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McLaren AMR, Kawaja MD. Olfactory Dysfunction and Alzheimer's Disease: A Review. J Alzheimers Dis 2024; 99:811-827. [PMID: 38728185 DOI: 10.3233/jad-231377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
Alzheimer's disease is the most common cause of dementia, and it is one of the leading causes of death globally. Identification and validation of biomarkers that herald the onset and progression of Alzheimer's disease is of paramount importance for early reliable diagnosis and effective pharmacological therapy commencement. A substantial body of evidence has emerged demonstrating that olfactory dysfunction is a preclinical symptom of neurodegenerative diseases including Alzheimer's disease. While a correlation between olfactory dysfunction and Alzheimer's disease onset and progression in humans exists, the mechanism underlying this relationship remains unknown. The aim of this article is to review the current state of knowledge regarding the range of potential factors that may contribute to the development of Alzheimer's disease-related olfactory dysfunction. This review predominantly focuses on genetic mutations associated with Alzheimer's disease including amyloid-β protein precursor, presenilin 1 and 2, and apolipoprotein E mutations, that may (in varying ways) drive the cellular events that lead to and sustain olfactory dysfunction.
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Affiliation(s)
| | - Michael D Kawaja
- Centre for Neuroscience Studies, Queen's University, Kingston, Ontario, ON, Canada
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, ON, Canada
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2
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Garcia-Segura ME, Durainayagam BR, Liggi S, Graça G, Jimenez B, Dehghan A, Tzoulaki I, Karaman I, Elliott P, Griffin JL. Pathway-based integration of multi-omics data reveals lipidomics alterations validated in an Alzheimer's disease mouse model and risk loci carriers. J Neurochem 2023; 164:57-76. [PMID: 36326588 PMCID: PMC10107183 DOI: 10.1111/jnc.15719] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 11/06/2022]
Abstract
Alzheimer's disease (AD) is a highly prevalent neurodegenerative disorder. Despite increasing evidence of the importance of metabolic dysregulation in AD, the underlying metabolic changes that may impact amyloid plaque formation are not understood, particularly for late-onset AD. This study analyzed genome-wide association studies (GWAS), transcriptomics, and proteomics data obtained from several data repositories to obtain differentially expressed (DE) multi-omics elements in mouse models of AD. We characterized the metabolic modulation in these data sets using gene ontology, transcription factor, pathway, and cell-type enrichment analyses. A predicted lipid signature was extracted from genome-scale metabolic networks (GSMN) and subsequently validated in a lipidomic data set derived from cortical tissue of ABCA-7 null mice, a mouse model of one of the genes associated with late-onset AD. Moreover, a metabolome-wide association study (MWAS) was performed to further characterize the association between dysregulated lipid metabolism in human blood serum and genes associated with AD risk. We found 203 DE transcripts, 164 DE proteins, and 58 DE GWAS-derived mouse orthologs associated with significantly enriched metabolic biological processes. Lipid and bioenergetic metabolic pathways were significantly over-represented across the AD multi-omics data sets. Microglia and astrocytes were significantly enriched in the lipid-predominant AD-metabolic transcriptome. We also extracted a predicted lipid signature that was validated and robustly modeled class separation in the ABCA7 mice cortical lipidome, with 11 of these lipid species exhibiting statistically significant modulations. MWAS revealed 298 AD single nucleotide polymorphisms-metabolite associations, of which 70% corresponded to lipid classes. These results support the importance of lipid metabolism dysregulation in AD and highlight the suitability of mapping AD multi-omics data into GSMNs to identify metabolic alterations.
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Affiliation(s)
- Monica Emili Garcia-Segura
- Department of Brain Sciences, Imperial College London, London, UK.,Section of Biomolecular Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Brenan R Durainayagam
- Section of Biomolecular Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.,UK-Dementia Research Institute (UK-DRI) at Imperial College London, London, UK
| | - Sonia Liggi
- Section of Biomolecular Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Gonçalo Graça
- Section of Bioinformatics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Beatriz Jimenez
- Section of Bioanalytical Chemistry and the National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Abbas Dehghan
- UK-Dementia Research Institute (UK-DRI) at Imperial College London, London, UK.,Department of Epidemiology and Biostatistics, Imperial College London, London, UK.,MRC Centre for Environment and Health, Imperial College London, London, UK
| | - Ioanna Tzoulaki
- UK-Dementia Research Institute (UK-DRI) at Imperial College London, London, UK.,Department of Epidemiology and Biostatistics, Imperial College London, London, UK.,National Institute for Health Research Imperial Biomedical Research Centre, Imperial College London, UK.,Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece
| | - Ibrahim Karaman
- Section of Bioinformatics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.,Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Paul Elliott
- UK-Dementia Research Institute (UK-DRI) at Imperial College London, London, UK.,Department of Epidemiology and Biostatistics, Imperial College London, London, UK.,MRC Centre for Environment and Health, Imperial College London, London, UK.,National Institute for Health Research Imperial Biomedical Research Centre, Imperial College London, UK
| | - Julian L Griffin
- Section of Biomolecular Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.,UK-Dementia Research Institute (UK-DRI) at Imperial College London, London, UK.,Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.,The Rowett Institute, University of Aberdeen, Aberdeen, Scotland
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3
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Garcia-Segura ME, Durainayagam BR, Liggi S, Graça G, Jimenez B, Dehghan A, Tzoulaki I, Karaman I, Elliott P, Griffin JL. Pathway-based integration of multi-omics data reveals lipidomics alterations validated in an Alzheimer's disease mouse model and risk loci carriers. J Neurochem 2023. [PMID: 36326588 DOI: 10.1101/2021.05.10.21255052v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Alzheimer's disease (AD) is a highly prevalent neurodegenerative disorder. Despite increasing evidence of the importance of metabolic dysregulation in AD, the underlying metabolic changes that may impact amyloid plaque formation are not understood, particularly for late-onset AD. This study analyzed genome-wide association studies (GWAS), transcriptomics, and proteomics data obtained from several data repositories to obtain differentially expressed (DE) multi-omics elements in mouse models of AD. We characterized the metabolic modulation in these data sets using gene ontology, transcription factor, pathway, and cell-type enrichment analyses. A predicted lipid signature was extracted from genome-scale metabolic networks (GSMN) and subsequently validated in a lipidomic data set derived from cortical tissue of ABCA-7 null mice, a mouse model of one of the genes associated with late-onset AD. Moreover, a metabolome-wide association study (MWAS) was performed to further characterize the association between dysregulated lipid metabolism in human blood serum and genes associated with AD risk. We found 203 DE transcripts, 164 DE proteins, and 58 DE GWAS-derived mouse orthologs associated with significantly enriched metabolic biological processes. Lipid and bioenergetic metabolic pathways were significantly over-represented across the AD multi-omics data sets. Microglia and astrocytes were significantly enriched in the lipid-predominant AD-metabolic transcriptome. We also extracted a predicted lipid signature that was validated and robustly modeled class separation in the ABCA7 mice cortical lipidome, with 11 of these lipid species exhibiting statistically significant modulations. MWAS revealed 298 AD single nucleotide polymorphisms-metabolite associations, of which 70% corresponded to lipid classes. These results support the importance of lipid metabolism dysregulation in AD and highlight the suitability of mapping AD multi-omics data into GSMNs to identify metabolic alterations.
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Affiliation(s)
- Monica Emili Garcia-Segura
- Department of Brain Sciences, Imperial College London, London, UK
- Section of Biomolecular Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Brenan R Durainayagam
- Section of Biomolecular Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- UK-Dementia Research Institute (UK-DRI) at Imperial College London, London, UK
| | - Sonia Liggi
- Section of Biomolecular Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Gonçalo Graça
- Section of Bioinformatics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Beatriz Jimenez
- Section of Bioanalytical Chemistry and the National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Abbas Dehghan
- UK-Dementia Research Institute (UK-DRI) at Imperial College London, London, UK
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- MRC Centre for Environment and Health, Imperial College London, London, UK
| | - Ioanna Tzoulaki
- UK-Dementia Research Institute (UK-DRI) at Imperial College London, London, UK
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- National Institute for Health Research Imperial Biomedical Research Centre, Imperial College London, UK
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece
| | - Ibrahim Karaman
- Section of Bioinformatics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Paul Elliott
- UK-Dementia Research Institute (UK-DRI) at Imperial College London, London, UK
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- MRC Centre for Environment and Health, Imperial College London, London, UK
- National Institute for Health Research Imperial Biomedical Research Centre, Imperial College London, UK
| | - Julian L Griffin
- Section of Biomolecular Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- UK-Dementia Research Institute (UK-DRI) at Imperial College London, London, UK
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
- The Rowett Institute, University of Aberdeen, Aberdeen, Scotland
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Ge X, Yao T, Zhang C, Wang Q, Wang X, Xu LC. Human microRNA-4433 (hsa-miR-4443) Targets 18 Genes to be a Risk Factor of Neurodegenerative Diseases. Curr Alzheimer Res 2022; 19:511-522. [PMID: 35929619 PMCID: PMC9906632 DOI: 10.2174/1567205019666220805120303] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 01/27/2023]
Abstract
BACKGROUND Neurodegenerative diseases, such as Alzheimer's disease patients (AD), Huntington's disease (HD) and Parkinson's disease (PD), are common causes of morbidity, mortality, and cognitive impairment in older adults. OBJECTIVE We aimed to understand the transcriptome characteristics of the cortex of neurodegenerative diseases and to provide an insight into the target genes of differently expressed microRNAs in the occurrence and development of neurodegenerative diseases. METHODS The Limma package of R software was used to analyze GSE33000, GSE157239, GSE64977 and GSE72962 datasets to identify the differentially expressed genes (DEGs) and microRNAs in the cortex of neurodegenerative diseases. Bioinformatics methods, such as GO enrichment analysis, KEGG enrichment analysis and gene interaction network analysis, were used to explore the biological functions of DEGs. Weighted gene co-expression network analysis (WGCNA) was used to cluster DEGs into modules. RNA22, miRDB, miRNet 2.0 and TargetScan7 databases were performed to predict the target genes of microRNAs. RESULTS Among 310 Alzheimer's disease (AD) patients, 157 Huntington's disease (HD) patients and 157 non-demented control (Con) individuals, 214 co-DEGs were identified. Those co-DEGs were filtered into 2 different interaction network complexes, representing immune-related genes and synapserelated genes. The WGCNA results identified five modules: yellow, blue, green, turquoise, and brown. Most of the co-DEGs were clustered into the turquoise module and blue module, which respectively regulated synapse-related function and immune-related function. In addition, human microRNA-4433 (hsa-miR-4443), which targets 18 co-DEGs, was the only 1 co-up-regulated microRNA identified in the cortex of neurodegenerative diseases. CONCLUSION 214 DEGs and 5 modules regulate the immune-related and synapse-related function of the cortex in neurodegenerative diseases. Hsa-miR-4443 targets 18 co-DEGs and may be a potential molecular mechanism in neurodegenerative diseases' occurrence and development.
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Affiliation(s)
- Xing Ge
- Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu 221002, China;
| | - Tingting Yao
- School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu 221002, China;
| | - Chaoran Zhang
- School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu 221002, China;
| | - Qingqing Wang
- Department of Nephrology, Xuzhou Children’s Hospital, Xuzhou, Jiangsu 221000, China
| | - Xuxu Wang
- School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu 221002, China;
| | - Li-Chun Xu
- School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu 221002, China; ,Address correspondence to this author at the School of Public Health, Xuzhou Medical University, Xuzhou, 209 Tong-Shan Road, Xuzhou, Jiangsu, 221002, China; Tel: +86-516-83262650; Fax: +86-516-83262650; E-mail:
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5
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Rodriguez Ospina S, Blazier DM, Criado-Marrero M, Gould LA, Gebru NT, Beaulieu-Abdelahad D, Wang X, Remily-Wood E, Chaput D, Stevens S, Uversky VN, Bickford PC, Dickey CA, Blair LJ. Small Heat Shock Protein 22 Improves Cognition and Learning in the Tauopathic Brain. Int J Mol Sci 2022; 23:ijms23020851. [PMID: 35055033 PMCID: PMC8775832 DOI: 10.3390/ijms23020851] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/05/2022] [Accepted: 01/10/2022] [Indexed: 02/04/2023] Open
Abstract
The microtubule-associated protein tau pathologically accumulates and aggregates in Alzheimer's disease (AD) and other tauopathies, leading to cognitive dysfunction and neuronal loss. Molecular chaperones, like small heat-shock proteins (sHsps), can help deter the accumulation of misfolded proteins, such as tau. Here, we tested the hypothesis that the overexpression of wild-type Hsp22 (wtHsp22) and its phosphomimetic (S24,57D) Hsp22 mutant (mtHsp22) could slow tau accumulation and preserve memory in a murine model of tauopathy, rTg4510. Our results show that Hsp22 protected against deficits in synaptic plasticity and cognition in the tauopathic brain. However, we did not detect a significant change in tau phosphorylation or levels in these mice. This led us to hypothesize that the functional benefit was realized through the restoration of dysfunctional pathways in hippocampi of tau transgenic mice since no significant benefit was measured in non-transgenic mice expressing wtHsp22 or mtHsp22. To identify these pathways, we performed mass spectrometry of tissue lysates from the injection site. Overall, our data reveal that Hsp22 overexpression in neurons promotes synaptic plasticity by regulating canonical pathways and upstream regulators that have been characterized as potential AD markers and synaptogenesis regulators, like EIF4E and NFKBIA.
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Affiliation(s)
- Santiago Rodriguez Ospina
- USF Health Byrd Alzheimer’s Institute, University of South Florida, Tampa, FL 33613, USA; (S.R.O.); (D.M.B.); (M.C.-M.); (L.A.G.); (N.T.G.); (D.B.-A.); (X.W.); (V.N.U.)
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA;
| | - Danielle M. Blazier
- USF Health Byrd Alzheimer’s Institute, University of South Florida, Tampa, FL 33613, USA; (S.R.O.); (D.M.B.); (M.C.-M.); (L.A.G.); (N.T.G.); (D.B.-A.); (X.W.); (V.N.U.)
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA;
| | - Marangelie Criado-Marrero
- USF Health Byrd Alzheimer’s Institute, University of South Florida, Tampa, FL 33613, USA; (S.R.O.); (D.M.B.); (M.C.-M.); (L.A.G.); (N.T.G.); (D.B.-A.); (X.W.); (V.N.U.)
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA;
| | - Lauren A. Gould
- USF Health Byrd Alzheimer’s Institute, University of South Florida, Tampa, FL 33613, USA; (S.R.O.); (D.M.B.); (M.C.-M.); (L.A.G.); (N.T.G.); (D.B.-A.); (X.W.); (V.N.U.)
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA;
| | - Niat T. Gebru
- USF Health Byrd Alzheimer’s Institute, University of South Florida, Tampa, FL 33613, USA; (S.R.O.); (D.M.B.); (M.C.-M.); (L.A.G.); (N.T.G.); (D.B.-A.); (X.W.); (V.N.U.)
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA;
| | - David Beaulieu-Abdelahad
- USF Health Byrd Alzheimer’s Institute, University of South Florida, Tampa, FL 33613, USA; (S.R.O.); (D.M.B.); (M.C.-M.); (L.A.G.); (N.T.G.); (D.B.-A.); (X.W.); (V.N.U.)
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA;
| | - Xinming Wang
- USF Health Byrd Alzheimer’s Institute, University of South Florida, Tampa, FL 33613, USA; (S.R.O.); (D.M.B.); (M.C.-M.); (L.A.G.); (N.T.G.); (D.B.-A.); (X.W.); (V.N.U.)
- Department of Molecular Pharmacology and Physiology, University of South Florida, Tampa, FL 33612, USA;
| | - Elizabeth Remily-Wood
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA;
| | - Dale Chaput
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA; (D.C.); (S.S.Jr.)
| | - Stanley Stevens
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA; (D.C.); (S.S.Jr.)
| | - Vladimir N. Uversky
- USF Health Byrd Alzheimer’s Institute, University of South Florida, Tampa, FL 33613, USA; (S.R.O.); (D.M.B.); (M.C.-M.); (L.A.G.); (N.T.G.); (D.B.-A.); (X.W.); (V.N.U.)
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA;
- Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy Pereulok, 9, 141700 Dolgoprudny, Russia
| | - Paula C. Bickford
- Department of Molecular Pharmacology and Physiology, University of South Florida, Tampa, FL 33612, USA;
- Research Service, James A. Haley Veterans’ Hospital, Tampa, FL 33620, USA
- Department of Neurosurgery and Brain Repair, University of South Florida, Tampa, FL 33613, USA
| | - Chad A. Dickey
- USF Health Byrd Alzheimer’s Institute, University of South Florida, Tampa, FL 33613, USA; (S.R.O.); (D.M.B.); (M.C.-M.); (L.A.G.); (N.T.G.); (D.B.-A.); (X.W.); (V.N.U.)
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA;
| | - Laura J. Blair
- USF Health Byrd Alzheimer’s Institute, University of South Florida, Tampa, FL 33613, USA; (S.R.O.); (D.M.B.); (M.C.-M.); (L.A.G.); (N.T.G.); (D.B.-A.); (X.W.); (V.N.U.)
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA;
- Research Service, James A. Haley Veterans’ Hospital, Tampa, FL 33620, USA
- Correspondence: ; Tel.: +1-813-369-0639
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Lachén-Montes M, Mendizuri N, Ausín K, Pérez-Mediavilla A, Azkargorta M, Iloro I, Elortza F, Kondo H, Ohigashi I, Ferrer I, de la Torre R, Robledo P, Fernández-Irigoyen J, Santamaría E. Smelling the Dark Proteome: Functional Characterization of PITH Domain-Containing Protein 1 (C1orf128) in Olfactory Metabolism. J Proteome Res 2020; 19:4826-4843. [PMID: 33185454 DOI: 10.1021/acs.jproteome.0c00452] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The Human Proteome Project (HPP) consortium aims to functionally characterize the dark proteome. On the basis of the relevance of olfaction in early neurodegeneration, we have analyzed the dark proteome using data mining in public resources and omics data sets derived from the human olfactory system. Multiple dark proteins localize at synaptic terminals and may be involved in amyloidopathies such as Alzheimer's disease (AD). We have characterized the dark PITH domain-containing protein 1 (PITHD1) in olfactory metabolism using bioinformatics, proteomics, in vitro and in vivo studies, and neuropathology. PITHD1-/- mice exhibit olfactory bulb (OB) proteome changes related to synaptic transmission, cognition, and memory. OB PITHD1 expression increases with age in wild-type (WT) mice and decreases in Tg2576 AD mice at late stages. The analysis across 6 neurological disorders reveals that olfactory tract (OT) PITHD1 is specifically upregulated in human AD. Stimulation of olfactory neuroepithelial (ON) cells with PITHD1 alters the ON phosphoproteome, modifies the proliferation rate, and induces a pro-inflammatory phenotype. This workflow applied by the Spanish C-HPP and Human Brain Proteome Project (HBPP) teams across the ON-OB-OT axis can be adapted as a guidance to decipher functional features of dark proteins. Data are available via ProteomeXchange with identifiers PXD018784 and PXD021634.
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Affiliation(s)
- Mercedes Lachén-Montes
- Clinical Neuroproteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,Proteored-ISCIII, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008 Pamplona, Spain
| | - Naroa Mendizuri
- Clinical Neuroproteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,Proteored-ISCIII, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008 Pamplona, Spain
| | - Karina Ausín
- Clinical Neuroproteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,Proteored-ISCIII, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008 Pamplona, Spain
| | - Alberto Pérez-Mediavilla
- IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008 Pamplona, Spain.,Neurobiology of Alzheimer's Disease, Department of Biochemistry, Center for Applied Medical Research (CIMA), Neurosciences Division, University of Navarra, 31008 Pamplona, Spain
| | - Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Ibon Iloro
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Felix Elortza
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Hiroyuki Kondo
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, Tokushima University, Tokushima 770-8503, Japan
| | - Izumi Ohigashi
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, Tokushima University, Tokushima 770-8503, Japan
| | - Isidre Ferrer
- Bellvitge Biomedical Research Institute (IDIBELL), 08908 Hospitalet de Llobregat, Spain.,CIBERNED (Network Centre of Biomedical Research of Neurodegenerative Diseases), Institute of Health Carlos III, 28029 Madrid, Spain.,Department of Pathology and Experimental Therapeutics, University of Barcelona, 08908 Hospitalet de Llobregat, Spain.,Institute of Neurosciences, University of Barcelona, 08007 Barcelona, Spain
| | - Rafael de la Torre
- Integrative Pharmacology and Systems Neuroscience Research Group, Neurosciences Research Program, IMIM (Hospital del Mar Medical Research Institute), 08003 Barcelona, Spain.,Department of Experimental and Health Sciences, Pompeu Fabra University (CEXS-UPF), 08002 Barcelona, Spain.,School of Medicine, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,CIBER de Fisiopatología de la Obesidad y Nutrición (CB06/03), CIBEROBN, 28029 Madrid, Spain
| | - Patricia Robledo
- Integrative Pharmacology and Systems Neuroscience Research Group, Neurosciences Research Program, IMIM (Hospital del Mar Medical Research Institute), 08003 Barcelona, Spain.,Department of Experimental and Health Sciences, Pompeu Fabra University (CEXS-UPF), 08002 Barcelona, Spain
| | - Joaquín Fernández-Irigoyen
- Clinical Neuroproteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,Proteored-ISCIII, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008 Pamplona, Spain
| | - Enrique Santamaría
- Clinical Neuroproteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,Proteored-ISCIII, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008 Pamplona, Spain
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7
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Proteomic Characterization of the Olfactory Molecular Imbalance in Dementia with Lewy Bodies. Int J Mol Sci 2020; 21:ijms21176371. [PMID: 32887355 PMCID: PMC7503830 DOI: 10.3390/ijms21176371] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/18/2020] [Accepted: 09/01/2020] [Indexed: 02/07/2023] Open
Abstract
Olfactory dysfunction is one of the prodromal symptoms in dementia with Lewy bodies (DLB). However, the molecular pathogenesis associated with decreased smell function remains largely undeciphered. We generated quantitative proteome maps to detect molecular alterations in olfactory bulbs (OB) derived from DLB subjects compared to neurologically intact controls. A total of 3214 olfactory proteins were quantified, and 99 proteins showed significant alterations in DLB cases. Protein interaction networks disrupted in DLB indicated an imbalance in translation and the synaptic vesicle cycle. These alterations were accompanied by alterations in AKT/MAPK/SEK1/p38 MAPK signaling pathways that showed a distinct expression profile across the OB–olfactory tract (OT) axis. Taken together, our data partially reflect the missing links in the biochemical understanding of olfactory dysfunction in DLB.
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8
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Ubeda-Bañon I, Saiz-Sanchez D, Flores-Cuadrado A, Rioja-Corroto E, Gonzalez-Rodriguez M, Villar-Conde S, Astillero-Lopez V, Cabello-de la Rosa JP, Gallardo-Alcañiz MJ, Vaamonde-Gamo J, Relea-Calatayud F, Gonzalez-Lopez L, Mohedano-Moriano A, Rabano A, Martinez-Marcos A. The human olfactory system in two proteinopathies: Alzheimer's and Parkinson's diseases. Transl Neurodegener 2020; 9:22. [PMID: 32493457 PMCID: PMC7271529 DOI: 10.1186/s40035-020-00200-7] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 05/20/2020] [Indexed: 12/31/2022] Open
Abstract
Alzheimer's and Parkinson's diseases are the most prevalent neurodegenerative disorders. Their etiologies are idiopathic, and treatments are symptomatic and orientated towards cognitive or motor deficits. Neuropathologically, both are proteinopathies with pathological aggregates (plaques of amyloid-β peptide and neurofibrillary tangles of tau protein in Alzheimer's disease, and Lewy bodies mostly composed of α-synuclein in Parkinson's disease). These deposits appear in the nervous system in a predictable and accumulative sequence with six neuropathological stages. Both disorders present a long prodromal period, characterized by preclinical signs including hyposmia. Interestingly, the olfactory system, particularly the anterior olfactory nucleus, is initially and preferentially affected by the pathology. Cerebral atrophy revealed by magnetic resonance imaging must be complemented by histological analyses to ascertain whether neuronal and/or glial loss or neuropil remodeling are responsible for volumetric changes. It has been proposed that these proteinopathies could act in a prion-like manner in which a misfolded protein would be able to force native proteins into pathogenic folding (seeding), which then propagates through neurons and glia (spreading). Existing data have been examined to establish why some neuronal populations are vulnerable while others are resistant to pathology and to what extent glia prevent and/or facilitate proteinopathy spreading. Connectomic approaches reveal a number of hubs in the olfactory system (anterior olfactory nucleus, olfactory entorhinal cortex and cortical amygdala) that are key interconnectors with the main hubs (the entorhinal-hippocampal-cortical and amygdala-dorsal motor vagal nucleus) of network dysfunction in Alzheimer's and Parkinson's diseases.
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Affiliation(s)
- Isabel Ubeda-Bañon
- Neuroplasticity and Neurodegeneration Laboratory, Ciudad Real Medical School, CRIB, University of Castilla-La Mancha, 13005 Ciudad Real, Spain
| | - Daniel Saiz-Sanchez
- Neuroplasticity and Neurodegeneration Laboratory, Ciudad Real Medical School, CRIB, University of Castilla-La Mancha, 13005 Ciudad Real, Spain
| | - Alicia Flores-Cuadrado
- Neuroplasticity and Neurodegeneration Laboratory, Ciudad Real Medical School, CRIB, University of Castilla-La Mancha, 13005 Ciudad Real, Spain
| | - Ernesto Rioja-Corroto
- Neuroplasticity and Neurodegeneration Laboratory, Ciudad Real Medical School, CRIB, University of Castilla-La Mancha, 13005 Ciudad Real, Spain
| | - Melania Gonzalez-Rodriguez
- Neuroplasticity and Neurodegeneration Laboratory, Ciudad Real Medical School, CRIB, University of Castilla-La Mancha, 13005 Ciudad Real, Spain
| | - Sandra Villar-Conde
- Neuroplasticity and Neurodegeneration Laboratory, Ciudad Real Medical School, CRIB, University of Castilla-La Mancha, 13005 Ciudad Real, Spain
| | - Veronica Astillero-Lopez
- Neuroplasticity and Neurodegeneration Laboratory, Ciudad Real Medical School, CRIB, University of Castilla-La Mancha, 13005 Ciudad Real, Spain
| | | | | | - Julia Vaamonde-Gamo
- Neurology Service, Ciudad Real General University Hospital, 13005 Ciudad Real, Spain
| | | | - Lucia Gonzalez-Lopez
- Pathology Service, Ciudad Real General University Hospital, 13005 Ciudad Real, Spain
| | | | - Alberto Rabano
- Neuropathology Department and Tissue Bank, CIEN Foundation, Carlos III Health Institute, Madrid, Spain
| | - Alino Martinez-Marcos
- Neuroplasticity and Neurodegeneration Laboratory, Ciudad Real Medical School, CRIB, University of Castilla-La Mancha, 13005 Ciudad Real, Spain
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9
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Lachen-Montes M, González-Morales A, Palomino M, Ausin K, Gómez-Ochoa M, Zelaya MV, Ferrer I, Pérez-Mediavilla A, Fernández-Irigoyen J, Santamaría E. Early-Onset Molecular Derangements in the Olfactory Bulb of Tg2576 Mice: Novel Insights Into the Stress-Responsive Olfactory Kinase Dynamics in Alzheimer's Disease. Front Aging Neurosci 2019; 11:141. [PMID: 31244650 PMCID: PMC6579864 DOI: 10.3389/fnagi.2019.00141] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 05/23/2019] [Indexed: 11/13/2022] Open
Abstract
The olfactory bulb (OB) is the first processing station in the olfactory pathway. Despite smell impairment, which is considered an early event in Alzheimer’s disease (AD), little is known about the initial molecular disturbances that accompany the AD development at olfactory level. We have interrogated the time-dependent OB molecular landscape in Tg2576 AD mice prior to the appearance of neuropathological amyloid plaques (2-, and 6-month-old), using combinatorial omics analysis. The metabolic modulation induced by overproduction of human mutated amyloid precursor protein (APP) clearly differs between both time points. Besides the progressive perturbation of the APP interactome, functional network analysis unveiled an inverse regulation of downstream extracellular signal-regulated kinase (ERK1/2), and p38 mitogen-activated protein kinase (MAPK) routes in 2-month-old Tg2576 mice with respect to wild-type (WT) mice. In contrast, Akt and MAPK kinase 4 (SEK1)/ stress-activated protein kinase (SAPK) axis were parallel activated in the OB of 6-months-old-Tg2576 mice. Furthermore, a survival kinome profiling performed during the aging process (2-, 6-, and 18-month-old) revealed that olfactory APP overexpression leads to changes in the activation dynamics of protein kinase A (PKA), and SEK1/MKK4-SAPK/JNK between 6 and 18 months of age, when memory deficits appear and AD pathology is well established in transgenic mice. Interestingly, both olfactory pathways were differentially activated in a stage-dependent manner in human sporadic AD subjects with different neuropathological grading. Taken together, our data reflect the early impact of mutated APP on the OB molecular homeostasis, highlighting the progressive modulation of specific signaling pathways during the olfactory amyloidogenic pathology.
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Affiliation(s)
- Mercedes Lachen-Montes
- Clinical Neuroproteomics Group, NavarraBiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Pamplona, Spain.,Proteored-ISCIII Proteomics Unit, NavarraBiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Pamplona, Spain.,IDISNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Andrea González-Morales
- Clinical Neuroproteomics Group, NavarraBiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Pamplona, Spain.,Proteored-ISCIII Proteomics Unit, NavarraBiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Pamplona, Spain.,IDISNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Maialen Palomino
- Clinical Neuroproteomics Group, NavarraBiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Pamplona, Spain
| | - Karina Ausin
- Proteored-ISCIII Proteomics Unit, NavarraBiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Pamplona, Spain.,IDISNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Marta Gómez-Ochoa
- Department of Pathology, Complejo Hospitalario de Navarra, Pamplona, Spain
| | - María Victoria Zelaya
- Clinical Neuroproteomics Group, NavarraBiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Pamplona, Spain.,IDISNA, Navarra Institute for Health Research, Pamplona, Spain.,Department of Pathology, Complejo Hospitalario de Navarra, Pamplona, Spain
| | - Isidro Ferrer
- Institut de Neuropatologia, IDIBELL-Hospital Universitari de Bellvitge, Universitat de Barcelona, L'Hospitalet de Llobregat, Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain
| | - Alberto Pérez-Mediavilla
- IDISNA, Navarra Institute for Health Research, Pamplona, Spain.,Neurobiology of Alzheimer's Disease, Department of Biochemistry, Center for Applied Medical Research (CIMA), Neurosciences Division, University of Navarra, Pamplona, Spain
| | - Joaquín Fernández-Irigoyen
- Clinical Neuroproteomics Group, NavarraBiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Pamplona, Spain.,Proteored-ISCIII Proteomics Unit, NavarraBiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Pamplona, Spain.,IDISNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Enrique Santamaría
- Clinical Neuroproteomics Group, NavarraBiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Pamplona, Spain.,Proteored-ISCIII Proteomics Unit, NavarraBiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Pamplona, Spain.,IDISNA, Navarra Institute for Health Research, Pamplona, Spain
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10
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Lachén-Montes M, González-Morales A, Fernández-Irigoyen J, Santamaría E. Deployment of Label-Free Quantitative Olfactory Proteomics to Detect Cerebrospinal Fluid Biomarker Candidates in Synucleinopathies. Methods Mol Biol 2019; 2044:273-289. [PMID: 31432419 DOI: 10.1007/978-1-4939-9706-0_17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Nowadays, diagnosis of neurodegenerative disorders is mainly based on neuroimaging and clinical symptoms, although postmortem neuropathological confirmation remains the gold standard diagnostic technique. Therefore, cerebrospinal fluid (CSF) proteome is considered a valuable molecular repository for diagnosing and targeting the neurodegenerative process. It is well known that olfactory dysfunction is among the earliest features of synucleinopathies such as Parkinson's disease (PD). Consequently, we consider that the application of tissue proteomics in primary olfactory structures is an ideal approach to explore early pathophysiological changes, detecting olfactory proteins that might be tested in CSF as potential biomarkers. Data mining of mass spectrometry-generated datasets has revealed that 30% of the olfactory bulb (OB) proteome is also localized in CSF. In this chapter, we describe a method that utilizes label-free quantitative proteomics and computational analysis to characterize human OB proteomes and potential cerebrospinal fluid (CSF) biomarkers associated with neurodegenerative syndromes. For that, we applied peptide fractionation methods, followed by tandem mass spectrometry (nanoLC-MS/MS), in silico analysis, and semi-quantitative orthogonal techniques in OB derived from PD subjects. After obtaining the differential OB proteome across Lewy-type alpha-synucleinopathy (LTS) stages and further validating the method, this workflow was applied to probe changes in NEGR1 (neuronal growth regulator 1) and GNPDA2 (glucosamine-6-phosphate deaminase 2) protein levels in CSF derived from parkinsonian subjects with respect to controls, observing an inverse correlation between both proteins and α-synuclein, the principal component analysis of Lewy pathology.
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Affiliation(s)
- Mercedes Lachén-Montes
- Proteomics Unit, Clinical Neuroproteomics Laboratory, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Proteored-ISCIII, Pamplona, Spain
| | - Andrea González-Morales
- Proteomics Unit, Clinical Neuroproteomics Laboratory, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Proteored-ISCIII, Pamplona, Spain
| | - Joaquín Fernández-Irigoyen
- Proteomics Unit, Clinical Neuroproteomics Laboratory, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Proteored-ISCIII, Pamplona, Spain
| | - Enrique Santamaría
- Proteomics Unit, Clinical Neuroproteomics Laboratory, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Proteored-ISCIII, Pamplona, Spain.
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11
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Nery TGM, Silva EM, Tavares R, Passetti F. The Challenge to Search for New Nervous System Disease Biomarker Candidates: the Opportunity to Use the Proteogenomics Approach. J Mol Neurosci 2018; 67:150-164. [PMID: 30554402 DOI: 10.1007/s12031-018-1220-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 11/18/2018] [Indexed: 12/14/2022]
Abstract
Alzheimer's disease, Parkinson's disease, prion diseases, schizophrenia, and multiple sclerosis are the most common nervous system diseases, affecting millions of people worldwide. The current scientific literature associates these pathological conditions to abnormal expression levels of certain proteins, which in turn improved the knowledge concerning normal and affected brains. However, there is no available cure or preventive therapy for any of these disorders. Proteogenomics is a recent approach defined as the data integration of both nucleotide high-throughput sequencing and protein mass spectrometry technologies. In the last years, proteogenomics studies in distinct diseases have emerged as a strategy for the identification of uncharacterized proteoforms, which are all the different protein forms derived from a single gene. For many of these diseases, at least one protein used as biomarker presents more than one proteoform, which fosters the analysis of publicly available data focusing proteoforms. Given this context, we describe the most important biomarkers for each neurodegenerative disease and how genomics, transcriptomics, and proteomics separately contributed to unveil them. Finally, we present a selection of proteogenomics studies in which the combination of nucleotide and proteome high-throughput data, from cell lines or brain tissue samples, is used to uncover proteoforms not previously described. We believe that this new approach may improve our knowledge about nervous system diseases and brain function and an opportunity to identify new biomarker candidates.
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Affiliation(s)
- Thais Guimarães Martins Nery
- Laboratory of Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Manguinhos, Rio de Janeiro, Brazil
- Laboratory of Gene Expression Regulation, Carlos Chagas Institute, Fundação Oswaldo Cruz (Fiocruz), Curitiba, Brazil
| | - Esdras Matheus Silva
- Laboratory of Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Manguinhos, Rio de Janeiro, Brazil
- Laboratory of Gene Expression Regulation, Carlos Chagas Institute, Fundação Oswaldo Cruz (Fiocruz), Curitiba, Brazil
| | - Raphael Tavares
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Fabio Passetti
- Laboratory of Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Manguinhos, Rio de Janeiro, Brazil.
- Laboratory of Gene Expression Regulation, Carlos Chagas Institute, Fundação Oswaldo Cruz (Fiocruz), Curitiba, Brazil.
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12
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Molecular and Cellular Mechanisms of Aging and Age-related Disorders. Int J Mol Sci 2018; 19:ijms19072049. [PMID: 30011889 PMCID: PMC6073633 DOI: 10.3390/ijms19072049] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 07/13/2018] [Indexed: 12/12/2022] Open
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