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Alizadeh S, Khamse S, Vafadar S, Bernhart SH, Afshar H, Vahedi M, Rezaei O, Delbari A, Ohadi M. The human SMAD9 (GCC) repeat links to natural selection and late-onset neurocognitive disorders. Neurol Sci 2024; 45:5241-5251. [PMID: 38877206 DOI: 10.1007/s10072-024-07637-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 06/05/2024] [Indexed: 06/16/2024]
Abstract
INTRODUCTION Whereas (GCC)-repeats are overrepresented in genic regions, and mutation hotspots, they are largely unexplored with regard to their link with natural selection. Across numerous primate species and tissues, SMAD9 (SMAD Family Member 9) reaches highest level of expression in the human brain. This gene contains a (GCC)-repeat in the interval between + 1 and + 60 of the transcription start site, which is in the high-ranking (GCC)-repeats with respect to length. METHODS Here we sequenced this (GCC)-repeat in 396 Iranian individuals, consisting of late-onset neurocognitive disorder (NCD) (N = 181) and controls (N = 215). RESULTS We detected two predominantly abundant alleles of 7 and 9 repeats, forming 96.2% of the allele pool. The (GCC)7/(GCC)9 ratio was in the reverse order in the NCD group versus controls (p = 0.005), resulting from excess of (GCC)7 in the NCD group (p = 0.003) and (GCC)9 in the controls (p = 0.01). Five genotypes, predominantly consisting of (GCC)7 and lacking (GCC)9 were detected in the NCD group only (p = 0.008). The patients harboring those genotypes received the diagnoses of Alzheimer's disease (AD) and vascular dementia (VD). Five genotypes consisting of (GCC)9 and lacking (GCC)7 were detected in the control group only (p = 0.002). The group-specific genotypes formed approximately 4% of the genotype pool in the human samples studied. CONCLUSION We propose natural selection and a novel locus for late-onset AD and VD at the SMAD9 (GCC)-repeat in humans.
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Affiliation(s)
- Samira Alizadeh
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Daneshjoo Blvd. Koodakyar St, Tehran, 1985713871, Iran
| | - Safoura Khamse
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Daneshjoo Blvd. Koodakyar St, Tehran, 1985713871, Iran
| | - Sara Vafadar
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Daneshjoo Blvd. Koodakyar St, Tehran, 1985713871, Iran
| | - Stephan H Bernhart
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16-18, 04107, Leipzig, Germany
| | - Hossein Afshar
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Daneshjoo Blvd. Koodakyar St, Tehran, 1985713871, Iran
| | - Mohsen Vahedi
- Department of Biostatistics and Epidemiology, Paediatric Neurorehabilitation Research Centre, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Omid Rezaei
- Department of Psychiatry, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Ahmad Delbari
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Daneshjoo Blvd. Koodakyar St, Tehran, 1985713871, Iran.
| | - Mina Ohadi
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Daneshjoo Blvd. Koodakyar St, Tehran, 1985713871, Iran.
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Li YB, Fu Q, Guo M, Du Y, Chen Y, Cheng Y. MicroRNAs: pioneering regulators in Alzheimer's disease pathogenesis, diagnosis, and therapy. Transl Psychiatry 2024; 14:367. [PMID: 39256358 PMCID: PMC11387755 DOI: 10.1038/s41398-024-03075-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 08/21/2024] [Accepted: 08/27/2024] [Indexed: 09/12/2024] Open
Abstract
This article delves into Alzheimer's disease (AD), a prevalent neurodegenerative condition primarily affecting the elderly. It is characterized by progressive memory and cognitive impairments, severely disrupting daily life. Recent research highlights the potential involvement of microRNAs in the pathogenesis of AD. MicroRNAs (MiRNAs), short non-coding RNAs comprising 20-24 nucleotides, significantly influence gene regulation by hindering translation or promoting degradation of target genes. This review explores the role of specific miRNAs in AD progression, focusing on their impact on β-amyloid (Aβ) peptide accumulation, intracellular aggregation of hyperphosphorylated tau proteins, mitochondrial dysfunction, neuroinflammation, oxidative stress, and the expression of the APOE4 gene. Our insights contribute to understanding AD's pathology, offering new avenues for identifying diagnostic markers and developing novel therapeutic targets.
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Affiliation(s)
- Yao-Bo Li
- Center on Translational Neuroscience, College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Qiang Fu
- Institute of National Security, Minzu University of China, Beijing, China
| | - Mei Guo
- Key Laboratory of Ethnomedicine of Ministry of Education, School of Pharmacy, Minzu University of China, Beijing, China
| | - Yang Du
- Institute of National Security, Minzu University of China, Beijing, China
| | - Yuewen Chen
- Chinese Academy of Sciences Key Laboratory of Brain Connectome and Manipulation, Shenzhen Key Laboratory of Translational Research for Brain Diseases, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, China.
- Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development, HKUST Shenzhen Research Institute, Shenzhen, China.
| | - Yong Cheng
- Center on Translational Neuroscience, College of Life and Environmental Sciences, Minzu University of China, Beijing, China.
- Institute of National Security, Minzu University of China, Beijing, China.
- Key Laboratory of Ethnomedicine of Ministry of Education, School of Pharmacy, Minzu University of China, Beijing, China.
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Khamse S, Alizadeh S, Khorshid HRK, Delbari A, Tajeddin N, Ohadi M. A Hypermutable Region in the DISP2 Gene Links to Natural Selection and Late-Onset Neurocognitive Disorders in Humans. Mol Neurobiol 2024:10.1007/s12035-024-04155-y. [PMID: 38565786 DOI: 10.1007/s12035-024-04155-y] [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: 05/28/2023] [Accepted: 03/25/2024] [Indexed: 04/04/2024]
Abstract
(CCG) short tandem repeats (STRs) are predominantly enriched in genic regions, mutation hotspots for C to T truncating substitutions, and involved in various neurological and neurodevelopmental disorders. However, intact blocks of this class of STRs are widely overlooked with respect to their link with natural selection. The human neuron-specific gene, DISP2 (dispatched RND transporter family member 2), contains a (CCG) repeat in its 5' untranslated region. Here, we sequenced this STR in a sample of 448 Iranian individuals, consisting of late-onset neurocognitive disorder (NCD) (N = 203) and controls (N = 245). We found that the region spanning the (CCG) repeat was highly mutated, resulting in several flanking (CCG) residues. However, an 8-repeat of the (CCG) repeat was predominantly abundant (frequency = 0.92) across the two groups. While the overall distribution of genotypes was not different between the two groups (p > 0.05), we detected four genotypes in the NCD group only (2% of the NCD genotypes, Mid-p = 0.02), consisting of extreme short alleles, 5- and 6-repeats, that were not detected in the control group. The patients harboring those genotypes received the diagnoses of probable Alzheimer's disease and vascular dementia. We also found six genotypes in the control group only (2.5% of the control genotypes, Mid-p = 0.01) that consisted of the 8-repeat and extreme long alleles, 9- and 10-repeats, of which the 10-repeat was not detected in the NCD group. The (CCG) repeat specifically expanded in primates. In conclusion, we report an indication of natural selection at a novel hypermutable region in the human genome and divergent alleles and genotypes in late-onset NhCDs and controls. These findings reinforce the hypothesis that a collection of rare alleles and genotypes in a number of genes may unambiguously contribute to the cognition impairment component of late-onset NCDs.
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Affiliation(s)
- S Khamse
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - S Alizadeh
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - H R Khorram Khorshid
- Personalized Medicine and Genometabolomics Research Center, Hope Generation Foundation, Tehran, Iran
| | - A Delbari
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
| | - N Tajeddin
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
- Department of Biology, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - M Ohadi
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
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Alizadeh S, Khamse S, Tajeddin N, Khorram Khorshid HR, Delbari A, Ohadi M. A GCC repeat in RAB26 undergoes natural selection in human and harbors divergent genotypes in late-onset Alzheimer's disease. Gene 2024; 893:147968. [PMID: 37931854 DOI: 10.1016/j.gene.2023.147968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 10/28/2023] [Accepted: 11/03/2023] [Indexed: 11/08/2023]
Abstract
Although mainly located in genic regions and being mutation hotspots, intact blocks of CG-rich trinucleotide short tandem repeats (STRs) are largely overlooked with respect to their link with natural selection. The human RAB26 (member RAS oncogene family) directs synaptic and secretory vesicles into preautophagosomal structures, inhibition of which specifically disrupts axonal transport of degradative organelles and leads to an axonal dystrophy, resembling Alzheimer's disease (AD). Human RAB26 contains a GCC repeat in the top 1st percent in respect of length. Here we sequenced this STR in 441 Iranian individuals, consisting of late-onset neurocognitive disorder (NCD) (N = 216) and controls (N = 225). In both groups, the 12-repeat allele and the 12/12 genotype were predominantly abundant. We found excess of homozygosity for non-12 alleles in the NCD group (Mid-P exact = 0.027). Furthermore, divergent genotypes were detected that were specific to the NCD group (2.8% of genotypes) (Mid-P exact = 0.006) or controls (3.1% of genotypes) (Mid-P exact = 0.004). The patients harboring divergent genotypes received the diagnosis of AD. Based on the predominant abundance of the 12-repeat and 12/12 genotype in both groups, excess of non-12 homozygosity in the NCD group, and divergent genotypes across the NCD and control groups, we propose natural selection at this locus and link with late-onset AD. Our findings strengthen the hypothesis that a collection of rare genotypes unambiguously contribute to the pathogenesis of late-onset NCDs, such as AD.
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Affiliation(s)
- S Alizadeh
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - S Khamse
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - N Tajeddin
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - H R Khorram Khorshid
- Personalized Medicine and Genometabolomics Research Center, Hope Generation Foundation, Tehran, Iran
| | - A Delbari
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
| | - M Ohadi
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
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Zhao J, Han Z, Ding L, Wang P, He X, Lin L. The molecular mechanism of aging and the role in neurodegenerative diseases. Heliyon 2024; 10:e24751. [PMID: 38312598 PMCID: PMC10835255 DOI: 10.1016/j.heliyon.2024.e24751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 12/09/2023] [Accepted: 01/12/2024] [Indexed: 02/06/2024] Open
Abstract
Aging is a complex and inevitable biological process affected by a combination of external environmental and genetic factors. Humans are currently living longer than ever before, accompanied with aging-related alterations such as diminished autophagy, decreased immunological function, mitochondrial malfunction, stem cell failure, accumulation of somatic and mitochondrial DNA mutations, loss of telomere, and altered nutrient metabolism. Aging leads to a decline in body functions and age-related diseases, for example, Alzheimer's disease, which adversely affects human health and longevity. The quality of life of the elderly is greatly diminished by the increase in their life expectancy rather than healthy life expectancy. With the rise in the age of the global population, aging and related diseases have become the focus of attention worldwide. In this review, we discuss several major mechanisms of aging, including DNA damage and repair, free radical oxidation, telomeres and telomerase, mitochondrial damage, inflammation, and their role in neurodegenerative diseases to provide a reference for the prevention of aging and its related diseases.
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Affiliation(s)
- Juanli Zhao
- Laboratory of Medical Molecular and Cellular Biology, College of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan, 430065, China
- Department of Pharmacology, College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Zhenjie Han
- Laboratory of Medical Molecular and Cellular Biology, College of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Li Ding
- Department of Pharmacology, College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Ping Wang
- Hubei Research Institute of Geriatrics, Collaborative Innovation Center of Hubei Province, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Xiutang He
- Center for Monitoring and Evaluation of Teaching Quality, Jingchu University of Technology, Jingmen, 448000, China
| | - Li Lin
- Laboratory of Medical Molecular and Cellular Biology, College of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan, 430065, China
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Chen J, Gao G, Zhang Y, Dai P, Huang Y. Comprehensive analysis and validation of SNX7 as a novel biomarker for the diagnosis, prognosis, and prediction of chemotherapy and immunotherapy response in hepatocellular carcinoma. BMC Cancer 2023; 23:899. [PMID: 37743471 PMCID: PMC10519071 DOI: 10.1186/s12885-023-11405-0] [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: 03/17/2023] [Accepted: 09/14/2023] [Indexed: 09/26/2023] Open
Abstract
BACKGROUND Studies have demonstrated that Sorting nexin 7 (SNX7) functions as an anti-apoptotic protein in liver tissue and plays a crucial role in the survival of hepatocytes during early embryonic development. However, its diagnostic and prognostic value as well as the predictive value of chemotherapy and immunotherapy have not been reported in hepatocellular carcinoma (HCC). METHODS SNX7 mRNA expression and its diagnostic efficacy were examined in GEO datasets, and the findings were further confirmed in TCGA, ICGC cohorts, and cell lines. The protein level of SNX7 was determined using CPTAC and HPA databases, and the results were validated through immunohistochemistry (IHC). Survival analyses were performed in TCGA and ICGC cohorts, and the results were subsequently validated via Kaplan-Meier Plotter. The response to chemotherapy and immunotherapy was predicted via GDSC dataset and TIDE algorithm, respectively. R packages were employed to explore the relationship between SNX7 expression and immune infiltration, m6A modification, as well as the functional enrichment of differentially expressed genes (DEGs). RESULTS The expression of SNX7 at both mRNA and protein levels was significantly upregulated in HCC tissues. SNX7 exhibited superior diagnostic efficacy compared to AFP alone for HCC detection, and combining it with AFP improved the diagnostic accuracy for HCC. High SNX7 was associated with unfavorable outcomes, including poor overall survival, disease-specific survival, progression-free survival, and advanced pathological stage, in patients with HCC, and SNX7 was identified as an independent risk factor for HCC. Moreover, elevated SNX7 expression was positively correlated with increased sensitivity to various chemotherapy drugs, including sorafenib, while it was associated with resistance to immunotherapy in HCC patients. Correlation analysis revealed a relationship between SNX7 and multiple m6A-related genes and various immune cells. Finally, enrichment analysis demonstrated strong associations of SNX7 with critical biological processes, such as cell cycle regulation, cellular senescence, cell adhesion, DNA replication, and mismatch repair pathway in HCC. CONCLUSIONS Our study highlights the association of SNX7 with the immune microenvironment and its potential influence on HCC progression. SNX7 emerges as a promising novel biomarker for the diagnosis, prognosis, and prediction of response to chemotherapy and immunotherapy in patients with HCC.
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Affiliation(s)
- Jianlin Chen
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, Fujian, 350001, China
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fuzhou, Fujian, 350001, China
- Central Laboratory, Fujian Provincial Hospital, Fuzhou, Fujian, 350001, China
- Center for Experimental Research in Clinical Medicine, Fujian Provincial Hospital, Fuzhou, Fujian, 350001, China
| | - Gan Gao
- Departments of Clinical Laboratory of Liuzhou Hospital of Guangzhou Women and Children's Medical Center, Liuzhou, 545616, Guangxi, China
| | - Yi Zhang
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, Fujian, 350001, China
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fuzhou, Fujian, 350001, China
| | - Peng Dai
- Departments of Anesthesiology, The First People's Hospital of Foshan, Foshan, 528000, Guangdong, China
| | - Yi Huang
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, Fujian, 350001, China.
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fuzhou, Fujian, 350001, China.
- Central Laboratory, Fujian Provincial Hospital, Fuzhou, Fujian, 350001, China.
- Center for Experimental Research in Clinical Medicine, Fujian Provincial Hospital, Fuzhou, Fujian, 350001, China.
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Zhang Y, Li X, Hu Y, Yuan H, Wu X, Yang Y, Zhao T, Hu K, Wang Z, Wang G, Zhang K, Liu H. Evaluation of mild cognitive impairment genetic susceptibility risks in a Chinese population. BMC Psychiatry 2022; 22:93. [PMID: 35135506 PMCID: PMC8822756 DOI: 10.1186/s12888-022-03756-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 02/02/2022] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Mild cognitive impairment (MCI) is a kind of non-functional cognitive decline between normal aging and dementia. With the increase of individual age, the quality of cognitive function has become a more and more important topic. The study of gene loci in patients with MCI is essential for the prevention of dementia. In this study, we evaluate the gene polymorphism in Chinese Han patients with MCI by propensity score matching (PSM) and comparing them to healthy control (HC) subjects. METHODS Four hundred seventeen patients with mild cognitive impairment and 508 healthy people were included. The two groups were matched by applying one-to-one PSM, and the matching tolerance was set to 0.002. The matching covariates included gender,age,occupation,marital status,living mode. Then, a case-control associated analysis was conducted to analyze the genotype and allele frequencies of single nucleotide polymorphisms (SNPs) in the MCI group and the control group. RESULTS Three hundred eleven cases were successfully matched in each group, and there was no statistical difference on all the matching variables, gender, age, occupation, marital status, living mode between two groups after the match (P > 0.05). The allele frequency of bridging integrator 1(BIN1) rs7561528 showed minimal association with MCI in the Han Chinese population (P = 0.01). Compared with the healthy control (HC) group, A allele frequency of MCI group patients was significantly decreased. The genotype frequency of BIN1 rs6733839 showed minimal association with MCI in the recessive model (P = 0.03). The genotype frequency of rs7561528 showed minimal association with MCI in the codominant, dominant, overdominant, and log-additive model (P < 0.05). The genotype frequencies of StAR-related lipid transfer domain 6 (STARD6) rs10164112 showed nominal association with MCI in the codominant, dominant, and log-additive model (P < 0.05). Unfortunately, the significant differences did not survive Benjamini-Hochberg false discovery rate correction (adjusted P > 0.05). The patients with SPI1 rs1057233 may be the protective factor of MCI (OR = 0.733, 95%CI 0.625-0.859, P < 0.001), and patients with APOE rs10164112 may be a risk factor for MCI (OR = 1.323, 95%CI 1.023-1.711, P = 0.033). CONCLUSIONS The polymorphisms of rs7561528, rs6733839 loci in the BIN1 gene, and rs1057233 loci in the SPI1 gene may be associated with the MCI in Chinese Han population. APOE gene was the risk factor of MCI, but further verification in a large sample population is still needed.
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Affiliation(s)
- Yelei Zhang
- grid.186775.a0000 0000 9490 772XDepartment of Psychiatry, Chaohu Hospital, Anhui Medical University, 64 North Chaohu Road, Hefei, 238000 China ,grid.186775.a0000 0000 9490 772XAnhui Psychiatric Center, Anhui Medical University, Hefei, 238000 China ,grid.268099.c0000 0001 0348 3990The Affiliated Kangning Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325007 China
| | - Xiaoyue Li
- grid.186775.a0000 0000 9490 772XDepartment of Psychiatry, Chaohu Hospital, Anhui Medical University, 64 North Chaohu Road, Hefei, 238000 China ,grid.186775.a0000 0000 9490 772XAnhui Psychiatric Center, Anhui Medical University, Hefei, 238000 China
| | - Yu Hu
- grid.186775.a0000 0000 9490 772XDepartment of Psychiatry, Chaohu Hospital, Anhui Medical University, 64 North Chaohu Road, Hefei, 238000 China ,grid.186775.a0000 0000 9490 772XAnhui Psychiatric Center, Anhui Medical University, Hefei, 238000 China
| | - Hongwei Yuan
- grid.89957.3a0000 0000 9255 8984Department of Psychiatry, Wuxi Mental Health Center, Nanjing Medical University, Wuxi, 214151 China
| | - Xiaodong Wu
- grid.186775.a0000 0000 9490 772XDepartment of Psychiatry, Chaohu Hospital, Anhui Medical University, 64 North Chaohu Road, Hefei, 238000 China ,grid.186775.a0000 0000 9490 772XAnhui Psychiatric Center, Anhui Medical University, Hefei, 238000 China
| | - Yating Yang
- grid.186775.a0000 0000 9490 772XDepartment of Psychiatry, Chaohu Hospital, Anhui Medical University, 64 North Chaohu Road, Hefei, 238000 China ,grid.186775.a0000 0000 9490 772XAnhui Psychiatric Center, Anhui Medical University, Hefei, 238000 China
| | - Tongtong Zhao
- grid.186775.a0000 0000 9490 772XDepartment of Psychiatry, Chaohu Hospital, Anhui Medical University, 64 North Chaohu Road, Hefei, 238000 China ,grid.186775.a0000 0000 9490 772XAnhui Psychiatric Center, Anhui Medical University, Hefei, 238000 China
| | - Ke Hu
- grid.89957.3a0000 0000 9255 8984Department of Psychiatry, Wuxi Mental Health Center, Nanjing Medical University, Wuxi, 214151 China
| | - Zhiqiang Wang
- grid.89957.3a0000 0000 9255 8984Department of Psychiatry, Wuxi Mental Health Center, Nanjing Medical University, Wuxi, 214151 China
| | - Guoqiang Wang
- grid.89957.3a0000 0000 9255 8984Department of Psychiatry, Wuxi Mental Health Center, Nanjing Medical University, Wuxi, 214151 China
| | - Kai Zhang
- Department of Psychiatry, Chaohu Hospital, Anhui Medical University, 64 North Chaohu Road, Hefei, 238000, China. .,Anhui Psychiatric Center, Anhui Medical University, Hefei, 238000, China.
| | - Huanzhong Liu
- Department of Psychiatry, Chaohu Hospital, Anhui Medical University, 64 North Chaohu Road, Hefei, 238000, China. .,Anhui Psychiatric Center, Anhui Medical University, Hefei, 238000, China.
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Mapping the gene network landscape of Alzheimer's disease through integrating genomics and transcriptomics. PLoS Comput Biol 2022; 18:e1009903. [PMID: 35213535 PMCID: PMC8906581 DOI: 10.1371/journal.pcbi.1009903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 03/09/2022] [Accepted: 02/08/2022] [Indexed: 01/08/2023] Open
Abstract
Integration of multi-omics data with molecular interaction networks enables elucidation of the pathophysiology of Alzheimer's disease (AD). Using the latest genome-wide association studies (GWAS) including proxy cases and the STRING interactome, we identified an AD network of 142 risk genes and 646 network-proximal genes, many of which were linked to synaptic functions annotated by mouse knockout data. The proximal genes were confirmed to be enriched in a replication GWAS of autopsy-documented cases. By integrating the AD gene network with transcriptomic data of AD and healthy temporal cortices, we identified 17 gene clusters of pathways, such as up-regulated complement activation and lipid metabolism, down-regulated cholinergic activity, and dysregulated RNA metabolism and proteostasis. The relationships among these pathways were further organized by a hierarchy of the AD network pinpointing major parent nodes in graph structure including endocytosis and immune reaction. Control analyses were performed using transcriptomics from cerebellum and a brain-specific interactome. Further integration with cell-specific RNA sequencing data demonstrated genes in our clusters of immunoregulation and complement activation were highly expressed in microglia.
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Neuroimmune contributions to Alzheimer's disease: a focus on human data. Mol Psychiatry 2022; 27:3164-3181. [PMID: 35668160 PMCID: PMC9168642 DOI: 10.1038/s41380-022-01637-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 05/05/2022] [Accepted: 05/18/2022] [Indexed: 12/12/2022]
Abstract
The past decade has seen the convergence of a series of new insights that arose from genetic and systems analyses of Alzheimer's disease (AD) with a wealth of epidemiological data from a variety of fields; this resulted in renewed interest in immune responses as important, potentially causal components of AD. Here, we focus primarily on a review of human data which has recently yielded a set of robust, reproducible results that exist in a much larger universe of conflicting reports stemming from small studies with important limitations in their study design. Thus, we are at an important crossroads in efforts to first understand at which step of the long, multiphasic course of AD a given immune response may play a causal role and then modulate this response to slow or block the pathophysiology of AD. We have a wealth of new experimental tools, analysis methods, and capacity to sample human participants at large scale longitudinally; these resources, when coupled to a foundation of reproducible results and novel study designs, will enable us to monitor human immune function in the CNS at the level of complexity that is required while simultaneously capturing the state of the peripheral immune system. This integration of peripheral and central perturbations in immune responses results in pathologic responses in the central nervous system parenchyma where specialized cellular microenvironments composed of multiple cell subtypes respond to these immune perturbations as well as to environmental exposures, comorbidities and the impact of the advancing life course. Here, we offer an overview that seeks to illustrate the large number of interconnecting factors that ultimately yield the neuroimmune component of AD.
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Natural selection at the RASGEF1C (GGC) repeat in human and divergent genotypes in late-onset neurocognitive disorder. Sci Rep 2021; 11:19235. [PMID: 34584172 PMCID: PMC8479062 DOI: 10.1038/s41598-021-98725-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 09/14/2021] [Indexed: 12/17/2022] Open
Abstract
Expression dysregulation of the neuron-specific gene, RASGEF1C (RasGEF Domain Family Member 1C), occurs in late-onset neurocognitive disorders (NCDs), such as Alzheimer's disease. This gene contains a (GGC)13, spanning its core promoter and 5' untranslated region (RASGEF1C-201 ENST00000361132.9). Here we sequenced the (GGC)-repeat in a sample of human subjects (N = 269), consisting of late-onset NCDs (N = 115) and controls (N = 154). We also studied the status of this STR across various primate and non-primate species based on Ensembl 103. The 6-repeat allele was the predominant allele in the controls (frequency = 0.85) and NCD patients (frequency = 0.78). The NCD genotype compartment consisted of an excess of genotypes that lacked the 6-repeat (divergent genotypes) (Mid-P exact = 0.004). A number of those genotypes were not detected in the control group (Mid-P exact = 0.007). The RASGEF1C (GGC)-repeat expanded beyond 2-repeats specifically in primates, and was at maximum length in human. We conclude that there is natural selection for the 6-repeat allele of the RASGEF1C (GGC)-repeat in human, and significant divergence from that allele in late-onset NCDs. STR alleles that are predominantly abundant and genotypes that deviate from those alleles are underappreciated features, which may have deep evolutionary and pathological consequences.
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Evolving evidence on a link between the ZMYM3 exceptionally long GA-STR and human cognition. Sci Rep 2020; 10:19454. [PMID: 33173136 PMCID: PMC7655811 DOI: 10.1038/s41598-020-76461-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 10/29/2020] [Indexed: 02/06/2023] Open
Abstract
The human X-linked zinc finger MYM-type protein 3 (ZMYM3) contains the longest GA-STR identified across protein-coding gene 5′ UTR sequences, at 32-repeats. This exceptionally long GA-STR is located at a complex string of GA-STRs with a human-specific formula across the complex as follows: (GA)8-(GA)4-(GA)6-(GA)32 (ZMYM3-207 ENST00000373998.5). ZMYM3 was previously reported among the top three genes involved in the progression of late-onset Alzheimer’s disease. Here we sequenced the ZMYM3 GA-STR complex in 750 human male subjects, consisting of late-onset neurocognitive disorder (NCD) as a clinical entity (n = 268) and matched controls (n = 482). We detected strict monomorphism of the GA-STR complex, except of the exceptionally long STR, which was architecturally skewed in respect of allele distribution between the NCD cases and controls [F (1, 50) = 12.283; p = 0.001]. Moreover, extreme alleles of this STR at 17, 20, 42, and 43 repeats were detected in seven NCD patients and not in the control group (Mid-P exact = 0.0003). A number of these alleles overlapped with alleles previously found in schizophrenia and bipolar disorder patients. In conclusion, we propose selective advantage for the exceptional length of the ZMYM3 GA-STR in human, and its link to a spectrum of diseases in which major cognition impairment is a predominant phenotype.
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12
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Marquez DX, Glover CM, Lamar M, Leurgans SE, Shah RC, Barnes LL, Aggarwal NT, Buchman AS, Bennett DA. Representation of Older Latinxs in Cohort Studies at the Rush Alzheimer's Disease Center. Neuroepidemiology 2020; 54:404-418. [PMID: 32906123 PMCID: PMC7572552 DOI: 10.1159/000509626] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 06/20/2020] [Indexed: 12/31/2022] Open
Abstract
The Rush Alzheimer's Disease Center (RADC) conducts 5 harmonized prospective clinical-pathologic cohort studies of aging - with 1 study, the Latino Core, focused exclusively on Latinxs, 2 studies consisting of mostly non-Latinx whites, and 2 studies of mostly non-Latinx blacks. This paper contextualizes the Latino Core within the other 4 harmonized RADC cohort studies. The overall aim of the paper is to provide information from the RADC, so that researchers can learn from our participants and procedures to better advance the science of Alzheimer's disease and related dementias in Latinxs. We describe an annual clinical evaluation that assesses risk factors for Alzheimer's dementia among older adults without known dementia at enrollment. As all RADC cohort studies offer brain donation as a part of research participation, we discuss our approach to brain donation and subsequent participant decision-making among older Latinxs. We also summarize baseline characteristics of older Latinxs across the 5 RADC cohort studies in relation to the baseline characteristics of non-Latinx blacks and non-Latinx whites. Finally, we outline challenges and considerations as well as potential next steps in cognitive aging research with older Latinxs.
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Affiliation(s)
- David X Marquez
- Rush Alzheimer's Disease Center, Chicago, Illinois, USA,
- Department of Kinesiology and Nutrition, University of Illinois at Chicago, Chicago, Illinois, USA,
| | - Crystal M Glover
- Rush Alzheimer's Disease Center, Chicago, Illinois, USA
- Department of Psychiatry and Behavioral Sciences, Rush Medical College, Chicago, Illinois, USA
| | - Melissa Lamar
- Rush Alzheimer's Disease Center, Chicago, Illinois, USA
- Department of Psychiatry and Behavioral Sciences, Rush Medical College, Chicago, Illinois, USA
| | - Sue E Leurgans
- Rush Alzheimer's Disease Center, Chicago, Illinois, USA
- Department of Neurological Sciences, Rush Medical College, Chicago, Illinois, USA
| | - Raj C Shah
- Rush Alzheimer's Disease Center, Chicago, Illinois, USA
- Department of Family Medicine, Rush Medical College, Chicago, Illinois, USA
| | - Lisa L Barnes
- Rush Alzheimer's Disease Center, Chicago, Illinois, USA
- Department of Neurological Sciences, Rush Medical College, Chicago, Illinois, USA
| | - Neelum T Aggarwal
- Rush Alzheimer's Disease Center, Chicago, Illinois, USA
- Department of Neurological Sciences, Rush Medical College, Chicago, Illinois, USA
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13
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Afshar H, Adelirad F, Kowsari A, Kalhor N, Delbari A, Najafipour R, Foroughan M, Bozorgmehr A, Khamse S, Nazaripanah N, Ohadi M. Natural Selection at the NHLH2 Core Promoter Exceptionally Long CA-Repeat in Human and Disease-Only Genotypes in Late-Onset Neurocognitive Disorder. Gerontology 2020; 66:514-522. [PMID: 32877896 DOI: 10.1159/000509471] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 06/17/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Approximately 2% of the human core promoter short tandem repeats (STRs) reach lengths of ≥6 repeats, which may in part be a result of adaptive evolutionary processes and natural selection. A single-exon transcript of the human nescient helix loop helix 2 (NHLH2) gene is flanked by the longest CA-repeat detected in a human protein-coding gene core promoter (Ensembl transcript ID: ENST00000369506.1). NHLH2 is involved in several biological and pathological pathways, such as motivated exercise, obesity, and diabetes. METHODS The allele and genotype distribution of the NHLH2 CA-repeat were investigated by sequencing in 655 Iranian subjects, consisting of late-onset neurocognitive disorder (NCD) as a clinical entity (n = 290) and matched controls (n = 365). The evolutionary trend of the CA-repeat was also studied across vertebrates. RESULTS The allele range was between 9 and 25 repeats in the NCD cases, and 12 and 24 repeats in the controls. At the frequency of 0.56, the 21-repeat allele was the predominant allele in the controls. While the 21-repeat was also the predominant allele in the NCD patients, we detected significant decline of the frequency (p < 0.0001) and homozygosity (p < 0.006) of this allele in this group. Furthermore, 12 genotypes were detected across 16 patients (5.5% of the entire NCD sample) and not in the controls (disease-only genotypes; p < 0.0003), consisting of at least one extreme allele. The extreme alleles were at 9, 12, 13, 18, and 19 repeats (extreme short end), and 23, 24, and 25 repeats (extreme long end), and their frequencies ranged between 0.001 and 0.04. The frequency of the 21-repeat allele significantly dropped to 0.09 in the disease-only genotype compartment (p < 0.0001). Evolutionarily, while the maximum length of the NHLH2 CA-repeat was 11 repeats in non-primates, this CA-repeat was ≥14 repeats in primates and reached maximum length in human. CONCLUSION We propose a novel locus for late-onset NCD at the NHLH2 core promoter exceptionally long CA-STR and natural selection at this locus. Furthermore, there was indication of genotypes at this locus that unambiguously linked to late-onset NCD. This is the first instance of natural selection in favor of a predominantly abundant STR allele in human and its differential distribution in late-onset NCD.
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Affiliation(s)
- Hossein Afshar
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Fatemeh Adelirad
- Department of Health Education and Promotion, Faculty of Health Sciences Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Kowsari
- Department of Mesenchymal Stem Cell, The Academic Center for Education, Culture and Research, Qom, Iran
| | - Naser Kalhor
- Department of Mesenchymal Stem Cell, The Academic Center for Education, Culture and Research, Qom, Iran
| | - Ahmad Delbari
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Reza Najafipour
- Cellular and Molecular Research Centre, Research Institute for Prevention of Non Communicable Disease, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Mahshid Foroughan
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Ali Bozorgmehr
- Department of Neuroscience, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Safoura Khamse
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Neda Nazaripanah
- Department of Health Education and Promotion, Faculty of Health Sciences Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mina Ohadi
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran,
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14
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Ni X, Zhou M, Wang H, He KY, Broeckel U, Hanis C, Kardia S, Redline S, Cooper RS, Tang H, Zhu X. Detecting fitness epistasis in recently admixed populations with genome-wide data. BMC Genomics 2020; 21:476. [PMID: 32652930 PMCID: PMC7353720 DOI: 10.1186/s12864-020-06874-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 06/30/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fitness epistasis, the interaction effect of genes at different loci on fitness, makes an important contribution to adaptive evolution. Although fitness interaction evidence has been observed in model organisms, it is more difficult to detect and remains poorly understood in human populations as a result of limited statistical power and experimental constraints. Fitness epistasis is inferred from non-independence between unlinked loci. We previously observed ancestral block correlation between chromosomes 4 and 6 in African Americans. The same approach fails when examining ancestral blocks on the same chromosome due to the strong confounding effect observed in a recently admixed population. RESULTS We developed a novel approach to eliminate the bias caused by admixture linkage disequilibrium when searching for fitness epistasis on the same chromosome. We applied this approach in 16,252 unrelated African Americans and identified significant ancestral correlations in two pairs of genomic regions (P-value< 8.11 × 10- 7) on chromosomes 1 and 10. The ancestral correlations were not explained by population admixture. Historical African-European crossover events are reduced between pairs of epistatic regions. We observed multiple pairs of co-expressed genes shared by the two regions on each chromosome, including ADAR being co-expressed with IFI44 in almost all tissues and DARC being co-expressed with VCAM1, S1PR1 and ELTD1 in multiple tissues in the Genotype-Tissue Expression (GTEx) data. Moreover, the co-expressed gene pairs are associated with the same diseases/traits in the GWAS Catalog, such as white blood cell count, blood pressure, lung function, inflammatory bowel disease and educational attainment. CONCLUSIONS Our analyses revealed two instances of fitness epistasis on chromosomes 1 and 10, and the findings suggest a potential approach to improving our understanding of adaptive evolution.
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Affiliation(s)
- Xumin Ni
- Department of Mathematics, School of Science, Beijing Jiaotong University, Beijing, 100044, China
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Mengshi Zhou
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Heming Wang
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Karen Y He
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Uli Broeckel
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Craig Hanis
- Department of Epidemiology, Human Genetics and Environmental Sciences, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Sharon Kardia
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Richard S Cooper
- Department of Public Health Science, Loyola University Medical Center, Maywood, IL, USA
| | - Hua Tang
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Xiaofeng Zhu
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA.
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15
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Badhwar A, McFall GP, Sapkota S, Black SE, Chertkow H, Duchesne S, Masellis M, Li L, Dixon RA, Bellec P. A multiomics approach to heterogeneity in Alzheimer's disease: focused review and roadmap. Brain 2020; 143:1315-1331. [PMID: 31891371 PMCID: PMC7241959 DOI: 10.1093/brain/awz384] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 10/04/2019] [Accepted: 10/07/2019] [Indexed: 11/14/2022] Open
Abstract
Aetiological and clinical heterogeneity is increasingly recognized as a common characteristic of Alzheimer's disease and related dementias. This heterogeneity complicates diagnosis, treatment, and the design and testing of new drugs. An important line of research is discovery of multimodal biomarkers that will facilitate the targeting of subpopulations with homogeneous pathophysiological signatures. High-throughput 'omics' are unbiased data-driven techniques that probe the complex aetiology of Alzheimer's disease from multiple levels (e.g. network, cellular, and molecular) and thereby account for pathophysiological heterogeneity in clinical populations. This review focuses on data reduction analyses that identify complementary disease-relevant perturbations for three omics techniques: neuroimaging-based subtypes, metabolomics-derived metabolite panels, and genomics-related polygenic risk scores. Neuroimaging can track accrued neurodegeneration and other sources of network impairments, metabolomics provides a global small-molecule snapshot that is sensitive to ongoing pathological processes, and genomics characterizes relatively invariant genetic risk factors representing key pathways associated with Alzheimer's disease. Following this focused review, we present a roadmap for assembling these multiomics measurements into a diagnostic tool highly predictive of individual clinical trajectories, to further the goal of personalized medicine in Alzheimer's disease.
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Affiliation(s)
- AmanPreet Badhwar
- Centre de Recherche de l’Institut Universitaire de Gériatrie de Montréal, Montreal, Canada
- Université de Montréal, Montreal, Canada
| | - G Peggy McFall
- Department of Psychology, University of Alberta, Edmonton, Canada
| | - Shraddha Sapkota
- Hurvitz Brain Sciences Research Program, Sunnybrook Research Institute, University of Toronto, Toronto, Canada
| | - Sandra E Black
- Hurvitz Brain Sciences Research Program, Sunnybrook Research Institute, University of Toronto, Toronto, Canada
- Department of Medicine (Neurology), Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Canada
| | - Howard Chertkow
- Baycrest Health Sciences and the Rotman Research Institute, University of Toronto, Toronto, Canada
| | - Simon Duchesne
- Centre CERVO, Quebec City Mental Health Institute, Quebec, Quebec City, Canada
- Department of Radiology, Faculty of Medicine, Université Laval, Quebec City, Canada
| | - Mario Masellis
- Department of Medicine (Neurology), Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Canada
| | - Roger A Dixon
- Department of Psychology, University of Alberta, Edmonton, Canada
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Canada
| | - Pierre Bellec
- Centre de Recherche de l’Institut Universitaire de Gériatrie de Montréal, Montreal, Canada
- Université de Montréal, Montreal, Canada
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16
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Li X, Zhu X, Zhang W, Yang F, Hui J, Tan J, Xie H, Peng D, Ma L, Cui L, Zhang S, Lv Z, Sun L, Yuan H, Zhou Q, Wang L, Qi S, Wang Z, Hu C, Yang Z. The etiological effect of a new low-frequency ESR1 variant on Mild Cognitive Impairment and Alzheimer's Disease: a population-based study. Aging (Albany NY) 2019; 10:2316-2337. [PMID: 30222591 PMCID: PMC6188501 DOI: 10.18632/aging.101548] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 09/06/2018] [Indexed: 11/25/2022]
Abstract
Latent genetic variations of cholesterol metabolism-related genes in late-onset Alzheimer’s disease, especially, as well as in mild cognitive impairment pathogenesis are still to be studied extensively. Thus, we performed the targeted-sequencing of 12 nuclear receptor genes plus APOE which were involved in cholesterol content modulation to screen susceptible genetic variants and focused on a new risk variant ESR1 rs9340803 at 6q25.1 for both late-onset Alzheimer’s disease (OR=3.30[1.84~4.22], p<0.001) and mild cognitive impairment (OR=3.08[1.75~3.89], p<0.001). This low-frequency variant was validated in three independent cohorts totaling 854 late-onset Alzheimer’s disease cases, 1059 mild cognitive impairment cases and 1254 controls from nine provinces of China mainland. Preliminary functional study on it revealed decreased ESR1 expression in vitro. Besides, we detected higher serum Aβ1-40 concentration in participants carrying this variant (p=0.038) and lower plasma total cholesterol level in this variant carriers with late-onset Alzheimer’s disease (p=0.009). In summary, we identified a susceptible variant which might contribute to developing mild cognitive impairment at earlier stage and Alzheimer’s Disease later. Our study would provide new insight into the disease causation of late-onset Alzheimer’s disease and could be exploited therapeutically.
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Affiliation(s)
- Xiaoling Li
- Graduate School of Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100001, P.R.China.,The MOH Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, 100730, P.R.China
| | - Xiaoquan Zhu
- The MOH Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, 100730, P.R.China
| | - Wandong Zhang
- Department of Pathology and Laboratory of Medicine, Faculty of Medicine, University of Ottawa, Ottawa, K1H 8M5, Canada.,Human Health Therapeutics, National Research Council of Canada, Ottawa, K1A 0R6, Canada
| | - Fan Yang
- The MOH Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, 100730, P.R.China
| | - Juan Hui
- The MOH Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, 100730, P.R.China
| | - Jiping Tan
- Department of Geriatric Neurology, Chinese PLA General Hospital, Beijing, 100730, P.R.China
| | - Haiqun Xie
- Department of Neurology, Affiliated Foshan Hospital of Sun Yat-sen University, Foshan, 528000, P.R.China
| | - Dantao Peng
- China-Japan Friendship Hospital, Beijing, 100029, P.R.China
| | - Lihua Ma
- 253 Hospital of PLA, Huhehot,, 010051, P.R.China
| | - Lianqi Cui
- Department of Neurology, 401 Hospital of PLA, Qingdao, Shandong 266100, P.R.China
| | - Shouzi Zhang
- Department of Neurology of Beijing Geriatric Hospital, Beijing, 100095, P.R.China
| | - Zeping Lv
- National Rehabilitation Aids Research Center, Ministry of Civil Affairs, Beijing, 100176, P.R.China
| | - Liang Sun
- The MOH Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, 100730, P.R.China
| | - Huiping Yuan
- The MOH Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, 100730, P.R.China
| | - Qi Zhou
- The MOH Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, 100730, P.R.China
| | - Luning Wang
- Department of Geriatric Neurology, Chinese PLA General Hospital, Beijing, 100730, P.R.China
| | - Shige Qi
- National Center for Chronic and Non-communicable Diseae Control and Prevention, Chinease CDC, Beijing, 100050, P.R.China
| | - Zhihui Wang
- National Center for Chronic and Non-communicable Diseae Control and Prevention, Chinease CDC, Beijing, 100050, P.R.China
| | - Caiyou Hu
- Department of Neurology, Jiangbin Hospital, Guangxi Zhuang Autonomous Region, Nanning, 530021, P.R.China
| | - Ze Yang
- Graduate School of Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100001, P.R.China.,The MOH Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, 100730, P.R.China
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17
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Meta-Analysis of Gene Expression Changes in the Blood of Patients with Mild Cognitive Impairment and Alzheimer's Disease Dementia. Int J Mol Sci 2019; 20:ijms20215403. [PMID: 31671574 PMCID: PMC6862214 DOI: 10.3390/ijms20215403] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/25/2019] [Accepted: 10/28/2019] [Indexed: 12/11/2022] Open
Abstract
Background: Dementia is a major public health concern affecting approximately 47 million people worldwide. Mild cognitive impairment (MCI) is one form of dementia that affects an individual’s memory with or without affecting their daily life. Alzheimer’s disease dementia (ADD) is a more severe form of dementia that usually affects elderly individuals. It remains unclear whether MCI is a distinct disorder from or an early stage of ADD. Methods: Gene expression data from blood were analyzed to identify potential biomarkers that may be useful for distinguishing between these two forms of dementia. Results: A meta-analysis revealed 91 genes dysregulated in individuals with MCI and 387 genes dysregulated in ADD. Pathway analysis identified seven pathways shared between MCI and ADD and nine ADD-specific pathways. Fifteen transcription factors were associated with MCI and ADD, whereas seven transcription factors were specific for ADD. Mir-335-5p was specific for ADD, suggesting that it may be useful as a biomarker. Diseases that are associated with MCI and ADD included developmental delays, cognition impairment, and movement disorders. Conclusion: These results provide a better molecular understanding of peripheral changes that occur in MCI and ADD patients and may be useful in the identification of diagnostic and prognostic biomarkers.
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18
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Network Analysis of a Membrane-Enriched Brain Proteome across Stages of Alzheimer's Disease. Proteomes 2019; 7:proteomes7030030. [PMID: 31461916 PMCID: PMC6789842 DOI: 10.3390/proteomes7030030] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/20/2019] [Accepted: 08/22/2019] [Indexed: 12/12/2022] Open
Abstract
Previous systems-based proteomic approaches have characterized alterations in protein co-expression networks of unfractionated asymptomatic (AsymAD) and symptomatic Alzheimer’s disease (AD) brains. However, it remains unclear how sample fractionation and sub-proteomic analysis influences the organization of these protein networks and their relationship to clinicopathological traits of disease. In this proof-of-concept study, we performed a systems-based sub-proteomic analysis of membrane-enriched post-mortem brain samples from pathology-free control, AsymAD, and AD brains (n = 6 per group). Label-free mass spectrometry based on peptide ion intensity was used to quantify the 18 membrane-enriched fractions. Differential expression and weighted protein co-expression network analysis (WPCNA) were then used to identify and characterize modules of co-expressed proteins most significantly altered between the groups. We identified a total of 27 modules of co-expressed membrane-associated proteins. In contrast to the unfractionated proteome, these networks did not map strongly to cell-type specific markers. Instead, these modules were principally organized by their associations with a wide variety of membrane-bound compartments and organelles. Of these, the mitochondrion was associated with the greatest number of modules, followed by modules linked to the cell surface compartment. In addition, we resolved networks with strong associations to the endoplasmic reticulum, Golgi apparatus, and other membrane-bound organelles. A total of 14 of the 27 modules demonstrated significant correlations with clinical and pathological AD phenotypes. These results revealed that the proteins within individual compartments feature a heterogeneous array of AD-associated expression patterns, particularly during the preclinical stages of disease. In conclusion, this systems-based analysis of the membrane-associated AsymAD brain proteome yielded a unique network organization highly linked to cellular compartmentalization. Further study of this membrane-associated proteome may reveal novel insight into the complex pathways governing the earliest stages of disease.
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19
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Morgan S, Duguez S, Duddy W. Personalized Medicine and Molecular Interaction Networks in Amyotrophic Lateral Sclerosis (ALS): Current Knowledge. J Pers Med 2018; 8:E44. [PMID: 30551677 PMCID: PMC6313785 DOI: 10.3390/jpm8040044] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/27/2018] [Accepted: 12/05/2018] [Indexed: 12/12/2022] Open
Abstract
Multiple genes and mechanisms of pathophysiology have been implicated in amyotrophic lateral sclerosis (ALS), suggesting it is a complex systemic disease. With this in mind, applying personalized medicine (PM) approaches to tailor treatment pipelines for ALS patients may be necessary. The modelling and analysis of molecular interaction networks could represent valuable resources in defining ALS-associated pathways and discovering novel therapeutic targets. Here we review existing omics datasets and analytical approaches, in order to consider how molecular interaction networks could improve our understanding of the molecular pathophysiology of this fatal neuromuscular disorder.
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Affiliation(s)
- Stephen Morgan
- Northern Ireland Centre for Stratified Medicine, Altnagelvin Hospital Campus, Ulster University, Londonderry, BT47 6SB, Northern Ireland, UK.
| | - Stephanie Duguez
- Northern Ireland Centre for Stratified Medicine, Altnagelvin Hospital Campus, Ulster University, Londonderry, BT47 6SB, Northern Ireland, UK.
| | - William Duddy
- Northern Ireland Centre for Stratified Medicine, Altnagelvin Hospital Campus, Ulster University, Londonderry, BT47 6SB, Northern Ireland, UK.
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20
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Raj T, Li YI, Wong G, Humphrey J, Wang M, Ramdhani S, Wang YC, Ng B, Gupta I, Haroutunian V, Schadt EE, Young-Pearse T, Mostafavi S, Zhang B, Sklar P, Bennett DA, De Jager PL. Integrative transcriptome analyses of the aging brain implicate altered splicing in Alzheimer's disease susceptibility. Nat Genet 2018; 50:1584-1592. [PMID: 30297968 PMCID: PMC6354244 DOI: 10.1038/s41588-018-0238-1] [Citation(s) in RCA: 251] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 08/16/2018] [Indexed: 12/12/2022]
Abstract
Here we use deep sequencing to identify sources of variation in mRNA splicing in the dorsolateral prefrontal cortex (DLPFC) of 450 subjects from two aging cohorts. Hundreds of aberrant pre-mRNA splicing events are reproducibly associated with Alzheimer's disease. We also generate a catalog of splicing quantitative trait loci (sQTL) effects: splicing of 3,006 genes is influenced by genetic variation. We report that altered splicing is the mechanism for the effects of the PICALM, CLU and PTK2B susceptibility alleles. Furthermore, we performed a transcriptome-wide association study and identified 21 genes with significant associations with Alzheimer's disease, many of which are found in known loci, whereas 8 are in novel loci. These results highlight the convergence of old and new genes associated with Alzheimer's disease in autophagy-lysosomal-related pathways. Overall, this study of the transcriptome of the aging brain provides evidence that dysregulation of mRNA splicing is a feature of Alzheimer's disease and is, in some cases, genetically driven.
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Affiliation(s)
- Towfique Raj
- Ronald M. Loeb Center for Alzheimer's Disease, Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Yang I Li
- Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
| | - Garrett Wong
- Ronald M. Loeb Center for Alzheimer's Disease, Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jack Humphrey
- Genetics Institute, University College London, London, UK
- Department of Neurodegenerative Disease, Institute of Neurology, University College London, London, UK
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Satesh Ramdhani
- Ronald M. Loeb Center for Alzheimer's Disease, Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ying-Chih Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bernard Ng
- Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ishaan Gupta
- Ronald M. Loeb Center for Alzheimer's Disease, Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vahram Haroutunian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- James J. Peters VA Medical Center, New York, NY, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tracy Young-Pearse
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sara Mostafavi
- Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pamela Sklar
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA.
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Bishof I, Dammer EB, Duong DM, Kundinger SR, Gearing M, Lah JJ, Levey AI, Seyfried NT. RNA-binding proteins with basic-acidic dipeptide (BAD) domains self-assemble and aggregate in Alzheimer's disease. J Biol Chem 2018; 293:11047-11066. [PMID: 29802200 PMCID: PMC6052236 DOI: 10.1074/jbc.ra118.001747] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 05/23/2018] [Indexed: 12/12/2022] Open
Abstract
The U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and other RNA-binding proteins (RBPs) are mislocalized to cytoplasmic neurofibrillary Tau aggregates in Alzheimer's disease (AD), yet the co-aggregation mechanisms are incompletely understood. U1-70K harbors two disordered low-complexity domains (LC1 and LC2) that are necessary for aggregation in AD brain extracts. The LC1 domain contains highly repetitive basic (Arg/Lys) and acidic (Asp/Glu) residues, referred to as a basic-acidic dipeptide (BAD) domain. We report here that this domain shares many of the properties of the Gln/Asn-rich LC domains in RBPs that also aggregate in neurodegenerative disease. These properties included self-assembly into oligomers and localization to nuclear granules. Co-immunoprecipitations of recombinant U1-70K and deletions lacking the LC domain(s) followed by quantitative proteomic analyses were used to resolve functional classes of U1-70K-interacting proteins that depend on the BAD domain for their interaction. Within this interaction network, we identified a class of RBPs with BAD domains nearly identical to that found in U1-70K. Two members of this class, LUC7L3 and RBM25, required their respective BAD domains for reciprocal interactions with U1-70K and nuclear granule localization. Strikingly, a significant proportion of RBPs with BAD domains had elevated insolubility in the AD brain proteome. Furthermore, we show that the BAD domain of U1-70K can interact with Tau from AD brains but not from other tauopathies. These findings highlight a mechanistic role for BAD domains in stabilizing RBP interactions and in potentially mediating co-aggregation with the pathological AD-specific Tau isoforms.
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Affiliation(s)
- Isaac Bishof
- From the Departments of Biochemistry
- the Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Eric B Dammer
- From the Departments of Biochemistry
- the Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Duc M Duong
- From the Departments of Biochemistry
- the Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Sean R Kundinger
- From the Departments of Biochemistry
- the Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Marla Gearing
- the Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, Georgia 30322
- Pathology and Laboratory Medicine and
| | - James J Lah
- the Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, Georgia 30322
- Neurology, and
| | - Allan I Levey
- the Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, Georgia 30322
- Neurology, and
| | - Nicholas T Seyfried
- From the Departments of Biochemistry,
- the Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, Georgia 30322
- Neurology, and
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22
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Corona E, Wang L, Ko D, Patel CJ. Systematic detection of positive selection in the human-pathogen interactome and lasting effects on infectious disease susceptibility. PLoS One 2018; 13:e0196676. [PMID: 29799843 PMCID: PMC5969750 DOI: 10.1371/journal.pone.0196676] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Accepted: 04/17/2018] [Indexed: 01/07/2023] Open
Abstract
Infectious disease has shaped the natural genetic diversity of humans throughout the world. A new approach to capture positive selection driven by pathogens would provide information regarding pathogen exposure in distinct human populations and the constantly evolving arms race between host and disease-causing agents. We created a human pathogen interaction database and used the integrated haplotype score (iHS) to detect recent positive selection in genes that interact with proteins from 26 different pathogens. We used the Human Genome Diversity Panel to identify specific populations harboring pathogen-interacting genes that have undergone positive selection. We found that human genes that interact with 9 pathogen species show evidence of recent positive selection. These pathogens are Yersenia pestis, human immunodeficiency virus (HIV) 1, Zaire ebolavirus, Francisella tularensis, dengue virus, human respiratory syncytial virus, measles virus, Rubella virus, and Bacillus anthracis. For HIV-1, GWAS demonstrate that some naturally selected variants in the host-pathogen protein interaction networks continue to have functional consequences for susceptibility to these pathogens. We show that selected human genes were enriched for HIV susceptibility variants (identified through GWAS), providing further support for the hypothesis that ancient humans were exposed to lentivirus pandemics. Human genes in the Italian, Miao, and Biaka Pygmy populations that interact with Y. pestis show significant signs of selection. These results reveal some of the genetic footprints created by pathogens in the human genome that may have left lasting marks on susceptibility to infectious disease.
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Affiliation(s)
- Erik Corona
- Department of Biomedical Informatics, RTI International, Durham, NC, United States of America
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, United States of America
- * E-mail:
| | - Liuyang Wang
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, United States of America
| | - Dennis Ko
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, United States of America
- Department of Medicine, Duke University Medical Center, Durham, NC, United States of America
| | - Chirag J. Patel
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, United States of America
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Jabbari K, Heger P, Sharma R, Wiehe T. The Diverging Routes of BORIS and CTCF: An Interactomic and Phylogenomic Analysis. Life (Basel) 2018; 8:life8010004. [PMID: 29385718 PMCID: PMC5871936 DOI: 10.3390/life8010004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 01/25/2018] [Accepted: 01/25/2018] [Indexed: 12/11/2022] Open
Abstract
The CCCTC-binding factor (CTCF) is multi-functional, ubiquitously expressed, and highly conserved from Drosophila to human. It has important roles in transcriptional insulation and the formation of a high-dimensional chromatin structure. CTCF has a paralog called “Brother of Regulator of Imprinted Sites” (BORIS) or “CTCF-like” (CTCFL). It binds DNA at sites similar to those of CTCF. However, the expression profiles of the two proteins are quite different. We investigated the evolutionary trajectories of the two proteins after the duplication event using a phylogenomic and interactomic approach. We find that CTCF has 52 direct interaction partners while CTCFL only has 19. Almost all interactors already existed before the emergence of CTCF and CTCFL. The unique secondary loss of CTCF from several nematodes is paralleled by a loss of two of its interactors, the polycomb repressive complex subunit SuZ12 and the multifunctional transcription factor TYY1. In contrast to earlier studies reporting the absence of BORIS from birds, we present evidence for a multigene synteny block containing CTCFL that is conserved in mammals, reptiles, and several species of birds, indicating that not the entire lineage of birds experienced a loss of CTCFL. Within this synteny block, BORIS and its genomic neighbors seem to be partitioned into two nested chromatin loops. The high expression of SPO11, RAE1, RBM38, and PMEPA1 in male tissues suggests a possible link between CTCFL, meiotic recombination, and fertility-associated phenotypes. Using the 65,700 exomes and the 1000 genomes data, we observed a higher number of intergenic, non-synonymous, and loss-of-function mutations in CTCFL than in CTCF, suggesting a reduced strength of purifying selection, perhaps due to less functional constraint.
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Affiliation(s)
- Kamel Jabbari
- Cologne Biocenter, Institute for Genetics, University of Cologne, Zülpicher Straße 47a, 50674 Köln, Germany.
| | - Peter Heger
- Cologne Biocenter, Institute for Genetics, University of Cologne, Zülpicher Straße 47a, 50674 Köln, Germany.
| | - Ranu Sharma
- Cologne Biocenter, Institute for Genetics, University of Cologne, Zülpicher Straße 47a, 50674 Köln, Germany.
| | - Thomas Wiehe
- Cologne Biocenter, Institute for Genetics, University of Cologne, Zülpicher Straße 47a, 50674 Köln, Germany.
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24
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Bennett DA, Buchman AS, Boyle PA, Barnes LL, Wilson RS, Schneider JA. Religious Orders Study and Rush Memory and Aging Project. J Alzheimers Dis 2018; 64:S161-S189. [PMID: 29865057 PMCID: PMC6380522 DOI: 10.3233/jad-179939] [Citation(s) in RCA: 681] [Impact Index Per Article: 113.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND The Religious Orders Study and Rush Memory and Aging Project are both ongoing longitudinal clinical-pathologic cohort studies of aging and Alzheimer's disease (AD). OBJECTIVES To summarize progress over the past five years and its implications for understanding neurodegenerative diseases. METHODS Participants in both studies are older adults who enroll without dementia and agree to detailed longitudinal clinical evaluations and organ donation. The last review summarized findings through the end of 2011. Here we summarize progress and study findings over the past five years and discuss new directions for how these studies can inform on aging and AD in the future. RESULTS We summarize 1) findings on the relation of neurobiology to clinical AD; 2) neurobiologic pathways linking risk factors to clinical AD; 3) non-cognitive AD phenotypes including motor function and decision making; 4) the development of a novel drug discovery platform. CONCLUSION Complexity at multiple levels needs to be understood and overcome to develop effective treatments and preventions for cognitive decline and AD dementia.
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Affiliation(s)
- David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL., USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL., USA
| | - Aron S. Buchman
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL., USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL., USA
| | - Patricia A. Boyle
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL., USA
- Department of Behavioral Sciences, Rush University Medical Center, Chicago, IL., USA
| | - Lisa L. Barnes
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL., USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL., USA
- Department of Behavioral Sciences, Rush University Medical Center, Chicago, IL., USA
| | - Robert S. Wilson
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL., USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL., USA
- Department of Behavioral Sciences, Rush University Medical Center, Chicago, IL., USA
| | - Julie A Schneider
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL., USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL., USA
- Department of Pathology (Neuropathology), Rush University Medical Center, Chicago, IL., USA
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25
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Abstract
High-throughput, low-cost sequencing technologies have begun to yield new insights into biology and medicine. New data enable the interrogation of the molecular biology of disease from DNA to RNA to protein, charting the central dogma. This chapter reviews some of the key advances and resources in the application of bioinformatics to understanding, and ultimately diagnosing and treating, diseases of the nervous system. Array genotyping, exome sequencing, and whole-genome sequencing, in both disease and healthy populations, have enabled the interpretation of new genetic data. Profiling of epigenetic markers, such as histone modifications, has added to our understanding of the regulatory machinery of the genome. Downstream, mRNA, and protein expression data from published experiments and high-throughput studies enable complex analyses of gene function across many experimental conditions and tissues. Further delineation of molecular mechanism arises from the concept of genes working together in pathways or networks, reflecting direct protein interactions and regulatory relationships. The rapidly moving field of bioinformatics has made significant contributions to neurology in these early days; continued advances promise to transform medicine from basic science to clinical practice, as more genomics data are generated, combined, and analyzed in the future.
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Affiliation(s)
- Jason Chen
- Interdepartmental Program in Bioinformatics and Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, United States
| | - Giovanni Coppola
- Interdepartmental Program in Bioinformatics and Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, United States.
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26
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Xu S, Zhang L, Brodin L. Overexpression of SNX7 reduces Aβ production by enhancing lysosomal degradation of APP. Biochem Biophys Res Commun 2017; 495:12-19. [PMID: 29080748 DOI: 10.1016/j.bbrc.2017.10.127] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 10/23/2017] [Indexed: 01/01/2023]
Abstract
Abnormal production of amyloid-β peptides (Aβ) by proteolytic processing of amyloid precursor protein (APP) is thought to be central to the pathogenesis of Alzheimer's disease (AD). Although many efforts have been made to investigate mechanisms that regulate APP processing, many details remain incompletely understood. Sorting nexins (SNXs) are a family of proteins which are involved in many intracellular trafficking events. Several SNXs have been implicated in APP processing and Aβ production. In this study, we extended the investigation to SNX7. We found that overexpression of SNX7 in HEK293T cells reduces the levels of secreted Aβ and β-cleaved N-terminal APP fragments (sAPPβ). Moreover, SNX7 overexpression caused a significant reduction of the steady-state levels of APP as well as of the cell surface APP levels. By using NH4Cl and Bafilomycin A1 to inhibit the lysosomal degradative pathway, we found that the reduction of APP induced by SNX7 overexpression was prevented by such inhibition. No change in the cell surface distribution or steady-state levels of BACE1 was detected after overexpression of SNX7. Taken together, these results suggest that SNX7 regulates Aβ production by directing APP for degradation.
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Affiliation(s)
- Shaohua Xu
- Department of Neuroscience, Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Lu Zhang
- Department of Medicine, Karolinska Institutet, SE-171 76, Stockholm, Sweden
| | - Lennart Brodin
- Department of Neuroscience, Karolinska Institutet, SE-171 77, Stockholm, Sweden.
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27
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He Y, Luo J, Chen Y, Zhou X, Yu S, Jin L, Xiao X, Jia S, Liu Q. ARHGAP18 is a novel gene under positive natural selection that influences HbF levels in β-thalassaemia. Mol Genet Genomics 2017; 293:207-216. [DOI: 10.1007/s00438-017-1377-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 09/25/2017] [Indexed: 10/18/2022]
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28
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Carter CJ. Genetic, Transcriptome, Proteomic, and Epidemiological Evidence for Blood-Brain Barrier Disruption and Polymicrobial Brain Invasion as Determinant Factors in Alzheimer's Disease. J Alzheimers Dis Rep 2017; 1:125-157. [PMID: 30480234 PMCID: PMC6159731 DOI: 10.3233/adr-170017] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Diverse pathogens are detected in Alzheimer's disease (AD) brains. A bioinformatics survey showed that AD genome-wide association study (GWAS) genes (localized in bone marrow, immune locations and microglia) relate to multiple host/pathogen interactomes (Candida albicans, Cryptococcus neoformans, Bornavirus, Borrelia burgdorferri, cytomegalovirus, Ebola virus, HSV-1, HERV-W, HIV-1, Epstein-Barr, hepatitis C, influenza, Chlamydia pneumoniae, Porphyrymonas gingivalis, Helicobacter pylori, Toxoplasma gondii, Trypanosoma cruzi). These interactomes also relate to the AD hippocampal transcriptome and to plaque or tangle proteins. Upregulated AD hippocampal genes match those upregulated by multiple bacteria, viruses, fungi, or protozoa in immunocompetent cells. AD genes are enriched in GWAS datasets reflecting pathogen diversity, suggesting selection for pathogen resistance, as supported by the old age of AD patients, implying resistance to earlier infections. APOE4 is concentrated in regions of high parasitic burden and protects against childhood tropical infections and hepatitis C. Immune/inflammatory gain of function applies to APOE4, CR1, and TREM2 variants. AD genes are also expressed in the blood-brain barrier (BBB), which is disrupted by AD risk factors (age, alcohol, aluminum, concussion, cerebral hypoperfusion, diabetes, homocysteine, hypercholesterolemia, hypertension, obesity, pesticides, pollution, physical inactivity, sleep disruption, smoking) and by pathogens, directly or via olfactory routes to basal-forebrain BBB control centers. The BBB benefits from statins, NSAIDs, estrogen, melatonin, memantine, and the Mediterranean diet. Polymicrobial involvement is supported by upregulation of bacterial, viral, and fungal sensors/defenders in the AD brain, blood, or cerebrospinal fluid. AD serum amyloid-β autoantibodies may attenuate its antimicrobial effects favoring microbial survival and cerebral invasion leading to activation of neurodestructive immune/inflammatory processes, which may also be augmented by age-related immunosenescence. AD may thus respond to antibiotic, antifungal, or antiviral therapy.
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29
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Yu S, Chen Y, Lai K, Dewan RK, He Y. A Novel Variant with Positive Natural Selection Influenced Hb A 2 Levels in Chinese Individuals with β-Thalassemia. Hemoglobin 2017; 41:193-197. [PMID: 28747083 DOI: 10.1080/03630269.2017.1358177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
β-Thalassemia (β-thal) is the most common inherited hemolytic anemia worldwide. Elevated Hb A2 is a mark of β-thal carriers. The aim of this study was to identify the pathogenic variants associated with the Hb A2 levels. One thousand and thirty β-thal carriers were recruited for this study. Using positive natural expression quantitative trait loci (eQTL) analysis, a significant variant was selected. Genotyping for the rs231841 polymorphism was performed by the Sequenom MassARRAY IPLEX platform. All genetic association analyses were performed with the PLINK program. The linear regression analysis showed that rs231841 in the intron region of the potassium voltage-gated channel subfamily Q member 1 (KCNQ1) gene on chromosome 11p15 was significantly associated with Hb A2 levels. The presence of the C allele was associated with elevated Hb A2 levels. Our results suggest that rs231841 on the KCNQ1 gene with positive natural selection is related to Hb A2 levels in Chinese β-thal carriers, and KCNQ1 is probably associated with the expression of the β-like globin gene cluster.
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Affiliation(s)
- Shanjuan Yu
- a Department of Pediatrics , The First Affiliated Hospital of Guangxi Medical University , Nanning , Guangxi Province , People's Republic of China
| | - Yang Chen
- b School of Public Health, Guangxi Medical University , Nanning , Guangxi Province , People's Republic of China
| | - Ketong Lai
- c Guangxi Key Laboratory of Thalassemia Research , The First Affiliated Hospital of Guangxi Medical University , Nanning , Guangxi Province , People's Republic of China
| | - Roma Kajal Dewan
- a Department of Pediatrics , The First Affiliated Hospital of Guangxi Medical University , Nanning , Guangxi Province , People's Republic of China
| | - Yunyan He
- a Department of Pediatrics , The First Affiliated Hospital of Guangxi Medical University , Nanning , Guangxi Province , People's Republic of China
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30
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The bridging integrator 1 Gene rs7561528 polymorphism contributes to Alzheimer's disease susceptibility in East Asian and Caucasian populations. Clin Chim Acta 2017; 469:13-21. [PMID: 28302384 DOI: 10.1016/j.cca.2017.03.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 03/10/2017] [Accepted: 03/11/2017] [Indexed: 01/16/2023]
Abstract
Genetic variants of the bridging integrator 1 (BIN1) at the rs7561528 single nucleotide polymorphism were implicated in increased risk of Alzheimer's disease in several case-control association studies. However, the studies have reported apparently conflicting results. Here, we searched the PubMed and Google Scholar databases. In total, 17,179 AD patients and 17,448 healthy controls (HCs) from 18 studies are included in the current study to examine the association between this polymorphism and AD risk. Significant associations of the SNP rs242557 with AD are found under allelic [A vs. G: odds ratio (OR)=0.86, 95% confidence interval (CI)=0.78, 0.96, P=0.006], dominant (AA+AG vs. GG: OR=0.87, 95% CI=0.77, 0.97, P=0.01), recessive (AA vs. AG+GG: OR=0.86, 95% CI=0.76, 0.98, P=0.21), homozygous (AA vs. GG: OR=0.86, 95% CI=0.76, 0.99, P=0.03) and heterozygous (AG vs. GG: OR=0.87, 95% CI=0.83, 0.92, P<0.00001) models in the pooled populations, under allelic (OR=0.77, 95% CI=0.65, 0.91, P=0.002), dominant (OR=0.75, 95% CI=0.63, 0.90, P=0.001) and heterozygous (OR =0.79, 95% CI=0.70, 0.88, P<0.0001) models in East Asian population, under heterozygous (OR=0.89, 95% CI=0.84, 0.94, P<0.0001) model in Caucasian population. The results of the current meta-analysis suggest that the rs7561528 A allele carriers may be a protective factor against susceptibility to AD under all the genetic models in the pooled populations and under allelic and dominant model in East Asian population, and individuals with A/G heterozygous genotype are not prone to suffer from AD in both Asians and Caucasians.
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31
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Ponomareva NV, Andreeva TV, Protasova MS, Shagam LI, Malina DD, Goltsov AY, Fokin VF, Illarioshkin SN, Rogaev EI. Quantitative EEG during normal aging: association with the Alzheimer's disease genetic risk variant in PICALM gene. Neurobiol Aging 2017; 51:177.e1-177.e8. [DOI: 10.1016/j.neurobiolaging.2016.12.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 11/14/2016] [Accepted: 12/11/2016] [Indexed: 10/20/2022]
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32
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Kim DH, Gim JA, Mishra A, Lee K, Cho Y, Kim HS. SNP analysis of genes related to cholesterol metabolism and associated with late-onset Alzheimer’s disease. Genes Genomics 2017. [DOI: 10.1007/s13258-017-0524-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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33
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Wang H, Choi Y, Tayo B, Wang X, Morris N, Zhang X, Broeckel U, Hanis C, Kardia S, Redline S, Cooper RS, Tang H, Zhu X. Genome-wide survey in African Americans demonstrates potential epistasis of fitness in the human genome. Genet Epidemiol 2017; 41:122-135. [PMID: 27917522 PMCID: PMC5226866 DOI: 10.1002/gepi.22026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/30/2016] [Accepted: 10/03/2016] [Indexed: 11/07/2022]
Abstract
The role played by epistasis between alleles at unlinked loci in shaping population fitness has been debated for many years and the existing evidence has been mainly accumulated from model organisms. In model organisms, fitness epistasis can be systematically inferred by detecting nonindependence of genotypic values between loci in a population and confirmed through examining the number of offspring produced in two-locus genotype groups. No systematic study has been conducted to detect epistasis of fitness in humans owing to experimental constraints. In this study, we developed a novel method to detect fitness epistasis by testing the correlation between local ancestries on different chromosomes in an admixed population. We inferred local ancestry across the genome in 16,252 unrelated African Americans and systematically examined the pairwise correlations between the genomic regions on different chromosomes. Our analysis revealed a pair of genomic regions on chromosomes 4 and 6 that show significant local ancestry correlation (P-value = 4.01 × 10-8 ) that can be potentially attributed to fitness epistasis. However, we also observed substantial local ancestry correlation that cannot be explained by systemic ancestry inference bias. To our knowledge, this study is the first to systematically examine evidence of fitness epistasis across the human genome.
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Affiliation(s)
- Heming Wang
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Yoonha Choi
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Bamidele Tayo
- Department of Public Health Science, Loyola University Medical Center, Maywood, Illinois, United States of America
| | - Xuefeng Wang
- Departments of Preventive Medicine, Biomedical Informatics, and Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, United States of America
| | - Nathan Morris
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Xiang Zhang
- Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Uli Broeckel
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Craig Hanis
- Department of Epidemiology, Human Genetics and Environmental Sciences, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Sharon Kardia
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Susan Redline
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Richard S Cooper
- Department of Public Health Science, Loyola University Medical Center, Maywood, Illinois, United States of America
| | - Hua Tang
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Xiaofeng Zhu
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States of America
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34
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Dong HK, Gim JA, Yeo SH, Kim HS. Integrated late onset Alzheimer's disease (LOAD) susceptibility genes: Cholesterol metabolism and trafficking perspectives. Gene 2016; 597:10-16. [PMID: 27773727 DOI: 10.1016/j.gene.2016.10.022] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 10/09/2016] [Accepted: 10/18/2016] [Indexed: 12/21/2022]
Abstract
Late onset Alzheimer's disease (LOAD) is the most common type of dementia and is characterized by decreased amyloid-β (Aβ) clearance from the brain. Cholesterol regulates the production and clearance of Aβ. Genome-wide association study (GWAS) suggests that at least 20 genes are associated with LOAD. The genes APOE, CLU, SORL1, PICALM, and BIN1 have a relatively high LOAD susceptibility. Additional experimental and bioinformatic approaches to integrate data from genetics, epigenetics, and molecular networks may further increase our understanding of LOAD in relation to cholesterol metabolism and trafficking.
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Affiliation(s)
- Hee Kim Dong
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea; Department of Psychiatry, Hyungju Hospital, Yangsan-si, Gyeongsangnam-do, Republic of Korea
| | - Jeong-An Gim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea; Genetic Engineering Institute, Pusan National University, Busan 46241, Republic of Korea
| | - Seung Hyeon Yeo
- Department of Neurology, Gyeongsangnam Provincial Yangsan Hospital for the Elderly, Yangsan-si, Gyeongsangnam-do, Republic of Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea; Genetic Engineering Institute, Pusan National University, Busan 46241, Republic of Korea.
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Gaiteri C, Mostafavi S, Honey CJ, De Jager PL, Bennett DA. Genetic variants in Alzheimer disease - molecular and brain network approaches. Nat Rev Neurol 2016; 12:413-27. [PMID: 27282653 PMCID: PMC5017598 DOI: 10.1038/nrneurol.2016.84] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Genetic studies in late-onset Alzheimer disease (LOAD) are aimed at identifying core disease mechanisms and providing potential biomarkers and drug candidates to improve clinical care of AD. However, owing to the complexity of LOAD, including pathological heterogeneity and disease polygenicity, extraction of actionable guidance from LOAD genetics has been challenging. Past attempts to summarize the effects of LOAD-associated genetic variants have used pathway analysis and collections of small-scale experiments to hypothesize functional convergence across several variants. In this Review, we discuss how the study of molecular, cellular and brain networks provides additional information on the effects of LOAD-associated genetic variants. We then discuss emerging combinations of these omic data sets into multiscale models, which provide a more comprehensive representation of the effects of LOAD-associated genetic variants at multiple biophysical scales. Furthermore, we highlight the clinical potential of mechanistically coupling genetic variants and disease phenotypes with multiscale brain models.
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Affiliation(s)
- Chris Gaiteri
- Rush Alzheimer's Disease Center, Rush University Medical Center, 600 S Paulina Street, Chicago, Illinois 60612, USA
| | - Sara Mostafavi
- Department of Statistics, and Medical Genetics; Centre for Molecular and Medicine and Therapeutics, University of British Columbia, 950 West 28th Avenue, Vancouver, British Columbia V5Z 4H4, Canada
| | - Christopher J Honey
- Department of Psychology, University of Toronto, 100 St. George Street, 4th Floor Sidney Smith Hall, Toronto, Ontario M5S 3G3, Canada
| | - Philip L De Jager
- Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital, 75 Francis Street, Boston MA 02115, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, 600 S Paulina Street, Chicago, Illinois 60612, USA
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Qian DC, Byun J, Han Y, Greene CS, Field JK, Hung RJ, Brhane Y, Mclaughlin JR, Fehringer G, Landi MT, Rosenberger A, Bickeböller H, Malhotra J, Risch A, Heinrich J, Hunter DJ, Henderson BE, Haiman CA, Schumacher FR, Eeles RA, Easton DF, Seminara D, Amos CI. Identification of shared and unique susceptibility pathways among cancers of the lung, breast, and prostate from genome-wide association studies and tissue-specific protein interactions. Hum Mol Genet 2015; 24:7406-20. [PMID: 26483192 PMCID: PMC4664175 DOI: 10.1093/hmg/ddv440] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 09/11/2015] [Accepted: 10/12/2015] [Indexed: 12/18/2022] Open
Abstract
Results from genome-wide association studies (GWAS) have indicated that strong single-gene effects are the exception, not the rule, for most diseases. We assessed the joint effects of germline genetic variations through a pathway-based approach that considers the tissue-specific contexts of GWAS findings. From GWAS meta-analyses of lung cancer (12 160 cases/16 838 controls), breast cancer (15 748 cases/18 084 controls) and prostate cancer (14 160 cases/12 724 controls) in individuals of European ancestry, we determined the tissue-specific interaction networks of proteins expressed from genes that are likely to be affected by disease-associated variants. Reactome pathways exhibiting enrichment of proteins from each network were compared across the cancers. Our results show that pathways associated with all three cancers tend to be broad cellular processes required for growth and survival. Significant examples include the nerve growth factor (P = 7.86 × 10(-33)), epidermal growth factor (P = 1.18 × 10(-31)) and fibroblast growth factor (P = 2.47 × 10(-31)) signaling pathways. However, within these shared pathways, the genes that influence risk largely differ by cancer. Pathways found to be unique for a single cancer focus on more specific cellular functions, such as interleukin signaling in lung cancer (P = 1.69 × 10(-15)), apoptosis initiation by Bad in breast cancer (P = 3.14 × 10(-9)) and cellular responses to hypoxia in prostate cancer (P = 2.14 × 10(-9)). We present the largest comparative cross-cancer pathway analysis of GWAS to date. Our approach can also be applied to the study of inherited mechanisms underlying risk across multiple diseases in general.
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Affiliation(s)
- David C Qian
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Jinyoung Byun
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Younghun Han
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Casey S Greene
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John K Field
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool Cancer Research Centre, Liverpool L69 3GA, UK
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Yonathan Brhane
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - John R Mclaughlin
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
| | - Gordon Fehringer
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Maria Teresa Landi
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Albert Rosenberger
- Department of Genetic Epidemiology, University Medical Centre Göttingen, 37099 Göttingen, Germany
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Centre Göttingen, 37099 Göttingen, Germany
| | - Jyoti Malhotra
- Division of Hematology and Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Angela Risch
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Joachim Heinrich
- Institute of Epidemiology I, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - David J Hunter
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Brian E Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Fredrick R Schumacher
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Rosalind A Eeles
- Department of Cancer Genetics, Institute of Cancer Research, London SW7 3RP, UK and
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Daniela Seminara
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christopher I Amos
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA,
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Ramanathan A, Nelson AR, Sagare AP, Zlokovic BV. Impaired vascular-mediated clearance of brain amyloid beta in Alzheimer's disease: the role, regulation and restoration of LRP1. Front Aging Neurosci 2015; 7:136. [PMID: 26236233 PMCID: PMC4502358 DOI: 10.3389/fnagi.2015.00136] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 07/02/2015] [Indexed: 12/12/2022] Open
Abstract
Amyloid beta (Aβ) homeostasis in the brain is governed by its production and clearance mechanisms. An imbalance in this homeostasis results in pathological accumulations of cerebral Aβ, a characteristic of Alzheimer’s disease (AD). While Aβ may be cleared by several physiological mechanisms, a major route of Aβ clearance is the vascular-mediated removal of Aβ from the brain across the blood-brain barrier (BBB). Here, we discuss the role of the predominant Aβ clearance protein—low-density lipoprotein receptor-related protein 1 (LRP1)—in the efflux of Aβ from the brain. We also outline the multiple factors that influence the function of LRP1-mediated Aβ clearance, such as its expression, shedding, structural modification and transcriptional regulation by other genes. Finally, we summarize approaches aimed at restoring LRP1-mediated Aβ clearance from the brain.
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Affiliation(s)
- Anita Ramanathan
- Department of Physiology and Biophysics, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California Los Angeles, CA, USA
| | - Amy R Nelson
- Department of Physiology and Biophysics, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California Los Angeles, CA, USA
| | - Abhay P Sagare
- Department of Physiology and Biophysics, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California Los Angeles, CA, USA
| | - Berislav V Zlokovic
- Department of Physiology and Biophysics, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California Los Angeles, CA, USA
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Zhao Z, Sagare AP, Ma Q, Halliday MR, Kong P, Kisler K, Winkler EA, Ramanathan A, Kanekiyo T, Bu G, Owens NC, Rege SV, Si G, Ahuja A, Zhu D, Miller CA, Schneider JA, Maeda M, Maeda T, Sugawara T, Ichida JK, Zlokovic BV. Central role for PICALM in amyloid-β blood-brain barrier transcytosis and clearance. Nat Neurosci 2015; 18:978-87. [PMID: 26005850 PMCID: PMC4482781 DOI: 10.1038/nn.4025] [Citation(s) in RCA: 310] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 04/21/2015] [Indexed: 12/11/2022]
Abstract
PICALM is a highly validated genetic risk factor for Alzheimer's disease (AD). We found that reduced expression of PICALM in AD and murine brain endothelium correlated with amyloid-β (Aβ) pathology and cognitive impairment. Moreover, Picalm deficiency diminished Aβ clearance across the murine blood-brain barrier (BBB) and accelerated Aβ pathology in a manner that was reversible by endothelial PICALM re-expression. Using human brain endothelial monolayers, we found that PICALM regulated PICALM/clathrin-dependent internalization of Aβ bound to the low density lipoprotein receptor related protein-1, a key Aβ clearance receptor, and guided Aβ trafficking to Rab5 and Rab11, leading to Aβ endothelial transcytosis and clearance. PICALM levels and Aβ clearance were reduced in AD-derived endothelial monolayers, which was reversible by adenoviral-mediated PICALM transfer. Inducible pluripotent stem cell-derived human endothelial cells carrying the rs3851179 protective allele exhibited higher PICALM levels and enhanced Aβ clearance. Thus, PICALM regulates Aβ BBB transcytosis and clearance, which has implications for Aβ brain homeostasis and clearance therapy.
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Affiliation(s)
- Zhen Zhao
- Zilkha Neurogenetic Institute and Department of Physiology and Biophysics, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Abhay P. Sagare
- Zilkha Neurogenetic Institute and Department of Physiology and Biophysics, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Qingyi Ma
- Zilkha Neurogenetic Institute and Department of Physiology and Biophysics, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Matthew R. Halliday
- Zilkha Neurogenetic Institute and Department of Physiology and Biophysics, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Pan Kong
- Zilkha Neurogenetic Institute and Department of Physiology and Biophysics, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Kassandra Kisler
- Zilkha Neurogenetic Institute and Department of Physiology and Biophysics, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Ethan A. Winkler
- Zilkha Neurogenetic Institute and Department of Physiology and Biophysics, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94143, USA
| | - Anita Ramanathan
- Zilkha Neurogenetic Institute and Department of Physiology and Biophysics, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Takahisa Kanekiyo
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Guojun Bu
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Nelly Chuqui Owens
- Zilkha Neurogenetic Institute and Department of Physiology and Biophysics, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Sanket V. Rege
- Zilkha Neurogenetic Institute and Department of Physiology and Biophysics, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Gabriel Si
- Zilkha Neurogenetic Institute and Department of Physiology and Biophysics, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Ashim Ahuja
- Zilkha Neurogenetic Institute and Department of Physiology and Biophysics, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Donghui Zhu
- Department of Chemical, Biological and Bio–Engineering, North Carolina Agricultural and Technical State University, Greensboro, NC 27411, USA
| | - Carol A. Miller
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Julie A. Schneider
- Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL 60612, USA
| | - Manami Maeda
- Division of Hematopoietic Stem Cell and Leukemia Research, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
- Division of Hematology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Takahiro Maeda
- Division of Hematopoietic Stem Cell and Leukemia Research, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
- Division of Hematology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Tohru Sugawara
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, and Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, 1425 San Pablo Street, BCC 307, Los Angeles, CA 90089, USA
| | - Justin K. Ichida
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, and Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, 1425 San Pablo Street, BCC 307, Los Angeles, CA 90089, USA
| | - Berislav V. Zlokovic
- Zilkha Neurogenetic Institute and Department of Physiology and Biophysics, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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Chibnik LB, Yu L, Eaton ML, Srivastava G, Schneider JA, Kellis M, Bennett DA, De Jager PL. Alzheimer's loci: epigenetic associations and interaction with genetic factors. Ann Clin Transl Neurol 2015; 2:636-47. [PMID: 26125039 PMCID: PMC4479524 DOI: 10.1002/acn3.201] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 02/20/2015] [Accepted: 03/06/2015] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE We explore the role of DNA methylation in Alzheimer's disease (AD). To elucidate where DNA methylation falls along the causal pathway linking risk factors to disease, we examine causal models to assess its role in the pathology of AD. METHODS DNA methylation profiles were generated in 740 brain samples using the Illumina HumanMet450K beadset. We focused our analysis on CpG sites from 11 AD susceptibility gene regions. The primary outcome was a quantitative measure of neuritic amyloid plaque (NP), a key early element of AD pathology. We tested four causal models: (1) independent associations, (2) CpG mediating the association of a variant, (3) reverse causality, and (4) genetic variant by CpG interaction. RESULTS Six genes regions (17 CpGs) showed evidence of CpG associations with NP, independent of genetic variation - BIN1 (5), CLU (5), MS4A6A (3), ABCA7 (2), CD2AP (1), and APOE (1). Together they explained 16.8% of the variability in NP. An interaction effect was seen in the CR1 region for two CpGs, cg10021878 (P = 0.01) and cg05922028 (P = 0.001), in relation to NP. In both cases, subjects with the risk allele rs6656401(AT) (/) (AA) display more methylation being associated with more NP burden, whereas subjects with the rs6656401(TT) protective genotype have an inverse association with more methylation being associated with less NP. INTERPRETATION These observations suggest that, within known AD susceptibility loci, methylation is related to pathologic processes of AD and may play a largely independent role by influencing gene expression in AD susceptibility loci.
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Affiliation(s)
- Lori B Chibnik
- Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital Boston, Massachusetts, 02115 ; Department of Neurology, Harvard Medical School Boston, Massachusetts, 02115 ; Medical and Population Genetics, Broad Institute of MIT and Harvard Cambridge, Massachusetts, 02142 ; Department of Epidemiology, Harvard T.H. Chan School of Public Health Boston, Massachusetts, 02115
| | - Lei Yu
- Medical and Population Genetics, Broad Institute of MIT and Harvard Cambridge, Massachusetts, 02142 ; Rush Alzheimer's Disease Center, Rush University Medical Center Chicago, Illinois, 60612
| | - Matthew L Eaton
- Medical and Population Genetics, Broad Institute of MIT and Harvard Cambridge, Massachusetts, 02142 ; Computer Science and Artificial Intelligence Laboratory, MIT Cambridge, Massachusetts, 02124
| | - Gyan Srivastava
- Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital Boston, Massachusetts, 02115 ; Department of Neurology, Harvard Medical School Boston, Massachusetts, 02115 ; Medical and Population Genetics, Broad Institute of MIT and Harvard Cambridge, Massachusetts, 02142
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Rush University Medical Center Chicago, Illinois, 60612
| | - Manolis Kellis
- Medical and Population Genetics, Broad Institute of MIT and Harvard Cambridge, Massachusetts, 02142 ; Computer Science and Artificial Intelligence Laboratory, MIT Cambridge, Massachusetts, 02124
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center Chicago, Illinois, 60612
| | - Philip L De Jager
- Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital Boston, Massachusetts, 02115 ; Department of Neurology, Harvard Medical School Boston, Massachusetts, 02115 ; Medical and Population Genetics, Broad Institute of MIT and Harvard Cambridge, Massachusetts, 02142
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Dominant and Protective Role of the CYTH4 Primate-Specific GTTT-Repeat Longer Alleles Against Neurodegeneration. J Mol Neurosci 2015; 56:593-6. [PMID: 25823437 DOI: 10.1007/s12031-015-0542-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 03/06/2015] [Indexed: 12/25/2022]
Abstract
Primate-specific genes and regulatory mechanisms could provide insight into human brain functioning and disease. In a genome-scale analysis of the entire protein-coding genes listed in the GeneCards database, we have recently reported human genes that contain "exceptionally long" short tandem repeats (STRs) in their core promoter, which may be of adaptive/selective evolutionary advantage in this species. The longest tetra-nucleotide repeat identified in a human gene core promoter belongs to the CYTH4 gene. This GTTT-repeat is specific to Hominidae and Old World monkeys, and the shortest allele of this repeat, (GTTT)6, is linked with neural dysfunction and type I bipolar disorder in human. In the present study, we sought a possibly broader role for the CYTH4 gene core promoter GTTT-repeat in neural functioning and investigated its allelic distribution in a total of 949 human subjects, consisting of two neurodegenerative disorders, multiple sclerosis (MS) (n = 272) and Alzheimer's disease (AD) (n = 257), and controls (n = 420). The range of the alleles of this GTTT-repeat in the human sample studied was between 6- and 9-repeats. The shortest allele, (GTTT)6, was significantly in excess in the MS and AD patients in comparison with the controls (p < 0.004). The 6/6, 6/7, and 7/7 genotypes were in excess in the MS and AD patients, whereas the overall frequency of all other genotypes (consisting of at least one longer allele, i.e., 8- or 9-repeat) was higher in the controls (p < 0.005), indicating a dominant and protective effect for the longer alleles against neurodegeneration. This is the first indication of the involvement of a primate-specific STR in neurodegeneration in humans. We propose an adaptive evolutionary role for the expansion of the CYTH4 gene core promoter GTTT-repeat in the human brain, which is supported by a link between the shortest allele of this repeat with neuropsychiatric disorders.
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Quitadamo A, Tian L, Hall B, Shi X. An integrated network of microRNA and gene expression in ovarian cancer. BMC Bioinformatics 2015; 16 Suppl 5:S5. [PMID: 25860109 PMCID: PMC4402579 DOI: 10.1186/1471-2105-16-s5-s5] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Background Ovarian cancer is a deadly female reproductive cancer. Understanding the biological mechanisms underlying ovarian cancer could help lead to quicker and more accurate diagnosis and more effective treatments. Both changes in microRNA(miRNA) expression and miRNA/mRNA dysregulation have been associated with ovarian cancer. With the availability of whole-genome miRNA and mRNA sequencing we now have new potentials to study these associations. In this study, we performed a comprehensive analysis of miRNA and mRNA expression in ovarian cancer using an integrative network approach combined with association analysis. Results We developed an integrative approach to construct a network that illustrates the complex interplay among miRNA and gene expression from a systems perspective. Our method is composed of expanding networks from eQTL associations, building network associations in eQTL analysis, and then combine the networks into an integrated network. This integrated network takes account of miRNA expression quantitative trait loci (eQTL) associations, miRNAs and their targets, protein-protein interactions, co-expressions among miRNAs and genes respectively. Applied to the ovarian cancer data set from The Cancer Genome Atlas (TCGA), we created an integrated network with 167 nodes containing 108 miRNA-target interactions and 145 from protein-protein interactions, starting from 44 initial eQTLs. This integrated network encompassed 26 genes and 14 miRNAs associated with cancer. In particular, 11 genes and 12 miRNAs in the integrated network are associated with ovarian cancer. Conclusion We demonstrated an integrated network approach that integrates multiple data sources at a systems level. We applied this approach to the TCGA ovarian cancer dataset, and constructed a network that provided a more inclusive view of miRNA and gene expression in ovarian cancer. This network included four separate types of interactions among miRNAs and genes. Simply analyzing each interaction component in isolation, such as the eQTL associations, the miRNA-target interactions or the protein-protein interactions, would create a much more limited network than the integrated one.
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Tan MS, Jiang T, Tan L, Yu JT. Genome-wide association studies in neurology. ANNALS OF TRANSLATIONAL MEDICINE 2015; 2:124. [PMID: 25568877 DOI: 10.3978/j.issn.2305-5839.2014.11.12] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Accepted: 03/04/2013] [Indexed: 12/11/2022]
Abstract
Genome-wide association studies (GWAS) are a powerful tool for understanding the genetic underpinnings of human disease. In this article, we briefly review the role and findings of GWAS in common neurological diseases, including Stroke, Alzheimer's disease, Parkinson's disease, epilepsy, multiple sclerosis, migraine, amyotrophic lateral sclerosis, frontotemporal lobar degeneration, restless legs syndrome, intracranial aneurysm, human prion diseases and moyamoya disease. We then discuss the present and future implications of these findings with regards to disease prediction, uncovering basic biology, and the development of potential therapeutic agents.
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Affiliation(s)
- Meng-Shan Tan
- 1 College of Medicine and Pharmaceutics, Ocean University of China, Qingdao 266071, China ; 2 Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, Qingdao 266071, China ; 3 Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao 266071, China
| | - Teng Jiang
- 1 College of Medicine and Pharmaceutics, Ocean University of China, Qingdao 266071, China ; 2 Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, Qingdao 266071, China ; 3 Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao 266071, China
| | - Lan Tan
- 1 College of Medicine and Pharmaceutics, Ocean University of China, Qingdao 266071, China ; 2 Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, Qingdao 266071, China ; 3 Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao 266071, China
| | - Jin-Tai Yu
- 1 College of Medicine and Pharmaceutics, Ocean University of China, Qingdao 266071, China ; 2 Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, Qingdao 266071, China ; 3 Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao 266071, China
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Venturini L, Perna S, Sardi F, Faliva M, Cavagna P, Bernardinelli L, Ricevuti G, Rondanelli M. Alzheimer's Disease: From Genes to Nutrition. EUR J INFLAMM 2014. [DOI: 10.1177/1721727x1401200301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Alzheimer's disease (AD) is widely identified as the most common cause of sporadic dementia. Its aetiology is still debated, as despite several hypotheses, different factors seem to play a role in its establishment and development. Recent studies have proposed a possible preventing role of nutrition. The weight loss typical of earlier phase of disease and the finding of malnutrition as a common trait between patients leads to hypothesize that a supplementation of specific nutrients seems to be useful and effective in terms of improvement of cognitive functions. Malnourished patients show also altered parameters when investigating inflammation markers: for example, hyperhomocysteinemia is a typical finding in elderly affected by dementia, and it can be prevented and corrected by using a proper nutrients supplementation. Pro-inflammatory state can be reduced with supplementation of polyunsaturated fatty acids, vitamins of the group B and phosphatidylserine, that can act reducing IL-1β (pro-inflammatory cytokine) and improving IL-10 (anti-inflammatory cytokine) synthesis. While investigating the role of nutrition, it seems to be deeply linked with genetic; a genetic onset AD-related could be latent and can be influenced by nutritional attitude. AD can be considered a sort of latent clinical condition that would disclose or not, depending also on micro-environment and nutritional parameters. The genetic expression can be influenced by assumptions or not of specific nutrients, with the promotion of different pro- or anti-inflammatory settings. The specific role of each micronutrient (in particular vitamins) and trace elements still needs to be punctuated, as they are involved in a pool of different reactions. Also genes acts not independently but in an interconnected pattern, in which the role of a single gene needs to be cleared, depending on others. This complex system of predisposing conditions and a possible role of nutrition as modulator of the inflammatory state is the object of this review.
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Affiliation(s)
- L. Venturini
- Department of Internal Medicine, Therapeutics, Cellular Phatophysiology and Clinical Immunology Laboratory, Azienda di Servizi alla Persona di Pavia, University of Pavia, Italy
| | - S. Perna
- Department of Public Health, Neuroscience, Experimental and Forensic Medicine, Section of Human Nutrition and Dietetics, Azienda di Servizi alla Persona di Pavia, University of Pavia, Italy
| | - F. Sardi
- Department of Internal Medicine, Therapeutics, Cellular Phatophysiology and Clinical Immunology Laboratory, Azienda di Servizi alla Persona di Pavia, University of Pavia, Italy
| | - M.A. Faliva
- Department of Public Health, Neuroscience, Experimental and Forensic Medicine, Section of Human Nutrition and Dietetics, Azienda di Servizi alla Persona di Pavia, University of Pavia, Italy
| | - P. Cavagna
- DSSAP Department of Applied and Phychic Behavioural Sciences, University of Pavia, Italy
| | - L. Bernardinelli
- DSSAP Department of Applied and Phychic Behavioural Sciences, University of Pavia, Italy
- Statistical Laboratory, Centre for Mathematical Sciences, University of Cambridge, Cambridge, UK
| | - G. Ricevuti
- Department of Internal Medicine, Therapeutics, Cellular Phatophysiology and Clinical Immunology Laboratory, Azienda di Servizi alla Persona di Pavia, University of Pavia, Italy
| | - M. Rondanelli
- Department of Public Health, Neuroscience, Experimental and Forensic Medicine, Section of Human Nutrition and Dietetics, Azienda di Servizi alla Persona di Pavia, University of Pavia, Italy
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De Jager PL, Srivastava G, Lunnon K, Burgess J, Schalkwyk LC, Yu L, Eaton ML, Keenan BT, Ernst J, McCabe C, Tang A, Raj T, Replogle J, Brodeur W, Gabriel S, Chai HS, Younkin C, Younkin SG, Zou F, Szyf M, Epstein CB, Schneider JA, Bernstein BE, Meissner A, Ertekin-Taner N, Chibnik LB, Kellis M, Mill J, Bennett DA. Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci. Nat Neurosci 2014; 17:1156-63. [PMID: 25129075 PMCID: PMC4292795 DOI: 10.1038/nn.3786] [Citation(s) in RCA: 638] [Impact Index Per Article: 63.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 07/16/2014] [Indexed: 02/07/2023]
Abstract
We used a collection of 708 prospectively collected autopsied brains to assess the methylation state of the brain's DNA in relation to Alzheimer's disease (AD). We found that the level of methylation at 71 of the 415,848 interrogated CpGs was significantly associated with the burden of AD pathology, including CpGs in the ABCA7 and BIN1 regions, which harbor known AD susceptibility variants. We validated 11 of the differentially methylated regions in an independent set of 117 subjects. Furthermore, we functionally validated these CpG associations and identified the nearby genes whose RNA expression was altered in AD: ANK1, CDH23, DIP2A, RHBDF2, RPL13, SERPINF1 and SERPINF2. Our analyses suggest that these DNA methylation changes may have a role in the onset of AD given that we observed them in presymptomatic subjects and that six of the validated genes connect to a known AD susceptibility gene network.
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Affiliation(s)
- PL De Jager
- Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital, 77 Avenue Louis Pasteur, NRB168, Boston, MA 02115
- Harvard Medical School, Boston, MA 02115
- Program in Medical and Population Genetics, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142
| | - G Srivastava
- Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital, 77 Avenue Louis Pasteur, NRB168, Boston, MA 02115
- Program in Medical and Population Genetics, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142
| | - K Lunnon
- University of Exeter Medical School, University of Exeter, RILD (Level 4), Barrack Rd, Exeter, UK
- Institute of Psychiatry, King's College London, De Crespigny Park, Denmark Hill, London. SE5 8AF. UK
| | - J Burgess
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224
- Department of Neurology, Mayo Clinic, Jacksonville, FL 32224
| | - LC Schalkwyk
- University of Exeter Medical School, University of Exeter, RILD (Level 4), Barrack Rd, Exeter, UK
- Institute of Psychiatry, King's College London, De Crespigny Park, Denmark Hill, London. SE5 8AF. UK
| | - L Yu
- Rush Alzheimer's Disease Center, Rush University Medical Center, 600 S Paulina St., Chicago, IL 60612; Computer Science and Artificial Intelligence Laboratory (CSAIL), Massachusetts Institute of Technology, 32 Vassar St., Cambridge, MA 02139
| | - ML Eaton
- Program in Medical and Population Genetics, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142
- Genetic Analysis Platform, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142
| | - BT Keenan
- Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital, 77 Avenue Louis Pasteur, NRB168, Boston, MA 02115
- Program in Medical and Population Genetics, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142
| | - J Ernst
- Program in Medical and Population Genetics, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142
- Genetic Analysis Platform, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142
| | - C McCabe
- Program in Medical and Population Genetics, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142
| | - A Tang
- Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital, 77 Avenue Louis Pasteur, NRB168, Boston, MA 02115
| | - T Raj
- Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital, 77 Avenue Louis Pasteur, NRB168, Boston, MA 02115
- Harvard Medical School, Boston, MA 02115
- Program in Medical and Population Genetics, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142
| | - J Replogle
- Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital, 77 Avenue Louis Pasteur, NRB168, Boston, MA 02115
- Harvard Medical School, Boston, MA 02115
- Program in Medical and Population Genetics, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142
| | - W Brodeur
- Genetic Analysis Platform, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142
| | - S Gabriel
- Genetic Analysis Platform, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142
| | - HS Chai
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224
- Department of Neurology, Mayo Clinic, Jacksonville, FL 32224
| | - C Younkin
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224
| | - SG Younkin
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224
| | - F Zou
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224
| | - M Szyf
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Québec, H3G 1Y6
| | - CB Epstein
- Epigenomics Program, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142
| | - JA Schneider
- Rush Alzheimer's Disease Center, Rush University Medical Center, 600 S Paulina St., Chicago, IL 60612; Computer Science and Artificial Intelligence Laboratory (CSAIL), Massachusetts Institute of Technology, 32 Vassar St., Cambridge, MA 02139
| | - BE Bernstein
- Harvard Medical School, Boston, MA 02115
- Epigenomics Program, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142
- Department of Pathology, Massachusetts General Hospital, 185 Cambridge St., Boston, MA 02114
| | - A Meissner
- Genetic Analysis Platform, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142
- Harvard Stem Cell Institute, Harvard University, 1350 Massachusetts Ave., Cambridge MA 02138
| | - N Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224
- Department of Neurology, Mayo Clinic, Jacksonville, FL 32224
| | - LB Chibnik
- Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital, 77 Avenue Louis Pasteur, NRB168, Boston, MA 02115
- Harvard Medical School, Boston, MA 02115
- Program in Medical and Population Genetics, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142
| | - M Kellis
- Program in Medical and Population Genetics, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142
- Genetic Analysis Platform, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142
| | - J Mill
- University of Exeter Medical School, University of Exeter, RILD (Level 4), Barrack Rd, Exeter, UK
- Institute of Psychiatry, King's College London, De Crespigny Park, Denmark Hill, London. SE5 8AF. UK
| | - DA Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, 600 S Paulina St., Chicago, IL 60612; Computer Science and Artificial Intelligence Laboratory (CSAIL), Massachusetts Institute of Technology, 32 Vassar St., Cambridge, MA 02139
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Sironi M, Biasin M, Cagliani R, Gnudi F, Saulle I, Ibba S, Filippi G, Yahyaei S, Tresoldi C, Riva S, Trabattoni D, De Gioia L, Lo Caputo S, Mazzotta F, Forni D, Pontremoli C, Pineda JA, Pozzoli U, Rivero-Juarez A, Caruz A, Clerici M. Evolutionary analysis identifies an MX2 haplotype associated with natural resistance to HIV-1 infection. Mol Biol Evol 2014; 31:2402-14. [PMID: 24930137 DOI: 10.1093/molbev/msu193] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The protein product of the myxovirus resistance 2 (MX2) gene restricts HIV-1 and simian retroviruses. We demonstrate that MX2 evolved adaptively in mammals with distinct sites representing selection targets in distinct branches; selection mainly involved residues in loop 4, previously shown to carry antiviral determinants. Modeling data indicated that positively selected sites form a continuous surface on loop 4, which folds into two antiparallel α-helices protruding from the stalk domain. A population genetics-phylogenetics approach indicated that the coding region of MX2 mainly evolved under negative selection in the human lineage. Nonetheless, population genetic analyses demonstrated that natural selection operated on MX2 during the recent history of human populations: distinct selective events drove the frequency increase of two haplotypes in the populations of Asian and European ancestry. The Asian haplotype carries a susceptibility allele for melanoma; the European haplotype is tagged by rs2074560, an intronic variant. Analyses performed on three independent European cohorts of HIV-1-exposed seronegative individuals with different geographic origin and distinct exposure route showed that the ancestral (G) allele of rs2074560 protects from HIV-1 infection with a recessive effect (combined P = 1.55 × 10(-4)). The same allele is associated with lower in vitro HIV-1 replication and increases MX2 expression levels in response to IFN-α. Data herein exploit evolutionary information to identify a novel host determinant of HIV-1 infection susceptibility.
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Affiliation(s)
- Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Mara Biasin
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Federica Gnudi
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Irma Saulle
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Salomè Ibba
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Giulia Filippi
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Milan, Italy
| | - Sarah Yahyaei
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Claudia Tresoldi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Stefania Riva
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Daria Trabattoni
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Luca De Gioia
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Milan, Italy
| | | | | | - Diego Forni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Chiara Pontremoli
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Juan Antonio Pineda
- Infectious Diseases and Microbiology Clinical Unit, Valme Hospital, Seville, Spain
| | - Uberto Pozzoli
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Antonio Rivero-Juarez
- Maimonides Institut for Biomedical Research (IMIBIC), Reina Sofia Universitary Hospital, University of Cordoba, Cordoba, Spain
| | - Antonio Caruz
- Immunogenetics Unit, Department of Experimental Biology, University of Jaen, Jaen, Spain
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, Milan, ItalyDon C. Gnocchi Foundation ONLUS, IRCCS, Milan, Italy
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Fumagalli M, Sironi M. Human genome variability, natural selection and infectious diseases. Curr Opin Immunol 2014; 30:9-16. [PMID: 24880709 DOI: 10.1016/j.coi.2014.05.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Revised: 04/29/2014] [Accepted: 05/02/2014] [Indexed: 01/04/2023]
Abstract
The recent availability of large-scale sequencing DNA data allowed researchers to investigate how genomic variation is distributed among populations. While demographic factors explain genome-wide population genetic diversity levels, scans for signatures of natural selection pinpointed several regions under non-neutral evolution. Recent studies found an enrichment of immune-related genes subjected to natural selection, suggesting that pathogens and infectious diseases have imposed a strong selective pressure throughout human history. Pathogen-mediated selection often targeted regulatory sites of genes belonging to the same biological pathway. Results from these studies have the potential to identify mutations that modulate infection susceptibility by integrating a population genomic approach with molecular immunology data and large-scale functional annotations.
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Affiliation(s)
- Matteo Fumagalli
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, United Kingdom.
| | - Manuela Sironi
- Bioinformatics - Scientific Institute IRCCS E.MEDEA, 23842 Bosisio Parini, Italy
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Bennett DA, Yu L, De Jager PL. Building a pipeline to discover and validate novel therapeutic targets and lead compounds for Alzheimer's disease. Biochem Pharmacol 2014; 88:617-30. [PMID: 24508835 PMCID: PMC4054869 DOI: 10.1016/j.bcp.2014.01.037] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 01/18/2014] [Accepted: 01/24/2014] [Indexed: 01/11/2023]
Abstract
Cognitive decline, Alzheimer's disease (AD) and other causes are major public health problems worldwide. With changing demographics, the number of persons with dementia will increase rapidly. The treatment and prevention of AD and other dementias, therefore, is an urgent unmet need. There have been considerable advances in understanding the biology of many age-related disorders that cause dementia. Gains in understanding AD have led to the development of ante-mortem biomarkers of traditional neuropathology and the conduct of several phase III interventions in the amyloid-β cascade early in the disease process. Many other intervention strategies are in various stages of development. However, efforts to date have met with limited success. A recent National Institute on Aging Research Summit led to a number of requests for applications. One was to establish multi-disciplinary teams of investigators who use systems biology approaches and stem cell technology to identify a new generation of AD targets. We were recently awarded one of three such grants to build a pipeline that integrates epidemiology, systems biology, and stem cell technology to discover and validate novel therapeutic targets and lead compounds for AD treatment and prevention. Here we describe the two cohorts that provide the data and biospecimens being exploited for our pipeline and describe the available unique datasets. Second, we present evidence in support of a chronic disease model of AD that informs our choice of phenotypes as the target outcome. Third, we provide an overview of our approach. Finally, we present the details of our planned drug discovery pipeline.
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Affiliation(s)
- David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, United States.
| | - Lei Yu
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, United States.
| | - Philip L De Jager
- Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, United States.
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Talwar P, Silla Y, Grover S, Gupta M, Agarwal R, Kushwaha S, Kukreti R. Genomic convergence and network analysis approach to identify candidate genes in Alzheimer's disease. BMC Genomics 2014; 15:199. [PMID: 24628925 PMCID: PMC4028079 DOI: 10.1186/1471-2164-15-199] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 02/21/2014] [Indexed: 01/28/2023] Open
Abstract
Background Alzheimer’s disease (AD) is one of the leading genetically complex and heterogeneous disorder that is influenced by both genetic and environmental factors. The underlying risk factors remain largely unclear for this heterogeneous disorder. In recent years, high throughput methodologies, such as genome-wide linkage analysis (GWL), genome-wide association (GWA) studies, and genome-wide expression profiling (GWE), have led to the identification of several candidate genes associated with AD. However, due to lack of consistency within their findings, an integrative approach is warranted. Here, we have designed a rank based gene prioritization approach involving convergent analysis of multi-dimensional data and protein-protein interaction (PPI) network modelling. Results Our approach employs integration of three different AD datasets- GWL,GWA and GWE to identify overlapping candidate genes ranked using a novel cumulative rank score (SR) based method followed by prioritization using clusters derived from PPI network. SR for each gene is calculated by addition of rank assigned to individual gene based on either p value or score in three datasets. This analysis yielded 108 plausible AD genes. Network modelling by creating PPI using proteins encoded by these genes and their direct interactors resulted in a layered network of 640 proteins. Clustering of these proteins further helped us in identifying 6 significant clusters with 7 proteins (EGFR, ACTB, CDC2, IRAK1, APOE, ABCA1 and AMPH) forming the central hub nodes. Functional annotation of 108 genes revealed their role in several biological activities such as neurogenesis, regulation of MAP kinase activity, response to calcium ion, endocytosis paralleling the AD specific attributes. Finally, 3 potential biochemical biomarkers were found from the overlap of 108 AD proteins with proteins from CSF and plasma proteome. EGFR and ACTB were found to be the two most significant AD risk genes. Conclusions With the assumption that common genetic signals obtained from different methodological platforms might serve as robust AD risk markers than candidates identified using single dimension approach, here we demonstrated an integrated genomic convergence approach for disease candidate gene prioritization from heterogeneous data sources linked to AD. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-199) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | - Ritushree Kukreti
- Genomics and Molecular Medicine Unit, Institute of Genomics and Integrative Biology (IGIB), Council of Scientific and Industrial Research (CSIR), Mall Road, Delhi 110 007, India.
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Amphiphysin 2 (BIN1) in physiology and diseases. J Mol Med (Berl) 2014; 92:453-63. [DOI: 10.1007/s00109-014-1138-1] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 02/11/2014] [Accepted: 02/17/2014] [Indexed: 12/15/2022]
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Jia P, Zhao Z. Network.assisted analysis to prioritize GWAS results: principles, methods and perspectives. Hum Genet 2014; 133:125-38. [PMID: 24122152 PMCID: PMC3943795 DOI: 10.1007/s00439-013-1377-1] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2012] [Accepted: 10/03/2013] [Indexed: 01/24/2023]
Abstract
Genome-wide association studies (GWAS) have rapidly become a powerful tool in genetic studies of complex diseases and traits. Traditionally, single marker-based tests have been used prevalently in GWAS and have uncovered tens of thousands of disease-associated SNPs. Network-assisted analysis (NAA) of GWAS data is an emerging area in which network-related approaches are developed and utilized to perform advanced analyses of GWAS data in order to study various human diseases or traits. Progress has been made in both methodology development and applications of NAA in GWAS data, and it has already been demonstrated that NAA results may enhance our interpretation and prioritization of candidate genes and markers. Inspired by the strong interest in and high demand for advanced GWAS data analysis, in this review article, we discuss the methodologies and strategies that have been reported for the NAA of GWAS data. Many NAA approaches search for subnetworks and assess the combined effects of multiple genes participating in the resultant subnetworks through a gene set analysis. With no restriction to pre-defined canonical pathways, NAA has the advantage of defining subnetworks with the guidance of the GWAS data under investigation. In addition, some NAA methods prioritize genes from GWAS data based on their interconnections in the reference network. Here, we summarize NAA applications to various diseases and discuss the available options and potential caveats related to their practical usage. Additionally, we provide perspectives regarding this rapidly growing research area.
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