department of Computer Science, Emory University, United States
| | - Zhaohui S. Qin
- Department of Biostatistics and Bioinformatics, Emory University, United States
- Corresponding author. @SteveQinEmory
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Suzuki S, Yamada S. Epigenetics in susceptibility, progression, and diagnosis of periodontitis. Jpn Dent Sci Rev 2022; 58:183-192. [PMID: 35754944 PMCID: PMC9218144 DOI: 10.1016/j.jdsr.2022.06.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/14/2022] [Accepted: 06/01/2022] [Indexed: 12/12/2022] Open
Abstract
Periodontitis is characterized by irreversible destruction of periodontal tissue. At present, the accepted etiology of periodontitis is based on a three-factor theory including pathogenic bacteria, host factors, and acquired factors. Periodontitis development usually takes a decade or longer and is therefore called chronic periodontitis (CP). To search for genetic factors associated with CP, several genome-wide association study (GWAS) analyses were conducted; however, polymorphisms associated with CP have not been identified. Epigenetics, on the other hand, involves acquired transcriptional regulatory mechanisms due to reversibly altered chromatin accessibility. Epigenetic status is a condition specific to each tissue and cell, mostly determined by the responses of host cells to stimulations by local factors, like bacterial inflammation, and systemic factors such as nutrition status, metabolic diseases, and health conditions. Significantly, epigenetic status has been linked with the onset and progression of several acquired diseases. Thus, epigenetic factors in periodontal tissues are attractive targets for periodontitis diagnosis and treatments. In this review, we introduce accumulating evidence to reveal the epigenetic background effects related to periodontitis caused by genetic factors, systemic diseases, and local environmental factors, such as smoking, and clarify the underlying mechanisms by which epigenetic alteration influences the susceptibility of periodontitis.
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Key Words
- 5mC, 5-methylcytocine
- AP, aggressive periodontitis
- ATAC-seq, assay for transposase-accessible chromatin sequencing
- CP, chronic periodontitis
- DNA methylation
- ECM, extracellular matrix
- Epigenetics
- Epigenome
- GWAS, genome-wide association study
- H3K27ac, acetylation of histone H3 lysine 27
- H3K27me3, trimethylation of histone H3 lysine 27
- H3K4me3, trimethylation of histone H3 lysine 4
- H3K9ac, histone H3 lysine 9
- HATs, histone acetyltransferases
- HDACs, histone deacetylases
- Histone modifications
- LPS, lipopolysaccharide
- PDL, periodontal ligament
- Periodontal ligament
- Periodontitis
- ceRNA, competing endogenous RNA
- lncRNAs, long ncRNAs
- m6A, N6-methyladenosine
- ncRNAs, non-coding RNAs
- sEV, small extracellular vesicles
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Affiliation(s)
- Shigeki Suzuki
- Department of Periodontology and Endodontology, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan
| | - Satoru Yamada
- Department of Periodontology and Endodontology, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan
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Chen X, Li H, Guo F, Hoffmeister M, Brenner H. Alcohol consumption, polygenic risk score, and early- and late-onset colorectal cancer risk. EClinicalMedicine 2022; 49:101460. [PMID: 35747198 PMCID: PMC9126769 DOI: 10.1016/j.eclinm.2022.101460] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/29/2022] [Accepted: 05/02/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Evidence is lacking on the impact of alcohol consumption on colorectal cancer (CRC) risk (overall and by age at diagnosis) by polygenic risk score (PRS) levels, and it is unclear how the magnitude of CRC risk associated with alcohol consumption compares to the magnitude of genetically determined risk. METHODS Multiple logistic regression was used to assess the association between alcohol consumption and colorectal cancer (CRC) across PRS levels based on 140 CRC-related loci among 5104 CRC cases and 4131 controls from a large population-based case-control study. We compared the effects for alcohol consumption and PRS on CRC risk using the "Genetic Risk Equivalent (GRE)" for effective risk communication. Specific analyses were conducted for early-onset CRC (EOCRC, <55 years) and late-onset CRC (LOCRC, ≥55 years). FINDINGS High alcohol consumption, and to a lower extent, also alcohol abstinence were associated with increased CRC risk. Compared to low alcohol consumption (0·1-<25 g/d), lifetime average alcohol consumption ≥25 g/d was more strongly associated with EOCRC [odds ratio (OR) 1·8, 95% confidence interval (CI) 1·2-2·8] than with LOCRC risk (OR 1·3, 95% CI 1·1-1·4) (P-value for interaction with age =0·011). Interactions between alcohol consumption and PRS did not reach statistical significance for either EOCRC or LOCRC risk. The estimated impact of high lifetime alcohol consumption on EOCRC was equivalent to the effect of having 47 percentiles higher PRS (GRE 47, 95% CI 12-82), stronger than the impact on LOCRC (GRE 18, 95% CI 8-29). INTERPRETATION Excessive alcohol use was strongly associated with EOCRC risk, independent of PRS levels. Abstaining from heavy drinking could reduce risk for CRC, in particular for EOCRC to an extent that would be equivalent to having a much lower genetically determined risk. FUNDING The first author (X.C.) was supported by the Guangzhou Elite Project (GEP). The DACHS study was supported by grants from the German Research Council (BR 1704/6-1, BR1704/6-3, BR 1704/6-4, BR 1704/6-6, CH 117/1-1, BR 1704/17-1, HO 5117/2-1) and the German Federal Ministry of Education and Research (01KH0404, 01ER0814, 01ER0815, 01GL1712).
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Key Words
- Alcohol consumption
- CI, confidence interval
- CRC, colorectal cancer
- DACHS, Darmkrebs: Chancen der Verhütung durch Screening
- EOCRC, early-onset colorectal cancer
- Early-onset colorectal cancer
- GRE, genetic risk equivalent
- GWAS, genome-wide association study
- Genetic risk equivalentt
- LOCRC, late-onset colorectal cancer
- Late-onset colorectal cancer
- NSAID, non-steroidal anti-inflammatory drug
- OR, odds ratio
- PRS, polygenic risk score
- Polygenic risk score
- SNP, single nucleotide polymorphisms
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Affiliation(s)
- Xuechen Chen
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Hengjing Li
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Feng Guo
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, Heidelberg, Germany
- Corresponding author at: Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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Trushina E, Trushin S, Hasan MF. Mitochondrial complex I as a therapeutic target for Alzheimer's disease. Acta Pharm Sin B 2022; 12:483-495. [PMID: 35256930 PMCID: PMC8897152 DOI: 10.1016/j.apsb.2021.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/01/2021] [Accepted: 10/25/2021] [Indexed: 02/08/2023] Open
Abstract
Alzheimer's disease (AD), the most prominent form of dementia in the elderly, has no cure. Strategies focused on the reduction of amyloid beta or hyperphosphorylated Tau protein have largely failed in clinical trials. Novel therapeutic targets and strategies are urgently needed. Emerging data suggest that in response to environmental stress, mitochondria initiate an integrated stress response (ISR) shown to be beneficial for healthy aging and neuroprotection. Here, we review data that implicate mitochondrial electron transport complexes involved in oxidative phosphorylation as a hub for small molecule-targeted therapeutics that could induce beneficial mitochondrial ISR. Specifically, partial inhibition of mitochondrial complex I has been exploited as a novel strategy for multiple human conditions, including AD, with several small molecules being tested in clinical trials. We discuss current understanding of the molecular mechanisms involved in this counterintuitive approach. Since this strategy has also been shown to enhance health and life span, the development of safe and efficacious complex I inhibitors could promote healthy aging, delaying the onset of age-related neurodegenerative diseases.
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Key Words
- AD, Alzheimer's disease
- ADP, adenosine diphosphate
- AIDS, acquired immunodeficiency syndrome
- AMP, adenosine monophosphate
- AMPK, AMP-activated protein kinase
- APP/PS1, amyloid precursor protein/presenilin 1
- ATP, adenosine triphosphate
- Alzheimer's disease
- Aβ, amyloid beta
- BBB, blood‒brain barrier
- BDNF, brain-derived neurotrophic factor
- CP2, tricyclic pyrone compound two
- Complex I inhibitors
- ER, endoplasmic reticulum
- ETC, electron transport chain
- FADH2, flavin adenine dinucleotide
- FDG-PET, fluorodeoxyglucose-positron emission tomography
- GWAS, genome-wide association study
- HD, Huntington's disease
- HIF-1α, hypoxia induced factor 1 α
- Healthy aging
- ISR, integrated stress response
- Integrated stress response
- LTP, long term potentiation
- MCI, mild cognitive impairment
- MPTP, 1-methyl 4-phenyl-1,2,3,6-tetrahydropyridine
- Mitochondria
- Mitochondria signaling
- Mitochondria targeted therapeutics
- NAD+ and NADH, nicotinamide adenine dinucleotide
- NF-κB, nuclear factor kappa-light-chain-enhancer of activated B cells
- NRF2, nuclear factor E2-related factor 2
- Neuroprotection
- OXPHOS, oxidative phosphorylation
- PD, Parkinson's disease
- PGC1α, peroxisome proliferator-activated receptor gamma coactivator 1 alpha
- PMF, proton-motive force
- RNAi, RNA interference
- ROS, reactive oxygen species
- T2DM, type II diabetes mellitus
- TCA, the tricarboxylic acid cycle
- mtDNA, mitochondrial DNA
- mtUPR, mitochondrial unfolded protein response
- pTau, hyper-phosphorylated Tau protein
- ΔpH, proton gradient
- Δψm, mitochondrial membrane potential
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Airaksinen L, Cerqueira JXM, Huhtala H, Saavalainen P, Yohannes DA, Mäki M, Kurppa K, Kilpeläinen E, Shcherban A, Palotie A, Kaukinen K, Lindfors K. Dissecting the contribution of single nucleotide polymorphisms in CCR9 and CCL25 genomic regions to the celiac disease phenotype. J Transl Autoimmun 2021; 4:100128. [PMID: 34901814 PMCID: PMC8640869 DOI: 10.1016/j.jtauto.2021.100128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/02/2021] [Accepted: 10/13/2021] [Indexed: 11/30/2022] Open
Abstract
PURPOSE AND OBJECTIVES Given their role in homing immune cells to the intestine, CC motif chemokine receptor 9 (CCR9) and its specific ligand CC motif chemokine ligand 25 (CCL25) are interesting candidate genes for celiac disease. These genes are located in regions previously shown to be associated with or linked to celiac disease, but no investigations on their association with various celiac disease phenotypes have so far been conducted. Here we studied such associations of both genotyped and imputed single nucleotide polymorphisms (SNPs) with either regulatory function or exonic location of the CCR9 and CCL25 loci. RESULTS Exploiting a carefully phenotyped cohort of 625 celiac disease patients and 1817 non-celiac controls, we identified that multiple SNPs with predicted regulatory function (RegulomeDB score ≤3a and/or eQTL effect) located between 100 kB upstream and downstream of CCR9 and CCL25 are associated with celiac disease and/or selected phenotypes. Of the genotyped SNPs in the CCR9 loci, rs213360 with an eQTL effect on CCR9 expression in blood was associated with celiac disease and all investigated phenotypes except high HLA risk. Rs1545985 with an eQTL on CCR9 expression and rs7652331 and rs12493471, both with RegulomeDB score ≤3a, were all associated with gastrointestinal symptoms and malabsorption and the latter additionally with anemia. The genotyped CCL25 SNPs rs952444 and rs882951, with RegulomeDB scores 1d and 1f respectively and eQTL effect on CCL25 expression in small intestine, were associated with gastrointestinal symptoms and malabsorption. The CCL25 SNP rs2303165 identified in sequencing followed by imputation was associated with partial villous atrophy. However, the association did not pass the permutation based multiple testing correction (PEMP2 > 0.05). CONCLUSIONS We conclude that SNPs in the region of CCR9 and CCL25 with predicted functional effect or exonic localization likely contribute only modestly to various celiac disease phenotypes.
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Key Words
- CCL25, CC motif chemokine ligand 25
- CCR9, CC motif chemokine receptor 9
- CI, confidence interval
- Celiac disease
- Chemokine receptor
- Clinical picture
- FUMA, Functional Mapping and Annotation of GWAS
- GWAS, genome-wide association study
- Genetic association
- Genetic variation
- HLA, human leukocyte antigen
- HWE, Hardy-Weinberg equilibrium
- MAF, minor allele frequency
- OR, odds ratio
- PBMC, peripheral blood mononuclear cell
- QC, quality control
- SNP, single nucleotide polymorphism
- TG2, transglutaminase 2
- eQTL, expression quantitative trait loci
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Affiliation(s)
- Laura Airaksinen
- Celiac Disease Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Juliana XM. Cerqueira
- Celiac Disease Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Faculty of Nutrition and Food Sciences, University of Porto, Porto, Portugal
| | - Heini Huhtala
- Faculty of Social Sciences, Tampere University, Tampere, Finland
| | - Päivi Saavalainen
- Translational Immunology Research Program, and Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Dawit A. Yohannes
- Translational Immunology Research Program, and Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Markku Mäki
- Celiac Disease Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Tampere Center for Child, Adolescent, and Maternal Health Research, Tampere University, and Department of Pediatrics, Tampere University Hospital, Tampere, Finland
| | - Kalle Kurppa
- Celiac Disease Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Tampere Center for Child, Adolescent, and Maternal Health Research, Tampere University, and Department of Pediatrics, Tampere University Hospital, Tampere, Finland
- University Consortium of Seinäjoki, Seinäjoki, Finland
| | - Elina Kilpeläinen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Anastasia Shcherban
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Psychiatric & Neurodevelopmental Genetics Unit, Department of Psychiatry, Analytic and Translational Genetics Unit, Department of Medicine, and the Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Katri Kaukinen
- Celiac Disease Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Internal Medicine, Tampere University Hospital, Tampere, Finland
| | - Katri Lindfors
- Celiac Disease Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
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Nakamura Y, Narita A, Sutoh Y, Imaeda N, Goto C, Matsui K, Takashima N, Kadota A, Miura K, Nakatochi M, Tamura T, Hishida A, Nakashima R, Ikezaki H, Hara M, Nishida Y, Takezaki T, Ibusuki R, Oze I, Ito H, Kuriyama N, Ozaki E, Mikami H, Kusakabe M, Nakagawa-Senda H, Suzuki S, Katsuura-Kamano S, Arisawa K, Kuriki K, Momozawa Y, Kubo M, Takeuchi K, Kita Y, Wakai K. A genome-wide association study on meat consumption in a Japanese population: the Japan Multi-Institutional Collaborative Cohort study. J Nutr Sci 2021; 10:e61. [PMID: 34733494 PMCID: PMC8532070 DOI: 10.1017/jns.2021.49] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/27/2021] [Accepted: 07/13/2021] [Indexed: 12/30/2022] Open
Abstract
Recent genome-wide association studies (GWAS) on the dietary habits of the Japanese population have shown that an effect rs671 allele was inversely associated with fish consumption, whereas it was directly associated with coffee consumption. Although meat is a major source of protein and fat in the diet, whether genetic factors that influence meat-eating habits in healthy populations are unknown. This study aimed to conduct a GWAS to find genetic variations that affect meat consumption in a Japanese population. We analysed GWAS data using 14 076 participants from the Japan Multi-Institutional Collaborative Cohort (J-MICC) study. We used a semi-quantitative food frequency questionnaire to estimate food intake that was validated previously. Association of the imputed variants with total meat consumption per 1000 kcal energy was performed by linear regression analysis with adjustments for age, sex, and principal component analysis components 1-10. We found that no genetic variant, including rs671, was associated with meat consumption. The previously reported single nucleotide polymorphisms that were associated with meat consumption in samples of European ancestry could not be replicated in our J-MICC data. In conclusion, significant genetic factors that affect meat consumption were not observed in a Japanese population.
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Affiliation(s)
- Yasuyuki Nakamura
- Department of Public Health, Shiga University of Medical Science, Otsu, Japan
- Yamashina Racto Clinic and Medical Examination Center, Kyoto, Japan
| | - Akira Narita
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Yoichi Sutoh
- Division of Biomedical Information Analysis, Institute for Biomedical Sciences, Iwate Medical University, Shiwa-gun, Iwate, Japan
| | - Nahomi Imaeda
- Department of Nutrition, Faculty of Wellness, Shigakkan University, Obu, Japan
- Department of Public Health, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Chiho Goto
- Department of Public Health, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
- Department of Health and Nutrition, School of Health and Human Life, Nagoya Bunri University, Inazawa, Japan
| | - Kenji Matsui
- Department of Public Health, Shiga University of Medical Science, Otsu, Japan
- Division of Bioethics and Healthcare Law, The National Cancer Center, Tokyo, Japan
| | - Naoyuki Takashima
- Department of Public Health, Shiga University of Medical Science, Otsu, Japan
- Department of Public Health, Faculty of Medicine, Kindai University, Osaka-Sayama, Osaka, Japan
| | - Aya Kadota
- Department of Public Health, Shiga University of Medical Science, Otsu, Japan
- NCD Epidemiology Center, Shiga University of Medical Science, Otsu, Japan
| | - Katsuyuki Miura
- Department of Public Health, Shiga University of Medical Science, Otsu, Japan
- NCD Epidemiology Center, Shiga University of Medical Science, Otsu, Japan
| | - Masahiro Nakatochi
- Public Health Informatics Unit, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takashi Tamura
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Asahi Hishida
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Ryoko Nakashima
- Department of General Internal Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Hiroaki Ikezaki
- Department of Comprehensive General Internal Medicine, Faculty of Medical Sciences, Kyushu University Graduate School, Fukuoka, Japan
| | - Megumi Hara
- Department of Preventive Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Yuichiro Nishida
- Department of Preventive Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Toshiro Takezaki
- Department of International Island and Community Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Rie Ibusuki
- Department of International Island and Community Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Isao Oze
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center, Nagoya, Japan
| | - Hidemi Ito
- Division of Cancer Information and Control, Aichi Cancer Center, Nagoya, Japan
- Division of Descriptive Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Nagato Kuriyama
- Department of Epidemiology for Community Health and Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Department of Social Health Medicine, Shizuoka Graduate University of Public Health, Shizuoka, Japan
| | - Etsuko Ozaki
- Department of Epidemiology for Community Health and Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Haruo Mikami
- Cancer Prevention Center, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Miho Kusakabe
- Cancer Prevention Center, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Hiroko Nakagawa-Senda
- Department of Public Health, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Sadao Suzuki
- Department of Public Health, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Sakurako Katsuura-Kamano
- Department of Preventive Medicine, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Kokichi Arisawa
- Department of Preventive Medicine, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Kiyonori Kuriki
- Laboratory of Public Health, Division of Nutritional Sciences, School of Food and Nutritional Sciences, University of Shizuoka, Shizuoka, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Michiaki Kubo
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Kenji Takeuchi
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshikuni Kita
- Department of Public Health, Shiga University of Medical Science, Otsu, Japan
- Faculty of Nursing Science, Tsuruga Nursing University, Tsuruga, Japan
| | - Kenji Wakai
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
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Zhang K, Zhu S, Li J, Jiang T, Feng L, Pei J, Wang G, Ouyang L, Liu B. Targeting autophagy using small-molecule compounds to improve potential therapy of Parkinson's disease. Acta Pharm Sin B 2021; 11:3015-3034. [PMID: 34729301 PMCID: PMC8546670 DOI: 10.1016/j.apsb.2021.02.016] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/28/2021] [Accepted: 02/19/2021] [Indexed: 02/08/2023] Open
Abstract
Parkinson's disease (PD), known as one of the most universal neurodegenerative diseases, is a serious threat to the health of the elderly. The current treatment has been demonstrated to relieve symptoms, and the discovery of new small-molecule compounds has been regarded as a promising strategy. Of note, the homeostasis of the autolysosome pathway (ALP) is closely associated with PD, and impaired autophagy may cause the death of neurons and thereby accelerating the progress of PD. Thus, pharmacological targeting autophagy with small-molecule compounds has been drawn a rising attention so far. In this review, we focus on summarizing several autophagy-associated targets, such as AMPK, mTORC1, ULK1, IMPase, LRRK2, beclin-1, TFEB, GCase, ERRα, C-Abelson, and as well as their relevant small-molecule compounds in PD models, which will shed light on a clue on exploiting more potential targeted small-molecule drugs tracking PD treatment in the near future.
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Key Words
- 3-MA, 3-methyladenine
- 5-HT2A, Serotonin 2A
- 5-HT2C, serotonin 2C
- A2A, adenosine 2A
- AADC, aromatic amino acid decarboxylase
- ALP, autophagy-lysosomal pathway
- AMPK, 5ʹAMP-activated protein kinase
- ATG, autophagy related protein
- ATP13A2, ATPase cation transporting 13A2
- ATTEC, autophagosome-tethering compound
- AUC, the area under the curve
- AUTAC, autophagy targeting chimera
- Autophagy
- BAF, bafilomycinA1
- BBB, blood−brain barrier
- CL, clearance rate
- CMA, chaperone-mediated autophagy
- CNS, central nervous system
- COMT, catechol-O-methyltransferase
- DA, dopamine
- DAT, dopamine transporter
- DJ-1, Parkinson protein 7
- DR, dopamine receptor
- ER, endoplasmic reticulum
- ERRα, estrogen-related receptor alpha
- F, oral bioavailability
- GAPDH, glyceraldehyde 3-phosphate dehydrogenase
- GBA, glucocerebrosidase β acid
- GWAS, genome-wide association study
- HDAC6, histone deacetylase 6
- HSC70, heat shock cognate 71 kDa protein
- HSPA8, heat shock 70 kDa protein 8
- IMPase, inositol monophosphatase
- IPPase, inositol polyphosphate 1-phosphatase
- KI, knockin
- LAMP2A, lysosome-associated membrane protein 2 A
- LC3, light chain 3
- LIMP-2, lysosomal integrated membrane protein-2
- LRRK2, leucine-rich repeat sequence kinase 2
- LRS, leucyl-tRNA synthetase
- LUHMES, lund human mesencephalic
- Lamp2a, type 2A lysosomal-associated membrane protein
- MAO-B, monoamine oxidase B
- MPP+, 1-methyl-4-phenylpyridinium
- MPTP, 1-methyl-4-phenyl-1,2,5,6-tetrahydropyridine
- MYCBP2, MYC-binding protein 2
- NMDA, N-methyl-d-aspartic acid
- ONRs, orphan nuclear receptors
- PD therapy
- PD, Parkinson's disease
- PDE4, phosphodiesterase 4
- PI3K, phosphatidylinositol 3-kinase
- PI3P, phosphatidylinositol 3-phosphate
- PINK1, PTEN-induced kinase 1
- PLC, phospholipase C
- PREP, prolyl oligopeptidase
- Parkin, parkin RBR E3 ubiquitin−protein ligase
- Parkinson's disease (PD)
- ROS, reactive oxygen species
- SAR, structure–activity relationship
- SAS, solvent accessible surface
- SN, substantia nigra
- SNCA, α-synuclein gene
- SYT11, synaptotagmin 11
- Small-molecule compound
- TFEB, transcription factor EB
- TSC2, tuberous sclerosis complex 2
- Target
- ULK1, UNC-51-like kinase 1
- UPS, ubiquitin−proteasome system
- mAChR, muscarinic acetylcholine receptor
- mTOR, the mammalian target of rapamycin
- α-syn, α-synuclein
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Kessler T, Schunkert H. Coronary Artery Disease Genetics Enlightened by Genome-Wide Association Studies. JACC Basic Transl Sci 2021; 6:610-623. [PMID: 34368511 PMCID: PMC8326228 DOI: 10.1016/j.jacbts.2021.04.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 03/04/2021] [Accepted: 04/01/2021] [Indexed: 12/12/2022]
Abstract
Many cardiovascular diseases are facilitated by strong inheritance. For example, large-scale genetic studies identified hundreds of genomic loci that affect the risk of coronary artery disease. At each of these loci, common variants are associated with disease risk with robust statistical evidence but individually small effect sizes. Only a minority of candidate genes found at these loci are involved in the pathophysiology of traditional risk factors, but experimental research is making progress in identifying novel, and, in part, unexpected mechanisms. Targets identified by genome-wide association studies have already led to the development of novel treatments, specifically in lipid metabolism. This review summarizes recent genetic and experimental findings in this field. In addition, the development and possible clinical usefulness of polygenic risk scores in risk prediction and individualization of treatment, particularly in lipid metabolism, are discussed.
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Affiliation(s)
- Thorsten Kessler
- German Heart Centre Munich, Department of Cardiology, Technical University of Munich, Munich, Germany.,German Centre for Cardiovascular Research (DZHK e.V.), partner site Munich Heart Alliance, Munich, Germany
| | - Heribert Schunkert
- German Heart Centre Munich, Department of Cardiology, Technical University of Munich, Munich, Germany.,German Centre for Cardiovascular Research (DZHK e.V.), partner site Munich Heart Alliance, Munich, Germany
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9
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Roberts R, Chang CC, Hadley T. Genetic Risk Stratification: A Paradigm Shift in Prevention of Coronary Artery Disease. ACTA ACUST UNITED AC 2021; 6:287-304. [PMID: 33778213 PMCID: PMC7987546 DOI: 10.1016/j.jacbts.2020.09.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/08/2020] [Accepted: 09/13/2020] [Indexed: 12/12/2022]
Abstract
CAD is a pandemic that can be prevented. Conventional risk factors are inadequate to detect who is at risk early in the asymptomatic stage. Genetic risk for CAD can be determined at birth, and those at highest genetic risk have been shown to respond to lifestyle changes and statin therapy with a 40% to 50% reduction in cardiac events. Genetic risk stratification for CAD should be brought to the bedside in an attempt to prevent this pandemic disease.
Coronary artery disease (CAD) is a pandemic disease that is highly preventable as shown by secondary prevention. Primary prevention is preferred knowing that 50% of the population can expect a cardiac event in their lifetime. Risk stratification for primary prevention using the American Heart Association/American College of Cardiology predicted 10-year risk based on conventional risk factors for CAD is less than optimal. Conventional risk factors such as hypertension, cholesterol, and age are age-dependent and not present until the sixth or seventh decade of life. The genetic risk score (GRS), which is estimated from the recently discovered genetic variants predisposed to CAD, offers a potential solution to this dilemma. The GRS, which is derived from genotyping the population with a microarray containing these genetic risk variants, has indicated that genetic risk stratification based on the GRS is superior to that of conventional risk factors in detecting those at high risk and who would benefit most from statin therapy. Studies performed in >1 million individuals confirmed genetic risk stratification is superior and primarily independent of conventional risk factors. Prospective clinical trials based on risk stratification for CAD using the GRS have shown lifestyle changes, physical activity, and statin therapy are associated with 40% to 50% reduction in cardiac events in the high genetic risk group (20%). Genetic risk stratification has the advantage of being innate to an individual’s DNA, and because DNA does not change in a lifetime, it is independent of age. Genetic risk stratification is inexpensive and can be performed worldwide, providing risk analysis at any age and thus has the potential to revolutionize primary prevention.
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Key Words
- ACC, American College of Cardiology
- AHA, American Heart Association
- ANRIL, antisense non-coding RNA in the INK4 Locust
- CAD, coronary artery disease
- GRS, genetic risk score
- GWAS, genome-wide association study
- LDL-C, low-density lipoprotein cholesterol
- MR, Mendelian randomization
- SNP, single nucleotide polymorphism
- bp, base pair
- cardiovascular genetics
- coronary artery disease
- genetic risk score for CAD
- genome-wide association studies
- prevention of CAD
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Affiliation(s)
- Robert Roberts
- Department of Medicine, Dignity Health at St. Joseph's Hospital and Medical Center, Phoenix, Arizona, USA
| | - Chih Chao Chang
- Department of Medicine, Dignity Health at St. Joseph's Hospital and Medical Center, Phoenix, Arizona, USA
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10
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Hong KU, Doll MA, Lykoudi A, Salazar-González RA, Habil MR, Walls KM, Bakr AF, Ghare SS, Barve SS, Arteel GE, Hein DW. Acetylator Genotype-Dependent Dyslipidemia in Rats Congenic for N-Acetyltransferase 2. Toxicol Rep 2020; 7:1319-1330. [PMID: 33083237 PMCID: PMC7553889 DOI: 10.1016/j.toxrep.2020.09.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/14/2020] [Accepted: 09/23/2020] [Indexed: 01/10/2023] Open
Abstract
Recent reports suggest that arylamine N-acetyltransferases (NAT1 and/or NAT2) serve important roles in regulation of energy utility and insulin sensitivity. We investigated the interaction between diet (control vs. high-fat diet) and acetylator phenotype (rapid vs. slow) using previously established congenic rat lines (in F344 background) that exhibit rapid or slow Nat2 (orthologous to human NAT1) acetylator genotypes. Male and female rats of each genotype were fed control or high-fat (Western-style) diet for 26 weeks. We then examined diet- and acetylator genotype-dependent changes in body and liver weights, systemic glucose tolerance, insulin sensitivity, and plasma lipid profile. Male and female rats on the high fat diet weighed approximately 10% more than rats on the control diet and the percentage liver to body weight was consistently higher in rapid than slow acetylator rats. Rapid acetylator rats were more prone to develop dyslipidemia overall (i.e., higher triglyceride; higher LDL; and lower HDL), compared to slow acetylator rats. Total cholesterol (TC)-to-HDL ratios were significantly higher and HDL-to-LDL ratios were significantly lower in rapid acetylator rats. Our data suggest that rats with rapid systemic Nat2 (NAT1 in humans) genotype exhibited higher dyslipidemia conferring risk for metabolic syndrome and cardiovascular dysfunction.
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Affiliation(s)
- Kyung U. Hong
- Department of Pharmacology & Toxicology, Center for Hepatobiology & Toxicology, University of Louisville School of Medicine, Louisville, KY, USA
| | - Mark A. Doll
- Department of Pharmacology & Toxicology, Center for Hepatobiology & Toxicology, University of Louisville School of Medicine, Louisville, KY, USA
| | - Angeliki Lykoudi
- Department of Pharmacology & Toxicology, Center for Hepatobiology & Toxicology, University of Louisville School of Medicine, Louisville, KY, USA
| | - Raúl A. Salazar-González
- Department of Pharmacology & Toxicology, Center for Hepatobiology & Toxicology, University of Louisville School of Medicine, Louisville, KY, USA
| | - Mariam R. Habil
- Department of Pharmacology & Toxicology, Center for Hepatobiology & Toxicology, University of Louisville School of Medicine, Louisville, KY, USA
| | - Kennedy M. Walls
- Department of Pharmacology & Toxicology, Center for Hepatobiology & Toxicology, University of Louisville School of Medicine, Louisville, KY, USA
| | - Alaa F. Bakr
- Department of Pharmacology & Toxicology, Center for Hepatobiology & Toxicology, University of Louisville School of Medicine, Louisville, KY, USA
| | - Smita S. Ghare
- Departments of Medicine and Pharmacology & Toxicology, Center for Hepatobiology & Toxicology, University of Louisville School of Medicine, Louisville, KY, USA
| | - Shirish S. Barve
- Department of Pharmacology & Toxicology, Center for Hepatobiology & Toxicology, University of Louisville School of Medicine, Louisville, KY, USA
- Departments of Medicine and Pharmacology & Toxicology, Center for Hepatobiology & Toxicology, University of Louisville School of Medicine, Louisville, KY, USA
| | - Gavin E. Arteel
- Department of Pharmacology & Toxicology, Center for Hepatobiology & Toxicology, University of Louisville School of Medicine, Louisville, KY, USA
| | - David W. Hein
- Department of Pharmacology & Toxicology, Center for Hepatobiology & Toxicology, University of Louisville School of Medicine, Louisville, KY, USA
- Departments of Medicine and Pharmacology & Toxicology, Center for Hepatobiology & Toxicology, University of Louisville School of Medicine, Louisville, KY, USA
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Komenoi S, Suzuki Y, Asami M, Murakami C, Hoshino F, Chiba S, Takahashi D, Kado S, Sakane F. Microarray analysis of gene expression in the diacylglycerol kinase η knockout mouse brain. Biochem Biophys Rep 2019; 19:100660. [PMID: 31297456 PMCID: PMC6597918 DOI: 10.1016/j.bbrep.2019.100660] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 06/17/2019] [Accepted: 06/19/2019] [Indexed: 12/18/2022] Open
Abstract
We have revealed that diacylglycerol kinase η (DGKη)-knockout (KO) mice display bipolar disorder (BPD) remedy-sensitive mania-like behaviors. However, the molecular mechanisms causing the mania-like abnormal behaviors remain unclear. In the present study, microarray analysis was performed to determine global changes in gene expression in the DGKη-KO mouse brain. We found that the DGKη-KO brain had 43 differentially expressed genes and the following five affected biological pathways: "neuroactive ligand-receptor interaction", "transcription by RNA polymerase II", "cytosolic calcium ion concentration", "Jak-STAT signaling pathway" and "ERK1/2 cascade". Interestingly, mRNA levels of prolactin and growth hormone, which are augmented in BPD patients and model animals, were most strongly increased. Notably, all five biological pathways include at least one gene among prolactin, growth hormone, forkhead box P3, glucagon-like peptide 1 receptor and interleukin 1β, which were previously implicated in BPD. Consistent with the microarray data, phosphorylated ERK1/2 levels were decreased in the DGKη-KO brain. Microarray analysis showed that the expression levels of several glycerolipid metabolism-related genes were also changed. Liquid chromatography-mass spectrometry revealed that several polyunsaturated fatty acid (PUFA)-containing phosphatidic acid (PA) molecular species were significantly decreased as a result of DGKη deficiency, suggesting that the decrease affects PUFA metabolism. Intriguingly, the PUFA-containing lysoPA species were markedly decreased in DGKη-KO mouse blood. Taken together, our study provides not only key broad knowledge to gain novel insights into the underlying mechanisms for the mania-like behaviors but also information for developing BPD diagnostics.
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Key Words
- BPD, bipolar disorder
- Bipolar disorder
- DAVID, Database for AnnotationVisualization and Integrated Discovery
- DG, diacylglycerol
- DGK, diacylglycerol kinase
- Diacylglycerol kinase
- ERK, extracellular signal-regulated kinase
- Fpr2, N-formyl peptide receptor 2
- GO:BP, Gene Ontology: Biological Process
- GWAS, genome-wide association study
- Gh, growth hormone
- Glp1r, glucagon-like peptide 1 receptor
- Growth hormone
- Il1b, interleukin 1β
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- KO, knockout
- LC-MS, liquid chromatography-mass spectrometry
- LPA, lysophosphatidic acid
- Lysophosphatidic acid
- MEK, mitogen-activated protein kinase/ERK kinase
- PA, phosphatidic acid
- PI, phosphatidylinositol
- PUFA, polyunsaturated fatty acid
- Phosphatidic acid
- Prl, prolactin
- Prolactin
- SERT, serotonin transporter
- WT, wild type
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Affiliation(s)
- Suguru Komenoi
- Department of Chemistry, Graduate School of Science, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan
| | - Yuji Suzuki
- Department of Chemistry, Graduate School of Science, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan
| | - Maho Asami
- Department of Chemistry, Graduate School of Science, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan
| | - Chiaki Murakami
- Department of Chemistry, Graduate School of Science, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan
| | - Fumi Hoshino
- Department of Chemistry, Graduate School of Science, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan
| | - Sohei Chiba
- Department of Chemistry, Graduate School of Science, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan
| | - Daisuke Takahashi
- Department of Chemistry, Graduate School of Science, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan
| | - Sayaka Kado
- Center for Analytical Instrumentation, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan
| | - Fumio Sakane
- Department of Chemistry, Graduate School of Science, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan
- Corresponding author. Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan.
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12
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Schooling CM, Ng JCM. Reproduction and longevity: A Mendelian randomization study of gonadotropin-releasing hormone and ischemic heart disease. SSM Popul Health 2019; 8:100411. [PMID: 31198836 PMCID: PMC6556548 DOI: 10.1016/j.ssmph.2019.100411] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/17/2019] [Accepted: 05/12/2019] [Indexed: 01/22/2023] Open
Abstract
Background According to well-established evolutionary biology theory there is a trade-off between reproduction and longevity, implying that upregulating the reproductive axis might drive major diseases. We assessed whether the central driver of reproduction gonadotropin-releasing hormone 1 (GnRH1) had a causal effect on the leading cause of global morbidity and mortality, i.e. ischemic heart disease (IHD). As a contrast we similarly examined the role of GnRH2 because it is more a driver of female sexual behavior. Methods We applied strong (p-value <5 × 10-6) and independent genetic predictors of GnRH1 and GnRH2 to an extensively genotyped IHD case (n = 76,014) - control (n = 264,785) study and combined the genetic variant specific Wald estimates using inverse variance weighting (IVW) with multiplicative random effects, and as a sensitivity analysis used weighted median, MR-Egger and MR-PRESSO estimates, and repeated the analysis only using genome wide significant genetic predictors. Findings GnRH1, predicted by 11 genetic variants, was positively associated with IHD (IVW odds ratio (OR) 1.04 per effect size, 95% confidence interval (CI) 1.01 to 1.08), but GnRH2, predicted by 15 genetic variants, was not (IVW OR 0.98, 95% CI 0.95 to 1.02). Estimates from sensitivity analysis were similar. Interpretation GnRH1 is a potential IHD genetic target. Apart from demonstrating a central tenet of evolutionary biology in humans, our study suggests that existing treatments and environmental factors targeting GnRH1, its drivers or consequences could be re-purposed to prevent and treat IHD. Given, the importance of reproduction to the human species, many such exposures likely exist.
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Affiliation(s)
- C M Schooling
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Graduate School of Public Health and Health Policy, The City University of New York, New York, USA
| | - Jack C M Ng
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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13
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van Rensburg SJ, Peeters AV, van Toorn R, Schoeman J, Moremi KE, van Heerden CJ, Kotze MJ. Identification of an iron-responsive subtype in two children diagnosed with relapsing-remitting multiple sclerosis using whole exome sequencing. Mol Genet Metab Rep 2019; 19:100465. [PMID: 30963028 DOI: 10.1016/j.ymgmr.2019.100465] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 03/16/2019] [Accepted: 03/16/2019] [Indexed: 12/26/2022] Open
Abstract
Background Multiple sclerosis is a disorder related to demyelination of axons. Iron is an essential cofactor in myelin synthesis. Previously, we described two children (males of mixed ancestry) with relapsing-remitting multiple sclerosis (RRMS) where long-term remission was achieved by regular iron supplementation. A genetic defect in iron metabolism was postulated, suggesting that more advanced genetic studies could shed new light on disease pathophysiology related to iron. Methods Whole exome sequencing (WES) was performed to identify causal pathways. Blood tests were performed over a 10 year period to monitor the long-term effect of a supplementation regimen. Clinical wellbeing was assessed quarterly by a pediatric neurologist and regular feedback was obtained from the schoolteachers. Results WES revealed gene variants involved in iron absorption and transport, in the transmembrane protease, serine 6 (TMPRSS6) and transferrin (TF) genes; multiple genetic variants in CUBN, which encodes cubilin (a receptor involved in the absorption of vitamin B12 as well as the reabsorption of transferrin-bound iron and vitamin D in the kidneys); SLC25A37 (involved in iron transport into mitochondria) and CD163 (a scavenger receptor involved in hemorrhage resolution). Variants were also found in COQ3, involved with synthesis of Coenzyme Q10 in mitochondria. Neither of the children had the HLA-DRB1*1501 allele associated with increased genetic risk for MS, suggesting that the genetic contribution of iron-related genetic variants may be instrumental in childhood MS. In both children the RRMS has remained stable without activity over the last 10 years since initiation of nutritional supplementation and maintenance of normal iron levels, confirming the role of iron deficiency in disease pathogenesis in these patients. Conclusion Our findings highlight the potential value of WES to identify heritable risk factors that could affect the reabsorption of transferrin-bound iron in the kidneys causing sustained iron loss, together with inhibition of vitamin B12 absorption and vitamin D reabsorption (CUBN) and iron transport into mitochondria (SLC25A37) as the sole site of heme synthesis. This supports a model for RRMS in children with an apparent iron-deficient biochemical subtype of MS, with oligodendrocyte cell death and impaired myelination possibly caused by deficits of energy- and antioxidant capacity in mitochondria.
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Key Words
- CNS, central nervous system
- CoQ, Coenzyme Q
- DFO, desferroxamine mesylate
- DIS, dissemination in space
- DIT, dissemination in time
- DMT, disease modifying therapy
- EDSS, Expanded Disability Status Scale
- ETC, electron transport chain
- GWAS, genome-wide association study
- Genetic variants
- HDL, high density lipoprotein
- HERV-W, human endogenous retrovirus W
- HLA, human leukocyte antigen
- HREC, human research ethics committee
- IPMSSG, International Pediatric Multiple Sclerosis Study Group
- IRE, iron-response element
- Iron deficiency
- MGA1, juvenile hereditary megaloblastic anemia 1
- MRI, magnetic resonance imaging
- MS, Multiple sclerosis
- MSRV, MS-associated retrovirus
- MST1R, macrophage stimulating-1 receptor
- Mitochondria
- Oxidative stress
- PSGT, pathology supported genetic testing
- Pediatric onset multiple sclerosis
- ROS, reactive oxygen species
- RRMS, relapsing-remitting MS
- SAMe, S-adenosyl methionine
- SDHB, iron-protein subunit of Complex II
- TF, transferrin
- TMPRSS6, transmembrane protease, serine 6
- WES, whole exome sequencing
- Whole exome sequencing
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Abstract
Heart failure (HF) is the end-stage of all heart disease and arguably constitutes the greatest unmet therapeutic need in cardiovascular medicine today. Classic epidemiological studies have established clinical risk factors for HF, but the cause remains poorly understood in many cases. Biochemical analyses of small case-control series and animal models have described a plethora of molecular characteristics of HF, but a single unifying pathogenic theory is lacking. Heart failure appears to result not only from cardiac overload or injury but also from a complex interplay among genetic, neurohormonal, metabolic, inflammatory, and other biochemical factors acting on the heart. Recent development of robust, high-throughput tools in molecular biology provides opportunity for deep molecular characterization of population-representative cohorts and HF cases (molecular epidemiology), including genome sequencing, profiling of myocardial gene expression and chromatin modifications, plasma composition of proteins and metabolites, and microbiomes. The integration of such detailed information holds promise for improving understanding of HF pathophysiology in humans, identification of therapeutic targets, and definition of disease subgroups beyond the current classification based on ejection fraction which may benefit from improved individual tailoring of therapy. Challenges include: 1) the need for large cohorts with deep, uniform phenotyping; 2) access to the relevant tissues, ideally with repeated sampling to capture dynamic processes; and 3) analytical issues related to integration and analysis of complex datasets. International research consortia have formed to address these challenges and combine datasets, and cohorts with up to 1 million participants are being collected. This paper describes the molecular epidemiology of HF and provides an overview of methods and tissue types and examples of published and ongoing efforts to systematically evaluate molecular determinants of HF in human populations.
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Affiliation(s)
- J Gustav Smith
- Department of Cardiology, Clinical Sciences, Lund University, Lund, Sweden.,Department of Heart Failure and Valvular Disease, Skåne University Hospital, Lund, Sweden.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
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Cnop M, Toivonen S, Igoillo-Esteve M, Salpea P. Endoplasmic reticulum stress and eIF2α phosphorylation: The Achilles heel of pancreatic β cells. Mol Metab 2017; 6:1024-1039. [PMID: 28951826 PMCID: PMC5605732 DOI: 10.1016/j.molmet.2017.06.001] [Citation(s) in RCA: 171] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 05/19/2017] [Accepted: 06/01/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Pancreatic β cell dysfunction and death are central in the pathogenesis of most if not all forms of diabetes. Understanding the molecular mechanisms underlying β cell failure is important to develop β cell protective approaches. SCOPE OF REVIEW Here we review the role of endoplasmic reticulum stress and dysregulated endoplasmic reticulum stress signaling in β cell failure in monogenic and polygenic forms of diabetes. There is substantial evidence for the presence of endoplasmic reticulum stress in β cells in type 1 and type 2 diabetes. Direct evidence for the importance of this stress response is provided by an increasing number of monogenic forms of diabetes. In particular, mutations in the PERK branch of the unfolded protein response provide insight into its importance for human β cell function and survival. The knowledge gained from different rodent models is reviewed. More disease- and patient-relevant models, using human induced pluripotent stem cells differentiated into β cells, will further advance our understanding of pathogenic mechanisms. Finally, we review the therapeutic modulation of endoplasmic reticulum stress and signaling in β cells. MAJOR CONCLUSIONS Pancreatic β cells are sensitive to excessive endoplasmic reticulum stress and dysregulated eIF2α phosphorylation, as indicated by transcriptome data, monogenic forms of diabetes and pharmacological studies. This should be taken into consideration when devising new therapeutic approaches for diabetes.
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Key Words
- ATF, activating transcription factor
- CHOP, C/EBP homologous protein
- CRISPR, clustered regularly interspaced short palindromic repeats
- CReP, constitutive repressor of eIF2α phosphorylation
- Diabetes
- ER, endoplasmic reticulum
- ERAD, ER-associated degradation
- Endoplasmic reticulum stress
- GCN2, general control non-derepressible-2
- GIP, glucose-dependent insulinotropic polypeptide
- GLP-1, glucagon-like peptide 1
- GWAS, genome-wide association study
- HNF1A, hepatocyte nuclear factor 1-α
- HRI, heme-regulated inhibitor kinase
- IAPP, islet amyloid polypeptide
- IER3IP1, immediate early response-3 interacting protein-1
- IRE1, inositol-requiring protein-1
- ISR, integrated stress response
- Insulin
- Islet
- MEHMO, mental retardation, epilepsy, hypogonadism and -genitalism, microcephaly and obesity
- MODY, maturity-onset diabetes of the young
- NRF2, nuclear factor, erythroid 2 like 2
- PBA, 4-phenyl butyric acid
- PERK, PKR-like ER kinase
- PKR, protein kinase RNA
- PP1, protein phosphatase 1
- PPA, phenylpropenoic acid glucoside
- Pancreatic β cell
- Pdx1, pancreatic duodenal homeobox 1
- RIDD, regulated IRE1-dependent decay
- RyR2, type 2 ryanodine receptor/Ca2+ release channel
- SERCA, sarcoendoplasmic reticulum Ca2+ ATPase
- TUDCA, taurine-conjugated ursodeoxycholic acid derivative
- UPR, unfolded protein response
- WFS, Wolfram syndrome
- XBP1, X-box binding protein 1
- eIF2, eukaryotic translation initiation factor 2
- eIF2α
- hESC, human embryonic stem cell
- hPSC, human pluripotent stem cell
- hiPSC, human induced pluripotent stem cell
- uORF, upstream open reading frame
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Affiliation(s)
- Miriam Cnop
- ULB Center for Diabetes Research, Faculty of Medicine, Université Libre de Bruxelles, Brussels, Belgium
- Division of Endocrinology, Erasmus Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Sanna Toivonen
- ULB Center for Diabetes Research, Faculty of Medicine, Université Libre de Bruxelles, Brussels, Belgium
| | - Mariana Igoillo-Esteve
- ULB Center for Diabetes Research, Faculty of Medicine, Université Libre de Bruxelles, Brussels, Belgium
| | - Paraskevi Salpea
- ULB Center for Diabetes Research, Faculty of Medicine, Université Libre de Bruxelles, Brussels, Belgium
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Tsai EA, Gilbert MA, Grochowski CM, Underkoffler LA, Meng H, Zhang X, Wang MM, Shitaye H, Hankenson KD, Piccoli D, Lin H, Kamath BM, Devoto M, Spinner NB, Loomes KM. THBS2 Is a Candidate Modifier of Liver Disease Severity in Alagille Syndrome. Cell Mol Gastroenterol Hepatol 2016; 2:663-675.e2. [PMID: 28090565 PMCID: PMC5042888 DOI: 10.1016/j.jcmgh.2016.05.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 05/17/2016] [Indexed: 01/03/2023]
Abstract
BACKGROUND & AIMS Alagille syndrome is an autosomal-dominant, multisystem disorder caused primarily by mutations in JAG1, resulting in bile duct paucity, cholestasis, cardiac disease, and other features. Liver disease severity in Alagille syndrome is highly variable, however, factors influencing the hepatic phenotype are unknown. We hypothesized that genetic modifiers may contribute to the variable expressivity of this disorder. METHODS We performed a genome-wide association study in a cohort of Caucasian subjects with known pathogenic JAG1 mutations, comparing patients with mild vs severe liver disease, followed by functional characterization of a candidate locus. RESULTS We identified a locus that reached suggestive genome-level significance upstream of the thrombospondin 2 (THBS2) gene. THBS2 codes for a secreted matricellular protein that regulates cell proliferation, apoptosis, and angiogenesis, and has been shown to affect Notch signaling. By using a reporter mouse line, we detected thrombospondin 2 expression in bile ducts and periportal regions of the mouse liver. Examination of Thbs2-null mouse livers showed increased microvessels in the portal regions of adult mice. We also showed that thrombospondin 2 interacts with NOTCH1 and NOTCH2 and can inhibit JAG1-NOTCH2 interactions. CONCLUSIONS Based on the genome-wide association study results, thrombospondin 2 localization within bile ducts, and demonstration of interactions of thrombospondin 2 with JAG1 and NOTCH2, we propose that changes in thrombospondin 2 expression may further perturb JAG1-NOTCH2 signaling in patients harboring a JAG1 mutation and lead to a more severe liver phenotype. These results implicate THBS2 as a plausible candidate genetic modifier of liver disease severity in Alagille syndrome.
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Key Words
- ALGS, Alagille syndrome
- BSA, bovine serum albumin
- CK19, cytokeratin 19
- ChiLDReN, Childhood Liver Disease Research Network
- Cholestasis
- GFP, green fluorescent protein
- GWAS, genome-wide association study
- Gene Modifier
- Genome-Wide Association Study
- JAG1
- NOTCH2
- PCR, polymerase chain reaction
- SNP, single-nucleotide polymorphism
- THBS2, thrombospondin 2
- cDNA, complementary DNA
- ddPCR, droplet digital polymerase chain reaction
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Affiliation(s)
- Ellen A Tsai
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania; Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Melissa A Gilbert
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Christopher M Grochowski
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Lara A Underkoffler
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania
| | - He Meng
- Department of Neurology, University of Michigan, Ann Arbor, Michigan
| | - Xiaojie Zhang
- Department of Neurology, University of Michigan, Ann Arbor, Michigan
| | - Michael M Wang
- Department of Neurology, University of Michigan, Ann Arbor, Michigan; Department of Physiology, University of Michigan, Ann Arbor, Michigan; VA Ann Arbor Healthcare System, Ann Arbor, Michigan
| | - Hailu Shitaye
- Medical Scientist Training Program, University of Michigan, Ann Arbor, Michigan
| | - Kurt D Hankenson
- Department of Physiology, Department of Small Animal Clinical Sciences, Colleges of Natural Science, Osteopathic Medicine, and Veterinary Medicine, Michigan State University, East Lansing, Michigan; Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - David Piccoli
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Henry Lin
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Binita M Kamath
- Division of Gastroenterology, Hepatology, and Nutrition, Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Marcella Devoto
- Division of Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | - Nancy B Spinner
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kathleen M Loomes
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania
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17
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Taylor KC, Evans DS, Edwards DRV, Edwards TL, Sofer T, Li G, Liu Y, Franceschini N, Jackson RD, Giri A, Donneyong M, Psaty B, Rotter JI, LaCroix AZ, Jordan JM, Robbins JA, Lewis B, Stefanick ML, Liu Y, Garcia M, Harris T, Cauley JA, North KE. A genome-wide association study meta-analysis of clinical fracture in 10,012 African American women. Bone Rep 2016; 5:233-242. [PMID: 28580392 PMCID: PMC5440953 DOI: 10.1016/j.bonr.2016.08.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 08/25/2016] [Indexed: 01/01/2023] Open
Abstract
Background Osteoporosis is a major public health problem associated with excess disability and mortality. It is estimated that 50–70% of the variation in osteoporotic fracture risk is attributable to genetic factors. The purpose of this hypothesis-generating study was to identify possible genetic determinants of fracture among African American (AA) women in a GWAS meta-analysis. Methods Data on clinical fractures (all fractures except fingers, toes, face, skull or sternum) were analyzed among AA female participants in the Women's Health Initiative (WHI) (N = 8155), Cardiovascular Health Study (CHS) (N = 504), BioVU (N = 704), Health ABC (N = 651), and the Johnston County Osteoarthritis Project (JoCoOA) (N = 291). Affymetrix (WHI) and Illumina (Health ABC, JoCoOA, BioVU, CHS) GWAS panels were used for genotyping, and a 1:1 ratio of YRI:CEU HapMap haplotypes was used as an imputation reference panel. We used Cox proportional hazard models or logistic regression to evaluate the association of ~ 2.5 million SNPs with fracture risk, adjusting for ancestry, age, and geographic region where applicable. We conducted a fixed-effects, inverse variance-weighted meta-analysis. Genome-wide significance was set at P < 5 × 10− 8. Results One SNP, rs12775980 in an intron of SVIL on chromosome 10p11.2, reached genome-wide significance (P = 4.0 × 10− 8). Although this SNP has a low minor allele frequency (0.03), there was no evidence for heterogeneity of effects across the studies (I2 = 0). This locus was not reported in any previous osteoporosis-related GWA studies. We also interrogated previously reported GWA-significant loci associated with fracture or bone mineral density in our data. One locus (SMOC1) generalized, but overall there was not substantial evidence of generalization. Possible reasons for the lack of generalization are discussed. Conclusion This GWAS meta-analysis of fractures in African American women identified a potentially novel locus in the supervillin gene, which encodes a platelet-associated factor and was previously associated with platelet thrombus formation in African Americans. If validated in other populations of African descent, these findings suggest potential new mechanisms involved in fracture that may be particularly important among African Americans. This was a hypothesis-generating GWAS for fracture in African Americans. One potentially novel locus (SVIL) was identified at GWA-significant levels. SVIL has been associated with platelet thrombus formation in African-Americans.
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Key Words
- AA, African American
- ASW, African ancestry individuals from Southwest USA
- African American
- BMD, bone mineral density
- BMI, body mass index
- BMP, bone morphogenetic protein
- CES-D, Center for Epidemiological Studies-Depression scale
- CEU, CEPH-Utah (Utah residents with ancestors from central and western Europe)
- CHS, Cardiovascular Health Study
- DNA, deoxyribonucleic acid
- EAF, effect allele frequency
- Fracture
- GEFOS, Genetic Factors of Osteoporosis
- GPGE, genetically predicted gene expression
- GTEx Project, Genotype-Tissue Expression project
- GWAS, genome-wide association study
- Genetic association study
- Genome-wide association study (GWAS)
- JoCoOA, Johnston County Osteoarthritis Project
- MAC, minor allele count
- MAF, minor allele frequency
- Meta-analysis
- OF, osteoporotic fracture
- Osteoporosis
- RNA, ribonucleic acid
- SD, standard deviation
- SHARe, SNP Health Association Resource
- SNP, single nucleotide polymorphism
- WHI, Women's Health Initiative
- YRI, Yoruban (Nigeria)
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Affiliation(s)
- Kira C Taylor
- School of Public Health and Information Sciences, University of Louisville, 485 E Gray St., Louisville, KY 40202, USA.,Gillings School of Global Public Health, University of North Carolina at Chapel Hill, 137 E. Franklin St., Chapel Hill, NC 27514, USA
| | - Daniel S Evans
- California Pacific Medical Center Research Institute, 550 16th Street, Box 0560, San Francisco, CA 94158-2549, USA
| | - Digna R Velez Edwards
- Vanderbilt Epidemiology Center, Department of Obstetrics and Gynecology, Vanderbilt Genetics Institute, Vanderbilt University, 2525 West End Avenue, Nashville, TN 37203, USA
| | - Todd L Edwards
- Vanderbilt Genetics Institute, Division of Epidemiology, Department of Medicine, Vanderbilt University, 2525 West End Avenue, Nashville, TN 37203, USA
| | - Tamar Sofer
- Department of Biostatistics, University of Washington, UW Tower 15th floor, 4333 Brooklyn Ave NE, Seattle 98105, USA
| | - Guo Li
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Metropolitan Park East Tower, 1730 Minor Ave, Suite 1360, Seattle, WA 98101, USA
| | - Youfang Liu
- Thurston Arthritis Research Center, University of North Carolina at Chapel Hill, 3300 Thurston Bldg., CB# 7280, Chapel Hill NC 27599-7280, NC, USA
| | - Nora Franceschini
- University of North Carolina at Chapel Hill, 137 E. Franklin St., Chapel Hill, NC 27514, USA
| | - Rebecca D Jackson
- The Ohio State University, 376 W 10th Avenue, Suite 260, Columbus, OH 43210, USA
| | - Ayush Giri
- Vanderbilt Genetics Institute, Division of Epidemiology, Department of Medicine, Vanderbilt University, 2525 West End Avenue, Nashville, TN 37203, USA
| | - Macarius Donneyong
- School of Public Health and Information Sciences, University of Louisville, 485 E Gray St., Louisville, KY 40202, USA.,Division of Pharmacoepidemiology and Pharmacoeconomics, Department of Medicine, Brigham and Women's Hospital, 1620 Tremont St, St 3030, Boston, MA 02120, USA
| | - Bruce Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology and Health Services, University of Washington; Group Health Research Institute, Group Health Cooperative, Metropolitan Park East Tower, 1730 Minor Ave, Suite 1360, Seattle, WA 98101, USA
| | - Jerome I Rotter
- Institute of Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics, Harbor-UCLA Medical Center, 1124 W. Carson Street, Bldg., E-5, Torrance, CA 90502, USA
| | - Andrea Z LaCroix
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Joanne M Jordan
- Department of Medicine, University of California at Davis Medical Center, PSSB Building, 4150 V St., Sacramento, CA 95817, USA
| | - John A Robbins
- Thurston Arthritis Research Center, University of North Carolina at Chapel Hill, 3300 Thurston Bldg., CB# 7280, Chapel Hill NC 27599-7280, NC, USA
| | - Beth Lewis
- University of Alabama, Medical Towers 614, 1717 11th Avenue South, Birmingham, AL 35205, USA
| | - Marcia L Stefanick
- Stanford Prevention Research Center, Stanford University School of Medicine, Medical School Office Building, 1265 Welch Road, Mail Code 5411, Stanford, CA 94305, USA
| | - Yongmei Liu
- Wake Forest Baptist Medical Center, Medical Center Boulevard, Winston-Salem, NC 27157, USA
| | - Melissa Garcia
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, 7201 Wisconsin Ave, Suite 3C309, Bethesda, MD 20892, USA
| | - Tamara Harris
- Laboratory of Epidemiology and Population Science, Intramural Research Program, National Institute on Aging, National Institutes of Health, 31 Center Drive, Bethesda, MD 20892, USA
| | - Jane A Cauley
- University of Pittsburgh Graduate School of Public Health, Department of Epidemiology, A510 Crabtree Hall, Pittsburgh, PA 15261, USA
| | - Kari E North
- Carolina Center for Genome Sciences, 250 Bell Tower Dr., Chapel Hill, NC 27514, USA.,Gillings School of Global Public Health, University of North Carolina at Chapel Hill, 137 E. Franklin St., Chapel Hill, NC 27514, USA
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Oliver VF, Jaffe AE, Song J, Wang G, Zhang P, Branham KE, Swaroop A, Eberhart CG, Zack DJ, Qian J, Merbs SL. Differential DNA methylation identified in the blood and retina of AMD patients. Epigenetics 2016; 10:698-707. [PMID: 26067391 DOI: 10.1080/15592294.2015.1060388] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Age-related macular degeneration (AMD) is a major cause of blindness in the western world. While genetic studies have linked both common and rare variants in genes involved in regulation of the complement system to increased risk of development of AMD, environmental factors, such as smoking and nutrition, can also significantly affect the risk of developing the disease and the rate of disease progression. Since epigenetics has been implicated in mediating, in part, the disease risk associated with some environmental factors, we investigated a possible epigenetic contribution to AMD. We performed genome-wide DNA methylation profiling of blood from AMD patients and controls. No differential methylation site reached genome-wide significance; however, when epigenetic changes in and around known GWAS-defined AMD risk loci were explored, we found small but significant DNA methylation differences in the blood of neovascular AMD patients near age-related maculopathy susceptibility 2 (ARMS2), a top-ranked GWAS locus preferentially associated with neovascular AMD. The methylation level of one of the CpG sites significantly correlated with the genotype of the risk SNP rs10490924, suggesting a possible epigenetic mechanism of risk. Integrating genome-wide DNA methylation analysis of retina samples with and without AMD together with blood samples, we further identified a consistent, replicable change in DNA methylation in the promoter region of protease serine 50 (PRSS50). These methylation changes may identify sites in novel genes that are susceptible to non-genetic factors known to contribute to AMD development and progression.
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Key Words
- AMD, Age-related macular degeneration
- AMD-MMAP, Michigan, Mayo
- AREDS, Age-Related Eye Disease Study
- AREDS, and Pennsylvania
- DNA methylation
- DNAm, DNA methylation
- GA, geographic atrophy
- GWAS, genome-wide association study
- KEC, Kellogg Eye Center
- LCLs, lymphoblastoid cell lines
- NV, choroidal neovascularization
- RPE, retinal pigment epithelium
- age-related macular degeneration
- genome-wide methylation
- meQTL, methylation quantitative trait loci
- methyl-QTL
- peripheral blood leukocytes
- retina
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Affiliation(s)
- Verity F Oliver
- a Department of Ophthalmology; Johns Hopkins University; School of Medicine ; Baltimore , MD USA
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Sun C, Wei H, Chen X, Zhao Z, Du H, Song W, Yang Y, Zhang M, Lu W, Pei Z, Xi L, Yan J, Zhi D, Cheng R, Luo F. ERBB3-rs2292239 as primary type 1 diabetes association locus among non-HLA genes in Chinese. Meta Gene 2016; 9:120-3. [PMID: 27331016 DOI: 10.1016/j.mgene.2016.05.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 04/18/2016] [Accepted: 05/11/2016] [Indexed: 12/13/2022] Open
Abstract
Type 1 diabetes (T1D) is an autoimmune disease that has strong contribution of genetic factors to its etiology. We aimed to assess the genetic association between non-HLA genes and T1D in a Chinese case-control cohort recruited from multiple centers consisting of 364 patients with T1D and 719 unrelated healthy children. We genotyped 55 single nucleotide polymorphisms (SNP) markers located in 16 non-HLA genes (VTCN1, PTPN22, CTLA4, SUMO4, CD274, IL2RA, INS, DHCR7, ERBB3, VDR, CYP27B1, CD69, CD276, PTPN2, UBASH3A, and IL2RB) using SNaPshot multiple single-base extension methods. After multivariate analysis and correction for multiple comparisons, we identified the SNP rs2292239 in ERBB3 gene were significantly associated with T1D. The frequency of the major G allele was significantly decreased in patients with T1D (68.8% in T1D vs 77.3% in controls, OR 0.65, 95% CI 0.53–0.79, P = 0.02), and the minor allele T was associated with an increased risk of T1D (OR 1.55, 95% CI 1.26–1.90, P = 0.02). Our haplotype analysis confirmed that rs2292239 was the primary T1D association locus in our current investigation. These results indicated that the ERBB3-rs2292239 was the primary T1D association locus among the investigated 55 SNPs in 16 non-HLA genes in Chinese Han population. A large scale case-control genetic association study on type 1 diabetes in Chinese investigating on-HLA genes. rs2292239 in the ERBB3 gene conferred the primary non-HLA association in Chinese type 1 diabetes. Markers in the common candidate genes, such as PTPN22, CTLA4, IL2RA, and INS, were not significantly associated with T1D in our Chinese cohort.
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Key Words
- CI, confidence interval
- DNA, deoxyribonucleic acid
- EGFR, epidermal growth factor receptor
- ERBB3
- GWAS, genome-wide association study
- Genetic association
- HLA, human leukocyte antigen
- HWE, Hardy-Weinberg equilibrium
- OR, odds ratio
- SBE, single-base extension
- SNP, single nucleotide polymorphism
- Single nucleotide polymorphism
- T1D, type 1 diabetes
- Type 1 diabetes
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Abstract
The development and progression of melanoma have been attributed to independent or combined genetic and epigenetic events. There has been remarkable progress in understanding melanoma pathogenesis in terms of genetic alterations. However, recent studies have revealed a complex involvement of epigenetic mechanisms in the regulation of gene expression, including methylation, chromatin modification and remodeling, and the diverse activities of non-coding RNAs. The roles of gene methylation and miRNAs have been relatively well studied in melanoma, but other studies have shown that changes in chromatin status and in the differential expression of long non-coding RNAs can lead to altered regulation of key genes. Taken together, they affect the functioning of signaling pathways that influence each other, intersect, and form networks in which local perturbations disturb the activity of the whole system. Here, we focus on how epigenetic events intertwine with these pathways and contribute to the molecular pathogenesis of melanoma.
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Key Words
- 5hmC, 5-hydroxymethylcytosine
- 5mC, 5-methylcytosine
- ACE, angiotensin converting enzyme
- ANCR, anti-differentiation non-coding RNA
- ANRIL, antisense noncoding RNA in INK4 locus
- ASK1, apoptosis signal-regulating kinase 1
- ATRA, all-trans retinoic acid
- BANCR, BRAF-activated non-coding RNA
- BCL-2, B-cell lymphoma 2
- BRAF, B-Raf proto-oncogene, serine/threonine kinase
- BRG1, ATP-dependent helicase SMARCA4
- CAF-1, chromatin assembly factor-1
- CBX7, chromobox homolog 7
- CCND1, cyclin D1
- CD28, cluster of differentiation 28
- CDK, cyclin-dependent kinase
- CDKN2A/B, cyclin-dependent kinase inhibitor 2A/B
- CHD8, chromodomain-helicase DNA-binding protein 8
- CREB, cAMP response element-binding protein
- CUDR, cancer upregulated drug resistant
- Cdc6, cell division cycle 6
- DNA methylation/demethylation
- DNMT, DNA methyltransferase
- EMT, epithelial-mesenchymal transition
- ERK, extracellular signal-regulated kinase
- EZH2, enhancer of zeste homolog 2
- GPCRs, G-protein coupled receptors
- GSK3a, glycogen synthase kinase 3 α
- GWAS, genome-wide association study
- HDAC, histone deacetylase
- HOTAIR, HOX antisense intergenic RNA
- IAP, inhibitor of apoptosis
- IDH2, isocitrate dehydrogenase
- IFN, interferon, interleukin 23
- JNK, Jun N-terminal kinase
- Jak/STAT, Janus kinase/signal transducer and activator of transcription
- MAFG, v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog G
- MALAT1, metastasis-associated lung adenocarcinoma transcript 1
- MAPK, mitogen-activated protein kinase
- MC1R, melanocortin-1 receptor
- MGMT, O6-methylguanine-DNA methyltransferase
- MIF, macrophage migration inhibitory factor
- MITF, microphthalmia-associated transcription factor
- MRE, miRNA recognition element
- MeCP2, methyl CpG binding protein 2
- NF-κB, nuclear factor kappa-light-chain-enhancer of activated B cells
- NOD, nucleotide-binding and oligomerization domain
- PBX, pre-B-cell leukemia homeobox
- PEDF, pigment epithelium derived factor
- PI3K, phosphatidylinositol-4, 5-bisphosphate 3-kinase
- PIB5PA, phosphatidylinositol-4, 5-biphosphate 5-phosphatase A
- PKA, protein kinase A
- PRC, polycomb repressor complex
- PSF, PTB associated splicing factor
- PTB, polypyrimidine tract-binding
- PTEN, phosphatase and tensin homolog
- RARB, retinoic acid receptor-β2
- RASSF1A, Ras association domain family 1A
- SETDB1, SET Domain, bifurcated 1
- SPRY4, Sprouty 4
- STAU1, Staufen1
- SWI/SNF, SWItch/Sucrose Non-Fermentable
- TCR, T-cell receptor
- TET, ten eleven translocase
- TGF β, transforming growth factor β
- TINCR, tissue differentiation-inducing non-protein coding RNA
- TOR, target of rapamycin
- TP53, tumor protein 53
- TRAF6, TNF receptor-associated factor 6
- UCA1, urothelial carcinoma-associated 1
- ceRNA, competitive endogenous RNAs
- chromatin modification
- chromatin remodeling
- epigenetics
- gene regulation
- lncRNA, long ncRNA
- melanoma
- miRNA, micro RNA
- ncRNA, non-coding RNA
- ncRNAs
- p14ARF, p14 alternative reading frame
- p16INK4a, p16 inhibitor of CDK4
- pRB, retinoblastoma protein
- snoRNA, small nucleolar RNA
- α-MSHm, α-melanocyte stimulating hormone
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Affiliation(s)
- Debina Sarkar
- a Auckland Cancer Society Research Center ; University of Auckland ; Auckland , New Zealand
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21
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He YH, Lu X, Bi MX, Yang LQ, Xu LY, Kong QP. The reduction of vascular disease risk mutations contributes to longevity in the Chinese population. Meta Gene 2014; 2:761-8. [PMID: 25606459 PMCID: PMC4287879 DOI: 10.1016/j.mgene.2014.09.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 09/18/2014] [Accepted: 09/23/2014] [Indexed: 12/05/2022] Open
Abstract
Aim Genetic factors play important roles in determining human lifespan. Although some “longevity genes” have been identified to be implicated in human longevity, many disease-associated variants were also observed in the long-lived individuals. The oldest old and their offspring usually have a lower prevalence of age-related diseases, which is likely attributed to a reduction or an absence of disease risk variants. Methods and results To test this hypothesis, 23 disease risk single nucleotide polymorphisms (SNPs), identified by previous genome-wide association studies (GWASs), were selected and genotyped in 1074 samples consisting of 574 longevity subjects (over 90 years old) and 500 younger controls. Our results revealed that 5 SNPs (rs2144300, rs1864163, rs2200733, rs1967017, and rs7193343) displayed significantly lower allelic frequencies and odds ratios (ORs) in the longevity group than that in the control group. The frequencies of homozygous mutation genotypes and corresponding ORs of the rs1864163, rs2200733, rs127430, rs1967017, and rs12413409 were lower in the longevity subjects. Interestingly, most of the abovementioned SNPs convey susceptibility to cardiovascular disease (CVD), which is the leading cause of deaths in old adults but shows a much lower incidence in the longevity individuals and their offspring. Conclusion Taking into account the observation that the longevity subjects and their offspring have lower rate of cardiovascular mortality, it is then most plausible that the lack of disease risk variants, especially the CVD, is a genetic contributor to longevity in the Chinese population. 23 disease risk gene polymorphisms were determined in 1074 subjects. 5 polymorphisms displayed lower allelic frequencies in longevity subjects. Lack of disease risk variants contributes to longevity.
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Affiliation(s)
- Yong-Han He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming 650223, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming 650223, China
| | - Xiang Lu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming 650223, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming 650223, China
| | - Ming-Xin Bi
- Department of Nutrition and Food Hygiene, Public Health College, Harbin Medical University, 157 Baojian Road, Nangang District, Harbin 150081, China
| | - Li-Qin Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming 650223, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming 650223, China
| | - Liang-You Xu
- Dujiangyan Longevity Research Centre, Dujiangyan 611830, China
| | - Qing-Peng Kong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming 650223, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming 650223, China
- Corresponding author at: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming 650223, China. Tel./fax: + 86 871 65197967.
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Guillemot J, Essalmani R, Hamelin J, Seidah NG. Is there a link between proprotein convertase PC7 activity and human lipid homeostasis? FEBS Open Bio 2014; 4:741-5. [PMID: 25349778 DOI: 10.1016/j.fob.2014.08.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 08/08/2014] [Accepted: 08/26/2014] [Indexed: 11/23/2022] Open
Abstract
A R504H mutation in human proprotein convertase PC7 is associated with increased HDL and reduced triglycerides. Wild-type PC7 and its R504H mutant have identical cellular enzymatic activities. In situ hybridization revealed co-localization of mouse ApoF and PC7 mRNAs in liver. WT and PC7 KO mice do not exhibit changes in circulating levels of insulin or glucose. WT and PC7 KO mice do not exhibit changes in circulating levels of HDL, TG and LDL.
A genome-wide association study suggested that a R504H mutation in the proprotein convertase PC7 is associated with increased circulating levels of HDL and reduced triglycerides in black Africans. Our present results show that PC7 and PC7-R504H exhibit similar processing of transferrin receptor-1, proSortilin, and apolipoprotein-F. Plasma analyses revealed no change in the lipid profiles, insulin or glucose of wild type and PC7 KO mice. Thus, the R504H mutation does not modify the proteolytic activity of PC7. The mechanisms behind the implication of PC7 in the regulation of human HDL, triglycerides and in modifying the levels of atherogenic small dense LDL remain to be elucidated.
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Key Words
- ANGPTL3, angiopoietin-like 3
- ANGPTL4, angiopoietin-like 4
- ApoF, apolipoprotein-F
- Apolipoprotein F
- GOF, gain of function
- GWAS, genome-wide association study
- HDL, high-density lipoprotein
- HDL/LDL
- KO, knockout
- LDL, low-density lipoprotein
- PCs, proprotein convertases
- Proprotein convertase PC7
- SNP, single nucleotide polymorphism
- Sortilin
- TGN, trans Golgi network
- TMD, transmembrane domain
- Transferrin receptor 1
- Triglycerides
- VLDL, very low-density lipoprotein
- hTfR1, human PC7-substrates: transferrin receptor 1
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Enya M, Horikawa Y, Iizuka K, Takeda J. Association of genetic variants of the incretin-related genes with quantitative traits and occurrence of type 2 diabetes in Japanese. Mol Genet Metab Rep 2014; 1:350-61. [PMID: 27896108 DOI: 10.1016/j.ymgmr.2014.07.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 07/26/2014] [Accepted: 07/26/2014] [Indexed: 02/08/2023] Open
Abstract
Background None of the high frequency variants of the incretin-related genes has been found by genome-wide association study (GWAS) for association with occurrence of type 2 diabetes in Japanese. However, low frequency and rare and/or high frequency variants affecting glucose metabolic traits remain to be investigated. Method We screened all exons of the incretin-related genes (GCG, GLP1R, DPP4, PCSK1, GIP, and GIPR) in 96 patients with type 2 diabetes and investigated for association of genetic variants of these genes with quantitative metabolic traits upon test meal with 38 young healthy volunteers and with the occurrence of type 2 diabetes in Japanese subjects comprising 1303 patients with type 2 diabetes and 1014 controls. Result Two mutations of GIPR, p.Thr3Alafsx21 and Arg183Gln, were found only in patients with type 2 diabetes, and both of them were treated with insulin. Of ten tagSNPs, we found that risk allele C of SNP393 (rs6235) of PCSK1 was nominally associated with higher fasting insulin and HOMA-R (P = 0.034 and P = 0.030), but not with proinsulin level, incretin level or BMI. The variant showed significant association with occurrence of type 2 diabetes after adjustment for age, sex, and BMI (P = 0.0043). Conclusion Rare variants of GIPR may contribute to the development of type 2 diabetes, possibly through insulin secretory defects. Furthermore, the genetic variant of PCSK1 might influence glucose homeostasis by altered insulin resistance independently of BMI, incretin level or proinsulin conversion, and may be associated with the occurrence of type 2 diabetes in Japanese.
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Key Words
- BMI, body mass index
- CPR, c-peptide immunoreactivity
- DPP4, dipeptidyl peptidase 4
- GCG, proglucagon gene
- GIP, glucose-dependent insulinotropic peptide
- GIPR, GIP receptor
- GLP-1, glucagon-like peptide 1
- GLP1R, GLP-1 receptor
- GWAS, genome-wide association study
- HOMA-B, homeostasis model assessment as an index of insulin secretion
- HOMA-R, homeostasis model assessment as an index of insulin resistance
- HbA1c, hemoglobin A1c
- IRI, immunoreactive insulin
- Incretin
- LD, linkage disequilibrium
- OR, odds ratio
- Obesity
- PCR, polymerase chain reaction
- PCSK1
- PCSK1, prohormone convertase (PC) enzymes. PC1/3
- Polymorphism
- SNP, single nucleotide polymorphism
- Type 2 diabetes
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Abstract
The recommended treatment for patients with chronic hepatitis C, pegylated interferon α (PEG-IFN-α) plus rebavirin (RBV), does not provide a sustained virologic response in all patients, especially those with hepatitis C virus (HCV) genotype 1. It is therefore important to predict whether or not a new patient with HCV genotype 1 will be cured by the recommended treatment. We propose a prediction method for a new patient using a decision tree learning model based on SNPs evaluated in a genome-wide association study. By the decision tree learning for 142 Japanese patients with HCV genotype 1 (78 with null virologic response and 64 with virologic response), we can predict with high probability (93%) whether or not a new patient with HCV will be helped by the recommended treatment.
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Key Words
- Chronic hepatitis C genotype 1
- Decision tree learning
- GDI, Gini diversity index
- GWAS, genome-wide association study
- Genome-wide association study
- HCV, hepatitis C virus
- Het, one major and one minor genotype
- MM, both major genotypes
- NVR, null virologic response
- Null virologic response
- OR, Odds ratio
- PEG-IFN-α, pegylated interferon α
- Pegylated interferon α
- RBV, ribavirin
- Rebavirin
- SNPs, single nucleotide polymorphisms
- SVR, sustained virologic response
- Single nucleotide polymorphism
- Sustained virologic response
- mm, both minor genotypes
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Affiliation(s)
- Yoshihiro Kawamura
- The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, 1-7-1 Konodai, Ichikawa, Chiba 272-8516, Japan
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