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Guo S, Yang J. Bayesian genome-wide TWAS with reference transcriptomic data of brain and blood tissues identified 141 risk genes for Alzheimer's disease dementia. Alzheimers Res Ther 2024; 16:120. [PMID: 38824563 PMCID: PMC11144322 DOI: 10.1186/s13195-024-01488-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 05/27/2024] [Indexed: 06/03/2024]
Abstract
BACKGROUND Transcriptome-wide association study (TWAS) is an influential tool for identifying genes associated with complex diseases whose genetic effects are likely mediated through transcriptome. TWAS utilizes reference genetic and transcriptomic data to estimate effect sizes of genetic variants on gene expression (i.e., effect sizes of a broad sense of expression quantitative trait loci, eQTL). These estimated effect sizes are employed as variant weights in gene-based association tests, facilitating the mapping of risk genes with genome-wide association study (GWAS) data. However, most existing TWAS of Alzheimer's disease (AD) dementia are limited to studying only cis-eQTL proximal to the test gene. To overcome this limitation, we applied the Bayesian Genome-wide TWAS (BGW-TWAS) method to leveraging both cis- and trans- eQTL of brain and blood tissues, in order to enhance mapping risk genes for AD dementia. METHODS We first applied BGW-TWAS to the Genotype-Tissue Expression (GTEx) V8 dataset to estimate cis- and trans- eQTL effect sizes of the prefrontal cortex, cortex, and whole blood tissues. Estimated eQTL effect sizes were integrated with the summary data of the most recent GWAS of AD dementia to obtain BGW-TWAS (i.e., gene-based association test) p-values of AD dementia per gene per tissue type. Then we used the aggregated Cauchy association test to combine TWAS p-values across three tissues to obtain omnibus TWAS p-values per gene. RESULTS We identified 85 significant genes in prefrontal cortex, 82 in cortex, and 76 in whole blood that were significantly associated with AD dementia. By combining BGW-TWAS p-values across these three tissues, we obtained 141 significant risk genes including 34 genes primarily due to trans-eQTL and 35 mapped risk genes in GWAS Catalog. With these 141 significant risk genes, we detected functional clusters comprised of both known mapped GWAS risk genes of AD in GWAS Catalog and our identified TWAS risk genes by protein-protein interaction network analysis, as well as several enriched phenotypes related to AD. CONCLUSION We applied BGW-TWAS and aggregated Cauchy test methods to integrate both cis- and trans- eQTL data of brain and blood tissues with GWAS summary data, identifying 141 TWAS risk genes of AD dementia. These identified risk genes provide novel insights into the underlying biological mechanisms of AD dementia and potential gene targets for therapeutics development.
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Affiliation(s)
- Shuyi Guo
- Center for Computational and Quantitative Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Biostatistics and Data Science, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Jingjing Yang
- Center for Computational and Quantitative Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
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2
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Tumenbayar BI, Tutino VM, Brazzo JA, Yao P, Bae Y. FAK and p130Cas modulate stiffness-mediated early transcription and cellular metabolism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.15.575789. [PMID: 38293187 PMCID: PMC10827115 DOI: 10.1101/2024.01.15.575789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Cellular metabolism is influenced by the stiffness of the extracellular matrix. Focal adhesion kinase (FAK) and its binding partner, p130Cas, transmit biomechanical signals about substrate stiffness to the cell to regulate a variety of cellular responses, but their roles in early transcriptional and metabolic responses remain largely unexplored. We cultured mouse embryonic fibroblasts with or without siRNA-mediated FAK or p130Cas knockdown and assessed the early transcriptional responses of these cells to placement on soft and stiff substrates by RNA sequencing and bioinformatics analyses. Exposure to the stiff ECM altered the expression of genes important for metabolic and biosynthetic processes, and these responses were influenced by knockdown of FAK and p130Cas. Our findings reveal that FAK-p130Cas signaling mechanotransduces ECM stiffness to early transcriptional changes that alter cellular metabolism and biosynthesis.
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Affiliation(s)
- Bat-Ider Tumenbayar
- Department of Pharmacology and Toxicology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA
| | - Vincent M. Tutino
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA
- Department of Biomedical Engineering, School of Engineering and Applied Sciences, University at Buffalo, Buffalo, NY 14260, USA
- Department of Neurosurgery, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA
| | - Joseph A. Brazzo
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA
| | - Peng Yao
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Yongho Bae
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA
- Department of Biomedical Engineering, School of Engineering and Applied Sciences, University at Buffalo, Buffalo, NY 14260, USA
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3
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Llaurador-Coll M, Rios S, García-Gavilán JF, Babio N, Vilella E, Salas-Salvadó J. Plasma levels of neurology-related proteins are associated with cognitive performance in an older population with overweight/obesity and metabolic syndrome. GeroScience 2023; 45:2457-2470. [PMID: 36964401 PMCID: PMC10651568 DOI: 10.1007/s11357-023-00764-y] [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: 10/04/2022] [Accepted: 01/17/2023] [Indexed: 03/26/2023] Open
Abstract
Cognitive impairment is present in a broad spectrum of medical conditions and in aging. Here, we aimed to identify plasma proteins related to cognitive function in a sample of older adults with overweight/obesity and metabolic syndrome. A total of 129 subjects (mean age 64.7 years; 36% females) were grouped according to low (l-GCF, N=65) or high (h-GCF, N=64) global cognitive function and matched according to education, sex, age, and body mass index. Cognitive performance was assessed using neuropsychological tests. Plasma levels of 92 neurology-related proteins were assessed using a proximity extension assay. An elastic net regression analysis was used to identify proteins more associated with cognitive performance. Additionally, the protein expression levels were compared between the two groups by means of a t-test with false discovery rate correction. Pearson correlations were used to assess associations between the protein levels and scores from the neurocognitive tests. Six proteins (alpha-2-MRAP, HAGH, Siglec-9, MDGA1, IL12, and EDA2R) were identified as potential contributors to cognitive performance, remaining significantly increased in l-GCF compared to h-GCF participants after correction for multiple testing. Negative correlations (r= -0.23 to -0.18, i.e., lower protein levels, higher cognitive function) were found between global cognitive function and Siglec-9, NMNAT1, HAGH, LXN, gal-8, alpha-2-MRAP, IL12, PDGF-R-alpha, NAAA, EDA2R, CLEC1B, and LAT. Mini-mental state examination z scores showed the strongest correlations with protein levels, specifically negative correlations with CLEC1b, LXN, LAT, PLXNB3, NMNAT1, gal-8, HAGH, NAAA, CTSS, EZR, KYNU, MANF (r=-0.38 to -0.26) and a positive correlation with ADAM23 (r= 0.26). In summary, we identified several plasma proteins that were significantly associated with cognitive performance in older adults with obesity and metabolic syndrome, although further research is needed to replicate the results in larger samples and to include a predictive perspective.
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Affiliation(s)
- Martí Llaurador-Coll
- Universitat Rovira i Virgili, Departament de Medicina i Cirurgia, Reus, Spain
- Hospital Universitari Institut Pere Mata, Reus, Spain
- Institut d'Investigació Sanitària Pere Virgili-CERCA, Reus, Spain
| | - Santiago Rios
- Institut d'Investigació Sanitària Pere Virgili-CERCA, Reus, Spain
- Universitat Rovira i Virgili, Departament de Bioquímica i Biotecnologia, Alimentació, Nutrició, Desenvolupament i Salut Mental ANUT-DSM, Reus, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
| | - Jesus F García-Gavilán
- Institut d'Investigació Sanitària Pere Virgili-CERCA, Reus, Spain
- Universitat Rovira i Virgili, Departament de Bioquímica i Biotecnologia, Alimentació, Nutrició, Desenvolupament i Salut Mental ANUT-DSM, Reus, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
| | - Nancy Babio
- Institut d'Investigació Sanitària Pere Virgili-CERCA, Reus, Spain
- Universitat Rovira i Virgili, Departament de Bioquímica i Biotecnologia, Alimentació, Nutrició, Desenvolupament i Salut Mental ANUT-DSM, Reus, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
| | - Elisabet Vilella
- Universitat Rovira i Virgili, Departament de Medicina i Cirurgia, Reus, Spain.
- Hospital Universitari Institut Pere Mata, Reus, Spain.
- Institut d'Investigació Sanitària Pere Virgili-CERCA, Reus, Spain.
- Centro de Investigación Biomédica en Red de Salud Mental, Instituto de Salud Carlos III, Madrid, Spain.
| | - Jordi Salas-Salvadó
- Institut d'Investigació Sanitària Pere Virgili-CERCA, Reus, Spain.
- Universitat Rovira i Virgili, Departament de Bioquímica i Biotecnologia, Alimentació, Nutrició, Desenvolupament i Salut Mental ANUT-DSM, Reus, Spain.
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain.
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Cheng F, Li W, Ji Z, Li J, Hu W, Zhao M, Yu D, Simayijiang H, Yan J. Estimation of bloodstain deposition time within a 24-h day-night cycle with rhythmic mRNA based on a machine learning algorithm. Forensic Sci Int Genet 2023; 66:102910. [PMID: 37406538 DOI: 10.1016/j.fsigen.2023.102910] [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: 12/06/2022] [Revised: 04/15/2023] [Accepted: 06/22/2023] [Indexed: 07/07/2023]
Abstract
Estimating the time that bloodstains are left at a crime scene can provide invaluable evidence for law enforcement investigations, including determining the time of the crime, linking the perpetrator to the crime scene, narrowing the pool of possible suspects, and verifying witness statements. There have been some attempts to estimate the time since deposition of bloodstains, i.e., how much time has passed since the bloodstain was left at a crime scene. However, most studies focus on the time interval of days. As far as we know, previous study have been conducted to estimate the deposition time of blood within a 24-h day-night cycle. To date, there is a lack of studies on whether rhythmic mRNA of blood is suitable for bloodstain samples. In this study, we estimated the bloodstain deposition time within a 24-h day-night cycle based on the expression of messenger RNAs (mRNAs) by real-time quantitative polymerase chain reaction. Bloodstain samples were prepared from eight individuals at eight time points under real and uncontrolled conditions. Four mRNAs expressed rhythmically and were used to construct a regression model using the k-nearest neighbor (KNN) algorithm, resulting in a mean absolute error of 3.92 h. Overall, using the rhythmic mRNAs, a machine learning model was developed which has allowed us to predict the deposition time of bloodstains within the 24-h day-night cycle in East Asian populations. This study demonstrates that mRNA biomarkers can be used to estimate the bloodstain deposition time within a 24-h period. Furthermore, rhythmic mRNA biomarkers provide a potential method and perspective for estimating the deposition time of forensic traces in forensic investigation. Case samples in forensic analysis are usually limited or degraded, so the stability and sensitivity of rhythmic biomarkers need to be further investigated.
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Affiliation(s)
- Feng Cheng
- School of Forensic Medicine, Shanxi Medical University, Taiyuan 030009, Shanxi, PR China
| | - Wanting Li
- School of Forensic Medicine, Shanxi Medical University, Taiyuan 030009, Shanxi, PR China
| | - Zhimin Ji
- School of Forensic Medicine, Shanxi Medical University, Taiyuan 030009, Shanxi, PR China
| | - Junli Li
- School of Forensic Medicine, Shanxi Medical University, Taiyuan 030009, Shanxi, PR China
| | - Wenjing Hu
- School of Forensic Medicine, Shanxi Medical University, Taiyuan 030009, Shanxi, PR China
| | - Mengyang Zhao
- School of Forensic Medicine, Shanxi Medical University, Taiyuan 030009, Shanxi, PR China
| | - Daijing Yu
- School of Forensic Medicine, Shanxi Medical University, Taiyuan 030009, Shanxi, PR China
| | - Halimureti Simayijiang
- School of Forensic Medicine, Shanxi Medical University, Taiyuan 030009, Shanxi, PR China.
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Taiyuan 030009, Shanxi, PR China.
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5
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Bhardwaj A, Liyanage SI, Weaver DF. Cancer and Alzheimer's Inverse Correlation: an Immunogenetic Analysis. Mol Neurobiol 2023; 60:3086-3099. [PMID: 36797545 DOI: 10.1007/s12035-023-03260-8] [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: 12/06/2022] [Accepted: 02/05/2023] [Indexed: 02/18/2023]
Abstract
Numerous studies have demonstrated an inverse link between cancer and Alzheimer's disease (AD), with data suggesting that people with Alzheimer's have a decreased risk of cancer and vice versa. Although other studies have investigated mechanisms to explain this relationship, the connection between these two diseases remains largely unexplained. Processes seen in cancer, such as decreased apoptosis and increased cell proliferation, seem to be reversed in AD. Given the need for effective therapeutic strategies for AD, comparisons with cancer could yield valuable insights into the disease process and perhaps result in new treatments. Here, through a review of existing literature, we compared the expressions of genes involved in cell proliferation and apoptosis to establish a genetic basis for the reciprocal association between AD and cancer. We discuss an array of genes involved in the aforementioned processes, their relevance to both diseases, and how changes in those genes produce varying effects in either disease.
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Affiliation(s)
- Aditya Bhardwaj
- Krembil Discovery Tower, Krembil Brain Institute, Toronto Western Hospital, University Health Network, 60 Leonard Avenue, Toronto, ON, M5T 0S8, Canada
| | - S Imindu Liyanage
- Krembil Discovery Tower, Krembil Brain Institute, Toronto Western Hospital, University Health Network, 60 Leonard Avenue, Toronto, ON, M5T 0S8, Canada
| | - Donald F Weaver
- Krembil Discovery Tower, Krembil Brain Institute, Toronto Western Hospital, University Health Network, 60 Leonard Avenue, Toronto, ON, M5T 0S8, Canada.
- Departments of Medicine and Chemistry, University of Toronto, Toronto, Canada.
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6
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Sharp FR, DeCarli CS, Jin LW, Zhan X. White matter injury, cholesterol dysmetabolism, and APP/Abeta dysmetabolism interact to produce Alzheimer's disease (AD) neuropathology: A hypothesis and review. Front Aging Neurosci 2023; 15:1096206. [PMID: 36845656 PMCID: PMC9950279 DOI: 10.3389/fnagi.2023.1096206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/30/2023] [Indexed: 02/12/2023] Open
Abstract
We postulate that myelin injury contributes to cholesterol release from myelin and cholesterol dysmetabolism which contributes to Abeta dysmetabolism, and combined with genetic and AD risk factors, leads to increased Abeta and amyloid plaques. Increased Abeta damages myelin to form a vicious injury cycle. Thus, white matter injury, cholesterol dysmetabolism and Abeta dysmetabolism interact to produce or worsen AD neuropathology. The amyloid cascade is the leading hypothesis for the cause of Alzheimer's disease (AD). The failure of clinical trials based on this hypothesis has raised other possibilities. Even with a possible new success (Lecanemab), it is not clear whether this is a cause or a result of the disease. With the discovery in 1993 that the apolipoprotein E type 4 allele (APOE4) was the major risk factor for sporadic, late-onset AD (LOAD), there has been increasing interest in cholesterol in AD since APOE is a major cholesterol transporter. Recent studies show that cholesterol metabolism is intricately involved with Abeta (Aβ)/amyloid transport and metabolism, with cholesterol down-regulating the Aβ LRP1 transporter and upregulating the Aβ RAGE receptor, both of which would increase brain Aβ. Moreover, manipulating cholesterol transport and metabolism in rodent AD models can ameliorate pathology and cognitive deficits, or worsen them depending upon the manipulation. Though white matter (WM) injury has been noted in AD brain since Alzheimer's initial observations, recent studies have shown abnormal white matter in every AD brain. Moreover, there is age-related WM injury in normal individuals that occurs earlier and is worse with the APOE4 genotype. Moreover, WM injury precedes formation of plaques and tangles in human Familial Alzheimer's disease (FAD) and precedes plaque formation in rodent AD models. Restoring WM in rodent AD models improves cognition without affecting AD pathology. Thus, we postulate that the amyloid cascade, cholesterol dysmetabolism and white matter injury interact to produce and/or worsen AD pathology. We further postulate that the primary initiating event could be related to any of the three, with age a major factor for WM injury, diet and APOE4 and other genes a factor for cholesterol dysmetabolism, and FAD and other genes for Abeta dysmetabolism.
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Affiliation(s)
| | - Charles S. DeCarli
- Department of Neurology, The MIND Institute, University of California at Davis Medical Center, Sacramento, CA, United States
| | - Lee-Way Jin
- Department of Neurology, The MIND Institute, University of California at Davis Medical Center, Sacramento, CA, United States
| | - Xinhua Zhan
- Department of Neurology, The MIND Institute, University of California at Davis Medical Center, Sacramento, CA, United States
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7
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Shao X, Vishweswaraiah S, Čuperlović-Culf M, Yilmaz A, Greenwood CMT, Surendra A, McGuinness B, Passmore P, Kehoe PG, Maddens ME, Bennett SAL, Green BD, Radhakrishna U, Graham SF. Dementia with Lewy bodies post-mortem brains reveal differentially methylated CpG sites with biomarker potential. Commun Biol 2022; 5:1279. [PMID: 36418427 PMCID: PMC9684551 DOI: 10.1038/s42003-022-03965-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 09/08/2022] [Indexed: 11/25/2022] Open
Abstract
Dementia with Lewy bodies (DLB) is a common form of dementia with known genetic and environmental interactions. However, the underlying epigenetic mechanisms which reflect these gene-environment interactions are poorly studied. Herein, we measure genome-wide DNA methylation profiles of post-mortem brain tissue (Broadmann area 7) from 15 pathologically confirmed DLB brains and compare them with 16 cognitively normal controls using Illumina MethylationEPIC arrays. We identify 17 significantly differentially methylated CpGs (DMCs) and 17 differentially methylated regions (DMRs) between the groups. The DMCs are mainly located at the CpG islands, promoter and first exon regions. Genes associated with the DMCs are linked to "Parkinson's disease" and "metabolic pathway", as well as the diseases of "severe intellectual disability" and "mood disorders". Overall, our study highlights previously unreported DMCs offering insights into DLB pathogenesis with the possibility that some of these could be used as biomarkers of DLB in the future.
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Affiliation(s)
- Xiaojian Shao
- National Research Council of Canada, Digital Technologies Research Centre, Ottawa, Canada.
| | | | - Miroslava Čuperlović-Culf
- National Research Council of Canada, Digital Technologies Research Centre, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology, sand Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Ali Yilmaz
- Oakland University-William Beaumont School of Medicine, Rochester, MI, 48309, USA
- Beaumont Research Institute, Royal Oak, MI, 48073, USA
| | - Celia M T Greenwood
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montréal, Canada
| | - Anuradha Surendra
- National Research Council of Canada, Digital Technologies Research Centre, Ottawa, Canada
| | - Bernadette McGuinness
- Centre for Public Health, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Peter Passmore
- Centre for Public Health, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Patrick G Kehoe
- Dementia Research Group, Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Michael E Maddens
- Oakland University-William Beaumont School of Medicine, Rochester, MI, 48309, USA
- Beaumont Research Institute, Royal Oak, MI, 48073, USA
| | - Steffany A L Bennett
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology, sand Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Brian D Green
- Institute for Global Food Security, School of Biological Sciences, Faculty of Medicine, Health and Life Sciences, Queen's University Belfast, Northern Ireland, UK
| | - Uppala Radhakrishna
- Oakland University-William Beaumont School of Medicine, Rochester, MI, 48309, USA
- Beaumont Research Institute, Royal Oak, MI, 48073, USA
| | - Stewart F Graham
- Oakland University-William Beaumont School of Medicine, Rochester, MI, 48309, USA.
- Beaumont Research Institute, Royal Oak, MI, 48073, USA.
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8
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Liu S, Chen T, Chen B, Liu Y, Lu X, Li J. Lrpap1 deficiency leads to myopia through TGF-β-induced apoptosis in zebrafish. Cell Commun Signal 2022; 20:162. [PMID: 36261846 PMCID: PMC9580148 DOI: 10.1186/s12964-022-00970-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/03/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Frameshift mutations in LRPAP1 are responsible for autosomal recessive high myopia in human beings but its underlying mechanism remains elusive. This study aims to investigate the effect of LRPAP1 defect on ocular refractive development and its involved mechanism. METHODS A lrpap1 mutant zebrafish line with homozygous frameshift mutation was generated by CRISPR/Cas9 technology and confirmed by Sanger sequencing. The ocular refractive phenotype was analyzed by calculating the relative refractive error (RRE) with vivo photography and histological analysis at different development stages, together with examining ocular structure change via transmission electron microscopy. Further, RNA sequencing and bioinformatics analysis were performed. The potentially involved signaling pathway as well as the interacted protein were investigated in vivo. RESULTS The lrpap1 homozygous mutant zebrafish line showed myopic phenotype. Specifically, the mutant lines showed larger eye axial length-to-body length in one-month old individuals and a myopic shift with an RRE that changed after two months. Collagen fibers became thinning and disordered in the sclera. Further, RNA sequencing and bioinformatics analysis indicated that apoptosis signaling was activated in mutant line; this was further confirmed by acridine orange and TUNEL staining. Moreover, the expression of TGF-β protein was elevated in the mutant lines. Finally, the treatment of wild-type embryos with a TGF-β agonist aggravated the degree of eyeball apoptosis; conversely, the use of a TGF-β inhibitor mitigated apoptosis in mutant embryos. CONCLUSION The study provides functional evidence of a link between lrpap1 and myopia, suggesting that lrpap1 deficiency could lead to myopia through TGF-β-induced apoptosis signaling. Video abstract.
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Affiliation(s)
- Shanshan Liu
- grid.284723.80000 0000 8877 7471Department of Ophthalmology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Ting Chen
- grid.284723.80000 0000 8877 7471Department of Ophthalmology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Binghao Chen
- grid.459579.30000 0004 0625 057XDepartment of Orthopedics, Guangdong Women and Children Hospital, Guangzhou, China
| | - Yijun Liu
- grid.413107.0Department of Foot and Ankle Surgery, Center for Orthopedic Surgery, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Xiaohe Lu
- grid.284723.80000 0000 8877 7471Department of Ophthalmology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jiali Li
- grid.284723.80000 0000 8877 7471Department of Ophthalmology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
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9
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Hou J, Bi H, Ge Q, Teng H, Wan G, Yu B, Jiang Q, Gu X. Heterogeneity analysis of astrocytes following spinal cord injury at single-cell resolution. FASEB J 2022; 36:e22442. [PMID: 35816276 DOI: 10.1096/fj.202200463r] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/21/2022] [Accepted: 06/24/2022] [Indexed: 12/11/2022]
Abstract
Astrocytes play many important functions in response to spinal cord injury (SCI) in an activated manner, including clearance of necrotic tissue, formation of protective barrier, maintenance of microenvironment balance, interaction with immune cells, and formation of the glial scar. More and more studies have shown that the astrocytes are heterogeneous, such as inflammatory astrocyte 1 (A1) and neuroprotective astrocyte 2 (A2) types. However, the subtypes of astrocyte resulting from SCI have not been clearly defined. In this study, using single-cell RNA sequencing, we constructed the transcriptomic profile of astrocytes from uninjured spinal cord tissue and injured tissue nearby the lesion epicenter at 0.5, 1, 3, 7, 14, 60, and 90 days after mouse hemisection spinal cord surgery. Our analysis uncovered six transcriptionally distinct astrocyte states, including Atp1b2+ , S100a4+ , Gpr84+ , C3+ /G0s2+ , GFAP+ /Tm4sf1+ , and Gss+ /Cryab+ astrocytes. We used these new signatures combined with canonical astrocyte markers to determine the distribution of morphologically and physiologically distinct astrocyte population at injured sites by immunofluorescence staining. Then we identified the dynamic evolution process of each astrocyte subtype following SCI. Finally, we also revealed the evolution of highly expressed genes in these astrocyte subtypes at different phases of SCI. Together, we provided six astrocyte subtypes at single-cell resolution following SCI. These data not only contribute to understand the heterogeneity of astrocytes during SCI but also help to find new astrocyte subtypes as a target for SCI repair.
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Affiliation(s)
- Jinxing Hou
- State Key Laboratory of Pharmaceutical Biotechnology, Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China.,Branch of National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Nanjing, People's Republic of China
| | - Huiru Bi
- State Key Laboratory of Pharmaceutical Biotechnology, Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China.,Branch of National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Nanjing, People's Republic of China
| | - Qiting Ge
- State Key Laboratory of Pharmaceutical Biotechnology, Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China.,Branch of National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Nanjing, People's Republic of China
| | - Huajian Teng
- State Key Laboratory of Pharmaceutical Biotechnology, Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China.,Branch of National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Nanjing, People's Republic of China
| | - Guoqiang Wan
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, People's Republic of China
| | - Bin Yu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, People's Republic of China
| | - Qing Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China.,Branch of National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Nanjing, People's Republic of China
| | - Xiaosong Gu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, People's Republic of China
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10
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Tejada Moreno JA, Villegas Lanau A, Madrigal Zapata L, Baena Pineda AY, Velez Hernandez J, Campo Nieto O, Soto Ospina A, Araque Marín P, Rishishwar L, Norris ET, Chande AT, Jordan IK, Bedoya Berrio G. Mutations in SORL1 and MTHFDL1 possibly contribute to the development of Alzheimer's disease in a multigenerational Colombian Family. PLoS One 2022; 17:e0269955. [PMID: 35905044 PMCID: PMC9337667 DOI: 10.1371/journal.pone.0269955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 05/31/2022] [Indexed: 11/19/2022] Open
Abstract
Alzheimer's disease (AD) is the most common cause of dementia in the elderly, affecting over 50 million people worldwide in 2020 and this number will triple to 152 million by 2050. Much of the increase will be in developing countries like Colombia. In familial forms, highly penetrant mutations have been identified in three genes, APP, PSEN1, and PSEN2, supporting a role for amyloid-β peptide. In sporadic forms, more than 30 risk genes involved in the lipid metabolism, the immune system, and synaptic functioning mechanisms. We used whole-exome sequencing (WES) to evaluate a family of 97 members, spanning three generations, with a familiar AD, and without mutations in APP, PSEN1, or PSEN2. We sequenced two affected and one unaffected member with the aim of identifying genetic variants that could explain the presence of the disease in the family and the candidate variants were validated in eleven members. We also built a structural model to try to determine the effect on protein function. WES analysis identified two rare variants in SORL1 and MTHFD1L genes segregating in the family with other potential risk variants in APOE, ABCA7, and CHAT, suggesting an oligogenic inheritance. Additionally, the structural 3D models of SORL1 and MTHFD1L variants shows that these variants produce polarity changes that favor hydrophobic interactions, resulting in local structural changes that could affect the protein function and may contribute to the development of the disease in this family.
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Affiliation(s)
| | | | | | | | | | - Omer Campo Nieto
- Molecular Genetics Research Group, University of Antioquia, Medellin, Colombia
| | | | - Pedronel Araque Marín
- Research and Innovation Group in Chemical Formulations, EIA University, Medellin, Colombia
| | - Lavanya Rishishwar
- IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, Georgia, United States of America
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
| | - Emily T. Norris
- IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, Georgia, United States of America
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Aroon T. Chande
- IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, Georgia, United States of America
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - I. King Jordan
- IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, Georgia, United States of America
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
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11
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Bottero V, Alrafati F, Santiago JA, Potashkin JA. Transcriptomic and Network Meta-Analysis of Frontotemporal Dementias. Front Mol Neurosci 2021; 14:747798. [PMID: 34720873 PMCID: PMC8554122 DOI: 10.3389/fnmol.2021.747798] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/28/2021] [Indexed: 11/30/2022] Open
Abstract
Frontotemporal lobar degeneration (FTLD), also known as frontotemporal dementia (FTD), results in a progressive decline in executive function, leading to behavioral changes, speech problems, and movement disorders. FTD is the second most common cause of young-onset dementia affecting approximately 50–60,000 Americans. FTD exists in familial and sporadic forms, with GRN progranulin and C9orf72 mutations being the most common causes. In this study, we compared the sporadic and familial transcriptome within the cerebellum, frontal cortex, hippocampus, and Brodmann’s area 8 of patients with FTD to determine genes and pathways involved in the disease process. Most dysregulated genes expression occurred in the frontal cortex and Brodmann’s area 8 for genetic and sporadic forms of FTD, respectively. A meta-analysis revealed 50 genes and 95 genes are dysregulated in at least three brain regions in patients with familial mutations and sporadic FTD patients, respectively. Familial FTD genes centered on the Wnt signaling pathway, whereas genes associated with the sporadic form of FTD centered on MAPK signaling. The results reveal the similarities and differences between sporadic and familial FTD. In addition, valproic acid and additional therapeutic agents may be beneficial in treating patients with FTD.
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Affiliation(s)
- Virginie Bottero
- Center for Neurodegenerative Diseases and Therapeutics, Chicago Medical School, Discipline of Cellular and Molecular Pharmacology, Rosalind Franklin University of Medicine and Science, North Chicago, IL, United States
| | - Fahed Alrafati
- Center for Neurodegenerative Diseases and Therapeutics, Chicago Medical School, Discipline of Cellular and Molecular Pharmacology, Rosalind Franklin University of Medicine and Science, North Chicago, IL, United States
| | | | - Judith A Potashkin
- Center for Neurodegenerative Diseases and Therapeutics, Chicago Medical School, Discipline of Cellular and Molecular Pharmacology, Rosalind Franklin University of Medicine and Science, North Chicago, IL, United States
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12
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Robbins M, Clayton E, Kaminski Schierle GS. Synaptic tau: A pathological or physiological phenomenon? Acta Neuropathol Commun 2021; 9:149. [PMID: 34503576 PMCID: PMC8428049 DOI: 10.1186/s40478-021-01246-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 12/17/2022] Open
Abstract
In this review, we discuss the synaptic aspects of Tau pathology occurring during Alzheimer's disease (AD) and how this may relate to memory impairment, a major hallmark of AD. Whilst the clinical diagnosis of AD patients is a loss of working memory and long-term declarative memory, the histological diagnosis is the presence of neurofibrillary tangles of hyperphosphorylated Tau and Amyloid-beta plaques. Tau pathology spreads through synaptically connected neurons to impair synaptic function preceding the formation of neurofibrillary tangles, synaptic loss, axonal retraction and cell death. Alongside synaptic pathology, recent data suggest that Tau has physiological roles in the pre- or post- synaptic compartments. Thus, we have seen a shift in the research focus from Tau as a microtubule-stabilising protein in axons, to Tau as a synaptic protein with roles in accelerating spine formation, dendritic elongation, and in synaptic plasticity coordinating memory pathways. We collate here the myriad of emerging interactions and physiological roles of synaptic Tau, and discuss the current evidence that synaptic Tau contributes to pathology in AD.
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13
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Wang C, Yang Z, Xu E, Shen X, Wang X, Li Z, Yu H, Chen K, Hu Q, Xia X, Liu S, Guan W. Apolipoprotein C-II induces EMT to promote gastric cancer peritoneal metastasis via PI3K/AKT/mTOR pathway. Clin Transl Med 2021; 11:e522. [PMID: 34459127 PMCID: PMC8351524 DOI: 10.1002/ctm2.522] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 07/18/2021] [Accepted: 07/22/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Peritoneal metastasis (PM) occurs frequently in patients with gastric cancer (GC) and confers poor survival. Lipid metabolism acts as a non-negligible regulator in epithelial-mesenchymal transition (EMT), which is crucial for the metastasis of GC. As apolipoprotein C2 (APOC2) is a key activator of lipoprotein lipase for triglyceride metabolism, the exact mechanism of APOC2 remains largely unknown in GC. METHODS Tandem mass tags identified differentially expressed proteins between human PM and GC tissues, and showed that APOC2 overexpressed in PM tissues, which was further confirmed by immunoblotting, immunohistochemistry, and ELISA. Global gene expression changes were identified in APOC2 knockdown cells via RNA-sequencing. The role of APOC2 in lipid metabolism of GC cells was assessed via the Seahorse XF analyzer and lipid staining assays. The biological role of APOC2 in GC cells was determined by 3D Spheroid invasion, apoptosis, colony formation, wound healing, transwell assay, and mouse models. The interaction between APOC2 and CD36 was analyzed by co-immunoprecipitation and biolayer interferometry. The underlying mechanisms were investigated using western blot technique. RESULTS APOC2 overexpressed in GC PM tissues. Upregulation of APOC2 correlated with a poor prognosis in GC patients. APOC2 promoted GC cell invasion, migration, and proliferation via CD36-mediated PI3K/AKT/mTOR signaling activation. Furthermore, APOC2-CD36 axis upregulated EMT markers of GC cells via increasing the phosphorylation of PI3K, AKT, and mTOR. Knockdown either APOC2 or CD36 inhibited the malignant phenotype of cancer cells, and delayed GC PM progression in murine GC models. CONCLUSION APOC2 cooperates with CD36 to induce EMT to promote GC PM via PI3K/AKT/mTOR pathway. APOC2-CD36 axis may be a potential target for the treatment of aggressive GC.
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Affiliation(s)
- Chao Wang
- Department of General Surgery, Nanjing Drum Tower HospitalThe Affiliated Hospital of Nanjing University Medical SchoolNanjingChina
| | - Zhi Yang
- Department of General SurgeryNanjing Drum Tower Hospital Clinical College of Nanjing Medical UniversityNanjingChina
| | - En Xu
- Department of General Surgery, Nanjing Drum Tower HospitalThe Affiliated Hospital of Nanjing University Medical SchoolNanjingChina
| | - Xiaofei Shen
- Department of General Surgery, Nanjing Drum Tower HospitalThe Affiliated Hospital of Nanjing University Medical SchoolNanjingChina
| | - Xingzhou Wang
- Department of General Surgery, Nanjing Drum Tower HospitalThe Affiliated Hospital of Nanjing University Medical SchoolNanjingChina
| | - Zijian Li
- Department of General SurgeryNanjing Drum Tower Hospital Clinical College of Nanjing Medical UniversityNanjingChina
| | - Heng Yu
- Department of General SurgeryNanjing Drum Tower Hospital Clinical College of Nanjing Medical UniversityNanjingChina
| | - Kai Chen
- Department of General Surgery, Nanjing Drum Tower HospitalThe Affiliated Hospital of Nanjing University Medical SchoolNanjingChina
| | - Qiongyuan Hu
- Department of General Surgery, Nanjing Drum Tower HospitalThe Affiliated Hospital of Nanjing University Medical SchoolNanjingChina
| | - Xuefeng Xia
- Department of General Surgery, Nanjing Drum Tower HospitalThe Affiliated Hospital of Nanjing University Medical SchoolNanjingChina
| | - Song Liu
- Department of General Surgery, Nanjing Drum Tower HospitalThe Affiliated Hospital of Nanjing University Medical SchoolNanjingChina
| | - Wenxian Guan
- Department of General Surgery, Nanjing Drum Tower HospitalThe Affiliated Hospital of Nanjing University Medical SchoolNanjingChina
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14
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Sandoval‐Sierra JV, Helbing AHB, Williams EG, Ashbrook DG, Roy S, Williams RW, Mozhui K. Body weight and high-fat diet are associated with epigenetic aging in female members of the BXD murine family. Aging Cell 2020; 19:e13207. [PMID: 32790008 PMCID: PMC7511861 DOI: 10.1111/acel.13207] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 06/03/2020] [Accepted: 07/03/2020] [Indexed: 01/23/2023] Open
Abstract
DNA methylation (DNAm) is shaped by genetic and environmental factors and modulated by aging. Here, we examine interrelations between epigenetic aging, body weight (BW), and life span in 12 isogenic strains from the BXD family of mice that exhibit over twofold variation in longevity. Genome-wide DNAm was assayed in 70 liver specimens from predominantly female cases, 6-25 months old, that were maintained on normal chow or high-fat diet (HFD). We defined subsets of CpG regions associated with age, BW at young adulthood, and strain-by-diet-dependent life span. These age-associated differentially methylated CpG regions (age-DMRs) featured distinct genomic characteristics, with DNAm gains over time occurring in sites such as promoters and exons that have high CpG density and low average methylation. CpG regions associated with BW were enriched in introns, tended to have lower methylation in mice with higher BW, and were inversely correlated with gene expression (i.e., higher mRNA levels in mice with higher BW). CpG regions associated with life span were linked to genes involved in life span modulation, including the telomerase reverse transcriptase gene, Tert, which had both lower methylation and higher expression in long-lived strains. An epigenetic clock defined from age-DMRs revealed accelerated aging in mice belonging to strains with shorter life spans. Both higher BW and the HFD were associated with accelerated epigenetic aging. Our results highlight the age-accelerating effect of heavier BW. Furthermore, we demonstrate that the measure of epigenetic aging derived from age-DMRs can predict genotype and diet-induced differences in life span among female BXD members.
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Affiliation(s)
| | - Alexandra H. B. Helbing
- Department of Preventive Medicine University of Tennessee Health Science Center College of Medicine Memphis TN USA
| | - Evan G. Williams
- Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
| | - David G. Ashbrook
- Department of Genetics, Genomics and Informatics University of Tennessee Health Science Center College of Medicine Memphis TN USA
| | - Suheeta Roy
- Department of Genetics, Genomics and Informatics University of Tennessee Health Science Center College of Medicine Memphis TN USA
| | - Robert W. Williams
- Department of Genetics, Genomics and Informatics University of Tennessee Health Science Center College of Medicine Memphis TN USA
| | - Khyobeni Mozhui
- Department of Preventive Medicine University of Tennessee Health Science Center College of Medicine Memphis TN USA
- Department of Genetics, Genomics and Informatics University of Tennessee Health Science Center College of Medicine Memphis TN USA
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15
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Bahrami A, Barreto GE, Lombardi G, Pirro M, Sahebkar A. Emerging roles for high-density lipoproteins in neurodegenerative disorders. Biofactors 2019; 45:725-739. [PMID: 31301192 DOI: 10.1002/biof.1541] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 06/18/2019] [Indexed: 12/24/2022]
Abstract
Lipoproteins are the complexes of different lipids and proteins, which are devoted to the transport and clearance of lipids or lipid-related molecules in the circulation. Lipoproteins have been found to play a crucial role in brain function and may influence myelination process. Among lipoproteins, high-density lipoproteins (HDLs) and their major protein component, apoA-I, are directly involved in cholesterol efflux in the brain. It has been suggested that inadequate or dysfunctional brain HDLs may contribute to cerebrovascular dysfunctions, neurodegeneration, or neurovascular instability. HDL deficiency could also promote cognitive decline through impacting on atherosclerotic risk. The focus of this review is to discuss knowledge on HDL dysregulation in neurological disorders. A better understanding on how changes in cellular HDL and apolipoprotein homeostasis affect central nervous system function may provide promising novel avenues for the treatment of specific HDL-related neurological disorders.
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Affiliation(s)
- Afsane Bahrami
- Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - George E Barreto
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá D.C., Colombia
- Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | - Gemma Lombardi
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, Florence, Italy
| | - Matteo Pirro
- Unit of Internal Medicine, Department of Medicine, University of Perugia, Perugia, Italy
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Neurogenic Inflammation Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
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16
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Talwar P, Gupta R, Kushwaha S, Agarwal R, Saso L, Kukreti S, Kukreti R. Viral Induced Oxidative and Inflammatory Response in Alzheimer's Disease Pathogenesis with Identification of Potential Drug Candidates: A Systematic Review using Systems Biology Approach. Curr Neuropharmacol 2019; 17:352-365. [PMID: 29676229 PMCID: PMC6482477 DOI: 10.2174/1570159x16666180419124508] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 03/19/2018] [Accepted: 04/10/2018] [Indexed: 02/07/2023] Open
Abstract
Alzheimer's disease (AD) is genetically complex with multifactorial etiology. Here, we aim to identify the potential viral pathogens leading to aberrant inflammatory and oxidative stress response in AD along with potential drug candidates using systems biology approach. We retrieved protein interactions of amyloid precursor protein (APP) and tau protein (MAPT) from NCBI and genes for oxidative stress from NetAge, for inflammation from NetAge and InnateDB databases. Genes implicated in aging were retrieved from GenAge database and two GEO expression datasets. These genes were individually used to create protein-protein interaction network using STRING database (score≥0.7). The interactions of candidate genes with known viruses were mapped using virhostnet v2.0 database. Drug molecules targeting candidate genes were retrieved using the Drug- Gene Interaction Database (DGIdb). Data mining resulted in 2095 APP, 116 MAPT, 214 oxidative stress, 1269 inflammatory genes. After STRING PPIN analysis, 404 APP, 109 MAPT, 204 oxidative stress and 1014 inflammation related high confidence proteins were identified. The overlap among all datasets yielded eight common markers (AKT1, GSK3B, APP, APOE, EGFR, PIN1, CASP8 and SNCA). These genes showed association with hepatitis C virus (HCV), Epstein- Barr virus (EBV), human herpes virus 8 and Human papillomavirus (HPV). Further, screening of drugs targeting candidate genes, and possessing anti-inflammatory property, antiviral activity along with a suggested role in AD pathophysiology yielded 12 potential drug candidates. Our study demonstrated the role of viral etiology in AD pathogenesis by elucidating interaction of oxidative stress and inflammation causing candidate genes with common viruses along with the identification of potential AD drug candidates.
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Affiliation(s)
- Puneet Talwar
- Genomics and Molecular Medicine Unit, Institute of Genomics and Integrative Biology (IGIB), Council of Scientific and Industrial Research (CSIR), Delhi, India
| | - Renu Gupta
- Institute of Human Behaviour & Allied Sciences (IHBAS), Dilshad Garden, Delhi 110 095, India
| | - Suman Kushwaha
- Institute of Human Behaviour & Allied Sciences (IHBAS), Dilshad Garden, Delhi 110 095, India
| | - Rachna Agarwal
- Institute of Human Behaviour & Allied Sciences (IHBAS), Dilshad Garden, Delhi 110 095, India
| | - Luciano Saso
- Department of Physiology and Pharmacology, Sapienza University of Rome, Italy
| | | | - Ritushree Kukreti
- Genomics and Molecular Medicine Unit, Institute of Genomics and Integrative Biology (IGIB), Council of Scientific and Industrial Research (CSIR), Delhi, India
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17
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Pinu FR, Goldansaz SA, Jaine J. Translational Metabolomics: Current Challenges and Future Opportunities. Metabolites 2019; 9:E108. [PMID: 31174372 PMCID: PMC6631405 DOI: 10.3390/metabo9060108] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 06/04/2019] [Accepted: 06/04/2019] [Indexed: 02/06/2023] Open
Abstract
Metabolomics is one of the latest omics technologies that has been applied successfully in many areas of life sciences. Despite being relatively new, a plethora of publications over the years have exploited the opportunities provided through this data and question driven approach. Most importantly, metabolomics studies have produced great breakthroughs in biomarker discovery, identification of novel metabolites and more detailed characterisation of biological pathways in many organisms. However, translation of the research outcomes into clinical tests and user-friendly interfaces has been hindered due to many factors, some of which have been outlined hereafter. This position paper is the summary of discussion on translational metabolomics undertaken during a peer session of the Australian and New Zealand Metabolomics Conference (ANZMET 2018) held in Auckland, New Zealand. Here, we discuss some of the key areas in translational metabolomics including existing challenges and suggested solutions, as well as how to expand the clinical and industrial application of metabolomics. In addition, we share our perspective on how full translational capability of metabolomics research can be explored.
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Affiliation(s)
- Farhana R Pinu
- The New Zealand Institute for Plant and Food Research, Private Bag 92169, Auckland 1142, New Zealand.
| | - Seyed Ali Goldansaz
- Department of Agriculture, Food and Nutritional Sciences, University of Alberta, Edmonton, AB T6G 2P5, Canada.
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
| | - Jacob Jaine
- Analytica Laboratories Ltd., Ruakura Research Centre, Hamilton 3216, New Zealand.
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18
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Zhu Z, Hu Y, Zhou Y, Zhang Y, Yu L, Tao L, Guo A, Fang Q. Macrophage Migration Inhibitory Factor Promotes Chemotaxis of Astrocytes through Regulation of Cholesterol 25-Hydroxylase Following Rat Spinal Cord Injury. Neuroscience 2019; 408:349-360. [PMID: 31026565 DOI: 10.1016/j.neuroscience.2019.04.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 03/29/2019] [Accepted: 04/08/2019] [Indexed: 11/25/2022]
Abstract
Oxysterol derived from cholesterol metabolism is involved in the inflammatory activation, and consequently in development of major chronic diseases. Multiple cytokines have been found to induce the expression of cholesterol metabolism-related enzymes. Several studies have shown that the protein level of cholesterol-25-hydroxylase (CH25H) is remarkably increased in response to injury of central nervous system (CNS), but little is known about the mechanisms of cytokine-induced expression of CH25H in specific cell types, and the resultant effects. In the present study, we demonstrated that ch25h expression was significantly upregulated in the astrocytes of rat injured spinal cord, in parallel with those of MIF. Administration of MIF inhibitor 4-IPP in the lesion sites attenuated injury-induced ch25h expression. MIF facilitated ch25h expression of astrocytes through interaction with CD74 membrane receptor, which in turn promoted production of chemokines, as identified by transcriptome profiles. MIF-induced release of oxysterol 25-hydroxycholesterol (25-HC) from astrocytes affects cell migration, but inhibited cell viability in dose-dependent manner, suggesting that MIF aggravates progressive neuropathology through regulation of cholesterol metabolism following CNS injury. These results have provided a novel mechanism and a potential therapeutic strategy for injured CNS.
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Affiliation(s)
- Zhenjie Zhu
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou 215006, PR China; Department of Rehabilitation Medicine, Affiliated Hospital of Nantong University, Nantong 226001, PR China
| | - Yuming Hu
- Department of Rehabilitation Medicine, Affiliated Hospital of Nantong University, Nantong 226001, PR China
| | - Yue Zhou
- Department of Rehabilitation Medicine, Affiliated Hospital of Nantong University, Nantong 226001, PR China
| | - Yuxin Zhang
- Department of Rehabilitation Medicine, Affiliated Hospital of Nantong University, Nantong 226001, PR China
| | - Liqiang Yu
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou 215006, PR China.
| | - Lihong Tao
- Department of Neurology, The Affiliated Hospital of Yangzhou University, Yangzhou 225012, PR China
| | - Aisong Guo
- Department of Rehabilitation Medicine, Affiliated Hospital of Nantong University, Nantong 226001, PR China
| | - Qi Fang
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou 215006, PR China.
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19
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Ye R, Gordillo R, Shao M, Onodera T, Chen Z, Chen S, Lin X, SoRelle JA, Li X, Tang M, Keller MP, Kuliawat R, Attie AD, Gupta RK, Holland WL, Beutler B, Herz J, Scherer PE. Intracellular lipid metabolism impairs β cell compensation during diet-induced obesity. J Clin Invest 2018; 128:1178-1189. [PMID: 29457786 DOI: 10.1172/jci97702] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 01/09/2018] [Indexed: 12/16/2022] Open
Abstract
The compensatory proliferation of insulin-producing β cells is critical to maintaining glucose homeostasis at the early stage of type 2 diabetes. Failure of β cells to proliferate results in hyperglycemia and insulin dependence in patients. To understand the effect of the interplay between β cell compensation and lipid metabolism upon obesity and peripheral insulin resistance, we eliminated LDL receptor-related protein 1 (LRP1), a pleiotropic mediator of cholesterol, insulin, energy metabolism, and other cellular processes, in β cells. Upon high-fat diet exposure, LRP1 ablation significantly impaired insulin secretion and proliferation of β cells. The diminished insulin signaling was partly contributed to by the hypersensitivity to glucose-induced, Ca2+-dependent activation of Erk and the mTORC1 effector p85 S6K1. Surprisingly, in LRP1-deficient islets, lipotoxic sphingolipids were mitigated by improved lipid metabolism, mediated at least in part by the master transcriptional regulator PPARγ2. Acute overexpression of PPARγ2 in β cells impaired insulin signaling and insulin secretion. Elimination of Apbb2, a functional regulator of LRP1 cytoplasmic domain, also impaired β cell function in a similar fashion. In summary, our results uncover the double-edged effects of intracellular lipid metabolism on β cell function and viability in obesity and type 2 diabetes and highlight LRP1 as an essential regulator of these processes.
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Affiliation(s)
- Risheng Ye
- Touchstone Diabetes Center, Department of Internal Medicine, University of Texas Southwestern (UTSW) Medical Center, Dallas, Texas, USA.,Department of Medical Education, Texas Tech University Health Sciences Center Paul L. Foster School of Medicine, El Paso, Texas, USA
| | - Ruth Gordillo
- Touchstone Diabetes Center, Department of Internal Medicine, University of Texas Southwestern (UTSW) Medical Center, Dallas, Texas, USA
| | - Mengle Shao
- Touchstone Diabetes Center, Department of Internal Medicine, University of Texas Southwestern (UTSW) Medical Center, Dallas, Texas, USA
| | - Toshiharu Onodera
- Touchstone Diabetes Center, Department of Internal Medicine, University of Texas Southwestern (UTSW) Medical Center, Dallas, Texas, USA
| | - Zhe Chen
- Touchstone Diabetes Center, Department of Internal Medicine, University of Texas Southwestern (UTSW) Medical Center, Dallas, Texas, USA.,Center for the Genetics of Host Defense, UTSW Medical Center, Dallas, Texas, USA
| | - Shiuhwei Chen
- Touchstone Diabetes Center, Department of Internal Medicine, University of Texas Southwestern (UTSW) Medical Center, Dallas, Texas, USA
| | - Xiaoli Lin
- Touchstone Diabetes Center, Department of Internal Medicine, University of Texas Southwestern (UTSW) Medical Center, Dallas, Texas, USA
| | - Jeffrey A SoRelle
- Center for the Genetics of Host Defense, UTSW Medical Center, Dallas, Texas, USA
| | - Xiaohong Li
- Center for the Genetics of Host Defense, UTSW Medical Center, Dallas, Texas, USA
| | - Miao Tang
- Center for the Genetics of Host Defense, UTSW Medical Center, Dallas, Texas, USA
| | - Mark P Keller
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Regina Kuliawat
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, New York, New York, USA
| | - Alan D Attie
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Rana K Gupta
- Touchstone Diabetes Center, Department of Internal Medicine, University of Texas Southwestern (UTSW) Medical Center, Dallas, Texas, USA
| | - William L Holland
- Touchstone Diabetes Center, Department of Internal Medicine, University of Texas Southwestern (UTSW) Medical Center, Dallas, Texas, USA
| | - Bruce Beutler
- Center for the Genetics of Host Defense, UTSW Medical Center, Dallas, Texas, USA
| | - Joachim Herz
- Departments of Molecular Genetics, Neuroscience, Neurology and Neurotherapeutics, and Center for Translational Neurodegeneration Research, UTSW Medical Center, Dallas, Texas, USA.,Center for Neuroscience, Department of Neuroanatomy, Albert Ludwig University, Freiburg, Germany
| | - Philipp E Scherer
- Touchstone Diabetes Center, Department of Internal Medicine, University of Texas Southwestern (UTSW) Medical Center, Dallas, Texas, USA
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20
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Lin JP, Mironova YA, Shrager P, Giger RJ. LRP1 regulates peroxisome biogenesis and cholesterol homeostasis in oligodendrocytes and is required for proper CNS myelin development and repair. eLife 2017; 6:30498. [PMID: 29251594 PMCID: PMC5752207 DOI: 10.7554/elife.30498] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 12/15/2017] [Indexed: 01/01/2023] Open
Abstract
Low-density lipoprotein receptor-related protein-1 (LRP1) is a large endocytic and signaling molecule broadly expressed by neurons and glia. In adult mice, global inducible (Lrp1flox/flox;CAG-CreER) or oligodendrocyte (OL)-lineage specific ablation (Lrp1flox/flox;Pdgfra-CreER) of Lrp1 attenuates repair of damaged white matter. In oligodendrocyte progenitor cells (OPCs), Lrp1 is required for cholesterol homeostasis and differentiation into mature OLs. Lrp1-deficient OPC/OLs show a strong increase in the sterol-regulatory element-binding protein-2 yet are unable to maintain normal cholesterol levels, suggesting more global metabolic deficits. Mechanistic studies revealed a decrease in peroxisomal biogenesis factor-2 and fewer peroxisomes in OL processes. Treatment of Lrp1−/− OPCs with cholesterol or activation of peroxisome proliferator-activated receptor-γ with pioglitazone alone is not sufficient to promote differentiation; however, when combined, cholesterol and pioglitazone enhance OPC differentiation into mature OLs. Collectively, our studies reveal a novel role for Lrp1 in peroxisome biogenesis, lipid homeostasis, and OPC differentiation during white matter development and repair.
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Affiliation(s)
- Jing-Ping Lin
- Department of Cell and Developmental Biology, University of Michigan School of Medicine, Ann Arbor, MI, United States
| | - Yevgeniya A Mironova
- Cellular and Molecular Biology Graduate Program, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Peter Shrager
- Department of Neuroscience, University of Rochester Medical Center, Rochester, NY, United States
| | - Roman J Giger
- Department of Cell and Developmental Biology, University of Michigan School of Medicine, Ann Arbor, MI, United States.,Cellular and Molecular Biology Graduate Program, University of Michigan Medical School, Ann Arbor, MI, United States.,Department of Neurology, University of Michigan Medical School, Ann Arbor, MI, United States.,Interdepartmental Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI, United States
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21
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Rebaї M, Kallel I, Abdelhedi R, kharrat N, Abdemoula Bouayed N, Abid L, Rebaї A. Association analysis of polymorphisms in EGFR , HER2 , ESR1 and THRA genes with coronary artery diseases. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2017. [DOI: 10.1016/j.ejmhg.2016.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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22
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Li GC, Zhang L, Yu M, Jia H, Tian T, Wang J, Wang F, Zhou L. Identification of novel biomarker and therapeutic target candidates for acute intracerebral hemorrhage by quantitative plasma proteomics. Clin Proteomics 2017; 14:14. [PMID: 28450824 PMCID: PMC5406897 DOI: 10.1186/s12014-017-9149-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 04/14/2017] [Indexed: 12/19/2022] Open
Abstract
Background The systematic mechanisms of acute intracerebral hemorrhage are still unknown and unverified, although many recent researches have indicated the secondary insults. This study was aimed to disclose the pathological mechanism and identify novel biomarker and therapeutic target candidates by plasma proteome. Methods Patients with AICH (n = 8) who demographically matched healthy controls (n = 4) were prospectively enrolled, and their plasma samples were obtained. The TMT-LC–MS/MS-based proteomics approach was used to quantify the differential proteome across plasma samples, and the results were analyzed by Ingenuity Pathway Analysis to explore canonical pathways and the relationship involved in the uploaded data. Results Compared with healthy controls, there were 31 differentially expressed proteins in the ICH group (P < 0.05), of which 21 proteins increased while 10 proteins decreased in abundance. These proteins are involved in 21 canonical pathways. One network with high confidence level was selected by the function network analysis, in which 23 proteins, P38MAPK and NFκB signaling pathways participated. Upstream regulator analysis found two regulators, IL6 and TNF, with an activation z-score. Seven biomarker candidates: APCS, FGB, LBP, MGMT, IGFBP2, LYZ, and APOA4 were found. Six candidate proteins were selected to assess the validity of the results by subsequent Western blotting analysis. Conclusion Our analysis provided several intriguing pathways involved in ICH, like LXR/RXR activation, acute phase response signaling, and production of NO and ROS in macrophages pathways. The three upstream regulators: IL-6, TNF, LPS, and seven biomarker candidates: APCS, APOA4, FGB, IGFBP2, LBP, LYZ, and MGMT were uncovered. LPS, APOA4, IGFBP2, LBP, LYZ, and MGMT are novel potential biomarkers in ICH development. The identified proteins and pathways provide new perspectives to the potential pathological mechanism and therapeutic targets underlying ICH. Electronic supplementary material The online version of this article (doi:10.1186/s12014-017-9149-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guo-Chun Li
- College of Medicine and Life Sciences, Nanjing University of Chinese Medicine, Nanjing, 210023 People's Republic of China
| | - Lina Zhang
- The Third Hospital of Zhangzhou, Zhangzhou, 363005 People's Republic of China
| | - Ming Yu
- Department of Neurology, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001 People's Republic of China
| | - Haiyu Jia
- Department of Neurology, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001 People's Republic of China
| | - Ting Tian
- College of Medicine and Life Sciences, Nanjing University of Chinese Medicine, Nanjing, 210023 People's Republic of China
| | - Junqin Wang
- College of Medicine and Life Sciences, Nanjing University of Chinese Medicine, Nanjing, 210023 People's Republic of China
| | - Fuqiang Wang
- School of Public Health, Nanjing Medical University, Nanjing, 211166 People's Republic of China
| | - Ling Zhou
- School of Public Health, Nanjing Medical University, Nanjing, 211166 People's Republic of China
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23
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Deatherage CL, Lu Z, Kroncke BM, Ma S, Smith JA, Voehler MW, McFeeters RL, Sanders CR. Structural and biochemical differences between the Notch and the amyloid precursor protein transmembrane domains. SCIENCE ADVANCES 2017; 3:e1602794. [PMID: 28439555 PMCID: PMC5389784 DOI: 10.1126/sciadv.1602794] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 02/13/2017] [Indexed: 05/11/2023]
Abstract
γ-Secretase cleavage of the Notch receptor transmembrane domain is a critical signaling event for various cellular processes. Efforts to develop inhibitors of γ-secretase cleavage of the amyloid-β precursor C99 protein as potential Alzheimer's disease therapeutics have been confounded by toxicity resulting from the inhibition of normal cleavage of Notch. We present biochemical and structural data for the combined transmembrane and juxtamembrane Notch domains (Notch-TMD) that illuminate Notch signaling and that can be compared and contrasted with the corresponding traits of C99. The Notch-TMD and C99 have very different conformations, adapt differently to changes in model membrane hydrophobic span, and exhibit different cholesterol-binding properties. These differences may be exploited in the design of agents that inhibit cleavage of C99 while allowing Notch cleavage.
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Affiliation(s)
- Catherine L. Deatherage
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
- Center for Structural Biology and Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Zhenwei Lu
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
- Center for Structural Biology and Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Brett M. Kroncke
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
- Center for Structural Biology and Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Sirui Ma
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
- Center for Structural Biology and Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Jarrod A. Smith
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
- Center for Structural Biology and Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Markus W. Voehler
- Center for Structural Biology and Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Robert L. McFeeters
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Charles R. Sanders
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
- Center for Structural Biology and Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Corresponding author.
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24
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Xu EG, Mager EM, Grosell M, Hazard ES, Hardiman G, Schlenk D. Novel transcriptome assembly and comparative toxicity pathway analysis in mahi-mahi (Coryphaena hippurus) embryos and larvae exposed to Deepwater Horizon oil. Sci Rep 2017; 7:44546. [PMID: 28295044 PMCID: PMC5353654 DOI: 10.1038/srep44546] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 02/10/2017] [Indexed: 12/13/2022] Open
Abstract
The impacts of Deepwater Horizon (DWH) oil on morphology and function during embryonic development have been documented for a number of fish species, including the economically and ecologically important pelagic species, mahi-mahi (Coryphaena hippurus). However, further investigations on molecular events and pathways responsible for developmental toxicity have been largely restricted due to the limited molecular data available for this species. We sought to establish the de novo transcriptomic database from the embryos and larvae of mahi-mahi exposed to water accommodated fractions (HEWAFs) of two DWH oil types (weathered and source oil), in an effort to advance our understanding of the molecular aspects involved during specific toxicity responses. By high throughput sequencing (HTS), we obtained the first de novo transcriptome of mahi-mahi, with 60,842 assembled transcripts and 30,518 BLAST hits. Among them, 2,345 genes were significantly regulated in 96hpf larvae after exposure to weathered oil. With comparative analysis to a reference-transcriptome-guided approach on gene ontology and tox-pathways, we confirmed the novel approach effective for exploring tox-pathways in non-model species, and also identified a list of co-expressed genes as potential biomarkers which will provide information for the construction of an Adverse Outcome Pathway which could be useful in Ecological Risk Assessments.
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Affiliation(s)
- Elvis Genbo Xu
- Department of Environmental Sciences, University of California, Riverside, CA 92521, USA
| | - Edward M Mager
- Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA
| | - Martin Grosell
- Department of Marine Biology and Ecology, University of Miami, Miami, FL 33149, USA
| | - E Starr Hazard
- Center for Genomic Medicine, Medical University of South Carolina, Charleston, SC 29403, USA.,Computational Biology Resource Center, Medical University of South Carolina, Charleston, SC 29403, USA
| | - Gary Hardiman
- Center for Genomic Medicine, Medical University of South Carolina, Charleston, SC 29403, USA.,Departments of Medicine &Public Health Sciences, Medical University of South Carolina, Charleston, SC 29403, USA.,Laboratory for Marine Systems Biology, Hollings Marine Laboratory, Charleston, SC 29412, USA
| | - Daniel Schlenk
- Department of Environmental Sciences, University of California, Riverside, CA 92521, USA
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25
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Massafra V, Milona A, Vos HR, Burgering BMT, van Mil SWC. Quantitative liver proteomics identifies FGF19 targets that couple metabolism and proliferation. PLoS One 2017; 12:e0171185. [PMID: 28178326 PMCID: PMC5298232 DOI: 10.1371/journal.pone.0171185] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/18/2017] [Indexed: 12/14/2022] Open
Abstract
Fibroblast growth factor 19 (FGF19) is a gut-derived peptide hormone that is produced following activation of Farnesoid X Receptor (FXR). FGF19 is secreted and signals to the liver, where it contributes to the homeostasis of bile acid (BA), lipid and carbohydrate metabolism. FGF19 is a promising therapeutic target for the metabolic syndrome and cholestatic diseases, but enthusiasm for its use has been tempered by FGF19-mediated induction of proliferation and hepatocellular carcinoma. To inform future rational design of FGF19-variants, we have conducted temporal quantitative proteomic and gene expression analyses to identify FGF19-targets related to metabolism and proliferation. Mice were fasted for 16 hours, and injected with human FGF19 (1 mg/kg body weight) or vehicle. Liver protein extracts (containing “light” lysine) were mixed 1:1 with a spike-in protein extract from 13C6-lysine metabolically labelled mouse liver (containing “heavy” lysine) and analysed by LC-MS/MS. Our analyses provide a resource of FGF19 target proteins in the liver. 189 proteins were upregulated (≥ 1.5 folds) and 73 proteins were downregulated (≤ -1.5 folds) by FGF19. FGF19 treatment decreased the expression of proteins involved in fatty acid (FA) synthesis, i.e., Fabp5, Scd1, and Acsl3 and increased the expression of Acox1, involved in FA oxidation. As expected, FGF19 increased the expression of proteins known to drive proliferation (i.e., Tgfbi, Vcam1, Anxa2 and Hdlbp). Importantly, many of the FGF19 targets (i.e., Pdk4, Apoa4, Fas and Stat3) have a dual function in both metabolism and cell proliferation. Therefore, our findings challenge the development of FGF19-variants that fully uncouple metabolic benefit from mitogenic potential.
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Affiliation(s)
- Vittoria Massafra
- Center for Molecular Medicine, UMC Utrecht, Utrecht, The Netherlands
| | - Alexandra Milona
- Center for Molecular Medicine, UMC Utrecht, Utrecht, The Netherlands
| | - Harmjan R. Vos
- Center for Molecular Medicine, UMC Utrecht, Utrecht, The Netherlands
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26
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Oliveira FFD, Chen ES, Smith MC, Bertolucci PH. Associations of cerebrovascular metabolism genotypes with neuropsychiatric symptoms and age at onset of Alzheimer's disease dementia. ACTA ACUST UNITED AC 2017; 39:95-103. [PMID: 28099631 PMCID: PMC7111454 DOI: 10.1590/1516-4446-2016-1991] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 07/05/2016] [Indexed: 12/03/2022]
Abstract
Objective: To study associations of cerebrovascular metabolism genotypes and haplotypes with age at Alzheimer’s disease dementia (AD) onset and with neuropsychiatric symptoms according to each dementia stage. Methods: Consecutive outpatients with late-onset AD were assessed for age at dementia onset and Neuropsychiatric Inventory scores according to Clinical Dementia Rating scores, apolipoprotein E gene (APOE) haplotypes, angiotensin-converting enzyme gene (ACE) variants rs1800764 and rs4291, low-density lipoprotein cholesterol receptor gene (LDLR) variants rs11669576 and rs5930, cholesteryl ester transfer protein gene (CETP) variants I422V and TaqIB, and liver X receptor beta gene (NR1H2) polymorphism rs2695121. Results: Considering 201 patients, only APOE-ɛ4 carriers had earlier dementia onset in multiple correlations, as well as less apathy, more delusions, and more aberrant motor behavior. Both ACE polymorphisms were associated with less intense frontally mediated behaviors. Regarding LDLR variants, carriers of the A allele of rs11669576 had less anxiety and more aberrant motor behavior, whereas carriers of the A allele of rs5930 had less delusions, less anxiety, more apathy, and more irritability. CETP variants that included G alleles of I422V and TaqIB were mostly associated with less intense frontally mediated behaviors, while severely impaired carriers of the T allele of rs2695121 had more anxiety and more aberrant motor behavior. Conclusion: Though only APOE haplotypes affected AD onset, cerebrovascular metabolism genotypes were associated with differences in several neuropsychiatric manifestations of AD.
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Affiliation(s)
- Fabricio F de Oliveira
- Departamento de Neurologia e Neurocirurgia, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo, SP, Brazil
| | - Elizabeth S Chen
- Departamento de Morfologia e Genética, EPM, UNIFESP, São Paulo, SP, Brazil
| | - Marilia C Smith
- Departamento de Morfologia e Genética, EPM, UNIFESP, São Paulo, SP, Brazil
| | - Paulo H Bertolucci
- Departamento de Neurologia e Neurocirurgia, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo, SP, Brazil
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27
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Chen YC, Hsiao CJ, Jung CC, Hu HH, Chen JH, Lee WC, Chiou JM, Chen TF, Sun Y, Wen LL, Yip PK, Chu YM, Chen CJ, Yang HI. Performance Metrics for Selecting Single Nucleotide Polymorphisms in Late-onset Alzheimer's Disease. Sci Rep 2016; 6:36155. [PMID: 27805002 PMCID: PMC5090242 DOI: 10.1038/srep36155] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 10/10/2016] [Indexed: 12/13/2022] Open
Abstract
Previous genome-wide association studies using P-values to select single nucleotide polymorphisms (SNPs) have suffered from high false-positive and false-negative results. This case-control study recruited 713 late-onset Alzheimer's disease (LOAD) cases and controls aged ≥65 from three teaching hospitals in northern Taiwan from 2007 to 2010. Performance metrics were used to select SNPs in stage 1, which were then genotyped to another dataset (stage 2). Four SNPs (CPXM2 rs2362967, APOC1 rs4420638, ZNF521 rs7230380, and rs12965520) were identified for LOAD by both traditional P-values (without correcting for multiple tests) and performance metrics. After correction for multiple tests, no SNPs were identified by traditional P-values. Simultaneous testing of APOE e4 and APOC1 rs4420638 (the SNP with the best performance in the performance metrics) significantly improved the low sensitivity of APOE e4 from 0.50 to 0.78. A point-based genetic model including these 2 SNPs and important covariates was constructed. Compared with elders with low-risks score (0-6), elders belonging to moderate-risk (score = 7-11) and high-risk (score = 12-18) groups showed a significantly increased risk of LOAD (adjusted odds ratio = 7.80 and 46.93, respectively; Ptrend < 0.0001). Performance metrics allow for identification of markers with moderate effect and are useful for creating genetic tests with clinical and public health implications.
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Affiliation(s)
- Yen-Ching Chen
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
- Department of Public Health, College of Public Health, National Taiwan University, Taipei, Taiwan
- Research Center for Genes, Environment and Human Health, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Chi-Jung Hsiao
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Chien-Cheng Jung
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Hui-Han Hu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Jen-Hau Chen
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
- Department of Geriatrics and Gerontology, National Taiwan University, Taipei, Taiwan
| | - Wen-Chung Lee
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
- Department of Public Health, College of Public Health, National Taiwan University, Taipei, Taiwan
- Research Center for Genes, Environment and Human Health, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Jeng-Min Chiou
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Ta-Fu Chen
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
| | - Yu Sun
- Department of Neurology, En Chu Kong Hospital, Taipei, Taiwan
| | - Li-Li Wen
- Department of Laboratory Medicine, En Chu Kong Hospital, Taipei, Taiwan
| | - Ping-Keung Yip
- Center of Neurological Medicine, Cardinal Tien Hospital, Taipei, Taiwan
- School of Medicine, Fu-Jen Catholic University, New Taipei City, Taiwan
| | - Yi-Min Chu
- Department of Laboratory Medicine, Cardinal Tien Hospital, Taipei, Taiwan
| | - Chien-Jen Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Hwai-I Yang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
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28
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Georgakis MK, Papadopoulos FC, Protogerou AD, Pagonari I, Sarigianni F, Biniaris-Georgallis SI, Kalogirou EΙ, Thomopoulos TP, Kapaki E, Papageorgiou C, Papageorgiou SG, Tousoulis D, Petridou ET. Comorbidity of Cognitive Impairment and Late-Life Depression Increase Mortality: Results From a Cohort of Community-Dwelling Elderly Individuals in Rural Greece. J Geriatr Psychiatry Neurol 2016; 29:195-204. [PMID: 26917554 DOI: 10.1177/0891988716632913] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 01/19/2016] [Indexed: 12/20/2022]
Abstract
OBJECTIVE To investigate the association of cognitive impairment (COGI) and depression with all-cause mortality and cardiovascular-specific mortality among community-dwelling elderly individuals in rural Greece. METHODS Cognition and depressive symptomatology of 676 Velestino town residents aged ≥60 years were assessed using Mini-Mental State Examination (MMSE) and Geriatric Depression Scale (GDS), respectively. Eight-year all-cause mortality and cardiovascular mortality were explored by multivariate Cox regression models controlling for major confounders. RESULTS Two hundred and one patients died during follow-up. Cognitive impairment (MMSE ≤ 23) was independently associated with all-cause mortality (hazard ratio [HR]: 1.57, 95% confidence interval [CI]: 1.13-2.18) and cardiovascular mortality (HR: 1.57, 95%CI: 1.03-2.41). Moderate to severe depression (GDS > 10) was significantly associated only with a 51% increase in all-cause mortality. A male-specific association was noted for moderate to severe depression, whereas the effect of COGI was limited to females. Noteworthy, COGI and depression comorbidity, rather than their sole presence, increased all-cause mortality and cardiovascular mortality by 66% and 72%, respectively. The mortality effect of COGI was augmented among patients with depression and of depression among patients with COGI. CONCLUSION COGI and depression, 2 entities often coexisting among elderly individuals, appear to increase all-cause mortality and cardiovascular mortality. Gender-specific modes may prevail but their comorbidity should be carefully assessed, as it seems to represent an independent index of increased frailty, which eventually shortens life expectancy.
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Affiliation(s)
- Marios K Georgakis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Greece
| | - Fotios C Papadopoulos
- Department of Neuroscience, Psychiatry, Uppsala University, Uppsala University Hospital, Athens, Greece
| | - Athanasios D Protogerou
- Department of Pathophysiology, Medical School, National and Kapodistrian University of Athens, Greece
| | - Ioanna Pagonari
- Health Centre of Velestino, Ahillopouleio General Hospital of Volos, Greece
| | - Fani Sarigianni
- Health Centre of Velestino, Ahillopouleio General Hospital of Volos, Greece
| | | | - Eleni Ι Kalogirou
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Greece
| | - Thomas P Thomopoulos
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Greece
| | - Elisabeth Kapaki
- First Department of Neurology, Eginition Hospital, Medical School, National and Kapodistrian University of Athens, Greece
| | - Charalampos Papageorgiou
- First Department of Psychiatry, Eginition Hospital, Medical School, National and Kapodistrian University of Athens, Greece
| | - Socratis G Papageorgiou
- Second Department of Neurology, Attikon University General Hospital, Medical School, National and Kapodistrian University of Athens, Greece
| | - Dimitrios Tousoulis
- First Department of Cardiology, Hippokrateion Hospital, Medical School, National and Kapodistrian University of Athens, Greece
| | - Eleni Th Petridou
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Greece
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29
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Vitamin D interacts with Esr1 and Igf1 to regulate molecular pathways relevant to Alzheimer's disease. Mol Neurodegener 2016; 11:22. [PMID: 26932723 PMCID: PMC4774101 DOI: 10.1186/s13024-016-0087-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 02/23/2016] [Indexed: 01/05/2023] Open
Abstract
Background Increasing evidence suggests a potential therapeutic benefit of vitamin D supplementation against Alzheimer’s disease (AD). Although studies have shown improvements in cognitive performance and decreases in markers of the pathology after chronic treatment, the mechanisms by which vitamin D acts on brain cells are multiple and remain to be thoroughly studied. We analyzed the molecular changes observed after 5 months of vitamin D3 supplementation in the brains of transgenic 5xFAD (Tg) mice, a recognized mouse model of AD, and their wild type (Wt) littermates. We first performed a kinematic behavioural examination at 4, 6 and 8 months of age (M4, M6 and M8) followed by a histologic assessment of AD markers. We then performed a comparative transcriptomic analysis of mRNA regulation in the neocortex and hippocampus of 9 months old (M9) female mice. Results Transcriptomic analysis of the hippocampus and neocortex of both Wt and Tg mice at M9, following 5 months of vitamin D3 treatment, reveals a large panel of dysregulated pathways related to i) immune and inflammatory response, ii) neurotransmitter activity, iii) endothelial and vascular processes and iv) hormonal alterations. The differentially expressed genes are not all direct targets of the vitamin D-VDR pathway and it appears that vitamin D action engages in the crosstalk with estrogen and insulin signaling. The misexpression of the large number of genes observed in this study translates into improved learning and memory performance and a decrease in amyloid plaques and astrogliosis in Tg animals. Conclusions This study underlies the multiplicity of action of this potent neurosteroid in an aging and AD-like brain. The classical and non-classical actions of vitamin D3 can act in an additive and possibly synergistic manner to induce neuroprotective activities in a context-specific way. Electronic supplementary material The online version of this article (doi:10.1186/s13024-016-0087-2) contains supplementary material, which is available to authorized users.
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30
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Label-free based quantitative proteomics analysis of primary neonatal porcine Leydig cells exposed to the persistent contaminant 3-methylsulfonyl-DDE. J Proteomics 2016; 137:68-82. [DOI: 10.1016/j.jprot.2015.12.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 11/25/2015] [Accepted: 12/05/2015] [Indexed: 01/08/2023]
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31
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Abstract
The cholesterol transporting protein apolipoprotein E (ApoE) occurs in three allelic variants in humans unlike in other species. The resulting protein isoforms E2, E3 and E4 exhibit differences in lipid binding, integrating into lipoprotein particles and affinity for lipoprotein receptors. ApoE isoforms confer genetic risk for several diseases of aging including atherosclerosis, Alzheimer's disease, and age-related macular degeneration (AMD). A single E4 allele increases the risk of developing Alzheimer's disease, whereas the E2 allele is protective. Intriguingly, the E4 allele is protective in AMD. Current thinking about different functions of ApoE isoforms comes largely from studies on Alzheimer's disease. These data cannot be directly extrapolated to AMD since the primary cells affected in these diseases (neurons vs. retinal pigment epithelium) are so different. Here, we propose that ApoE serves a fundamentally different purpose in regulating cholesterol homeostasis in the retinal pigment epithelium and this could explain why allelic risk factors are flipped for AMD compared to Alzheimer's disease.
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32
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Colon K, Perez-Laspiur J, Quiles R, Rodriguez Y, Wojna V, Shaffer SA, Leszyk J, Skolasky RL, Melendez LM. Macrophage secretome from women with HIV-associated neurocognitive disorders. Proteomics Clin Appl 2015. [PMID: 26220577 DOI: 10.1002/prca.201400203] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
PURPOSE Thirty to 50% of HIV patients develop HIV-associated neurocognitive disorders (HANDs) despite combined antiretroviral therapy. HIV-1-infected macrophages release viral and cellular proteins that induce neuronal degeneration and death. We hypothesize that changes in the macrophage secretome of HIV-1 seropositive patients with HAND may dissect proteins related to neurotoxicity. EXPERIMENTAL DESIGN Monocyte-derived macrophages (MDMs) were isolated from the peripheral blood of 12 HIV+ and four HIV- women characterized for neurocognitive function. Serum-free MDM supernatants were collected for protein isolation and quantification with iTRAQ® labeling. Protein identification was performed using a LTQ Orbitrap Velos mass spectrometer and validated in MDM supernatants and in plasma using ELISA. RESULTS Three proteins were different between normal cognition (NC) and asymptomatic neurocognitive disorders (ANI), six between NC and HIV-associated dementia (HAD), and six between NC and HAD. Among these, S100A9 was decreased in plasma from patients with ANI, and metalloproteinase 9 was decreased in the plasma of all HIV+ patients regardless of cognitive status, and was significantly reduced in supernatant of MDM isolated from patients with ANI. CONCLUSIONS AND CLINICAL RELEVANCE S100A9 and metalloproteinase 9 have been associated with inflammation and cognitive impairment, and therefore represent potential targets for HAND treatment.
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Affiliation(s)
- Krystal Colon
- Department of Microbiology, Medical Sciences Campus, University of Puerto Rico, San Juan, PR, USA
| | - Juliana Perez-Laspiur
- RCMI Translational Proteomics Center, Medical Sciences Campus, University of Puerto Rico, San Juan, PR, USA
| | - Raymond Quiles
- Metropolitan Campus, Interamerican University, San Juan, PR, USA
| | - Yolanda Rodriguez
- Department of Microbiology, Medical Sciences Campus, University of Puerto Rico, San Juan, PR, USA
| | - Valerie Wojna
- Division of Neurology, Medical Sciences Campus, University of Puerto Rico, San Juan, PR, USA
| | - Scott A Shaffer
- Proteomics and Mass Spectrometry Facility, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - John Leszyk
- Proteomics and Mass Spectrometry Facility, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Richard L Skolasky
- Department of Orthopaedic Surgery, John Hopkins University, Baltimore, MD, USA
| | - Loyda M Melendez
- Department of Microbiology, Medical Sciences Campus, University of Puerto Rico, San Juan, PR, USA.,RCMI Translational Proteomics Center, Medical Sciences Campus, University of Puerto Rico, San Juan, PR, USA
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Salminen LE, Schofield PR, Pierce KD, Luo X, Zhao Y, Laidlaw DH, Cabeen RP, Conturo TE, Lane EM, Heaps JM, Bolzenius JD, Baker LM, Cooley SA, Scott S, Cagle LM, Paul RH. Genetic markers of cholesterol transport and gray matter diffusion: a preliminary study of the CETP I405V polymorphism. J Neural Transm (Vienna) 2015; 122:1581-92. [PMID: 26253899 PMCID: PMC4618053 DOI: 10.1007/s00702-015-1434-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 07/24/2015] [Indexed: 12/14/2022]
Abstract
Variations of the cholesteryl ester transfer protein polymorphism (CETP I405V/rs5882) have been associated with an increased risk for neurodegeneration, particularly when examined in conjunction with the epsilon 4 isoform of apolipoprotein E (ApoE4). Despite these identified relationships, the impact of I405V on gray matter microstructure remains unknown. The present study examined the impact of the CETP I405V polymorphism on gray matter integrity among 52 healthy adults between ages 51 and 85. Gray matter was measured bilaterally using diffusion tensor imaging (DTI) metrics of fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD), and radial diffusivity (RD). Participants were grouped according to a dominant statistical model (II genotype vs. IV/VV genotypes) and secondary analyses were completed to examine the interactive effects of CETP and ApoE4 on DTI metrics. Compared to individuals with the IV/VV genotypes, II homozygotes demonstrated significantly higher MD in bilateral temporal, parietal, and occipital gray matter. Secondary analyses revealed higher FA and AD in the left temporal lobe of IV/VV genotypes with an ApoE4 allele. Our results provide preliminary evidence that CETP II homozygosity is a predisposing risk factor for gray matter abnormalities in posterior brain regions in healthy older adults, independent of an ApoE4 allele.
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Affiliation(s)
- Lauren E Salminen
- Department of Psychological Sciences, University of Missouri-St. Louis, 1 University Blvd., Stadler Hall 442A, St. Louis, MO, 63121, USA.
| | - Peter R Schofield
- Neuroscience Research Australia, Barker Street Randwick, Sydney, NSW, 2031, Australia
- School of Medical Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Kerrie D Pierce
- Neuroscience Research Australia, Barker Street Randwick, Sydney, NSW, 2031, Australia
| | - Xi Luo
- Department of Biostatistics and Center for Statistical Sciences, Brown University, Providence, RI, 02912, USA
| | - Yi Zhao
- Department of Biostatistics and Center for Statistical Sciences, Brown University, Providence, RI, 02912, USA
| | - David H Laidlaw
- Computer Science Department, Brown University, Providence, RI, 02912, USA
| | - Ryan P Cabeen
- Computer Science Department, Brown University, Providence, RI, 02912, USA
| | - Thomas E Conturo
- Washington University School of Medicine, Mallinckrodt Institute of Radiology, 510 S. Kingshighway, St. Louis, MO, 63110, USA
| | - Elizabeth M Lane
- Vanderbilt University Medical Center, 1211 Medical Center Drive, Nashville, TN, 37232, USA
| | - Jodi M Heaps
- Missouri Institute of Mental Health, 4633 World Parkway Circle, Berkeley, MO, 63134-3115, USA
| | - Jacob D Bolzenius
- Department of Psychological Sciences, University of Missouri-St. Louis, 1 University Blvd., Stadler Hall 442A, St. Louis, MO, 63121, USA
| | - Laurie M Baker
- Department of Psychological Sciences, University of Missouri-St. Louis, 1 University Blvd., Stadler Hall 442A, St. Louis, MO, 63121, USA
| | - Sarah A Cooley
- Department of Psychological Sciences, University of Missouri-St. Louis, 1 University Blvd., Stadler Hall 442A, St. Louis, MO, 63121, USA
| | - Staci Scott
- Missouri Institute of Mental Health, 4633 World Parkway Circle, Berkeley, MO, 63134-3115, USA
| | - Lee M Cagle
- Department of Psychological Sciences, University of Missouri-St. Louis, 1 University Blvd., Stadler Hall 442A, St. Louis, MO, 63121, USA
| | - Robert H Paul
- Department of Psychological Sciences, University of Missouri-St. Louis, 1 University Blvd., Stadler Hall 442A, St. Louis, MO, 63121, USA
- Missouri Institute of Mental Health, 4633 World Parkway Circle, Berkeley, MO, 63134-3115, USA
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Lin Q, Cao Y, Gao J. Decreased expression of the APOA1-APOC3-APOA4 gene cluster is associated with risk of Alzheimer's disease. DRUG DESIGN DEVELOPMENT AND THERAPY 2015; 9:5421-31. [PMID: 26491253 PMCID: PMC4598222 DOI: 10.2147/dddt.s89279] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Background Apolipoprotein is genetically associated with the risk of Alzheimer’s disease (AD). The APOA1, APOC3, and APOA4 genes are closely linked and located on human chromosome 11. Therefore, this gene cluster may be related to the risk of AD. Patients and methods A total of 147 AD patients and 160 healthy controls were randomly recruited from June 2013 to August 2014. APOA1, APOC3, and APOA4 levels were measured using real-time quantitative reverse-transcriptase polymerase chain reaction and enzyme-linked immunosorbent assay. Results APOA1, APOC3 and APOA4 levels were significantly lower in AD patients than controls (P<0.01). APOA1, APOC3, and APOA4 levels were negatively related with the severities of AD determined by Clinical Dementia Rating scores (P<0.01). APOA1, APOC3, and APOA4 levels showed a negative relation with Montgomery–Åsberg Depression Rating Scale scores and a positive relation with RAND 36-item health-survey scores (P<0.01). There was a decreased trend for levels of APOA1, APOC3, and APOA4 in AD patients. Conclusion Low levels of APOA1, APOC3, and APOA4 are associated with risk of AD. APOA1, APOC3, and APOA4 should be developed as combined drugs for the therapy of AD.
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Affiliation(s)
- Qiao Lin
- Department of Internal Medicine, Fourth Affiliated Hospital of China Medical University, Shenyang, People's Republic of China
| | - Yunpeng Cao
- Neural Department of Internal Medicine, First Affiliated Hospital of China Medical University, Shenyang, People's Republic of China
| | - Jie Gao
- Department of Anatomy, First Affiliated Hospital of China Medical University, Shenyang, People's Republic of China
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Hooli BV, Kovacs-Vajna ZM, Mullin K, Blumenthal MA, Mattheisen M, Zhang C, Lange C, Mohapatra G, Bertram L, Tanzi RE. Rare autosomal copy number variations in early-onset familial Alzheimer's disease. Mol Psychiatry 2014; 19:676-81. [PMID: 23752245 DOI: 10.1038/mp.2013.77] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 03/19/2013] [Accepted: 04/15/2013] [Indexed: 01/08/2023]
Abstract
Over 200 rare and fully penetrant pathogenic mutations in amyloid precursor protein (APP), presenilin 1 and 2 (PSEN1 and PSEN2) cause a subset of early-onset familial Alzheimer's disease (EO-FAD). Of these, 21 cases of EO-FAD families carrying unique APP locus duplications remain the only pathogenic copy number variations (CNVs) identified to date in Alzheimer's disease (AD). Using high-density DNA microarrays, we performed a comprehensive genome-wide analysis for the presence of rare CNVs in 261 EO-FAD and early/mixed-onset pedigrees. Our analysis revealed 10 novel private CNVs in 10 EO-FAD families overlapping a set of genes that includes: A2BP1, ABAT, CDH2, CRMP1, DMRT1, EPHA5, EPHA6, ERMP1, EVC, EVC2, FLJ35024 and VLDLR. In addition, CNVs encompassing two known frontotemporal dementia genes, CHMP2B and MAPT were found. To our knowledge, this is the first study reporting rare gene-rich CNVs in EO-FAD and early/mixed-onset AD that are likely to underlie pathogenicity in familial AD and perhaps related dementias.
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Affiliation(s)
- B V Hooli
- Department of Neurology, Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Charlestown, MA, USA
| | - Z M Kovacs-Vajna
- Department of Information Engineering, University of Brescia, Brescia, Italy
| | - K Mullin
- Department of Neurology, Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Charlestown, MA, USA
| | - M A Blumenthal
- Department of Neurology, Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Charlestown, MA, USA
| | - M Mattheisen
- Channing Laboratory, Brigham and Women's Hospital, Boston MA, USA
| | - C Zhang
- Department of Neurology, Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Charlestown, MA, USA
| | - C Lange
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | - G Mohapatra
- Molecular Pathology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - L Bertram
- Max-Planck Institute for Molecular Genetics, Neuropsychiatric Genetics Group, Berlin, Germany
| | - R E Tanzi
- Department of Neurology, Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Charlestown, MA, USA
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Gao HH, Gao LB, Wen JM. Genetic polymorphisms in the ESR1 gene and cerebral infarction risk: a meta-analysis. DNA Cell Biol 2014; 33:605-15. [PMID: 24772998 DOI: 10.1089/dna.2013.2270] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
A number of studies have documented that estrogen receptor α (ESR1) may play an important role in the development and progression of cerebral infarction, but many existing studies have yielded inconclusive results. This meta-analysis was performed to evaluate the relationships between ESR1 genetic polymorphisms and cerebral infarction risk. The PubMed, CISCOM, CINAHL, Web of Science, Google Scholar, EBSCO, Cochrane Library, and CBM databases were searched for relevant articles published before October 1, 2013, without any language restrictions. Meta-analysis was conducted using the STATA 12.0 software. Seven case-control studies were included with a total of 1471 patients with cerebral infarction and 4688 healthy control subjects. Two common single-nucleotide polymorphisms (SNPs) in the ESR1 gene (rs2234693 T>C and rs9340799 A>G) were assessed. Our meta-analysis results revealed that ESR1 genetic polymorphisms might increase the risk of cerebral infarction. Subgroup analysis by SNP type indicated that both rs2234693 and rs9340799 polymorphisms in the ESR1 gene were strongly associated with an increased risk of cerebral infarction. Further subgroup analysis by ethnicity showed significant associations between ESR1 genetic polymorphisms and increased risk of cerebral infarction among both Asians and Caucasians. In the stratified subgroup analysis by gender, the results suggested that ESR1 genetic polymorphisms were associated with an increased risk of cerebral infarction in the female population. However, there were no statistically significant associations between ESR1 genetic polymorphisms and cerebral infarction risk in the male population. Meta-regression analyses also confirmed that gender might be a main source of heterogeneity. Our findings indicate that ESR1 genetic polymorphisms may contribute to the development of cerebral infarction, especially in the female population.
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Affiliation(s)
- Hong-Hua Gao
- Department of Neurology, The Fourth Affiliated Hospital of China Medical University , Shenyang, People's Republic of China
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Ferrer DG, Jaldín-Fincati JR, Amigone JL, Capra RH, Collino CJ, Albertini RA, Chiabrando GA. Standardized flow cytometry assay for identification of human monocytic heterogeneity and LRP1 expression in monocyte subpopulations: decreased expression of this receptor in nonclassical monocytes. Cytometry A 2014; 85:601-10. [PMID: 24639232 DOI: 10.1002/cyto.a.22455] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 12/27/2013] [Accepted: 02/18/2014] [Indexed: 12/12/2022]
Abstract
In this article, we present a flow cytometry assay by which human blood monocyte subpopulations-classical (CD14(++) CD16(-)), intermediate (CD14(++) CD16(+)), and nonclassical (CD14(+) CD16(++)) monocytes-can be determined. Monocytic cells were selected from CD45(+) leukocyte subsets by differential staining of the low-density lipoprotein receptor-related protein 1 (LRP1), which allows reducing the spill-over of natural killer cells and granulocytes into the CD16(+) monocyte gate. Percentages of monocyte subpopulations established by this procedure were significantly comparable with those obtained by a well-standardized flow cytometry assay based on the HLA-DR monocyte-gating strategy. We also demonstrated that LRP1 is differentially expressed at cell surface of monocyte subpopulations, being significantly lower in nonclassical monocytes than in classical and intermediate monocytes. Cell surface expression of LRP1 accounts for only 20% of the total cellular content in each monocyte subpopulation. Finally, we established the within-individual biological variation (bCV%) of circulating monocyte subpopulations in healthy donors, obtaining values of 21%, 20%, and 17% for nonclassical, intermediate, and classical monocytes, respectively. Similar values of bCV% for LRP1 measured in each monocyte subpopulation were also obtained, suggesting that its variability is mainly influenced by the intrinsic biological variation of circulating monocytes. Thus, we conclude that LRP1 can be used as a third pan-monocytic marker together with CD14 and CD16 to properly identify monocyte subpopulations. The combined determination of monocyte subpopulations and LRP1 monocytic expression may be relevant for clinical studies of inflammatory processes, with special interest in atherosclerosis and cardiovascular disease.
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Affiliation(s)
- Darío G Ferrer
- Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI-CONICET), Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
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Solomon A, Kivipelto M. Cholesterol-modifying strategies for Alzheimer’s disease. Expert Rev Neurother 2014; 9:695-709. [DOI: 10.1586/ern.09.25] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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McBride WJ, Kimpel MW, McClintick JN, Ding ZM, Hauser SR, Edenberg HJ, Bell RL, Rodd ZA. Changes in gene expression within the ventral tegmental area following repeated excessive binge-like alcohol drinking by alcohol-preferring (P) rats. Alcohol 2013; 47:367-80. [PMID: 23714385 DOI: 10.1016/j.alcohol.2013.04.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 04/02/2013] [Accepted: 04/17/2013] [Indexed: 12/11/2022]
Abstract
The objective of this study was to detect changes in gene expression in the ventral tegmental area (VTA) following repeated excessive binge-like ('loss-of-control') alcohol drinking by alcohol-preferring (P) rats. Adult female P rats (n = 7) were given concurrent access to 10, 20, and 30% EtOH for 4 1-h sessions daily for 10 weeks followed by 2 cycles of 2 weeks of abstinence and 2 weeks of EtOH access. Rats were sacrificed by decapitation 3 h after the 4th daily EtOH-access session at the end of the second 2-week relapse period. A water-control group of female P rats (n = 8) was also sacrificed. RNA was prepared from micro-punch samples of the VTA from individual rats; analyses were conducted with Affymetrix Rat 230.2 GeneChips. Ethanol intakes were 1.2-1.7 g/kg per session, resulting in blood levels >200 mg% at the end of the 4th session. There were 211 unique named genes that significantly differed (FDR = 0.1) between the water and EtOH groups. Bioinformatics analyses indicated alterations in a) transcription factors that reduced excitation-coupled transcription and promoted excitotoxic neuronal damage involving clusters of genes associated with Nfkbia, Fos, and Srebf1, b) genes that reduced cholesterol and fatty acid synthesis, and increased protein degradation, and c) genes involved in cell-to-cell interactions and regulation of the actin cytoskeleton. Among the named genes, there were 62 genes that showed differences between alcohol-naïve P and non-preferring (NP) rats, with 43 of the genes changing toward NP-like expression levels following excessive binge-like drinking in the P rats. These genes are involved in a pro-inflammatory response, and enhanced response to glucocorticoids and steroid hormones. Overall, the results of this study indicate that the repeated excessive binge-like alcohol drinking can change the expression of genes that may alter neuronal function in several ways, some of which may be deleterious.
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Affiliation(s)
- William J McBride
- Institute of Psychiatric Research, Department of Psychiatry, Indiana University School of Medicine, Indiana University-Purdue University at Indianapolis, Indianapolis, IN 46202, USA.
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Ryan MM, Morris GP, Mockett BG, Bourne K, Abraham WC, Tate WP, Williams JM. Time-dependent changes in gene expression induced by secreted amyloid precursor protein-alpha in the rat hippocampus. BMC Genomics 2013; 14:376. [PMID: 23742273 PMCID: PMC3691674 DOI: 10.1186/1471-2164-14-376] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 05/24/2013] [Indexed: 01/19/2023] Open
Abstract
Background Differential processing of the amyloid precursor protein liberates either amyloid-ß, a causative agent of Alzheimer’s disease, or secreted amyloid precursor protein-alpha (sAPPα), which promotes neuroprotection, neurotrophism, neurogenesis and synaptic plasticity. The underlying molecular mechanisms recruited by sAPPα that underpin these considerable cellular effects are not well elucidated. As these effects are enduring, we hypothesised that regulation of gene expression may be of importance and examined temporally specific gene networks and pathways induced by sAPPα in rat hippocampal organotypic slice cultures. Slices were exposed to 1 nM sAPPα or phosphate buffered saline for 15 min, 2 h or 24 h and sAPPα-associated gene expression profiles were produced for each time-point using Affymetrix Rat Gene 1.0 ST arrays (moderated t-test using Limma: p < 0.05, and fold change ± 1.15). Results Treatment of organotypic hippocampal slice cultures with 1 nM sAPPα induced temporally distinct gene expression profiles, including mRNA and microRNA associated with Alzheimer’s disease. Having demonstrated that treatment with human recombinant sAPPα was protective against N-methyl d-aspartate-induced toxicity, we next explored the sAPPα-induced gene expression profiles. Ingenuity Pathway Analysis predicted that short-term exposure to sAPPα elicited a multi-level transcriptional response, including upregulation of immediate early gene transcription factors (AP-1, Egr1), modulation of the chromatin environment, and apparent activation of the constitutive transcription factors CREB and NF-κB. Importantly, dynamic regulation of NF-κB appears to be integral to the transcriptional response across all time-points. In contrast, medium and long exposure to sAPPα resulted in an overall downregulation of gene expression. While these results suggest commonality between sAPPα and our previously reported analysis of plasticity-related gene expression, we found little crossover between these datasets. The gene networks formed following medium and long exposure to sAPPα were associated with inflammatory response, apoptosis, neurogenesis and cell survival; functions likely to be the basis of the neuroprotective effects of sAPPα. Conclusions Our results demonstrate that sAPPα rapidly and persistently regulates gene expression in rat hippocampus. This regulation is multi-level, temporally specific and is likely to underpin the neuroprotective effects of sAPPα.
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Affiliation(s)
- Margaret M Ryan
- Brain Health Research Centre, University of Otago, PO Box 56, Dunedin New Zealand.
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Wiwanitkit V. Physiological genomics analysis for Alzheimer's disease. Ann Indian Acad Neurol 2013; 16:72-4. [PMID: 23661967 PMCID: PMC3644786 DOI: 10.4103/0972-2327.107711] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 01/26/2012] [Accepted: 06/21/2012] [Indexed: 11/18/2022] Open
Abstract
Alzheimer's disease is a common kind of dementia. This disorder can be detected in all countries around the world. This neurological disorder affects millions of population and becomes an important concern in modern neurology. There are many researches on the pathogenesis of Alzheimer's disease. Although it has been determined for a long time, there is no clear-cut that this is a case with genetic disorder or not. A physiological genomics is a new application that is useful for track function to genes within the human genome and can be applied for answering the problem of underlying pathobiology of complex diseases. The physiogenomics can be helpful for study of systemic approach on the pathophysiology, and genomics might provide useful information to better understand the pathogenesis of Alzheimer's disease. The present advent in genomics technique makes it possible to trace for the underlying genomics of disease. In this work, physiological genomics analysis for Alzheimer's disease was performed. The standard published technique is used for assessment. According to this work, there are 20 identified physiogenomics relationship on several chromosomes. Considering the results, the HADH2 gene on chromosome X, APBA1 gene on chromosome 9, AGER gene on chromosome 6, GSK3B gene on chromosome 3, CDKHR1 gene on chromosome 17, APPBP1 gene on chromosome 16, APBA2 gene on chromosome 15, GAL gene on chromosome 11, and APLP2 gene on chromosome 11 have the highest physiogenomics score (9.26) while the CASP3 gene on chromosome 4 and the SNCA gene on chromosome 4 have the lowest physiogenomics score (7.44). The results from this study confirm that Alzheimer's disease has a polygenomic origin.
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Carter CJ. Toxoplasmosis and Polygenic Disease Susceptibility Genes: Extensive Toxoplasma gondii Host/Pathogen Interactome Enrichment in Nine Psychiatric or Neurological Disorders. J Pathog 2013; 2013:965046. [PMID: 23533776 PMCID: PMC3603208 DOI: 10.1155/2013/965046] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 08/18/2012] [Accepted: 09/10/2012] [Indexed: 01/04/2023] Open
Abstract
Toxoplasma gondii is not only implicated in schizophrenia and related disorders, but also in Alzheimer's or Parkinson's disease, cancer, cardiac myopathies, and autoimmune disorders. During its life cycle, the pathogen interacts with ~3000 host genes or proteins. Susceptibility genes for multiple sclerosis, Alzheimer's disease, schizophrenia, bipolar disorder, depression, childhood obesity, Parkinson's disease, attention deficit hyperactivity disorder (P from 8.01E - 05 (ADHD) to 1.22E - 71) (multiple sclerosis), and autism (P = 0.013), but not anorexia or chronic fatigue are highly enriched in the human arm of this interactome and 18 (ADHD) to 33% (MS) of the susceptibility genes relate to it. The signalling pathways involved in the susceptibility gene/interactome overlaps are relatively specific and relevant to each disease suggesting a means whereby susceptibility genes could orient the attentions of a single pathogen towards disruption of the specific pathways that together contribute (positively or negatively) to the endophenotypes of different diseases. Conditional protein knockdown, orchestrated by T. gondii proteins or antibodies binding to those of the host (pathogen derived autoimmunity) and metabolite exchange, may contribute to this disruption. Susceptibility genes may thus be related to the causes and influencers of disease, rather than (and as well as) to the disease itself.
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Affiliation(s)
- C. J. Carter
- Polygenic Pathways, Flat 2, 40 Baldslow Road, Hastings, East Sussex TN34 2EY, UK
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Zhao W, Marchani EE, Cheung CYK, Steinbart EJ, Schellenberg GD, Bird TD, Wijsman EM. Genome scan in familial late-onset Alzheimer's disease: a locus on chromosome 6 contributes to age-at-onset. Am J Med Genet B Neuropsychiatr Genet 2013; 162B:201-12. [PMID: 23355194 PMCID: PMC3654841 DOI: 10.1002/ajmg.b.32133] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 12/26/2012] [Indexed: 01/31/2023]
Abstract
Alzheimer's disease (AD) is a common, genetically complex, fatal neurodegenerative disorder of late life. Although several genes are known to play a role in early-onset AD, identification of the genetic basis of late onset AD (LOAD) has been challenging, with only the APOE gene known to have a high contribution to both AD risk and age-at-onset. Here, we present the first genome-scan analysis of the complete, well-characterized University of Washington LOAD sample of 119 pedigrees, using age-at-onset as the trait of interest. The analysis approach used allows for a multilocus trait model while at the same time accommodating age censoring, effects of APOE as a known genetic covariate, and full pedigree and marker information. The results provide strong evidence for linkage of loci contributing to age-at-onset to genomic regions on chromosome 6q16.3, and to 19q13.42 in the region of the APOE locus. There was evidence for interaction between APOE and the locus on chromosome 6q and suggestive evidence for linkage to chromosomes 11p13, 15q12-14, and 19p13.12. These results provide the first independent confirmation of an AD age-at-onset locus on chromosome 6 and suggest that further efforts towards identifying the underlying causal locus or loci are warranted.
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Affiliation(s)
- Wei Zhao
- Department of Biostatistics, University of Washington, Seattle, WA
| | - Elizabeth E. Marchani
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA
| | | | - Ellen J. Steinbart
- Geriatric Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle Division, Seattle, WA,Department of Neurology, University of Washington, Seattle, WA
| | - Gerard D. Schellenberg
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia PA
| | - Thomas D. Bird
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA,Geriatric Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle Division, Seattle, WA,Department of Neurology, University of Washington, Seattle, WA
| | - Ellen M. Wijsman
- Department of Biostatistics, University of Washington, Seattle, WA,Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA,Department of Genome Sciences, University of Washington, Seattle, WA
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Abad-Rodríguez J. ApoE isoform-related behavioral defects. Is chronic cholesterol loss-driven membrane disorganization behind? Exp Neurol 2013; 241:1-4. [DOI: 10.1016/j.expneurol.2012.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Revised: 11/30/2012] [Accepted: 12/07/2012] [Indexed: 10/27/2022]
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Keeney JTR, Swomley AM, Förster S, Harris JL, Sultana R, Butterfield DA. Apolipoprotein A-I: insights from redox proteomics for its role in neurodegeneration. Proteomics Clin Appl 2013; 7:109-22. [PMID: 23027708 PMCID: PMC3760000 DOI: 10.1002/prca.201200087] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Accepted: 09/03/2012] [Indexed: 01/03/2023]
Abstract
Proteomics has a wide range of applications, including determination of differences in the proteome in terms of expression and post-translational protein modifications. Redox proteomics allows the identification of specific targets of protein oxidation in a biological sample. Using proteomic techniques, apolipoprotein A-I (ApoA-I) has been found at decreased levels in subjects with a variety of neurodegenerative disorders including in the serum and cerebrospinal fluid (CSF) of Alzheimer disease (AD), Parkinson disease (PD), and Down syndrome (DS) with gout subjects. ApoA-I plays roles in cholesterol transport and regulation of inflammation. Redox proteomics further showed ApoA-I to be highly oxidatively modified and particularly susceptible to modification by 4-hydroxy-2-trans-nonenal (HNE), a lipid peroxidation product. In the current review, we discuss the consequences of oxidation of ApoA-I in terms of neurodegeneration. ROS-associated chemotherapy related ApoA-I oxidation leads to elevation of peripheral levels of tumor necrosis factor-α (TNF-α) that can cross the blood-brain barrier (BBB) causing a signaling cascade that can contribute to neuronal death, likely a contributor to what patients refer to as "chemobrain." Current evidence suggests ApoA-I to be a promising diagnostic marker as well as a potential target for therapeutic strategies in these neurodegenerative disorders.
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Affiliation(s)
- Jeriel T. R. Keeney
- Department of Chemistry, Center of Membrane Sciences, Sanders Brown Center on Aging, University of Kentucky, Lexington, KY 40506, USA
| | - Aaron M. Swomley
- Department of Chemistry, Center of Membrane Sciences, Sanders Brown Center on Aging, University of Kentucky, Lexington, KY 40506, USA
| | - Sarah Förster
- Department of Chemistry, Center of Membrane Sciences, Sanders Brown Center on Aging, University of Kentucky, Lexington, KY 40506, USA
- Institute of Animal Sciences, Department of Biochemistry, University of Bonn, 53115 Bonn, Germany
| | - Jessica L. Harris
- Department of Chemistry, Center of Membrane Sciences, Sanders Brown Center on Aging, University of Kentucky, Lexington, KY 40506, USA
| | - Rukhsana Sultana
- Department of Chemistry, Center of Membrane Sciences, Sanders Brown Center on Aging, University of Kentucky, Lexington, KY 40506, USA
| | - D. Allan Butterfield
- Department of Chemistry, Center of Membrane Sciences, Sanders Brown Center on Aging, University of Kentucky, Lexington, KY 40506, USA
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Application of an integrative computational framework in trancriptomic data of atherosclerotic mice suggests numerous molecular players. Adv Bioinformatics 2012; 2012:453513. [PMID: 23193398 PMCID: PMC3502768 DOI: 10.1155/2012/453513] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 09/21/2012] [Indexed: 01/09/2023] Open
Abstract
Atherosclerosis is a multifactorial disease involving a lot of genes and proteins recruited throughout its manifestation. The present study aims to exploit bioinformatic tools in order to analyze microarray data of atherosclerotic aortic lesions of ApoE knockout mice, a model widely used in atherosclerosis research. In particular, a dynamic analysis was performed among young and aged animals, resulting in a list of 852 significantly altered genes. Pathway analysis indicated alterations in critical cellular processes related to cell communication and signal transduction, immune response, lipid transport, and metabolism. Cluster analysis partitioned the significantly differentiated genes in three major clusters of similar expression profile. Promoter analysis applied to functional related groups of the same cluster revealed shared putative cis-elements potentially contributing to a common regulatory mechanism. Finally, by reverse engineering the functional relevance of differentially expressed genes with specific cellular pathways, putative genes acting as hubs, were identified, linking functionally disparate cellular processes in the context of traditional molecular description.
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Wu H, Lu Y, Shen C, Patel N, Gan L, Xiong WC, Mei L. Distinct roles of muscle and motoneuron LRP4 in neuromuscular junction formation. Neuron 2012; 75:94-107. [PMID: 22794264 DOI: 10.1016/j.neuron.2012.04.033] [Citation(s) in RCA: 127] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/23/2012] [Indexed: 01/07/2023]
Abstract
Neuromuscular junction (NMJ) formation requires precise interaction between motoneurons and muscle fibers. LRP4 is a receptor of agrin that is thought to act in cis to stimulate MuSK in muscle fibers for postsynaptic differentiation. Here we dissected the roles of LRP4 in muscle fibers and motoneurons in NMJ formation by cell-specific mutation. Studies of muscle-specific mutants suggest that LRP4 is involved in deciding where to form AChR clusters in muscle fibers, postsynaptic differentiation, and axon terminal development. LRP4 in HEK293 cells increased synapsin or SV2 puncta in contacting axons of cocultured neurons, suggesting a synaptogenic function. Analysis of LRP4 muscle and motoneuron double mutants and mechanistic studies suggest that NMJ formation may also be regulated by LRP4 in motoneurons, which could serve as agrin's receptor in trans to induce AChR clusters. These observations uncovered distinct roles of LRP4 in motoneurons and muscles in NMJ development.
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Affiliation(s)
- Haitao Wu
- Institute of Molecular Medicine and Genetics and Department of Neurology, Medical College of Georgia, Georgia Health Sciences University, Augusta, GA 30912, USA
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Gamba P, Testa G, Sottero B, Gargiulo S, Poli G, Leonarduzzi G. The link between altered cholesterol metabolism and Alzheimer's disease. Ann N Y Acad Sci 2012; 1259:54-64. [PMID: 22758637 DOI: 10.1111/j.1749-6632.2012.06513.x] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Alzheimer's disease (AD), the most common form of dementia, is characterized by the progressive loss of neurons and synapses, and by extracellular deposits of amyloid-β (Aβ) as senile plaques, Aβ deposits in the cerebral blood vessels, and intracellular inclusions of hyperphosphorylated tau in the form of neurofibrillary tangles. Several mechanisms contribute to AD development and progression, and increasing epidemiological and molecular evidence suggests a key role of cholesterol in its initiation and progression. Altered cholesterol metabolism and hypercholesterolemia appear to play fundamental roles in amyloid plaque formation and tau hyperphosphorylation. Over the last decade, growing evidence supports the idea that cholesterol oxidation products, known as oxysterols, may be the missing link between altered brain cholesterol metabolism and AD pathogenesis, as their involvement in neurotoxicity, mainly by interacting with Aβ peptides, is reported.
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Affiliation(s)
- Paola Gamba
- Department of Clinical and Biological Sciences, Faculty of Medicine San Luigi Gonzaga, University of Turin, Turin, Italy
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Chakrabarti A, Mukhopadhyay D. Novel adaptors of amyloid precursor protein intracellular domain and their functional implications. GENOMICS PROTEOMICS & BIOINFORMATICS 2012; 10:208-16. [PMID: 23084776 PMCID: PMC5054717 DOI: 10.1016/j.gpb.2012.07.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Revised: 03/19/2012] [Accepted: 03/21/2012] [Indexed: 01/20/2023]
Abstract
Amyloid precursor protein intracellular domain (AICD) is one of the potential candidates in deciphering the complexity of Alzheimer’s disease. It plays important roles in determining cell fate and neurodegeneration through its interactions with several adaptors. The presence or absence of phosphorylation at specific sites determines the choice of partners. In this study, we identified 20 novel AICD-interacting proteins by in vitro pull down experiments followed by 2D gel electrophoresis and MALDI-MS analysis. The identified proteins can be grouped into different functional classes including molecular chaperones, structural proteins, signaling and transport molecules, adaptors, motor proteins and apoptosis determinants. Interactions of nine proteins were further validated either by colocalization using confocal imaging or by co-immunoprecipitation followed by immunoblotting. The cellular functions of most of the proteins can be correlated with AD. Hence, illustration of their interactions with AICD may shed some light on the disease pathophysiology.
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Affiliation(s)
- Arunabha Chakrabarti
- Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, West Bengal, India
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Hwang T, Atluri G, Xie M, Dey S, Hong C, Kumar V, Kuang R. Co-clustering phenome-genome for phenotype classification and disease gene discovery. Nucleic Acids Res 2012; 40:e146. [PMID: 22735708 PMCID: PMC3479160 DOI: 10.1093/nar/gks615] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Understanding the categorization of human diseases is critical for reliably identifying disease causal genes. Recently, genome-wide studies of abnormal chromosomal locations related to diseases have mapped >2000 phenotype–gene relations, which provide valuable information for classifying diseases and identifying candidate genes as drug targets. In this article, a regularized non-negative matrix tri-factorization (R-NMTF) algorithm is introduced to co-cluster phenotypes and genes, and simultaneously detect associations between the detected phenotype clusters and gene clusters. The R-NMTF algorithm factorizes the phenotype–gene association matrix under the prior knowledge from phenotype similarity network and protein–protein interaction network, supervised by the label information from known disease classes and biological pathways. In the experiments on disease phenotype–gene associations in OMIM and KEGG disease pathways, R-NMTF significantly improved the classification of disease phenotypes and disease pathway genes compared with support vector machines and Label Propagation in cross-validation on the annotated phenotypes and genes. The newly predicted phenotypes in each disease class are highly consistent with human phenotype ontology annotations. The roles of the new member genes in the disease pathways are examined and validated in the protein–protein interaction subnetworks. Extensive literature review also confirmed many new members of the disease classes and pathways as well as the predicted associations between disease phenotype classes and pathways.
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Affiliation(s)
- TaeHyun Hwang
- Bioinformatics core at Masonic Cancer Center, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
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