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Veteleanu A, Stevenson-Hoare J, Keat S, Daskoulidou N, Zetterberg H, Heslegrave A, Escott-Price V, Williams J, Sims R, Zelek WM, Carpanini SM, Morgan BP. Alzheimer's disease-associated complement gene variants influence plasma complement protein levels. J Neuroinflammation 2023; 20:169. [PMID: 37480051 PMCID: PMC10362776 DOI: 10.1186/s12974-023-02850-6] [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: 04/17/2023] [Accepted: 07/08/2023] [Indexed: 07/23/2023] Open
Abstract
BACKGROUND Alzheimer's disease (AD) has been associated with immune dysregulation in biomarker and genome-wide association studies (GWAS). GWAS hits include the genes encoding complement regulators clusterin (CLU) and complement receptor 1 (CR1), recognised as key players in AD pathology, and complement proteins have been proposed as biomarkers. MAIN BODY To address whether changes in plasma complement protein levels in AD relate to AD-associated complement gene variants we first measured relevant plasma complement proteins (clusterin, C1q, C1s, CR1, factor H) in a large cohort comprising early onset AD (EOAD; n = 912), late onset AD (LOAD; n = 492) and control (n = 504) donors. Clusterin and C1q were significantly increased (p < 0.001) and sCR1 and factor H reduced (p < 0.01) in AD plasma versus controls. ROC analyses were performed to assess utility of the measured complement biomarkers, alone or in combination with amyloid beta, in predicting AD. C1q was the most predictive single complement biomarker (AUC 0.655 LOAD, 0.601 EOAD); combining C1q with other complement or neurodegeneration makers through stepAIC-informed models improved predictive values slightly. Effects of GWS SNPs (rs6656401, rs6691117 in CR1; rs11136000, rs9331888 in CLU; rs3919533 in C1S) on protein concentrations were assessed by comparing protein levels in carriers of the minor vs major allele. To identify new associations between SNPs and changes in plasma protein levels, we performed a GWAS combining genotyping data in the cohort with complement protein levels as endophenotype. SNPs in CR1 (rs6656401), C1S (rs3919533) and CFH (rs6664877) reached significance and influenced plasma levels of the corresponding protein, whereas SNPs in CLU did not influence clusterin levels. CONCLUSION Complement dysregulation is evident in AD and may contribute to pathology. AD-associated SNPs in CR1, C1S and CFH impact plasma levels of the encoded proteins, suggesting a mechanism for impact on disease risk.
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Affiliation(s)
- Aurora Veteleanu
- UK Dementia Research Institute Cardiff, School of Medicine, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ UK
| | | | - Samuel Keat
- UK Dementia Research Institute Cardiff, School of Medicine, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ UK
| | - Nikoleta Daskoulidou
- UK Dementia Research Institute Cardiff, School of Medicine, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ UK
| | - Henrik Zetterberg
- UK Dementia Research Institute at University College London, London, WC1E6BT UK
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Psychology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, WC1N3BG UK
- Hong Kong Center for Neurodegenerative Diseases, Clear Water Bay, Hong Kong, China
| | - Amanda Heslegrave
- UK Dementia Research Institute at University College London, London, WC1E6BT UK
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, WC1N3BG UK
| | | | - Julie Williams
- UK Dementia Research Institute Cardiff, School of Medicine, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ UK
| | - Rebecca Sims
- Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, CF244HQ UK
| | - Wioleta M. Zelek
- UK Dementia Research Institute Cardiff, School of Medicine, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ UK
| | - Sarah M. Carpanini
- UK Dementia Research Institute Cardiff, School of Medicine, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ UK
| | - Bryan Paul Morgan
- UK Dementia Research Institute Cardiff, School of Medicine, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ UK
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Bradley J, Gorijala P, Schindler SE, Sung YJ, Ances B, Fernandez MV, Cruchaga C. Genetic architecture of plasma Alzheimer disease biomarkers. Hum Mol Genet 2023; 32:2532-2543. [PMID: 37208024 PMCID: PMC10360384 DOI: 10.1093/hmg/ddad087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 04/29/2023] [Accepted: 05/16/2023] [Indexed: 05/21/2023] Open
Abstract
Genome-wide association studies (GWAS) of cerebrospinal fluid (CSF) Alzheimer's Disease (AD) biomarker levels have identified novel genes implicated in disease risk, onset and progression. However, lumbar punctures have limited availability and may be perceived as invasive. Blood collection is readily available and well accepted, but it is not clear whether plasma biomarkers will be informative for genetic studies. Here we perform genetic analyses on concentrations of plasma amyloid-β peptides Aβ40 (n = 1,467) and Aβ42 (n = 1,484), Aβ42/40 (n = 1467) total tau (n = 504), tau phosphorylated (p-tau181; n = 1079) and neurofilament light (NfL; n = 2,058). GWAS and gene-based analysis was used to identify single variant and genes associated with plasma levels. Finally, polygenic risk score and summary statistics were used to investigate overlapping genetic architecture between plasma biomarkers, CSF biomarkers and AD risk. We found a total of six genome-wide significant signals. APOE was associated with plasma Aβ42, Aβ42/40, tau, p-tau181 and NfL. We proposed 10 candidate functional genes on the basis of 12 single nucleotide polymorphism-biomarker pairs and brain differential gene expression analysis. We found a significant genetic overlap between CSF and plasma biomarkers. We also demonstrate that it is possible to improve the specificity and sensitivity of these biomarkers, when genetic variants regulating protein levels are included in the model. This current study using plasma biomarker levels as quantitative traits can be critical to identification of novel genes that impact AD and more accurate interpretation of plasma biomarker levels.
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Affiliation(s)
- Joseph Bradley
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO 63110, USA
- Hope Center for Neurologic Diseases, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Priyanka Gorijala
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Suzanne E Schindler
- Hope Center for Neurologic Diseases, Washington University in St. Louis, St. Louis, MO 63110, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yun J Sung
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO 63110, USA
- Hope Center for Neurologic Diseases, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Beau Ances
- Hope Center for Neurologic Diseases, Washington University in St. Louis, St. Louis, MO 63110, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Maria V Fernandez
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO 63110, USA
- Hope Center for Neurologic Diseases, Washington University in St. Louis, St. Louis, MO 63110, USA
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Cong W, Meng X, Li J, Zhang Q, Chen F, Liu W, Wang Y, Cheng S, Yao X, Yan J, Kim S, Saykin AJ, Liang H, Shen L. Genome-wide network-based pathway analysis of CSF t-tau/Aβ1-42 ratio in the ADNI cohort. BMC Genomics 2017; 18:421. [PMID: 28558704 PMCID: PMC5450240 DOI: 10.1186/s12864-017-3798-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 05/16/2017] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The cerebrospinal fluid (CSF) levels of total tau (t-tau) and Aβ1-42 are potential early diagnostic markers for probable Alzheimer's disease (AD). The influence of genetic variation on these CSF biomarkers has been investigated in candidate or genome-wide association studies (GWAS). However, the investigation of statistically modest associations in GWAS in the context of biological networks is still an under-explored topic in AD studies. The main objective of this study is to gain further biological insights via the integration of statistical gene associations in AD with physical protein interaction networks. RESULTS The CSF and genotyping data of 843 study subjects (199 CN, 85 SMC, 239 EMCI, 207 LMCI, 113 AD) from the Alzheimer's Disease Neuroimaging Initiative (ADNI) were analyzed. PLINK was used to perform GWAS on the t-tau/Aβ1-42 ratio using quality controlled genotype data, including 563,980 single nucleotide polymorphisms (SNPs), with age, sex and diagnosis as covariates. Gene-level p-values were obtained by VEGAS2. Genes with p-value ≤ 0.05 were mapped on to a protein-protein interaction (PPI) network (9,617 nodes, 39,240 edges, from the HPRD Database). We integrated a consensus model strategy into the iPINBPA network analysis framework, and named it as CM-iPINBPA. Four consensus modules (CMs) were discovered by CM-iPINBPA, and were functionally annotated using the pathway analysis tool Enrichr. The intersection of four CMs forms a common subnetwork of 29 genes, including those related to tau phosphorylation (GSK3B, SUMO1, AKAP5, CALM1 and DLG4), amyloid beta production (CASP8, PIK3R1, PPA1, PARP1, CSNK2A1, NGFR, and RHOA), and AD (BCL3, CFLAR, SMAD1, and HIF1A). CONCLUSIONS This study coupled a consensus module (CM) strategy with the iPINBPA network analysis framework, and applied it to the GWAS of CSF t-tau/Aβ1-42 ratio in an AD study. The genome-wide network analysis yielded 4 enriched CMs that share not only genes related to tau phosphorylation or amyloid beta production but also multiple genes enriching several KEGG pathways such as Alzheimer's disease, colorectal cancer, gliomas, renal cell carcinoma, Huntington's disease, and others. This study demonstrated that integration of gene-level associations with CMs could yield statistically significant findings to offer valuable biological insights (e.g., functional interaction among the protein products of these genes) and suggest high confidence candidates for subsequent analyses.
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Affiliation(s)
- Wang Cong
- College of Automation, Harbin Engineering University, 145 Nantong Street, BLDG 61-5029, Harbin, 150001 China
| | - Xianglian Meng
- College of Automation, Harbin Engineering University, 145 Nantong Street, BLDG 61-5029, Harbin, 150001 China
- Harbin Huade University, No.288 Xue Yuan Rd. Limin Development Zone, Harbin, 150025 China
| | - Jin Li
- College of Automation, Harbin Engineering University, 145 Nantong Street, BLDG 61-5029, Harbin, 150001 China
| | - Qiushi Zhang
- College of Automation, Harbin Engineering University, 145 Nantong Street, BLDG 61-5029, Harbin, 150001 China
- College of Information Engineering, Northeast Dianli University, 169 Changchun Street, Jilin City, Jilin 132012 China
| | - Feng Chen
- College of Automation, Harbin Engineering University, 145 Nantong Street, BLDG 61-5029, Harbin, 150001 China
| | - Wenjie Liu
- College of Automation, Harbin Engineering University, 145 Nantong Street, BLDG 61-5029, Harbin, 150001 China
| | - Ying Wang
- College of Automation, Harbin Engineering University, 145 Nantong Street, BLDG 61-5029, Harbin, 150001 China
| | - Sipu Cheng
- College of Automation, Harbin Engineering University, 145 Nantong Street, BLDG 61-5029, Harbin, 150001 China
| | - Xiaohui Yao
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, 355 W 16th St, Suite 4100, Indianapolis, IN 46202 USA
- School of Informatics and Computing, Indiana University, 719 Indiana Avenue, Indianapolis, IN 46202 USA
| | - Jingwen Yan
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, 355 W 16th St, Suite 4100, Indianapolis, IN 46202 USA
- School of Informatics and Computing, Indiana University, 719 Indiana Avenue, Indianapolis, IN 46202 USA
- Indiana University Network Science Institute, Bloomington, IN 47405 USA
| | - Sungeun Kim
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, 355 W 16th St, Suite 4100, Indianapolis, IN 46202 USA
- Indiana University Network Science Institute, Bloomington, IN 47405 USA
| | - Andrew J. Saykin
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, 355 W 16th St, Suite 4100, Indianapolis, IN 46202 USA
- Indiana University Network Science Institute, Bloomington, IN 47405 USA
| | - Hong Liang
- College of Automation, Harbin Engineering University, 145 Nantong Street, BLDG 61-5029, Harbin, 150001 China
| | - Li Shen
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, 355 W 16th St, Suite 4100, Indianapolis, IN 46202 USA
- School of Informatics and Computing, Indiana University, 719 Indiana Avenue, Indianapolis, IN 46202 USA
| | - for the Alzheimer’s Disease Neuroimaging Initiative
- College of Automation, Harbin Engineering University, 145 Nantong Street, BLDG 61-5029, Harbin, 150001 China
- Harbin Huade University, No.288 Xue Yuan Rd. Limin Development Zone, Harbin, 150025 China
- College of Information Engineering, Northeast Dianli University, 169 Changchun Street, Jilin City, Jilin 132012 China
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, 355 W 16th St, Suite 4100, Indianapolis, IN 46202 USA
- School of Informatics and Computing, Indiana University, 719 Indiana Avenue, Indianapolis, IN 46202 USA
- Indiana University Network Science Institute, Bloomington, IN 47405 USA
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Voyle N, Patel H, Folarin A, Newhouse S, Johnston C, Visser PJ, Dobson RJ, Kiddle SJ. Genetic Risk as a Marker of Amyloid-β and Tau Burden in Cerebrospinal Fluid. J Alzheimers Dis 2017; 55:1417-1427. [PMID: 27834776 PMCID: PMC5181674 DOI: 10.3233/jad-160707] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2016] [Indexed: 12/31/2022]
Abstract
BACKGROUND The search for a biomarker of Alzheimer's disease (AD) pathology (amyloid-β (Aβ) and tau) is ongoing, with the best markers currently being measurements of Aβ and tau in cerebrospinal fluid (CSF) and via positron emission tomography (PET) scanning. These methods are relatively invasive, costly, and often have high screening failure rates. Consequently, research is aiming to elucidate blood biomarkers of Aβ and tau. OBJECTIVE This study aims to investigate a case/control polygenic risk score (PGRS) as a marker of tau and investigate blood markers of a combined Aβ and tau outcome for the first time. A sub-study also considers plasma tau as markers of Aβ and tau pathology in CSF. METHODS We used data from the EDAR*, DESCRIPA**, and Alzheimer's Disease Neuroimaging Initiative (ADNI) cohorts in a logistic regression analysis to investigate blood markers of Aβ and tau in CSF. In particular, we investigated the extent to which a case/control PGRS is predictive of CSF tau, CSF amyloid, and a combined amyloid and tau outcome. The predictive ability of models was compared to that of age, gender, and APOE genotype ('basic model'). RESULTS In EDAR and DESCRIPA test data, inclusion of a case/control PGRS was no more predictive of Aβ, and a combined Aβ and tau endpoint than the basic models (accuracies of 66.0%, and 73.3% respectively). The tau model saw a small increase in accuracy compared to basic models (59.6%). ADNI 2 test data also showed a slight increase in accuracy for the Aβ model when compared to the basic models (61.4%). CONCLUSION We see some evidence that a case/control PGRS is marginally more predictive of Aβ and tau pathology than the basic models. The search for predictive factors of Aβ and tau pathologies, above and beyond demographic information, is still ongoing. Better understanding of AD risk alleles, development of more sensitive assays, and studies of larger sample size are three avenues that may provide such factors. However, the clinical utility of possible predictors of brain Aβ and tau pathologies must also be investigated.*'Beta amyloid oligomers in the early diagnosis of AD and as marker for treatment response'**'Development of screening guidelines and criteria for pre-dementia Alzheimer's disease'.
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Affiliation(s)
- Nicola Voyle
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
| | - Hamel Patel
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
| | - Amos Folarin
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
| | - Stephen Newhouse
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
| | - Caroline Johnston
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
| | - Pieter Jelle Visser
- Department of Neurology and Alzheimer Center, VU University Medical Center, Amsterdam, The Netherlands
- Helen Wills Neuroscience Institute, University of California, Berkeley, CA, USA
| | - Richard J.B. Dobson
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
- NIHR Biomedical Research Centre for Mental Health and Biomedical Research Unit for Dementia at South London and Maudsley NHS Foundation, London, UK
- Farr Institute of Health Informatics Research, UCL Institute of Health Informatics, University College London, London, UK
| | - Steven J. Kiddle
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
- MRC Biostatistics Unit, Cambridge Biomedical Campus, Cambridge Institute of Public Health, Forvie Site, Robinson Way, Cambridge, UK
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Abstract
Genetic characterization of individuals at risk of Alzheimer's disease (AD), i.e. people having amyloid deposits in the brain without symptoms, people suffering from subjective cognitive decline (SCD) or mild cognitive impairment (MCI), has spurred the interests of researchers. However, their pre-dementia genetic profile remains mostly unexplored. In this study, we reviewed the loci related to phenotypes of AD, MCI and SCD from literature and performed the first meta-analyses evaluating the role of apolipoprotein E (APOE) in the risk of conversion from a healthy status to MCI and SCD. For AD dementia risk, an increased number of loci have been identified; to date, 28 genes have been associated with Late Onset AD. In MCI syndrome, APOE is confirmed as a pheno-conversion factor leading from MCI to AD, and clusterin is a promising candidate. Additionally, our meta-analyses revealed APOE as genetic risk factor to convert from a healthy status to MCI [OR = 1.849 (1.587-2.153); P = 2.80 × 10-15] and to a lesser extent from healthy status to SCD [OR = 1.151 (1.015-1.304); P = 0.028]. Thus, we believe that genetic studies in longitudinal SCD and MCI series may provide new therapeutic targets and improve the existing knowledge of AD. This type of studies must be completed on healthy subjects to better understand the natural disease resistance to brain insults and neurodegeneration.
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Ravikumar KE, Wagholikar KB, Li D, Kocher JP, Liu H. Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature. BMC Bioinformatics 2015; 16:185. [PMID: 26047637 PMCID: PMC4457984 DOI: 10.1186/s12859-015-0609-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 04/30/2015] [Indexed: 12/03/2022] Open
Abstract
Background Advances in the next generation sequencing technology has accelerated the pace of individualized medicine (IM), which aims to incorporate genetic/genomic information into medicine. One immediate need in interpreting sequencing data is the assembly of information about genetic variants and their corresponding associations with other entities (e.g., diseases or medications). Even with dedicated effort to capture such information in biological databases, much of this information remains ‘locked’ in the unstructured text of biomedical publications. There is a substantial lag between the publication and the subsequent abstraction of such information into databases. Multiple text mining systems have been developed, but most of them focus on the sentence level association extraction with performance evaluation based on gold standard text annotations specifically prepared for text mining systems. Results We developed and evaluated a text mining system, MutD, which extracts protein mutation-disease associations from MEDLINE abstracts by incorporating discourse level analysis, using a benchmark data set extracted from curated database records. MutD achieves an F-measure of 64.3 % for reconstructing protein mutation disease associations in curated database records. Discourse level analysis component of MutD contributed to a gain of more than 10 % in F-measure when compared against the sentence level association extraction. Our error analysis indicates that 23 of the 64 precision errors are true associations that were not captured by database curators and 68 of the 113 recall errors are caused by the absence of associated disease entities in the abstract. After adjusting for the defects in the curated database, the revised F-measure of MutD in association detection reaches 81.5 %. Conclusions Our quantitative analysis reveals that MutD can effectively extract protein mutation disease associations when benchmarking based on curated database records. The analysis also demonstrates that incorporating discourse level analysis significantly improved the performance of extracting the protein-mutation-disease association. Future work includes the extension of MutD for full text articles.
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Affiliation(s)
- Komandur Elayavilli Ravikumar
- Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First St SW, Harvick 3rd, Rochester, MN, 55905, USA.
| | - Kavishwar B Wagholikar
- Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First St SW, Harvick 3rd, Rochester, MN, 55905, USA.
| | - Dingcheng Li
- Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First St SW, Harvick 3rd, Rochester, MN, 55905, USA.
| | - Jean-Pierre Kocher
- Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First St SW, Harvick 3rd, Rochester, MN, 55905, USA.
| | - Hongfang Liu
- Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First St SW, Harvick 3rd, Rochester, MN, 55905, USA.
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Tabassum S, Sheikh AM, Yano S, Ikeue T, Handa M, Nagai A. A carboxylated Zn-phthalocyanine inhibits fibril formation of Alzheimer's amyloid β peptide. FEBS J 2014; 282:463-76. [PMID: 25404240 DOI: 10.1111/febs.13151] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 11/07/2014] [Accepted: 11/14/2014] [Indexed: 12/31/2022]
Abstract
Amyloid β (Aβ), a 39-42 amino acid peptide derived from amyloid precursor protein, is deposited as fibrils in Alzheimer's disease brains, and is considered to play a major role in the pathogenesis of the disease. We have investigated the effects of a water-soluble Zn-phthalocyanine, ZnPc(COONa)₈, a macrocyclic compound with near-infrared optical properties, on Aβ fibril formation in vitro. A thioflavin T fluorescence assay showed that ZnPc(COONa)₈ significantly inhibited Aβ fibril formation, increasing the lag time and dose-dependently decreasing the plateau level of fibril formation. Moreover, it destabilized pre-formed Aβ fibrils, resulting in an increase in low-molecular-weight species. After fibril formation in the presence of ZnPc(COONa)₈, immunoprecipitation of Aβ₁₋₄₂ using Aβ-specific antibody followed by near-infrared scanning demonstrated binding of ZnPc(COONa)₈ to Aβ₁₋₄₂. A study using the hydrophobic fluorescent probe 8-anilino-1-naphthalenesulfonic acid showed that ZnPc(COONa)8 decreased the hydrophobicity during Aβ₁₋₄₂ fibril formation. CD spectroscopy showed an increase in the α helix structure and a decrease in the β sheet structure of Aβ₁₋₄₀ in fibril-forming buffer containing ZnPc(COONa)₈. SDS/PAGE and a dot-blot immunoassay showed that ZnPc(COONa)₈ delayed the disappearance of low-molecular-weight species and the appearance of higher-molecular-weight oligomeric species of Aβ₁₋₄₂. A cell viability assay showed that ZnPc(COONa)₈ was not toxic to a neuronal cell line (A1), but instead protected A1 cells against Aβ₁₋₄₂-induced toxicity. Overall, our results indicate that ZnPc(COONa)₈ binds to Aβ and decreases the hydrophobicity, and this change is unfavorable for Aβ oligomerization and fibril formation.
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Affiliation(s)
- Shatera Tabassum
- Department of Laboratory Medicine, Shimane University School of Medicine, Izumo, Japan
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8
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Kauwe JSK, Bailey MH, Ridge PG, Perry R, Wadsworth ME, Hoyt KL, Staley LA, Karch CM, Harari O, Cruchaga C, Ainscough BJ, Bales K, Pickering EH, Bertelsen S, Fagan AM, Holtzman DM, Morris JC, Goate AM. Genome-wide association study of CSF levels of 59 alzheimer's disease candidate proteins: significant associations with proteins involved in amyloid processing and inflammation. PLoS Genet 2014; 10:e1004758. [PMID: 25340798 PMCID: PMC4207667 DOI: 10.1371/journal.pgen.1004758] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 09/16/2014] [Indexed: 01/25/2023] Open
Abstract
Cerebrospinal fluid (CSF) 42 amino acid species of amyloid beta (Aβ42) and tau levels are strongly correlated with the presence of Alzheimer's disease (AD) neuropathology including amyloid plaques and neurodegeneration and have been successfully used as endophenotypes for genetic studies of AD. Additional CSF analytes may also serve as useful endophenotypes that capture other aspects of AD pathophysiology. Here we have conducted a genome-wide association study of CSF levels of 59 AD-related analytes. All analytes were measured using the Rules Based Medicine Human DiscoveryMAP Panel, which includes analytes relevant to several disease-related processes. Data from two independently collected and measured datasets, the Knight Alzheimer's Disease Research Center (ADRC) and Alzheimer's Disease Neuroimaging Initiative (ADNI), were analyzed separately, and combined results were obtained using meta-analysis. We identified genetic associations with CSF levels of 5 proteins (Angiotensin-converting enzyme (ACE), Chemokine (C-C motif) ligand 2 (CCL2), Chemokine (C-C motif) ligand 4 (CCL4), Interleukin 6 receptor (IL6R) and Matrix metalloproteinase-3 (MMP3)) with study-wide significant p-values (p<1.46×10−10) and significant, consistent evidence for association in both the Knight ADRC and the ADNI samples. These proteins are involved in amyloid processing and pro-inflammatory signaling. SNPs associated with ACE, IL6R and MMP3 protein levels are located within the coding regions of the corresponding structural gene. The SNPs associated with CSF levels of CCL4 and CCL2 are located in known chemokine binding proteins. The genetic associations reported here are novel and suggest mechanisms for genetic control of CSF and plasma levels of these disease-related proteins. Significant SNPs in ACE and MMP3 also showed association with AD risk. Our findings suggest that these proteins/pathways may be valuable therapeutic targets for AD. Robust associations in cognitively normal individuals suggest that these SNPs also influence regulation of these proteins more generally and may therefore be relevant to other diseases. The use of quantitative endophenotypes from cerebrospinal fluid has led to the identification of several genetic variants that alter risk or rate of progression of Alzheimer's disease. Here we have analyzed the levels of 58 disease-related proteins in the cerebrospinal fluid for association with millions of variants across the human genome. We have identified significant, replicable associations with 5 analytes, Angiotensin-converting enzyme, Chemokine (C-C motif) ligand 2, Chemokine (C-C motif) ligand 4, Interleukin 6 receptor and Matrix metalloproteinase-3. Our results suggest that these variants play a regulatory role in the respective protein levels and are relevant to the inflammatory and amyloid processing pathways. Variants in associated with ACE and those associated with MMP3 levels also show association with risk for Alzheimer's disease in the expected directions. These associations are consistent in cerebrospinal fluid and plasma and in samples with only cognitively normal individuals suggesting that they are relevant in the regulation of these protein levels beyond the context of Alzheimer's disease.
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Affiliation(s)
- John S. K. Kauwe
- Department of Biology, Brigham Young University, Provo, Utah, United States of America
| | - Matthew H. Bailey
- Department of Biology, Brigham Young University, Provo, Utah, United States of America
| | - Perry G. Ridge
- Department of Biology, Brigham Young University, Provo, Utah, United States of America
| | - Rachel Perry
- Department of Biology, Brigham Young University, Provo, Utah, United States of America
| | - Mark E. Wadsworth
- Department of Biology, Brigham Young University, Provo, Utah, United States of America
| | - Kaitlyn L. Hoyt
- Department of Biology, Brigham Young University, Provo, Utah, United States of America
| | - Lyndsay A. Staley
- Department of Biology, Brigham Young University, Provo, Utah, United States of America
| | - Celeste M. Karch
- Department of Psychiatry, Washington University School of Medicine, St Louis, Missouri, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Oscar Harari
- Department of Psychiatry, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St Louis, Missouri, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Benjamin J. Ainscough
- The Genome Institute, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Kelly Bales
- Neuroscience Research Unit, Worldwide Research and Development, Pfizer Inc., Groton, Connecticut, United States of America
| | - Eve H. Pickering
- Neuroscience Research Unit, Worldwide Research and Development, Pfizer Inc., Groton, Connecticut, United States of America
| | - Sarah Bertelsen
- Department of Psychiatry, Washington University School of Medicine, St Louis, Missouri, United States of America
| | | | - Anne M. Fagan
- Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, Missouri, United States of America
- Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St Louis, Missouri, United States of America
- Department of Neurology, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - David M. Holtzman
- Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, Missouri, United States of America
- Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St Louis, Missouri, United States of America
- Department of Neurology, Washington University School of Medicine, St Louis, Missouri, United States of America
- Department of Developmental Biology, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - John C. Morris
- Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, Missouri, United States of America
- Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St Louis, Missouri, United States of America
- Department of Neurology, Washington University School of Medicine, St Louis, Missouri, United States of America
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Alison M. Goate
- Department of Psychiatry, Washington University School of Medicine, St Louis, Missouri, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, Missouri, United States of America
- Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St Louis, Missouri, United States of America
- Department of Neurology, Washington University School of Medicine, St Louis, Missouri, United States of America
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri, United States of America
- * E-mail:
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Intracellular clusterin interacts with brain isoforms of the bridging integrator 1 and with the microtubule-associated protein Tau in Alzheimer's disease. PLoS One 2014; 9:e103187. [PMID: 25051234 PMCID: PMC4106906 DOI: 10.1371/journal.pone.0103187] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 06/26/2014] [Indexed: 12/11/2022] Open
Abstract
Sporadic or late-onset Alzheimer's disease (AD) is expected to affect 50% of individuals reaching 85 years of age. The most significant genetic risk factor for late-onset AD is the e4 allele of APOE gene encoding apolipoprotein E, a lipid carrier shown to modulate brain amyloid burden. Recent genome-wide association studies have uncovered additional single nucleotide polymorphisms (SNPs) linked to AD susceptibility, including those in the CLU and BIN1 genes encoding for clusterin (CLU) and the bridging integrator 1 (BIN1) proteins, respectively. Because CLU has been implicated in brain amyloid-β (Aβ) clearance in mouse models of amyloid deposition, we sought to investigate whether an AD-linked SNP in the CLU gene altered Aβ42 biomarker levels in the cerebrospinal fluid (CSF). Instead, we found that the CLU rs11136000 SNP modified CSF levels of the microtubule-associated protein Tau in AD patients. We also found that an intracellular form of CLU (iCLU) was upregulated in the brain of Tau overexpressing Tg4510 mice, but not in Tg2576 amyloid mouse model. By overexpressing iCLU and Tau in cell culture systems we discovered that iCLU was a Tau-interacting protein and that iCLU associated with brain-specific isoforms of BIN1, also recently identified as a Tau-binding protein. Through expression analysis of CLU and BIN1 variants, we found that CLU and BIN1 interacted via their coiled-coil motifs. In co-immunoprecipitation studies using human brain tissue, we showed that iCLU and the major BIN1 isoform expressed in neurons were associated with modified Tau species found in AD. Finally, we showed that expression of certain coding CLU variants linked to AD risk led to increased levels of iCLU. Together, our findings suggest that iCLU and BIN1 interaction might impact Tau function in neurons and uncover potential new mechanisms underlying the etiology of Tau pathology in AD.
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