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Zhang X, Zhu Z, Huang Y, Shang X, O'Brien TJ, Kwan P, Ha J, Wang W, Liu S, Zhang X, Kiburg K, Bao Y, Wang J, Yu H, He M, Zhang L. Shared genetic aetiology of Alzheimer's disease and age-related macular degeneration by APOC1 and APOE genes. BMJ Neurol Open 2024; 6:e000570. [PMID: 38646507 PMCID: PMC11029327 DOI: 10.1136/bmjno-2023-000570] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 04/04/2024] [Indexed: 04/23/2024] Open
Abstract
Background Alzheimer's disease (AD) and age-related macular degeneration (AMD) share similar pathological features, suggesting common genetic aetiologies between the two. Investigating gene associations between AD and AMD may provide useful insights into the underlying pathogenesis and inform integrated prevention and treatment for both diseases. Methods A stratified quantile-quantile (QQ) plot was constructed to detect the pleiotropy among AD and AMD based on genome-wide association studies data from 17 008 patients with AD and 30 178 patients with AMD. A Bayesian conditional false discovery rate-based (cFDR) method was used to identify pleiotropic genes. UK Biobank was used to verify the pleiotropy analysis. Biological network and enrichment analysis were conducted to explain the biological reason for pleiotropy phenomena. A diagnostic test based on gene expression data was used to predict biomarkers for AD and AMD based on pleiotropic genes and their regulators. Results Significant pleiotropy was found between AD and AMD (significant leftward shift on QQ plots). APOC1 and APOE were identified as pleiotropic genes for AD-AMD (cFDR <0.01). Network analysis revealed that APOC1 and APOE occupied borderline positions on the gene co-expression networks. Both APOC1 and APOE genes were enriched on the herpes simplex virus 1 infection pathway. Further, machine learning-based diagnostic tests identified that APOC1, APOE (areas under the curve (AUCs) >0.65) and their upstream regulators, especially ZNF131, ADNP2 and HINFP, could be potential biomarkers for both AD and AMD (AUCs >0.8). Conclusion In this study, we confirmed the genetic pleiotropy between AD and AMD and identified APOC1 and APOE as pleiotropic genes. Further, the integration of multiomics data identified ZNF131, ADNP2 and HINFP as novel diagnostic biomarkers for AD and AMD.
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Affiliation(s)
- Xueli Zhang
- Guangdong Eye Institute, Department of Ophthalmology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, People's Republic of China
| | - Zhuoting Zhu
- Guangdong Eye Institute, Department of Ophthalmology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Yu Huang
- Guangdong Eye Institute, Department of Ophthalmology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Xianwen Shang
- Guangdong Eye Institute, Department of Ophthalmology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Terence J O'Brien
- Department of Neuroscience, School of Translational Medicine, Monash University, Melbourne, Victoria, Australia
| | - Patrick Kwan
- Department of Neuroscience, School of Translational Medicine, Monash University, Melbourne, Victoria, Australia
| | - Jason Ha
- Alfred Health, Melbourne, Victoria, Australia
| | - Wei Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Shunming Liu
- Guangdong Eye Institute, Department of Ophthalmology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Xiayin Zhang
- Guangdong Eye Institute, Department of Ophthalmology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Katerina Kiburg
- Centre for Eye Research, University of Melbourne, East Melbourne, Victoria, Australia
| | - Yining Bao
- China-Australia Joint Research Center for Infectious Diseases, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Jing Wang
- China-Australia Joint Research Center for Infectious Diseases, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Honghua Yu
- Guangdong Eye Institute, Department of Ophthalmology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Mingguang He
- Guangdong Eye Institute, Department of Ophthalmology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Lei Zhang
- Clinical Medical Research Center, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
- School of Translational Medicine, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
- Artificial Intelligence and Modelling in Epidemiology Program, Melbourne Sexual Health Centre, Alfred Health, Melbourne, VIC, Australia
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Lausser L, Szekely R, Klimmek A, Schmid F, Kestler HA. Constraining classifiers in molecular analysis: invariance and robustness. J R Soc Interface 2020; 17:20190612. [PMID: 32019472 PMCID: PMC7061712 DOI: 10.1098/rsif.2019.0612] [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: 01/03/2020] [Accepted: 01/09/2020] [Indexed: 12/02/2022] Open
Abstract
Analysing molecular profiles requires the selection of classification models that can cope with the high dimensionality and variability of these data. Also, improper reference point choice and scaling pose additional challenges. Often model selection is somewhat guided by ad hoc simulations rather than by sophisticated considerations on the properties of a categorization model. Here, we derive and report four linked linear concept classes/models with distinct invariance properties for high-dimensional molecular classification. We can further show that these concept classes also form a half-order of complexity classes in terms of Vapnik-Chervonenkis dimensions, which also implies increased generalization abilities. We implemented support vector machines with these properties. Surprisingly, we were able to attain comparable or even superior generalization abilities to the standard linear one on the 27 investigated RNA-Seq and microarray datasets. Our results indicate that a priori chosen invariant models can replace ad hoc robustness analysis by interpretable and theoretically guaranteed properties in molecular categorization.
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Affiliation(s)
- Ludwig Lausser
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Robin Szekely
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Attila Klimmek
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Florian Schmid
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Hans A. Kestler
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
- Leibniz Institute on Aging, Jena, Germany
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Chu XK, Meyerle CB, Liang X, Chew EY, Chan CC, Tuo J. In-depth analyses unveil the association and possible functional involvement of novel RAD51B polymorphisms in age-related macular degeneration. Age (Dordr) 2014; 36:9627. [PMID: 24526414 PMCID: PMC4082603 DOI: 10.1007/s11357-014-9627-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 02/03/2014] [Indexed: 05/02/2023]
Abstract
The contribution of DNA damage to the pathogenesis of age-related macular degeneration (AMD) has been reported. Recently, a genomewide association study detected the association of a single-nucleotide polymorphism (SNP) in RAD51B (rs8017304 A>G) with AMD. RAD51B is involved in recombinational repair of DNA double-strand breaks. We analyzed RAD51B influence on AMD using two cohorts from Caucasian and Han Chinese populations. The Caucasian set replicated the rs8017304 A>G association and revealed two novel AMD-associated SNPs in RAD51B, rs17105278 T>C and rs4902566 C>T. Under the dominant model, these two SNPs exhibit highly significant disease risk. SNP-SNP interaction analysis on rs17105278 T>C and rs4902566 C>T homozygous demonstrated a synergistic effect on AMD risk, reaching an odds ratio multifold higher than well-established AMD susceptibility loci in genes such as CFH, HTRA1, and ARMS2. Functional study revealed lower RAD51B mRNA expression in cultured primary human fetal retinal pigment epithelium (hfRPE) carrying rs17105278 T>C variants than in hfRPE carrying rs17105278 wild type. We concluded that the risk of developing AMD exhibits dose dependency as well as an epistatic combined effect in rs17105278 T>C and rs4902566 C>T carriers and that the elevated risk for rs17105278 T>C carriers may be due to decreased transcription of RAD51B. This study further confirms the role of DNA damage/DNA repair in AMD pathogenesis.
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Affiliation(s)
- Xi K. Chu
- />Laboratory of Immunology, National Eye Institute, National Institutes of Health, 10/10N103, 10 Center Dr., Bethesda, MD 20892-1857 USA
| | - Catherine B. Meyerle
- />Division of Epidemiology and Clinical Applications, National Eye Institute, National Institutes of Health, 10/10N103, 10 Center Dr., Bethesda, MD USA
| | - Xiaoling Liang
- />State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangzhou, China
| | - Emily Y. Chew
- />Division of Epidemiology and Clinical Applications, National Eye Institute, National Institutes of Health, 10/10N103, 10 Center Dr., Bethesda, MD USA
| | - Chi-Chao Chan
- />Laboratory of Immunology, National Eye Institute, National Institutes of Health, 10/10N103, 10 Center Dr., Bethesda, MD 20892-1857 USA
| | - Jingsheng Tuo
- />Laboratory of Immunology, National Eye Institute, National Institutes of Health, 10/10N103, 10 Center Dr., Bethesda, MD 20892-1857 USA
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Blasiak J, Glowacki S, Kauppinen A, Kaarniranta K. Mitochondrial and nuclear DNA damage and repair in age-related macular degeneration. Int J Mol Sci 2013; 14:2996-3010. [PMID: 23434654 DOI: 10.3390/ijms14022996] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 01/04/2013] [Accepted: 01/25/2013] [Indexed: 12/28/2022] Open
Abstract
Aging and oxidative stress seem to be the most important factors in the pathogenesis of age-related macular degeneration (AMD), a condition affecting many elderly people in the developed world. However, aging is associated with the accumulation of oxidative damage in many biomolecules, including DNA. Furthermore, mitochondria may be especially important in this process because the reactive oxygen species produced in their electron transport chain can damage cellular components. Therefore, the cellular response to DNA damage, expressed mainly through DNA repair, may play an important role in AMD etiology. In several studies the increase in mitochondrial DNA (mtDNA) damage and mutations, and the decrease in the efficacy of DNA repair have been correlated with the occurrence and the stage of AMD. It has also been shown that mitochondrial DNA accumulates more DNA lesions than nuclear DNA in AMD. However, the DNA damage response in mitochondria is executed by nucleus-encoded proteins, and thus mutagenesis in nuclear DNA (nDNA) may affect the ability to respond to mutagenesis in its mitochondrial counterpart. We reported that lymphocytes from AMD patients displayed a higher amount of total endogenous basal and oxidative DNA damage, exhibited a higher sensitivity to hydrogen peroxide and UV radiation, and repaired the lesions induced by these factors less effectively than did cells from control individuals. We postulate that poor efficacy of DNA repair (i.e., is impaired above average for a particular age) when combined with the enhanced sensitivity of retinal pigment epithelium cells to environmental stress factors, contributes to the pathogenesis of AMD. Collectively, these data suggest that the cellular response to both mitochondrial and nuclear DNA damage may play an important role in AMD pathogenesis.
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Keller MA, Watschinger K, Lange K, Golderer G, Werner-Felmayer G, Hermetter A, Wanders RJA, Werner ER. Studying fatty aldehyde metabolism in living cells with pyrene-labeled compounds. J Lipid Res 2012; 53:1410-6. [PMID: 22508945 PMCID: PMC3371253 DOI: 10.1194/jlr.d025650] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The lack of fatty aldehyde dehydrogenase function in Sjögren Larsson Syndrome
(SLS) patient cells not only impairs the conversion of fatty aldehydes into their
corresponding fatty acid but also has an effect on connected pathways. Alteration of
the lipid profile in these cells is thought to be responsible for severe symptoms
such as ichtyosis, mental retardation, and spasticity. Here we present a novel
approach to examine fatty aldehyde metabolism in a time-dependent manner by measuring
pyrene-labeled fatty aldehyde, fatty alcohol, fatty acid, and alkylglycerol in the
culture medium of living cells using HPLC separation and fluorescence detection. Our
results show that in fibroblasts from SLS patients, fatty aldehyde is not
accumulating but is converted readily into fatty alcohol. In control cells, in
contrast, exclusively the corresponding fatty acid is formed. SLS patient cells did
not display a hypersensitivity toward hexadecanal or hexadecanol, but 3-fold lower
concentrations of the fatty alcohol than the corresponding fatty aldehyde were needed
to induce toxicity in SLS patient and in control cells.
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Affiliation(s)
- Markus A Keller
- Division of Biological Chemistry, Biocenter, Innsbruck Medical University, 6020 Innsbruck, Austria
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Kim M, Cho SB, Kim JH. Mixture-model based estimation of gene expression variance from public database improves identification of differentially expressed genes in small sized microarray data. Bioinformatics 2010; 26:486-92. [PMID: 20015947 PMCID: PMC2820675 DOI: 10.1093/bioinformatics/btp685] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Motivation: The small number of samples in many microarray experiments is a challenge for the correct identification of differentially expressed gens (DEGs) by conventional statistical means. Information from public microarray databases can help more efficient identification of DEGs. To model various experimental conditions of a public microarray database, we applied Gaussian mixture model and extracted bi- or tri-modal distributions of gene expression. Prior variance of Baldi's Bayesian framework was estimate for the analysis of the small sample-sized datasets. Results: First, we estimated the prior variance of a gene expression by pooling variances obtained from mixture modeling of large samples in the public microarray database. Then, using the prior variance, we identified DEGs in small sample-sized test datasets using the Baldi's framework. For benchmark study, we generated test datasets having several samples from relatively large datasets. Our proposed method outperformed other benchmark methods in terms of detecting gold-standard DEGs from the test datasets. The results may be a challenging evidence for usage of public microarray databases in microarray data analysis. Availability:Supplementary data are available at http://www.snubi.org/publication/MixBayes Contact:juhan@snu.ac.kr
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Affiliation(s)
- Mingoo Kim
- Seoul National University Biomedical Informatics (SNUBI), Seoul National University College of Medicine, Seoul 110-799, Korea
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