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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.
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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
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2
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Downs M, Zaia J, Sethi MK. Mass spectrometry methods for analysis of extracellular matrix components in neurological diseases. MASS SPECTROMETRY REVIEWS 2023; 42:1848-1875. [PMID: 35719114 PMCID: PMC9763553 DOI: 10.1002/mas.21792] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/12/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
The brain extracellular matrix (ECM) is a highly glycosylated environment and plays important roles in many processes including cell communication, growth factor binding, and scaffolding. The formation of structures such as perineuronal nets (PNNs) is critical in neuroprotection and neural plasticity, and the formation of molecular networks is dependent in part on glycans. The ECM is also implicated in the neuropathophysiology of disorders such as Alzheimer's disease (AD), Parkinson's disease (PD), and Schizophrenia (SZ). As such, it is of interest to understand both the proteomic and glycomic makeup of healthy and diseased brain ECM. Further, there is a growing need for site-specific glycoproteomic information. Over the past decade, sample preparation, mass spectrometry, and bioinformatic methods have been developed and refined to provide comprehensive information about the glycoproteome. Core ECM molecules including versican, hyaluronan and proteoglycan link proteins, and tenascin are dysregulated in AD, PD, and SZ. Glycomic changes such as differential sialylation, sulfation, and branching are also associated with neurodegeneration. A more thorough understanding of the ECM and its proteomic, glycomic, and glycoproteomic changes in brain diseases may provide pathways to new therapeutic options.
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Affiliation(s)
- Margaret Downs
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University, Boston, Massachusetts, USA
| | - Joseph Zaia
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University, Boston, Massachusetts, USA
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA
| | - Manveen K Sethi
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University, Boston, Massachusetts, USA
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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.
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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.
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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.
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Radford RAW, Rayner SL, Szwaja P, Morsch M, Cheng F, Zhu T, Widagdo J, Anggono V, Pountney DL, Chung R, Lee A. Identification of phosphorylated tau protein interactors in progressive supranuclear palsy (PSP) reveals networks involved in protein degradation, stress response, cytoskeletal dynamics, metabolic processes, and neurotransmission. J Neurochem 2023; 165:563-586. [PMID: 36847488 PMCID: PMC10953353 DOI: 10.1111/jnc.15796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/27/2023] [Accepted: 02/21/2023] [Indexed: 03/01/2023]
Abstract
Progressive supranuclear palsy (PSP) is a late-onset neurodegenerative disease defined pathologically by the presence of insoluble phosphorylated-Tau (p-Tau) in neurons and glia. Identifying co-aggregating proteins within p-Tau inclusions may reveal important insights into processes affected by the aggregation of Tau. We used a proteomic approach, which combines antibody-mediated biotinylation and mass spectrometry (MS) to identify proteins proximal to p-Tau in PSP. Using this proof-of-concept workflow for identifying interacting proteins of interest, we characterized proteins proximal to p-Tau in PSP cases, identifying >84% of previously identified interaction partners of Tau and known modifiers of Tau aggregation, while 19 novel proteins not previously found associated with Tau were identified. Furthermore, our data also identified confidently assigned phosphorylation sites that have been previously reported on p-Tau. Additionally, using ingenuity pathway analysis (IPA) and human RNA-seq datasets, we identified proteins previously associated with neurological disorders and pathways involved in protein degradation, stress responses, cytoskeletal dynamics, metabolism, and neurotransmission. Together, our study demonstrates the utility of biotinylation by antibody recognition (BAR) approach to answer a fundamental question to rapidly identify proteins in proximity to p-Tau from post-mortem tissue. The application of this workflow opens up the opportunity to identify novel protein targets to give us insight into the biological process at the onset and progression of tauopathies.
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Affiliation(s)
- Rowan A. W. Radford
- Centre for Motor Neuron Disease ResearchMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversityNew South WalesNorth RydeAustralia
| | - Stephanie L. Rayner
- Centre for Motor Neuron Disease ResearchMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversityNew South WalesNorth RydeAustralia
| | - Paulina Szwaja
- Centre for Motor Neuron Disease ResearchMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversityNew South WalesNorth RydeAustralia
| | - Marco Morsch
- Centre for Motor Neuron Disease ResearchMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversityNew South WalesNorth RydeAustralia
| | - Flora Cheng
- Centre for Motor Neuron Disease ResearchMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversityNew South WalesNorth RydeAustralia
| | - Tianyi Zhu
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain InstituteThe University of QueenslandQueenslandBrisbaneAustralia
| | - Jocelyn Widagdo
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain InstituteThe University of QueenslandQueenslandBrisbaneAustralia
| | - Victor Anggono
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain InstituteThe University of QueenslandQueenslandBrisbaneAustralia
| | - Dean L. Pountney
- School of Pharmacy and Medical SciencesGriffith UniversityQueenslandGold CoastAustralia
| | - Roger Chung
- Centre for Motor Neuron Disease ResearchMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversityNew South WalesNorth RydeAustralia
| | - Albert Lee
- Centre for Motor Neuron Disease ResearchMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversityNew South WalesNorth RydeAustralia
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Arora D, Hackenberg Y, Li J, Winter D. Updates on the study of lysosomal protein dynamics: possibilities for the clinic. Expert Rev Proteomics 2023; 20:47-55. [PMID: 36919490 DOI: 10.1080/14789450.2023.2190515] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
INTRODUCTION The lysosome is the main degradative organelle of almost all mammalian cells, fulfilling important functions in macromolecule recycling, metabolism, and signaling. Lysosomal dysfunction is connected to a continuously growing number of pathologic conditions, and lysosomal proteins present potential biomarkers for a variety of diseases. Therefore, there is an increasing interest in their analysis in patient samples. AREAS COVERED We provide an overview of OMICs studies which identified lysosomal proteins as potential biomarkers for pathological conditions, covering proteomics, genomics, and transcriptomics approaches, identified through PubMed searches. With respect to discovery proteomics analyses, mainly lysosomal luminal and associated proteins were detected, while membrane proteins were found less frequently. Comprehensive coverage of the lysosomal proteome was only achieved by ultra-deep-coverage studies, but targeted approaches allowed for the reproducible quantification of lysosomal proteins in diverse sample types. EXPERT OPINION The low abundance of lysosomal proteins complicates their reproducible analysis in patient samples. Whole proteome shotgun analyses fail in many instances to cover the lysosomal proteome, which is due to under-sampling and/or a lack of sensitivity. With the current state of the art, targeted proteomics assays provide the best performance for the characterization of lysosomal proteins in patient samples.
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Affiliation(s)
- Dhriti Arora
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Yannic Hackenberg
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Jiaran Li
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Dominic Winter
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Bonn, Germany
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Obi EN, Tellock DA, Thomas GJ, Veenstra TD. Biomarker Analysis of Formalin-Fixed Paraffin-Embedded Clinical Tissues Using Proteomics. Biomolecules 2023; 13:biom13010096. [PMID: 36671481 PMCID: PMC9855471 DOI: 10.3390/biom13010096] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 01/06/2023] Open
Abstract
The relatively recent developments in mass spectrometry (MS) have provided novel opportunities for this technology to impact modern medicine. One of those opportunities is in biomarker discovery and diagnostics. Key developments in sample preparation have enabled a greater range of clinical samples to be characterized at a deeper level using MS. While most of these developments have focused on blood, tissues have also been an important resource. Fresh tissues, however, are difficult to obtain for research purposes and require significant resources for long-term storage. There are millions of archived formalin-fixed paraffin-embedded (FFPE) tissues within pathology departments worldwide representing every possible tissue type including tumors that are rare or very small. Owing to the chemical technique used to preserve FFPE tissues, they were considered intractable to many newer proteomics techniques and primarily only useful for immunohistochemistry. In the past couple of decades, however, researchers have been able to develop methods to extract proteins from FFPE tissues in a form making them analyzable using state-of-the-art technologies such as MS and protein arrays. This review will discuss the history of these developments and provide examples of how they are currently being used to identify biomarkers and diagnose diseases such as cancer.
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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.
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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.
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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.
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Capturing the third dimension in drug discovery: Spatially-resolved tools for interrogation of complex 3D cell models. Biotechnol Adv 2021; 55:107883. [PMID: 34875362 DOI: 10.1016/j.biotechadv.2021.107883] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 11/22/2021] [Accepted: 11/30/2021] [Indexed: 02/07/2023]
Abstract
Advanced three-dimensional (3D) cell models have proven to be capable of depicting architectural and microenvironmental features of several tissues. By providing data of higher physiological and pathophysiological relevance, 3D cell models have been contributing to a better understanding of human development, pathology onset and progression mechanisms, as well as for 3D cell-based assays for drug discovery. Nonetheless, the characterization and interrogation of these tissue-like structures pose major challenges on the conventional analytical methods, pushing the development of spatially-resolved technologies. Herein, we review recent advances and pioneering technologies suitable for the interrogation of multicellular 3D models, while capable of retaining biological spatial information. We focused on imaging technologies and omics tools, namely transcriptomics, proteomics and metabolomics. The advantages and shortcomings of these novel methodologies are discussed, alongside the opportunities to intertwine data from the different tools.
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11
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Stavenhagen K, Laan LC, Gao C, Mehta AY, Heimburg-Molinaro J, Glickman JN, van Die I, Cummings RD. Tumor cells express pauci- and oligomannosidic N-glycans in glycoproteins recognized by the mannose receptor (CD206). Cell Mol Life Sci 2021; 78:5569-5585. [PMID: 34089345 PMCID: PMC11072813 DOI: 10.1007/s00018-021-03863-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 05/07/2021] [Accepted: 05/22/2021] [Indexed: 01/21/2023]
Abstract
The macrophage mannose receptor (CD206, MR) is an endocytic lectin receptor which plays an important role in homeostasis and innate immunity, however, the endogenous glycan and glycoprotein ligands recognized by its C-type lectin domains (CTLD) have not been well studied. Here we used the murine MR CTLD4-7 coupled to the Fc-portion of human IgG (MR-Fc) to investigate the MR glycan and glycoprotein recognition. We probed 16 different cancer and control tissues using the MR-Fc, and observed cell- and tissue-specific binding with varying intensity. All cancer tissues and several control tissues exhibited MR-Fc ligands, intracellular and/or surface-located. We further confirmed the presence of ligands on the surface of cancer cells by flow cytometry. To characterize the fine specificity of the MR for glycans, we screened a panel of glycan microarrays. Remarkably, the results indicate that the CTLD4-7 of the MR is highly selective for specific types of pauci- and oligomannose N-glycans among hundreds of glycans tested. As lung cancer tissue and the lung cancer cell line A549 showed intense MR-Fc binding, we further investigated the MR glycoprotein ligands in those cells by immunoprecipitation and glycoproteomic analysis. All enriched glycoproteins, of which 42 were identified, contained pauci- or oligomannose N-glycans, confirming the microarray results. Our study demonstrates that the MR CTLD4-7 is highly selective for pauci- and oligomannosidic N-glycans, structures that are often elevated in tumor cells, and suggest a potential role for the MR in tumor biology.
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Affiliation(s)
- Kathrin Stavenhagen
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, CLS 11087 - 3 Blackfan Circle, Boston, MA, 02115, USA
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC (VU Medical Center), Amsterdam, The Netherlands
| | - Lisa C Laan
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC (VU Medical Center), Amsterdam, The Netherlands
| | - Chao Gao
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, CLS 11087 - 3 Blackfan Circle, Boston, MA, 02115, USA
| | - Akul Y Mehta
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, CLS 11087 - 3 Blackfan Circle, Boston, MA, 02115, USA
| | - Jamie Heimburg-Molinaro
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, CLS 11087 - 3 Blackfan Circle, Boston, MA, 02115, USA
| | - Jonathan N Glickman
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Irma van Die
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC (VU Medical Center), Amsterdam, The Netherlands
| | - Richard D Cummings
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, CLS 11087 - 3 Blackfan Circle, Boston, MA, 02115, USA.
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12
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Friedrich C, Schallenberg S, Kirchner M, Ziehm M, Niquet S, Haji M, Beier C, Neudecker J, Klauschen F, Mertins P. Comprehensive micro-scaled proteome and phosphoproteome characterization of archived retrospective cancer repositories. Nat Commun 2021; 12:3576. [PMID: 34117251 PMCID: PMC8196151 DOI: 10.1038/s41467-021-23855-w] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 05/17/2021] [Indexed: 02/07/2023] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues are a valuable resource for retrospective clinical studies. Here, we evaluate the feasibility of (phospho-)proteomics on FFPE lung tissue regarding protein extraction, quantification, pre-analytics, and sample size. After comparing protein extraction protocols, we use the best-performing protocol for the acquisition of deep (phospho-)proteomes from lung squamous cell and adenocarcinoma with >8,000 quantified proteins and >14,000 phosphosites with a tandem mass tag (TMT) approach. With a microscaled approach, we quantify 7,000 phosphosites, enabling the analysis of FFPE biopsies with limited tissue amounts. We also investigate the influence of pre-analytical variables including fixation time and heat-assisted de-crosslinking on protein extraction efficiency and proteome coverage. Our improved workflows provide quantitative information on protein abundance and phosphosite regulation for the most relevant oncogenes, tumor suppressors, and signaling pathways in lung cancer. Finally, we present general guidelines to which methods are best suited for different applications, highlighting TMT methods for comprehensive (phospho-)proteome profiling for focused clinical studies and label-free methods for large cohorts.
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Affiliation(s)
- Corinna Friedrich
- German Cancer Consortium (DKTK), partner site Berlin, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7468.d0000 0001 2248 7639Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany ,grid.419491.00000 0001 1014 0849Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), MDC graduate school, Berlin, Germany ,grid.7468.d0000 0001 2248 7639Humboldt Universität zu Berlin, Institute of Chemistry, Berlin, Germany
| | - Simon Schallenberg
- grid.7468.d0000 0001 2248 7639Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Marieluise Kirchner
- grid.419491.00000 0001 1014 0849Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Proteomics Platform, Berlin, Germany ,grid.484013.aBerlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Matthias Ziehm
- grid.419491.00000 0001 1014 0849Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Proteomics Platform, Berlin, Germany ,grid.484013.aBerlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Sylvia Niquet
- grid.419491.00000 0001 1014 0849Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Proteomics Platform, Berlin, Germany ,grid.484013.aBerlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Mohamed Haji
- grid.419491.00000 0001 1014 0849Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Proteomics Platform, Berlin, Germany
| | - Christin Beier
- grid.419491.00000 0001 1014 0849Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Proteomics Platform, Berlin, Germany
| | - Jens Neudecker
- grid.6363.00000 0001 2218 4662Department of Surgery - Campus Charité Mitte and Campus Virchow-Klinikum, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Frederick Klauschen
- German Cancer Consortium (DKTK), partner site Berlin, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7468.d0000 0001 2248 7639Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany ,grid.484013.aBerlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany ,grid.5252.00000 0004 1936 973XInstitute of Pathology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Philipp Mertins
- German Cancer Consortium (DKTK), partner site Berlin, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.419491.00000 0001 1014 0849Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Proteomics Platform, Berlin, Germany ,grid.484013.aBerlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
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13
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Matos B, Publicover SJ, Castro LFC, Esteves PJ, Fardilha M. Brain and testis: more alike than previously thought? Open Biol 2021; 11:200322. [PMID: 34062096 PMCID: PMC8169208 DOI: 10.1098/rsob.200322] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Several strands of evidence indicate the presence of marked similarities between human brain and testis. Understanding these similarities and their implications has become a topic of interest among the scientific community. Indeed, an association of intelligence with some semen quality parameters has been reported and a relation between dysfunctions of the human brain and testis has also been evident. Numerous common molecular features are evident when these tissues are compared, which is reflected in the huge number of common proteins. At the functional level, human neurons and sperm share a number of characteristics, including the importance of the exocytotic process and the presence of similar receptors and signalling pathways. The common proteins are mainly involved in exocytosis, tissue development and neuron/brain-associated biological processes. With this analysis, we conclude that human brain and testis share several biochemical characteristics which, in addition to their involvement in the speciation process, could, at least in part, be responsible for the expression of a huge number of common proteins. Nonetheless, this is an underexplored topic, and the connection between these tissues needs to be clarified, which could help to understand the dysfunctions affecting brain and testis, as well as to develop improved therapeutic strategies.
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Affiliation(s)
- Bárbara Matos
- Laboratory of Signal Transduction, Department of Medical Sciences, Institute of Biomedicine-iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Stephen J Publicover
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Luis Filipe C Castro
- CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal.,Department of Biology, FCUP-Faculty of Sciences, University of Porto, Porto, Portugal
| | - Pedro J Esteves
- Department of Biology, FCUP-Faculty of Sciences, University of Porto, Porto, Portugal.,CIBIO-InBIO, Research Centre in Biodiversity and Genetic Resources, Campus Agrico de Vairão, University of Porto, 4485-661 Vairão, Portugal
| | - Margarida Fardilha
- Laboratory of Signal Transduction, Department of Medical Sciences, Institute of Biomedicine-iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
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14
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Leitner DF, Mills JD, Pires G, Faustin A, Drummond E, Kanshin E, Nayak S, Askenazi M, Verducci C, Chen BJ, Janitz M, Anink JJ, Baayen JC, Idema S, van Vliet EA, Devore S, Friedman D, Diehl B, Scott C, Thijs R, Wisniewski T, Ueberheide B, Thom M, Aronica E, Devinsky O. Proteomics and Transcriptomics of the Hippocampus and Cortex in SUDEP and High-Risk SUDEP Patients. Neurology 2021; 96:e2639-e2652. [PMID: 33910938 PMCID: PMC8205452 DOI: 10.1212/wnl.0000000000011999] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 02/26/2021] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVE To identify the molecular signaling pathways underlying sudden unexpected death in epilepsy (SUDEP) and high-risk SUDEP compared to control patients with epilepsy. METHODS For proteomics analyses, we evaluated the hippocampus and frontal cortex from microdissected postmortem brain tissue of 12 patients with SUDEP and 14 with non-SUDEP epilepsy. For transcriptomics analyses, we evaluated hippocampus and temporal cortex surgical brain tissue from patients with mesial temporal lobe epilepsy: 6 low-risk and 8 high-risk SUDEP as determined by a short (<50 seconds) or prolonged (≥50 seconds) postictal generalized EEG suppression (PGES) that may indicate severely depressed brain activity impairing respiration, arousal, and protective reflexes. RESULTS In autopsy hippocampus and cortex, we observed no proteomic differences between patients with SUDEP and those with non-SUDEP epilepsy, contrasting with our previously reported robust differences between epilepsy and controls without epilepsy. Transcriptomics in hippocampus and cortex from patients with surgical epilepsy segregated by PGES identified 55 differentially expressed genes (37 protein-coding, 15 long noncoding RNAs, 3 pending) in hippocampus. CONCLUSION The SUDEP proteome and high-risk SUDEP transcriptome were similar to those in other patients with epilepsy in hippocampus and cortex, consistent with diverse epilepsy syndromes and comorbid conditions associated with SUDEP. Studies with larger cohorts and different epilepsy syndromes, as well as additional anatomic regions, may identify molecular mechanisms of SUDEP.
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Affiliation(s)
- Dominique F Leitner
- From the Comprehensive Epilepsy Center (D.F.L., C.V., S.D., D.F., O.D.), Proteomics Laboratory (E.K., S.N., B.U.), Division of Advanced Research Technologies, and Department of Biochemistry and Molecular Pharmacology (B.U.), NYU School of Medicine; Department of Neurology (D.F.L., G.P., A.F., E.D., S.D., D.F., T.W., B.U., O.D.), Center for Cognitive Neurology (G.P., A.F., E.D., T.W.), Department of Pathology (T.W.), and Department of Psychiatry (T.W.), NYU Langone Health and School of Medicine, New York; Department of (Neuro)Pathology (J.D.M., J.J.A., E.A.v.V., E.A.), Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, the Netherlands; Alzheimer's and Prion Diseases Team (G.P.), Paris Brain Institute, CNRS, UMR 7225, INSERM 1127, Sorbonne University UM75, Paris, France; Brain & Mind Centre and School of Medical Sciences (E.D.), Faculty of Medicine and Health, University of Sydney, Australia; Biomedical Hosting LLC (M.A.), Arlington, MA; School of Biotechnology and Biomolecular Sciences (B.J.C., M.J.), University of New South Wales, Sydney, Australia; Amsterdam UMC (J.C.B., S.I.), Vrije Universiteit Amsterdam, Department of Neurosurgery, Amsterdam Neuroscience, De Boelelaan 1117; Swammerdam Institute for Life Sciences (E.A.v.V.), Center for Neuroscience, University of Amsterdam, the Netherlands; Department of Clinical and Experimental Epilepsy (B.D., C.S., M.T.), University College London Institute of Neurology, UK; and Stichting Epilepsie Instellingen Nederland (R.T., E.A.), Heemstede, the Netherlands
| | - James D Mills
- From the Comprehensive Epilepsy Center (D.F.L., C.V., S.D., D.F., O.D.), Proteomics Laboratory (E.K., S.N., B.U.), Division of Advanced Research Technologies, and Department of Biochemistry and Molecular Pharmacology (B.U.), NYU School of Medicine; Department of Neurology (D.F.L., G.P., A.F., E.D., S.D., D.F., T.W., B.U., O.D.), Center for Cognitive Neurology (G.P., A.F., E.D., T.W.), Department of Pathology (T.W.), and Department of Psychiatry (T.W.), NYU Langone Health and School of Medicine, New York; Department of (Neuro)Pathology (J.D.M., J.J.A., E.A.v.V., E.A.), Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, the Netherlands; Alzheimer's and Prion Diseases Team (G.P.), Paris Brain Institute, CNRS, UMR 7225, INSERM 1127, Sorbonne University UM75, Paris, France; Brain & Mind Centre and School of Medical Sciences (E.D.), Faculty of Medicine and Health, University of Sydney, Australia; Biomedical Hosting LLC (M.A.), Arlington, MA; School of Biotechnology and Biomolecular Sciences (B.J.C., M.J.), University of New South Wales, Sydney, Australia; Amsterdam UMC (J.C.B., S.I.), Vrije Universiteit Amsterdam, Department of Neurosurgery, Amsterdam Neuroscience, De Boelelaan 1117; Swammerdam Institute for Life Sciences (E.A.v.V.), Center for Neuroscience, University of Amsterdam, the Netherlands; Department of Clinical and Experimental Epilepsy (B.D., C.S., M.T.), University College London Institute of Neurology, UK; and Stichting Epilepsie Instellingen Nederland (R.T., E.A.), Heemstede, the Netherlands
| | - Geoffrey Pires
- From the Comprehensive Epilepsy Center (D.F.L., C.V., S.D., D.F., O.D.), Proteomics Laboratory (E.K., S.N., B.U.), Division of Advanced Research Technologies, and Department of Biochemistry and Molecular Pharmacology (B.U.), NYU School of Medicine; Department of Neurology (D.F.L., G.P., A.F., E.D., S.D., D.F., T.W., B.U., O.D.), Center for Cognitive Neurology (G.P., A.F., E.D., T.W.), Department of Pathology (T.W.), and Department of Psychiatry (T.W.), NYU Langone Health and School of Medicine, New York; Department of (Neuro)Pathology (J.D.M., J.J.A., E.A.v.V., E.A.), Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, the Netherlands; Alzheimer's and Prion Diseases Team (G.P.), Paris Brain Institute, CNRS, UMR 7225, INSERM 1127, Sorbonne University UM75, Paris, France; Brain & Mind Centre and School of Medical Sciences (E.D.), Faculty of Medicine and Health, University of Sydney, Australia; Biomedical Hosting LLC (M.A.), Arlington, MA; School of Biotechnology and Biomolecular Sciences (B.J.C., M.J.), University of New South Wales, Sydney, Australia; Amsterdam UMC (J.C.B., S.I.), Vrije Universiteit Amsterdam, Department of Neurosurgery, Amsterdam Neuroscience, De Boelelaan 1117; Swammerdam Institute for Life Sciences (E.A.v.V.), Center for Neuroscience, University of Amsterdam, the Netherlands; Department of Clinical and Experimental Epilepsy (B.D., C.S., M.T.), University College London Institute of Neurology, UK; and Stichting Epilepsie Instellingen Nederland (R.T., E.A.), Heemstede, the Netherlands
| | - Arline Faustin
- From the Comprehensive Epilepsy Center (D.F.L., C.V., S.D., D.F., O.D.), Proteomics Laboratory (E.K., S.N., B.U.), Division of Advanced Research Technologies, and Department of Biochemistry and Molecular Pharmacology (B.U.), NYU School of Medicine; Department of Neurology (D.F.L., G.P., A.F., E.D., S.D., D.F., T.W., B.U., O.D.), Center for Cognitive Neurology (G.P., A.F., E.D., T.W.), Department of Pathology (T.W.), and Department of Psychiatry (T.W.), NYU Langone Health and School of Medicine, New York; Department of (Neuro)Pathology (J.D.M., J.J.A., E.A.v.V., E.A.), Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, the Netherlands; Alzheimer's and Prion Diseases Team (G.P.), Paris Brain Institute, CNRS, UMR 7225, INSERM 1127, Sorbonne University UM75, Paris, France; Brain & Mind Centre and School of Medical Sciences (E.D.), Faculty of Medicine and Health, University of Sydney, Australia; Biomedical Hosting LLC (M.A.), Arlington, MA; School of Biotechnology and Biomolecular Sciences (B.J.C., M.J.), University of New South Wales, Sydney, Australia; Amsterdam UMC (J.C.B., S.I.), Vrije Universiteit Amsterdam, Department of Neurosurgery, Amsterdam Neuroscience, De Boelelaan 1117; Swammerdam Institute for Life Sciences (E.A.v.V.), Center for Neuroscience, University of Amsterdam, the Netherlands; Department of Clinical and Experimental Epilepsy (B.D., C.S., M.T.), University College London Institute of Neurology, UK; and Stichting Epilepsie Instellingen Nederland (R.T., E.A.), Heemstede, the Netherlands
| | - Eleanor Drummond
- From the Comprehensive Epilepsy Center (D.F.L., C.V., S.D., D.F., O.D.), Proteomics Laboratory (E.K., S.N., B.U.), Division of Advanced Research Technologies, and Department of Biochemistry and Molecular Pharmacology (B.U.), NYU School of Medicine; Department of Neurology (D.F.L., G.P., A.F., E.D., S.D., D.F., T.W., B.U., O.D.), Center for Cognitive Neurology (G.P., A.F., E.D., T.W.), Department of Pathology (T.W.), and Department of Psychiatry (T.W.), NYU Langone Health and School of Medicine, New York; Department of (Neuro)Pathology (J.D.M., J.J.A., E.A.v.V., E.A.), Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, the Netherlands; Alzheimer's and Prion Diseases Team (G.P.), Paris Brain Institute, CNRS, UMR 7225, INSERM 1127, Sorbonne University UM75, Paris, France; Brain & Mind Centre and School of Medical Sciences (E.D.), Faculty of Medicine and Health, University of Sydney, Australia; Biomedical Hosting LLC (M.A.), Arlington, MA; School of Biotechnology and Biomolecular Sciences (B.J.C., M.J.), University of New South Wales, Sydney, Australia; Amsterdam UMC (J.C.B., S.I.), Vrije Universiteit Amsterdam, Department of Neurosurgery, Amsterdam Neuroscience, De Boelelaan 1117; Swammerdam Institute for Life Sciences (E.A.v.V.), Center for Neuroscience, University of Amsterdam, the Netherlands; Department of Clinical and Experimental Epilepsy (B.D., C.S., M.T.), University College London Institute of Neurology, UK; and Stichting Epilepsie Instellingen Nederland (R.T., E.A.), Heemstede, the Netherlands
| | - Evgeny Kanshin
- From the Comprehensive Epilepsy Center (D.F.L., C.V., S.D., D.F., O.D.), Proteomics Laboratory (E.K., S.N., B.U.), Division of Advanced Research Technologies, and Department of Biochemistry and Molecular Pharmacology (B.U.), NYU School of Medicine; Department of Neurology (D.F.L., G.P., A.F., E.D., S.D., D.F., T.W., B.U., O.D.), Center for Cognitive Neurology (G.P., A.F., E.D., T.W.), Department of Pathology (T.W.), and Department of Psychiatry (T.W.), NYU Langone Health and School of Medicine, New York; Department of (Neuro)Pathology (J.D.M., J.J.A., E.A.v.V., E.A.), Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, the Netherlands; Alzheimer's and Prion Diseases Team (G.P.), Paris Brain Institute, CNRS, UMR 7225, INSERM 1127, Sorbonne University UM75, Paris, France; Brain & Mind Centre and School of Medical Sciences (E.D.), Faculty of Medicine and Health, University of Sydney, Australia; Biomedical Hosting LLC (M.A.), Arlington, MA; School of Biotechnology and Biomolecular Sciences (B.J.C., M.J.), University of New South Wales, Sydney, Australia; Amsterdam UMC (J.C.B., S.I.), Vrije Universiteit Amsterdam, Department of Neurosurgery, Amsterdam Neuroscience, De Boelelaan 1117; Swammerdam Institute for Life Sciences (E.A.v.V.), Center for Neuroscience, University of Amsterdam, the Netherlands; Department of Clinical and Experimental Epilepsy (B.D., C.S., M.T.), University College London Institute of Neurology, UK; and Stichting Epilepsie Instellingen Nederland (R.T., E.A.), Heemstede, the Netherlands
| | - Shruti Nayak
- From the Comprehensive Epilepsy Center (D.F.L., C.V., S.D., D.F., O.D.), Proteomics Laboratory (E.K., S.N., B.U.), Division of Advanced Research Technologies, and Department of Biochemistry and Molecular Pharmacology (B.U.), NYU School of Medicine; Department of Neurology (D.F.L., G.P., A.F., E.D., S.D., D.F., T.W., B.U., O.D.), Center for Cognitive Neurology (G.P., A.F., E.D., T.W.), Department of Pathology (T.W.), and Department of Psychiatry (T.W.), NYU Langone Health and School of Medicine, New York; Department of (Neuro)Pathology (J.D.M., J.J.A., E.A.v.V., E.A.), Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, the Netherlands; Alzheimer's and Prion Diseases Team (G.P.), Paris Brain Institute, CNRS, UMR 7225, INSERM 1127, Sorbonne University UM75, Paris, France; Brain & Mind Centre and School of Medical Sciences (E.D.), Faculty of Medicine and Health, University of Sydney, Australia; Biomedical Hosting LLC (M.A.), Arlington, MA; School of Biotechnology and Biomolecular Sciences (B.J.C., M.J.), University of New South Wales, Sydney, Australia; Amsterdam UMC (J.C.B., S.I.), Vrije Universiteit Amsterdam, Department of Neurosurgery, Amsterdam Neuroscience, De Boelelaan 1117; Swammerdam Institute for Life Sciences (E.A.v.V.), Center for Neuroscience, University of Amsterdam, the Netherlands; Department of Clinical and Experimental Epilepsy (B.D., C.S., M.T.), University College London Institute of Neurology, UK; and Stichting Epilepsie Instellingen Nederland (R.T., E.A.), Heemstede, the Netherlands
| | - Manor Askenazi
- From the Comprehensive Epilepsy Center (D.F.L., C.V., S.D., D.F., O.D.), Proteomics Laboratory (E.K., S.N., B.U.), Division of Advanced Research Technologies, and Department of Biochemistry and Molecular Pharmacology (B.U.), NYU School of Medicine; Department of Neurology (D.F.L., G.P., A.F., E.D., S.D., D.F., T.W., B.U., O.D.), Center for Cognitive Neurology (G.P., A.F., E.D., T.W.), Department of Pathology (T.W.), and Department of Psychiatry (T.W.), NYU Langone Health and School of Medicine, New York; Department of (Neuro)Pathology (J.D.M., J.J.A., E.A.v.V., E.A.), Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, the Netherlands; Alzheimer's and Prion Diseases Team (G.P.), Paris Brain Institute, CNRS, UMR 7225, INSERM 1127, Sorbonne University UM75, Paris, France; Brain & Mind Centre and School of Medical Sciences (E.D.), Faculty of Medicine and Health, University of Sydney, Australia; Biomedical Hosting LLC (M.A.), Arlington, MA; School of Biotechnology and Biomolecular Sciences (B.J.C., M.J.), University of New South Wales, Sydney, Australia; Amsterdam UMC (J.C.B., S.I.), Vrije Universiteit Amsterdam, Department of Neurosurgery, Amsterdam Neuroscience, De Boelelaan 1117; Swammerdam Institute for Life Sciences (E.A.v.V.), Center for Neuroscience, University of Amsterdam, the Netherlands; Department of Clinical and Experimental Epilepsy (B.D., C.S., M.T.), University College London Institute of Neurology, UK; and Stichting Epilepsie Instellingen Nederland (R.T., E.A.), Heemstede, the Netherlands
| | - Chloe Verducci
- From the Comprehensive Epilepsy Center (D.F.L., C.V., S.D., D.F., O.D.), Proteomics Laboratory (E.K., S.N., B.U.), Division of Advanced Research Technologies, and Department of Biochemistry and Molecular Pharmacology (B.U.), NYU School of Medicine; Department of Neurology (D.F.L., G.P., A.F., E.D., S.D., D.F., T.W., B.U., O.D.), Center for Cognitive Neurology (G.P., A.F., E.D., T.W.), Department of Pathology (T.W.), and Department of Psychiatry (T.W.), NYU Langone Health and School of Medicine, New York; Department of (Neuro)Pathology (J.D.M., J.J.A., E.A.v.V., E.A.), Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, the Netherlands; Alzheimer's and Prion Diseases Team (G.P.), Paris Brain Institute, CNRS, UMR 7225, INSERM 1127, Sorbonne University UM75, Paris, France; Brain & Mind Centre and School of Medical Sciences (E.D.), Faculty of Medicine and Health, University of Sydney, Australia; Biomedical Hosting LLC (M.A.), Arlington, MA; School of Biotechnology and Biomolecular Sciences (B.J.C., M.J.), University of New South Wales, Sydney, Australia; Amsterdam UMC (J.C.B., S.I.), Vrije Universiteit Amsterdam, Department of Neurosurgery, Amsterdam Neuroscience, De Boelelaan 1117; Swammerdam Institute for Life Sciences (E.A.v.V.), Center for Neuroscience, University of Amsterdam, the Netherlands; Department of Clinical and Experimental Epilepsy (B.D., C.S., M.T.), University College London Institute of Neurology, UK; and Stichting Epilepsie Instellingen Nederland (R.T., E.A.), Heemstede, the Netherlands
| | - Bei Jun Chen
- From the Comprehensive Epilepsy Center (D.F.L., C.V., S.D., D.F., O.D.), Proteomics Laboratory (E.K., S.N., B.U.), Division of Advanced Research Technologies, and Department of Biochemistry and Molecular Pharmacology (B.U.), NYU School of Medicine; Department of Neurology (D.F.L., G.P., A.F., E.D., S.D., D.F., T.W., B.U., O.D.), Center for Cognitive Neurology (G.P., A.F., E.D., T.W.), Department of Pathology (T.W.), and Department of Psychiatry (T.W.), NYU Langone Health and School of Medicine, New York; Department of (Neuro)Pathology (J.D.M., J.J.A., E.A.v.V., E.A.), Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, the Netherlands; Alzheimer's and Prion Diseases Team (G.P.), Paris Brain Institute, CNRS, UMR 7225, INSERM 1127, Sorbonne University UM75, Paris, France; Brain & Mind Centre and School of Medical Sciences (E.D.), Faculty of Medicine and Health, University of Sydney, Australia; Biomedical Hosting LLC (M.A.), Arlington, MA; School of Biotechnology and Biomolecular Sciences (B.J.C., M.J.), University of New South Wales, Sydney, Australia; Amsterdam UMC (J.C.B., S.I.), Vrije Universiteit Amsterdam, Department of Neurosurgery, Amsterdam Neuroscience, De Boelelaan 1117; Swammerdam Institute for Life Sciences (E.A.v.V.), Center for Neuroscience, University of Amsterdam, the Netherlands; Department of Clinical and Experimental Epilepsy (B.D., C.S., M.T.), University College London Institute of Neurology, UK; and Stichting Epilepsie Instellingen Nederland (R.T., E.A.), Heemstede, the Netherlands
| | - Michael Janitz
- From the Comprehensive Epilepsy Center (D.F.L., C.V., S.D., D.F., O.D.), Proteomics Laboratory (E.K., S.N., B.U.), Division of Advanced Research Technologies, and Department of Biochemistry and Molecular Pharmacology (B.U.), NYU School of Medicine; Department of Neurology (D.F.L., G.P., A.F., E.D., S.D., D.F., T.W., B.U., O.D.), Center for Cognitive Neurology (G.P., A.F., E.D., T.W.), Department of Pathology (T.W.), and Department of Psychiatry (T.W.), NYU Langone Health and School of Medicine, New York; Department of (Neuro)Pathology (J.D.M., J.J.A., E.A.v.V., E.A.), Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, the Netherlands; Alzheimer's and Prion Diseases Team (G.P.), Paris Brain Institute, CNRS, UMR 7225, INSERM 1127, Sorbonne University UM75, Paris, France; Brain & Mind Centre and School of Medical Sciences (E.D.), Faculty of Medicine and Health, University of Sydney, Australia; Biomedical Hosting LLC (M.A.), Arlington, MA; School of Biotechnology and Biomolecular Sciences (B.J.C., M.J.), University of New South Wales, Sydney, Australia; Amsterdam UMC (J.C.B., S.I.), Vrije Universiteit Amsterdam, Department of Neurosurgery, Amsterdam Neuroscience, De Boelelaan 1117; Swammerdam Institute for Life Sciences (E.A.v.V.), Center for Neuroscience, University of Amsterdam, the Netherlands; Department of Clinical and Experimental Epilepsy (B.D., C.S., M.T.), University College London Institute of Neurology, UK; and Stichting Epilepsie Instellingen Nederland (R.T., E.A.), Heemstede, the Netherlands
| | - Jasper J Anink
- From the Comprehensive Epilepsy Center (D.F.L., C.V., S.D., D.F., O.D.), Proteomics Laboratory (E.K., S.N., B.U.), Division of Advanced Research Technologies, and Department of Biochemistry and Molecular Pharmacology (B.U.), NYU School of Medicine; Department of Neurology (D.F.L., G.P., A.F., E.D., S.D., D.F., T.W., B.U., O.D.), Center for Cognitive Neurology (G.P., A.F., E.D., T.W.), Department of Pathology (T.W.), and Department of Psychiatry (T.W.), NYU Langone Health and School of Medicine, New York; Department of (Neuro)Pathology (J.D.M., J.J.A., E.A.v.V., E.A.), Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, the Netherlands; Alzheimer's and Prion Diseases Team (G.P.), Paris Brain Institute, CNRS, UMR 7225, INSERM 1127, Sorbonne University UM75, Paris, France; Brain & Mind Centre and School of Medical Sciences (E.D.), Faculty of Medicine and Health, University of Sydney, Australia; Biomedical Hosting LLC (M.A.), Arlington, MA; School of Biotechnology and Biomolecular Sciences (B.J.C., M.J.), University of New South Wales, Sydney, Australia; Amsterdam UMC (J.C.B., S.I.), Vrije Universiteit Amsterdam, Department of Neurosurgery, Amsterdam Neuroscience, De Boelelaan 1117; Swammerdam Institute for Life Sciences (E.A.v.V.), Center for Neuroscience, University of Amsterdam, the Netherlands; Department of Clinical and Experimental Epilepsy (B.D., C.S., M.T.), University College London Institute of Neurology, UK; and Stichting Epilepsie Instellingen Nederland (R.T., E.A.), Heemstede, the Netherlands
| | - Johannes C Baayen
- From the Comprehensive Epilepsy Center (D.F.L., C.V., S.D., D.F., O.D.), Proteomics Laboratory (E.K., S.N., B.U.), Division of Advanced Research Technologies, and Department of Biochemistry and Molecular Pharmacology (B.U.), NYU School of Medicine; Department of Neurology (D.F.L., G.P., A.F., E.D., S.D., D.F., T.W., B.U., O.D.), Center for Cognitive Neurology (G.P., A.F., E.D., T.W.), Department of Pathology (T.W.), and Department of Psychiatry (T.W.), NYU Langone Health and School of Medicine, New York; Department of (Neuro)Pathology (J.D.M., J.J.A., E.A.v.V., E.A.), Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, the Netherlands; Alzheimer's and Prion Diseases Team (G.P.), Paris Brain Institute, CNRS, UMR 7225, INSERM 1127, Sorbonne University UM75, Paris, France; Brain & Mind Centre and School of Medical Sciences (E.D.), Faculty of Medicine and Health, University of Sydney, Australia; Biomedical Hosting LLC (M.A.), Arlington, MA; School of Biotechnology and Biomolecular Sciences (B.J.C., M.J.), University of New South Wales, Sydney, Australia; Amsterdam UMC (J.C.B., S.I.), Vrije Universiteit Amsterdam, Department of Neurosurgery, Amsterdam Neuroscience, De Boelelaan 1117; Swammerdam Institute for Life Sciences (E.A.v.V.), Center for Neuroscience, University of Amsterdam, the Netherlands; Department of Clinical and Experimental Epilepsy (B.D., C.S., M.T.), University College London Institute of Neurology, UK; and Stichting Epilepsie Instellingen Nederland (R.T., E.A.), Heemstede, the Netherlands
| | - Sander Idema
- From the Comprehensive Epilepsy Center (D.F.L., C.V., S.D., D.F., O.D.), Proteomics Laboratory (E.K., S.N., B.U.), Division of Advanced Research Technologies, and Department of Biochemistry and Molecular Pharmacology (B.U.), NYU School of Medicine; Department of Neurology (D.F.L., G.P., A.F., E.D., S.D., D.F., T.W., B.U., O.D.), Center for Cognitive Neurology (G.P., A.F., E.D., T.W.), Department of Pathology (T.W.), and Department of Psychiatry (T.W.), NYU Langone Health and School of Medicine, New York; Department of (Neuro)Pathology (J.D.M., J.J.A., E.A.v.V., E.A.), Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, the Netherlands; Alzheimer's and Prion Diseases Team (G.P.), Paris Brain Institute, CNRS, UMR 7225, INSERM 1127, Sorbonne University UM75, Paris, France; Brain & Mind Centre and School of Medical Sciences (E.D.), Faculty of Medicine and Health, University of Sydney, Australia; Biomedical Hosting LLC (M.A.), Arlington, MA; School of Biotechnology and Biomolecular Sciences (B.J.C., M.J.), University of New South Wales, Sydney, Australia; Amsterdam UMC (J.C.B., S.I.), Vrije Universiteit Amsterdam, Department of Neurosurgery, Amsterdam Neuroscience, De Boelelaan 1117; Swammerdam Institute for Life Sciences (E.A.v.V.), Center for Neuroscience, University of Amsterdam, the Netherlands; Department of Clinical and Experimental Epilepsy (B.D., C.S., M.T.), University College London Institute of Neurology, UK; and Stichting Epilepsie Instellingen Nederland (R.T., E.A.), Heemstede, the Netherlands
| | - Erwin A van Vliet
- From the Comprehensive Epilepsy Center (D.F.L., C.V., S.D., D.F., O.D.), Proteomics Laboratory (E.K., S.N., B.U.), Division of Advanced Research Technologies, and Department of Biochemistry and Molecular Pharmacology (B.U.), NYU School of Medicine; Department of Neurology (D.F.L., G.P., A.F., E.D., S.D., D.F., T.W., B.U., O.D.), Center for Cognitive Neurology (G.P., A.F., E.D., T.W.), Department of Pathology (T.W.), and Department of Psychiatry (T.W.), NYU Langone Health and School of Medicine, New York; Department of (Neuro)Pathology (J.D.M., J.J.A., E.A.v.V., E.A.), Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, the Netherlands; Alzheimer's and Prion Diseases Team (G.P.), Paris Brain Institute, CNRS, UMR 7225, INSERM 1127, Sorbonne University UM75, Paris, France; Brain & Mind Centre and School of Medical Sciences (E.D.), Faculty of Medicine and Health, University of Sydney, Australia; Biomedical Hosting LLC (M.A.), Arlington, MA; School of Biotechnology and Biomolecular Sciences (B.J.C., M.J.), University of New South Wales, Sydney, Australia; Amsterdam UMC (J.C.B., S.I.), Vrije Universiteit Amsterdam, Department of Neurosurgery, Amsterdam Neuroscience, De Boelelaan 1117; Swammerdam Institute for Life Sciences (E.A.v.V.), Center for Neuroscience, University of Amsterdam, the Netherlands; Department of Clinical and Experimental Epilepsy (B.D., C.S., M.T.), University College London Institute of Neurology, UK; and Stichting Epilepsie Instellingen Nederland (R.T., E.A.), Heemstede, the Netherlands
| | - Sasha Devore
- From the Comprehensive Epilepsy Center (D.F.L., C.V., S.D., D.F., O.D.), Proteomics Laboratory (E.K., S.N., B.U.), Division of Advanced Research Technologies, and Department of Biochemistry and Molecular Pharmacology (B.U.), NYU School of Medicine; Department of Neurology (D.F.L., G.P., A.F., E.D., S.D., D.F., T.W., B.U., O.D.), Center for Cognitive Neurology (G.P., A.F., E.D., T.W.), Department of Pathology (T.W.), and Department of Psychiatry (T.W.), NYU Langone Health and School of Medicine, New York; Department of (Neuro)Pathology (J.D.M., J.J.A., E.A.v.V., E.A.), Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, the Netherlands; Alzheimer's and Prion Diseases Team (G.P.), Paris Brain Institute, CNRS, UMR 7225, INSERM 1127, Sorbonne University UM75, Paris, France; Brain & Mind Centre and School of Medical Sciences (E.D.), Faculty of Medicine and Health, University of Sydney, Australia; Biomedical Hosting LLC (M.A.), Arlington, MA; School of Biotechnology and Biomolecular Sciences (B.J.C., M.J.), University of New South Wales, Sydney, Australia; Amsterdam UMC (J.C.B., S.I.), Vrije Universiteit Amsterdam, Department of Neurosurgery, Amsterdam Neuroscience, De Boelelaan 1117; Swammerdam Institute for Life Sciences (E.A.v.V.), Center for Neuroscience, University of Amsterdam, the Netherlands; Department of Clinical and Experimental Epilepsy (B.D., C.S., M.T.), University College London Institute of Neurology, UK; and Stichting Epilepsie Instellingen Nederland (R.T., E.A.), Heemstede, the Netherlands
| | - Daniel Friedman
- From the Comprehensive Epilepsy Center (D.F.L., C.V., S.D., D.F., O.D.), Proteomics Laboratory (E.K., S.N., B.U.), Division of Advanced Research Technologies, and Department of Biochemistry and Molecular Pharmacology (B.U.), NYU School of Medicine; Department of Neurology (D.F.L., G.P., A.F., E.D., S.D., D.F., T.W., B.U., O.D.), Center for Cognitive Neurology (G.P., A.F., E.D., T.W.), Department of Pathology (T.W.), and Department of Psychiatry (T.W.), NYU Langone Health and School of Medicine, New York; Department of (Neuro)Pathology (J.D.M., J.J.A., E.A.v.V., E.A.), Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, the Netherlands; Alzheimer's and Prion Diseases Team (G.P.), Paris Brain Institute, CNRS, UMR 7225, INSERM 1127, Sorbonne University UM75, Paris, France; Brain & Mind Centre and School of Medical Sciences (E.D.), Faculty of Medicine and Health, University of Sydney, Australia; Biomedical Hosting LLC (M.A.), Arlington, MA; School of Biotechnology and Biomolecular Sciences (B.J.C., M.J.), University of New South Wales, Sydney, Australia; Amsterdam UMC (J.C.B., S.I.), Vrije Universiteit Amsterdam, Department of Neurosurgery, Amsterdam Neuroscience, De Boelelaan 1117; Swammerdam Institute for Life Sciences (E.A.v.V.), Center for Neuroscience, University of Amsterdam, the Netherlands; Department of Clinical and Experimental Epilepsy (B.D., C.S., M.T.), University College London Institute of Neurology, UK; and Stichting Epilepsie Instellingen Nederland (R.T., E.A.), Heemstede, the Netherlands
| | - Beate Diehl
- From the Comprehensive Epilepsy Center (D.F.L., C.V., S.D., D.F., O.D.), Proteomics Laboratory (E.K., S.N., B.U.), Division of Advanced Research Technologies, and Department of Biochemistry and Molecular Pharmacology (B.U.), NYU School of Medicine; Department of Neurology (D.F.L., G.P., A.F., E.D., S.D., D.F., T.W., B.U., O.D.), Center for Cognitive Neurology (G.P., A.F., E.D., T.W.), Department of Pathology (T.W.), and Department of Psychiatry (T.W.), NYU Langone Health and School of Medicine, New York; Department of (Neuro)Pathology (J.D.M., J.J.A., E.A.v.V., E.A.), Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, the Netherlands; Alzheimer's and Prion Diseases Team (G.P.), Paris Brain Institute, CNRS, UMR 7225, INSERM 1127, Sorbonne University UM75, Paris, France; Brain & Mind Centre and School of Medical Sciences (E.D.), Faculty of Medicine and Health, University of Sydney, Australia; Biomedical Hosting LLC (M.A.), Arlington, MA; School of Biotechnology and Biomolecular Sciences (B.J.C., M.J.), University of New South Wales, Sydney, Australia; Amsterdam UMC (J.C.B., S.I.), Vrije Universiteit Amsterdam, Department of Neurosurgery, Amsterdam Neuroscience, De Boelelaan 1117; Swammerdam Institute for Life Sciences (E.A.v.V.), Center for Neuroscience, University of Amsterdam, the Netherlands; Department of Clinical and Experimental Epilepsy (B.D., C.S., M.T.), University College London Institute of Neurology, UK; and Stichting Epilepsie Instellingen Nederland (R.T., E.A.), Heemstede, the Netherlands
| | - Catherine Scott
- From the Comprehensive Epilepsy Center (D.F.L., C.V., S.D., D.F., O.D.), Proteomics Laboratory (E.K., S.N., B.U.), Division of Advanced Research Technologies, and Department of Biochemistry and Molecular Pharmacology (B.U.), NYU School of Medicine; Department of Neurology (D.F.L., G.P., A.F., E.D., S.D., D.F., T.W., B.U., O.D.), Center for Cognitive Neurology (G.P., A.F., E.D., T.W.), Department of Pathology (T.W.), and Department of Psychiatry (T.W.), NYU Langone Health and School of Medicine, New York; Department of (Neuro)Pathology (J.D.M., J.J.A., E.A.v.V., E.A.), Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, the Netherlands; Alzheimer's and Prion Diseases Team (G.P.), Paris Brain Institute, CNRS, UMR 7225, INSERM 1127, Sorbonne University UM75, Paris, France; Brain & Mind Centre and School of Medical Sciences (E.D.), Faculty of Medicine and Health, University of Sydney, Australia; Biomedical Hosting LLC (M.A.), Arlington, MA; School of Biotechnology and Biomolecular Sciences (B.J.C., M.J.), University of New South Wales, Sydney, Australia; Amsterdam UMC (J.C.B., S.I.), Vrije Universiteit Amsterdam, Department of Neurosurgery, Amsterdam Neuroscience, De Boelelaan 1117; Swammerdam Institute for Life Sciences (E.A.v.V.), Center for Neuroscience, University of Amsterdam, the Netherlands; Department of Clinical and Experimental Epilepsy (B.D., C.S., M.T.), University College London Institute of Neurology, UK; and Stichting Epilepsie Instellingen Nederland (R.T., E.A.), Heemstede, the Netherlands
| | - Roland Thijs
- From the Comprehensive Epilepsy Center (D.F.L., C.V., S.D., D.F., O.D.), Proteomics Laboratory (E.K., S.N., B.U.), Division of Advanced Research Technologies, and Department of Biochemistry and Molecular Pharmacology (B.U.), NYU School of Medicine; Department of Neurology (D.F.L., G.P., A.F., E.D., S.D., D.F., T.W., B.U., O.D.), Center for Cognitive Neurology (G.P., A.F., E.D., T.W.), Department of Pathology (T.W.), and Department of Psychiatry (T.W.), NYU Langone Health and School of Medicine, New York; Department of (Neuro)Pathology (J.D.M., J.J.A., E.A.v.V., E.A.), Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, the Netherlands; Alzheimer's and Prion Diseases Team (G.P.), Paris Brain Institute, CNRS, UMR 7225, INSERM 1127, Sorbonne University UM75, Paris, France; Brain & Mind Centre and School of Medical Sciences (E.D.), Faculty of Medicine and Health, University of Sydney, Australia; Biomedical Hosting LLC (M.A.), Arlington, MA; School of Biotechnology and Biomolecular Sciences (B.J.C., M.J.), University of New South Wales, Sydney, Australia; Amsterdam UMC (J.C.B., S.I.), Vrije Universiteit Amsterdam, Department of Neurosurgery, Amsterdam Neuroscience, De Boelelaan 1117; Swammerdam Institute for Life Sciences (E.A.v.V.), Center for Neuroscience, University of Amsterdam, the Netherlands; Department of Clinical and Experimental Epilepsy (B.D., C.S., M.T.), University College London Institute of Neurology, UK; and Stichting Epilepsie Instellingen Nederland (R.T., E.A.), Heemstede, the Netherlands
| | - Thomas Wisniewski
- From the Comprehensive Epilepsy Center (D.F.L., C.V., S.D., D.F., O.D.), Proteomics Laboratory (E.K., S.N., B.U.), Division of Advanced Research Technologies, and Department of Biochemistry and Molecular Pharmacology (B.U.), NYU School of Medicine; Department of Neurology (D.F.L., G.P., A.F., E.D., S.D., D.F., T.W., B.U., O.D.), Center for Cognitive Neurology (G.P., A.F., E.D., T.W.), Department of Pathology (T.W.), and Department of Psychiatry (T.W.), NYU Langone Health and School of Medicine, New York; Department of (Neuro)Pathology (J.D.M., J.J.A., E.A.v.V., E.A.), Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, the Netherlands; Alzheimer's and Prion Diseases Team (G.P.), Paris Brain Institute, CNRS, UMR 7225, INSERM 1127, Sorbonne University UM75, Paris, France; Brain & Mind Centre and School of Medical Sciences (E.D.), Faculty of Medicine and Health, University of Sydney, Australia; Biomedical Hosting LLC (M.A.), Arlington, MA; School of Biotechnology and Biomolecular Sciences (B.J.C., M.J.), University of New South Wales, Sydney, Australia; Amsterdam UMC (J.C.B., S.I.), Vrije Universiteit Amsterdam, Department of Neurosurgery, Amsterdam Neuroscience, De Boelelaan 1117; Swammerdam Institute for Life Sciences (E.A.v.V.), Center for Neuroscience, University of Amsterdam, the Netherlands; Department of Clinical and Experimental Epilepsy (B.D., C.S., M.T.), University College London Institute of Neurology, UK; and Stichting Epilepsie Instellingen Nederland (R.T., E.A.), Heemstede, the Netherlands
| | - Beatrix Ueberheide
- From the Comprehensive Epilepsy Center (D.F.L., C.V., S.D., D.F., O.D.), Proteomics Laboratory (E.K., S.N., B.U.), Division of Advanced Research Technologies, and Department of Biochemistry and Molecular Pharmacology (B.U.), NYU School of Medicine; Department of Neurology (D.F.L., G.P., A.F., E.D., S.D., D.F., T.W., B.U., O.D.), Center for Cognitive Neurology (G.P., A.F., E.D., T.W.), Department of Pathology (T.W.), and Department of Psychiatry (T.W.), NYU Langone Health and School of Medicine, New York; Department of (Neuro)Pathology (J.D.M., J.J.A., E.A.v.V., E.A.), Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, the Netherlands; Alzheimer's and Prion Diseases Team (G.P.), Paris Brain Institute, CNRS, UMR 7225, INSERM 1127, Sorbonne University UM75, Paris, France; Brain & Mind Centre and School of Medical Sciences (E.D.), Faculty of Medicine and Health, University of Sydney, Australia; Biomedical Hosting LLC (M.A.), Arlington, MA; School of Biotechnology and Biomolecular Sciences (B.J.C., M.J.), University of New South Wales, Sydney, Australia; Amsterdam UMC (J.C.B., S.I.), Vrije Universiteit Amsterdam, Department of Neurosurgery, Amsterdam Neuroscience, De Boelelaan 1117; Swammerdam Institute for Life Sciences (E.A.v.V.), Center for Neuroscience, University of Amsterdam, the Netherlands; Department of Clinical and Experimental Epilepsy (B.D., C.S., M.T.), University College London Institute of Neurology, UK; and Stichting Epilepsie Instellingen Nederland (R.T., E.A.), Heemstede, the Netherlands
| | - Maria Thom
- From the Comprehensive Epilepsy Center (D.F.L., C.V., S.D., D.F., O.D.), Proteomics Laboratory (E.K., S.N., B.U.), Division of Advanced Research Technologies, and Department of Biochemistry and Molecular Pharmacology (B.U.), NYU School of Medicine; Department of Neurology (D.F.L., G.P., A.F., E.D., S.D., D.F., T.W., B.U., O.D.), Center for Cognitive Neurology (G.P., A.F., E.D., T.W.), Department of Pathology (T.W.), and Department of Psychiatry (T.W.), NYU Langone Health and School of Medicine, New York; Department of (Neuro)Pathology (J.D.M., J.J.A., E.A.v.V., E.A.), Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, the Netherlands; Alzheimer's and Prion Diseases Team (G.P.), Paris Brain Institute, CNRS, UMR 7225, INSERM 1127, Sorbonne University UM75, Paris, France; Brain & Mind Centre and School of Medical Sciences (E.D.), Faculty of Medicine and Health, University of Sydney, Australia; Biomedical Hosting LLC (M.A.), Arlington, MA; School of Biotechnology and Biomolecular Sciences (B.J.C., M.J.), University of New South Wales, Sydney, Australia; Amsterdam UMC (J.C.B., S.I.), Vrije Universiteit Amsterdam, Department of Neurosurgery, Amsterdam Neuroscience, De Boelelaan 1117; Swammerdam Institute for Life Sciences (E.A.v.V.), Center for Neuroscience, University of Amsterdam, the Netherlands; Department of Clinical and Experimental Epilepsy (B.D., C.S., M.T.), University College London Institute of Neurology, UK; and Stichting Epilepsie Instellingen Nederland (R.T., E.A.), Heemstede, the Netherlands
| | - Eleonora Aronica
- From the Comprehensive Epilepsy Center (D.F.L., C.V., S.D., D.F., O.D.), Proteomics Laboratory (E.K., S.N., B.U.), Division of Advanced Research Technologies, and Department of Biochemistry and Molecular Pharmacology (B.U.), NYU School of Medicine; Department of Neurology (D.F.L., G.P., A.F., E.D., S.D., D.F., T.W., B.U., O.D.), Center for Cognitive Neurology (G.P., A.F., E.D., T.W.), Department of Pathology (T.W.), and Department of Psychiatry (T.W.), NYU Langone Health and School of Medicine, New York; Department of (Neuro)Pathology (J.D.M., J.J.A., E.A.v.V., E.A.), Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, the Netherlands; Alzheimer's and Prion Diseases Team (G.P.), Paris Brain Institute, CNRS, UMR 7225, INSERM 1127, Sorbonne University UM75, Paris, France; Brain & Mind Centre and School of Medical Sciences (E.D.), Faculty of Medicine and Health, University of Sydney, Australia; Biomedical Hosting LLC (M.A.), Arlington, MA; School of Biotechnology and Biomolecular Sciences (B.J.C., M.J.), University of New South Wales, Sydney, Australia; Amsterdam UMC (J.C.B., S.I.), Vrije Universiteit Amsterdam, Department of Neurosurgery, Amsterdam Neuroscience, De Boelelaan 1117; Swammerdam Institute for Life Sciences (E.A.v.V.), Center for Neuroscience, University of Amsterdam, the Netherlands; Department of Clinical and Experimental Epilepsy (B.D., C.S., M.T.), University College London Institute of Neurology, UK; and Stichting Epilepsie Instellingen Nederland (R.T., E.A.), Heemstede, the Netherlands
| | - Orrin Devinsky
- From the Comprehensive Epilepsy Center (D.F.L., C.V., S.D., D.F., O.D.), Proteomics Laboratory (E.K., S.N., B.U.), Division of Advanced Research Technologies, and Department of Biochemistry and Molecular Pharmacology (B.U.), NYU School of Medicine; Department of Neurology (D.F.L., G.P., A.F., E.D., S.D., D.F., T.W., B.U., O.D.), Center for Cognitive Neurology (G.P., A.F., E.D., T.W.), Department of Pathology (T.W.), and Department of Psychiatry (T.W.), NYU Langone Health and School of Medicine, New York; Department of (Neuro)Pathology (J.D.M., J.J.A., E.A.v.V., E.A.), Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, the Netherlands; Alzheimer's and Prion Diseases Team (G.P.), Paris Brain Institute, CNRS, UMR 7225, INSERM 1127, Sorbonne University UM75, Paris, France; Brain & Mind Centre and School of Medical Sciences (E.D.), Faculty of Medicine and Health, University of Sydney, Australia; Biomedical Hosting LLC (M.A.), Arlington, MA; School of Biotechnology and Biomolecular Sciences (B.J.C., M.J.), University of New South Wales, Sydney, Australia; Amsterdam UMC (J.C.B., S.I.), Vrije Universiteit Amsterdam, Department of Neurosurgery, Amsterdam Neuroscience, De Boelelaan 1117; Swammerdam Institute for Life Sciences (E.A.v.V.), Center for Neuroscience, University of Amsterdam, the Netherlands; Department of Clinical and Experimental Epilepsy (B.D., C.S., M.T.), University College London Institute of Neurology, UK; and Stichting Epilepsie Instellingen Nederland (R.T., E.A.), Heemstede, the Netherlands
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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.
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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:
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16
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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: 27] [Impact Index Per Article: 9.0] [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.
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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
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17
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Davalieva K, Kiprijanovska S, Dimovski A, Rosoklija G, Dwork AJ. Comparative evaluation of two methods for LC-MS/MS proteomic analysis of formalin fixed and paraffin embedded tissues. J Proteomics 2021; 235:104117. [PMID: 33453434 DOI: 10.1016/j.jprot.2021.104117] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/05/2021] [Accepted: 01/05/2021] [Indexed: 10/22/2022]
Abstract
The proteomics of formalin-fixed, paraffin-embedded (FFPE) samples has advanced significantly during the last two decades, but there are many protocols and few studies comparing them directly. There is no consensus on the most effective protocol for shotgun proteomic analysis. We compared the in-solution digestion with RapiGest and Filter Aided Sample Preparation (FASP) of FFPE prostate tissues stored 7 years and mirroring fresh frozen samples, using two label-free data-independent LC-MS/MS acquisitions. RapiGest identified more proteins than FASP, with almost identical numbers of proteins from fresh and FFPE tissues and 69% overlap, good preservation of high-MW proteins, no bias regarding isoelectric point, and greater technical reproducibility. On the other hand, FASP yielded 20% fewer protein identifications in FFPE than in fresh tissue, with 64-69% overlap, depletion of proteins >70 kDa, lower efficiency in acidic and neutral range, and lower technical reproducibility. Both protocols showed highly similar subcellular compartments distribution, highly similar percentages of extracted unique peptides from FFPE and fresh tissues and high positive correlation between the absolute quantitation values of fresh and FFPE proteins. In conclusion, RapiGest extraction of FFPE tissues delivers a proteome that closely resembles the fresh frozen proteome and should be preferred over FASP in biomarker and quantification studies. SIGNIFICANCE: Here we analyzed the performance of two sample preparation methods for shotgun proteomic analysis of FFPE tissues to give a comprehensive overview of the obtained proteomes and the resemblance to its matching fresh frozen counterparts. These findings give us better understanding towards competent proteomics analysis of FFPE tissues. It is hoped that it will encourage further assessments of available protocols before establishing the most effective protocol for shotgun proteomic FFPE tissue analysis.
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Affiliation(s)
- Katarina Davalieva
- Research Centre for Genetic Engineering and Biotechnology "Georgi D Efremov", Macedonian Academy of Sciences and Arts, Krste Misirkov 2, 1000 Skopje, North Macedonia.
| | - Sanja Kiprijanovska
- Research Centre for Genetic Engineering and Biotechnology "Georgi D Efremov", Macedonian Academy of Sciences and Arts, Krste Misirkov 2, 1000 Skopje, North Macedonia
| | - Aleksandar Dimovski
- Research Centre for Genetic Engineering and Biotechnology "Georgi D Efremov", Macedonian Academy of Sciences and Arts, Krste Misirkov 2, 1000 Skopje, North Macedonia; Faculty of Pharmacy, University "St. Cyril and Methodius", 50ta Divizija 6, 1000 Skopje, North Macedonia
| | - Gorazd Rosoklija
- Department of Psychiatry, Columbia University, New York, USA; Molecular Imaging and Neuropathology Division, New York State Psychiatric Institute, 1051 Riverside Drive, Unit 42, New York, NY 10032, USA
| | - Andrew J Dwork
- Department of Psychiatry, Columbia University, New York, USA; Molecular Imaging and Neuropathology Division, New York State Psychiatric Institute, 1051 Riverside Drive, Unit 42, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University, New York, USA
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18
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Utilization of Laser Capture Microdissection Coupled to Mass Spectrometry to Uncover the Proteome of Cellular Protrusions. Methods Mol Biol 2021; 2259:25-45. [PMID: 33687707 DOI: 10.1007/978-1-0716-1178-4_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Laser capture microdissection (LCM) provides a fast, specific, and versatile method to isolate and enrich cells in mixed populations and/or subcellular structures, for further proteomic study. Furthermore, mass spectrometry (MS) can quickly and accurately generate differential protein expression profiles from small amounts of samples. Although cellular protrusions-such as tunneling nanotubes, filopodia, growth cones, invadopodia, etc.-are involved in essential physiological and pathological actions such as phagocytosis or cancer-cell invasion, the study of their protein composition is progressing slowly due to their fragility and transient nature. The method described herein, combining LCM and MS, has been designed to identify the proteome of different cellular protrusions. First, cells are fixed with a novel fixative method to preserve the cellular protrusions, which are isolated by LCM. Next, the extraction of proteins from the enriched sample is optimized to de-crosslink the fixative agent to improve the identification of proteins by MS. The efficient protein recovery and high sample quality of this method enable the protein profiling of these small and diverse subcellular structures.
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19
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Rayaprolu S, Higginbotham L, Bagchi P, Watson CM, Zhang T, Levey AI, Rangaraju S, Seyfried NT. Systems-based proteomics to resolve the biology of Alzheimer's disease beyond amyloid and tau. Neuropsychopharmacology 2021; 46:98-115. [PMID: 32898852 PMCID: PMC7689445 DOI: 10.1038/s41386-020-00840-3] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/05/2020] [Accepted: 08/19/2020] [Indexed: 02/07/2023]
Abstract
The repeated failures of amyloid-targeting therapies have challenged our narrow understanding of Alzheimer's disease (AD) pathogenesis and inspired wide-ranging investigations into the underlying mechanisms of disease. Increasing evidence indicates that AD develops from an intricate web of biochemical and cellular processes that extend far beyond amyloid and tau accumulation. This growing recognition surrounding the diversity of AD pathophysiology underscores the need for holistic systems-based approaches to explore AD pathogenesis. Here we describe how network-based proteomics has emerged as a powerful tool and how its application to the AD brain has provided an informative framework for the complex protein pathophysiology underlying the disease. Furthermore, we outline how the AD brain network proteome can be leveraged to advance additional scientific and translational efforts, including the discovery of novel protein biomarkers of disease.
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Affiliation(s)
- Sruti Rayaprolu
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Lenora Higginbotham
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Pritha Bagchi
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Caroline M Watson
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Tian Zhang
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Allan I Levey
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Srikant Rangaraju
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Nicholas T Seyfried
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA.
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, 30322, USA.
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA.
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20
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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.
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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.
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21
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Buczak K, Kirkpatrick JM, Truckenmueller F, Santinha D, Ferreira L, Roessler S, Singer S, Beck M, Ori A. Spatially resolved analysis of FFPE tissue proteomes by quantitative mass spectrometry. Nat Protoc 2020; 15:2956-2979. [PMID: 32737464 DOI: 10.1038/s41596-020-0356-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 05/14/2020] [Indexed: 01/09/2023]
Abstract
Bottom-up mass spectrometry-based proteomics relies on protein digestion and peptide purification. The application of such methods to broadly available clinical samples such as formalin-fixed and paraffin-embedded (FFPE) tissues requires reversal of chemical crosslinking and the removal of reagents that are incompatible with mass spectrometry. Here, we describe in detail a protocol that combines tissue disruption by ultrasonication, heat-induced antigen retrieval and two alternative methods for efficient detergent removal to enable quantitative proteomic analysis of limited amounts of FFPE material. To show the applicability of our approach, we used hepatocellular carcinoma (HCC) as a model system. By combining the described protocol with laser-capture microdissection, we were able to quantify the intra-tumor heterogeneity of a tumor specimen on the proteome level using a single slide with tissue of 10-µm thickness. We also demonstrate broader applicability to other tissues, including human gallbladder and heart. The procedure described in this protocol can be completed within 8 d.
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Affiliation(s)
- Katarzyna Buczak
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Biozentrum, University of Basel, Basel, Switzerland
| | - Joanna M Kirkpatrick
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany.,Proteomics Science Technology Platform, The Francis Crick Institute, London, UK
| | | | - Deolinda Santinha
- Center for Neuroscience and Cell Biology and Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Lino Ferreira
- Center for Neuroscience and Cell Biology and Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Stephanie Roessler
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Stephan Singer
- Institute of Pathology, University Hospital Tuebingen, Tuebingen, Germany
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany. .,Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
| | - Alessandro Ori
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany.
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22
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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 2020; 143:2803-2817. [PMID: 32812023 PMCID: PMC7526722 DOI: 10.1093/brain/awaa223] [Citation(s) in RCA: 185] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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.
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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
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23
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Griesser E, Wyatt H, Ten Have S, Stierstorfer B, Lenter M, Lamond AI. Quantitative Profiling of the Human Substantia Nigra Proteome from Laser-capture Microdissected FFPE Tissue. Mol Cell Proteomics 2020; 19:839-851. [PMID: 32132230 PMCID: PMC7196589 DOI: 10.1074/mcp.ra119.001889] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/19/2020] [Indexed: 11/10/2022] Open
Abstract
Laser-capture microdissection (LCM) allows the visualization and isolation of morphologically distinct subpopulations of cells from heterogeneous tissue specimens. In combination with formalin-fixed and paraffin-embedded (FFPE) tissue it provides a powerful tool for retrospective and clinically relevant studies of tissue proteins in a healthy and diseased context. We first optimized the protocol for efficient LCM analysis of FFPE tissue specimens. The use of SDS containing extraction buffer in combination with the single-pot solid-phase-enhanced sample preparation (SP3) digest method gave the best results regarding protein yield and protein/peptide identifications. Microdissected FFPE human substantia nigra tissue samples (∼3,000 cells) were then analyzed, using tandem mass tag (TMT) labeling and LC-MS/MS, resulting in the quantification of >5,600 protein groups. Nigral proteins were classified and analyzed by abundance, showing an enrichment of extracellular exosome and neuron-specific gene ontology (GO) terms among the higher abundance proteins. Comparison of microdissected samples with intact tissue sections, using a label-free shotgun approach, revealed an enrichment of neuronal cell type markers, such as tyrosine hydroxylase and alpha-synuclein, as well as proteins annotated with neuron-specific GO terms. Overall, this study provides a detailed protocol for laser-capture proteomics using FFPE tissue and demonstrates the efficiency of LCM analysis of distinct cell subpopulations for proteomic analysis using low sample amounts.
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Affiliation(s)
- Eva Griesser
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom; Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Hannah Wyatt
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Sara Ten Have
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom
| | - Birgit Stierstorfer
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Martin Lenter
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Angus I Lamond
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom.
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24
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Early intraneuronal amyloid triggers neuron-derived inflammatory signaling in APP transgenic rats and human brain. Proc Natl Acad Sci U S A 2020; 117:6844-6854. [PMID: 32144141 PMCID: PMC7104377 DOI: 10.1073/pnas.1914593117] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
This work provides evidence that soluble and oligomeric amyloid protein stokes neuronal inflammation during the earliest stages of Alzheimer’s disease. Identifying neuron-derived factors that engage the brain’s immune system will provide insight into how vulnerable neurons might interact with other immune cells to propagate cytotoxic signaling cascades and cellular dysfunction during disease development. Chronic inflammation during Alzheimer’s disease (AD) is most often attributed to sustained microglial activation in response to amyloid-β (Aβ) plaque deposits and cell death. However, cytokine release and microgliosis are consistently observed in AD transgenic animal models devoid of such pathologies, bringing into question the underlying processes that may be at play during the earliest AD-related immune response. We propose that this plaque-independent inflammatory reaction originates from neurons burdened with increasing levels of soluble and oligomeric Aβ, which are known to be the most toxic amyloid species within the brain. Laser microdissected neurons extracted from preplaque amyloid precursor protein (APP) transgenic rats were found to produce a variety of potent immune factors, both at the transcript and protein levels. Neuron-derived cytokines correlated with the extent of microglial activation and mobilization, even in the absence of extracellular plaques and cell death. Importantly, we identified an inflammatory profile unique to Aβ-burdened neurons, since neighboring glial cells did not express similar molecules. Moreover, we demonstrate within disease-vulnerable regions of the human brain that a neuron-specific inflammatory response may precede insoluble Aβ plaque and tau tangle formation. Thus, we reveal the Aβ-burdened neuron as a primary proinflammatory agent, implicating the intraneuronal accumulation of Aβ as a significant immunological component in the AD pathogenesis.
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25
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Legrès LG. [Laser microdissection applications in histology: an open way to molecular studies]. Med Sci (Paris) 2019; 35:871-879. [PMID: 31845879 DOI: 10.1051/medsci/2019166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
One of the most fascinating aspects of the use of a laser beam in the field of biology has emerged with the development of devices able to perform fine dissections of biological tissues. Laser microdissection can collect phenotypically identical cells from tissue regions laid on a microscope slide in order to make differential molecular analyses on these microdissected cells. Laser microdissection can be used many areas including oncology to specify molecular mechanisms that enable to adapt a treatment related to diagnosis and research in biology, but also forensic science for tissue selection, neurology for post-mortem studies on patients with Alzheimer's disease, for clonality studies from cell cultures and cytogenetics to decipher chromosomal rearrangements. This technology represents the missing link between clinical observations and the intrinsic physiological mechanisms of biological tissues and its major applications will be addressed here.
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Affiliation(s)
- Luc G Legrès
- Institut de recherche Saint-Louis, Paris, France, UMR_S 976 Inserm, Université de Paris, Hôpital Saint-Louis, 1 avenue Claude-Vellefaux, F-75010 Paris, France
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26
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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.
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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.
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Dapic I, Baljeu-Neuman L, Uwugiaren N, Kers J, Goodlett DR, Corthals GL. Proteome analysis of tissues by mass spectrometry. MASS SPECTROMETRY REVIEWS 2019; 38:403-441. [PMID: 31390493 DOI: 10.1002/mas.21598] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 06/17/2019] [Indexed: 06/10/2023]
Abstract
Tissues and biofluids are important sources of information used for the detection of diseases and decisions on patient therapies. There are several accepted methods for preservation of tissues, among which the most popular are fresh-frozen and formalin-fixed paraffin embedded methods. Depending on the preservation method and the amount of sample available, various specific protocols are available for tissue processing for subsequent proteomic analysis. Protocols are tailored to answer various biological questions, and as such vary in lysis and digestion conditions, as well as duration. The existence of diverse tissue-sample protocols has led to confusion in how to choose the best protocol for a given tissue and made it difficult to compare results across sample types. Here, we summarize procedures used for tissue processing for subsequent bottom-up proteomic analysis. Furthermore, we compare protocols for their variations in the composition of lysis buffers, digestion procedures, and purification steps. For example, reports have shown that lysis buffer composition plays an important role in the profile of extracted proteins: the most common are tris(hydroxymethyl)aminomethane, radioimmunoprecipitation assay, and ammonium bicarbonate buffers. Although, trypsin is the most commonly used enzyme for proteolysis, in some protocols it is supplemented with Lys-C and/or chymotrypsin, which will often lead to an increase in proteome coverage. Data show that the selection of the lysis procedure might need to be tissue-specific to produce distinct protocols for individual tissue types. Finally, selection of the procedures is also influenced by the amount of sample available, which range from biopsies or the size of a few dozen of mm2 obtained with laser capture microdissection to much larger amounts that weight several milligrams.
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Affiliation(s)
- Irena Dapic
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | | | - Naomi Uwugiaren
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Jesper Kers
- Department of Pathology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam Cardiovascular Sciences (ACS), Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - David R Goodlett
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
- University of Maryland, 20N. Pine Street, Baltimore, MD 21201
| | - Garry L Corthals
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
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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.
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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
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Li P, Marshall L, Oh G, Jakubowski JL, Groot D, He Y, Wang T, Petronis A, Labrie V. Epigenetic dysregulation of enhancers in neurons is associated with Alzheimer's disease pathology and cognitive symptoms. Nat Commun 2019; 10:2246. [PMID: 31113950 PMCID: PMC6529540 DOI: 10.1038/s41467-019-10101-7] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 04/18/2019] [Indexed: 12/23/2022] Open
Abstract
Epigenetic control of enhancers alters neuronal functions and may be involved in Alzheimer’s disease (AD). Here, we identify enhancers in neurons contributing to AD by comprehensive fine-mapping of DNA methylation at enhancers, genome-wide. We examine 1.2 million CpG and CpH sites in enhancers in prefrontal cortex neurons of individuals with no/mild, moderate, and severe AD pathology (n = 101). We identify 1224 differentially methylated enhancer regions; most of which are hypomethylated at CpH sites in AD neurons. CpH methylation losses occur in normal aging neurons, but are accelerated in AD. Integration of epigenetic and transcriptomic data demonstrates a pro-apoptotic reactivation of the cell cycle in post-mitotic AD neurons. Furthermore, AD neurons have a large cluster of significantly hypomethylated enhancers in the DSCAML1 gene that targets BACE1. Hypomethylation of these enhancers in AD is associated with an upregulation of BACE1 transcripts and an increase in amyloid plaques, neurofibrillary tangles, and cognitive decline. Epigenetic control of enhancers may contribute to neurological disease. Here the authors carry out genome-wide analysis of DNA methylation in neurons isolated postmortem from patients with Alzheimer’s disease.
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Affiliation(s)
- Peipei Li
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Lee Marshall
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Gabriel Oh
- Centre for Addiction and Mental Health, Toronto, M5T 1R8, ON, Canada
| | - Jennifer L Jakubowski
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Daniel Groot
- Centre for Addiction and Mental Health, Toronto, M5T 1R8, ON, Canada
| | - Yu He
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Ting Wang
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Arturas Petronis
- Centre for Addiction and Mental Health, Toronto, M5T 1R8, ON, Canada.,Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257, Vilnius, Lithuania
| | - Viviane Labrie
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, 49503, USA. .,Centre for Addiction and Mental Health, Toronto, M5T 1R8, ON, Canada. .,Division of Psychiatry and Behavioral Medicine, College of Human Medicine, Michigan State University, Grand Rapids, MI, 49503, USA.
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A novel Microproteomic Approach Using Laser Capture Microdissection to Study Cellular Protrusions. Int J Mol Sci 2019; 20:ijms20051172. [PMID: 30866487 PMCID: PMC6429397 DOI: 10.3390/ijms20051172] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 02/17/2019] [Accepted: 02/28/2019] [Indexed: 12/28/2022] Open
Abstract
Cell–cell communication is vital to multicellular organisms, and distinct types of cellular protrusions play critical roles during development, cell signaling, and the spreading of pathogens and cancer. The differences in the structure and protein composition of these different types of protrusions and their specific functions have not been elucidated due to the lack of a method for their specific isolation and analysis. In this paper, we described, for the first time, a method to specifically isolate distinct protrusion subtypes, based on their morphological structures or fluorescent markers, using laser capture microdissection (LCM). Combined with a unique fixation and protein extraction protocol, we pushed the limits of microproteomics and demonstrate that proteins from LCM-isolated protrusions can successfully and reproducibly be identified by mass spectrometry using ultra-high field Orbitrap technologies. Our method confirmed that different types of protrusions have distinct proteomes and it promises to advance the characterization and the understanding of these unique structures to shed light on their possible role in health and disease.
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Thom M, Boldrini M, Bundock E, Sheppard MN, Devinsky O. Review: The past, present and future challenges in epilepsy-related and sudden deaths and biobanking. Neuropathol Appl Neurobiol 2019; 44:32-55. [PMID: 29178443 PMCID: PMC5820128 DOI: 10.1111/nan.12453] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 11/14/2017] [Indexed: 12/14/2022]
Abstract
Awareness and research on epilepsy-related deaths (ERD), in particular Sudden Unexpected Death in Epilepsy (SUDEP), have exponentially increased over the last two decades. Most publications have focused on guidelines that inform clinicians dealing with these deaths, educating patients, potential risk factors and mechanisms. There is a relative paucity of information available for pathologists who conduct these autopsies regarding appropriate post mortem practice and investigations. As we move from recognizing SUDEP as the most common form of ERD toward in-depth investigations into its causes and prevention, health professionals involved with these autopsies and post mortem procedure must remain fully informed. Systematizing a more comprehensive and consistent practice of examining these cases will facilitate (i) more precise determination of cause of death, (ii) identification of SUDEP for improved epidemiological surveillance (the first step for an intervention study), and (iii) biobanking and cell-based research. This article reviews how pathologists and healthcare professionals have approached ERD, current practices, logistical problems and areas to improve and harmonize. The main neuropathology, cardiac and genetic findings in SUDEP are outlined, providing a framework for best practices, integration of clinical, pathological and molecular genetic investigations in SUDEP, and ultimately prevention.
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Affiliation(s)
- M Thom
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, London, UK
| | - M Boldrini
- Department of Psychiatry, Columbia University Medical Centre, Divisions of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, USA
| | - E Bundock
- Office of the Chief Medical Examiner, Burlington, VT, USA
| | - M N Sheppard
- Department of Pathology, St George's University Hospitals NHS Foundation Trust, London, UK
| | - O Devinsky
- Department of Neurology, NYU Epilepsy Center, New York, NY, USA
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32
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Wisniewski T, Drummond E. Future horizons in Alzheimer's disease research. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2019; 168:223-241. [PMID: 31699317 DOI: 10.1016/bs.pmbts.2019.08.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
There are growing genetic, transcriptomic and proteomic data pointing to the complexity of Alzheimer's disease (AD) pathogenesis. Unbiased "omics" approaches are essential for the future development of effective AD research, which will need to be combined and personalized, given that multiple distinct pathways can drive AD pathology. It is essential to gain a better understanding of the AD pathogenesis subtype variety and to develop several distinct therapeutic approaches tailored to address this diversity, as well as the common presence of mixed pathologies. These nonmutually exclusive therapeutic approaches include the targeting of multiple toxic oligomeric species concurrently, targeting the apolipoprotein E/amyloid β interaction and the modulation of innate immunity, as well as more "out of the box" ideas such as targeting infectious agents that may play a role in AD.
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Affiliation(s)
- Thomas Wisniewski
- Departments of Neurology, Pathology and Psychiatry, Center for Cognitive Neurology, NYU School of Medicine, New York, NY, United States.
| | - Eleanor Drummond
- Central Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
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Thompson AG, Gray E, Mager I, Fischer R, Thézénas ML, Charles PD, Talbot K, El Andaloussi S, Kessler BM, Wood M, Turner MR. UFLC-Derived CSF Extracellular Vesicle Origin and Proteome. Proteomics 2018; 18:e1800257. [PMID: 30411858 DOI: 10.1002/pmic.201800257] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 10/18/2018] [Indexed: 12/25/2022]
Abstract
Cerebrospinal fluid (CSF) extracellular vesicles (EVs) show promise as a source of neurological disease biomarkers, although their precise origin is poorly understood. Current extraction techniques produce disappointing yield and purity. This study describes the application of ultrafiltration LC (UFLC) to CSF-EVs, compared with ultracentrifugation (UC), and explores CSF-EV origin. EVs are extracted from human CSF by UC and UFLC and characterized using nanoparticle tracking analysis, electron microscopy, and immunoblotting. EV and CSF proteomes are analyzed by LC-MS/MS. UFLC-isolated particles have size, morphology, and marker expression characteristic of EVs. UFLC provides greater EV yield (UFLC 7.90 × 108 ± SD 1.31 × 108 EVs mL-1 CSF, UC 1.06 × 108 ± 0.57 × 108 p < 0.001). UFLC enhances purity, proteomic depth (UFLC 622 ± 49, UC 298 ± 50, p = 0.001), and consistency of quantification (CV 17% vs 23%). EVs contain more intracellular proteins (Odds ratio [OR] 2.63 p < 0.001) and fewer plasma proteins than CSF (OR 0.60, p < 0.001). CSF and EV-enriched proteomes show overrepresentation of brain-specific proteins (EV OR 3.18, p < 0.001; CSF OR 3.37, p < 0.001). Overrepresentation of cerebral white matter (OR 1.99, p = 0.015) and choroid plexus proteins (OR 1.87, p<0.001) is observed in EVs. UFLC improves yield and purity of CSF-EVs. The EV-enriched proteome better reflects the intracellular and white matter proteome than whole CSF.
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Affiliation(s)
- Alexander G Thompson
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Elizabeth Gray
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Imre Mager
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Roman Fischer
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Marie-Laëtitia Thézénas
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Philip D Charles
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Kevin Talbot
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Samir El Andaloussi
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom.,Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Benedikt M Kessler
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Matthew Wood
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Martin R Turner
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
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Wilson RS, Nairn AC. Cell-Type-Specific Proteomics: A Neuroscience Perspective. Proteomes 2018; 6:51. [PMID: 30544872 PMCID: PMC6313874 DOI: 10.3390/proteomes6040051] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/04/2018] [Accepted: 12/05/2018] [Indexed: 12/18/2022] Open
Abstract
Cell-type-specific analysis has become a major focus for many investigators in the field of neuroscience, particularly because of the large number of different cell populations found in brain tissue that play roles in a variety of developmental and behavioral disorders. However, isolation of these specific cell types can be challenging due to their nonuniformity and complex projections to different brain regions. Moreover, many analytical techniques used for protein detection and quantitation remain insensitive to the low amounts of protein extracted from specific cell populations. Despite these challenges, methods to improve proteomic yield and increase resolution continue to develop at a rapid rate. In this review, we highlight the importance of cell-type-specific proteomics in neuroscience and the technical difficulties associated. Furthermore, current progress and technological advancements in cell-type-specific proteomics research are discussed with an emphasis in neuroscience.
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Affiliation(s)
- Rashaun S Wilson
- Yale/NIDA Neuroproteomics Center, 300 George St., New Haven, CT 06511, USA.
| | - Angus C Nairn
- Yale/NIDA Neuroproteomics Center, 300 George St., New Haven, CT 06511, USA.
- Department of Psychiatry, Yale School of Medicine, Connecticut Mental Health Center, New Haven, CT 06511, USA.
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Kole K, Celikel T. Neocortical Microdissection at Columnar and Laminar Resolution for Molecular Interrogation. ACTA ACUST UNITED AC 2018; 86:e55. [PMID: 30285322 DOI: 10.1002/cpns.55] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The heterogeneous organization of the mammalian neocortex poses a challenge for elucidating the molecular mechanisms underlying its physiological processes. Although high-throughput molecular methods are increasingly deployed in neuroscience, their anatomical specificity is often lacking. In this unit, we introduce a targeted microdissection technique that enables extraction of high-quality RNA and proteins at high anatomical resolution from acutely prepared brain slices. We exemplify its utility by isolating single cortical columns and laminae from the mouse primary somatosensory (barrel) cortex. Tissues can be isolated from living slices in minutes, and the extracted RNA and protein are of sufficient quantity and quality to be used for RNA sequencing and mass spectrometry. This technique will help to increase the anatomical specificity of molecular studies of the neocortex, and the brain in general, as it is applicable to any brain structure that can be identified using optical landmarks in living slices. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Koen Kole
- Department of Neurophysiology, Donders Institute for Brain, Cognition, and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Tansu Celikel
- Department of Neurophysiology, Donders Institute for Brain, Cognition, and Behaviour, Radboud University, Nijmegen, The Netherlands
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Föll MC, Fahrner M, Oria VO, Kühs M, Biniossek ML, Werner M, Bronsert P, Schilling O. Reproducible proteomics sample preparation for single FFPE tissue slices using acid-labile surfactant and direct trypsinization. Clin Proteomics 2018. [PMID: 29527141 PMCID: PMC5838928 DOI: 10.1186/s12014-018-9188-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background Proteomic analyses of clinical specimens often rely on human tissues preserved through formalin-fixation and paraffin embedding (FFPE). Minimal sample consumption is the key to preserve the integrity of pathological archives but also to deal with minimal invasive core biopsies. This has been achieved by using the acid-labile surfactant RapiGest in combination with a direct trypsinization (DTR) strategy. A critical comparison of the DTR protocol with the most commonly used filter aided sample preparation (FASP) protocol is lacking. Furthermore, it is unknown how common histological stainings influence the outcome of the DTR protocol. Methods Four single consecutive murine kidney tissue specimens were prepared with the DTR approach or with the FASP protocol using both 10 and 30 k filter devices and analyzed by label-free, quantitative liquid chromatography–tandem mass spectrometry (LC–MS/MS). We compared the different protocols in terms of proteome coverage, relative label-free quantitation, missed cleavages, physicochemical properties and gene ontology term annotations of the proteins. Additionally, we probed compatibility of the DTR protocol for the analysis of common used histological stainings, namely hematoxylin & eosin (H&E), hematoxylin and hemalaun. These were proteomically compared to an unstained control by analyzing four human tonsil FFPE tissue specimens per condition. Results On average, the DTR protocol identified 1841 ± 22 proteins in a single, non-fractionated LC–MS/MS analysis, whereas these numbers were 1857 ± 120 and 1970 ± 28 proteins for the FASP 10 and 30 k protocol. The DTR protocol showed 15% more missed cleavages, which did not adversely affect quantitation and intersample comparability. Hematoxylin or hemalaun staining did not adversely impact the performance of the DTR protocol. A minor perturbation was observed for H&E staining, decreasing overall protein identification by 13%. Conclusions In essence, the DTR protocol can keep up with the FASP protocol in terms of qualitative and quantitative reproducibility and performed almost as well in terms of proteome coverage and missed cleavages. We highlight the suitability of the DTR protocol as a viable and straightforward alternative to the FASP protocol for proteomics-based clinical research. Electronic supplementary material The online version of this article (10.1186/s12014-018-9188-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Melanie Christine Föll
- 1Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Stefan Meier Strasse 17, 79104 Freiburg, Germany.,2Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Matthias Fahrner
- 1Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Stefan Meier Strasse 17, 79104 Freiburg, Germany.,2Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany.,3Spemann Graduate School of Biology and Medicine (SGBM), Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Victor Oginga Oria
- 1Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Stefan Meier Strasse 17, 79104 Freiburg, Germany.,2Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany.,3Spemann Graduate School of Biology and Medicine (SGBM), Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Markus Kühs
- 4Institute for Surgical Pathology, Medical Center - University of Freiburg, Freiburg, Germany.,5Comprehensive Cancer Center Freiburg, Medical Center - University of Freiburg, Freiburg, Germany.,6Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Martin Lothar Biniossek
- 1Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Stefan Meier Strasse 17, 79104 Freiburg, Germany
| | - Martin Werner
- 4Institute for Surgical Pathology, Medical Center - University of Freiburg, Freiburg, Germany.,5Comprehensive Cancer Center Freiburg, Medical Center - University of Freiburg, Freiburg, Germany.,6Faculty of Medicine, University of Freiburg, Freiburg, Germany.,7German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Peter Bronsert
- 4Institute for Surgical Pathology, Medical Center - University of Freiburg, Freiburg, Germany.,5Comprehensive Cancer Center Freiburg, Medical Center - University of Freiburg, Freiburg, Germany.,6Faculty of Medicine, University of Freiburg, Freiburg, Germany.,7German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oliver Schilling
- 1Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Stefan Meier Strasse 17, 79104 Freiburg, Germany.,7German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,8BIOSS Centre for Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany
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Wilson RS, Nairn AC. Making brain proteomics true to type. Nat Biotechnol 2018; 36:149-150. [DOI: 10.1038/nbt.4077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Isolation of Amyloid Plaques and Neurofibrillary Tangles from Archived Alzheimer's Disease Tissue Using Laser-Capture Microdissection for Downstream Proteomics. Methods Mol Biol 2018; 1723:319-334. [PMID: 29344869 DOI: 10.1007/978-1-4939-7558-7_18] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Here, we describe a new method that allows localized proteomics of amyloid plaques and neurofibrillary tangles (NFTs), which are the two pathological hallmarks of Alzheimer's disease (AD). Amyloid plaques and NFTs are visualized using immunohistochemistry and microdissected from archived, formalin-fixed paraffin-embedded (FFPE) human tissue samples using laser-capture microdissection. The majority of human tissue specimens are FFPE; hence the use of this type of tissue is a particular advantage of this technique. Microdissected tissue samples are solubilized with formic acid and deparaffinized, reduced, alkylated, proteolytically digested, and desalted. The resulting protein content of plaques and NFTs is determined using label-free quantitative LC-MS. This results in the unbiased and simultaneous quantification of ~900 proteins in plaques and ~500 proteins in NFTs. This approach permits downstream pathway and network analysis, hence providing a comprehensive overview of pathological protein accumulation found in neuropathological features in AD.
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Abstract
Among various methods now available to isolate distinct cell populations or even single cells for DNA/RNA and proteomic analysis, laser capture microdissection (LCM) offers a unique opportunity to study cells in their topological contexts. This chapter focuses on the preparation of LCM membrane slides, tissue staining and laser microdissection of cells of interest from frozen or formalin-fixed, paraffin-embedded glioblastoma tissue.
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Affinity purification mass spectrometry analysis of PD-1 uncovers SAP as a new checkpoint inhibitor. Proc Natl Acad Sci U S A 2017; 115:E468-E477. [PMID: 29282323 DOI: 10.1073/pnas.1710437115] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Programmed cell death-1 (PD-1) is an essential inhibitory receptor in T cells. Antibodies targeting PD-1 elicit durable clinical responses in patients with multiple tumor indications. Nevertheless, a significant proportion of patients do not respond to anti-PD-1 treatment, and a better understanding of the signaling pathways downstream of PD-1 could provide biomarkers for those whose tumors respond and new therapeutic approaches for those whose tumors do not. We used affinity purification mass spectrometry to uncover multiple proteins associated with PD-1. Among these proteins, signaling lymphocytic activation molecule-associated protein (SAP) was functionally and mechanistically analyzed for its contribution to PD-1 inhibitory responses. Silencing of SAP augmented and overexpression blocked PD-1 function. T cells from patients with X-linked lymphoproliferative disease (XLP), who lack functional SAP, were hyperresponsive to PD-1 signaling, confirming its inhibitory role downstream of PD-1. Strikingly, signaling downstream of PD-1 in purified T cell subsets did not correlate with PD-1 surface expression but was inversely correlated with intracellular SAP levels. Mechanistically, SAP opposed PD-1 function by acting as a molecular shield of key tyrosine residues that are targets for the tyrosine phosphatase SHP2, which mediates PD-1 inhibitory properties. Our results identify SAP as an inhibitor of PD-1 function and SHP2 as a potential therapeutic target in patients with XLP.
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Yi L, Piehowski PD, Shi T, Smith RD, Qian WJ. Advances in microscale separations towards nanoproteomics applications. J Chromatogr A 2017; 1523:40-48. [PMID: 28765000 PMCID: PMC6042839 DOI: 10.1016/j.chroma.2017.07.055] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 07/14/2017] [Accepted: 07/17/2017] [Indexed: 01/22/2023]
Abstract
Microscale separation (e.g., liquid chromatography or capillary electrophoresis) coupled with mass spectrometry (MS) has become the primary tool for advanced proteomics, an indispensable technology for gaining understanding of complex biological processes. In recent decades significant advances have been achieved in MS-based proteomics. However, the current proteomics platforms still face an analytical challenge in overall sensitivity towards nanoproteomics applications for starting materials of less than 1μg total proteins (e.g., cellular heterogeneity in tissue pathologies). Herein, we review recent advances in microscale separation techniques and integrated sample processing strategies that improve the overall sensitivity and proteome coverage of the proteomics workflow, and their contributions towards nanoproteomics applications.
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Affiliation(s)
- Lian Yi
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, United States
| | - Paul D Piehowski
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, United States
| | - Tujin Shi
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, United States
| | - Richard D Smith
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, United States
| | - Wei-Jun Qian
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, United States.
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Hosp F, Mann M. A Primer on Concepts and Applications of Proteomics in Neuroscience. Neuron 2017; 96:558-571. [DOI: 10.1016/j.neuron.2017.09.025] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/29/2017] [Accepted: 09/14/2017] [Indexed: 02/06/2023]
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Dapic I, Uwugiaren N, Jansen PJ, Corthals GL. Fast and Simple Protocols for Mass Spectrometry-Based Proteomics of Small Fresh Frozen Uterine Tissue Sections. Anal Chem 2017; 89:10769-10775. [PMID: 28910098 PMCID: PMC5647562 DOI: 10.1021/acs.analchem.7b01937] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Human
tissues are an important link between organ-specific spatial
molecular information, patient pathology, and patient treatment options.
However, patient tissues are uniquely obtained by time and location,
and limited in their availability and size. Currently, little knowledge
exists about appropriate and simplified protocols for routine MS-based
analysis of the various types and sizes of tissues. Following standard
procedures used in pathology, we selected small fresh frozen uterine
tissue samples to investigate how the tissue preparation protocol
affected the subsequent proteomics analysis. First, we observed that
protein extraction with 0.1% SDS followed by extraction with a 30%
ACN/urea resulted in a decrease in the number of identified proteins,
when compared to extraction with 30% ACN/urea only. The decrease in
the number of proteins was approximately 55% and 20%, for 10 and 16
μm thick tissue, respectively. Interestingly, the relative abundance
of the proteins shared between the two methods was higher when SDS/ACN/urea
was used, compared to the 30% ACN/urea extraction, indicating the
role of SDS to be beneficial for protein solubility. Second, the influence
of tissue thickness was investigated by comparing the results obtained
for 10, 16, and 20 μm thick (1 mm2) tissue using
urea/30% ACN. We observed an increase in the number of identified
proteins and corresponding quantity with an increase in the tissue
thickness. Finally, by analyzing very small amounts of tissues (∼0.2
mm2) of 10, 16, and 20 μm thickness, we observed
that the increase in tissue thickness resulted in a higher number
of protein identifications and corresponding quantitative values.
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Affiliation(s)
- Irena Dapic
- University of Amsterdam, Van 't Hoff Institute for Molecular Sciences (HIMS) , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Naomi Uwugiaren
- University of Amsterdam, Van 't Hoff Institute for Molecular Sciences (HIMS) , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Petra J Jansen
- University of Amsterdam, Van 't Hoff Institute for Molecular Sciences (HIMS) , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Garry L Corthals
- University of Amsterdam, Van 't Hoff Institute for Molecular Sciences (HIMS) , Science Park 904, 1098 XH Amsterdam, The Netherlands
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Localized Proteomics of Individual Neurons Isolated from Formalin-Fixed, Paraffin-Embedded Tissue Sections Using Laser Capture Microdissection. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/978-1-4939-7119-0_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Scifo E, Calza G, Fuhrmann M, Soliymani R, Baumann M, Lalowski M. Recent advances in applying mass spectrometry and systems biology to determine brain dynamics. Expert Rev Proteomics 2017; 14:545-559. [PMID: 28539064 DOI: 10.1080/14789450.2017.1335200] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
INTRODUCTION Neurological disorders encompass various pathologies which disrupt normal brain physiology and function. Poor understanding of their underlying molecular mechanisms and their societal burden argues for the necessity of novel prevention strategies, early diagnostic techniques and alternative treatment options to reduce the scale of their expected increase. Areas covered: This review scrutinizes mass spectrometry based approaches used to investigate brain dynamics in various conditions, including neurodegenerative and neuropsychiatric disorders. Different proteomics workflows for isolation/enrichment of specific cell populations or brain regions, sample processing; mass spectrometry technologies, for differential proteome quantitation, analysis of post-translational modifications and imaging approaches in the brain are critically deliberated. Future directions, including analysis of cellular sub-compartments, targeted MS platforms (selected/parallel reaction monitoring) and use of mass cytometry are also discussed. Expert commentary: Here, we summarize and evaluate current mass spectrometry based approaches for determining brain dynamics in health and diseases states, with a focus on neurological disorders. Furthermore, we provide insight on current trends and new MS technologies with potential to improve this analysis.
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Affiliation(s)
- Enzo Scifo
- a Department of Psychiatry, and of Pharmacology and Toxicology , University of Toronto, Campbell Family Mental Health Research Institute of CAMH , Toronto , Canada
| | - Giulio Calza
- b Medicum, Meilahti Clinical Proteomics Core Facility, Biochemistry/Developmental Biology, Faculty of Medicine , FI-00014 University of Helsinki , Helsinki , Finland
| | - Martin Fuhrmann
- c Neuroimmunology and Imaging Group , German Center for Neurodegenerative Diseases (DZNE) , Bonn , Germany
| | - Rabah Soliymani
- b Medicum, Meilahti Clinical Proteomics Core Facility, Biochemistry/Developmental Biology, Faculty of Medicine , FI-00014 University of Helsinki , Helsinki , Finland
| | - Marc Baumann
- b Medicum, Meilahti Clinical Proteomics Core Facility, Biochemistry/Developmental Biology, Faculty of Medicine , FI-00014 University of Helsinki , Helsinki , Finland
| | - Maciej Lalowski
- b Medicum, Meilahti Clinical Proteomics Core Facility, Biochemistry/Developmental Biology, Faculty of Medicine , FI-00014 University of Helsinki , Helsinki , Finland
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Proteomic differences in amyloid plaques in rapidly progressive and sporadic Alzheimer's disease. Acta Neuropathol 2017; 133:933-954. [PMID: 28258398 DOI: 10.1007/s00401-017-1691-0] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 02/22/2017] [Accepted: 02/26/2017] [Indexed: 12/16/2022]
Abstract
Rapidly progressive Alzheimer's disease (rpAD) is a particularly aggressive form of Alzheimer's disease, with a median survival time of 7-10 months after diagnosis. Why these patients have such a rapid progression of Alzheimer's disease is currently unknown. To further understand pathological differences between rpAD and typical sporadic Alzheimer's disease (sAD) we used localized proteomics to analyze the protein differences in amyloid plaques in rpAD and sAD. Label-free quantitative LC-MS/MS was performed on amyloid plaques microdissected from rpAD and sAD patients (n = 22 for each patient group) and protein expression differences were quantified. On average, 913 ± 30 (mean ± SEM) proteins were quantified in plaques from each patient and 279 of these proteins were consistently found in plaques from every patient. We found significant differences in protein composition between rpAD and sAD plaques. We found that rpAD plaques contained significantly higher levels of neuronal proteins (p = 0.0017) and significantly lower levels of astrocytic proteins (p = 1.08 × 10-6). Unexpectedly, cumulative protein differences in rpAD plaques did not suggest accelerated typical sAD. Plaques from patients with rpAD were particularly abundant in synaptic proteins, especially those involved in synaptic vesicle release, highlighting the potential importance of synaptic dysfunction in the accelerated development of plaque pathology in rpAD. Combined, our data provide new direct evidence that amyloid plaques do not all have the same protein composition and that the proteomic differences in plaques could provide important insight into the factors that contribute to plaque development. The cumulative protein differences in rpAD plaques suggest rpAD may be a novel subtype of Alzheimer's disease.
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Cohen M, Appleby B, Safar JG. Distinct prion-like strains of amyloid beta implicated in phenotypic diversity of Alzheimer's disease. Prion 2017; 10:9-17. [PMID: 26809345 DOI: 10.1080/19336896.2015.1123371] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Vast evidence on human prions demonstrates that variable disease phenotypes, rates of propagation, and targeting of distinct brain structures are determined by unique conformers (strains) of pathogenic prion protein (PrP(Sc)). Recent progress in the development of advanced biophysical tools that inventory structural characteristics of amyloid beta (Aβ) in the brain cortex of phenotypically diverse Alzheimer's disease (AD) patients, revealed unique spectrum of oligomeric particles in the cortex of rapidly progressive cases, implicating these structures in variable rates of propagation in the brain, and in distict disease manifestation. Since only ∼30% of phenotypic diversity of AD can be explained by polymorphisms in risk genes, these and transgenic bioassay data argue that structurally distinct Aβ particles play a major role in the diverse pathogenesis of AD, and may behave as distinct prion-like strains encoding diverse phenotypes. From these observations and our growing understanding of prions, there is a critical need for new strain-specific diagnostic strategies for misfolded proteins causing these elusive disorders. Since targeted drug therapy can induce mutation and evolution of prions into new strains, effective treatments of AD will require drugs that enhance clearance of pathogenic conformers, reduce the precursor protein, or inhibit the conversion of precursors into prion-like states.
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Affiliation(s)
- Mark Cohen
- a National Prion Disease Pathology Surveillance Center, Case Western Reserve University School of Medicine , Cleveland , OH , USA.,b Department of Pathology , Case Western Reserve University School of Medicine , Cleveland , OH , USA
| | - Brian Appleby
- a National Prion Disease Pathology Surveillance Center, Case Western Reserve University School of Medicine , Cleveland , OH , USA.,c Department of Neurology , Case Western Reserve University School of Medicine , Cleveland , OH , USA.,d Department of Psychiatry , Case Western Reserve University School of Medicine , Cleveland , OH , USA
| | - Jiri G Safar
- a National Prion Disease Pathology Surveillance Center, Case Western Reserve University School of Medicine , Cleveland , OH , USA.,b Department of Pathology , Case Western Reserve University School of Medicine , Cleveland , OH , USA.,c Department of Neurology , Case Western Reserve University School of Medicine , Cleveland , OH , USA
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48
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Drummond E, Wisniewski T. The use of localized proteomics to identify the drivers of Alzheimer's disease pathogenesis. Neural Regen Res 2017; 12:912-913. [PMID: 28761421 PMCID: PMC5514863 DOI: 10.4103/1673-5374.208570] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Eleanor Drummond
- Center for Cognitive Neurology, Department of Neurology, New York University School of Medicine, New York, NY, USA
| | - Thomas Wisniewski
- Department of Neurology, Pathology and Psychiatry, New York University School of Medicine, New York, NY, USA
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Corgiat BA, Mueller C. Using Laser Capture Microdissection to Isolate Cortical Laminae in Nonhuman Primate Brain. Methods Mol Biol 2017; 1606:115-132. [PMID: 28501997 DOI: 10.1007/978-1-4939-6990-6_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Laser capture microdissection (LCM) is a technique that allows procurement of an enriched cell population from a heterogeneous tissue sample under direct microscopic visualization. Fundamentally, laser capture microdissection consists of three main steps: (1) visualizing the desired cell population by microscopy, (2) melting a thermolabile polymer onto the desired cell populations using infrared laser energy to form a polymer-cell composite (capture method) or photovolatizing a region of tissue using ultraviolet laser energy (cutting method), and (3) removing the desired cell population from the heterogeneous tissue. In this chapter, we discuss the infrared capture method only. LCM technology is compatible with a wide range of downstream applications such as mass spectrometry, DNA genotyping and RNA transcript profiling, cDNA library generation, proteomics discovery, and signal pathway mapping. This chapter profiles the ArcturusXT™ laser capture microdissection instrument, using isolation of specific cortical lamina from nonhuman primate brain regions, and sample preparation methods for downstream proteomic applications.
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Affiliation(s)
- Brian A Corgiat
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, MS1A9, Manassas, VA, 20110, USA.
| | - Claudius Mueller
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, MS1A9, Manassas, VA, 20110, USA
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50
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Iacono D, Geraci-Erck M, Peng H, Bouffard JP. Symmetric Bihemispheric Postmortem Brain Cutting to Study Healthy and Pathological Brain Conditions in Humans. J Vis Exp 2016. [PMID: 28060309 DOI: 10.3791/54602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Neuropathologists, at times, feel intimidated by the amount of knowledge needed to generate definitive diagnoses for complex neuropsychiatric phenomena described in those patients for whom a brain autopsy has been requested. Although the advancements of biomedical sciences and neuroimaging have revolutionized the neuropsychiatric field, they have also generated the misleading idea that brain autopsies have only a confirmatory value. This false idea created a drastic reduction of autopsy rates and, consequently, a reduced possibility to perform more detailed and extensive neuropathological investigations, which are necessary to comprehend numerous normal and pathological aspects yet unknown of the human brain. The traditional inferential method of correlation between observed neuropsychiatric phenomena and corresponding localization/characterization of their possible neurohistological correlates continues to have an undeniable value. In the context of neuropsychiatric diseases, the traditional clinicopathological method is still the best possible methodology (and often the only available) to link unique neuropsychiatric features to their corresponding neuropathological substrates, since it relies specifically upon the direct physical assessment of brain tissues. The assessment of postmortem brains is based on brain cutting procedures that vary across different neuropathology centers. Brain cuttings are performed in a relatively extensive and systematic way based on the various clinical and academic contingencies present in each institution. A more anatomically inclusive and symmetric bi-hemispheric brain cutting methodology should at least be used for research purposes in human neuropathology to coherently investigate, in depth, normal and pathological conditions with the peculiarities of the human brain (i.e., hemispheric specialization and lateralization for specific functions). Such a method would provide a more comprehensive collection of neuropathologically well-characterized brains available for current and future biotechnological and neuroimaging techniques. We describe a symmetric bi-hemispheric brain cutting procedure for the investigation of hemispheric differences in human brain pathologies and for use with current as well as future biomolecular/neuroimaging techniques.
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Affiliation(s)
- Diego Iacono
- Neuropathology Research, Biomedical Research Institute of New Jersey (BRInj);
| | - Maria Geraci-Erck
- Neuropathology Research, Biomedical Research Institute of New Jersey (BRInj)
| | - Hui Peng
- Neuropathology Research, Biomedical Research Institute of New Jersey (BRInj)
| | - John Paul Bouffard
- Department of Pathology, Atlantic Health System (AHS), Overlook Medical Center
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