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Zolotareva K, Dotsenko PA, Podkolodnyy N, Ivanov R, Makarova AL, Chadaeva I, Bogomolov A, Demenkov PS, Ivanisenko V, Oshchepkov D, Ponomarenko M. Candidate SNP Markers Significantly Altering the Affinity of the TATA-Binding Protein for the Promoters of Human Genes Associated with Primary Open-Angle Glaucoma. Int J Mol Sci 2024; 25:12802. [PMID: 39684516 DOI: 10.3390/ijms252312802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2024] [Revised: 11/20/2024] [Accepted: 11/25/2024] [Indexed: 12/18/2024] Open
Abstract
Primary open-angle glaucoma (POAG) is the most common form of glaucoma. This condition leads to optic nerve degeneration and eventually to blindness. Tobacco smoking, alcohol consumption, fast-food diets, obesity, heavy weight lifting, high-intensity physical exercises, and many other bad habits are lifestyle-related risk factors for POAG. By contrast, moderate-intensity aerobic exercise and the Mediterranean diet can alleviate POAG. In this work, we for the first time estimated the phylostratigraphic age indices (PAIs) of all 153 POAG-related human genes in the NCBI Gene Database. This allowed us to separate them into two groups: POAG-related genes that appeared before and after the phylum Chordata, that is, ophthalmologically speaking, before and after the camera-type eye evolved. Next, in the POAG-related genes' promoters, we in silico predicted all 3835 candidate SNP markers that significantly change the TATA-binding protein (TBP) affinity for these promoters and, through this molecular mechanism, the expression levels of these genes. Finally, we verified our results against five independent web services-PANTHER, DAVID, STRING, MetaScape, and GeneMANIA-as well as the ClinVar database. It was concluded that POAG is likely to be a symptom of the human self-domestication syndrome, a downside of being civilized.
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Affiliation(s)
- Karina Zolotareva
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences (ICG SB RAS), Novosibirsk 630090, Russia
- Kurchatov Genome Center at the ICG SB RAS, Novosibirsk 630090, Russia
| | - Polina A Dotsenko
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences (ICG SB RAS), Novosibirsk 630090, Russia
- Kurchatov Genome Center at the ICG SB RAS, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Nikolay Podkolodnyy
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences (ICG SB RAS), Novosibirsk 630090, Russia
- Kurchatov Genome Center at the ICG SB RAS, Novosibirsk 630090, Russia
- Institute of Computational Mathematics and Mathematical Geophysics, SB RAS, Novosibirsk 630090, Russia
| | - Roman Ivanov
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences (ICG SB RAS), Novosibirsk 630090, Russia
| | - Aelita-Luiza Makarova
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences (ICG SB RAS), Novosibirsk 630090, Russia
| | - Irina Chadaeva
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences (ICG SB RAS), Novosibirsk 630090, Russia
- Kurchatov Genome Center at the ICG SB RAS, Novosibirsk 630090, Russia
| | - Anton Bogomolov
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences (ICG SB RAS), Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Pavel S Demenkov
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences (ICG SB RAS), Novosibirsk 630090, Russia
- Kurchatov Genome Center at the ICG SB RAS, Novosibirsk 630090, Russia
| | - Vladimir Ivanisenko
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences (ICG SB RAS), Novosibirsk 630090, Russia
- Kurchatov Genome Center at the ICG SB RAS, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Dmitry Oshchepkov
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences (ICG SB RAS), Novosibirsk 630090, Russia
- Kurchatov Genome Center at the ICG SB RAS, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Mikhail Ponomarenko
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences (ICG SB RAS), Novosibirsk 630090, Russia
- Kurchatov Genome Center at the ICG SB RAS, Novosibirsk 630090, Russia
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Teng M, Wang J, Su X, Tian Y, Wang J, Zhang Y. Causal associations between rheumatoid arthritis, cataract and glaucoma in European and East Asian populations: A bidirectional two-sample mendelian randomization study. PLoS One 2024; 19:e0299192. [PMID: 38437213 PMCID: PMC10911615 DOI: 10.1371/journal.pone.0299192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 02/06/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND Previous studies have indicated a heightened susceptibility to cataract and glaucoma among rheumatoid arthritis (RA) patients, while it remains uncertain whether RA is causally associated with cataract and glaucoma. A two-sample mendelian randomization (MR) analysis was used to investigate the causal associations between RA, cataract and glaucoma in European and East Asian populations. METHODS In the European population, genome-wide association study (GWAS) summary statistics for cataract (372,386 individuals) and glaucoma (377,277 individuals) were obtained from the FinnGen consortium (R9), while RA summary data were derived from a meta-analysis of GWAS encompassing 97173 samples. In the East Asian population, summary data for cataract (212453 individuals), glaucoma (212453 individuals), and RA (22515 individuals) were sourced from the IEU Open GWAS project. Inverse-variance weighted (IVW, random-effects) method served as the primary analysis, complemented by MR‒Egger regression, weighted median, weighted mode and simple mode methods. Additionally, various sensitivity tests, including Cochran's Q test, MR‒Egger intercept, MR pleiotropy Residual Sum and Outlier test and leave-one-out test were performed to detect the heterogeneity, horizontal pleiotropy and stability of the analysis results. RESULTS Following stringent screening, the number of selected instrumental variables ranged from 8 to 56. The IVW results revealed that RA had an increased risk of cataract (OR = 1.041, 95% CI = 1.019-1.064; P = 2.08×10-4) and glaucoma (OR = 1.029, 95% CI = 1.003-1.057; P = 2.94×10-2) in European populations, and RA displayed a positive association with cataract (OR = 1.021, 95% CI = 1.004-1.039; P = 1.64×10-2) in East Asian populations. Other methods also supported those results by IVW, and sensitivity tests showed that our analysis results were credible and stable. CONCLUSIONS This study revealed a positive causality between RA and the increased risk of cataract and glaucoma, which provides guidance for the early prevention of cataracts and glaucoma in patients with RA and furnishes evidence for the impact of RA-induced inflammation on ophthalmic diseases.
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Affiliation(s)
- Menghao Teng
- Department of Orthopedics, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Jiachen Wang
- Department of Joint Surgery, HongHui Hospital, Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Xiaochen Su
- Department of Orthopedics, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Ye Tian
- Healthy Food Evaluation Research Center, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jiqing Wang
- Department of Orthopedics, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Yingang Zhang
- Department of Orthopedics, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
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West CE, Karim M, Falaguera MJ, Speidel L, Green CJ, Logie L, Schwartzentruber J, Ochoa D, Lord JM, Ferguson MAJ, Bountra C, Wilkinson GF, Vaughan B, Leach AR, Dunham I, Marsden BD. Integrative GWAS and co-localisation analysis suggests novel genes associated with age-related multimorbidity. Sci Data 2023; 10:655. [PMID: 37749083 PMCID: PMC10520009 DOI: 10.1038/s41597-023-02513-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 08/22/2023] [Indexed: 09/27/2023] Open
Abstract
Advancing age is the greatest risk factor for developing multiple age-related diseases. Therapeutic approaches targeting the underlying pathways of ageing, rather than individual diseases, may be an effective way to treat and prevent age-related morbidity while reducing the burden of polypharmacy. We harness the Open Targets Genetics Portal to perform a systematic analysis of nearly 1,400 genome-wide association studies (GWAS) mapped to 34 age-related diseases and traits, identifying genetic signals that are shared between two or more of these traits. Using locus-to-gene (L2G) mapping, we identify 995 targets with shared genetic links to age-related diseases and traits, which are enriched in mechanisms of ageing and include known ageing and longevity-related genes. Of these 995 genes, 128 are the target of an approved or investigational drug, 526 have experimental evidence of binding pockets or are predicted to be tractable, and 341 have no existing tractability evidence, representing underexplored genes which may reveal novel biological insights and therapeutic opportunities. We present these candidate targets for exploration and prioritisation in a web application.
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Affiliation(s)
- Clare E West
- Centre for Medicines Discovery, University of Oxford, Oxford, UK.
- Open Targets, Wellcome Genome Campus, Hinxton, UK.
| | - Mohd Karim
- Open Targets, Wellcome Genome Campus, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Maria J Falaguera
- Open Targets, Wellcome Genome Campus, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Leo Speidel
- Francis Crick Institute, London, UK
- Genetics Institute, University College London, London, UK
| | | | - Lisa Logie
- Drug Discovery Unit, University of Dundee, Dundee, UK
- Medicines Discovery Catapult, 35 Mereside Alderley Park, Macclesfield, Cheshire, UK
| | - Jeremy Schwartzentruber
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - David Ochoa
- Open Targets, Wellcome Genome Campus, Hinxton, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Janet M Lord
- MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | | | - Chas Bountra
- Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Graeme F Wilkinson
- Medicines Discovery Catapult, 35 Mereside Alderley Park, Macclesfield, Cheshire, UK
| | - Beverley Vaughan
- Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Andrew R Leach
- Open Targets, Wellcome Genome Campus, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Ian Dunham
- Open Targets, Wellcome Genome Campus, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Brian D Marsden
- Centre for Medicines Discovery, University of Oxford, Oxford, UK
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
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Impact of long-term care insurance on medical costs and utilization by patients with Parkinson's disease. Soc Sci Med 2023; 317:115563. [PMID: 36455406 DOI: 10.1016/j.socscimed.2022.115563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 11/09/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022]
Abstract
BACKGROUND In patients with Parkinson's disease (PD), long-term care insurance (LTCI), which can provide physical activity, might affect medical costs and utilization. We investigated the impact of LTCI on medical costs and utilization among patients with PD aged ≥60 years. METHODS Data were derived from the 12-year Korean National Health Insurance Service‒Senior cohort. Among patients with newly developed PD, the intervention group receiving LTCI was matched with the control group using propensity score risk-set matching. As medical costs and utilization may increase markedly immediately before LTCI allocation, the baseline period was set from 5 years to 1 year prior to receiving LTCI. Medical costs and utilization were recorded in six 1-year intervals thereafter. We compared medical costs and utilization between groups using a comparative interrupted time-series analysis. RESULTS 5011 LTCI beneficiaries and 5011 propensity score- and risk-set-matched controls were included. The overall mean (standard deviation) age was 77.73 (5.7) years, and 66.2% were women, in both groups. LTCI benefit was associated with reduced overall direct medical costs for 5 years (post-intervention year 5: -270$, p = 0.033), and overall hospital length-of-stay (LOS) for 2 years post-LTCI (post-intervention year 2: -2.43 days, p = 0.002), although medical costs and LOS increased immediately pre-LTCI implementation. The long-term care hospital LOS of LTCI beneficiaries increased relatively by 3-years post-LTCI implementation, particularly in those with a high Charlson Comorbidity Index score (post-intervention year 3: +2.65 days, p = 0.04). CONCLUSIONS LTCI benefit stably decreased medical costs for patients with PD for 5 years, despite the steep increase immediately pre-LTCI benefit, but was limited in reducing medical utilization, particularly as reflected by LOS in long-term care hospitals and patients with comorbidities. LTCI could be a useful health policy to reduce PD disease burden. However, further development is required to provide services that can reduce LOS to PD patients with comorbidities.
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Increased risk of all-cause, Alzheimer's, and vascular dementia in adults with migraine in Korea: a population-based cohort study. J Headache Pain 2022; 23:108. [PMID: 36002812 PMCID: PMC9404580 DOI: 10.1186/s10194-022-01484-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/17/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Studies investigating the association between migraine and dementia have reported inconsistent findings. This study aimed to evaluate whether patients with migraine have an increased risk of dementia compared to individuals without migraine. METHODS We obtained data from the 2002-2019 Korean National Health Insurance Health Screening Cohort. Non-migraine controls were selected using a 1:1 risk-set matching with a time-dependent propensity score. The main outcome was the development of all-cause dementia, and the secondary outcome was the development of each cause of dementia (Alzheimer's, vascular, mixed or other specified, and unspecified dementia). The incidence rate of dementia was calculated using Poisson regression, and the association between migraine and dementia was evaluated using Cox proportional hazards regression. RESULTS Among 88,390 participants, 66.1% were female, and the mean baseline age was 55.3 ± 9.4 years. During the study period, dementia cases were identified in 4,800 of the 44,195 patients with migraine and 3,757 of the 44,915 matched controls. The incidence rate of dementia was 139.6 (95% confidence interval [CI], 135.7-143.5) and 107.7 (95% CI, 104.3-111.1) cases per 10,000 person-years in patients with migraine and matched controls, respectively. Patients with migraine had a 1.30 (hazard ratio [HR], 1.30; 95% CI, 1.25-1.35), 1.29 (HR, 1.29; 95% CI, 1.23-1.35), 1.35 (HR, 1.35; 95% CI, 1.19-1.54), 1.36 (HR, 1.36; 95% CI, 1.00-1.83), and 1.30 (HR, 1.30; 95% CI, 1.17-1.45) times higher risk of developing all-cause dementia, Alzheimer's dementia, vascular dementia, mixed or other specified dementias, and unspecified dementia than their matched controls, respectively. CONCLUSION Our results suggest that migraine is associated with an increased risk of subsequent dementia. Further research is warranted to confirm these findings and to reveal the underlying mechanisms.
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Jeong SH, Hoon Kim S, Lee DW, Park EC, Jang SY. Association between new-onset Parkinson's disease and suicide risk in South Korea: a nationwide cohort study. BMC Psychiatry 2022; 22:341. [PMID: 35581575 PMCID: PMC9115980 DOI: 10.1186/s12888-022-03990-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/12/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Parkinson's disease (PD) is an increasingly common neurodegenerative disease in an aging society. Whether PD is associated with an increased suicide risk is unclear. Thus, we investigated the effect of new-onset PD on suicide. METHODS Using the National Health Insurance Service Senior Sample Cohort of South Korea, 17,143 incident PD patients and 17,143 risk set controls, matched by propensity score, were selected for follow-up. The incidence rate of suicide and 95% confidence interval (CI) were calculated based on a generalized linear model of the Poisson distribution. Effect sizes were expressed as hazard ratios (HRs) using the Cox proportional hazards model with a robust variance estimator that incorporated clustering within matched pairs. RESULTS The incidence rate of suicide was 206.7 cases per 100,000 person-years (95% CI, 172.8-246.9) among the PD cohort. Compared to the matched controls, patients with PD were 2.64 times (HR, 2.64; 95% CI, 1.31-5.30) more likely to commit suicide during the first 180 days of follow-up and 2.47 times (HR, 2.47; 95% CI, 1.42-4.28) within the first 365 days of follow-up. During the entire follow-up period, patients with PD were 2.26 times more likely to commit suicide than were their matched controls (HR, 2.26; 95% CI, 1.67-3.06). CONCLUSION Our findings indicated an increased risk of suicide in patients with new-onset PD, regardless of the period after diagnosis. Incorporating mental health care with social and environmental interventions into primary care and PD-specialized care can help reduce suicide risk in people with PD, improving suicide prevention, identification, and risk assessment.
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Affiliation(s)
- Sung Hoon Jeong
- grid.15444.300000 0004 0470 5454Department of Public Health, Graduate School, Yonsei University, Seoul, Republic of Korea ,grid.15444.300000 0004 0470 5454Institute of Health Services Research, Yonsei University, Seoul, Republic of Korea
| | - Seung Hoon Kim
- grid.15444.300000 0004 0470 5454Institute of Health Services Research, Yonsei University, Seoul, Republic of Korea ,grid.15444.300000 0004 0470 5454Department of Preventive Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Doo Woong Lee
- grid.15444.300000 0004 0470 5454Institute of Health Services Research, Yonsei University, Seoul, Republic of Korea
| | - Eun-Cheol Park
- grid.15444.300000 0004 0470 5454Institute of Health Services Research, Yonsei University, Seoul, Republic of Korea ,grid.15444.300000 0004 0470 5454Department of Preventive Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Suk-Yong Jang
- Institute of Health Services Research, Yonsei University, Seoul, Republic of Korea. .,Department of Healthcare Management, Graduate School of Public Health, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
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