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Fan M, Hu J, Xu X, Chen J, Zhang W, Zheng X, Pan J, Xu W, Feng S. Mass spectrometry-based multi-omics analysis reveals distinct molecular features in early and advanced stages of hepatocellular carcinoma. Heliyon 2024; 10:e38182. [PMID: 39381095 PMCID: PMC11456867 DOI: 10.1016/j.heliyon.2024.e38182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 09/18/2024] [Accepted: 09/19/2024] [Indexed: 10/10/2024] Open
Abstract
Hepatocellular Carcinoma (HCC) is a serious primary solid tumor that is prevalent worldwide. Due to its high mortality rate, it is crucial to explore both early diagnosis and advanced treatment for HCC. In recent years, multi-omics approaches have emerged as promising tools to identify biomarkers and investigate molecular mechanisms of biological processes and diseases. In this study, we performed proteomics, phosphoproteomics, metabolomics, and lipidomics to reveal the molecular features of early- and advanced-stage HCC. The data obtained from these omics were analyzed separately and then integrated to provide a comprehensive understanding of the disease. The multi-omics results unveiled intricate biological pathways and interaction networks underlying the initiation and progression of HCC. Moreover, we proposed specific potential biomarker panels for both early- and advanced-stage HCC by overlapping our data with CPTAC database for HCC diagnosis, and deduced novel insights and mechanisms related to HCC origination and development, such as glucose depletion during tumor progression, ROCK1 deactivation and GSK3A activation.
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Affiliation(s)
- Mingzhu Fan
- Key Laboratory of Structural Biology of Zhejiang Province, Westlake University, Hangzhou, 310024, Zhejiang, China
- Mass Spectrometry & Metabolomics Core Facility, The Biomedical Research Core Facility, Westlake University, Hangzhou, 310024, Zhejiang, China
| | - Jin Hu
- Key Laboratory of Structural Biology of Zhejiang Province, Westlake University, Hangzhou, 310024, Zhejiang, China
- Mass Spectrometry & Metabolomics Core Facility, The Biomedical Research Core Facility, Westlake University, Hangzhou, 310024, Zhejiang, China
| | - Xiaoyan Xu
- Mass Spectrometry & Metabolomics Core Facility, The Biomedical Research Core Facility, Westlake University, Hangzhou, 310024, Zhejiang, China
| | - Jia Chen
- Mass Spectrometry & Metabolomics Core Facility, The Biomedical Research Core Facility, Westlake University, Hangzhou, 310024, Zhejiang, China
| | - Wenwen Zhang
- Mass Spectrometry & Metabolomics Core Facility, The Biomedical Research Core Facility, Westlake University, Hangzhou, 310024, Zhejiang, China
| | - Xiaoping Zheng
- Pathology Department, Shulan (Hangzhou) Hospital, Hangzhou, 311112, Zhejiang, China
| | - Jinheng Pan
- Key Laboratory of Structural Biology of Zhejiang Province, Westlake University, Hangzhou, 310024, Zhejiang, China
| | - Wei Xu
- College of Basic Medical Science, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, China
- Key Laboratory of Chinese Medicine Rheumatology of Zhejiang Province, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, China
- Hangzhou Tongchuang Medical Laboratory, Shulan Health Group, Hangzhou, 310015, Zhejiang, China
| | - Shan Feng
- Key Laboratory of Structural Biology of Zhejiang Province, Westlake University, Hangzhou, 310024, Zhejiang, China
- Mass Spectrometry & Metabolomics Core Facility, The Biomedical Research Core Facility, Westlake University, Hangzhou, 310024, Zhejiang, China
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2
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Kolobova E, Petrushanko I, Mitkevich V, Makarov AA, Grigorova IL. β-Amyloids and Immune Responses Associated with Alzheimer's Disease. Cells 2024; 13:1624. [PMID: 39404388 PMCID: PMC11475064 DOI: 10.3390/cells13191624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2024] [Revised: 09/24/2024] [Accepted: 09/25/2024] [Indexed: 10/19/2024] Open
Abstract
Alzheimer's disease (AD) is associated with the accumulation of β-amyloids (Aβs) and the formation of Aβ plaques in the brain. Various structural forms and isoforms of Aβs that have variable propensities for oligomerization and toxicity and may differentially affect the development of AD have been identified. In addition, there is evidence that β-amyloids are engaged in complex interactions with the innate and adaptive immune systems, both of which may also play a role in the regulation of AD onset and progression. In this review, we discuss what is currently known about the intricate interplay between β-amyloids and the immune response to Aβs with a more in-depth focus on the possible roles of B cells in the pathogenesis of AD.
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Affiliation(s)
- Elizaveta Kolobova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.K.); (I.P.); (V.M.); (A.A.M.)
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117513 Moscow, Russia
| | - Irina Petrushanko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.K.); (I.P.); (V.M.); (A.A.M.)
| | - Vladimir Mitkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.K.); (I.P.); (V.M.); (A.A.M.)
| | - Alexander A Makarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.K.); (I.P.); (V.M.); (A.A.M.)
| | - Irina L Grigorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.K.); (I.P.); (V.M.); (A.A.M.)
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117513 Moscow, Russia
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3
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Xu M, Wang X, Zhang Y, Ji N, Wang Q, Zhao T, Zhou C, Jia C. Profiling of the Proteins Interacting with Amyloid Beta Peptides in Clinical Samples by PACTS-TPP. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1310-1319. [PMID: 38780475 DOI: 10.1021/jasms.4c00083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
The accumulation of amyloid beta (Aβ1-42) results in neurotoxicity and is strongly related to neurodegenerative disorders, especially Alzheimer's disease (AD), but the underlying molecular mechanism is still poorly understood. Therefore, there is an urgent need for researchers to discover the proteins that interact with Aβ1-42 to determine the molecular basis. Previously, we developed peptide-ligand-induced changes in the abundance of proTeinS (PACTS)-assisted thermal proteome profiling (TPP) to identify proteins that interact with peptide ligands. In the present study, we applied this technique to analyze clinical samples to identify Aβ1-42-interacting proteins. We detected 115 proteins that interact with Aβ1-42 in human frontal lobe tissue. Pathway enrichment analysis revealed that the differentially expressed proteins were involved mainly in neurodegenerative diseases. Further orthogonal validation revealed that Aβ1-42 interacted with the AD-associated protein mitogen-activated protein kinase 3 (MAPK3), and knockdown of the Aβ1-42 amyloid precursor protein (APP) inhibited the MAPK signaling pathway, suggesting potential functional roles for Aβ1-42 in interacting with MAPK3. Overall, this study demonstrated the application of the PACTS-TPP in clinical samples and provided a valuable data source for research on neurodegenerative diseases.
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Affiliation(s)
- Mengting Xu
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences-Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, 102206, China
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui 230032, China
| | - Xiankun Wang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences-Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Yang Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China
| | - Nan Ji
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Beijing, 100070, China
| | - Qianqian Wang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences-Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Ting Zhao
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences-Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Congli Zhou
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences-Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Chenxi Jia
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences-Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, 102206, China
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Soares Martins T, Pelech S, Ferreira M, Pinho B, Leandro K, de Almeida LP, Breitling B, Hansen N, Esselmann H, Wiltfang J, da Cruz e Silva OAB, Henriques AG. Phosphoproteome Microarray Analysis of Extracellular Particles as a Tool to Explore Novel Biomarker Candidates for Alzheimer's Disease. Int J Mol Sci 2024; 25:1584. [PMID: 38338863 PMCID: PMC10855802 DOI: 10.3390/ijms25031584] [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: 11/30/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Phosphorylation plays a key role in Alzheimer's disease (AD) pathogenesis, impacting distinct processes such as amyloid-beta (Aβ) peptide production and tau phosphorylation. Impaired phosphorylation events contribute to senile plaques and neurofibrillary tangles' formation, two major histopathological hallmarks of AD. Blood-derived extracellular particles (bdEP) can represent a disease-related source of phosphobiomarker candidates, and hence, in this pilot study, bdEP of Control and AD cases were analyzed by a targeted phosphoproteomics approach using a high-density microarray that featured at least 1145 pan-specific and 913 phosphosite-specific antibodies. This approach, innovatively applied to bdEP, allowed the identification of 150 proteins whose expression levels and/or phosphorylation patterns were significantly altered across AD cases. Gene Ontology enrichment and Reactome pathway analysis unraveled potentially relevant molecular targets and disease-associated pathways, and protein-protein interaction networks were constructed to highlight key targets. The discriminatory value of both the total proteome and the phosphoproteome was evaluated by univariate and multivariate approaches. This pilot experiment supports that bdEP are enriched in phosphotargets relevant in an AD context, holding value as peripheral biomarker candidates for disease diagnosis.
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Affiliation(s)
- Tânia Soares Martins
- Neurosciences and Signaling Group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal; (T.S.M.)
| | - Steven Pelech
- Department of Medicine, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
- Kinexus Bioinformatics Corporation, Vancouver, BC V6P 6T3, Canada
| | - Maria Ferreira
- Neurosciences and Signaling Group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal; (T.S.M.)
| | - Beatriz Pinho
- Neurosciences and Signaling Group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal; (T.S.M.)
| | - Kevin Leandro
- Center for Neuroscience and Cell Biology, Faculty of Pharmacy, University of Coimbra, 3004-504 Coimbra, Portugal
- ViraVector–Viral Vector for Gene Transfer Core Facility, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Luís Pereira de Almeida
- Center for Neuroscience and Cell Biology, Faculty of Pharmacy, University of Coimbra, 3004-504 Coimbra, Portugal
- ViraVector–Viral Vector for Gene Transfer Core Facility, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Benedict Breitling
- Department of Psychiatry and Psychotherapy, University Medical Center Goettingen (UMG), Georg-August University, 37075 Goettingen, Germany
| | - Niels Hansen
- Department of Psychiatry and Psychotherapy, University Medical Center Goettingen (UMG), Georg-August University, 37075 Goettingen, Germany
| | - Hermann Esselmann
- Department of Psychiatry and Psychotherapy, University Medical Center Goettingen (UMG), Georg-August University, 37075 Goettingen, Germany
| | - Jens Wiltfang
- Neurosciences and Signaling Group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal; (T.S.M.)
- Department of Psychiatry and Psychotherapy, University Medical Center Goettingen (UMG), Georg-August University, 37075 Goettingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), 37075 Goettingen, Germany
| | - Odete A. B. da Cruz e Silva
- Neurosciences and Signaling Group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal; (T.S.M.)
| | - Ana Gabriela Henriques
- Neurosciences and Signaling Group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal; (T.S.M.)
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Lin L, Liu X, Cheng X, Li Y, Gearing M, Levey A, Huang X, Li Y, Jin P, Li X. MicroRNA-650 Regulates the Pathogenesis of Alzheimer's Disease Through Targeting Cyclin-Dependent Kinase 5. Mol Neurobiol 2023; 60:2426-2441. [PMID: 36656459 PMCID: PMC10039829 DOI: 10.1007/s12035-023-03224-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 01/06/2023] [Indexed: 01/20/2023]
Abstract
Alzheimer's disease (AD) pathogenesis feature progressive neurodegeneration, amyloid-β plaque formation, and neurofibrillary tangles. Ample evidence has indicated the involvement of epigenetic pathways in AD pathogenesis. Here, we show that the expression of microRNA 650 (miR-650) is altered in brains from AD patients. Furthermore, we found that the processing of primary miR-650 to mature miR-650 is misregulated. Bioinformatic analysis predicted that miR-650 targets the expression of three AD-associated components: Apolipoprotein E (APOE), Presenilin 1 (PSEN1), and Cyclin-Dependent Kinase 5 (CDK5), and we have experimentally confirmed that miR-650 is able to significantly reduce the expression of APOE, PSEN1, and CDK5 in vitro. Importantly, the overexpression of miR-650 was further shown to significantly alter the CDK5 level and ameliorate AD pathologies in APP-PSEN1 transgenic mice. Overall, our results indicate that miR-650 influences AD pathogenesis through regulation of CDK5.
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Affiliation(s)
- Li Lin
- Guangdong-Hongkong-Macau Institute of CNS Regeneration, Guangdong Key Laboratory of Nonhuman Primate Models of Human Diseases, Key Laboratory of CNS Regeneration (Ministry of Education), Jinan University, Guangzhou, 510632, China.
| | - Xiaodong Liu
- Guangdong-Hongkong-Macau Institute of CNS Regeneration, Guangdong Key Laboratory of Nonhuman Primate Models of Human Diseases, Key Laboratory of CNS Regeneration (Ministry of Education), Jinan University, Guangzhou, 510632, China
| | - Xuejun Cheng
- The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
- The Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Yujing Li
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Marla Gearing
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Allan Levey
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Xiaoli Huang
- The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
- The Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Ying Li
- The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
- The Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
| | - Xuekun Li
- The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China.
- The Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, 310003, China.
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6
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Pandey RS, Kotredes KP, Sasner M, Howell GR, Carter GW. Differential splicing of neuronal genes in a Trem2*R47H mouse model mimics alterations associated with Alzheimer's disease. BMC Genomics 2023; 24:172. [PMID: 37016304 PMCID: PMC10074678 DOI: 10.1186/s12864-023-09280-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 03/29/2023] [Indexed: 04/06/2023] Open
Abstract
BACKGROUND Molecular characterization of late-onset Alzheimer's disease (LOAD), the leading cause of age-related dementia, has revealed transcripts, proteins, and pathway alterations associated with disease. Assessing these postmortem signatures of LOAD in experimental model systems can further elucidate their relevance to disease origins and progression. Model organisms engineered with human genetic factors further link these signatures to disease-associated variants, especially when studies are designed to leverage homology across species. Here we assess differential gene splicing patterns in aging mouse models carrying humanized APOE4 and/or the Trem2*R47H variant on a C57BL/6J background. We performed a differential expression of gene (DEG) and differential splicing analyses on whole brain transcriptomes at multiple ages. To better understand the difference between differentially expressed and differentially spliced genes, we evaluated enrichment of KEGG pathways and cell-type specific gene signatures of the adult brain from each alteration type. To determine LOAD relevance, we compared differential splicing results from mouse models with multiple human AD splicing studies. RESULTS We found that differentially expressed genes in Trem2*R47H mice were significantly enriched in multiple AD-related pathways, including immune response, osteoclast differentiation, and metabolism, whereas differentially spliced genes were enriched for neuronal related functions, including GABAergic synapse and glutamatergic synapse. These results were reinforced by the enrichment of microglial genes in DEGs and neuronal genes in differentially spliced genes in Trem2*R47H mice. We observed significant overlap between differentially spliced genes in Trem2*R47H mice and brains from human AD subjects. These effects were absent in APOE4 mice and suppressed in APOE4.Trem2*R47H double mutant mice relative to Trem2*R47H mice. CONCLUSIONS The cross-species observation that alternative splicing observed in LOAD are present in Trem2*R47H mouse models suggests a novel link between this candidate risk gene and molecular signatures of LOAD in neurons and demonstrates how deep molecular analysis of new genetic models links molecular disease outcomes to a human candidate gene.
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Affiliation(s)
- Ravi S Pandey
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Kevin P Kotredes
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Michael Sasner
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Gareth R Howell
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Gregory W Carter
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA.
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA.
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Ando K, Nagaraj S, Küçükali F, de Fisenne MA, Kosa AC, Doeraene E, Lopez Gutierrez L, Brion JP, Leroy K. PICALM and Alzheimer's Disease: An Update and Perspectives. Cells 2022; 11:3994. [PMID: 36552756 PMCID: PMC9776874 DOI: 10.3390/cells11243994] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/30/2022] [Accepted: 12/04/2022] [Indexed: 12/14/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified the PICALM (Phosphatidylinositol binding clathrin-assembly protein) gene as the most significant genetic susceptibility locus after APOE and BIN1. PICALM is a clathrin-adaptor protein that plays a critical role in clathrin-mediated endocytosis and autophagy. Since the effects of genetic variants of PICALM as AD-susceptibility loci have been confirmed by independent genetic studies in several distinct cohorts, there has been a number of in vitro and in vivo studies attempting to elucidate the underlying mechanism by which PICALM modulates AD risk. While differential modulation of APP processing and Aβ transcytosis by PICALM has been reported, significant effects of PICALM modulation of tau pathology progression have also been evidenced in Alzheimer's disease models. In this review, we summarize the current knowledge about PICALM, its physiological functions, genetic variants, post-translational modifications and relevance to AD pathogenesis.
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Affiliation(s)
- Kunie Ando
- Laboratory of Histology, Neuropathology and Neuroanatomy, Faculty of Medicine, Université Libre de Bruxelles, ULB Neuroscience Institute, 808 Route de Lennik, 1070 Brussels, Belgium
| | - Siranjeevi Nagaraj
- Laboratory of Histology, Neuropathology and Neuroanatomy, Faculty of Medicine, Université Libre de Bruxelles, ULB Neuroscience Institute, 808 Route de Lennik, 1070 Brussels, Belgium
| | - Fahri Küçükali
- Complex Genetics of Alzheimer’s Disease Group, VIB Center for Molecular Neurology, VIB Antwerp, Department of Biomedical Sciences, University of Antwerp, 2000 Antwerp, Belgium
| | - Marie-Ange de Fisenne
- Laboratory of Histology, Neuropathology and Neuroanatomy, Faculty of Medicine, Université Libre de Bruxelles, ULB Neuroscience Institute, 808 Route de Lennik, 1070 Brussels, Belgium
| | - Andreea-Claudia Kosa
- Laboratory of Histology, Neuropathology and Neuroanatomy, Faculty of Medicine, Université Libre de Bruxelles, ULB Neuroscience Institute, 808 Route de Lennik, 1070 Brussels, Belgium
| | - Emilie Doeraene
- Laboratory of Histology, Neuropathology and Neuroanatomy, Faculty of Medicine, Université Libre de Bruxelles, ULB Neuroscience Institute, 808 Route de Lennik, 1070 Brussels, Belgium
| | - Lidia Lopez Gutierrez
- Laboratory of Histology, Neuropathology and Neuroanatomy, Faculty of Medicine, Université Libre de Bruxelles, ULB Neuroscience Institute, 808 Route de Lennik, 1070 Brussels, Belgium
| | - Jean-Pierre Brion
- Laboratory of Histology, Neuropathology and Neuroanatomy, Faculty of Medicine, Université Libre de Bruxelles, ULB Neuroscience Institute, 808 Route de Lennik, 1070 Brussels, Belgium
| | - Karelle Leroy
- Laboratory of Histology, Neuropathology and Neuroanatomy, Faculty of Medicine, Université Libre de Bruxelles, ULB Neuroscience Institute, 808 Route de Lennik, 1070 Brussels, Belgium
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Bahado-Singh RO, Radhakrishna U, Gordevičius J, Aydas B, Yilmaz A, Jafar F, Imam K, Maddens M, Challapalli K, Metpally RP, Berrettini WH, Crist RC, Graham SF, Vishweswaraiah S. Artificial Intelligence and Circulating Cell-Free DNA Methylation Profiling: Mechanism and Detection of Alzheimer's Disease. Cells 2022; 11:1744. [PMID: 35681440 PMCID: PMC9179874 DOI: 10.3390/cells11111744] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/13/2022] [Accepted: 05/17/2022] [Indexed: 02/01/2023] Open
Abstract
Background: Despite extensive efforts, significant gaps remain in our understanding of Alzheimer’s disease (AD) pathophysiology. Novel approaches using circulating cell-free DNA (cfDNA) have the potential to revolutionize our understanding of neurodegenerative disorders. Methods: We performed DNA methylation profiling of cfDNA from AD patients and compared them to cognitively normal controls. Six Artificial Intelligence (AI) platforms were utilized for the diagnosis of AD while enrichment analysis was used to elucidate the pathogenesis of AD. Results: A total of 3684 CpGs were significantly (adj. p-value < 0.05) differentially methylated in AD versus controls. All six AI algorithms achieved high predictive accuracy (AUC = 0.949−0.998) in an independent test group. As an example, Deep Learning (DL) achieved an AUC (95% CI) = 0.99 (0.95−1.0), with 94.5% sensitivity and specificity. Conclusion: We describe numerous epigenetically altered genes which were previously reported to be differentially expressed in the brain of AD sufferers. Genes identified by AI to be the best predictors of AD were either known to be expressed in the brain or have been previously linked to AD. We highlight enrichment in the Calcium signaling pathway, Glutamatergic synapse, Hedgehog signaling pathway, Axon guidance and Olfactory transduction in AD sufferers. To the best of our knowledge, this is the first reported genome-wide DNA methylation study using cfDNA to detect AD.
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Affiliation(s)
- Ray O. Bahado-Singh
- Department of Obstetrics and Gynecology, Oakland University-William Beaumont School of Medicine, Royal Oak, MI 48309, USA; (R.O.B.-S.); (A.Y.); (S.F.G.)
- Department of Obstetrics and Gynecology, Beaumont Health, 3601 W. 13 Mile Road, Royal Oak, MI 48073, USA; (F.J.); (K.C.)
| | - Uppala Radhakrishna
- Department of Obstetrics and Gynecology, Beaumont Health, 3601 W. 13 Mile Road, Royal Oak, MI 48073, USA; (F.J.); (K.C.)
| | - Juozas Gordevičius
- Vugene, LLC, 625 Kenmoor Ave Suite 301 PMB 96578, Grand Rapids, MI 49546, USA;
| | - Buket Aydas
- Department of Care Management Analytics, Blue Cross Blue Shield of Michigan, Detroit, MI 48226, USA;
| | - Ali Yilmaz
- Department of Obstetrics and Gynecology, Oakland University-William Beaumont School of Medicine, Royal Oak, MI 48309, USA; (R.O.B.-S.); (A.Y.); (S.F.G.)
- Department of Alzheimer’s Disease Research, Beaumont Research Institute, 3811 W. 13 Mile Road, Royal Oak, MI 48073, USA
| | - Faryal Jafar
- Department of Obstetrics and Gynecology, Beaumont Health, 3601 W. 13 Mile Road, Royal Oak, MI 48073, USA; (F.J.); (K.C.)
| | - Khaled Imam
- Department of Internal Medicine, Beaumont Health, 3601 W. 13 Mile Road, Royal Oak, MI 48073, USA; (K.I.); (M.M.)
| | - Michael Maddens
- Department of Internal Medicine, Beaumont Health, 3601 W. 13 Mile Road, Royal Oak, MI 48073, USA; (K.I.); (M.M.)
| | - Kshetra Challapalli
- Department of Obstetrics and Gynecology, Beaumont Health, 3601 W. 13 Mile Road, Royal Oak, MI 48073, USA; (F.J.); (K.C.)
| | - Raghu P. Metpally
- Department of Molecular and Functional Genomics, Geisinger, Danville, PA 17821, USA; (R.P.M.); (W.H.B.)
| | - Wade H. Berrettini
- Department of Molecular and Functional Genomics, Geisinger, Danville, PA 17821, USA; (R.P.M.); (W.H.B.)
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Richard C. Crist
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Stewart F. Graham
- Department of Obstetrics and Gynecology, Oakland University-William Beaumont School of Medicine, Royal Oak, MI 48309, USA; (R.O.B.-S.); (A.Y.); (S.F.G.)
- Department of Obstetrics and Gynecology, Beaumont Health, 3601 W. 13 Mile Road, Royal Oak, MI 48073, USA; (F.J.); (K.C.)
- Department of Alzheimer’s Disease Research, Beaumont Research Institute, 3811 W. 13 Mile Road, Royal Oak, MI 48073, USA
| | - Sangeetha Vishweswaraiah
- Department of Obstetrics and Gynecology, Beaumont Health, 3601 W. 13 Mile Road, Royal Oak, MI 48073, USA; (F.J.); (K.C.)
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9
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Alves SR, da Cruz e Silva C, Martins I, Henriques AG, da Cruz e Silva OA. A Bioinformatics Approach Toward Unravelling the Synaptic Molecular Crosstalk Between Alzheimer’s Disease and Diabetes. J Alzheimers Dis 2022; 86:1917-1933. [PMID: 35253743 PMCID: PMC9108712 DOI: 10.3233/jad-215059] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Background: Increasing evidence links impaired brain insulin signaling and insulin resistance to the development of Alzheimer’s disease (AD). Objective: This evidence prompted a search for molecular players common to AD and diabetes mellitus (DM). Methods: The work incorporated studies based on a primary care-based cohort (pcb-Cohort) and a bioinformatics analysis to identify central nodes, that are key players in AD and insulin signaling (IS) pathways. The interactome for each of these key proteins was retrieved and network maps were developed for AD and IS. Synaptic enrichment was performed to reveal synaptic common hubs. Results: Cohort analysis showed that individuals with DM exhibited a correlation with poor performance in the Mini-Mental State Examination (MMSE) cognitive test. Additionally, APOE ɛ2 allele carriers appear to potentially be relatively more protected against both DM and cognitive deficits. Ten clusters were identified in this network and 32 key synaptic proteins were common to AD and IS. Given the relevance of signaling pathways, another network was constructed focusing on protein kinases and protein phosphatases, and the top 6 kinase nodes (LRRK2, GSK3B, AKT1, EGFR, MAPK1, and FYN) were further analyzed. Conclusion: This allowed the elaboration of signaling cascades directly impacting AβPP and tau, whereby distinct signaling pathway play a major role and strengthen an AD-IS link at a molecular level.
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Affiliation(s)
- Steven R. Alves
- Department of Medical Sciences, Neurosciences and Signalling Group, Institute of Biomedicine, University of Aveiro, Aveiro, Portugal
| | | | - Ilka Martins
- Department of Medical Sciences, Neurosciences and Signalling Group, Institute of Biomedicine, University of Aveiro, Aveiro, Portugal
| | - Ana Gabriela Henriques
- Department of Medical Sciences, Neurosciences and Signalling Group, Institute of Biomedicine, University of Aveiro, Aveiro, Portugal
| | - Odete A.B. da Cruz e Silva
- Department of Medical Sciences, Neurosciences and Signalling Group, Institute of Biomedicine, University of Aveiro, Aveiro, Portugal
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10
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Soares Martins T, Marçalo R, da Cruz E Silva CB, Trindade D, Catita J, Amado F, Melo T, Rosa IM, Vogelgsang J, Wiltfang J, da Cruz E Silva OAB, Henriques AG. Novel Exosome Biomarker Candidates for Alzheimer's Disease Unravelled Through Mass Spectrometry Analysis. Mol Neurobiol 2022; 59:2838-2854. [PMID: 35212939 PMCID: PMC9016047 DOI: 10.1007/s12035-022-02762-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 01/28/2022] [Indexed: 01/03/2023]
Abstract
Exosomes are small extracellular vesicles (EVs) present in human biofluids that can transport specific disease-associated molecules. Consequently blood-derived exosomes have emerged as important peripheral biomarker sources for a wide range of diseases, among them Alzheimer’s disease (AD). Although there is no effective cure for AD, an accurate diagnosis, relying on easily accessible peripheral biofluids, is still necessary to discriminate this disease from other dementias, test potential therapies and even monitor rate of disease progression. The ultimate goal is to produce a cost-effective and widely available alternative, which can also be employed as a first clinical screen. In this study, EVs with exosome-like characteristics were isolated from serum of Controls and AD cases through precipitation- and column-based methods, followed by mass spectrometry analysis. The resulting proteomes were characterized by Gene Ontology (GO) and multivariate analyses. Although GO terms were similar for exosomes’ proteomes of Controls and ADs, using both methodologies, a clear segregation of disease cases was obtained when using the precipitation-based method. Nine significantly different abundant proteins were identified between Controls and AD cases, representing putative biomarker candidate targets. Among them are AACT and C4BPα, two Aβ-binding proteins, whose exosome levels were further validated in individuals from independent cohorts using antibody-based approaches. The findings discussed represent an important contribution to the identification of novel exosomal biomarker candidates useful as potential blood-based tools for AD diagnosis.
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Affiliation(s)
- Tânia Soares Martins
- Neuroscience and Signalling Group, Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro (UA), 3810-193, Aveiro, Portugal
| | - Rui Marçalo
- Neuroscience and Signalling Group, Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro (UA), 3810-193, Aveiro, Portugal
| | - Cristóvão B da Cruz E Silva
- Laboratory of Instrumentation and Experimental Particle Physics-LIP, Av. Elias Garcia 14-1º, 1000-149, Lisbon, Portugal
| | - Dário Trindade
- Neuroscience and Signalling Group, Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro (UA), 3810-193, Aveiro, Portugal
| | - José Catita
- CEBIMED-Faculty of Health Sciences, University Fernando Pessoa, 4249-004, Porto, Portugal.,Paralab SA, 4420-437, Gondomar, Portugal
| | - Francisco Amado
- Department of Chemistry, QOPNA (Organic Chemistry Natural and Agrofood Products and LAVQ REQUIMTE), University of Aveiro, 3810-193, Aveiro, Portugal
| | - Tânia Melo
- Department of Chemistry, QOPNA (Organic Chemistry Natural and Agrofood Products and LAVQ REQUIMTE), University of Aveiro, 3810-193, Aveiro, Portugal
| | - Ilka Martins Rosa
- Neuroscience and Signalling Group, Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro (UA), 3810-193, Aveiro, Portugal
| | - Jonathan Vogelgsang
- Department of Psychiatry and Psychotherapy, University Medical Center Goettingen (UMG), Georg-August University, Von-Siebold-Str. 5, 37075, Goettingen, Germany.,Translational Neuroscience Laboratory, McLean Hospital, Harvard Medical School, Belmont, MA, 02478, USA
| | - Jens Wiltfang
- Neuroscience and Signalling Group, Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro (UA), 3810-193, Aveiro, Portugal.,Department of Psychiatry and Psychotherapy, University Medical Center Goettingen (UMG), Georg-August University, Von-Siebold-Str. 5, 37075, Goettingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075, Goettingen, Germany
| | - Odete A B da Cruz E Silva
- Neuroscience and Signalling Group, Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro (UA), 3810-193, Aveiro, Portugal
| | - Ana Gabriela Henriques
- Neuroscience and Signalling Group, Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro (UA), 3810-193, Aveiro, Portugal.
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11
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Gutiérrez‑Vargas J, Castro‑Álvarez J, Zapata‑Berruecos J, Abdul‑Rahim K, Arteaga‑Noriega A. Neurodegeneration and convergent factors contributing to the deterioration of the cytoskeleton in Alzheimer's disease, cerebral ischemia and multiple sclerosis (Review). Biomed Rep 2022; 16:27. [PMID: 35251614 PMCID: PMC8889542 DOI: 10.3892/br.2022.1510] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/21/2022] [Indexed: 11/26/2022] Open
Abstract
The cytoskeleton is the main intracellular structure that determines the morphology of neurons and maintains their integrity. Therefore, disruption of its structure and function may underlie several neurodegenerative diseases. This review summarizes the current literature on the tau protein, microtubule-associated protein 2 (MAP2) and neurofilaments as common denominators in pathological conditions such as Alzheimer's disease (AD), cerebral ischemia, and multiple sclerosis (MS). Insights obtained from experimental models using biochemical and immunocytochemical techniques highlight that changes in these proteins may be potentially used as protein targets in clinical settings, which provides novel opportunities for the detection, monitoring and treatment of patients with these neurodegenerative diseases.
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Affiliation(s)
- Johanna Gutiérrez‑Vargas
- Neuroscience and Aging Group (GISAM), Faculty of Health Sciences, Life Sciences Laboratory, Remington University Corporation, Medellín 050023, Colombia
| | - John Castro‑Álvarez
- Neuroscience and Aging Group (GISAM), Faculty of Health Sciences, Life Sciences Laboratory, Remington University Corporation, Medellín 050023, Colombia
| | - Jose Zapata‑Berruecos
- INDEC‑CES Research Group, Neurological Institute of Colombia, Medellín 050023, Colombia
| | | | - Anibal Arteaga‑Noriega
- Family and Community Health Group, Faculty of Health Sciences, Life Sciences Laboratory, Remington University Corporation, Medellín 050023, Colombia
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12
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Smith BJ, Silva-Costa LC, Martins-de-Souza D. Human disease biomarker panels through systems biology. Biophys Rev 2021; 13:1179-1190. [PMID: 35059036 PMCID: PMC8724340 DOI: 10.1007/s12551-021-00849-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/01/2021] [Indexed: 12/23/2022] Open
Abstract
As more uses for biomarkers are sought after for an increasing number of disease targets, single-target biomarkers are slowly giving way for biomarker panels. These panels incorporate various sources of biomolecular and clinical data to guarantee a higher robustness and power of separation for a clinical test. Multifactorial diseases such as psychiatric disorders show great potential for clinical use, assisting medical professionals during the analysis of risk and predisposition, disease diagnosis and prognosis, and treatment applicability and efficacy. More specific tests are also being developed to assist in ruling out, distinguishing between, and confirming suspicions of multifactorial diseases, as well as to predict which therapy option may be the best option for a given patient's biochemical profile. As more complex datasets are entering the field, involving multi-omic approaches, systems biology has stepped in to facilitate the discovery and validation steps during biomarker panel generation. Filtering biomolecules and clinical data, pre-validating and cross-validating potential biomarkers, generating final biomarker panels, and testing the robustness and applicability of those panels are all beginning to rely on machine learning and systems biology and research in this area will only benefit from advances in these approaches.
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Affiliation(s)
- Bradley J. Smith
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Licia C. Silva-Costa
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- Instituto Nacional de Biomarcadores Em Neuropsiquiatria (INBION), Conselho Nacional de Desenvolvimento Científico E Tecnológico, Sao Paulo, Brazil
- Experimental Medicine Research Cluster (EMRC), University of Campinas, Campinas, Brazil
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13
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Soares Martins T, Magalhães S, Rosa IM, Vogelgsang J, Wiltfang J, Delgadillo I, Catita J, da Cruz E Silva OAB, Nunes A, Henriques AG. Potential of FTIR Spectroscopy Applied to Exosomes for Alzheimer's Disease Discrimination: A Pilot Study. J Alzheimers Dis 2021; 74:391-405. [PMID: 32039849 DOI: 10.3233/jad-191034] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Alzheimer's disease (AD) diagnosis is based on psychological and imaging tests but can also include monitoring cerebrospinal fluid (CSF) biomarkers. However, CSF based-neurochemical approaches are expensive and invasive, limiting their use to well-equipped settings. In contrast, blood-based biomarkers are minimally invasive, cost-effective, and a widely accessible alternative. Blood-derived exosomes have recently emerged as a reliable AD biomarker source, carrying disease-specific cargo. Fourier-transformed infrared (FTIR) spectroscopy meets the criteria for an ideal diagnostic methodology since it is rapid, easy to implement, and has high reproducibility. This metabolome-based technique is useful for diagnosing a broad range of diseases, although to our knowledge, no reports for FTIR spectroscopy applied to exosomes in AD exist. In this ground-breaking pilot study, FTIR spectra of serum and serum-derived exosomes from two independent cohorts were acquired and analyzed using multivariate analysis. The regional UA-cohort includes 9 individuals, clinically diagnosed with AD, mean age of 78.7 years old; and the UMG-cohort comprises 12 individuals, clinically diagnosed with AD (based on molecular and/or imaging data), mean age of 73.2 years old. Unsupervised principal component analysis of FTIR spectra of serum-derived exosomes revealed higher discriminatory value for AD cases when compared to serum as a whole. Consistently, the partial least-squares analysis revealed that serum-derived exosomes present higher correlations than serum. In addition, the second derivative peak area calculation also revealed significant differences among Controls and AD cases. The results obtained suggest that this methodology can discriminate cases from Controls and thus be potential useful to assist in AD clinical diagnosis.
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Affiliation(s)
- Tânia Soares Martins
- Neurosciences and Signalling Group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Sandra Magalhães
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal.,CICECO -Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Ilka Martins Rosa
- Neurosciences and Signalling Group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Jonathan Vogelgsang
- Department of Psychiatry and Psychotherapy, University Medical Center Goettingen (UMG), Georg-August University, Goettingen, Germany.,Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, MA, USA
| | - Jens Wiltfang
- Neurosciences and Signalling Group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal.,Department of Psychiatry and Psychotherapy, University Medical Center Goettingen (UMG), Georg-August University, Goettingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), Goettingen, Germany
| | | | - José Catita
- CEBIMED-Faculty of Health Sciences; University Fernando Pessoa, Porto, Portugal.,Paralab SA, Gondomar, Portugal
| | - Odete A B da Cruz E Silva
- Neurosciences and Signalling Group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal.,The Discovery CTR, University of Aveiro Campus, Aveiro, Portugal
| | - Alexandra Nunes
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Ana Gabriela Henriques
- Neurosciences and Signalling Group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
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14
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Morshed N, Ralvenius WT, Nott A, Watson LA, Rodriguez FH, Akay LA, Joughin BA, Pao P, Penney J, LaRocque L, Mastroeni D, Tsai L, White FM. Phosphoproteomics identifies microglial Siglec-F inflammatory response during neurodegeneration. Mol Syst Biol 2020; 16:e9819. [PMID: 33289969 PMCID: PMC7722784 DOI: 10.15252/msb.20209819] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 10/02/2020] [Accepted: 10/06/2020] [Indexed: 12/20/2022] Open
Abstract
Alzheimer's disease (AD) is characterized by the appearance of amyloid-β plaques, neurofibrillary tangles, and inflammation in brain regions involved in memory. Using mass spectrometry, we have quantified the phosphoproteome of the CK-p25, 5XFAD, and Tau P301S mouse models of neurodegeneration. We identified a shared response involving Siglec-F which was upregulated on a subset of reactive microglia. The human paralog Siglec-8 was also upregulated on microglia in AD. Siglec-F and Siglec-8 were upregulated following microglial activation with interferon gamma (IFNγ) in BV-2 cell line and human stem cell-derived microglia models. Siglec-F overexpression activates an endocytic and pyroptotic inflammatory response in BV-2 cells, dependent on its sialic acid substrates and immunoreceptor tyrosine-based inhibition motif (ITIM) phosphorylation sites. Related human Siglecs induced a similar response in BV-2 cells. Collectively, our results point to an important role for mouse Siglec-F and human Siglec-8 in regulating microglial activation during neurodegeneration.
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Affiliation(s)
- Nader Morshed
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMAUSA
| | - William T Ralvenius
- Picower Institute for Learning and MemoryMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of Brain and Cognitive SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Alexi Nott
- Picower Institute for Learning and MemoryMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of Brain and Cognitive SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of Brain SciencesImperial College LondonUK
- UK Dementia Research Institute at Imperial College LondonLondonUK
| | - L Ashley Watson
- Picower Institute for Learning and MemoryMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of Brain and Cognitive SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Felicia H Rodriguez
- Department of Chemical and Materials EngineeringNew Mexico State UniversityLas CrucesNMUSA
| | - Leyla A Akay
- Picower Institute for Learning and MemoryMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of Brain and Cognitive SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Brian A Joughin
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Ping‐Chieh Pao
- Picower Institute for Learning and MemoryMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of Brain and Cognitive SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Jay Penney
- Picower Institute for Learning and MemoryMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of Brain and Cognitive SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Lauren LaRocque
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Diego Mastroeni
- ASU‐Banner Neurodegenerative Disease Research CenterTempeAZUSA
| | - Li‐Huei Tsai
- Picower Institute for Learning and MemoryMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of Brain and Cognitive SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
- Broad Institute of MIT and HarvardCambridgeMAUSA
| | - Forest M White
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMAUSA
- Center for Precision Cancer MedicineMassachusetts Institute of TechnologyCambridgeMAUSA
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15
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16
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Soares Martins T, Trindade D, Vaz M, Campelo I, Almeida M, Trigo G, da Cruz E Silva OAB, Henriques AG. Diagnostic and therapeutic potential of exosomes in Alzheimer's disease. J Neurochem 2020; 156:162-181. [PMID: 32618370 DOI: 10.1111/jnc.15112] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/20/2020] [Accepted: 06/18/2020] [Indexed: 12/12/2022]
Abstract
Exosomes are small extracellular vesicles released by almost all cell types in physiological and pathological conditions. The exosomal potential to unravel disease mechanisms, or to be used as a source of biomarkers, is being explored, in particularly in the field of neurodegenerative diseases. Alzheimer's disease (AD) is the most prevalent neurodegenerative disease in the world and exosomes appear to have a relevant role in disease pathogenesis. This review summarizes the current knowledge on exosome contributions to AD as well as their use as disease biomarker resources or therapeutic targets. The most recent findings with respect to both protein and miRNA biomarker candidates for AD, herein described, highlight the state of the art in this field and encourage the use of exosomes derived from biofluids in clinical practice in the near future.
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Affiliation(s)
- Tânia Soares Martins
- Neurosciences and Signalling Group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Dário Trindade
- Neurosciences and Signalling Group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Margarida Vaz
- Neurosciences and Signalling Group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Inês Campelo
- Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Martim Almeida
- Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Guilherme Trigo
- Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Odete A B da Cruz E Silva
- Neurosciences and Signalling Group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal.,The Discovery CTR, University of Aveiro Campus, Aveiro, Portugal
| | - Ana Gabriela Henriques
- Neurosciences and Signalling Group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
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17
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Soleimani Zakeri NS, Pashazadeh S, MotieGhader H. Gene biomarker discovery at different stages of Alzheimer using gene co-expression network approach. Sci Rep 2020; 10:12210. [PMID: 32699331 PMCID: PMC7376049 DOI: 10.1038/s41598-020-69249-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 07/08/2020] [Indexed: 12/24/2022] Open
Abstract
Alzheimer's disease (AD) is a chronic neurodegenerative disorder. It is the most common type of dementia that has remained as an incurable disease in the world, which destroys the brain cells irreversibly. In this study, a systems biology approach was adopted to discover novel micro-RNA and gene-based biomarkers of the diagnosis of Alzheimer's disease. The gene expression data from three AD stages (Normal, Mild Cognitive Impairment, and Alzheimer) were used to reconstruct co-expression networks. After preprocessing and normalization, Weighted Gene Co-Expression Network Analysis (WGCNA) was used on a total of 329 samples, including 145 samples of Alzheimer stage, 80 samples of Mild Cognitive Impairment (MCI) stage, and 104 samples of the Normal stage. Next, three gene-miRNA bipartite networks were reconstructed by comparing the changes in module groups. Then, the functional enrichment analyses of extracted genes of three bipartite networks and miRNAs were done, respectively. Finally, a detailed analysis of the authentic studies was performed to discuss the obtained biomarkers. The outcomes addressed proposed novel genes, including MBOAT1, ARMC7, RABL2B, HNRNPUL1, LAMTOR1, PLAGL2, CREBRF, LCOR, and MRI1and novel miRNAs comprising miR-615-3p, miR-4722-5p, miR-4768-3p, miR-1827, miR-940 and miR-30b-3p which were related to AD. These biomarkers were proposed to be related to AD for the first time and should be examined in future clinical studies.
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Affiliation(s)
| | - Saeid Pashazadeh
- Faculty of Electrical and Computer Engineering, University of Tabriz, Tabriz, Iran.
| | - Habib MotieGhader
- Department of Computer Engineering, Gowgan Educational Center, Tabriz Branch, Islamic Azad University, Tabriz, Iran
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18
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Ahmad S, Milan MDC, Hansson O, Demirkan A, Agustin R, Sáez ME, Giagtzoglou N, Cabrera-Socorro A, Bakker MHM, Ramirez A, Hankemeier T, Stomrud E, Mattsson-Carlgren N, Scheltens P, van der Flier WM, Ikram MA, Malarstig A, Teunissen CE, Amin N, van Duijn CM. CDH6 and HAGH protein levels in plasma associate with Alzheimer's disease in APOE ε4 carriers. Sci Rep 2020; 10:8233. [PMID: 32427856 PMCID: PMC7237496 DOI: 10.1038/s41598-020-65038-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 04/24/2020] [Indexed: 02/06/2023] Open
Abstract
Many Alzheimer’s disease (AD) genes including Apolipoprotein E (APOE) are found to be expressed in blood-derived macrophages and thus may alter blood protein levels. We measured 91 neuro-proteins in plasma from 316 participants of the Rotterdam Study (incident AD = 161) using Proximity Extension Ligation assay. We studied the association of plasma proteins with AD in the overall sample and stratified by APOE. Findings from the Rotterdam study were replicated in 186 AD patients of the BioFINDER study. We further evaluated the correlation of these protein biomarkers with total tau (t-tau), phosphorylated tau (p-tau) and amyloid-beta (Aβ) 42 levels in cerebrospinal fluid (CSF) in the Amsterdam Dementia Cohort (N = 441). Finally, we conducted a genome-wide association study (GWAS) to identify the genetic variants determining the blood levels of AD-associated proteins. Plasma levels of the proteins, CDH6 (β = 0.638, P = 3.33 × 10−4) and HAGH (β = 0.481, P = 7.20 × 10−4), were significantly elevated in APOE ε4 carrier AD patients. The findings in the Rotterdam Study were replicated in the BioFINDER study for both CDH6 (β = 1.365, P = 3.97 × 10−3) and HAGH proteins (β = 0.506, P = 9.31 × 10−7) when comparing cases and controls in APOE ε4 carriers. In the CSF, CDH6 levels were positively correlated with t-tau and p-tau in the total sample as well as in APOE ε4 stratum (P < 1 × 10−3). The HAGH protein was not detected in CSF. GWAS of plasma CDH6 protein levels showed significant association with a cis-regulatory locus (rs111283466, P = 1.92 × 10−9). CDH6 protein is implicated in cell adhesion and synaptogenesis while HAGH protein is related to the oxidative stress pathway. Our findings suggest that these pathways may be altered during presymptomatic AD and that CDH6 and HAGH may be new blood-based biomarkers.
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Affiliation(s)
- Shahzad Ahmad
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands.
| | - Marta Del Campo Milan
- Neurochemistry laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam University Medical Centers (AUMC), Vrije Universiteit, Amsterdam, The Netherlands
| | - Oskar Hansson
- Clinical Memory Research Unit, Faculty of Medicine, Lund University, Lund, Sweden.,Memory Clinic, Skåne University Hospital, Malmö, Sweden
| | - Ayse Demirkan
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Ruiz Agustin
- Research Center and Memory clinic Fundació ACE. Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain.,CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Maria E Sáez
- Centro Andaluz de Estudios Bioinformáticos CAEBi, Sevilla, Spain
| | | | | | - Margot H M Bakker
- Discovery Research, AbbVie Deutschland GmbH & Co. KG, Knollstrasse, 67061, Ludwigshafen, Germany
| | - Alfredo Ramirez
- Department of Neurodegeneration and Geriatric Psychiatry, University of Bonn, 53127, Bonn, Germany.,Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, University of Cologne, Medical Faculty, 50937, Cologne, Germany.,German Center for Neurodegenerative Diseases (DZNE), 53127, Bonn, Germany
| | - Thomas Hankemeier
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Erik Stomrud
- Clinical Memory Research Unit, Faculty of Medicine, Lund University, Lund, Sweden.,Memory Clinic, Skåne University Hospital, Malmö, Sweden
| | - Niklas Mattsson-Carlgren
- Clinical Memory Research Unit, Faculty of Medicine, Lund University, Lund, Sweden.,Memory Clinic, Skåne University Hospital, Malmö, Sweden
| | - Philip Scheltens
- Alzheimer center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, UMC, The Netherlands
| | - Wiesje M van der Flier
- Alzheimer center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, UMC, The Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Anders Malarstig
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,Pfizer Worldwide R&D, Stockholm, Sweden
| | - Charlotte E Teunissen
- Neurochemistry laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam University Medical Centers (AUMC), Vrije Universiteit, Amsterdam, The Netherlands
| | - Najaf Amin
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands. .,Nuffield Department of Population Health, Oxford University, Oxford, UK.
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Mechanistic investigation of phosphoprotein enrichment by fly ash-based chromatography. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1118-1119:1-6. [PMID: 31005769 DOI: 10.1016/j.jchromb.2019.04.035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/22/2019] [Accepted: 04/15/2019] [Indexed: 11/22/2022]
Abstract
In this work, the mechanistic details contributing to the binding of phosphoproteins on fly ash (FA) has been investigated. The effects of factors influencing adsorption of phosphoprotein, i.e., contact time, pH, ionic strength, initial concentration of proteins, and contribution of ligand exchange, were thoroughly examined. Results showed that the adsorption efficiency of phosphoproteins to FA was enhanced with increasing contact time. Intriguingly, the adsorption of phosphoproteins to FA was not profoundly affected by high ionic strength, suggesting that electrostatic interaction does not play a pivotal role in phosphoprotein binding on the surface of FA particles. The interaction between phosphoproteins and FA could be instead disturbed when NaF and phosphate ion were used as competing electrolytes/ions. Also, it was found that at a high pH condition has a substantial effect on the adsorption of phosphoproteins through ligand exchange mechanism. To this end, our results clearly indicated that ligand exchange mechanism exerted by F-, phosphate ion and hydroxide ion with the metal oxide surface of FA is the mechanism that majorly contributed to the phosphoprotein binding on the surface of FA particles.
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20
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Using Next-Generation Sequencing Transcriptomics To Determine Markers of Post-traumatic Symptoms: Preliminary Findings from a Post-deployment Cohort of Soldiers. G3-GENES GENOMES GENETICS 2019; 9:463-471. [PMID: 30622122 PMCID: PMC6385974 DOI: 10.1534/g3.118.200516] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Post-traumatic stress disorder is a concerning psychobehavioral disorder thought to emerge from the complex interaction between genetic and environmental factors. For soldiers exposed to combat, the risk of developing this disorder is twofold and diagnosis is often late, when much sequela has set in. To be able to identify and diagnose in advance those at “risk” of developing post-traumatic stress disorder, would greatly taper the gap between late sequelae and treatment. Therefore, this study sought to determine whether the transcriptome can be used to track the development of post-traumatic stress disorder in this unique and susceptible cohort of individuals. Gene expression levels in peripheral blood samples from 85 Canadian infantry soldiers (n = 58 participants negative for symptoms of post-traumatic stress disorder and n = 27 participants with symptoms of post-traumatic stress disorder) following return from deployment to Afghanistan were determined using RNA sequencing technology. Count-based gene expression quantification, normalization and differential analysis (with thorough correction for confounders) revealed genes associated to PTSD; LRP8 and GOLM1. These preliminary results provide a proof-of-principle for the diagnostic utility of blood-based gene expression profiles for tracking symptoms of post-traumatic stress disorder in soldiers returning from tour. It is also the first to report transcriptome-wide expression profiles alongside a post-traumatic symptom checklist.
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Rezvykh AP, Yurinskaya MM, Vinokurov MG, Krasnov GS, Mitkevich VA, Makarov AA, Evgen’ev MB, Zatsepina OG. The Effect of Beta-Amyloid Peptides and Main Stress Protein HSP70 on Human SH-SY5Y Neuroblastoma Proteome. Mol Biol 2018. [DOI: 10.1134/s0026893318060158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Thawornpan P, Thanapongpichat S, Tun AW, Phongdara A, de Jong L, Buncherd H. Fly-ash as a low-cost material for isolation of phosphoproteins. CHEMOSPHERE 2018; 213:124-132. [PMID: 30216812 DOI: 10.1016/j.chemosphere.2018.08.150] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 08/27/2018] [Accepted: 08/29/2018] [Indexed: 06/08/2023]
Abstract
Metal oxide affinity chromatography (MOAC) is one of the most commonly used techniques for selective isolation phosphoproteins and phosphopeptides. This technique is capable of capturing the phosphorylated biomolecules through the affinity of the phosphoryl group for metal oxides/hydroxides. Fly-ash (FA), a by-product of coal-combustion power plants, is primarily composed of oxides of silicon and metals, among which iron and titanium. A number of studies have demonstrated the potential of these metal oxides for phosphoprotein and phosphopeptide enrichment. FA is annually produced over hundred million tons worldwide and generally considered as hazardous waste. It is thus of great importance to enhance its utilization. Here we present the first demonstration of the utility of FA as a low-cost MOAC material for the enrichment of phosphoproteins. With an FA-microcolumn, phosphoproteins can be successfully sequestered from other proteins. FA-microcolumns are shown to be simple, cheap and selective devices for phosphoprotein enrichment from a small volume of mixtures.
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Affiliation(s)
- Pongsakorn Thawornpan
- Department of Molecular Biotechnology and Bioinformatics, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | | | - Aung Win Tun
- Faculty of Graduate Studies, Mahidol University, Thailand
| | - Amornrat Phongdara
- Faculty of Medical Technology, Prince of Songkla University, Songkhla, Thailand; Center for Genomics and Bioinformatics Research, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Luitzen de Jong
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1090 GE Amsterdam, the Netherlands
| | - Hansuk Buncherd
- Faculty of Medical Technology, Prince of Songkla University, Songkhla, Thailand.
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23
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Rosa IM, Henriques AG, Wiltfang J, da Cruz E Silva OAB. Putative Dementia Cases Fluctuate as a Function of Mini-Mental State Examination Cut-Off Points. J Alzheimers Dis 2018; 61:157-167. [PMID: 29125486 DOI: 10.3233/jad-170501] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
As the population ages, there is a growing need to quickly and accurately identify putative dementia cases. Many cognitive tests are available; among those commonly used are the Cognitive Dementia Rating (CDR) and the Mini-Mental Status Examination (MMSE). The aim of this work was to compare the validity and reliability of these cognitive tests in a primary care based cohort (pcb-Cohort). The MMSE and the CDR were applied to 568 volunteers in the pcb-Cohort. Distinct cut-off points for the MMSE were considered, namely MMSE 27, MMSE 24, and MMSE PT (adapted for the Portuguese population). The MMSE 27 identified the greatest number of putative dementia cases, and, as determined by the ROC curve, it was the most sensitive and specific of the MMSE cut-offs considered. Putative predictive or risk factors identified included age, literacy, depression, and diabetes mellitus (DM). DM has previously been indicated as a risk factor for dementia and Alzheimer's disease. Comparatively, the MMSE 27 cut-off has the greatest sensibility (94.9%) and specificity (66.3%) when compared to MMSE PT and MMSE 24. Upon comparing MMSE and CDR scores, the latter identified a further 146 putative dementia cases, thus permitting one to propose that in an ideal situation, both tests should be employed. This increases the likelihood of identifying putative dementia cases for subsequent follow up work, thus these cognitive tests represent important tools in patient care. Further, this is a significant study for Portuguese populations, where few of these studies have been carried out.
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Affiliation(s)
- Ilka M Rosa
- Department of Medical Sciences, Neuroscience and Signalling Laboratory, Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - Ana G Henriques
- Department of Medical Sciences, Neuroscience and Signalling Laboratory, Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - Jens Wiltfang
- Department of Medical Sciences, Neuroscience and Signalling Laboratory, Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal.,Department of Psychiatry and Psychotherapy, University Medicine Göttingen, Göttingen, Germany
| | - Odete A B da Cruz E Silva
- Department of Medical Sciences, Neuroscience and Signalling Laboratory, Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
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24
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Rosa IM, Henriques AG, Carvalho L, Oliveira J, da Cruz E Silva OAB. Screening Younger Individuals in a Primary Care Setting Flags Putative Dementia Cases and Correlates Gastrointestinal Diseases with Poor Cognitive Performance. Dement Geriatr Cogn Disord 2018; 43:15-28. [PMID: 27907913 DOI: 10.1159/000452485] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/13/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND/AIMS Diagnosing dementia is challenging in many primary care settings, given the limited human resources and the lack of current diagnostic tools. With this in mind, a primary care-based cohort was established in the Aveiro district of Portugal. METHODS A total of 568 participants were evaluated using cognitive tests and APOE genotyping. RESULTS The findings revealed a dementia prevalence of 12%. A strong correlation between increasing Clinical Dementia Rating (CDR) scores and education was clearly evident. Other highly relevant risk factors were activities of daily living (ADL), instrumental ADL, aging, depression, gender, the APOE ε4 allele, and comorbidities (depression as well as gastrointestinal, osteoarticular, and neurodegenerative diseases). A hitherto unreported, significant correlation between gastrointestinal disease and high CDR score was clearly observable. CONCLUSIONS This study shows the merit of carrying out a dementia screening on younger subjects. Significantly, 71 subjects in the age group of 50-65 years were flagged for follow-up studies; furthermore, these cases with a potentially early onset of dementia were identified in a primary care setting.
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Affiliation(s)
- Ilka M Rosa
- Neuroscience and Signalling Laboratory, Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
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25
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Amyloid-β with isomerized Asp7 cytotoxicity is coupled to protein phosphorylation. Sci Rep 2018; 8:3518. [PMID: 29476081 PMCID: PMC5824883 DOI: 10.1038/s41598-018-21815-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 01/18/2018] [Indexed: 01/08/2023] Open
Abstract
Neuronal dysfunction and loss associated with the accumulation of amyloid-β (Aβ) in the form of extracellular amyloid plaques and hyperphosphorylated tau in the form of intraneuronal neurofibrillary tangles represent key features of Alzheimer's disease (AD). Amyloid plaques found in the brains of AD patients are predominantly composed of Aβ42 and its multiple chemically or structurally modified isoforms. Recently, we demonstrated that Aβ42 with isomerised Asp7 (isoAβ42) which is one of the most abundant Aβ isoform in plaques, exhibited high neurotoxicity in human neuronal cells. Here, we show that, in SH-SY5Y neuroblastoma cells, the administration of synthetic isoAβ42 rather than intact Aβ42 resulted in a significantly higher level of protein phosphorylation, especially the phosphorylation of tau, tubulins, and matrin 3. IsoAβ42 induced a drastic reduction of tau protein levels. Our data demonstrate, for the first time, that isoAβ42, being to date the only known synthetic Aβ species to cause AD-like amyloidogenesis in an animal AD model, induced cell death by disabling structural proteins in a manner characteristic of that observed in the neurons of AD patients. The data emphasize an important role of isoAβ42 in AD progression and provide possible neurotoxicity paths for this particular isoform.
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26
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Functions and dysfunctions of Ca2+/calmodulin-dependent protein kinase phosphatase (CaMKP/PPM1F) and CaMKP-N/PPM1E. Arch Biochem Biophys 2018; 640:83-92. [DOI: 10.1016/j.abb.2018.01.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 12/28/2017] [Accepted: 01/04/2018] [Indexed: 12/22/2022]
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27
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Shinde S, Selvalatchmanan J, Incel A, Akhoundian M, Bendt AK, Torta F. Mesoporous polymeric microspheres with high affinity for phosphorylated biomolecules. NEW J CHEM 2018. [DOI: 10.1039/c8nj01114a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bis-imidazolium functionalized mesoporous microspheres selectively extract phosphorylated peptides/lipids from biofluids.
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Affiliation(s)
- Sudhirkumar Shinde
- Department of Biomedical Sciences
- Faculty of Health and Society
- Malmö University
- SE 205 06 Malmö
- Sweden
| | - Jayashree Selvalatchmanan
- Singapore Lipidomics Incubator (SLING)
- Life Sciences Institute
- National University of Singapore
- Singapore 117456
- Singapore
| | - Anil Incel
- Department of Biomedical Sciences
- Faculty of Health and Society
- Malmö University
- SE 205 06 Malmö
- Sweden
| | - Maedeh Akhoundian
- Department of Biomedical Sciences
- Faculty of Health and Society
- Malmö University
- SE 205 06 Malmö
- Sweden
| | - Anne K. Bendt
- Singapore Lipidomics Incubator (SLING)
- Life Sciences Institute
- National University of Singapore
- Singapore 117456
- Singapore
| | - Federico Torta
- Singapore Lipidomics Incubator (SLING)
- Department of Biochemistry
- YLL School of Medicine
- National University of Singapore
- Singapore 11745
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28
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Oliveira JM, da Cruz e Silva CB, Müller T, Martins TS, Cova M, da Cruz e Silva OAB, Henriques AG. Toward Neuroproteomics in Biological Psychiatry: A Systems Approach Unravels Okadaic Acid-Induced Alterations in the Neuronal Phosphoproteome. ACTA ACUST UNITED AC 2017; 21:550-563. [DOI: 10.1089/omi.2017.0108] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Joana Machado Oliveira
- Neurosciences and Signalling Laboratory, Department of Medical Sciences and Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal
| | | | - Thorsten Müller
- Cell Signaling, Biochemistry II—Molecular Biochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Tânia Soares Martins
- Neurosciences and Signalling Laboratory, Department of Medical Sciences and Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal
| | - Marta Cova
- Neurosciences and Signalling Laboratory, Department of Medical Sciences and Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal
| | - Odete A. B. da Cruz e Silva
- Neurosciences and Signalling Laboratory, Department of Medical Sciences and Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal
| | - Ana Gabriela Henriques
- Neurosciences and Signalling Laboratory, Department of Medical Sciences and Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal
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29
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Oliveira J, Costa M, de Almeida MSC, da Cruz e Silva OA, Henriques AG. Protein Phosphorylation is a Key Mechanism in Alzheimer’s Disease. J Alzheimers Dis 2017; 58:953-978. [DOI: 10.3233/jad-170176] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Joana Oliveira
- Department of Medical Sciences, Neuroscience and Signalling Laboratory, iBiMED, University of Aveiro, Aveiro, Portugal
| | - Márcio Costa
- Department of Medical Sciences, Neuroscience and Signalling Laboratory, iBiMED, University of Aveiro, Aveiro, Portugal
| | | | - Odete A.B. da Cruz e Silva
- Department of Medical Sciences, Neuroscience and Signalling Laboratory, iBiMED, University of Aveiro, Aveiro, Portugal
| | - Ana Gabriela Henriques
- Department of Medical Sciences, Neuroscience and Signalling Laboratory, iBiMED, University of Aveiro, Aveiro, Portugal
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