1
|
Thierry M, Ponce J, Martà-Ariza M, Askenazi M, Faustin A, Leitner D, Pires G, Kanshin E, Drummond E, Ueberheide B, Wisniewski T. The influence of APOE ε4 on the pTau interactome in sporadic Alzheimer's disease. Acta Neuropathol 2024; 147:91. [PMID: 38772917 PMCID: PMC11108952 DOI: 10.1007/s00401-024-02744-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/12/2024] [Accepted: 05/12/2024] [Indexed: 05/23/2024]
Abstract
APOEε4 is the major genetic risk factor for sporadic Alzheimer's disease (AD). Although APOEε4 is known to promote Aβ pathology, recent data also support an effect of APOE polymorphism on phosphorylated Tau (pTau) pathology. To elucidate these potential effects, the pTau interactome was analyzed across APOE genotypes in the frontal cortex of 10 advanced AD cases (n = 5 APOEε3/ε3 and n = 5 APOEε4/ε4), using a combination of anti-pTau pS396/pS404 (PHF1) immunoprecipitation (IP) and mass spectrometry (MS). This proteomic approach was complemented by an analysis of anti-pTau PHF1 and anti-Aβ 4G8 immunohistochemistry, performed in the frontal cortex of 21 advanced AD cases (n = 11 APOEε3/ε3 and n = 10 APOEε4/ε4). Our dataset includes 1130 and 1330 proteins enriched in IPPHF1 samples from APOEε3/ε3 and APOEε4/ε4 groups (fold change ≥ 1.50, IPPHF1 vs IPIgG ctrl). We identified 80 and 68 proteins as probable pTau interactors in APOEε3/ε3 and APOEε4/ε4 groups, respectively (SAINT score ≥ 0.80; false discovery rate (FDR) ≤ 5%). A total of 47/80 proteins were identified as more likely to interact with pTau in APOEε3/ε3 vs APOEε4/ε4 cases. Functional enrichment analyses showed that they were significantly associated with the nucleoplasm compartment and involved in RNA processing. In contrast, 35/68 proteins were identified as more likely to interact with pTau in APOEε4/ε4 vs APOEε3/ε3 cases. They were significantly associated with the synaptic compartment and involved in cellular transport. A characterization of Tau pathology in the frontal cortex showed a higher density of plaque-associated neuritic crowns, made of dystrophic axons and synapses, in APOEε4 carriers. Cerebral amyloid angiopathy was more frequent and severe in APOEε4/ε4 cases. Our study supports an influence of APOE genotype on pTau-subcellular location in AD. These results suggest a facilitation of pTau progression to Aβ-affected brain regions in APOEε4 carriers, paving the way to the identification of new therapeutic targets.
Collapse
Affiliation(s)
- Manon Thierry
- Department of Neurology, Center for Cognitive Neurology, Grossman School of Medicine, New York University, Science Building, Rm 1023J, 435 East 30th Street, New York, NY, USA.
| | - Jackeline Ponce
- Department of Biochemistry and Molecular Pharmacology, Proteomics Laboratory, Grossman School of Medicine, New York University, New York, NY, USA
| | - Mitchell Martà-Ariza
- Department of Neurology, Center for Cognitive Neurology, Grossman School of Medicine, New York University, Science Building, Rm 1023J, 435 East 30th Street, New York, NY, USA
- Institut de Neurociències, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Arline Faustin
- Department of Neurology, Center for Cognitive Neurology, Grossman School of Medicine, New York University, Science Building, Rm 1023J, 435 East 30th Street, New York, NY, USA
| | - Dominique Leitner
- Department of Neurology, Center for Cognitive Neurology, Grossman School of Medicine, New York University, Science Building, Rm 1023J, 435 East 30th Street, New York, NY, USA
- Department of Neurology, Comprehensive Epilepsy Center, Grossman School of Medicine, New York University, New York, NY, USA
| | - Geoffrey Pires
- Department of Neurology, Center for Cognitive Neurology, Grossman School of Medicine, New York University, Science Building, Rm 1023J, 435 East 30th Street, New York, NY, USA
| | - Evgeny Kanshin
- Department of Biochemistry and Molecular Pharmacology, Proteomics Laboratory, Grossman School of Medicine, New York University, New York, NY, USA
| | - Eleanor Drummond
- Brain and Mind Centre, School of Medical Science, University of Sydney, Sydney, Australia
| | - Beatrix Ueberheide
- Department of Biochemistry and Molecular Pharmacology, Proteomics Laboratory, Grossman School of Medicine, New York University, New York, NY, USA
| | - Thomas Wisniewski
- Department of Neurology, Center for Cognitive Neurology, Grossman School of Medicine, New York University, Science Building, Rm 1023J, 435 East 30th Street, New York, NY, USA.
- Departments of Pathology and Psychiatry, Grossman School of Medicine, New York University, Science Building, Rm 1017, 435 East 30 Street, New York, NY, 10016, USA.
| |
Collapse
|
2
|
Liang Z, Zhuang H, Cao X, Ma G, Shen L. Subcellular proteomics insights into Alzheimer's disease development. Proteomics Clin Appl 2024; 18:e2200112. [PMID: 37650321 DOI: 10.1002/prca.202200112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 07/27/2023] [Accepted: 08/12/2023] [Indexed: 09/01/2023]
Abstract
Alzheimer's disease (AD), one of the most common dementias, is a neurodegenerative disease characterized by cognitive impairment and decreased judgment function. The expected number of AD patient is increasing in the context of the world's advancing medical care and increasing human life expectancy. Since current molecular mechanism studies on AD pathogenesis are incomplete, there is no specific and effective therapeutic agent. Mass spectrometry (MS)-based unbiased proteomics studies provide an effective and comprehensive approach. Many advances have been made in the study of the mechanism, diagnostic markers, and drug targets of AD using proteomics. This paper focus on subcellular level studies, reviews studies using proteomics to study AD-associated mitochondrial dysfunction, synaptic, and myelin damage, the protein composition of amyloid plaques (APs) and neurofibrillary tangles (NFTs), changes in tissue extracellular vehicles (EVs) and exosome proteome, and the protein changes in ribosomes and lysosomes. The methods of sample separation and preparation and proteomic analysis as well as the main findings of these studies are involved. The results of these proteomics studies provide insights into the pathogenesis of AD and provide theoretical resource and direction for future research in AD, helping to identify new biomarkers and drugs targets for AD.
Collapse
Affiliation(s)
- Zhiyuan Liang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, P. R. China
| | - Hongbin Zhuang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, P. R. China
| | - Xueshan Cao
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, P. R. China
- College of Physics and Optoelectronics Engineering, Shenzhen University, Shenzhen, P. R. China
| | - Guanwei Ma
- School of Public Health, the key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, P. R. China
| | - Liming Shen
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, P. R. China
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, P. R. China
| |
Collapse
|
3
|
Cartas-Cejudo P, Cortés A, Lachén-Montes M, Anaya-Cubero E, Peral E, Ausín K, Díaz-Peña R, Fernández-Irigoyen J, Santamaría E. Mapping the human brain proteome: opportunities, challenges, and clinical potential. Expert Rev Proteomics 2024; 21:55-63. [PMID: 38299555 DOI: 10.1080/14789450.2024.2313073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/24/2024] [Indexed: 02/02/2024]
Abstract
INTRODUCTION Due to the segmented functions and complexity of the human brain, the characterization of molecular profiles within specific areas such as brain structures and biofluids is essential to unveil the molecular basis for structure specialization as well as the molecular imbalance associated with neurodegenerative and psychiatric diseases. AREAS COVERED Much of our knowledge about brain functionality derives from neurophysiological, anatomical, and transcriptomic approaches. More recently, laser capture and imaging proteomics, technological and computational developments in LC-MS/MS, as well as antibody/aptamer-based platforms have allowed the generation of novel cellular, spatial, and posttranslational dimensions as well as innovative facets in biomarker validation and druggable target identification. EXPERT OPINION Proteomics is a powerful toolbox to functionally characterize, quantify, and localize the extensive protein catalog of the human brain across physiological and pathological states. Brain function depends on multi-dimensional protein homeostasis, and its elucidation will help us to characterize biological pathways that are essential to properly maintain cognitive functions. In addition, comprehensive human brain pathological proteomes may be the basis in computational drug-repositioning methods as a strategy for unveiling potential new therapies in neurodegenerative and psychiatric disorders.
Collapse
Affiliation(s)
- Paz Cartas-Cejudo
- Clinical Neuroproteomics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Adriana Cortés
- Clinical Neuroproteomics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Mercedes Lachén-Montes
- Clinical Neuroproteomics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Elena Anaya-Cubero
- Clinical Neuroproteomics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Erika Peral
- Proteomics Platform, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Karina Ausín
- Proteomics Platform, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Ramón Díaz-Peña
- Proteomics Platform, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Joaquín Fernández-Irigoyen
- Proteomics Platform, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Enrique Santamaría
- Clinical Neuroproteomics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| |
Collapse
|
4
|
Anderton E, Chamoli M, Bhaumik D, King CD, Xie X, Foulger A, Andersen JK, Schilling B, Lithgow GJ. Amyloid β accelerates age-related proteome-wide protein insolubility. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.13.548937. [PMID: 37503138 PMCID: PMC10369951 DOI: 10.1101/2023.07.13.548937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Loss of proteostasis is a highly conserved feature of aging across model organisms and typically results in the accumulation of insoluble protein aggregates. Protein insolubility is a central feature of major age-related neurodegenerative diseases, including Alzheimer's Disease (AD), where hundreds of insoluble proteins associate with aggregated amyloid beta (Aβ) in senile plaques. Moreover, proteins that become insoluble during aging in model organisms are capable of accelerating Aβ aggregation in vitro. Despite the connection between aging and AD risk, therapeutic approaches to date have overlooked aging-driven protein insolubility as a contributory factor. Here, using an unbiased proteomics approach, we questioned the relationship between Aβ and age-related protein insolubility. We demonstrate that Aβ expression drives proteome-wide protein insolubility in C. elegans and this insoluble proteome closely resembles the insoluble proteome driven by normal aging, suggesting the possibility of a vicious feedforward cycle of aggregation in the context of AD. Importantly, using human genome-wide association studies (GWAS), we show that the CIP is replete with biological processes implicated not only in neurodegenerative diseases but also across a broad array of chronic, age-related diseases (CARDs). This provides suggestive evidence that age-related loss of proteostasis could play a role in general CARD risk. Finally, we show that the CIP is enriched with proteins that modulate the toxic effects of Aβ and that the gut-derived metabolite, Urolithin A, relieves Aβ toxicity, supporting its use in clinical trials for dementia and other age-related diseases.
Collapse
Affiliation(s)
- Edward Anderton
- The Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA 94945
- USC Leonard Davis School of Gerontology, University of Southern California, 3715 McClintock Ave., Los Angeles, CA 90191
| | - Manish Chamoli
- The Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA 94945
| | - Dipa Bhaumik
- The Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA 94945
| | - Christina D. King
- The Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA 94945
| | - Xueshu Xie
- The Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA 94945
| | - Anna Foulger
- The Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA 94945
| | - Julie K. Andersen
- The Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA 94945
| | - Birgit Schilling
- The Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA 94945
| | - Gordon J. Lithgow
- The Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA 94945
| |
Collapse
|
5
|
Lu K, Li C, Liu J, Wang J, Li Y, He B, Li J, Zhang X, Wei M, Tian Y, Zhang R, Zhang C, Zhang Y. Impairments in endogenous AMPA receptor dynamics correlates with learning deficits in Alzheimer's disease model mice. Proc Natl Acad Sci U S A 2023; 120:e2303878120. [PMID: 37748061 PMCID: PMC10556575 DOI: 10.1073/pnas.2303878120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 08/29/2023] [Indexed: 09/27/2023] Open
Abstract
AMPA receptors (AMPARs) play a critical role in synaptic plasticity and learning and memory, and dysfunction or dysregulation of AMPARs could lead to various neurological and psychiatric disorders, such as Alzheimer's disease (AD). However, the dynamics and/or longitudinal changes of AMPARs in vivo during AD pathogenesis remain elusive. Here, employing 5xFAD SEP-GluA1 KI mice, we investigated endogenous AMPA receptor dynamics in a whisker deflection-associated Go/No-go learning paradigm. We found a significant increase in synaptosomal AMPA receptor subunits GluA1 in WT mice after learning, while no such changes were detected in 7-mo-old 5xFAD mice. Daily training led to an increase in endogenous spine surface GluA1 in Control mice, while this increase was absent in 5xFAD-KI mice which correlates with its learning defects in Go/No-go paradigm. Furthermore, we demonstrated that the onset of abnormal AMPAR dynamics corresponds temporally with microglia and astrocyte overactivation. Our results have shown that impairments in endogenous AMPA receptor dynamics play an important role in learning deficits in 5xFAD mice and AD pathogenesis.
Collapse
Affiliation(s)
- Kongjie Lu
- Neuroscience Research Institute and Department of Neurobiology, School of Basic Medical Sciences, Peking University, Key Laboratory for Neuroscience, Ministry of Education of China and National Health Commission of the People’s Republic of China, Beijing100083, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing100871, China
| | - Chenyang Li
- Neuroscience Research Institute and Department of Neurobiology, School of Basic Medical Sciences, Peking University, Key Laboratory for Neuroscience, Ministry of Education of China and National Health Commission of the People’s Republic of China, Beijing100083, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing100871, China
| | - Jiao Liu
- Center of Medical and Health Analysis, Peking University Health Science Center, Beijing100083, China
| | - Jinpeng Wang
- Neuroscience Research Institute and Department of Neurobiology, School of Basic Medical Sciences, Peking University, Key Laboratory for Neuroscience, Ministry of Education of China and National Health Commission of the People’s Republic of China, Beijing100083, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing100871, China
| | - Yongfeng Li
- Neuroscience Research Institute and Department of Neurobiology, School of Basic Medical Sciences, Peking University, Key Laboratory for Neuroscience, Ministry of Education of China and National Health Commission of the People’s Republic of China, Beijing100083, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing100871, China
| | - Bin He
- Neuroscience Research Institute and Department of Neurobiology, School of Basic Medical Sciences, Peking University, Key Laboratory for Neuroscience, Ministry of Education of China and National Health Commission of the People’s Republic of China, Beijing100083, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing100871, China
| | - Junzhao Li
- Neuroscience Research Institute and Department of Neurobiology, School of Basic Medical Sciences, Peking University, Key Laboratory for Neuroscience, Ministry of Education of China and National Health Commission of the People’s Republic of China, Beijing100083, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing100871, China
| | - Xiaochen Zhang
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin300072, China
| | - Mengping Wei
- School of Basic Medical Sciences, Beijing Key Laboratory of Neural Regeneration and Repair, Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing100069, China
| | - Yonglu Tian
- PKU-IDG/McGovern Institute for Brain Research, Beijing100871, China
- School of Psychological and Cognitive Sciences, Peking University, Beijing100871, China
| | - Rong Zhang
- Neuroscience Research Institute and Department of Neurobiology, School of Basic Medical Sciences, Peking University, Key Laboratory for Neuroscience, Ministry of Education of China and National Health Commission of the People’s Republic of China, Beijing100083, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing100871, China
| | - Chen Zhang
- School of Basic Medical Sciences, Beijing Key Laboratory of Neural Regeneration and Repair, Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing100069, China
| | - Yong Zhang
- Neuroscience Research Institute and Department of Neurobiology, School of Basic Medical Sciences, Peking University, Key Laboratory for Neuroscience, Ministry of Education of China and National Health Commission of the People’s Republic of China, Beijing100083, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing100871, China
| |
Collapse
|
6
|
Guo W, Hu Y, Qian J, Zhu L, Cheng J, Liao J, Fan X. Laser capture microdissection for biomedical research: towards high-throughput, multi-omics, and single-cell resolution. J Genet Genomics 2023; 50:641-651. [PMID: 37544594 DOI: 10.1016/j.jgg.2023.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/28/2023] [Accepted: 07/28/2023] [Indexed: 08/08/2023]
Abstract
Spatial omics technologies have become powerful methods to provide valuable insights into cells and tissues within a complex context, significantly enhancing our understanding of the intricate and multifaceted biological system. With an increasing focus on spatial heterogeneity, there is a growing need for unbiased, spatially resolved omics technologies. Laser capture microdissection (LCM) is a cutting-edge method for acquiring spatial information that can quickly collect regions of interest (ROIs) from heterogeneous tissues, with resolutions ranging from single cells to cell populations. Thus, LCM has been widely used for studying the cellular and molecular mechanisms of diseases. This review focuses on the differences among four types of commonly used LCM technologies and their applications in omics and disease research. Key attributes of application cases are also highlighted, such as throughput and spatial resolution. In addition, we comprehensively discuss the existing challenges and the great potential of LCM in biomedical research, disease diagnosis, and targeted therapy from the perspective of high-throughput, multi-omics, and single-cell resolution.
Collapse
Affiliation(s)
- Wenbo Guo
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, Zhejiang 314100, China
| | - Yining Hu
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, Zhejiang 314100, China
| | - Jingyang Qian
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, Zhejiang 314100, China
| | - Lidan Zhu
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, Zhejiang 314100, China
| | - Junyun Cheng
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, Zhejiang 314100, China
| | - Jie Liao
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, Zhejiang 314100, China.
| | - Xiaohui Fan
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, Zhejiang 314100, China.
| |
Collapse
|
7
|
Cardoso dos Santos LM, Avila Y, Schvartz D, Rougemont AL, Bochaton-Piallat ML, Ruchonnet-Metrailler I. Laser microdissection, proteomics, and multiplex immunohistochemistry: a bumpy ride into the study of paraffin-embedded fetal and pediatric lung tissues. Front Med (Lausanne) 2023; 10:1191205. [PMID: 37706027 PMCID: PMC10495683 DOI: 10.3389/fmed.2023.1191205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 07/28/2023] [Indexed: 09/15/2023] Open
Abstract
Background Knowledge about lung development or lung disease is mainly derived from data extrapolated from mouse models. This has obvious drawbacks in developmental diseases, particularly due to species differences. Our objective is to describe the development of complementary analysis methods that will allow a better understanding of the molecular mechanisms involved in the pathogenesis of rare congenital diseases. Methods Paraffin-embedded human pediatric and fetal lung samples were laser microdissected to enrich different lung regions, namely, bronchioli or alveoli. These samples were analyzed by data-independent acquisition-based quantitative proteomics, and the lung structures were subsequently compared. To confirm the proteomic data, we employed an optimized Sequential ImmunoPeroxidase Labeling and Erasing (SIMPLE) staining for specific proteins of interest. Results By quantitative proteomics, we identified typical pulmonary proteins from being differentially expressed in different regions. While the receptor for advanced glycation end products (RAGE) and the surfactant protein C (SFTPC) were downregulated, tubulin beta 4B (TUBB4B) was upregulated in bronchioli, compared to alveoli. In fetal tissues, CD31 was downregulated in fetal bronchioli compared to canaliculi. Moreover, we confirmed their presence using SIMPLE staining. Some expected proteins did not show up in the proteomic data, such as SOX-9, which was only detected by means of immunohistochemistry in the SIMPLE analysis. Conclusion Our data underline the robustness and applicability of this type of experimental approach, especially for rare paraffin-embedded tissue samples. It also strengthens the importance of these methods for future studies, particularly when considering developmental lung diseases, such as congenital lung anomalies.
Collapse
Affiliation(s)
- Luis M. Cardoso dos Santos
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Pediatric Pulmonary Unit, Department of Pediatrics, Gynecology, and Obstetrics, University Hospital of Geneva, Geneva, Switzerland
| | - Yannick Avila
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Pediatric Pulmonary Unit, Department of Pediatrics, Gynecology, and Obstetrics, University Hospital of Geneva, Geneva, Switzerland
| | - Domitille Schvartz
- Proteomics Core Facility, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Bioinformatic Support Platform, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | | | | | - Isabelle Ruchonnet-Metrailler
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Pediatric Pulmonary Unit, Department of Pediatrics, Gynecology, and Obstetrics, University Hospital of Geneva, Geneva, Switzerland
| |
Collapse
|
8
|
Wang Y, Xu H, Geng Z, Geng G, Zhang F. Dementia and the history of disease in older adults in community. BMC Public Health 2023; 23:1555. [PMID: 37582737 PMCID: PMC10428616 DOI: 10.1186/s12889-023-16494-x] [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: 12/26/2022] [Accepted: 08/09/2023] [Indexed: 08/17/2023] Open
Abstract
INTRODUCTION Many studies have revealed the effect of medical history on dementia. The aim of this study was to explore the relationship between the history of disease and onset of dementia. METHODS This was a multi-center, cross-sectional study, with 2595 older adults enrolled. The onset of dementia was evaluated with Revised Hasegawa Dementia Scale (HDS-R). The diagnosed diseases after the age of 40 of the participants were investigated, including respiratory system diseases, digestive system diseases, cardiovascular diseases, endocrine disorders, genitourinary system diseases, nervous system disease, sensory system diseases, dental/oral diseases, bone/joint diseases and mental illnesses. RESULTS Data of 2458 older adults were analyzed. Univariate analysis showed that diabetes, thyroid disease, mental illness, hearing loss, stroke, dental/oral disease, Denture use, fracture/osteoporosis, kidney disease and number of diseases were risk factors for dementia. After controlling for demographic sociological variables, diabetes, dental/oral disease, and denture use were independent risk factors for dementia. Thyroid disease (P = 0.313), mental illnesses (P = 0.067), hearing loss (P = 0.595), stroke (P = 0.538), fractures/osteoporosis (P = 0.069), kidney disease (P = 0.168) were no longer significant to dementia. CONCLUSION Diabetes, dental/oral disease and denture use were main risk factors for dementia.
Collapse
Affiliation(s)
- Yuan Wang
- Medical College of Nantong University, 19 QiXiu Road, Nantong City, Jiangsu Province, China
| | - Honglian Xu
- Nantong North Rehabilitation Hospital, Nantong City, Jiangsu Province, China
| | - Zihan Geng
- Medical College of Nantong University, 19 QiXiu Road, Nantong City, Jiangsu Province, China
| | - Guiling Geng
- Medical College of Nantong University, 19 QiXiu Road, Nantong City, Jiangsu Province, China
| | - Feng Zhang
- Medical College of Nantong University, 19 QiXiu Road, Nantong City, Jiangsu Province, China.
| |
Collapse
|
9
|
Kitata RB, Velickovic M, Xu Z, Zhao R, Scholten D, Chu RK, Orton DJ, Chrisler WB, Mathews JV, Piehowski PD, Liu T, Smith RD, Liu H, Wasserfall CH, Tsai CF, Shi T. Robust collection and processing for label-free single voxel proteomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.14.553333. [PMID: 37645907 PMCID: PMC10462033 DOI: 10.1101/2023.08.14.553333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
With advanced mass spectrometry (MS)-based proteomics, genome-scale proteome coverage can be achieved from bulk tissues. However, such bulk measurement lacks spatial resolution and obscures important tissue heterogeneity, which make it impossible for proteome mapping of tissue microenvironment. Here we report an integrated wet collection of single tissue voxel and Surfactant-assisted One-Pot voxel processing method termed wcSOP for robust label-free single voxel proteomics. wcSOP capitalizes on buffer droplet-assisted wet collection of single tissue voxel dissected by LCM into the PCR tube cap and MS-compatible surfactant-assisted one-pot voxel processing in the collection cap. This convenient method allows reproducible label-free quantification of ∼900 and ∼4,600 proteins for single voxel from fresh frozen human spleen tissue at 20 μm × 20 μm × 10 μm (close to single cells) and 200 μm × 200 μm × 10 μm (∼100 cells), respectively. 100s-1000s of protein signatures with differential expression levels were identified to be spatially resolved between spleen red and white pulp regions depending on the voxel size. Region-specific signaling pathways were enriched from single voxel proteomics data. Antibody-based CODEX imaging was used to validate label-free MS quantitation for single voxel analysis. The wcSOP-MS method paves the way for routine robust single voxel proteomics and spatial proteomics.
Collapse
|
10
|
Askenazi M, Kavanagh T, Pires G, Ueberheide B, Wisniewski T, Drummond E. Compilation of reported protein changes in the brain in Alzheimer's disease. Nat Commun 2023; 14:4466. [PMID: 37491476 PMCID: PMC10368642 DOI: 10.1038/s41467-023-40208-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 07/14/2023] [Indexed: 07/27/2023] Open
Abstract
Proteomic studies of human Alzheimer's disease brain tissue have potential to identify protein changes that drive disease, and to identify new drug targets. Here, we analyse 38 published Alzheimer's disease proteomic studies, generating a map of protein changes in human brain tissue across thirteen brain regions, three disease stages (preclinical Alzheimer's disease, mild cognitive impairment, advanced Alzheimer's disease), and proteins enriched in amyloid plaques, neurofibrillary tangles, and cerebral amyloid angiopathy. Our dataset is compiled into a searchable database (NeuroPro). We found 848 proteins were consistently altered in 5 or more studies. Comparison of protein changes in early-stage and advanced Alzheimer's disease revealed proteins associated with synapse, vesicle, and lysosomal pathways show change early in disease, but widespread changes in mitochondrial associated protein expression change are only seen in advanced Alzheimer's disease. Protein changes were similar for brain regions considered vulnerable and regions considered resistant. This resource provides insight into Alzheimer's disease brain protein changes and highlights proteins of interest for further study.
Collapse
Affiliation(s)
| | - Tomas Kavanagh
- Brain and Mind Centre and School of Medical Sciences, University of Sydney, Camperdown, NSW, 2050, Australia
| | - Geoffrey Pires
- Center for Cognitive Neurology, Department of Neurology, Grossman School of Medicine, New York University, New York, NY, 10016, USA
| | - Beatrix Ueberheide
- Center for Cognitive Neurology, Department of Neurology, Grossman School of Medicine, New York University, New York, NY, 10016, USA
- Proteomics Laboratory, Division of Advanced Research Technologies, Grossman School of Medicine, New York University, New York, NY, 10016, USA
- Biochemistry and Molecular Pharmacology, Grossman School of Medicine, New York University, New York, NY, 10016, USA
| | - Thomas Wisniewski
- Center for Cognitive Neurology, Department of Neurology, Grossman School of Medicine, New York University, New York, NY, 10016, USA
| | - Eleanor Drummond
- Brain and Mind Centre and School of Medical Sciences, University of Sydney, Camperdown, NSW, 2050, Australia.
- Center for Cognitive Neurology, Department of Neurology, Grossman School of Medicine, New York University, New York, NY, 10016, USA.
| |
Collapse
|
11
|
Marshall CR, Farrow MA, Djambazova KV, Spraggins JM. Untangling Alzheimer's disease with spatial multi-omics: a brief review. Front Aging Neurosci 2023; 15:1150512. [PMID: 37533766 PMCID: PMC10390637 DOI: 10.3389/fnagi.2023.1150512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 06/13/2023] [Indexed: 08/04/2023] Open
Abstract
Alzheimer's disease (AD) is the most common form of neurological dementia, specified by extracellular β-amyloid plaque deposition, neurofibrillary tangles, and cognitive impairment. AD-associated pathologies like cerebral amyloid angiopathy (CAA) are also affiliated with cognitive impairment and have overlapping molecular drivers, including amyloid buildup. Discerning the complexity of these neurological disorders remains a significant challenge, and the spatiomolecular relationships between pathogenic features of AD and AD-associated pathologies remain poorly understood. This review highlights recent developments in spatial omics, including profiling and molecular imaging methods, and how they are applied to AD. These emerging technologies aim to characterize the relationship between how specific cell types and tissue features are organized in combination with mapping molecular distributions to provide a systems biology view of the tissue microenvironment around these neuropathologies. As spatial omics methods achieve greater resolution and improved molecular coverage, they are enabling deeper characterization of the molecular drivers of AD, leading to new possibilities for the prediction, diagnosis, and mitigation of this debilitating disease.
Collapse
Affiliation(s)
- Cody R. Marshall
- Chemical and Physical Biology Program, Vanderbilt University School of Medicine, Nashville, TN, United States
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Melissa A. Farrow
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN, United States
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Katerina V. Djambazova
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN, United States
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Jeffrey M. Spraggins
- Chemical and Physical Biology Program, Vanderbilt University School of Medicine, Nashville, TN, United States
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN, United States
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, United States
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, United States
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
| |
Collapse
|
12
|
Leitner DF, Kanshin E, Faustin A, Thierry M, Friedman D, Devore S, Ueberheide B, Devinsky O, Wisniewski T. Localized proteomic differences in the choroid plexus of Alzheimer's disease and epilepsy patients. Front Neurol 2023; 14:1221775. [PMID: 37521285 PMCID: PMC10379643 DOI: 10.3389/fneur.2023.1221775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/22/2023] [Indexed: 08/01/2023] Open
Abstract
Introduction Alzheimer's disease (AD) and epilepsy are reciprocally related. Among sporadic AD patients, clinical seizures occur in 10-22% and subclinical epileptiform abnormalities occur in 22-54%. Cognitive deficits, especially short-term memory impairments, occur in most epilepsy patients. Common neurophysiological and molecular mechanisms occur in AD and epilepsy. The choroid plexus undergoes pathological changes in aging, AD, and epilepsy, including decreased CSF turnover, amyloid beta (Aβ), and tau accumulation due to impaired clearance and disrupted CSF amino acid homeostasis. This pathology may contribute to synaptic dysfunction in AD and epilepsy. Methods We evaluated control (n = 8), severe AD (n = 8; A3, B3, C3 neuropathology), and epilepsy autopsy cases (n = 12) using laser capture microdissection (LCM) followed by label-free quantitative mass spectrometry on the choroid plexus adjacent to the hippocampus at the lateral geniculate nucleus level. Results Proteomics identified 2,459 proteins in the choroid plexus. At a 5% false discovery rate (FDR), 616 proteins were differentially expressed in AD vs. control, 1 protein in epilepsy vs. control, and 438 proteins in AD vs. epilepsy. There was more variability in the epilepsy group across syndromes. The top 20 signaling pathways associated with differentially expressed proteins in AD vs. control included cell metabolism pathways; activated fatty acid beta-oxidation (p = 2.00 x 10-7, z = 3.00), and inhibited glycolysis (p = 1.00 x 10-12, z = -3.46). For AD vs. epilepsy, the altered pathways included cell metabolism pathways, activated complement system (p = 5.62 x 10-5, z = 2.00), and pathogen-induced cytokine storm (p = 2.19 x 10-2, z = 3.61). Of the 617 altered proteins in AD and epilepsy vs. controls, 497 (81%) were positively correlated (p < 0.0001, R2 = 0.27). Discussion We found altered signaling pathways in the choroid plexus of severe AD cases and many correlated changes in the protein expression of cell metabolism pathways in AD and epilepsy cases. The shared molecular mechanisms should be investigated further to distinguish primary pathogenic changes from the secondary ones. These mechanisms could inform novel therapeutic strategies to prevent disease progression or restore normal function. A focus on dual-diagnosed AD/epilepsy cases, specific epilepsy syndromes, such as temporal lobe epilepsy, and changes across different severity levels in AD and epilepsy would add to our understanding.
Collapse
Affiliation(s)
- Dominique F. Leitner
- Comprehensive Epilepsy Center, New York University Grossman School of Medicine, New York, NY, United States
- Center for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, New York, NY, United States
- Department of Neurology, New York University Grossman School of Medicine, New York, NY, United States
| | - Evgeny Kanshin
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY, United States
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, United States
| | - Arline Faustin
- Center for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, New York, NY, United States
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, United States
| | - Manon Thierry
- Center for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, New York, NY, United States
- Department of Neurology, New York University Grossman School of Medicine, New York, NY, United States
| | - Daniel Friedman
- Comprehensive Epilepsy Center, New York University Grossman School of Medicine, New York, NY, United States
- Department of Neurology, New York University Grossman School of Medicine, New York, NY, United States
| | - Sasha Devore
- Comprehensive Epilepsy Center, New York University Grossman School of Medicine, New York, NY, United States
- Department of Neurology, New York University Grossman School of Medicine, New York, NY, United States
| | - Beatrix Ueberheide
- Center for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, New York, NY, United States
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY, United States
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, United States
| | - Orrin Devinsky
- Comprehensive Epilepsy Center, New York University Grossman School of Medicine, New York, NY, United States
- Department of Neurology, New York University Grossman School of Medicine, New York, NY, United States
| | - Thomas Wisniewski
- Center for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, New York, NY, United States
- Department of Neurology, New York University Grossman School of Medicine, New York, NY, United States
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, United States
- Department of Psychiatry, New York University Grossman School of Medicine, New York, NY, United States
| |
Collapse
|
13
|
Zhou XG, Qiu WQ, Yu L, Pan R, Teng JF, Sang ZP, Law BYK, Zhao Y, Zhang L, Yan L, Tang Y, Sun XL, Wong VKW, Yu CL, Wu JM, Qin DL, Wu AG. Targeting microglial autophagic degradation of the NLRP3 inflammasome for identification of thonningianin A in Alzheimer’s disease. Inflamm Regen 2022; 42:25. [PMID: 35918778 PMCID: PMC9347127 DOI: 10.1186/s41232-022-00209-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 04/05/2022] [Indexed: 02/08/2023] Open
Abstract
Background NLRP3 inflammasome-mediated neuroinflammation plays a critical role in the pathogenesis and development of Alzheimer’s disease (AD). Microglial autophagic degradation not only decreases the deposits of extracellular Aβ fibrils but also inhibits the activation of NRLP3 inflammasome. Here, we aimed to identify the potent autophagy enhancers from Penthorum chinense Pursh (PCP) that alleviate the pathology of AD via inhibiting the NLRP3 inflammasome. Methods At first, autophagic activity-guided isolation was performed to identify the autophagy enhancers in PCP. Secondly, the autophagy effect was monitored by detecting LC3 protein expression using Western blotting and the average number of GFP-LC3 puncta per microglial cell using confocal microscopy. Then, the activation of NLRP3 inflammasome was measured by detecting the protein expression and transfected fluorescence intensity of NLRP3, ASC, and caspase-1, as well as the secretion of proinflammatory cytokines. Finally, the behavioral performance was evaluated by measuring the paralysis in C. elegans, and the cognitive function was tested by Morris water maze (MWM) in APP/PS1 mice. Results Four ellagitannin flavonoids, including pinocembrin-7-O-[4″,6″-hexahydroxydiphenoyl]-glucoside (PHG), pinocembrin-7-O-[3″-O-galloyl-4″,6″-hexahydroxydiphenoyl]-glucoside (PGHG), thonningianin A (TA), and thonningianin B (TB), were identified to be autophagy enhancers in PCP. Among these, TA exhibited the strongest autophagy induction effect, and the mechanistic study demonstrated that TA activated autophagy via the AMPK/ULK1 and Raf/MEK/ERK signaling pathways. In addition, TA effectively promoted the autophagic degradation of NLRP3 inflammasome in Aβ(1–42)-induced microglial cells and ameliorated neuronal damage via autophagy induction. In vivo, TA activated autophagy and improved behavioral symptoms in C. elegans. Furthermore, TA might penetrate the blood-brain barrier and could improve cognitive function and ameliorate the Aβ pathology and the NLRP3 inflammasome-mediated neuroinflammation via the AMPK/ULK1 and Raf/MEK/ERK signaling pathways in APP/PS1 mice. Conclusion We identified TA as a potent microglial autophagy enhancer in PCP that promotes the autophagic degradation of the NLRP3 inflammasome to alleviate the pathology of AD via the AMPK/ULK1 and Raf/MEK/ERK signaling pathways, which provides novel insights for TA in the treatment of AD. Supplementary Information The online version contains supplementary material available at 10.1186/s41232-022-00209-7.
Collapse
|
14
|
Leitner DF, Kanshin E, Askenazi M, Faustin A, Friedman D, Devore S, Ueberheide B, Wisniewski T, Devinsky O. Raphe and ventrolateral medulla proteomics in epilepsy and sudden unexpected death in epilepsy. Brain Commun 2022; 4:fcac186. [PMID: 35928051 PMCID: PMC9344977 DOI: 10.1093/braincomms/fcac186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/29/2022] [Accepted: 07/11/2022] [Indexed: 12/26/2022] Open
Abstract
Brainstem nuclei dysfunction is implicated in sudden unexpected death in epilepsy. In animal models, deficient serotonergic activity is associated with seizure-induced respiratory arrest. In humans, glia are decreased in the ventrolateral medullary pre-Botzinger complex that modulate respiratory rhythm, as well as in the medial medullary raphe that modulate respiration and arousal. Finally, sudden unexpected death in epilepsy cases have decreased midbrain volume. To understand the potential role of brainstem nuclei in sudden unexpected death in epilepsy, we evaluated molecular signalling pathways using localized proteomics in microdissected midbrain dorsal raphe and medial medullary raphe serotonergic nuclei, as well as the ventrolateral medulla in brain tissue from epilepsy patients who died of sudden unexpected death in epilepsy and other causes in diverse epilepsy syndromes and non-epilepsy control cases (n = 15-16 cases per group/region). Compared with the dorsal raphe of non-epilepsy controls, we identified 89 proteins in non-sudden unexpected death in epilepsy and 219 proteins in sudden unexpected death in epilepsy that were differentially expressed. These proteins were associated with inhibition of EIF2 signalling (P-value of overlap = 1.29 × 10-8, z = -2.00) in non-sudden unexpected death in epilepsy. In sudden unexpected death in epilepsy, there were 10 activated pathways (top pathway: gluconeogenesis I, P-value of overlap = 3.02 × 10-6, z = 2.24) and 1 inhibited pathway (fatty acid beta-oxidation, P-value of overlap = 2.69 × 10-4, z = -2.00). Comparing sudden unexpected death in epilepsy and non-sudden unexpected death in epilepsy, 10 proteins were differentially expressed, but there were no associated signalling pathways. In both medullary regions, few proteins showed significant differences in pairwise comparisons. We identified altered proteins in the raphe and ventrolateral medulla of epilepsy patients, including some differentially expressed in sudden unexpected death in epilepsy cases. Altered signalling pathways in the dorsal raphe of sudden unexpected death in epilepsy indicate a shift in cellular energy production and activation of G-protein signalling, inflammatory response, stress response and neuronal migration/outgrowth. Future studies should assess the brain proteome in relation to additional clinical variables (e.g. recent tonic-clonic seizures) and in more of the reciprocally connected cortical and subcortical regions to better understand the pathophysiology of epilepsy and sudden unexpected death in epilepsy.
Collapse
Affiliation(s)
- Dominique F Leitner
- Comprehensive Epilepsy Center, Grossman School of Medicine, New York
University, 223 East 34th Street, New York, NY
10016, USA
| | - Evgeny Kanshin
- Proteomics Laboratory, Division of Advanced Research Technologies, Grossman
School of Medicine, New York University, 223 East 34th
Street, New York, NY 10016, USA
| | - Manor Askenazi
- Biomedical Hosting LLC, Arlington, MA
02140, USA
- Department of Biochemistry and Molecular Pharmacology, Grossman School of
Medicine, New York University, 223 East 34th Street, New
York, NY 10016, USA
| | - Arline Faustin
- Center for Cognitive Neurology, Department of Neurology, Grossman School of
Medicine, New York University, 223 East 34th Street, New
York, NY 10016, USA
- Department of Pathology, Grossman School of Medicine, New York
University, 223 East 34th Street, New York, NY
10016, USA
| | - Daniel Friedman
- Comprehensive Epilepsy Center, Grossman School of Medicine, New York
University, 223 East 34th Street, New York, NY
10016, USA
| | - Sasha Devore
- Comprehensive Epilepsy Center, Grossman School of Medicine, New York
University, 223 East 34th Street, New York, NY
10016, USA
| | - Beatrix Ueberheide
- Proteomics Laboratory, Division of Advanced Research Technologies, Grossman
School of Medicine, New York University, 223 East 34th
Street, New York, NY 10016, USA
- Department of Biochemistry and Molecular Pharmacology, Grossman School of
Medicine, New York University, 223 East 34th Street, New
York, NY 10016, USA
- Center for Cognitive Neurology, Department of Neurology, Grossman School of
Medicine, New York University, 223 East 34th Street, New
York, NY 10016, USA
| | - Thomas Wisniewski
- Center for Cognitive Neurology, Department of Neurology, Grossman School of
Medicine, New York University, 223 East 34th Street, New
York, NY 10016, USA
- Department of Pathology, Grossman School of Medicine, New York
University, 223 East 34th Street, New York, NY
10016, USA
- Department of Psychiatry, Grossman School of Medicine, New York
University, 223 East 34th Street, New York, NY
10016, USA
| | - Orrin Devinsky
- Comprehensive Epilepsy Center, Grossman School of Medicine, New York
University, 223 East 34th Street, New York, NY
10016, USA
| |
Collapse
|
15
|
Ganne A, Balasubramaniam M, Griffin WST, Shmookler Reis RJ, Ayyadevara S. Glial Fibrillary Acidic Protein: A Biomarker and Drug Target for Alzheimer’s Disease. Pharmaceutics 2022; 14:pharmaceutics14071354. [PMID: 35890250 PMCID: PMC9322874 DOI: 10.3390/pharmaceutics14071354] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 02/05/2023] Open
Abstract
Glial fibrillary acidic protein (GFAP) is an intermediate filament structural protein involved in cytoskeleton assembly and integrity, expressed in high abundance in activated glial cells. GFAP is neuroprotective, as knockout mice are hypersensitive to traumatic brain injury. GFAP in cerebrospinal fluid is a biomarker of Alzheimer’s disease (AD), dementia with Lewy bodies, and frontotemporal dementia (FTD). Here, we present novel evidence that GFAP is markedly overexpressed and differentially phosphorylated in AD hippocampus, especially in AD with the apolipoprotein E [ε4, ε4] genotype, relative to age-matched controls (AMCs). Kinases that phosphorylate GFAP are upregulated in AD relative to AMC. A knockdown of these kinases in SH-SY5Y-APPSw human neuroblastoma cells reduced amyloid accrual and lowered protein aggregation and associated behavioral traits in C. elegans models of polyglutamine aggregation (as observed in Huntington’s disease) and of Alzheimer’s-like amyloid formation. In silico screening of the ChemBridge structural library identified a small molecule, MSR1, with stable and specific binding to GFAP. Both MSR1 exposure and GF AP-specific RNAi knockdown reduce aggregation with remarkably high concordance of aggregate proteins depleted. These data imply that GFAP and its phosphorylation play key roles in neuropathic aggregate accrual and provide valuable new biomarkers, as well as novel therapeutic targets to alleviate, delay, or prevent AD.
Collapse
Affiliation(s)
- Akshatha Ganne
- Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA; (A.G.); (M.B.); (W.S.T.G.)
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | | | - W. Sue T. Griffin
- Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA; (A.G.); (M.B.); (W.S.T.G.)
- BioInformatics Program, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Robert J. Shmookler Reis
- Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA; (A.G.); (M.B.); (W.S.T.G.)
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- BioInformatics Program, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Department of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Correspondence: (R.J.S.R.); (S.A.); Tel.: +1-501-526-5820 (R.J.S.R.); +1-501-526-7282 (S.A.)
| | - Srinivas Ayyadevara
- Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA; (A.G.); (M.B.); (W.S.T.G.)
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- BioInformatics Program, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Correspondence: (R.J.S.R.); (S.A.); Tel.: +1-501-526-5820 (R.J.S.R.); +1-501-526-7282 (S.A.)
| |
Collapse
|
16
|
Leitner DF, William C, Faustin A, Askenazi M, Kanshin E, Snuderl M, McGuone D, Wisniewski T, Ueberheide B, Gould L, Devinsky O. Proteomic differences in hippocampus and cortex of sudden unexplained death in childhood. Acta Neuropathol 2022; 143:585-599. [PMID: 35333953 PMCID: PMC8953962 DOI: 10.1007/s00401-022-02414-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/18/2022] [Accepted: 03/19/2022] [Indexed: 11/01/2022]
Abstract
Sudden unexplained death in childhood (SUDC) is death of a child over 1 year of age that is unexplained after review of clinical history, circumstances of death, and complete autopsy with ancillary testing. Multiple etiologies may cause SUDC. SUDC and sudden unexpected death in epilepsy (SUDEP) share clinical and pathological features, suggesting some similarities in mechanism of death and possible abnormalities in hippocampus and cortex. To identify molecular signaling pathways, we performed label-free quantitative mass spectrometry on microdissected frontal cortex, hippocampal dentate gyrus (DG), and cornu ammonis (CA1-3) in SUDC (n = 19) and pediatric control cases (n = 19) with an explained cause of death. At a 5% false discovery rate (FDR), we found differential expression of 660 proteins in frontal cortex, 170 in DG, and 57 in CA1-3. Pathway analysis of altered proteins identified top signaling pathways associated with activated oxidative phosphorylation (p = 6.3 × 10-15, z = 4.08) and inhibited EIF2 signaling (p = 2.0 × 10-21, z = - 2.56) in frontal cortex, and activated acute phase response in DG (p = 8.5 × 10-6, z = 2.65) and CA1-3 (p = 4.7 × 10-6, z = 2.00). Weighted gene correlation network analysis (WGCNA) of clinical history indicated that SUDC-positive post-mortem virology (n = 4/17) had the most significant module in each brain region, with the top most significant associated with decreased mRNA metabolic processes (p = 2.8 × 10-5) in frontal cortex. Additional modules were associated with clinical history, including fever within 24 h of death (top: increased mitochondrial fission in DG, p = 1.8 × 10-3) and febrile seizure history (top: decreased small molecule metabolic processes in frontal cortex, p = 8.8 × 10-5) in all brain regions, neuropathological hippocampal findings in the DG (top: decreased focal adhesion, p = 1.9 × 10-3). Overall, cortical and hippocampal protein changes were present in SUDC cases and some correlated with clinical features. Our studies support that proteomic studies of SUDC cohorts can advance our understanding of the pathogenesis of these tragedies and may inform the development of preventive strategies.
Collapse
|
17
|
Drummond E, Kavanagh T, Pires G, Marta-Ariza M, Kanshin E, Nayak S, Faustin A, Berdah V, Ueberheide B, Wisniewski T. The amyloid plaque proteome in early onset Alzheimer's disease and Down syndrome. Acta Neuropathol Commun 2022; 10:53. [PMID: 35418158 PMCID: PMC9008934 DOI: 10.1186/s40478-022-01356-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/28/2022] [Indexed: 11/17/2022] Open
Abstract
Amyloid plaques contain many proteins in addition to beta amyloid (Aβ). Previous studies examining plaque-associated proteins have shown these additional proteins are important; they provide insight into the factors that drive amyloid plaque development and are potential biomarkers or therapeutic targets for Alzheimer's disease (AD). The aim of this study was to comprehensively identify proteins that are enriched in amyloid plaques using unbiased proteomics in two subtypes of early onset AD: sporadic early onset AD (EOAD) and Down Syndrome (DS) with AD. We focused our study on early onset AD as the drivers of the more aggressive pathology development in these cases is unknown and it is unclear whether amyloid-plaque enriched proteins differ between subtypes of early onset AD. Amyloid plaques and neighbouring non-plaque tissue were microdissected from human brain sections using laser capture microdissection and label-free LC-MS was used to quantify the proteins present. 48 proteins were consistently enriched in amyloid plaques in EOAD and DS. Many of these proteins were more significantly enriched in amyloid plaques than Aβ. The most enriched proteins in amyloid plaques in both EOAD and DS were: COL25A1, SMOC1, MDK, NTN1, OLFML3 and HTRA1. Endosomal/lysosomal proteins were particularly highly enriched in amyloid plaques. Fluorescent immunohistochemistry was used to validate the enrichment of four proteins in amyloid plaques (moesin, ezrin, ARL8B and SMOC1) and to compare the amount of total Aβ, Aβ40, Aβ42, phosphorylated Aβ, pyroglutamate Aβ species and oligomeric species in EOAD and DS. These studies showed that phosphorylated Aβ, pyroglutamate Aβ species and SMOC1 were significantly higher in DS plaques, while oligomers were significantly higher in EOAD. Overall, we observed that amyloid plaques in EOAD and DS largely contained the same proteins, however the amount of enrichment of some proteins was different in EOAD and DS. Our study highlights the significant enrichment of many proteins in amyloid plaques, many of which may be potential therapeutic targets and/or biomarkers for AD.
Collapse
Affiliation(s)
- Eleanor Drummond
- Brain and Mind Centre and School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, 94 Mallett Street, Camperdown, NSW, Australia.
- Centre for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, Science Building, Rm 1017, 435 East 30th Street, New York, NY, 10016, USA.
| | - Tomas Kavanagh
- Brain and Mind Centre and School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, 94 Mallett Street, Camperdown, NSW, Australia
| | - Geoffrey Pires
- Centre for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, Science Building, Rm 1017, 435 East 30th Street, New York, NY, 10016, USA
| | - Mitchell Marta-Ariza
- Centre for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, Science Building, Rm 1017, 435 East 30th Street, New York, NY, 10016, USA
| | - Evgeny Kanshin
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY, USA
| | - Shruti Nayak
- Merck & Co., Inc, Computational & Structural Chemistry, Kenilworth, NJ, USA
| | - Arline Faustin
- Centre for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, Science Building, Rm 1017, 435 East 30th Street, New York, NY, 10016, USA
| | - Valentin Berdah
- Centre for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, Science Building, Rm 1017, 435 East 30th Street, New York, NY, 10016, USA
| | - Beatrix Ueberheide
- Centre for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, Science Building, Rm 1017, 435 East 30th Street, New York, NY, 10016, USA
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Thomas Wisniewski
- Centre for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, Science Building, Rm 1017, 435 East 30th Street, New York, NY, 10016, USA.
- Departments of Pathology and Psychiatry, Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, USA.
| |
Collapse
|
18
|
Nargeh H, Aliabadi F, Ajami M, Pazoki-Toroudi H. Role of Polyphenols on Gut Microbiota and the Ubiquitin-Proteasome System in Neurodegenerative Diseases. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:6119-6144. [PMID: 34038102 DOI: 10.1021/acs.jafc.1c00923] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Today, neurodegenerative diseases have become a remarkable public health challenge due to their direct relation with aging. Accordingly, understanding the molecular and cellular mechanisms occurring in the pathogenesis of them is essential. Both protein aggregations as a result of the ubiquitin-proteasome system (UPS) inefficiency and gut microbiota alternation are the main pathogenic hallmarks. Polyphenols upregulating this system may decrease the developing rate of neurodegenerative diseases. Most of the dietary intake of polyphenols is converted into other microbial metabolites, which have completely different biological properties from the original polyphenols and should be thoroughly investigated. Herein, several prevalent neurodegenerative diseases are pinpointed to explain the role of gut microbiota alternations and the role of molecular changes, especially UPS down-regulation in their pathogenesis. Some of the most important polyphenols found in our diet are explained along with their microbial metabolites in the body.
Collapse
Affiliation(s)
- Hanieh Nargeh
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran 1417466191, Iran
| | - Fatemeh Aliabadi
- Physiology Research Center, Faculty of Medicine, Iran University of Medical Sciences, Tehran 14535, Iran
| | - Marjan Ajami
- Faculty of Nutrition Sciences & Food Technology, Shahid Beheshti University of Medical Sciences, 7th Floor, Bldg No. 2 SBUMS, Arabi Avenue, Daneshjoo Boulevard, Velenjak, Tehran 19839-63113, Iran
| | - Hamidreza Pazoki-Toroudi
- Physiology Research Center, Faculty of Medicine, Iran University of Medical Sciences, Tehran 14535, Iran
- Department of Physiology and Physiology Research Center, Faculty of Medicine, Iran University of Medical Sciences, Tehran 14535, Iran
| |
Collapse
|
19
|
Li X, Tsolis KC, Koper MJ, Ronisz A, Ospitalieri S, von Arnim CAF, Vandenberghe R, Tousseyn T, Scheuerle A, Economou A, Carpentier S, Otto M, Thal DR. Sequence of proteome profiles in preclinical and symptomatic Alzheimer's disease. Alzheimers Dement 2021; 17:946-958. [PMID: 33871169 DOI: 10.1002/alz.12345] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 03/03/2021] [Accepted: 03/11/2021] [Indexed: 12/15/2022]
Abstract
Proteome profile changes in Alzheimer's disease (AD) brains have been reported. However, it is unclear whether they represent a continuous process, or whether there is a sequential involvement of distinct proteins. To address this question, we used mass spectrometry. We analyzed soluble, dispersible, sodium dodecyl sulfate, and formic acid fractions of neocortex homogenates (mainly Brodmann area 17-19) from 18 pathologically diagnosed preclinical AD, 17 symptomatic AD, and 18 cases without signs of neurodegeneration. By doing so, we identified four groups of AD-related proteins being changed in levels in preclinical and symptomatic AD cases: early-responding, late-responding, gradually-changing, and fraction-shifting proteins. Gene ontology analysis of these proteins and all known AD-risk/causative genes identified vesicle endocytosis and the secretory pathway-related processes as an early-involved AD component. In conclusion, our findings suggest that subtle changes involving the secretory pathway and endocytosis precede severe proteome changes in symptomatic AD as part of the preclinical phase of AD. The respective early-responding proteins may also contribute to synaptic vesicle cycle alterations in symptomatic AD.
Collapse
Affiliation(s)
- Xiaohang Li
- Laboratory for Neuropathology, Department of Imaging and Pathology, KU Leuven (University of Leuven), Leuven, Belgium.,Leuven Brain Institute (LBI), KU Leuven (University of Leuven), Leuven, Belgium
| | - Konstantinos C Tsolis
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology, KU Leuven (University of Leuven), Leuven, Belgium
| | - Marta J Koper
- Laboratory for Neuropathology, Department of Imaging and Pathology, KU Leuven (University of Leuven), Leuven, Belgium.,Leuven Brain Institute (LBI), KU Leuven (University of Leuven), Leuven, Belgium.,Laboratory for the Research of Neurodegenerative Diseases, Department of Neurosciences, KU Leuven (University of Leuven), Leuven, Belgium.,Center for Brain and Disease Research, VIB, Leuven, Belgium
| | - Alicja Ronisz
- Laboratory for Neuropathology, Department of Imaging and Pathology, KU Leuven (University of Leuven), Leuven, Belgium.,Leuven Brain Institute (LBI), KU Leuven (University of Leuven), Leuven, Belgium
| | - Simona Ospitalieri
- Laboratory for Neuropathology, Department of Imaging and Pathology, KU Leuven (University of Leuven), Leuven, Belgium.,Leuven Brain Institute (LBI), KU Leuven (University of Leuven), Leuven, Belgium
| | - Christine A F von Arnim
- Department of Neurology, University of Ulm, Ulm, Germany.,Department of Geriatrics, University Medical Center Göttingen, Göttingen, Germany
| | - Rik Vandenberghe
- Department of Neurology, UZ Leuven (University Hospitals Leuven), Leuven, Belgium.,Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven (University of Leuven), Leuven, Belgium
| | - Thomas Tousseyn
- Department of Pathology, UZ Leuven (University Hospitals Leuven), Leuven, Belgium
| | | | - Anastassios Economou
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology, KU Leuven (University of Leuven), Leuven, Belgium
| | - Sebastien Carpentier
- BIOMED facility for SYstems BIOlogy based MAss spectrometry, KU Leuven (University of Leuven), Leuven, Belgium
| | - Markus Otto
- Department of Neurology, University of Ulm, Ulm, Germany
| | - Dietmar Rudolf Thal
- Laboratory for Neuropathology, Department of Imaging and Pathology, KU Leuven (University of Leuven), Leuven, Belgium.,Leuven Brain Institute (LBI), KU Leuven (University of Leuven), Leuven, Belgium.,Department of Pathology, UZ Leuven (University Hospitals Leuven), Leuven, Belgium
| |
Collapse
|
20
|
Jain AP, Sathe G. Proteomics Landscape of Alzheimer's Disease. Proteomes 2021; 9:proteomes9010013. [PMID: 33801961 PMCID: PMC8005944 DOI: 10.3390/proteomes9010013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/02/2021] [Accepted: 03/08/2021] [Indexed: 01/22/2023] Open
Abstract
Alzheimer’s disease (AD) is the most prevalent form of dementia, and the numbers of AD patients are expected to increase as human life expectancy improves. Deposition of β-amyloid protein (Aβ) in the extracellular matrix and intracellular neurofibrillary tangles are molecular hallmarks of the disease. Since the precise pathophysiology of AD has not been elucidated yet, effective treatment is not available. Thus, understanding the disease pathology, as well as identification and development of valid biomarkers, is imperative for early diagnosis as well as for monitoring disease progression and therapeutic responses. Keeping this goal in mind several studies using quantitative proteomics platform have been carried out on both clinical specimens including the brain, cerebrospinal fluid (CSF), plasma and on animal models of AD. In this review, we summarize the mass spectrometry (MS)-based proteomics studies on AD and discuss the discovery as well as validation stages in brief to identify candidate biomarkers.
Collapse
Affiliation(s)
- Ankit P. Jain
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India;
| | - Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India;
- Manipal Academy of Higher Education (MAHE), Manipal 576104, India
- Correspondence:
| |
Collapse
|
21
|
Pires G, Leitner D, Drummond E, Kanshin E, Nayak S, Askenazi M, Faustin A, Friedman D, Debure L, Ueberheide B, Wisniewski T, Devinsky O. Proteomic differences in the hippocampus and cortex of epilepsy brain tissue. Brain Commun 2021; 3:fcab021. [PMID: 34159317 DOI: 10.1093/braincomms/fcab021] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 12/22/2022] Open
Abstract
Epilepsy is a common neurological disorder affecting over 70 million people worldwide, with a high rate of pharmaco-resistance, diverse comorbidities including progressive cognitive and behavioural disorders, and increased mortality from direct (e.g. sudden unexpected death in epilepsy, accidents, drowning) or indirect effects of seizures and therapies. Extensive research with animal models and human studies provides limited insights into the mechanisms underlying seizures and epileptogenesis, and these have not translated into significant reductions in pharmaco-resistance, morbidities or mortality. To help define changes in molecular signalling networks associated with seizures in epilepsy with a broad range of aetiologies, we examined the proteome of brain samples from epilepsy and control cases. Label-free quantitative mass spectrometry was performed on the hippocampal cornu ammonis 1-3 region (CA1-3), frontal cortex and dentate gyrus microdissected from epilepsy and control cases (n = 14/group). Epilepsy cases had significant differences in the expression of 777 proteins in the hippocampal CA1 - 3 region, 296 proteins in the frontal cortex and 49 proteins in the dentate gyrus in comparison to control cases. Network analysis showed that proteins involved in protein synthesis, mitochondrial function, G-protein signalling and synaptic plasticity were particularly altered in epilepsy. While protein differences were most pronounced in the hippocampus, similar changes were observed in other brain regions indicating broad proteomic abnormalities in epilepsy. Among the most significantly altered proteins, G-protein subunit beta 1 (GNB1) was one of the most significantly decreased proteins in epilepsy in all regions studied, highlighting the importance of G-protein subunit signalling and G-protein-coupled receptors in epilepsy. Our results provide insights into common molecular mechanisms underlying epilepsy across various aetiologies, which may allow for novel targeted therapeutic strategies.
Collapse
Affiliation(s)
- Geoffrey Pires
- Comprehensive Epilepsy Center, New York University Grossman School of Medicine, New York, NY, USA.,Department of Neurology, Center for Cognitive Neurology, New York University Grossman School of Medicine, New York, NY, USA.,Alzheimer's and Prion Diseases Team, Paris Brain Institute, CNRS, UMR 7225, INSERM 1127, Sorbonne University UM75, Paris, France
| | - Dominique Leitner
- Comprehensive Epilepsy Center, New York University Grossman School of Medicine, New York, NY, USA
| | - Eleanor Drummond
- Department of Neurology, Center for Cognitive Neurology, New York University Grossman School of Medicine, New York, NY, USA.,Faculty of Medicine and Health, Brain and Mind Centre and School of Medical Sciences, University of Sydney, Sydney, Australia
| | - Evgeny Kanshin
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY, USA
| | - Shruti Nayak
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY, USA
| | - Manor Askenazi
- Biomedical Hosting LLC, USA.,Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Arline Faustin
- Department of Neurology, Center for Cognitive Neurology, New York University Grossman School of Medicine, New York, NY, USA
| | - Daniel Friedman
- Comprehensive Epilepsy Center, New York University Grossman School of Medicine, New York, NY, USA
| | - Ludovic Debure
- Department of Neurology, Center for Cognitive Neurology, New York University Grossman School of Medicine, New York, NY, USA
| | - Beatrix Ueberheide
- Department of Neurology, Center for Cognitive Neurology, New York University Grossman School of Medicine, New York, NY, USA.,Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY, USA.,Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Thomas Wisniewski
- Department of Neurology, Center for Cognitive Neurology, New York University Grossman School of Medicine, New York, NY, USA.,Department of Psychiatry, New York University Grossman School of Medicine, New York, NY, USA.,Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Orrin Devinsky
- Comprehensive Epilepsy Center, New York University Grossman School of Medicine, New York, NY, USA
| |
Collapse
|
22
|
Drummond E, Pires G, MacMurray C, Askenazi M, Nayak S, Bourdon M, Safar J, Ueberheide B, Wisniewski T. Phosphorylated tau interactome in the human Alzheimer's disease brain. Brain 2021; 143:2803-2817. [PMID: 32812023 DOI: 10.1093/brain/awaa223] [Citation(s) in RCA: 162] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 05/05/2020] [Accepted: 05/22/2020] [Indexed: 01/07/2023] Open
Abstract
Accumulation of phosphorylated tau is a key pathological feature of Alzheimer's disease. Phosphorylated tau accumulation causes synaptic impairment, neuronal dysfunction and formation of neurofibrillary tangles. The pathological actions of phosphorylated tau are mediated by surrounding neuronal proteins; however, a comprehensive understanding of the proteins that phosphorylated tau interacts with in Alzheimer's disease is surprisingly limited. Therefore, the aim of this study was to determine the phosphorylated tau interactome. To this end, we used two complementary proteomics approaches: (i) quantitative proteomics was performed on neurofibrillary tangles microdissected from patients with advanced Alzheimer's disease; and (ii) affinity purification-mass spectrometry was used to identify which of these proteins specifically bound to phosphorylated tau. We identified 542 proteins in neurofibrillary tangles. This included the abundant detection of many proteins known to be present in neurofibrillary tangles such as tau, ubiquitin, neurofilament proteins and apolipoprotein E. Affinity purification-mass spectrometry confirmed that 75 proteins present in neurofibrillary tangles interacted with PHF1-immunoreactive phosphorylated tau. Twenty-nine of these proteins have been previously associated with phosphorylated tau, therefore validating our proteomic approach. More importantly, 34 proteins had previously been associated with total tau, but not yet linked directly to phosphorylated tau (e.g. synaptic protein VAMP2, vacuolar-ATPase subunit ATP6V0D1); therefore, we provide new evidence that they directly interact with phosphorylated tau in Alzheimer's disease. In addition, we also identified 12 novel proteins, not previously known to be physiologically or pathologically associated with tau (e.g. RNA binding protein HNRNPA1). Network analysis showed that the phosphorylated tau interactome was enriched in proteins involved in the protein ubiquitination pathway and phagosome maturation. Importantly, we were able to pinpoint specific proteins that phosphorylated tau interacts with in these pathways for the first time, therefore providing novel potential pathogenic mechanisms that can be explored in future studies. Combined, our results reveal new potential drug targets for the treatment of tauopathies and provide insight into how phosphorylated tau mediates its toxicity in Alzheimer's disease.
Collapse
Affiliation(s)
- Eleanor Drummond
- Brain and Mind Centre and Central Clinical School, Faculty of Medicine and Health, University of Sydney, Australia.,Centre for Cognitive Neurology, Department of Neurology, New York University School of Medicine, New York, NY, USA
| | - Geoffrey Pires
- Centre for Cognitive Neurology, Department of Neurology, New York University School of Medicine, New York, NY, USA.,Alzheimer's and Prion Diseases Team, Paris Brain Institute, CNRS, UMR 7225, INSERM 1127, Sorbonne University UM75, Paris, France
| | - Claire MacMurray
- Centre for Cognitive Neurology, Department of Neurology, New York University School of Medicine, New York, NY, USA
| | | | - Shruti Nayak
- Proteomics Laboratory, Division of Advanced Research Technologies, NYU School of Medicine, New York, NY, USA
| | - Marie Bourdon
- Centre for Cognitive Neurology, Department of Neurology, New York University School of Medicine, New York, NY, USA
| | - Jiri Safar
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA.,Department of Neurology, Case Western Reserve University, Cleveland, OH, USA
| | - Beatrix Ueberheide
- Biomedical Hosting LLC, USA.,Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Thomas Wisniewski
- Centre for Cognitive Neurology, Department of Neurology, New York University School of Medicine, New York, NY, USA.,Department of Psychiatry, New York University School of Medicine, New York, NY, USA
| |
Collapse
|
23
|
Zheng Y, Yang C, Zheng X, Guan Q, Yu S. Acrylamide treatment alters the level of Ca 2+ and Ca 2+-related protein kinase in spinal cords of rats. Toxicol Ind Health 2021; 37:113-123. [PMID: 33487136 DOI: 10.1177/0748233720971879] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This study aimed to analyze the neurological changes induced by acrylamide (ACR) poisoning and their underlying mechanisms within the spinal cords of male adult Wistar rats. The rats were randomly divided into three groups (n = 9 rats per group). ACR was intraperitoneally injected to produce axonopathy according to the daily dosing schedules of 20 or 40 mg/kg/day of ACR for eight continuous weeks (three times per week). During the exposure period, body weights and gait scores were assessed, and the concentration of Ca2+ was calculated in 27 mice. Protein kinase A (PKA), protein kinase C (PKC), cyclin-dependent protein kinase 5 (CDK5), and P35 were assessed by electrophoretic resolution and Western blotting. The contents of 3'-cyclic adenosine monophosphate (cAMP) and calmodulin (CaM) were determined using ELISA kits, and the activities of calcium/calmodulin-dependent protein kinase II (CaMKII), PKA, and PKC were determined using the commercial Signa TECTPKAassay kits. Compared with control rats, treatment with 20 and 40 mg/kg of ACR decreased body weight and increased gait scores at 8 weeks. Intracellular Ca2+ levels increased significantly in treated rats; CaM, PKC, CDK5, and P35 levels were significantly decreased; and PKA and cAMP levels remained unchanged. CaMKII, PKA, and PKC activities increased significantly. The results indicated that ACR can damage neurofilaments by affecting the contents and activities of CaM, CaMKII, PKA, cAMP, PKC, CDK5, and P35, which could result in ACR toxic neuropathy.
Collapse
Affiliation(s)
- Yunhe Zheng
- Gansu Provincial Center for Disease Control and Prevention, West Lanzhou, Gansu, People's Republic of China
| | - Chen Yang
- Gansu Provincial Center for Disease Control and Prevention, West Lanzhou, Gansu, People's Republic of China
| | - Xiu'e Zheng
- Shandong food and Drug Administration, SDFDA, Jinan, People's Republic of China
| | - Qiangdong Guan
- School of Public Health, Nanjing Medical University, Jiangning District, Nanjing, People's Republic of China
| | - Sufang Yu
- School of Public Health, 12589Shandong University, Jinan, People's Republic of China
| |
Collapse
|
24
|
Gomez-Gomez A, Sabbaghi M, Haro N, Albanell J, Menéndez S, González M, Gil-Gómez G, Rovira A, Pozo OJ. Targeted metabolomics in formalin-fixed paraffin-embedded tissue specimens: Liquid chromatography-tandem mass spectrometry determination of acidic metabolites in cancer research. Talanta 2020; 223:121740. [PMID: 33298266 DOI: 10.1016/j.talanta.2020.121740] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 10/02/2020] [Accepted: 10/05/2020] [Indexed: 11/18/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues play an irreplaceable role in cancer research. Although extensive research has been conducted for the detection of DNA, RNA and proteins in FFPE samples, literature dealing with the FFPE determination of small molecules is scarce. In this study, we aimed to explore the potential of targeted metabolomics in FFPE specimens. For that purpose, we developed a LC-MS/MS method for the quantification of acidic metabolites in FFPE samples. The method involves trimming tissue slices from FFPE blocks, deparaffinization, lysis of the tissue, o-benzyl hydroxylamine derivatization and LC-MS/MS detection. Deparaffinization and lysis steps were optimized to maximize the analytes extraction and to minimize the effect of the ubiquitous presence of some metabolites in the paraffin. Two validation approaches were applied: (i) using blank paraffin as matrix and (ii) using actual human FFPE tissue samples by standard additions. The method quantified 40 metabolites with appropriate accuracy (commonly 80-120%) and precision (CV 2-19%) in both validation approaches. LLOQs ranging 0.88-2001 pg mg-1 with low-moderate matrix effects (commonly 85-115%) were obtained. FFPE samples from 15 patients with colorectal cancer were analyzed and metabolites concentrations in tumor vs matched normal FFPE tissues were compared. Results show that tumor tissues have a well-established fingerprint including an increase in ketogenesis, a decrease in lipogenesis and an imbalance in the tricarboxylic acid cycle.
Collapse
Affiliation(s)
- Alex Gomez-Gomez
- Integrative Pharmacology & Systems Neuroscience Group, IMIM (Hospital del Mar Medical Research Institute), Carrer Doctor Aiguader 88, 08003, Barcelona, Spain; Universitat Pompeu Fabra (CEXS-UPF), Carrer Doctor Aiguader 88, 08003, Barcelona, Spain
| | - MohammadA Sabbaghi
- Cancer Research Program, IMIM (Hospital del Mar Medical Research Institute), Carrer Doctor Aiguader 88, 08003, Barcelona, Spain
| | - Noemí Haro
- Integrative Pharmacology & Systems Neuroscience Group, IMIM (Hospital del Mar Medical Research Institute), Carrer Doctor Aiguader 88, 08003, Barcelona, Spain
| | - Joan Albanell
- Universitat Pompeu Fabra (CEXS-UPF), Carrer Doctor Aiguader 88, 08003, Barcelona, Spain; Cancer Research Program, IMIM (Hospital del Mar Medical Research Institute), Carrer Doctor Aiguader 88, 08003, Barcelona, Spain; Medical Oncology Department, Hospital del Mar, Passeig Marítim de la Barcelona, 25-29, 08003, Barcelona, Spain; CIBERONC, Hospital del Mar, Passeig Marítim de la Barcelona, 25-29, 08003, Barcelona, Spain
| | - Silvia Menéndez
- Cancer Research Program, IMIM (Hospital del Mar Medical Research Institute), Carrer Doctor Aiguader 88, 08003, Barcelona, Spain
| | - Mónica González
- Department of Pathology, Hospital del Mar, Passeig Marítim de la Barcelona, 25-29, 08003, Barcelona, Spain
| | - Gabriel Gil-Gómez
- Gastroesophageal Carcinogenesis Group, IMIM (Hospital del Mar Medical Research Institute), Carrer Doctor Aiguader 88, 08003, Barcelona, Spain
| | - Ana Rovira
- Cancer Research Program, IMIM (Hospital del Mar Medical Research Institute), Carrer Doctor Aiguader 88, 08003, Barcelona, Spain; Medical Oncology Department, Hospital del Mar, Passeig Marítim de la Barcelona, 25-29, 08003, Barcelona, Spain; CIBERONC, Hospital del Mar, Passeig Marítim de la Barcelona, 25-29, 08003, Barcelona, Spain
| | - Oscar J Pozo
- Integrative Pharmacology & Systems Neuroscience Group, IMIM (Hospital del Mar Medical Research Institute), Carrer Doctor Aiguader 88, 08003, Barcelona, Spain.
| |
Collapse
|
25
|
Patterns of Expression of Purinergic Receptor P2RY12, a Putative Marker for Non-Activated Microglia, in Aged and Alzheimer's Disease Brains. Int J Mol Sci 2020; 21:ijms21020678. [PMID: 31968618 PMCID: PMC7014248 DOI: 10.3390/ijms21020678] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/10/2020] [Accepted: 01/11/2020] [Indexed: 01/08/2023] Open
Abstract
Neuroinflammation is considered a key pathological process in neurodegenerative diseases of aging, including Alzheimer's disease (AD). Many studies have defined phenotypes of reactive microglia, the brain-resident macrophages, with different antigenic markers to identify those potentially causing inflammatory damage. We took an alternative approach with the goal of characterizing the distribution of purinergic receptor P2RY12-positive microglia, a marker previously defined as identifying homeostatic or non-activated microglia. We examined the expression of P2RY12 by dual-color light and fluorescence immunohistochemistry using sections of middle temporal gyrus from AD, high plaque and low plaque non-demented cases in relation to amyloid beta (Aβ) plaques and phosphorylated tau, markers of pathology, and HLA-DR, IBA-1, CD68, and progranulin, microglial phenotype markers. In low plaque cases, P2RY12-positive microglia mostly had non-activated morphologies, while the morphologies of P2RY12-positive microglia in AD brains were highly variable, suggesting its expression could encompass a wider range of phenotypes than originally hypothesized. P2RY12 expression by microglia differed depending on the types of plaques or tangles they were associated with. Areas of inflammation characterized by lack of P2RY12-positive microglia around mature plaques could be observed, but many diffuse plaques showed colocalization with P2RY12-positive microglia. Based on these results, P2RY12 expression by microglia should not be considered solely a marker of resting microglia as P2RY12 immunoreactivity was identifying microglia positive for CD68, progranulin and to a limited extent HLA-DR, markers of activation.
Collapse
|
26
|
Pires G, McElligott S, Drusinsky S, Halliday G, Potier MC, Wisniewski T, Drummond E. Secernin-1 is a novel phosphorylated tau binding protein that accumulates in Alzheimer's disease and not in other tauopathies. Acta Neuropathol Commun 2019; 7:195. [PMID: 31796108 PMCID: PMC6892024 DOI: 10.1186/s40478-019-0848-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 11/14/2019] [Indexed: 12/13/2022] Open
Abstract
We recently identified Secernin-1 (SCRN1) as a novel amyloid plaque associated protein using localized proteomics. Immunohistochemistry studies confirmed that SCRN1 was present in plaque-associated dystrophic neurites and also revealed distinct and abundant co-localization with neurofibrillary tangles (NFTs). Little is known about the physiological function of SCRN1 and its role in Alzheimer's disease (AD) and other neurodegenerative diseases has not been studied. Therefore, we performed a comprehensive study of SCRN1 distribution in neurodegenerative diseases. Immunohistochemistry was used to map SCRN1 accumulation throughout the progression of AD in a cohort of 58 patients with a range of NFT pathology (Abundant NFT, n = 21; Moderate NFT, n = 22; Low/No NFT, n = 15), who were clinically diagnosed as having AD, mild cognitive impairment or normal cognition. SCRN1 accumulation was also examined in two cases with both Frontotemporal Lobar Degeneration (FTLD)-Tau and AD-related neuropathology, cases of Down Syndrome (DS) with AD (n = 5), one case of hereditary cerebral hemorrhage with amyloidosis - Dutch type (HCHWA-D) and other non-AD tauopathies including: primary age-related tauopathy (PART, [n = 5]), Corticobasal Degeneration (CBD, [n = 5]), Progressive Supranuclear Palsy (PSP, [n = 5]) and Pick's disease (PiD, [n = 4]). Immunohistochemistry showed that SCRN1 was a neuronal protein that abundantly accumulated in NFTs and plaque-associated dystrophic neurites throughout the progression of AD. Quantification of SCRN1 immunohistochemistry confirmed that SCRN1 preferentially accumulated in NFTs in comparison to surrounding non-tangle containing neurons at both early and late stages of AD. Similar results were observed in DS with AD and PART. However, SCRN1 did not co-localize with phosphorylated tau inclusions in CBD, PSP or PiD. Co-immunoprecipitation revealed that SCRN1 interacted with phosphorylated tau in human AD brain tissue. Together, these results suggest that SCRN1 is uniquely associated with tau pathology in AD, DS and PART. As such, SCRN1 has potential as a novel therapeutic target and could serve as a useful biomarker to distinguish AD from other tauopathies.
Collapse
Affiliation(s)
- Geoffrey Pires
- Center for Cognitive Neurology and Department of Neurology, New York University School of Medicine, 435 East 30th Street, Rm 1017, New York, NY, 10016, USA
| | - Sacha McElligott
- Center for Cognitive Neurology and Department of Neurology, New York University School of Medicine, 435 East 30th Street, Rm 1017, New York, NY, 10016, USA
| | - Shiron Drusinsky
- Center for Cognitive Neurology and Department of Neurology, New York University School of Medicine, 435 East 30th Street, Rm 1017, New York, NY, 10016, USA
| | - Glenda Halliday
- Brain & Mind Centre and Central Clinical School, Faculty of Medicine and Health, University of Sydney, 94 Mallett Street, Camperdown, NSW, 2050, Australia
| | - Marie-Claude Potier
- Institut du Cerveau et de la Moelle épinière, CNRS UMR7225, INSERM U1127, UPMC, Hôpital de la Pitié-Salpêtrière, 47 Bd de l'Hôpital, Paris, France
| | - Thomas Wisniewski
- Center for Cognitive Neurology and Department of Neurology, New York University School of Medicine, 435 East 30th Street, Rm 1017, New York, NY, 10016, USA.
- Departments of Pathology and Psychiatry, New York University School of Medicine, 435 East 30th Street, Rm 1017, New York, NY, 10016, USA.
| | - Eleanor Drummond
- Center for Cognitive Neurology and Department of Neurology, New York University School of Medicine, 435 East 30th Street, Rm 1017, New York, NY, 10016, USA.
- Brain & Mind Centre and Central Clinical School, Faculty of Medicine and Health, University of Sydney, 94 Mallett Street, Camperdown, NSW, 2050, Australia.
| |
Collapse
|
27
|
Chapman J, Dogan A. Fibrinogen alpha amyloidosis: insights from proteomics. Expert Rev Proteomics 2019; 16:783-793. [PMID: 31443619 PMCID: PMC6788741 DOI: 10.1080/14789450.2019.1659137] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/20/2019] [Indexed: 12/17/2022]
Abstract
Introduction: Systemic amyloidosis is a diverse group of diseases that, although rare, pose a serious health issue and can lead to organ failure and death. Amyloid typing is essential in determining the causative protein and initiating proper treatment. Mass spectrometry-based proteomics is currently the most sensitive and accurate means of typing amyloid. Areas covered: Amyloidosis can be systemic or localized, acquired or hereditary, and can affect any organ or tissue. Diagnosis requires biopsy, histological analysis, and typing of the causative protein to determine treatment. The kidneys are the most commonly affected organ in systemic disease. Fibrinogen alpha chain amyloidosis (AFib) is the most prevalent form of hereditary renal amyloidosis. Select mutations in the fibrinogen Aα (FGA) gene lead to AFib. Expert commentary: Mass spectrometry is currently the most specific and sensitive method for amyloid typing. Identification of the mutated fibrinogen alpha chain can be difficult in the case of 'private' frameshift mutations, which dramatically change the sequences of the expressed fibrinogen alpha chain. A combination of expert pathologist review, mass spectrometry, and gene sequencing can allow for confident diagnosis and determination of the fibrinogen alpha chain mutated sequence.
Collapse
Affiliation(s)
- Jessica Chapman
- Hematopathology Service, Memorial Sloan Kettering Cancer Center , New York , NY , USA
| | - Ahmet Dogan
- Hematopathology Service, Memorial Sloan Kettering Cancer Center , New York , NY , USA
| |
Collapse
|
28
|
Penke B, Bogár F, Paragi G, Gera J, Fülöp L. Key Peptides and Proteins in Alzheimer's Disease. Curr Protein Pept Sci 2019; 20:577-599. [PMID: 30605056 DOI: 10.2174/1389203720666190103123434] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/03/2018] [Accepted: 12/27/2018] [Indexed: 02/02/2023]
Abstract
Alzheimer's Disease (AD) is a form of progressive dementia involving cognitive impairment, loss of learning and memory. Different proteins (such as amyloid precursor protein (APP), β- amyloid (Aβ) and tau protein) play a key role in the initiation and progression of AD. We review the role of the most important proteins and peptides in AD pathogenesis. The structure, biosynthesis and physiological role of APP are shortly summarized. The details of trafficking and processing of APP to Aβ, the cytosolic intracellular Aβ domain (AICD) and small soluble proteins are shown, together with other amyloid-forming proteins such as tau and α-synuclein (α-syn). Hypothetic physiological functions of Aβ are summarized. The mechanism of conformational change, the formation and the role of neurotoxic amyloid oligomeric (oAβ) are shown. The fibril formation process and the co-existence of different steric structures (U-shaped and S-shaped) of Aβ monomers in mature fibrils are demonstrated. We summarize the known pathogenic and non-pathogenic mutations and show the toxic interactions of Aβ species after binding to cellular receptors. Tau phosphorylation, fibrillation, the molecular structure of tau filaments and their toxic effect on microtubules are shown. Development of Aβ and tau imaging in AD brain and CSF as well as blood biomarkers is shortly summarized. The most probable pathomechanisms of AD including the toxic effects of oAβ and tau; the three (biochemical, cellular and clinical) phases of AD are shown. Finally, the last section summarizes the present state of Aβ- and tau-directed therapies and future directions of AD research and drug development.
Collapse
Affiliation(s)
- Botond Penke
- Department of Medical Chemistry, Interdisciplinary Excellence Centre, University of Szeged, Dom square 8, Szeged, H-6720, Hungary
| | - Ferenc Bogár
- Department of Medical Chemistry, Interdisciplinary Excellence Centre, University of Szeged, Dom square 8, Szeged, H-6720, Hungary.,MTA-SZTE Biomimetic Systems Research Group, University of Szeged, H-6720 Szeged, Dom square 8, Hungary
| | - Gábor Paragi
- MTA-SZTE Biomimetic Systems Research Group, University of Szeged, H-6720 Szeged, Dom square 8, Hungary.,Institute of Physics, University of Pécs, H-7624 Pecs, Ifjusag utja 6, Hungary
| | - János Gera
- Department of Medical Chemistry, Interdisciplinary Excellence Centre, University of Szeged, Dom square 8, Szeged, H-6720, Hungary
| | - Lívia Fülöp
- Department of Medical Chemistry, Interdisciplinary Excellence Centre, University of Szeged, Dom square 8, Szeged, H-6720, Hungary
| |
Collapse
|
29
|
Drummond E, Goñi F, Liu S, Prelli F, Scholtzova H, Wisniewski T. Potential Novel Approaches to Understand the Pathogenesis and Treat Alzheimer's Disease. J Alzheimers Dis 2019; 64:S299-S312. [PMID: 29562516 DOI: 10.3233/jad-179909] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
There is growing genetic and proteomic data highlighting the complexity of Alzheimer's disease (AD) pathogenesis. Greater use of unbiased "omics" approaches is being increasingly recognized as essential for the future development of effective AD research, that need to better reflect the multiple distinct pathway abnormalities that can drive AD pathology. The track record of success in AD clinical trials thus far has been very poor. In part, this high failure rate has been related to the premature translation of highly successful results in animal models that mirror only limited aspects of AD pathology to humans. We highlight our recent efforts to increase use of human tissue to gain a better understanding of the AD pathogenesis subtype variety and to develop several distinct therapeutic approaches tailored to address this diversity. These therapeutic approaches include the blocking of the Aβ/apoE interaction, stimulation of innate immunity, and the simultaneous blocking of Aβ/tau oligomer toxicity. We believe that future successful therapeutic approaches will need to be combined to better reflect the complexity of the abnormal pathways triggered in AD pathogenesis.
Collapse
Affiliation(s)
- Eleanor Drummond
- Department of Neurology, Center for Cognitive Neurology, NYU School of Medicine, New York, NY, USA
| | - Fernando Goñi
- Department of Neurology, Center for Cognitive Neurology, NYU School of Medicine, New York, NY, USA
| | - Shan Liu
- Department of Neurology, Center for Cognitive Neurology, NYU School of Medicine, New York, NY, USA
| | - Frances Prelli
- Department of Neurology, Center for Cognitive Neurology, NYU School of Medicine, New York, NY, USA
| | - Henrieta Scholtzova
- Department of Neurology, Center for Cognitive Neurology, NYU School of Medicine, New York, NY, USA
| | - Thomas Wisniewski
- Departments of Neurology, Pathology and Psychiatry, Center for Cognitive Neurology, NYU School of Medicine, New York, NY, USA
| |
Collapse
|
30
|
Lutz BM, Peng J. Deep Profiling of the Aggregated Proteome in Alzheimer's Disease: From Pathology to Disease Mechanisms. Proteomes 2018; 6:proteomes6040046. [PMID: 30424485 PMCID: PMC6313861 DOI: 10.3390/proteomes6040046] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 10/29/2018] [Accepted: 11/07/2018] [Indexed: 01/20/2023] Open
Abstract
Hallmarks of Alzheimer’s disease (AD), a progressive neurodegenerative disease causing dementia, include protein aggregates such as amyloid beta plaques and tau neurofibrillary tangles in a patient’s brain. Understanding the complete composition and structure of protein aggregates in AD can shed light on the as-yet unidentified underlying mechanisms of AD development and progression. Biochemical isolation of aggregates coupled with mass spectrometry (MS) provides a comprehensive proteomic analysis of aggregates in AD. Dissection of these AD-specific aggregate components, such as U1 small nuclear ribonucleoprotein complex (U1 snRNP), provides novel insights into the deregulation of RNA splicing in the disease. In this review, we summarize the methodologies of laser capture microdissection (LCM) and differential extraction to analyze the aggregated proteomes in AD samples, and discuss the derived novel insights that may contribute to AD pathogenesis.
Collapse
Affiliation(s)
- Brianna M Lutz
- Departments of Structural Biology and Developmental Neurobiology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| |
Collapse
|