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Faizan M, Sachan N, Verma O, Sarkar A, Rawat N, Pratap Singh M. Cerebrospinal fluid protein biomarkers in Parkinson's disease. Clin Chim Acta 2024; 556:117848. [PMID: 38417781 DOI: 10.1016/j.cca.2024.117848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/24/2024] [Accepted: 02/25/2024] [Indexed: 03/01/2024]
Abstract
Proteomic profiling is an effective way to identify biomarkers for Parkinson's disease (PD). Cerebrospinal fluid (CSF) has direct connectivity with the brain and could be a source of finding biomarkers and their clinical implications. Comparative proteomic profiling has shown that a group of differentially displayed proteins exist. The studies performed using conventional and classical tools also supported the occurrence of these proteins. Many studies have highlighted the potential of CSF proteomic profiling for biomarker identification and their clinical applications. Some of these proteins are useful for disease diagnosis and prediction. Proteomic profiling of CSF also has immense potential to distinguish PD from similar neurodegenerative disorders. A few protein biomarkers help in fundamental knowledge generation and clinical interpretation. However, the specific biomarker of PD is not yet known. The use of proteomic approaches in clinical settings is also rare. A large-scale, multi-centric, multi-population and multi-continental study using multiple proteomic tools is warranted. Such a study can provide valuable, comprehensive and reliable information for a better understanding of PD and the development of specific biomarkers. The current article sheds light on the role of CSF proteomic profiling in identifying biomarkers of PD and their clinical implications. The article also explains the achievements, obstacles and hopes for future directions of this approach.
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Affiliation(s)
- Mohd Faizan
- Systems Toxicology Group, FEST Division, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Nidhi Sachan
- Systems Toxicology Group, FEST Division, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India
| | - Oyashvi Verma
- Systems Toxicology Group, FEST Division, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Alika Sarkar
- Systems Toxicology Group, FEST Division, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Neeraj Rawat
- Systems Toxicology Group, FEST Division, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Mahendra Pratap Singh
- Systems Toxicology Group, FEST Division, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India; Capacity Building and Knowledge Services, ASSIST Division, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India.
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Chopra A, Outeiro TF. Aggregation and beyond: alpha-synuclein-based biomarkers in synucleinopathies. Brain 2024; 147:81-90. [PMID: 37526295 DOI: 10.1093/brain/awad260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 07/12/2023] [Accepted: 07/15/2023] [Indexed: 08/02/2023] Open
Abstract
Parkinson's disease is clinically known for the loss of dopaminergic neurons in the substantia nigra pars compacta and accumulation of intraneuronal cytoplasmic inclusions rich in alpha-synuclein called 'Lewy bodies' and 'Lewy neurites'. Together with dementia with Lewy bodies and multiple system atrophy, Parkinson's disease is part of a group of disorders called synucleinopathies. Currently, diagnosis of synucleinopathies is based on the clinical assessment which often takes place in advanced disease stages. While the causal role of alpha-synuclein aggregates in these disorders is still debatable, measuring the levels, types or seeding properties of different alpha-synuclein species hold great promise as biomarkers. Recent studies indicate significant differences in peptide, protein and RNA levels in blood samples from patients with Parkinson's disease. Seed amplification assays using CSF, blood, skin biopsy, olfactory swab samples show great promise for detecting synucleinopathies and even for discriminating between different synucleinopathies. Interestingly, small extracellular vesicles, such as exosomes, display differences in their cargoes in Parkinson's disease patients versus controls. In this update, we focus on alpha-synuclein aggregation and possible sources of disease-related species released in extracellular vesicles, which promise to revolutionize the diagnosis and the monitoring of disease progression.
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Affiliation(s)
- Avika Chopra
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Tiago Fleming Outeiro
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, 37073 Göttingen, Germany
- Max Planck Institute for Multidisciplinary Sciences, 37075 Göttingen, Germany
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, UK
- Scientific Employee with an Honorary Contract at Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 37075 Göttingen, Germany
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Harvey J, Pishva E, Chouliaras L, Lunnon K. Elucidating distinct molecular signatures of Lewy body dementias. Neurobiol Dis 2023; 188:106337. [PMID: 37918758 DOI: 10.1016/j.nbd.2023.106337] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/15/2023] [Accepted: 10/27/2023] [Indexed: 11/04/2023] Open
Abstract
Dementia with Lewy bodies and Parkinson's disease dementia are common neurodegenerative diseases that share similar neuropathological profiles and spectra of clinical symptoms but are primarily differentiated by the order in which symptoms manifest. The question of whether a distinct molecular pathological profile could distinguish these disorders is yet to be answered. However, in recent years, studies have begun to investigate genomic, epigenomic, transcriptomic and proteomic differences that may differentiate these disorders, providing novel insights in to disease etiology. In this review, we present an overview of the clinical and pathological hallmarks of Lewy body dementias before summarizing relevant research into genetic, epigenetic, transcriptional and protein signatures in these diseases, with a particular interest in those resolving "omic" level changes. We conclude by suggesting future research directions to address current gaps and questions present within the field.
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Affiliation(s)
- Joshua Harvey
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Ehsan Pishva
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK; Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, the Netherlands
| | - Leonidas Chouliaras
- Department of Psychiatry, School of Clinical Medicine, University of Cambridge, Cambridge, UK; Specialist Dementia and Frailty Service, Essex Partnership University NHS Foundation Trust, Epping, UK
| | - Katie Lunnon
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK.
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Del Campo M, Vermunt L, Peeters CFW, Sieben A, Hok-A-Hin YS, Lleó A, Alcolea D, van Nee M, Engelborghs S, van Alphen JL, Arezoumandan S, Chen-Plotkin A, Irwin DJ, van der Flier WM, Lemstra AW, Teunissen CE. CSF proteome profiling reveals biomarkers to discriminate dementia with Lewy bodies from Alzheimer´s disease. Nat Commun 2023; 14:5635. [PMID: 37704597 PMCID: PMC10499811 DOI: 10.1038/s41467-023-41122-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 08/22/2023] [Indexed: 09/15/2023] Open
Abstract
Diagnosis of dementia with Lewy bodies (DLB) is challenging and specific biofluid biomarkers are highly needed. We employed proximity extension-based assays to measure 665 proteins in the cerebrospinal fluid (CSF) from patients with DLB (n = 109), Alzheimer´s disease (AD, n = 235) and cognitively unimpaired controls (n = 190). We identified over 50 CSF proteins dysregulated in DLB, enriched in myelination processes among others. The dopamine biosynthesis enzyme DDC was the strongest dysregulated protein, and could efficiently discriminate DLB from controls and AD (AUC:0.91 and 0.81 respectively). Classification modeling unveiled a 7-CSF biomarker panel that better discriminate DLB from AD (AUC:0.93). A custom multiplex panel for six of these markers (DDC, CRH, MMP-3, ABL1, MMP-10, THOP1) was developed and validated in independent cohorts, including an AD and DLB autopsy cohort. This DLB CSF proteome study identifies DLB-specific protein changes and translates these findings to a practicable biomarker panel that accurately identifies DLB patients, providing promising diagnostic and clinical trial testing opportunities.
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Affiliation(s)
- Marta Del Campo
- Neurochemistry Laboratory and Biobank, Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location VUmc, Amsterdam, The Netherlands.
- Barcelonaßeta Brain Research Center, Pasqual Maragall Foundation, Barcelona, Spain.
- Departamento de Ciencias Farmacéuticas y de la Salud, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Madrid, Spain.
| | - Lisa Vermunt
- Neurochemistry Laboratory and Biobank, Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location VUmc, Amsterdam, The Netherlands
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location VUmc, Amsterdam, The Netherlands
| | - Carel F W Peeters
- Mathematical & Statistical Methods group (Biometris), Wageningen University & Research, Wageningen, The Netherlands
| | - Anne Sieben
- Lab of neuropathology, Neurobiobank, Institute Born-Bunge, Antwerp University, Edegem, Belgium
| | - Yanaika S Hok-A-Hin
- Neurochemistry Laboratory and Biobank, Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location VUmc, Amsterdam, The Netherlands
| | - Alberto Lleó
- Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau (IIB SANT PAU) - Hospital de Sant Pau, Universitat Autònoma de Barcelona, Hospital de la Santa Creu i Sant Pau, Barcelona, Catalunya, Spain
- Center of Biomedical Investigation Network for Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Daniel Alcolea
- Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau (IIB SANT PAU) - Hospital de Sant Pau, Universitat Autònoma de Barcelona, Hospital de la Santa Creu i Sant Pau, Barcelona, Catalunya, Spain
- Center of Biomedical Investigation Network for Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Mirrelijn van Nee
- Department of Epidemiology & Data Science, Amsterdam Public Health research institute, Amsterdam University Medical Centers, Location VUmc, Amsterdam, The Netherlands
| | - Sebastiaan Engelborghs
- Reference Center for Biological Markers of Dementia (BIODEM), Laboratory of Neurochemistry and Behavior, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
- Vrije Universiteit Brussel, Center for Neurosciences (C4N), Neuroprotection and Neuromodulation Research Group (NEUR), Brussels, Belgium
- Universitair Ziekenhuis Brussel, Department of Neurology, Brussels, Belgium
| | - Juliette L van Alphen
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location VUmc, Amsterdam, The Netherlands
| | - Sanaz Arezoumandan
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alice Chen-Plotkin
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David J Irwin
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Wiesje M van der Flier
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location VUmc, Amsterdam, The Netherlands
- Department of Epidemiology & Data Science, Amsterdam Public Health research institute, Amsterdam University Medical Centers, Location VUmc, Amsterdam, The Netherlands
| | - Afina W Lemstra
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location VUmc, Amsterdam, The Netherlands
| | - Charlotte E Teunissen
- Neurochemistry Laboratory and Biobank, Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location VUmc, Amsterdam, The Netherlands
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Sohaei D, Thebault S, Avery LM, Batruch I, Lam B, Xu W, Saadeh RS, Scarisbrick IA, Diamandis EP, Prassas I, Freedman MS. Cerebrospinal fluid camk2a levels at baseline predict long-term progression in multiple sclerosis. Clin Proteomics 2023; 20:33. [PMID: 37644477 PMCID: PMC10466840 DOI: 10.1186/s12014-023-09418-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/28/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Multiple sclerosis (MS) remains a highly unpredictable disease. Many hope that fluid biomarkers may contribute to better stratification of disease, aiding the personalisation of treatment decisions, ultimately improving patient outcomes. OBJECTIVE The objective of this study was to evaluate the predictive value of CSF brain-specific proteins from early in the disease course of MS on long term clinical outcomes. METHODS In this study, 34 MS patients had their CSF collected and stored within 5 years of disease onset and were then followed clinically for at least 15 years. CSF concentrations of 64 brain-specific proteins were analyzed in the 34 patient CSF, as well as 19 age and sex-matched controls, using a targeted liquid-chromatography tandem mass spectrometry approach. RESULTS We identified six CSF brain-specific proteins that significantly differentiated MS from controls (p < 0.05) and nine proteins that could predict disease course over the next decade. CAMK2A emerged as a biomarker candidate that could discriminate between MS and controls and could predict long-term disease progression. CONCLUSION Targeted approaches to identify and quantify biomarkers associated with MS in the CSF may inform on long term MS outcomes. CAMK2A may be one of several candidates, warranting further exploration.
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Affiliation(s)
- Dorsa Sohaei
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Simon Thebault
- Department of Medicine, The Ottawa Hospital, 01 Smyth Road, Box 601, Ottawa, ON, K1H 8L6, Canada
- The Ottawa Hospital Research Institute, Ottawa, Canada
| | - Lisa M Avery
- Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
- Department of Biostatistics, The Princess Margaret Cancer Centre, University of Toronto, Toronto, Canada
| | - Ihor Batruch
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada
| | - Brian Lam
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, United States of America
| | - Wei Xu
- Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
- Department of Biostatistics, The Princess Margaret Cancer Centre, University of Toronto, Toronto, Canada
| | - Rubah S Saadeh
- Department of Physical Medicine and Rehabilitation, Center for Multiple Sclerosis and Autoimmune Neurology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Isobel A Scarisbrick
- Department of Physical Medicine and Rehabilitation, Center for Multiple Sclerosis and Autoimmune Neurology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Eleftherios P Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Lunenfeld-Tanenbaum Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Department of Clinical Biochemistry, University Health Network, Toronto, Canada
| | - Ioannis Prassas
- Mount Sinai Hospital, Joseph & Wolf Lebovic Ctr, 60 Murray St [Box 32]; Flr 6 - Rm L6-201, Toronto, ON, M5T 3L9, Canada.
- Laboratory Medicine Program, University Health Network, Toronto, Canada.
| | - Mark S Freedman
- Department of Medicine, The Ottawa Hospital, 01 Smyth Road, Box 601, Ottawa, ON, K1H 8L6, Canada.
- The Ottawa Hospital Research Institute, Ottawa, Canada.
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Tiwari V, Shukla S. Lipidomics and proteomics: An integrative approach for early diagnosis of dementia and Alzheimer's disease. Front Genet 2023; 14:1057068. [PMID: 36845373 PMCID: PMC9946989 DOI: 10.3389/fgene.2023.1057068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 01/23/2023] [Indexed: 02/11/2023] Open
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disorder and considered to be responsible for majority of worldwide prevalent dementia cases. The number of patients suffering from dementia are estimated to increase up to 115.4 million cases worldwide in 2050. Hence, AD is contemplated to be one of the major healthcare challenge in current era. This disorder is characterized by impairment in various signaling molecules at cellular and nuclear level including aggregation of Aβ protein, tau hyper phosphorylation altered lipid metabolism, metabolites dysregulation, protein intensity alteration etc. Being heterogeneous and multifactorial in nature, the disease do not has any cure or any confirmed diagnosis before the onset of clinical manifestations. Hence, there is a requisite for early diagnosis of AD in order to downturn the progression/risk of the disorder and utilization of newer technologies developed in this field are aimed to provide an extraordinary assistance towards the same. The lipidomics and proteomics constitute large scale study of cellular lipids and proteomes in biological matrices at normal stage or any stage of a disease. The study involves high throughput quantification and detection techniques such as mass spectrometry, liquid chromatography, nuclear mass resonance spectroscopy, fluorescence spectroscopy etc. The early detection of altered levels of lipids and proteins in blood or any other biological matrices could aid in preventing the progression of AD and dementia. Therefore, the present review is designed to focus on the recent techniques and early diagnostic criteria for AD, revealing the role of lipids and proteins in this disease and their assessment through different techniques.
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Affiliation(s)
- Virendra Tiwari
- Division of Neuroscience and Ageing Biology, CSIR- Central Drug Research Institute, Lucknow, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Shubha Shukla
- Division of Neuroscience and Ageing Biology, CSIR- Central Drug Research Institute, Lucknow, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India,*Correspondence: Shubha Shukla,
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Chen R, Yi Y, Xiao W, Zhong B, Zhang L, Zeng Y. Urinary protein biomarkers based on LC-MS/MS analysis to discriminate vascular dementia from Alzheimer's disease in Han Chinese population. Front Aging Neurosci 2023; 15:1070854. [PMID: 36761180 PMCID: PMC9905227 DOI: 10.3389/fnagi.2023.1070854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 01/04/2023] [Indexed: 01/27/2023] Open
Abstract
Objective This study aimed to identify the potential urine biomarkers of vascular dementia (VD) and unravel the disease-associated mechanisms by applying Liquid chromatography tandem-mass spectrometry (LC-MS/MS). Methods LC-MS/MS proteomic analysis was applied to urine samples from 3 groups, including 14 patients with VD, 9 patients with AD, and 21 normal controls (NC). By searching the MS data by Proteome Discoverer software, analyzing the protein abundances qualitatively and quantitatively, comparing between groups, combining bioinformatics analysis using Gene Ontology (GO) and pathway crosstalk analysis using Kyoto Encyclopedia of Genes and Genomes (KEGG), and literature searching, the differentially expressed proteins (DEPs) of VD can be comprehensively determined at last and were further quantified by receiver operating characteristic (ROC) curve methods. Results The proteomic findings showed quantitative changes in patients with VD compared to patients with NC and AD groups; among 4,699 identified urine proteins, 939 and 1,147 proteins displayed quantitative changes unique to VD vs. NC and AD, respectively, including 484 overlapped common DEPs. Then, 10 unique proteins named in KEGG database (including PLOD3, SDCBP, SRC, GPRC5B, TSG101/STP22/VPS23, THY1/CD90, PLCD, CDH16, NARS/asnS, AGRN) were confirmed by a ROC curve method. Conclusion Our results suggested that urine proteins enable detection of VD from AD and VC, which may provide an opportunity for intervention.
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Affiliation(s)
- Ruijuan Chen
- Department of Geriatrics, Second Xiangya Hospital, Central South University, Changsha, Hunan, China,Department of Emergency, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou, Hainan, China
| | - Yuanjing Yi
- Department of Geriatrics, Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wenbiao Xiao
- Department of Geriatrics, Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Bowen Zhong
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Le Zhang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yi Zeng
- Department of Geriatrics, Second Xiangya Hospital, Central South University, Changsha, Hunan, China,*Correspondence: Yi Zeng,
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Tsamourgelis A, Swann P, Chouliaras L, O'Brien JT. From protein biomarkers to proteomics in dementia with Lewy Bodies. Ageing Res Rev 2023; 83:101771. [PMID: 36328346 DOI: 10.1016/j.arr.2022.101771] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 09/15/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022]
Abstract
Dementia with Lewy Bodies (DLB) is the second most common neurodegenerative dementia. Despite considerable research progress, there remain gaps in our understanding of the pathophysiology and there is no disease-modifying treatment. Proteomics is a powerful tool to elucidate complex biological pathways across heterogenous conditions. This review summarizes the widely used proteomic methods and presents evidence for protein dysregulation in the brain and peripheral tissues in DLB. Proteomics of post-mortem brain tissue shows that DLB shares common features with other dementias, such as synaptic dysfunction, but retains a unique protein signature. Promising diagnostic biomarkers are being identified in cerebrospinal fluid (CSF), blood, and peripheral tissues, such as serum Heart-type fatty acid binding protein. Research is needed to track these changes from the prodromal stage to established dementia, with standardized workflows to ensure replicability. Identifying novel protein targets in causative biological pathways could lead to the development of new targeted therapeutics or the stratification of participants for clinical trials.
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Gerstmann K, Kindbeiter K, Telley L, Bozon M, Reynaud F, Théoulle E, Charoy C, Jabaudon D, Moret F, Castellani V. A balance of noncanonical Semaphorin signaling from the cerebrospinal fluid regulates apical cell dynamics during corticogenesis. Sci Adv 2022; 8:eabo4552. [PMID: 36399562 PMCID: PMC9674300 DOI: 10.1126/sciadv.abo4552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 10/03/2022] [Indexed: 06/01/2023]
Abstract
During corticogenesis, dynamic regulation of apical adhesion is fundamental to generate correct numbers and cell identities. While radial glial cells (RGCs) maintain basal and apical anchors, basal progenitors and neurons detach and settle at distal positions from the apical border. Whether diffusible signals delivered from the cerebrospinal fluid (CSF) contribute to the regulation of apical adhesion dynamics remains fully unknown. Secreted class 3 Semaphorins (Semas) trigger cell responses via Plexin-Neuropilin (Nrp) membrane receptor complexes. Here, we report that unconventional Sema3-Nrp preformed complexes are delivered by the CSF from sources including the choroid plexus to Plexin-expressing RGCs via their apical endfeet. Through analysis of mutant mouse models and various ex vivo assays mimicking ventricular delivery to RGCs, we found that two different complexes, Sema3B/Nrp2 and Sema3F/Nrp1, exert dual effects on apical endfeet dynamics, nuclei positioning, and RGC progeny. This reveals unexpected balance of CSF-delivered guidance molecules during cortical development.
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Affiliation(s)
- Katrin Gerstmann
- MeLis, CNRS UMR 5284, INSERM U1314, University of Lyon, Université Claude Bernard Lyon 1, Institut NeuroMyoGène, 8 avenue Rockefeller, 69008 Lyon, France
| | - Karine Kindbeiter
- MeLis, CNRS UMR 5284, INSERM U1314, University of Lyon, Université Claude Bernard Lyon 1, Institut NeuroMyoGène, 8 avenue Rockefeller, 69008 Lyon, France
| | - Ludovic Telley
- Department of Basic Neuroscience, University of Geneva, 1211 Geneva 4, Switzerland
| | - Muriel Bozon
- MeLis, CNRS UMR 5284, INSERM U1314, University of Lyon, Université Claude Bernard Lyon 1, Institut NeuroMyoGène, 8 avenue Rockefeller, 69008 Lyon, France
| | - Florie Reynaud
- MeLis, CNRS UMR 5284, INSERM U1314, University of Lyon, Université Claude Bernard Lyon 1, Institut NeuroMyoGène, 8 avenue Rockefeller, 69008 Lyon, France
| | - Emy Théoulle
- MeLis, CNRS UMR 5284, INSERM U1314, University of Lyon, Université Claude Bernard Lyon 1, Institut NeuroMyoGène, 8 avenue Rockefeller, 69008 Lyon, France
| | - Camille Charoy
- UCL Institute of Ophthalmology, University College London, London, UK
| | - Denis Jabaudon
- Department of Basic Neuroscience, University of Geneva, 1211 Geneva 4, Switzerland
| | - Frédéric Moret
- MeLis, CNRS UMR 5284, INSERM U1314, University of Lyon, Université Claude Bernard Lyon 1, Institut NeuroMyoGène, 8 avenue Rockefeller, 69008 Lyon, France
| | - Valerie Castellani
- MeLis, CNRS UMR 5284, INSERM U1314, University of Lyon, Université Claude Bernard Lyon 1, Institut NeuroMyoGène, 8 avenue Rockefeller, 69008 Lyon, France
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Wang D, Ma M, Huang J, Gu TJ, Cui Y, Li M, Wang Z, Zetterberg H, Li L. Boost-DiLeu: Enhanced Isobaric N, N-Dimethyl Leucine Tagging Strategy for a Comprehensive Quantitative Glycoproteomic Analysis. Anal Chem 2022; 94:11773-11782. [PMID: 35960654 PMCID: PMC9966376 DOI: 10.1021/acs.analchem.2c01773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Intact glycopeptide analysis has been of great interest because it can elucidate glycosylation site information and glycan structural composition at the same time. However, mass spectrometry (MS)-based glycoproteomic analysis is hindered by the low abundance and poor ionization efficiency of glycopeptides. Relatively large amounts of starting materials are needed for the enrichment, which makes the identification and quantification of intact glycopeptides from samples with limited quantity more challenging. To overcome these limitations, we developed an improved isobaric labeling strategy with an additional boosting channel to enhance N,N-dimethyl leucine (DiLeu) tagging-based quantitative glycoproteomic analysis, termed as Boost-DiLeu. With the integration of a one-tube sample processing workflow and high-pH fractionation, 3514 quantifiable N-glycopeptides were identified from 30 μg HeLa cell tryptic digests with reliable quantification performance. Furthermore, this strategy was applied to human cerebrospinal fluid (CSF) samples to differentiate N-glycosylation profiles between Alzheimer's disease (AD) patients and non-AD donors. The results revealed processes and pathways affected by dysregulated N-glycosylation in AD, including platelet degranulation, cell adhesion, and extracellular matrix, which highlighted the involvement of N-glycosylation aberrations in AD pathogenesis. Moreover, weighted gene coexpression network analysis (WGCNA) showed nine modules of glycopeptides, two of which were associated with the AD phenotype. Our results demonstrated the feasibility of using this strategy for in-depth glycoproteomic analysis of size-limited clinical samples. Taken together, we developed and optimized a strategy for the enhanced comprehensive quantitative intact glycopeptide analysis with DiLeu labeling, showing significant promise for identifying novel therapeutic targets or biomarkers in biological systems with a limited sample quantity.
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Affiliation(s)
- Danqing Wang
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Min Ma
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Junfeng Huang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Ting-Jia Gu
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Yusi Cui
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Miyang Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Zicong Wang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Henrik Zetterberg
- Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 43141, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, 43130, Sweden.,Department of Molecular Neuroscience, UCL Institute of Neurology, London, WC1N 3BG, U.K.,UK Dementia Research Institute at UCL, London, WC1N 3BG, U.K.,Hong Kong Center for Neurodegenerative Diseases, Hong Kong, China
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.,School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA.,To whom correspondence should be addressed. . Phone: +1-(608)-265- 8491, Fax: +1-(608)-262-5345. Mailing Address: 5125 Rennebohm Hall, 777 Highland Avenue, Madison, WI 53705, USA
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11
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Lin H, Tang R, Fan L, Wang E. Exogenous Tetranectin Alleviates Pre-formed-fibrils-induced Synucleinopathies in SH-SY5Y Cells by Activating the Plasminogen Activation System. Neurochem Res 2022; 47:3192-3201. [PMID: 35895152 DOI: 10.1007/s11064-022-03673-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 06/25/2022] [Accepted: 06/28/2022] [Indexed: 10/16/2022]
Abstract
Parkinson's disease (PD) is a common neurodegenerative disease. Previously we identified tetranectin (TN) as a differentially expressed protein in the cerebrospinal fluid of PD patients, and we were surprised to find that TN knockout mice developed PD features. However, the specific role of TN in PD has not been clarified. In this study, we aimed to determine the effect of exogenous TN on cellular PD models and elucidate the underlying mechanisms. We found that exogenous TN could alleviate pre-formed-fibrils (PFFs)-induced synucleinopathies in SH-SY5Y cells and reduce the cell-to-cell transmission of α-synuclein (SYN). We also found that TN can promote the degradation of SYN by plasmin, which may account for its effect on cellular PD models. Moreover, administration of SYN/PFFs decreased the expression of TN and increased the expression of plasminogen activator inhibitor-1 (PAI-1) in SH-SY5Y cells, thereby reducing plasmin activity. Our findings depict a possible SYN-TN-plasmin interaction in which elevated levels of extracellular SYN monomers and aggregates in PD diminish the production of TN and PAI-1. Such changes lead to a reduced plasmin activity, which in turn reduces the degradation of extracellular SYN, thus forming a vicious cycle.
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Affiliation(s)
- Heng Lin
- Department of Neurosurgery, Jinshan Hospital, Fudan University, Shanghai, 201508, China
| | - Ri Tang
- Department of Neurosurgery, Jinshan Hospital, Fudan University, Shanghai, 201508, China.,Department of Critical Care Medicine, School of Medicine, Renji Hospital, Shanghai Jiaotong University, Shanghai, 200127, China
| | - Lijun Fan
- Department of Neurosurgery, Jinshan Hospital, Fudan University, Shanghai, 201508, China
| | - Ersong Wang
- Department of Neurosurgery, Jinshan Hospital, Fudan University, Shanghai, 201508, China.
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12
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Krance SH, Wu CY, Chan ACY, Kwong S, Song BX, Xiong LY, Ouk M, Chen MH, Zhang J, Yung A, Stanley M, Herrmann N, Lanctôt KL, Swardfager W. Endosomal-Lysosomal and Autophagy Pathway in Alzheimer's Disease: A Systematic Review and Meta-Analysis. J Alzheimers Dis 2022; 88:1279-1292. [PMID: 35754279 DOI: 10.3233/jad-220360] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND The endosomal-lysosomal and autophagy (ELA) pathway may be implicated in the progression of Alzheimer's disease (AD); however, findings thus far have been inconsistent. OBJECTIVE To systematically summarize differences in endosomal-lysosomal and autophagy proteins in the cerebrospinal fluid (CSF) of people with AD and healthy controls (HC). METHODS Studies measuring CSF concentrations of relevant proteins in the ELA pathway in AD and healthy controls were included. Standardized mean differences (SMD) with 95% confidence intervals (CI) between AD and healthy controls in CSF concentrations of relevant proteins were meta-analyzed using random-effects models. RESULTS Of 2,471 unique studies, 43 studies were included in the systematic review and meta-analysis. Differences in ELA protein levels in the CSF between AD and healthy controls were observed, particularly in lysosomal membrane (LAMP-1: NAD/NHC = 348/381, SMD [95% CI] = 0.599 [0.268, 0.930], I2 = 72.8% ; LAMP-2: NAD/NHC = 401/510, SMD [95% CI] = 0.480 [0.134, 0.826], I2 = 78.7%) and intra-lysosomal proteins (GM2A: NAD/NHC = 390/420, SMD [95% CI] = 0.496 [0.039, 0.954], I2 = 87.7% ; CTSB: NAD/NHC = 485/443, SMD [95% CI] = 0.201 [0.029, 0.374], I2 = 28.5% ; CTSZ: NAD/NHC = 535/820, SMD [95% CI] = -0.160 [-0.305, -0.015], I2 = 24.0%) and in proteins involved in endocytosis (AP2B1:NAD/NHC = 171/205, SMD [95% CI] = 0.513 [0.259, 0.768], I2 = 27.4% ; FLOT1: NAD/NHC = 41/45, SMD [95% CI] = -0.489 [-0.919, -0.058], I2 <0.01). LC3B, an autophagy marker, also showed a difference (NAD/NHC = 70/59, SMD [95% CI] = 0.648 [0.180, 1.116], I2 = 38.3%)), but overall there was limited evidence suggesting differences in proteins involved in endosomal function and autophagy. CONCLUSION Dysregulation of proteins in the ELA pathway may play an important role in AD pathogenesis. Some proteins within this pathway may be potential biomarkers for AD.
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Affiliation(s)
- Saffire H Krance
- Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada.,Sandra Black Centre for Brain Resilience and Recovery, Sunnybrook Research Institute, Toronto, Ontario, Canada.,Hurvitz Brain Sciences Program, Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Che-Yuan Wu
- Sandra Black Centre for Brain Resilience and Recovery, Sunnybrook Research Institute, Toronto, Ontario, Canada.,Hurvitz Brain Sciences Program, Sunnybrook Research Institute, Toronto, Ontario, Canada.,Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Alison C Y Chan
- Sandra Black Centre for Brain Resilience and Recovery, Sunnybrook Research Institute, Toronto, Ontario, Canada.,Hurvitz Brain Sciences Program, Sunnybrook Research Institute, Toronto, Ontario, Canada.,Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Stephanie Kwong
- Sandra Black Centre for Brain Resilience and Recovery, Sunnybrook Research Institute, Toronto, Ontario, Canada.,Hurvitz Brain Sciences Program, Sunnybrook Research Institute, Toronto, Ontario, Canada.,Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Bing Xin Song
- Hurvitz Brain Sciences Program, Sunnybrook Research Institute, Toronto, Ontario, Canada.,Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Lisa Y Xiong
- Sandra Black Centre for Brain Resilience and Recovery, Sunnybrook Research Institute, Toronto, Ontario, Canada.,Hurvitz Brain Sciences Program, Sunnybrook Research Institute, Toronto, Ontario, Canada.,Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Michael Ouk
- Sandra Black Centre for Brain Resilience and Recovery, Sunnybrook Research Institute, Toronto, Ontario, Canada.,Hurvitz Brain Sciences Program, Sunnybrook Research Institute, Toronto, Ontario, Canada.,Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Ming Hui Chen
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Jane Zhang
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Adrian Yung
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Meagan Stanley
- Western Libraries, University of Western Ontario, London, Ontario, Canada
| | - Nathan Herrmann
- Hurvitz Brain Sciences Program, Sunnybrook Research Institute, Toronto, Ontario, Canada.,Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada.,Department of Psychiatry, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Krista L Lanctôt
- Hurvitz Brain Sciences Program, Sunnybrook Research Institute, Toronto, Ontario, Canada.,Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada.,Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada.,Department of Psychiatry, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada.,University Health Network KITE Toronto Rehabilitation Institute, Toronto, Ontario, Canada.,Toronto Dementia Research Alliance, Toronto, Ontario, Canada
| | - Walter Swardfager
- Sandra Black Centre for Brain Resilience and Recovery, Sunnybrook Research Institute, Toronto, Ontario, Canada.,Hurvitz Brain Sciences Program, Sunnybrook Research Institute, Toronto, Ontario, Canada.,Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada.,University Health Network KITE Toronto Rehabilitation Institute, Toronto, Ontario, Canada
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13
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Liu Y, Pan X, Bao Y, Wei L, Gao Y. Many kinds of oxidized proteins are present more in the urine of the elderly. Clin Proteomics 2022; 19:22. [PMID: 35733114 PMCID: PMC9214981 DOI: 10.1186/s12014-022-09360-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 06/08/2022] [Indexed: 11/22/2022] Open
Abstract
Background Many studies have shown an association between aging and oxidation. To our knowledge, there have been no studies exploring aging-related urine proteome modifications. The purpose of this study was to explore differences in global chemical modifications of urinary protein at different ages. Methods Discovery (n=38) cohort MS data including children, young and old groups were downloaded from three published studies, and this data was analyzed using open-pFind for identifying modifications. Verification cohort human samples (n=28) including young, middle-aged, and old groups, rat samples (n=7) at three-time points after birth, adulthood, and old age were collected and processed in the laboratory simultaneously based on label-free quantification combined with pFind. Results Discovery cohort: there were 28 kinds of differential oxidations in the old group that were higher than those in the young or children group in. Verification cohort: there were 17 kinds of differential oxidations of 49 oxidized proteins in the middle and old groups, which were significantly higher than those in the young group. Both oxidations and oxidized proteins distinguished different age groups well. There were also 15 kinds of differential oxidations in old age higher than others in the rat cohort. The results showed that the validation experiment was basically consistent with the results of the discovery experiment, showing that the level of oxidized proteins in urine increased significantly with age. Conclusions Our study is the first to show that oxidative proteins occur in urine and that oxidations are higher in older than younger ages. Perhaps improving the degree of excretion of oxidative protein in vivo through the kidney is helpful for maintaining the homeostasis of the body’s internal environment, delaying aging and the occurrence of senile diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s12014-022-09360-2.
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Affiliation(s)
- Yongtao Liu
- Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Gene Engineering Drug and Biotechnology, Beijing Normal University, Beijing, 100875, China
| | - Xuanzhen Pan
- Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Gene Engineering Drug and Biotechnology, Beijing Normal University, Beijing, 100875, China
| | - Yijin Bao
- Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Gene Engineering Drug and Biotechnology, Beijing Normal University, Beijing, 100875, China
| | - Lilong Wei
- Clinical Laboratory, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Youhe Gao
- Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Gene Engineering Drug and Biotechnology, Beijing Normal University, Beijing, 100875, China.
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14
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Peinado JR, Chaplot K, Jarvela TS, Barbieri EM, Shorter J, Lindberg I. Sequestration of TDP-43 216-414 Aggregates by Cytoplasmic Expression of the proSAAS Chaperone. ACS Chem Neurosci 2022; 13:1651-1665. [PMID: 35549000 PMCID: PMC9731516 DOI: 10.1021/acschemneuro.2c00156] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
As neurons age, protein homeostasis becomes less efficient, resulting in misfolding and aggregation. Chaperone proteins perform vital functions in the maintenance of cellular proteostasis, and chaperone-based therapies that promote sequestration of toxic aggregates may prove useful in blocking the development of neurodegenerative disease. We previously demonstrated that proSAAS, a small secreted neuronal protein, exhibits potent chaperone activity against protein aggregation in vitro and blocks the cytotoxic effects of amyloid and synuclein oligomers in cell culture systems. We now examine whether cytoplasmic expression of proSAAS results in interactions with protein aggregates in this cellular compartment. We report that expression of proSAAS within the cytoplasm generates dense, membraneless 2 μm proSAAS spheres which progressively fuse to form larger spheres, suggesting liquid droplet-like properties. ProSAAS spheres selectively accumulate a C-terminally truncated fluorescently tagged form of TDP-43, initiating its cellular redistribution; these TDP-43-containing spheres also exhibit dynamic fusion. Efficient encapsulation of TDP-43 into proSAAS spheres is driven by its C-terminal prion-like domain; spheres must be formed for sequestration to occur. Three proSAAS sequences, a predicted coiled-coil, a conserved region (residues 158-169), and the positively charged sequence 181-185, are all required for proSAAS to form spheres able to encapsulate TDP-43 aggregates. Substitution of lysines for arginines in the 181-185 sequence results in nuclear translocation of proSAAS and encapsulation of nuclear-localized TDP-43216-414. As a functional output, we demonstrate that proSAAS expression results in cytoprotection against full-length TDP-43 toxicity in yeast. We conclude that proSAAS can act as a functional holdase for TDP-43 via this phase-separation property, representing a cytoprotectant whose unusual biochemical properties can potentially be exploited in the design of therapeutic molecules.
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Affiliation(s)
- Juan R. Peinado
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, University of Maryland, Baltimore, MD 21201 USA
| | - Kriti Chaplot
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, University of Maryland, Baltimore, MD 21201 USA
| | - Timothy S. Jarvela
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, University of Maryland, Baltimore, MD 21201 USA
| | - Edward M. Barbieri
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Iris Lindberg
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, University of Maryland, Baltimore, MD 21201 USA
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15
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Naskar A, Stezin A, Dharmappa A, Hegde S, Philip M, Kamble N, Saini J, Sandhya K, Tatu U, Yadav R, Pal PK, Alladi PA. Fibrinogen and Complement Factor H Are Promising CSF Protein Biomarkers for Parkinson's Disease with Cognitive Impairment─A Proteomics-ELISA-Based Study. ACS Chem Neurosci 2022; 13:1030-1045. [PMID: 35200010 DOI: 10.1021/acschemneuro.2c00019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Parkinson's disease (PD) with cognitive impairment (PDCI) is essentially diagnosed through clinical and neuropsychological examinations. There is a need to identify biomarkers to foresee cognitive decline in them. We performed label-free unbiased nontargeted proteomics (Q-TOF LC/MS-MS) on the CSF of non-neurological control; PDCI; PD; and normal pressure hydrocephalus (NPH) patients, followed by targeted ELISA for validation. Of the 281 proteins identified, 42 were differentially altered in PD, PDCI, and NPH. With a certain overlap, 28 proteins were altered in PDCI and 25 proteins were altered in NPH. Five significantly upregulated proteins in PDCI were fibrinogen, gelsolin, complement factor-H, and apolipoproteins A-I and A-IV, whereas carnosine dipeptidase-1, carboxypeptidase-E, dickkopf-3, and secretogranin-3 precursor proteins were downregulated. Those uniquely altered in NPH were the insulin-like growth factor-binding protein, ceruloplasmin, α-1 antitrypsin, VGF nerve growth factor, and neural cell adhesion molecule L1-like protein. The ELISA-derived protein concentrations correlated with neuropsychological scores of certain cognitive domains. In PDCI, the Wisconsin card sorting percentile correlated negatively with fibrinogen. Intraperitoneal injection of native fibrinogen caused motor deficits in C57BL/6J mice as assessed by the pole test. Thus, a battery of proteins such as fibrinogen-α-chain, CFAH, and APOA-I/APOA-IV alongside neuropsychological assessment could be reliable biomarkers to distinguish PDCI and NPH.
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Affiliation(s)
- Aditi Naskar
- Department of Clinical Psychopharmacology & Neurotoxicology, National Institute of Mental Health and Neuro Sciences, Bengaluru 560029, India
| | - Albert Stezin
- Department of Clinical Neurosciences, National Institute of Mental Health and Neuro Sciences, Bengaluru 560029, India
| | - Arpitha Dharmappa
- Department of Clinical Psychology, National Institute of Mental Health and Neuro Sciences, Bengaluru 560029, India
| | - Shantala Hegde
- Department of Clinical Psychology, National Institute of Mental Health and Neuro Sciences, Bengaluru 560029, India
| | - Mariamma Philip
- Department of Biostatistics, National Institute of Mental Health and Neuro Sciences, Bengaluru 560029, India
| | - Nitish Kamble
- Department of Neurology, National Institute of Mental Health and Neuro Sciences, Bengaluru 560029, India
| | - Jitender Saini
- Department of Neuroimaging & Interventional Radiology, National Institute of Mental Health and Neuro Sciences, Bengaluru 560029, India
| | - K. Sandhya
- Department of Anaesthesiology, Bangalore Medical College and Research Institute, Bengaluru 560002, India
| | - Utpal Tatu
- Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India
| | - Ravi Yadav
- Department of Neurology, National Institute of Mental Health and Neuro Sciences, Bengaluru 560029, India
| | - Pramod Kumar Pal
- Department of Neurology, National Institute of Mental Health and Neuro Sciences, Bengaluru 560029, India
| | - Phalguni Anand Alladi
- Department of Clinical Psychopharmacology & Neurotoxicology, National Institute of Mental Health and Neuro Sciences, Bengaluru 560029, India
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16
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Aljerian K. Saudi physicians’ perceptions of the validity of autopsy and its implications - Structural equation modeling. J Forensic Leg Med 2022; 86:102320. [DOI: 10.1016/j.jflm.2022.102320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 01/24/2022] [Accepted: 01/30/2022] [Indexed: 10/19/2022]
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17
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Laffoon SB, Doecke JD, Roberts AM, Vance JA, Reeves BD, Pertile KK, Rumble RL, Fowler CJ, Trounson B, Ames D, Martins R, Bush AI, Masters CL, Grieco PA, Dratz EA, Roberts BR. Analysis of plasma proteins using 2D gels and novel fluorescent probes: in search of blood based biomarkers for Alzheimer's disease. Proteome Sci 2022; 20:2. [PMID: 35081972 PMCID: PMC8790928 DOI: 10.1186/s12953-021-00185-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 12/23/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The Australian Imaging and Biomarker Lifestyle (AIBL) study of aging is designed to aid the discovery of biomarkers. The current study aimed to discover differentially expressed plasma proteins that could yield a blood-based screening tool for Alzheimer's disease. METHODS The concentration of proteins in plasma covers a vast range of 12 orders of magnitude. Therefore, to search for medium to low abundant biomarkers and elucidate mechanisms of AD, we immuno-depleted the most abundant plasma proteins and pre-fractionated the remaining proteins by HPLC, prior to two-dimensional gel electrophoresis. The relative levels of approximately 3400 protein species resolved on the 2D gels were compared using in-gel differential analysis with spectrally resolved fluorescent protein detection dyes (Zdyes™). Here we report on analysis of pooled plasma samples from an initial screen of a sex-matched cohort of 72 probable AD patients and 72 healthy controls from the baseline time point of AIBL. RESULTS We report significant changes in variants of apolipoprotein E, haptoglobin, α1 anti-trypsin, inter-α trypsin inhibitor, histidine-rich glycoprotein, and a protein of unknown identity. α1 anti-trypsin and α1 anti-chymotrypsin demonstrated plasma concentrations that were dependent on APOE ε4 allele dose. Our analysis also identified an association with the level of Vitamin D binding protein fragments and complement factor I with sex. We then conducted a preliminary validation study, on unique individual samples compared to the discovery cohort, using a targeted LC-MS/MS assay on a subset of discovered biomarkers. We found that targets that displayed a high degree of isoform specific changes in the 2D gels were not changed in the targeted MS assay which reports on the total level of the biomarker. CONCLUSIONS This demonstrates that further development of mass spectrometry assays is needed to capture the isoform complexity that exists in theses biological samples. However, this study indicates that a peripheral protein signature has potential to aid in the characterization of AD.
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Affiliation(s)
- Scott B. Laffoon
- Florey Institute of Neuroscience and Mental Health and The University of Melbourne Dementia Research Centre, Parkville, VIC 3010 Australia
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59715 USA
- Cooperative Research Centre for Mental Health, Carlton South, VIC Australia
| | - James D. Doecke
- Australian e-Health Research Centre, CSIRO and Cooperative Research Centre of Mental Health, Royal Brisbane and Women’s Hospital, Brisbane, QLD 4029 Australia
| | - Anne M. Roberts
- Department of Biochemistry, Emory School of Medicine, 4001 Rollins Research Building, Atlanta, GA 30322 USA
- Department of Neurology, Emory School of Medicine, 4001 Rollins Research Building, Atlanta, GA 30322 USA
| | | | - Benjamin D. Reeves
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59715 USA
| | - Kelly K. Pertile
- Florey Institute of Neuroscience and Mental Health and The University of Melbourne Dementia Research Centre, Parkville, VIC 3010 Australia
| | - Rebecca L. Rumble
- Florey Institute of Neuroscience and Mental Health and The University of Melbourne Dementia Research Centre, Parkville, VIC 3010 Australia
| | - Chris J. Fowler
- Florey Institute of Neuroscience and Mental Health and The University of Melbourne Dementia Research Centre, Parkville, VIC 3010 Australia
| | - Brett Trounson
- Florey Institute of Neuroscience and Mental Health and The University of Melbourne Dementia Research Centre, Parkville, VIC 3010 Australia
| | - David Ames
- Florey Institute of Neuroscience and Mental Health and The University of Melbourne Dementia Research Centre, Parkville, VIC 3010 Australia
| | - Ralph Martins
- Cooperative Research Centre for Mental Health, Carlton South, VIC Australia
- School of Medical Sciences, Edith Cowan University, Joondalup, WA Australia
- Department of Biomedical Sciences, Macquarie University, North Ryde, NSW Australia
| | - Ashley I. Bush
- Florey Institute of Neuroscience and Mental Health and The University of Melbourne Dementia Research Centre, Parkville, VIC 3010 Australia
- Cooperative Research Centre for Mental Health, Carlton South, VIC Australia
| | - Colin L. Masters
- Florey Institute of Neuroscience and Mental Health and The University of Melbourne Dementia Research Centre, Parkville, VIC 3010 Australia
- Cooperative Research Centre for Mental Health, Carlton South, VIC Australia
| | - Paul A. Grieco
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59715 USA
| | - Edward A. Dratz
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59715 USA
| | - Blaine R. Roberts
- Department of Biochemistry, Emory School of Medicine, 4001 Rollins Research Building, Atlanta, GA 30322 USA
- Department of Neurology, Emory School of Medicine, 4001 Rollins Research Building, Atlanta, GA 30322 USA
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18
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Camporesi E, Nilsson J, Vrillon A, Cognat E, Hourregue C, Zetterberg H, Blennow K, Becker B, Brinkmalm A, Paquet C, Brinkmalm G. Quantification of the trans-synaptic partners neurexin-neuroligin in CSF of neurodegenerative diseases by parallel reaction monitoring mass spectrometry. EBioMedicine 2022; 75:103793. [PMID: 34990894 PMCID: PMC8743209 DOI: 10.1016/j.ebiom.2021.103793] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Synaptic proteins are increasingly studied as biomarkers for synaptic dysfunction and loss, which are early and central events in Alzheimer's disease (AD) and strongly correlate with the degree of cognitive decline. In this study, we specifically investigated the synaptic binding partners neurexin (NRXN) and neuroligin (Nlgn) proteins, to assess their biomarker's potential. METHODS we developed a parallel reaction monitoring mass spectrometric method for the simultaneous quantification of NRXNs and Nlgns in cerebrospinal fluid (CSF) of neurodegenerative diseases, focusing on AD. Specifically, NRXN-1α, NRXN-1β, NRXN-2α, NRXN-3α and Nlgn1, Nlgn2, Nlgn3 and Nlgn4 proteins were targeted. FINDINGS The proteins were investigated in a clinical cohort including CSF from controls (n=22), mild cognitive impairment (MCI) due to AD (n=44), MCI due to other conditions (n=46), AD (n=77) and a group of non-AD dementia (n=28). No difference in levels of NRXNs and Nlgns was found between AD (both at dementia and MCI stages) or controls or the non-AD dementia group for any of the targeted proteins. NRXN and Nlgn proteins correlated strongly with each other, but only a weak correlation with the AD core biomarkers and the synaptic biomarkers neurogranin and growth-associated protein 43, was found, possibly reflecting different pathogenic processing at the synapse. INTERPRETATION we conclude that NRXN and Nlgn proteins do not represent suitable biomarkers for synaptic pathology in AD. The panel developed here could aid in future investigations of the potential involvement of NRXNs and Nlgns in synaptic dysfunction in other disorders of the central nervous system. FUNDING a full list of funding can be found under the acknowledgments section.
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Affiliation(s)
- Elena Camporesi
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at University of Gothenburg, Mölndal, Sweden; Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.
| | - Johanna Nilsson
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at University of Gothenburg, Mölndal, Sweden; Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Agathe Vrillon
- Université de Paris, Cognitive Neurology Center, GHU Nord APHP Hospital Lariboisière Fernand Widal, Paris, France; Université de Paris, Inserm UMR S11-44 Therapeutic Optimization in Neuropsychopharmacology, Paris, France
| | - Emmanuel Cognat
- Université de Paris, Cognitive Neurology Center, GHU Nord APHP Hospital Lariboisière Fernand Widal, Paris, France; Université de Paris, Inserm UMR S11-44 Therapeutic Optimization in Neuropsychopharmacology, Paris, France
| | - Claire Hourregue
- Université de Paris, Cognitive Neurology Center, GHU Nord APHP Hospital Lariboisière Fernand Widal, Paris, France
| | - Henrik Zetterberg
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at University of Gothenburg, Mölndal, Sweden; Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden; UK Dementia Research Institute at UCL, London, UK; Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, UK; Hong Kong Center for Neurodegenerative Diseases, Hong Kong, China
| | - Kaj Blennow
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at University of Gothenburg, Mölndal, Sweden; Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Bruno Becker
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at University of Gothenburg, Mölndal, Sweden; Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Ann Brinkmalm
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at University of Gothenburg, Mölndal, Sweden; Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Claire Paquet
- Université de Paris, Cognitive Neurology Center, GHU Nord APHP Hospital Lariboisière Fernand Widal, Paris, France; Université de Paris, Inserm UMR S11-44 Therapeutic Optimization in Neuropsychopharmacology, Paris, France
| | - Gunnar Brinkmalm
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at University of Gothenburg, Mölndal, Sweden; Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
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19
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Pan J, Ma N, Zhong J, Yu B, Wan J, Zhang W. Age-associated changes in microglia and astrocytes ameliorate blood-brain barrier dysfunction. Mol Ther Nucleic Acids 2021; 26:970-986. [PMID: 34760339 PMCID: PMC8561003 DOI: 10.1016/j.omtn.2021.08.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 08/30/2021] [Indexed: 02/06/2023]
Abstract
Blood-brain barrier (BBB) dysfunction is associated with an accumulation of neurotoxic molecules and increased infiltration of peripheral cells within the brain parenchyma. Accruing evidence suggests that microglia and astrocytes play a crucial role in the recovery of BBB integrity and the corralling of infiltrating cells into clusters after brain damage, but the mechanisms involved remain unclear. Intriguingly, the results of flow cytometry and immunofluorescence analyses have shown that BBB permeability to peripheral cells is substantially enhanced during normal aging at 12 months in mice. Thus, we used the SMART-seq2 method to perform RNA sequencing of microglia and astrocytes at five time points before and immediately after the BBB permeability change. Our comprehensive analyses revealed that microglia are characterized by marked alterations in the negative regulation of protein phosphorylation and phagocytic vesicles, whereas astrocytes show elevated enzyme or peptidase-inhibitor activity in the recovery of BBB function. Moreover, we identified a cassette of key genes that might ameliorate the insults of pathophysiological events in aging and neurodegenerative disease.
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Affiliation(s)
- Jie Pan
- Greater Bay Biomedical Innocenter, Shenzhen Bay Laboratory, Shenzhen, Guangdong Province, China.,Department of Pathology and Neuropathology, Stanford University School of Medicine, CA 94305, USA
| | - Nana Ma
- Greater Bay Biomedical Innocenter, Shenzhen Bay Laboratory, Shenzhen, Guangdong Province, China
| | - Jie Zhong
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center, Shenzhen, Guangdong Province, China
| | - Bo Yu
- Shenzhen Key Laboratory for Translational Medicine of Dermatology, Biomedical Research Institute, Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center, Shenzhen, Guangdong Province, China.,Department of Dermatology, Peking University Shenzhen Hospital, Shenzhen, Guangdong Province, China
| | - Jun Wan
- Greater Bay Biomedical Innocenter, Shenzhen Bay Laboratory, Shenzhen, Guangdong Province, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong Province, PRC
| | - Wei Zhang
- Greater Bay Biomedical Innocenter, Shenzhen Bay Laboratory, Shenzhen, Guangdong Province, China
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20
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Cai X, Yang C, Chen J, Gong W, Yi F, Liao W, Huang R, Xie L, Zhou J. Proteomic Insights Into Susceptibility and Resistance to Chronic-Stress-Induced Depression or Anxiety in the Rat Striatum. Front Mol Biosci 2021; 8:730473. [PMID: 34676246 PMCID: PMC8523913 DOI: 10.3389/fmolb.2021.730473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/27/2021] [Indexed: 11/13/2022] Open
Abstract
Chronic stress is a key factor for the onset of anxiety and depression disorders. However, the stress-induced common and unique molecular basis of the two psychiatric disorders is not fully known and still needs to be explored. Previously, we employed a chronic mild stress (CMS) procedure to induce a rat model including depression-susceptible (Dep-Sus), anxiety-susceptible (Anx-Sus), and insusceptible (Insus) cohorts. In this work, we continuously analyze the striatal proteomes of the three stressed cohorts by the use of comparative proteomics and bioinformatics approaches. Through isobaric tags for relative and absolute quantitation (iTRAQ)-based analysis, 386 abnormally expressed proteins in total were identified. These deregulated proteins are involved in various biological functions and significant pathways that are potentially connected with resistance and susceptibility to CMS-caused anxious- or depressive-like behaviors and, hence, could act as suggestive protein targets. A further parallel reaction monitoring-based independent investigation shows that alterations in Pak5, Dgkg, Scn4b, Rb1cc1, and Acin1; Ggps1, Fntb, Nudt19, Ufd1, and Ndufab1; and Dnajb12, Hbb2, Ap2s1, Ip6k1, and Stk4 were specifically connected with Dep-Sus, Anx-Sus, or Insus groups, respectively, potentially indicating that identical CMS treatment results in the different changes in the striatal protein regulations. Overall, our current proteomics study of the striatum provides an important molecular foundation and comprehensive insights into common and specific deregulations correlated with pathophysiological mechanisms that underlie resistance and susceptibility to chronic stress-induced anxiety or depression.
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Affiliation(s)
- Xiao Cai
- Basic Medical College, Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - Chen Yang
- Basic Medical College, Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - Jin Chen
- Basic Medical College, Institute of Neuroscience, Chongqing Medical University, Chongqing, China.,Department of Neurology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Weibo Gong
- Basic Medical College, Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - Faping Yi
- Basic Medical College, Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - Wei Liao
- Basic Medical College, Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - Rongzhong Huang
- Statistics Laboratory, ChuangXu Institute of Life Science, Chongqing, China.,Chongqing Institute of Life Science, Chongqing, China
| | - Liang Xie
- Basic Medical College, Institute of Neuroscience, Chongqing Medical University, Chongqing, China.,Department of Neurology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jian Zhou
- Basic Medical College, Institute of Neuroscience, Chongqing Medical University, Chongqing, China
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21
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Tian F, Liu D, Chen J, Liao W, Gong W, Huang R, Xie L, Yi F, Zhou J. Proteomic Response of Rat Pituitary Under Chronic Mild Stress Reveals Insights Into Vulnerability and Resistance to Anxiety or Depression. Front Genet 2021; 12:751999. [PMID: 34603401 PMCID: PMC8484759 DOI: 10.3389/fgene.2021.751999] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/01/2021] [Indexed: 12/31/2022] Open
Abstract
Chronic stress as one of the most significant risk factor can trigger overactivity of hypothalamic-pituitary-adrenal (HPA) axis in depression as well as anxiety. Yet, the shared and unique neurobiological underpinnings underlying the pituitary abnormality in these two disorders have not been made clear. We previously have established depression-susceptible, anxiety-susceptible and insusceptible groups using a valid chronic mild stress (CMS) model. In this work, the possible protein expression changes in the rat pituitary of these three groups were continuously investigated through the use of the comparative quantitative proteomics and bioinformatics approaches. The pituitary-proteome analysis identified totally 197 differential proteins as a CMS response. These deregulated proteins were involved in diverse biological functions and significant pathways potentially connected with the three different behavioral phenotypes, likely serving as new investigative protein targets. Afterwards, parallel reaction monitoring-based independent analysis found out that expression alterations in Oxct1, Sec24c, Ppp1cb, Dock1, and Coq3; Lama1, Glb1, Gapdh, Sccpdh, and Renbp; Sephs1, Nup188, Spp1, Prodh1, and Srm were specifically linked to depression-susceptible, anxiety-susceptible and insusceptible groups, respectively, suggesting that the same CMS had different impacts on the pituitary protein regulatory system. Collectively, the current proteomics research elucidated an important molecular basis and furnished new valuable insights into neurochemical commonalities and specificities of the pituitary dysfunctional mechanisms in HPA axis underlying vulnerability and resistance to stress-induced anxiety or depression.
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Affiliation(s)
- Fenfang Tian
- Institute of Neuroscience, Basic Medical College, Chongqing Medical University, Chongqing, China
| | - Dan Liu
- Institute of Neuroscience, Basic Medical College, Chongqing Medical University, Chongqing, China
| | - Jin Chen
- Institute of Neuroscience, Basic Medical College, Chongqing Medical University, Chongqing, China.,Department of Neurology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Wei Liao
- Institute of Neuroscience, Basic Medical College, Chongqing Medical University, Chongqing, China
| | - Weibo Gong
- Institute of Neuroscience, Basic Medical College, Chongqing Medical University, Chongqing, China
| | - Rongzhong Huang
- Statistics Laboratory, ChuangXu Institute of Life Science, Chongqing, China.,Chongqing Institute of Life Science, Chongqing, China
| | - Liang Xie
- Institute of Neuroscience, Basic Medical College, Chongqing Medical University, Chongqing, China.,Department of Neurology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Faping Yi
- Institute of Neuroscience, Basic Medical College, Chongqing Medical University, Chongqing, China
| | - Jian Zhou
- Institute of Neuroscience, Basic Medical College, Chongqing Medical University, Chongqing, China
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22
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Korecka M, Shaw LM. Mass spectrometry-based methods for robust measurement of Alzheimer's disease biomarkers in biological fluids. J Neurochem 2021; 159:211-233. [PMID: 34244999 PMCID: PMC9057379 DOI: 10.1111/jnc.15465] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 06/11/2021] [Accepted: 07/06/2021] [Indexed: 11/29/2022]
Abstract
Alzheimer's disease (AD) is the most common form of dementia affecting 60%-70% of people afflicted with this disease. Accurate antemortem diagnosis is urgently needed for early detection of AD to enable reliable estimation of prognosis, intervention, and monitoring of the disease. The National Institute on Aging/Alzheimer's Association sponsored the 'Research Framework: towards a biological definition of AD', which recommends using different biomarkers in living persons for a biomarker-based definition of AD regardless of clinical status. Fluid biomarkers represent one of key groups of them. Since cerebrospinal fluid (CSF) is in direct contact with brain and many proteins present in the brain can be detected in CSF, this fluid has been regarded as the best biofluid in which to measure AD biomarkers. Recently, technological advancements in protein detection made possible the effective study of plasma AD biomarkers despite their significantly lower concentrations versus to that in CSF. This and other challenges that face plasma-based biomarker measurements can be overcome by using mass spectrometry. In this review, we discuss AD biomarkers which can be reliably measured in CSF and plasma using targeted mass spectrometry coupled to liquid chromatography (LC/MS/MS). We describe progress in LC/MS/MS methods' development, emphasize the challenges, and summarize major findings. We also highlight the role of mass spectrometry and progress made in the process of global standardization of the measurement of Aβ42/Aβ40. Finally, we briefly describe exploratory proteomics which seek to identify new biomarkers that can contribute to detection of co-pathological processes that are common in sporadic AD.
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Affiliation(s)
- Magdalena Korecka
- Department of Pathology and Laboratory Medicine Perlman School of Medicine University of Pennsylvania Philadelphia PA USA
| | - Leslie M. Shaw
- Department of Pathology and Laboratory Medicine Perlman School of Medicine University of Pennsylvania Philadelphia PA USA
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23
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Liu D, Cai X, Wang L, Yi F, Liao W, Huang R, Fang C, Chen J, Zhou J. Comparative Proteomics of Rat Olfactory Bulb Reveal Insights into Susceptibility and Resiliency to Chronic-stress-induced Depression or Anxiety. Neuroscience 2021; 473:29-43. [PMID: 34425157 DOI: 10.1016/j.neuroscience.2021.08.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 08/05/2021] [Accepted: 08/16/2021] [Indexed: 01/10/2023]
Abstract
Chronic stress causes the abnormality of olfactory bulb (OB) in both anxiety and depression, however, the unique and common neurobiological underpinnings are still poorly understood. Previously, we built the three groups by chronic mild stress (CMS), depression-susceptible (Dep-Sus): with depression-like behavior, anxiety-susceptible (Anx-Sus): with anxiety-like behavior and insusceptible (Insus): without depression- and anxiety-like behaviors. To continuously explore the protein expression changes in these three groups, comparative quantitative proteomics analysis was conducted on the rat OB as crucial part of the olfactory system. Next, bioinformatics analyses were implemented whereas protein expressions were independently analyzed by parallel reaction monitoring (PRM) or Western blot (WB). The OB-proteome analysis identified totally 133 differentially expressed proteins as a CMS response. These deregulated proteins were involved in multiple functions and significant pathways potentially correlated with phenotypes of maladaptive behavior of depression or anxiety as well as adaptive behavior, and hence might act as potential candidate protein targets. The subsequent PRM-based or WB-based analyses showed that changes in Nefl, Mtmr7 and Tk2; Prkaca, Coa3, Cox6c2, Lamc1 and Tubal3; and Pabpn1, Nme3, Sos1 and Lum were uniquely associated with Dep-Sus, Anx-Sus, and Insus groups, respectively. These phenotype-specific deregulated proteins were primarily involved in multiple metabolic and signaling pathways, suggesting that the identical CMS differently impacted the olfactory protein regulation system and biological processes. To sum up, our present data as a useful proteomics underpinning provided the common and distinct molecular insights into the biochemical understanding of OB dysfunction underlying susceptibility and resiliency to chronic-stress-induced anxiety or depression.
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Affiliation(s)
- Dan Liu
- Institute of Neuroscience, Basic Medical College, Chongqing Medical University, Chongqing 400016, China
| | - Xiao Cai
- Institute of Neuroscience, Basic Medical College, Chongqing Medical University, Chongqing 400016, China
| | - Lixiang Wang
- Shenzhen Wininnovate Bio-Tech Co., Ltd, Shenzhen 410034, China
| | - Faping Yi
- Institute of Neuroscience, Basic Medical College, Chongqing Medical University, Chongqing 400016, China
| | - Wei Liao
- Institute of Neuroscience, Basic Medical College, Chongqing Medical University, Chongqing 400016, China
| | - Rongzhong Huang
- ChuangXu Institute of Life Science, Chongqing 400016, China; Chongqing Institute of Life Science, Chongqing 400016, China
| | - Chui Fang
- Shenzhen Wininnovate Bio-Tech Co., Ltd, Shenzhen 410034, China.
| | - Jin Chen
- Institute of Neuroscience, Basic Medical College, Chongqing Medical University, Chongqing 400016, China; Department of Neurology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, China.
| | - Jian Zhou
- Institute of Neuroscience, Basic Medical College, Chongqing Medical University, Chongqing 400016, China.
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Barranco N, Plá V, Alcolea D, Sánchez-Domínguez I, Fischer-Colbrie R, Ferrer I, Lleó A, Aguado F. Dense core vesicle markers in CSF and cortical tissues of patients with Alzheimer's disease. Transl Neurodegener 2021; 10:37. [PMID: 34565482 PMCID: PMC8466657 DOI: 10.1186/s40035-021-00263-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 09/14/2021] [Indexed: 12/19/2022] Open
Abstract
Background New fluid biomarkers for Alzheimer's disease (AD) that reveal synaptic and neural network dysfunctions are needed for clinical practice and therapeutic trial design. Dense core vesicle (DCV) cargos are promising cerebrospinal fluid (CSF) indicators of synaptic failure in AD patients. However, their value as biomarkers has not yet been determined. Methods Immunoassays were performed to analyze the secretory proteins prohormone convertases PC1/3 and PC2, carboxypeptidase E (CPE), secretogranins SgIII and SgII, and Cystatin C in the cerebral cortex (n = 45, provided by Bellvitge University Hospital) and CSF samples (n = 66, provided by The Sant Pau Initiative on Neurodegeneration cohort) from AD patients (n = 56) and age-matched controls (n = 55).
Results In AD tissues, most DCV proteins were aberrantly accumulated in dystrophic neurites and activated astrocytes, whereas PC1/3, PC2 and CPE were also specifically accumulated in hippocampal granulovacuolar degeneration bodies. AD individuals displayed an overall decline of secretory proteins in the CSF. Interestingly, in AD patients, the CSF levels of prohormone convertases strongly correlated inversely with those of neurodegeneration markers and directly with cognitive impairment status. Conclusions These results demonstrate marked alterations of neuronal-specific prohormone convertases in CSF and cortical tissues of AD patients. The neuronal DCV cargos are biomarker candidates for synaptic dysfunction and neurodegeneration in AD. Supplementary Information The online version contains supplementary material available at 10.1186/s40035-021-00263-0.
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Affiliation(s)
- Neus Barranco
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, 08028, Barcelona, Spain.,Institute of Neurosciences, University of Barcelona, 08028, Barcelona, Spain
| | - Virginia Plá
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, 08028, Barcelona, Spain.,Institute of Neurosciences, University of Barcelona, 08028, Barcelona, Spain.,Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Daniel Alcolea
- Memory Unit, Department of Neurology, Sant Pau Biomedical Research Institute. Sant Pau Hospital, Autonomous University of Barcelona, 08041, Barcelona, Spain.,Center for Networked Biomedical Research on Neurodegenerative Diseases (CIBERNED), 28031, Madrid, Spain
| | - Irene Sánchez-Domínguez
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, 08028, Barcelona, Spain.,Institute of Neurosciences, University of Barcelona, 08028, Barcelona, Spain
| | | | - Isidro Ferrer
- Institute of Neurosciences, University of Barcelona, 08028, Barcelona, Spain.,Center for Networked Biomedical Research on Neurodegenerative Diseases (CIBERNED), 28031, Madrid, Spain.,Department of Pathology and Experimental Therapeutics, University of Barcelona, and Bellvitge University Hospital, Bellvitge Biomedical Research Institute, Hospitalet de Llobregat, Spain
| | - Alberto Lleó
- Memory Unit, Department of Neurology, Sant Pau Biomedical Research Institute. Sant Pau Hospital, Autonomous University of Barcelona, 08041, Barcelona, Spain.,Center for Networked Biomedical Research on Neurodegenerative Diseases (CIBERNED), 28031, Madrid, Spain
| | - Fernando Aguado
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, 08028, Barcelona, Spain. .,Institute of Neurosciences, University of Barcelona, 08028, Barcelona, Spain.
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Wen G, Pang H, Wu X, Jiang E, Zhang X, Zhan X. Proteomic characterization of secretory granules in dopaminergic neurons indicates chromogranin/secretogranin-mediated protein processing impairment in Parkinson's disease. Aging (Albany NY) 2021; 13:20335-20358. [PMID: 34420933 PMCID: PMC8436928 DOI: 10.18632/aging.203415] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 08/03/2021] [Indexed: 11/25/2022]
Abstract
Parkinson’s disease (PD) is an aging disorder related to vesicle transport dysfunctions and neurotransmitter secretion. Secretory granules (SGs) are large dense-core vesicles for the biosynthesis of neuropeptides and hormones. At present, the involvement of SGs impairment in PD remains unclear. In the current study, we found that the number of SGs in tyrosine hydroxylase-positive neurons and the marker proteins secretogranin III (Scg3) significantly decreased in the substantia nigra and striatum regions of 1-methyl-4-phenyl-1, 2, 3, 6-tetrahydropyridine (MPTP) exposed mice. Proteomic study of SGs purified from the dopaminergic SH-sy5Y cells under 1-methyl-4-phenylpyridinium (MPP+) treatments (ProteomeXchange PXD023937) identified 536 significantly differentially expressed proteins. The result indicated that disabled lysosome and peroxisome, lipid and energy metabolism disorders are three characteristic features. Protein-protein interaction analysis of 56 secretory proteins and 140 secreted proteins suggested that the peptide processing mediated by chromogranin/secretogranin in SGs was remarkably compromised, accompanied by decreased candidate proteins and peptides neurosecretory protein (VGF), neuropeptide Y, apolipoprotein E, and an increased level of proenkephalin. The current study provided an extensive proteinogram of SGs in PD. It is helpful to understand the molecular mechanisms in the disease.
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Affiliation(s)
- Gehua Wen
- School of Forensic Medicine, China Medical University, Shenyang, PR China
| | - Hao Pang
- School of Forensic Medicine, China Medical University, Shenyang, PR China
| | - Xu Wu
- School of Forensic Medicine, China Medical University, Shenyang, PR China
| | - Enzhu Jiang
- School of Forensic Medicine, China Medical University, Shenyang, PR China
| | - Xique Zhang
- Department of Geriatrics, The First Affiliated Hospital of China Medical University, Shenyang, PR China
| | - Xiaoni Zhan
- School of Forensic Medicine, China Medical University, Shenyang, PR China
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Liu Y, Tian F, Li S, Chen W, Gong W, Xie H, Liu D, Huang R, Liao W, Yi F, Zhou J. Global effects of RAB3GAP1 dysexpression on the proteome of mouse cortical neurons. Amino Acids 2021. [PMID: 34363538 DOI: 10.1007/s00726-021-03058-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 07/30/2021] [Indexed: 12/15/2022]
Abstract
Mounting studies have demonstrated that RAB3GAP1 expression is modified in brain diseases with multiple neurobiological functions and processes and acts as a potentially significant target. However, the cellular and molecular events arising from RAB3GAP1 dysexpression are still incompletely understood. In this work, underexpression and overexpression of RAB3GAP1 were first induced into cultured mouse cortical neurons by transfection with lentivirus plasmids. Then we globally explored the effects of RAB3GAP1 dysexpression on the proteome of the neurons through the use of isobaric tag for relative and absolute quantitation (iTRAQ)-based quantitative proteomics with bioinformatics. A total of 364 proteins in the RAB3GAP1-underexpression group and 314 proteins in the RAB3GAP1-overexpression group were identified to be differentially expressed. Subsequent bioinformatics analysis indicated that the proteome functional expression profiles induced by RAB3GAP1 underexpression and overexpression were different, suggesting the potential differences in biological processes and cellular effects. Subsequent intergroup cross-comparison revealed some candidate target proteins regulated directly by RAB3GAP1. Further parallel reaction monitoring (PRM) analysis illustrated that Sub1, Ssrp1, and Top1 proteins might serve as new potentially important linkers in the RAB3GAP1-mediated autophagy pathway in the cortical neurons. Collectively, the current proteomics data furnished new valuable insights to better understand the regulatory molecular mechanism of neuronal RAB3GAP1.
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Kim JH, Park SH, Han J, Ko PW, Kwon D, Suk K. Gliome database: a comprehensive web-based tool to access and analyze glia secretome data. Database (Oxford) 2021; 2020:5879255. [PMID: 32743661 PMCID: PMC7396318 DOI: 10.1093/database/baaa057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/12/2020] [Accepted: 07/02/2020] [Indexed: 12/15/2022]
Abstract
Glial cells are phenotypically heterogeneous non-neuronal components of the central and peripheral nervous systems. These cells are endowed with diverse functions and molecular machineries to detect and regulate neuronal or their own activities by various secreted mediators, such as proteinaceous factors. In particular, glia-secreted proteins form a basis of a complex network of glia-neuron or glia-glia interactions in health and diseases. In recent years, the analysis and profiling of glial secretomes have raised new expectations for the diagnosis and treatment of neurological disorders due to the vital role of glia in numerous physiological or pathological processes of the nervous system. However, there is no online database of glia-secreted proteins available to facilitate glial research. Here, we developed a user-friendly 'Gliome' database (available at www.gliome.org), a web-based tool to access and analyze glia-secreted proteins. The database provides a vast collection of information on 3293 proteins that are released from glia of multiple species and have been reported to have differential functions under diverse experimental conditions. It contains a web-based interface with the following four key features regarding glia-secreted proteins: (i) fundamental information, such as signal peptide, SecretomeP value, functions and Gene Ontology category; (ii) differential expression patterns under distinct experimental conditions; (iii) disease association; and (iv) interacting proteins. In conclusion, the Gliome database is a comprehensive web-based tool to access and analyze glia-secretome data obtained from diverse experimental settings, whereby it may facilitate the integration of bioinformatics into glial research.
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Affiliation(s)
- Jong-Heon Kim
- Brain Science and Engineering Institute, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea
| | - Su-Hyeong Park
- Department of Pharmacology, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea.,D&P BIOTECH, 807 Hoguk-ro, Buk-gu, Daegu, 41404, Republic of Korea
| | - Jin Han
- Department of Pharmacology, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea
| | - Pan-Woo Ko
- Department of Neurology, Kyungpook National University Chilgok Hospital, 807 Hoguk-ro, Buk-gu, Daegu, 41404, Republic of Korea
| | - Dongseop Kwon
- School of Software Convergence, Myongji University, 34 Geobukgol-ro, Seodaemun-gu, Seoul, 03674, Republic of Korea
| | - Kyoungho Suk
- Brain Science and Engineering Institute, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea.,Department of Pharmacology, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea
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Vatansever S, Schlessinger A, Wacker D, Kaniskan HÜ, Jin J, Zhou M, Zhang B. Artificial intelligence and machine learning-aided drug discovery in central nervous system diseases: State-of-the-arts and future directions. Med Res Rev 2021; 41:1427-1473. [PMID: 33295676 PMCID: PMC8043990 DOI: 10.1002/med.21764] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/30/2020] [Accepted: 11/20/2020] [Indexed: 01/11/2023]
Abstract
Neurological disorders significantly outnumber diseases in other therapeutic areas. However, developing drugs for central nervous system (CNS) disorders remains the most challenging area in drug discovery, accompanied with the long timelines and high attrition rates. With the rapid growth of biomedical data enabled by advanced experimental technologies, artificial intelligence (AI) and machine learning (ML) have emerged as an indispensable tool to draw meaningful insights and improve decision making in drug discovery. Thanks to the advancements in AI and ML algorithms, now the AI/ML-driven solutions have an unprecedented potential to accelerate the process of CNS drug discovery with better success rate. In this review, we comprehensively summarize AI/ML-powered pharmaceutical discovery efforts and their implementations in the CNS area. After introducing the AI/ML models as well as the conceptualization and data preparation, we outline the applications of AI/ML technologies to several key procedures in drug discovery, including target identification, compound screening, hit/lead generation and optimization, drug response and synergy prediction, de novo drug design, and drug repurposing. We review the current state-of-the-art of AI/ML-guided CNS drug discovery, focusing on blood-brain barrier permeability prediction and implementation into therapeutic discovery for neurological diseases. Finally, we discuss the major challenges and limitations of current approaches and possible future directions that may provide resolutions to these difficulties.
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Affiliation(s)
- Sezen Vatansever
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Mount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Icahn Institute for Data Science and Genomic TechnologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Avner Schlessinger
- Department of Pharmacological SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Mount Sinai Center for Therapeutics DiscoveryIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Daniel Wacker
- Department of Pharmacological SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Mount Sinai Center for Therapeutics DiscoveryIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of NeuroscienceIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - H. Ümit Kaniskan
- Department of Pharmacological SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Mount Sinai Center for Therapeutics DiscoveryIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of Oncological Sciences, Tisch Cancer InstituteIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Jian Jin
- Department of Pharmacological SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Mount Sinai Center for Therapeutics DiscoveryIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of Oncological Sciences, Tisch Cancer InstituteIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Ming‐Ming Zhou
- Department of Pharmacological SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of Oncological Sciences, Tisch Cancer InstituteIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Bin Zhang
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Mount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Icahn Institute for Data Science and Genomic TechnologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of Pharmacological SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
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Chen Z, Yu Q, Yu Q, Johnson J, Shipman R, Zhong X, Huang J, Asthana S, Carlsson C, Okonkwo O, Li L. In-depth Site-specific Analysis of N-glycoproteome in Human Cerebrospinal Fluid and Glycosylation Landscape Changes in Alzheimer's Disease. Mol Cell Proteomics 2021; 20:100081. [PMID: 33862227 PMCID: PMC8724636 DOI: 10.1016/j.mcpro.2021.100081] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 04/02/2021] [Accepted: 04/03/2021] [Indexed: 01/22/2023] Open
Abstract
As the body fluid that directly interchanges with the extracellular fluid of the central nervous system (CNS), cerebrospinal fluid (CSF) serves as a rich source for CNS-related disease biomarker discovery. Extensive proteome profiling has been conducted for CSF, but studies aimed at unraveling site-specific CSF N-glycoproteome are lacking. Initial efforts into site-specific N-glycoproteomics study in CSF yield limited coverage, hindering further experimental design of glycosylation-based disease biomarker discovery in CSF. In the present study, we have developed an N-glycoproteomic approach that combines enhanced N-glycopeptide sequential enrichment by hydrophilic interaction chromatography (HILIC) and boronic acid enrichment with electron transfer and higher-energy collision dissociation (EThcD) for large-scale intact N-glycopeptide analysis. The application of the developed approach to the analyses of human CSF samples enabled identifications of a total of 2893 intact N-glycopeptides from 511 N-glycosites and 285 N-glycoproteins. To our knowledge, this is the largest site-specific N-glycoproteome dataset reported for CSF to date. Such dataset provides molecular basis for a better understanding of the structure-function relationships of glycoproteins and their roles in CNS-related physiological and pathological processes. As accumulating evidence suggests that defects in glycosylation are involved in Alzheimer's disease (AD) pathogenesis, in the present study, a comparative in-depth N-glycoproteomic analysis was conducted for CSF samples from healthy control and AD patients, which yielded a comparable N-glycoproteome coverage but a distinct expression pattern for different categories of glycoforms, such as decreased fucosylation in AD CSF samples. Altered glycosylation patterns were detected for a number of N-glycoproteins including alpha-1-antichymotrypsin, ephrin-A3 and carnosinase CN1 etc., which serve as potentially interesting targets for further glycosylation-based AD study and may eventually lead to molecular elucidation of the role of glycosylation in AD progression.
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Affiliation(s)
- Zhengwei Chen
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Qinying Yu
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Qing Yu
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Jillian Johnson
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Richard Shipman
- Department of Applied Science, University of Wisconsin-Stout, Menomonie, Wisconsin, USA
| | - Xiaofang Zhong
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Junfeng Huang
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Sanjay Asthana
- School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA
| | - Cynthia Carlsson
- School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA
| | - Ozioma Okonkwo
- School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, USA; School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA.
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Gong W, Liao W, Fang C, Liu Y, Xie H, Yi F, Huang R, Wang L, Zhou J. Analysis of Chronic Mild Stress-Induced Hypothalamic Proteome: Identification of Protein Dysregulations Associated With Vulnerability and Resiliency to Depression or Anxiety. Front Mol Neurosci 2021; 14:633398. [PMID: 33737865 PMCID: PMC7960925 DOI: 10.3389/fnmol.2021.633398] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/10/2021] [Indexed: 12/15/2022] Open
Abstract
Chronic stress as a known risk factor leads to hyperactivity of the hypothalamus-pituitary-adrenal (HPA) axis in both depression and anxiety. However, the stress-induced dysfunction of the HPA axis in these disorders especially the common and unique molecular dysregulations have not been well-explored. Previously, we utilized a chronic mild stress (CMS) paradigm to segregate and gain depression-susceptible, anxiety-susceptible, and insusceptible groups. In this study, we continue to examine the possible protein expression alterations of the hypothalamus as the center of the HPA axis in these three groups by using a proteomic approach. Though isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative analysis, a total of 593 dysregulated proteins were identified. These were potentially associated with vulnerability and adaptability of CMS-caused depression or anxiety and therefore might become novel investigative protein targets. Further independent analysis using parallel reaction monitoring (PRM) indicated that 5, 7, and 21 dysregulated proteins were specifically associated with depression-susceptible, anxiety-susceptible, and insusceptible groups, respectively, suggesting that the same CMS differently affected the regulation system of the rat hypothalamic proteome. In summary, the current proteomic research on the hypothalamus provided insights into the specific and common molecular basis for the HPA dysfunction mechanisms that underlie resiliency and vulnerability to stress-induced depression or anxiety.
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Affiliation(s)
- Weibo Gong
- Institute of Neuroscience, Chongqing Medical University, Chongqing, China.,Basic Medical College, Chongqing Medical University, Chongqing, China
| | - Wei Liao
- Institute of Neuroscience, Chongqing Medical University, Chongqing, China.,Basic Medical College, Chongqing Medical University, Chongqing, China
| | - Chui Fang
- Shenzhen Wininnovate Bio-Tech Co., Ltd., Shenzhen, China
| | - Yanchen Liu
- Institute of Neuroscience, Chongqing Medical University, Chongqing, China.,Basic Medical College, Chongqing Medical University, Chongqing, China
| | - Hong Xie
- Institute of Neuroscience, Chongqing Medical University, Chongqing, China.,Department of Pharmacy, Chongqing Renji Hospital, University of Chinese Academy of Sciences, Chongqing, China
| | - Faping Yi
- Institute of Neuroscience, Chongqing Medical University, Chongqing, China.,Basic Medical College, Chongqing Medical University, Chongqing, China
| | | | - Lixiang Wang
- Shenzhen Wininnovate Bio-Tech Co., Ltd., Shenzhen, China
| | - Jian Zhou
- Institute of Neuroscience, Chongqing Medical University, Chongqing, China.,Basic Medical College, Chongqing Medical University, Chongqing, China
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31
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Liao W, Liu Y, Wang L, Cai X, Xie H, Yi F, Huang R, Fang C, Xie P, Zhou J. Chronic mild stress-induced protein dysregulations correlated with susceptibility and resiliency to depression or anxiety revealed by quantitative proteomics of the rat prefrontal cortex. Transl Psychiatry 2021; 11:143. [PMID: 33627638 PMCID: PMC7904772 DOI: 10.1038/s41398-021-01267-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 01/22/2021] [Accepted: 02/02/2021] [Indexed: 11/09/2022] Open
Abstract
Chronic stress is a significant risk factor for depression as well as anxiety disorders. Yet, the stress-induced specific and common molecular dysregulations of these disorders have not been fully understood. Previously, we constructed a chronic mild stress (CMS) rat model to separate and obtain depression-susceptible, anxiety-susceptible, and insusceptible groups. In this study, the prefrontal cortical proteomes of the three stressed groups were comparatively profiled utilizing isobaric tags for relative and absolute quantitation (iTRAQ)-coupled tandem mass spectrometry approach. A total of 212 protein dysregulations were identified, potentially correlating to susceptibility or resilience to CMS-induced depression or anxiety, and thus might serve as potential protein targets for further investigation. In addition, independent analysis by parallel reaction monitoring identified changes in Gfap, Rhog, Gnai2, Ppp1r1b, and Uqcrh; Tubb6, Urod, Cul1, Spred1, and Gpcpd1; Acadl, Ppp1r1a, Grm2, Mtor, Lsm8, Cplx2, and Tsta3 that were distinctly correlated to depression-susceptible, anxiety-susceptible, or insusceptible groups, respectively. This suggested that identical CMS had different effects on the protein regulation system of the rat prefrontal cortex. Collectively, the present proteomics study of the prefrontal cortex established a significant molecular basis and offered new insights into the specificity and commonality of pathophysiologic mechanisms underlying susceptibility and resiliency to stress-induced depression or anxiety.
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Affiliation(s)
- Wei Liao
- grid.203458.80000 0000 8653 0555Institute of Neuroscience, Chongqing Medical University, 400016 Chongqing, China ,grid.203458.80000 0000 8653 0555Basic Medical College, Chongqing Medical University, 400016 Chongqing, China
| | - Yanchen Liu
- grid.203458.80000 0000 8653 0555Institute of Neuroscience, Chongqing Medical University, 400016 Chongqing, China ,grid.203458.80000 0000 8653 0555Basic Medical College, Chongqing Medical University, 400016 Chongqing, China
| | - Lixiang Wang
- Shenzhen Wininnovate Bio-Tech Co., Ltd, 410034 Shenzhen, China
| | - Xiao Cai
- grid.203458.80000 0000 8653 0555Institute of Neuroscience, Chongqing Medical University, 400016 Chongqing, China ,grid.203458.80000 0000 8653 0555Basic Medical College, Chongqing Medical University, 400016 Chongqing, China
| | - Hong Xie
- grid.203458.80000 0000 8653 0555Institute of Neuroscience, Chongqing Medical University, 400016 Chongqing, China ,grid.410726.60000 0004 1797 8419Department of Pharmacy, Chongqing Renji Hospital, University of Chinese Academy of Sciences, 400062 Chongqing, China
| | - Faping Yi
- grid.203458.80000 0000 8653 0555Institute of Neuroscience, Chongqing Medical University, 400016 Chongqing, China ,grid.203458.80000 0000 8653 0555Basic Medical College, Chongqing Medical University, 400016 Chongqing, China
| | | | - Chui Fang
- Shenzhen Wininnovate Bio-Tech Co., Ltd, 410034, Shenzhen, China.
| | - Peng Xie
- Institute of Neuroscience, Chongqing Medical University, 400016, Chongqing, China. .,Basic Medical College, Chongqing Medical University, 400016, Chongqing, China.
| | - Jian Zhou
- Institute of Neuroscience, Chongqing Medical University, 400016, Chongqing, China. .,Basic Medical College, Chongqing Medical University, 400016, Chongqing, China.
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Chen R, Yi Y, Xiao W, Zhong B, Shu Y, Zhang L, Zeng Y. Label-Free Liquid Chromatography-Mass Spectrometry Proteomic Analysis of Urinary Identification in Diabetic Vascular Dementia in a Han Chinese Population. Front Aging Neurosci 2021; 13:619945. [PMID: 33597859 PMCID: PMC7882624 DOI: 10.3389/fnagi.2021.619945] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/04/2021] [Indexed: 12/18/2022] Open
Abstract
Objective: This study aimed to identify potential diagnostic biomarkers of diabetic vascular dementia (DVD) and unravel the underlying mechanisms using mass spectrometry (MS). Methods: Label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomic analysis was applied to urine samples from four groups, including 14 patients with vascular dementia (VD), 22 patients with type 2 diabetes mellitus (T2DM), 12 patients with DVD, and 21 normal controls (NCs). Searching the MS data by Proteome Discoverer software (ThermoFisher Scientific; Waltham, MA, USA), protein abundances were analyzed qualitatively and quantitatively and compared between these groups. Combining bioinformatics analysis using Gene Ontology (GO), pathway crosstalk analysis using Kyoto Encyclopedia of Genes and Genomes (KEGG), protein–protein interaction (PPI) network analysis using STRING, and literature searching, the differentially expressed proteins (DEPs) of DVD can be comprehensively judged and were further quantified by receiver operating characteristic (ROC) curve methods. Results: The proteomic findings showed quantitative changes in patients with DVD compared to patients with NC, T2DM, and VD groups; among 4,744 identified urine proteins, 1,222, 1,152, and 1,180 proteins displayed quantitative changes unique to DVD vs. NC, T2DM, and VD, respectively, including 481 overlapped common DEPs. Then, nine unique proteins [including HP, SERPIND, ATP5PB, VNN2, ALDH3A1, U2AF2, C6, A0A5C2GRG5 (no name), and A0A5C2FZ29 (no name)] and two composite markers (CM) (A0A5C2GRG5+U2AF2 and U2AF2+C6) were confirmed by a ROC curve method. Conclusion: This study provided an insight into the potential pathogenesis of DVD and elucidated a method for early detection.
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Affiliation(s)
- Ruijuan Chen
- Department of Geriatrics, Second Xiangya Hospital, Central South University, Changsha, China
| | - Yuanjing Yi
- Department of Geriatrics, Second Xiangya Hospital, Central South University, Changsha, China
| | - Wenbiao Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Bowen Zhong
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Yi Shu
- Department of Neurology, Second Xiangya Hospital, Central South University, Changsha, China
| | - Le Zhang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yi Zeng
- Department of Geriatrics, Second Xiangya Hospital, Central South University, Changsha, China
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33
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Shakya M, Yildirim T, Lindberg I. Increased expression and retention of the secretory chaperone proSAAS following cell stress. Cell Stress Chaperones 2020; 25:929-941. [PMID: 32607937 PMCID: PMC7591655 DOI: 10.1007/s12192-020-01128-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 06/05/2020] [Accepted: 06/10/2020] [Indexed: 11/25/2022] Open
Abstract
The secretory pathway of neurons and endocrine cells contains a variety of mechanisms designed to combat cellular stress. These include not only the unfolded protein response pathways but also diverse chaperone proteins that collectively work to ensure proteostatic control of secreted and membrane-bound molecules. One of the least studied of these chaperones is the neural- and endocrine-specific molecule known as proSAAS. This small chaperone protein acts as a potent anti-aggregant both in vitro and in cellulo and also represents a cerebrospinal fluid biomarker in Alzheimer's disease. In the present study, we have examined the idea that proSAAS, like other secretory chaperones, might represent a stress-responsive protein. We find that exposure of neural and endocrine cells to the cell stressors tunicamycin and thapsigargin increases cellular proSAAS mRNA and protein in Neuro2A cells. Paradoxically, proSAAS secretion is inhibited by these same drugs. Exposure of Neuro2A cells to low concentrations of the hypoxic stress inducer cobalt chloride, or to sodium arsenite, an oxidative stressor, also increases cellular proSAAS content and reduces its secretion. We conclude that the cellular levels of the small secretory chaperone proSAAS are positively modulated by cell stress.
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Affiliation(s)
- Manita Shakya
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, 20 Penn St, HSF2, S267, Baltimore, MD, 21201, USA
| | - Taha Yildirim
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, 20 Penn St, HSF2, S267, Baltimore, MD, 21201, USA
| | - Iris Lindberg
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, 20 Penn St, HSF2, S267, Baltimore, MD, 21201, USA.
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34
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Ertilav E, Barcin NE, Ozdem S. Comparison of Serum Free and Bioavailable 25-Hydroxyvitamin D Levels in Alzheimer's Disease and Healthy Control Patients. Lab Med 2020; 52:219-225. [PMID: 32893866 DOI: 10.1093/labmed/lmaa066] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
OBJECTIVE Many studies have investigated lower 25-hydroxyvitamin D (25[OH]D) levels in patients with Alzheimer's disease (AD) compared with those in control patients. In the present study, we aimed to evaluate serum free and bioavailable 25(OH)D levels in patients with AD and in healthy control patients. METHODS The AD group consisted of 85 patients aged >60 years who were diagnosed with possible AD according to National Institute on Aging-Alzheimer's Association criteria and 85 healthy control patients. Serum levels of total 1,25-dihydroxyvitamin D, total 25(OH)D, vitamin D binding protein (VDBP), parathormone, calcium, phosphorus and albumin, free 25(OH)D, bioavailable 25(OH)D, and the bioavailable 25(OH)D/total 25(OH)D ratio were compared in both groups. RESULTS Total 25(OH)D, free 25(OH)D, bioavailable 25(OH)D, and the bioavailable 25(OH)D/total 25(OH)D ratio were significantly lower (P <.001, P <.001, P <.001, P <.05, respectively) in the AD group, whereas the VDBP level was significantly higher (P <.05) in the AD than in the control group. CONCLUSION Free and bioavailable 25(OH)D detected at lower levels in patients with AD limit the target central effects of 25(OH)D; this result suggests that reduced levels of the active free form of vitamin D may be a risk factor for AD and dementia.
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Affiliation(s)
- Esra Ertilav
- Department of Neurology, Adnan Menderes University Faculty of Medicine, Aydın, Turkey
| | - Nur Ebru Barcin
- Department of Neurology, and Akdeniz University Faculty of Medicine, Antalya, Turkey
| | - Sebahat Ozdem
- Department of Biochemistry, Akdeniz University Faculty of Medicine, Antalya, Turkey
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Abstract
Protein homeostasis, or proteostasis, is a combination of cellular processes that govern protein quality control, namely, protein translation, folding, processing, and degradation. Disruptions in these processes can lead to protein misfolding and aggregation. Proteostatic disruption can lead to cellular changes such as endoplasmic reticulum or oxidative stress; organelle dysfunction; and, if continued, to cell death. A majority of neurodegenerative diseases involve the pathologic aggregation of proteins that subverts normal neuronal function. While prior reviews of neuronal proteostasis in neurodegenerative processes have focused on cytoplasmic chaperones, there is increasing evidence that chaperones secreted both by neurons and other brain cells in the extracellular – including transsynaptic – space play important roles in neuronal proteostasis. In this review, we will introduce various secreted chaperones involved in neurodegeneration. We begin with clusterin and discuss its identification in various protein aggregates, and the use of increased cerebrospinal fluid (CSF) clusterin as a potential biomarker and as a potential therapeutic. Our next secreted chaperone is progranulin; polymorphisms in this gene represent a known genetic risk factor for frontotemporal lobar degeneration, and progranulin overexpression has been found to be effective in reducing Alzheimer’s- and Parkinson’s-like neurodegenerative phenotypes in mouse models. We move on to BRICHOS domain-containing proteins, a family of proteins containing highly potent anti-amyloidogenic activity; we summarize studies describing the biochemical mechanisms by which recombinant BRICHOS protein might serve as a therapeutic agent. The next section of the review is devoted to the secreted chaperones 7B2 and proSAAS, small neuronal proteins which are packaged together with neuropeptides and released during synaptic activity. Since proteins can be secreted by both classical secretory and non-classical mechanisms, we also review the small heat shock proteins (sHsps) that can be secreted from the cytoplasm to the extracellular environment and provide evidence for their involvement in extracellular proteostasis and neuroprotection. Our goal in this review focusing on extracellular chaperones in neurodegenerative disease is to summarize the most recent literature relating to neurodegeneration for each secreted chaperone; to identify any common mechanisms; and to point out areas of similarity as well as differences between the secreted chaperones identified to date.
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Affiliation(s)
- Kriti Chaplot
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, University of Maryland, Baltimore, Baltimore, MD, United States
| | - Timothy S Jarvela
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, University of Maryland, Baltimore, Baltimore, MD, United States
| | - Iris Lindberg
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, University of Maryland, Baltimore, Baltimore, MD, United States
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36
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Marcus K, Lelong C, Rabilloud T. What Room for Two-Dimensional Gel-Based Proteomics in a Shotgun Proteomics World? Proteomes 2020; 8:proteomes8030017. [PMID: 32781532 PMCID: PMC7563651 DOI: 10.3390/proteomes8030017] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 08/02/2020] [Accepted: 08/04/2020] [Indexed: 02/07/2023] Open
Abstract
Two-dimensional gel electrophoresis was instrumental in the birth of proteomics in the late 1980s. However, it is now often considered as an outdated technique for proteomics—a thing of the past. Although this opinion may be true for some biological questions, e.g., when analysis depth is of critical importance, for many others, two-dimensional gel electrophoresis-based proteomics still has a lot to offer. This is because of its robustness, its ability to separate proteoforms, and its easy interface with many powerful biochemistry techniques (including western blotting). This paper reviews where and why two-dimensional gel electrophoresis-based proteomics can still be profitably used. It emerges that, rather than being a thing of the past, two-dimensional gel electrophoresis-based proteomics is still highly valuable for many studies. Thus, its use cannot be dismissed on simple fashion arguments and, as usual, in science, the tree is to be judged by the fruit.
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Affiliation(s)
- Katrin Marcus
- Medizinisches Proteom-Center, Medical Faculty & Medical Proteome Analysis, Center for Proteindiagnostics (PRODI) Ruhr-University Bochum Gesundheitscampus, 4 44801 Bochum, Germany;
| | - Cécile Lelong
- CBM UMR CNRS5249, Université Grenoble Alpes, CEA, CNRS, 17 rue des Martyrs, CEDEX 9, 38054 Grenoble, France;
| | - Thierry Rabilloud
- Laboratory of Chemistry and Biology of Metals, UMR 5249, Université Grenoble Alpes, CNRS, 38054 Grenoble, France
- Correspondence: ; Tel.: +33-438-783-212
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Devanarayan P, Devanarayan V, Llano DA. Identification of a Simple and Novel Cut-Point Based Cerebrospinal Fluid and MRI Signature for Predicting Alzheimer's Disease Progression that Reinforces the 2018 NIA-AA Research Framework. J Alzheimers Dis 2020; 68:537-550. [PMID: 30775985 DOI: 10.3233/jad-180905] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The 2018 NIA-AA research framework proposes a classification system with Amyloid-β deposition, pathologic Tau, and Neurodegeneration (ATN) for diagnosis and staging of Alzheimer's disease (AD). Data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database can be utilized to identify diagnostic signatures for predicting AD progression, and to determine the utility of this NIA-AA research framework. Profiles of 320 peptides from baseline cerebrospinal fluid (CSF) samples of 287 normal, mild cognitive impairment (MCI), and AD subjects followed over a 3-10-year period were measured via multiple reaction monitoring mass spectrometry. CSF Aβ42, total-Tau (tTau), phosphorylated-Tau (pTau-181), and hippocampal volume were also measured. From these candidate markers, optimal signatures with decision thresholds to separate AD and normal subjects were first identified via unbiased regression and tree-based algorithms. The best performing signature determined via cross-validation was then tested in an independent group of MCI subjects to predict future progression. This multivariate analysis yielded a simple diagnostic signature comprising CSF pTau-181 to Aβ42 ratio, MRI hippocampal volume, and low CSF levels of a novel PTPRN peptide, with a decision threshold on each marker. When applied to a separate MCI group at baseline, subjects meeting these signature criteria experience 4.3-fold faster progression to AD compared to a 2.2-fold faster progression using only conventional markers. This novel 4-marker signature represents an advance over the current diagnostics based on widely used markers, and is easier to use in practice than recently published complex signatures. This signature also reinforces the ATN construct from the 2018 NIA-AA research framework.
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Affiliation(s)
| | - Viswanath Devanarayan
- Charles River Laboratories, Horsham, PA, USA.,Department of Mathematics, Statistics and Computer Science, University of Illinois at Chicago, IL, USA
| | - Daniel A Llano
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Champaign, IL, USA.,Carle Neuroscience Institute, Urbana, IL, USA
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Ibrahim AM, Pottoo FH, Dahiya ES, Khan FA, Kumar JBS. Neuron‐glia interactions: Molecular basis of alzheimer’s disease and applications of neuroproteomics. Eur J Neurosci 2020; 52:2931-2943. [DOI: 10.1111/ejn.14838] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 04/30/2020] [Accepted: 05/18/2020] [Indexed: 12/30/2022]
Affiliation(s)
- Abdallah Mohammad Ibrahim
- Fundamentals of Nursing Department College of Nursing Imam Abdulrahman Bin Faisal University Dammam Saudi Arabia
| | - Faheem Hyder Pottoo
- Department of Pharmacology College of Clinical Pharmacy Imam Abdulrahman Bin Faisal University Dammam Saudi Arabia
| | - Ekta Singh Dahiya
- National Institute of Stroke and Applied Neurosciences (NISAN) Auckland University of Technology Auckland New‐Zealand
| | - Firdos Alam Khan
- Department of Stem Cell Research Institute for Research and Medical Consultations Imam Abdulrahman Bin Faisal University Dammam Saudi Arabia
| | - J. B. Senthil Kumar
- Special centre for Molecular Medicine Jawaharlal Nehru University New‐Delhi India
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van Steenoven I, Koel-Simmelink MJA, Vergouw LJM, Tijms BM, Piersma SR, Pham TV, Bridel C, Ferri GL, Cocco C, Noli B, Worley PF, Xiao MF, Xu D, Oeckl P, Otto M, van der Flier WM, de Jong FJ, Jimenez CR, Lemstra AW, Teunissen CE. Identification of novel cerebrospinal fluid biomarker candidates for dementia with Lewy bodies: a proteomic approach. Mol Neurodegener 2020; 15:36. [PMID: 32552841 PMCID: PMC7301448 DOI: 10.1186/s13024-020-00388-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 06/08/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Diagnosis of dementia with Lewy bodies (DLB) is challenging, largely due to a lack of diagnostic tools. Cerebrospinal fluid (CSF) biomarkers have been proven useful in Alzheimer's disease (AD) diagnosis. Here, we aimed to identify novel CSF biomarkers for DLB using a high-throughput proteomic approach. METHODS We applied liquid chromatography/tandem mass spectrometry with label-free quantification to identify biomarker candidates to individual CSF samples from a well-characterized cohort comprising patients with DLB (n = 20) and controls (n = 20). Validation was performed using (1) the identical proteomic workflow in an independent cohort (n = 30), (2) proteomic data from patients with related neurodegenerative diseases (n = 149) and (3) orthogonal techniques in an extended cohort consisting of DLB patients and controls (n = 76). Additionally, we utilized random forest analysis to identify the subset of candidate markers that best distinguished DLB from all other groups. RESULTS In total, we identified 1995 proteins. In the discovery cohort, 69 proteins were differentially expressed in DLB compared to controls (p < 0.05). Independent cohort replication confirmed VGF, SCG2, NPTX2, NPTXR, PDYN and PCSK1N as candidate biomarkers for DLB. The downregulation of the candidate biomarkers was somewhat more pronounced in DLB in comparison with related neurodegenerative diseases. Using random forest analysis, we identified a panel of VGF, SCG2 and PDYN to best differentiate between DLB and other clinical groups (accuracy: 0.82 (95%CI: 0.75-0.89)). Moreover, we confirmed the decrease of VGF and NPTX2 in DLB by ELISA and SRM methods. Low CSF levels of all biomarker candidates, except PCSK1N, were associated with more pronounced cognitive decline (0.37 < r < 0.56, all p < 0.01). CONCLUSION We identified and validated six novel CSF biomarkers for DLB. These biomarkers, particularly when used as a panel, show promise to improve diagnostic accuracy and strengthen the importance of synaptic dysfunction in the pathophysiology of DLB.
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Affiliation(s)
- Inger van Steenoven
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands
| | - Marleen J. A. Koel-Simmelink
- Neurochemistry Laboratory and Biobank, Department of Clinical Chemistry, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Leonie J. M. Vergouw
- Alzheimer Center Erasmus MC, Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Betty M. Tijms
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands
| | - Sander R. Piersma
- OncoProteomics Laboratory, Department of Medical Oncology, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Thang V. Pham
- OncoProteomics Laboratory, Department of Medical Oncology, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Claire Bridel
- Neurochemistry Laboratory and Biobank, Department of Clinical Chemistry, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Gian-Luca Ferri
- NEF-laboratory, Department of Biomedical Sciences, University of Cagliari, Monserrato, Italy
| | - Cristina Cocco
- NEF-laboratory, Department of Biomedical Sciences, University of Cagliari, Monserrato, Italy
| | - Barbara Noli
- NEF-laboratory, Department of Biomedical Sciences, University of Cagliari, Monserrato, Italy
| | - Paul F. Worley
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Mei-Fang Xiao
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Desheng Xu
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Patrick Oeckl
- Department of Neurology, Ulm University Hospital, Ulm, Germany
| | - Markus Otto
- Department of Neurology, Ulm University Hospital, Ulm, Germany
| | - Wiesje M. van der Flier
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands
- Department of Epidemiology and Biostatistics, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Frank Jan de Jong
- Alzheimer Center Erasmus MC, Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Connie R. Jimenez
- OncoProteomics Laboratory, Department of Medical Oncology, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Afina W. Lemstra
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands
| | - Charlotte E. Teunissen
- Neurochemistry Laboratory and Biobank, Department of Clinical Chemistry, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
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Pedrero-Prieto CM, García-Carpintero S, Frontiñán-Rubio J, Llanos-González E, Aguilera García C, Alcaín FJ, Lindberg I, Durán-Prado M, Peinado JR, Rabanal-Ruiz Y. A comprehensive systematic review of CSF proteins and peptides that define Alzheimer's disease. Clin Proteomics 2020; 17:21. [PMID: 32518535 PMCID: PMC7273668 DOI: 10.1186/s12014-020-09276-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/09/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND During the last two decades, over 100 proteomics studies have identified a variety of potential biomarkers in CSF of Alzheimer's (AD) patients. Although several reviews have proposed specific biomarkers, to date, the statistical relevance of these proteins has not been investigated and no peptidomic analyses have been generated on the basis of specific up- or down- regulation. Herein, we perform an analysis of all unbiased explorative proteomics studies of CSF biomarkers in AD to critically evaluate whether proteins and peptides identified in each study are consistent in distribution; direction change; and significance, which would strengthen their potential use in studies of AD pathology and progression. METHODS We generated a database containing all CSF proteins whose levels are known to be significantly altered in human AD from 47 independent, validated, proteomics studies. Using this database, which contains 2022 AD and 2562 control human samples, we examined whether each protein is consistently present on the basis of reliable statistical studies; and if so, whether it is over- or under-represented in AD. Additionally, we performed a direct analysis of available mass spectrometric data of these proteins to generate an AD CSF peptide database with 3221 peptides for further analysis. RESULTS Of the 162 proteins that were identified in 2 or more studies, we investigated their enrichment or depletion in AD CSF. This allowed us to identify 23 proteins which were increased and 50 proteins which were decreased in AD, some of which have never been revealed as consistent AD biomarkers (i.e. SPRC or MUC18). Regarding the analysis of the tryptic peptide database, we identified 87 peptides corresponding to 13 proteins as the most highly consistently altered peptides in AD. Analysis of tryptic peptide fingerprinting revealed specific peptides encoded by CH3L1, VGF, SCG2, PCSK1N, FBLN3 and APOC2 with the highest probability of detection in AD. CONCLUSIONS Our study reveals a panel of 27 proteins and 21 peptides highly altered in AD with consistent statistical significance; this panel constitutes a potent tool for the classification and diagnosis of AD.
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Affiliation(s)
- Cristina M. Pedrero-Prieto
- Department of Medical Sciences, Ciudad Real Medical School, Oxidative Stress and Neurodegeneration Group, Regional Center for Biomedical Research, University of Castilla-La Mancha, Ciudad Real, Spain
| | - Sonia García-Carpintero
- Department of Medical Sciences, Ciudad Real Medical School, Oxidative Stress and Neurodegeneration Group, Regional Center for Biomedical Research, University of Castilla-La Mancha, Ciudad Real, Spain
| | - Javier Frontiñán-Rubio
- Department of Medical Sciences, Ciudad Real Medical School, Oxidative Stress and Neurodegeneration Group, Regional Center for Biomedical Research, University of Castilla-La Mancha, Ciudad Real, Spain
| | - Emilio Llanos-González
- Department of Medical Sciences, Ciudad Real Medical School, Oxidative Stress and Neurodegeneration Group, Regional Center for Biomedical Research, University of Castilla-La Mancha, Ciudad Real, Spain
| | - Cristina Aguilera García
- Department of Medical Sciences, Ciudad Real Medical School, Oxidative Stress and Neurodegeneration Group, Regional Center for Biomedical Research, University of Castilla-La Mancha, Ciudad Real, Spain
| | - Francisco J. Alcaín
- Department of Medical Sciences, Ciudad Real Medical School, Oxidative Stress and Neurodegeneration Group, Regional Center for Biomedical Research, University of Castilla-La Mancha, Ciudad Real, Spain
| | - Iris Lindberg
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, University of Maryland, Baltimore, MD 21201 USA
| | - Mario Durán-Prado
- Department of Medical Sciences, Ciudad Real Medical School, Oxidative Stress and Neurodegeneration Group, Regional Center for Biomedical Research, University of Castilla-La Mancha, Ciudad Real, Spain
| | - Juan R. Peinado
- Department of Medical Sciences, Ciudad Real Medical School, Oxidative Stress and Neurodegeneration Group, Regional Center for Biomedical Research, University of Castilla-La Mancha, Ciudad Real, Spain
| | - Yoana Rabanal-Ruiz
- Department of Medical Sciences, Ciudad Real Medical School, Oxidative Stress and Neurodegeneration Group, Regional Center for Biomedical Research, University of Castilla-La Mancha, Ciudad Real, Spain
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Ashton NJ, Hye A, Rajkumar AP, Leuzy A, Snowden S, Suárez-Calvet M, Karikari TK, Schöll M, La Joie R, Rabinovici GD, Höglund K, Ballard C, Hortobágyi T, Svenningsson P, Blennow K, Zetterberg H, Aarsland D. An update on blood-based biomarkers for non-Alzheimer neurodegenerative disorders. Nat Rev Neurol 2020; 16:265-284. [PMID: 32322100 DOI: 10.1038/s41582-020-0348-0] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2020] [Indexed: 01/11/2023]
Abstract
Cerebrospinal fluid analyses and neuroimaging can identify the underlying pathophysiology at the earliest stage of some neurodegenerative disorders, but do not have the scalability needed for population screening. Therefore, a blood-based marker for such pathophysiology would have greater utility in a primary care setting and in eligibility screening for clinical trials. Rapid advances in ultra-sensitive assays have enabled the levels of pathological proteins to be measured in blood samples, but research has been predominantly focused on Alzheimer disease (AD). Nonetheless, proteins that were identified as potential blood-based biomarkers for AD, for example, amyloid-β, tau, phosphorylated tau and neurofilament light chain, are likely to be relevant to other neurodegenerative disorders that involve similar pathological processes and could also be useful for the differential diagnosis of clinical symptoms. This Review outlines the neuropathological, clinical, molecular imaging and cerebrospinal fluid features of the most common neurodegenerative disorders outside the AD continuum and gives an overview of the current status of blood-based biomarkers for these disorders.
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Affiliation(s)
- Nicholas J Ashton
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience & Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.,Department of Old Age Psychiatry, Institute of Psychiatry, Psychology & Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK.,NIHR Biomedical Research Centre for Mental Health & Biomedical Research Unit for Dementia at South London & Maudsley NHS Foundation, London, UK
| | - Abdul Hye
- Department of Old Age Psychiatry, Institute of Psychiatry, Psychology & Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK.,NIHR Biomedical Research Centre for Mental Health & Biomedical Research Unit for Dementia at South London & Maudsley NHS Foundation, London, UK
| | - Anto P Rajkumar
- Department of Old Age Psychiatry, Institute of Psychiatry, Psychology & Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK.,NIHR Biomedical Research Centre for Mental Health & Biomedical Research Unit for Dementia at South London & Maudsley NHS Foundation, London, UK.,Institute of Mental Health, University of Nottingham, Nottingham, UK
| | - Antoine Leuzy
- Clinical Memory Research Unit, Lund University, Malmö, Sweden
| | - Stuart Snowden
- Core Metabolomics and Lipidomics Laboratory, Metabolic Research Laboratories, Institute of Metabolic Science, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Marc Suárez-Calvet
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience & Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Barcelonaβeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona, Catalonia, Spain.,Department of Neurology, Hospital del Mar, Barcelona, Catalonia, Spain
| | - Thomas K Karikari
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience & Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Michael Schöll
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience & Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.,Clinical Memory Research Unit, Lund University, Malmö, Sweden.,Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK
| | - Renaud La Joie
- Memory and Aging Center, University of California, San Francisco, San Francisco, CA, USA
| | - Gil D Rabinovici
- Memory and Aging Center, University of California, San Francisco, San Francisco, CA, USA
| | - Kina Höglund
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience & Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Disease Research, Neurogeriatrics Division, Karolinska Institutet, Novum, Huddinge, Stockholm, Sweden
| | | | - Tibor Hortobágyi
- Department of Old Age Psychiatry, Institute of Psychiatry, Psychology & Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK.,MTA-DE Cerebrovascular and Neurodegenerative Research Group, Department of Neurology, University of Debrecen, Debrecen, Hungary
| | - Per Svenningsson
- Department of Old Age Psychiatry, Institute of Psychiatry, Psychology & Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK.,Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience & Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience & Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.,Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, UK.,UK Dementia Research Institute at UCL, London, UK
| | - Dag Aarsland
- Department of Old Age Psychiatry, Institute of Psychiatry, Psychology & Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK. .,NIHR Biomedical Research Centre for Mental Health & Biomedical Research Unit for Dementia at South London & Maudsley NHS Foundation, London, UK. .,Centre for Age-Related Medicine, Stavanger University Hospital, Stavanger, Norway.
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Rotunno MS, Lane M, Zhang W, Wolf P, Oliva P, Viel C, Wills AM, Alcalay RN, Scherzer CR, Shihabuddin LS, Zhang K, Sardi SP. Cerebrospinal fluid proteomics implicates the granin family in Parkinson's disease. Sci Rep 2020; 10:2479. [PMID: 32051502 PMCID: PMC7015906 DOI: 10.1038/s41598-020-59414-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 01/24/2020] [Indexed: 12/25/2022] Open
Abstract
Parkinson's disease, the most common age-related movement disorder, is a progressive neurodegenerative disease with unclear etiology. Better understanding of the underlying disease mechanism(s) is an urgent need for the development of disease-modifying therapeutics. Limited studies have been performed in large patient cohorts to identify protein alterations in cerebrospinal fluid (CSF), a proximal site to pathology. We set out to identify disease-relevant protein changes in CSF to gain insights into the etiology of Parkinson's disease and potentially assist in disease biomarker identification. In this study, we used liquid chromatography-tandem mass spectrometry in data-independent acquisition (DIA) mode to identify Parkinson's-relevant biomarkers in cerebrospinal fluid. We quantified 341 protein groups in two independent cohorts (n = 196) and a longitudinal cohort (n = 105 samples, representing 40 patients) consisting of Parkinson's disease and healthy control samples from three different sources. A first cohort of 53 Parkinson's disease and 72 control samples was analyzed, identifying 53 proteins with significant changes (p < 0.05) in Parkinson's disease relative to healthy control. We established a biomarker signature and multiple protein ratios that differentiate Parkinson's disease from healthy controls and validated these results in an independent cohort. The second cohort included 28 Parkinson's disease and 43 control samples. Independent analysis of these samples identified 41 proteins with significant changes. Evaluation of the overlapping changes between the two cohorts identified 13 proteins with consistent and significant changes (p < 0.05). Importantly, we found the extended granin family proteins as reduced in disease, suggesting a potential common mechanism for the biological reduction in monoamine neurotransmission in Parkinson's patients. Our study identifies several novel protein changes in Parkinson's disease cerebrospinal fluid that may be exploited for understanding etiology of disease and for biomarker development.
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Affiliation(s)
- Melissa S Rotunno
- Rare and Neurologic Diseases Therapeutic Area, Sanofi, Inc., Framingham, MA, 01701, USA.,Biomarkers and Bioanalytics, Translational Sciences, Sanofi, Inc., Framingham, MA, 01701, USA
| | - Monica Lane
- Biomarkers and Bioanalytics, Translational Sciences, Sanofi, Inc., Framingham, MA, 01701, USA
| | - Wenfei Zhang
- Translational Medicine, Sanofi, Inc., Framingham, MA, 01701, USA
| | - Pavlina Wolf
- Biomarkers and Bioanalytics, Translational Sciences, Sanofi, Inc., Framingham, MA, 01701, USA.,Editas Medicine, Cambridge, MA, 02141, USA
| | - Petra Oliva
- Biomarkers and Bioanalytics, Translational Sciences, Sanofi, Inc., Framingham, MA, 01701, USA.,ARCHIMED Life Sciences GmbH, Leberstraße 20/2, 1110, Vienna, Austria
| | - Catherine Viel
- Rare and Neurologic Diseases Therapeutic Area, Sanofi, Inc., Framingham, MA, 01701, USA
| | - Anne-Marie Wills
- Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Roy N Alcalay
- Department of Neurology, Columbia University, New York, NY, 10032-3784, USA
| | - Clemens R Scherzer
- Precision Neurology Program, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, 02115, USA.,Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA.,APDA Center for Advance Parkinson Research, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, 02115, USA
| | - Lamya S Shihabuddin
- Rare and Neurologic Diseases Therapeutic Area, Sanofi, Inc., Framingham, MA, 01701, USA
| | - Kate Zhang
- Biomarkers and Bioanalytics, Translational Sciences, Sanofi, Inc., Framingham, MA, 01701, USA.,Editas Medicine, Cambridge, MA, 02141, USA
| | - S Pablo Sardi
- Rare and Neurologic Diseases Therapeutic Area, Sanofi, Inc., Framingham, MA, 01701, USA.
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Abstract
Background Arsenic (As) is an environmental contaminant, and As pollution in water and soil is a public health issue worldwide. As exposure is associated with the incidence of many disorders, such as arteriosclerosis, diabetes, neurodegenerative diseases, and renal dysfunction. However, the mechanism of As toxicity remains unclear. Material/Methods We investigated the changes in serum protein profiles of rats chronically exposed to As. Twenty healthy rats were randomly divided into 4 groups, and sodium arsenite of varying final concentrations (0, 2, 10, and 50 mg/L, respectively) was add into the drinking water for each group. The administration lasted for 3 months. Two proteomic strategies, isobaric tags for relative and absolute quantitation (iTRAQ), and 2-dimensional gel electrophoresis (2-DE), were employed to screen the differential serum proteins between control and arsenite exposure groups. Results We identified a total of 27 differentially-expressed proteins, among which 9 proteins were significantly upregulated and 18 were downregulated by As exposure. Many of the differentially-expressed proteins were related to fat digestion and absorption, including 5 apolipoproteins, which indicated lipid metabolism may be the most affected by As exposure. Conclusions This study revealed the influence of As on lipid metabolism, suggesting an increased potential risk of relevant diseases in subjects chronically exposed to As.
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Affiliation(s)
- Ling Zhang
- Division of Endemic Disease Prevention, Xinjiang Uighur Autonomous Region Center for Disease Control and Prevention, Urumqi, Xinjiang, China (mainland)
| | - Jia Huang
- Division of Endemic Disease Prevention, Xinjiang Uighur Autonomous Region Center for Disease Control and Prevention, Urumqi, Xinjiang, China (mainland).,School of Public Health, Xinjiang Medical University, Urumqi, Xinjiang, China (mainland)
| | - Qin Lin
- Division of Endemic Disease Prevention, Xinjiang Uighur Autonomous Region Center for Disease Control and Prevention, Urumqi, Xinjiang, China (mainland)
| | - Yan Ma
- School of Public Health, Xinjiang Medical University, Urumqi, Xinjiang, China (mainland)
| | - Rongxiang Xia
- Division of Endemic Disease Prevention, Xinjiang Uighur Autonomous Region Center for Disease Control and Prevention, Urumqi, Xinjiang, China (mainland)
| | - Yuming Zhu
- Division of Endemic Disease Prevention, Xinjiang Uighur Autonomous Region Center for Disease Control and Prevention, Urumqi, Xinjiang, China (mainland)
| | - Saimaitikari Abudubari
- School of Public Health, Xinjiang Medical University, Urumqi, Xinjiang, China (mainland)
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Wesenhagen KEJ, Teunissen CE, Visser PJ, Tijms BM. Cerebrospinal fluid proteomics and biological heterogeneity in Alzheimer's disease: A literature review. Crit Rev Clin Lab Sci 2019; 57:86-98. [PMID: 31694431 DOI: 10.1080/10408363.2019.1670613] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Alzheimer's disease (AD) is the most common cause of dementia and is characterized by aggregation of amyloid and tau proteins in the brain. Results from genetic studies suggest that the pathophysiology underlying AD is complex, but studying this complexity in patients remains difficult. The cerebrospinal fluid (CSF) proteome contains a large number of proteins that can reflect ongoing biological processes. Proteomics techniques can be used to measure many proteins simultaneously in individual patients and may therefore provide an opportunity to study AD disease mechanisms. Here, we review the CSF proteomics literature to identify proteins consistently associated with AD, and perform pathway analyses on these proteins to study which biological processes may be involved in the disease.We performed a literature search of studies that investigated CSF proteomic alterations related to AD. We included original research articles when they measured at least 10 proteins in (antemortem) CSF in at least 10 individuals with AD, mild cognitive impairment (MCI) or controls. We examined if proteins were consistently related to AD, defined as consistent increase or decrease in AD vs. controls across studies. Next, we used the proteins identified as input to pathway analyses using Reactome to investigate which biological processes were enriched.In total, 29 studies were included that investigated AD-related changes to the CSF proteome, including a total of 1434 individuals with AD (of whom 47.1% had a CSF biomarker profile and 9.6% a postmortem examination consistent with AD) and 1380 controls. The studies reported 1 to 138 proteins associated with AD, of which 97 proteins were reported by two or more studies. Among proteins that were measured in more than one study, 27 (27.8%) showed consistent increases, 15 (15.5%) consistent decreases and 55 (56.7%) had contrasting results. Pathway analyses showed that AD-related proteins were enriched for hemostasis, lipoprotein and extracellular matrix pathways.These results indicate that proteomic alterations in CSF associated with AD reflect involvement of various biological pathways. The frequent occurrence of inconsistent protein level changes reported by different studies suggests that additional biological and/or (pre)analytical factors may influence the CSF proteome in AD, which should be further investigated in order to improve understanding of the biological complexity underlying AD.
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Affiliation(s)
- Kirsten E J Wesenhagen
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Charlotte E Teunissen
- Neurochemistry Lab and Biobank, Department of Clinical Chemistry, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Pieter Jelle Visser
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Betty M Tijms
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
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Tang M, Huang H, Li S, Zhou M, Liu Z, Huang R, Liao W, Xie P, Zhou J. Hippocampal proteomic changes of susceptibility and resilience to depression or anxiety in a rat model of chronic mild stress. Transl Psychiatry 2019; 9:260. [PMID: 31624233 DOI: 10.1038/s41398-019-0605-4] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 07/15/2019] [Accepted: 08/01/2019] [Indexed: 01/21/2023] Open
Abstract
Chronic stressful occurrences are documented as a vital cause of both depression and anxiety disorders. However, the stress-induced molecular mechanisms underlying the common and distinct pathophysiology of these disorders remains largely unclear. We utilized a chronic mild stress (CMS) rat model to differentiate and subgroup depression-susceptible, anxiety-susceptible, and insusceptible rats. The hippocampus was analyzed for differential proteomes by combining mass spectrometry and the isobaric tags for relative and absolute quantitation (iTRAQ) labeling technique. Out of 2593 quantified proteins, 367 were aberrantly expressed. These hippocampal protein candidates might be associated with susceptibility to stress-induced depression or anxiety and stress resilience. They provide the potential protein systems involved in various metabolic pathways as novel investigative protein targets. Further, independent immunoblot analysis identified changes in Por, Idh2 and Esd; Glo1, G6pdx, Aldh2, and Dld; Dlat, Ogdhl, Anxal, Tpp2, and Sdha that were specifically associated to depression-susceptible, anxiety-susceptible, or insusceptible groups respectively, suggesting that identical CMS differently impacted the mitochondrial and metabolic processes in the hippocampus. Collectively, the observed alterations to protein abundance profiles of the hippocampus provided significant and novel insights into the stress regulation mechanism in a CMS rat model. This might serve as the molecular basis for further studies that would contributed to a better understanding of the similarities and differences in pathophysiologic mechanisms underlying stress-induced depression or anxiety, and stress resiliency.
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Parada CA, Osbun JW, Busald T, Karasozen Y, Kaur S, Shi M, Barber J, Adidharma W, Cimino PJ, Pan C, Gonzalez-cuyar LF, Rostomily R, Born DE, Zhang J, Ferreira M. Phosphoproteomic and Kinomic Signature of Clinically Aggressive Grade I (1.5) Meningiomas Reveals RB1 Signaling as a Novel Mediator and Biomarker. Clin Cancer Res 2020; 26:193-205. [DOI: 10.1158/1078-0432.ccr-18-0641] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 06/17/2018] [Accepted: 10/10/2019] [Indexed: 11/16/2022]
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Bueno D, Parvas M, Nabiuni M, Miyan J. Embryonic cerebrospinal fluid formation and regulation. Semin Cell Dev Biol 2019; 102:3-12. [PMID: 31615690 DOI: 10.1016/j.semcdb.2019.09.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/10/2019] [Accepted: 09/12/2019] [Indexed: 01/01/2023]
Abstract
The vertebrate brain is organized, from its embryonic origin and throughout adult life, around a dynamic and complex fluid, the cerebrospinal fluid (CSF). There is growing interest in the composition, dynamics and function of the CSF in brain development research. It has been demonstrated in higher vertebrates that CSF has key functions in delivering diffusible signals and nutrients to the developing brain, contributing to the proliferation, differentiation and survival of neural progenitor cells, and to the patterning of the brain. It has also been shown that the composition and the homeostasis of CSF are tightly regulated following the closure of the anterior neuropore, just before the initiation of primary neurogenesis in the neural tissue surrounding brain cavities, before the formation of functional choroid plexus. In this review we draw together existing literature about the composition and formation of embryonic cerebrospinal fluid in birds and mammals, from the closure of the anterior neuropore to the formation of functional fetal choroid plexus, including mechanisms regulating its composition and homeostasis. The significance of CSF regulation within embryonic brain is also discussed from an evolutionary perspective.
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Affiliation(s)
- David Bueno
- Section of Biomedical, Evolutionary and Developmental Genetics, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Av. Diagonal 643. Barcelona 08028, Catalonia Spain.
| | - Maryam Parvas
- Section of Biomedical, Evolutionary and Developmental Genetics, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Av. Diagonal 643. Barcelona 08028, Catalonia Spain
| | - Mohammad Nabiuni
- Division of Neuroscience & Experimental Psychology, Faculty of Biology, Medicine & Health, The University of Manchester, Stopford Building, Oxford Road. Manchester M13 9PT, UK
| | - Jaleel Miyan
- Division of Neuroscience & Experimental Psychology, Faculty of Biology, Medicine & Health, The University of Manchester, Stopford Building, Oxford Road. Manchester M13 9PT, UK
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Câmara AB. Receptores neurais e a doença de Alzheimer: uma revisão sistemática da literatura sobre as famílias de receptores mais associadas a doença, suas funções e áreas de expressão. J bras psiquiatr 2019. [DOI: 10.1590/0047-2085000000242] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
RESUMO Objetivo O artigo tem como objetivo determinar as famílias de receptores mais estudadas, envolvidas com a doença de Alzheimer, assim como determinar a região do sistema nervoso na qual mais tipos de receptores são expressos e quais funções dos receptores estão predominantemente associadas com a patologia em questão. O artigo busca mostrar os modelos e métodos mais utilizados nessas pesquisas, resumindo alguns achados e discutindo o impacto desses estudos no conhecimento científico. Métodos Esta revisão utilizou-se de uma metodologia sistemática (Prospero; ID 141957). Resultados Pode-se constatar que os receptores de transcrição nuclear foram os mais estudados. A maior parte desses receptores se expressa no córtex cerebral e hipocampo. Adicionalmente, a maioria das pesquisas avaliou os receptores relacionados com os efeitos benéficos na doença. A eliminação da proteína amiloide ou o bloqueio de vias relacionadas à síntese dessa proteína foram as principais funções desempenhadas por esses receptores. Por fim, as técnicas de imunoistoquímica e reação em cadeia de polimerase em tempo real (RT-PCR), respectivamente, foram as mais utilizadas, e os roedores consistiram no principal modelo de estudo. Conclusões Os receptores de transcrição nuclear, o córtex cerebral, o hipocampo, a micróglia e a proteína beta-amiloide mostraram importância na patogênese da doença de Alzheimer neste estudo.
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Gay M, Sánchez-Jiménez E, Villarreal L, Vilanova M, Huguet R, Arauz-Garofalo G, Díaz-Lobo M, López-Ferrer D, Vilaseca M. Top-Down Proteomics Applied to Human Cerebrospinal Fluid. Methods Mol Biol 2019; 2044:193-219. [PMID: 31432414 DOI: 10.1007/978-1-4939-9706-0_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Cerebrospinal fluid (CSF) is the fluid of choice to study pathologies and disorders of the central nervous system (CNS). Its composition, especially its proteins and peptides, holds the promise that it may reflect the pathological state of an individual. Traditionally, proteins and peptides in CSF have been analyzed using bottom-up proteomics technologies in the search of high proteome coverage. However, the limited protein sequence coverage of this technology means that information regarding post-translational modifications (PTMs) and alternative splice variants is lost. As an alternative technology, top-down proteomics offers low to medium proteome coverage, but high protein coverage enabling almost a full characterization of the proteins' primary structure. This allows us to precisely identify distinct molecular forms of proteins (proteoforms) as well as naturally occurring bioactive peptide fragments, which could be of critical biological relevance and would otherwise remain undetected with a classical proteomics approach.Here, we describe various strategies including sample preparation protocols, off-line intact protein prefractionation, and LC-MS/MS methods together with data analysis pipelines to analyze cerebrospinal fluid (CSF) by top-down proteomics. However, there is not a unique or standardized method and the selection of the top-down strategy will depend on the exact goal of the study. Here, we describe various top-down proteomics methods that enable rapid protein characterization and may be an excellent companion analytical workflow in the search for new protein biomarkers in neurodegenerative diseases.
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Dixit A, Mehta R, Singh AK. Proteomics in Human Parkinson’s Disease: Present Scenario and Future Directions. Cell Mol Neurobiol 2019; 39:901-15. [DOI: 10.1007/s10571-019-00700-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/04/2019] [Indexed: 12/26/2022]
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