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Lumi R, Petri S, Siwy J, Latosinska A, Raad J, Zürbig P, Skripuletz T, Mischak H, Beige J. Small peptide CSF fingerprint of amyotrophic lateral sclerosis. PLoS One 2024; 19:e0302280. [PMID: 38687737 PMCID: PMC11060592 DOI: 10.1371/journal.pone.0302280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 04/01/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by abnormal protein aggregation in the motor neurons. Present and earlier proteomic studies to characterize peptides in cerebrospinal fluid (CSF) associated with motoneuron pathology did not target low molecular weight proteins and peptides. We hypothesized that specific changes in CSF peptides or low molecular weight proteins are significantly altered in ALS, and that these changes may support deciphering molecular pathophysiology and even guide approaches towards therapeutic interventions. METHODS Cerebrospinal fluid (CSF) from 50 ALS patients and 50 non-ALS controls was collected, centrifuged immediately after collection, aliquoted into polypropylene test tubes, frozen within 30-40 min after the puncture, and stored at -80°C until use. Peptides were sequenced using capillary electrophoresis or liquid chromatography/mass spectrometry (CE-MS/MS or LC-MS/MS). FINDINGS In the CSF of 50 patients and 50 non-ALS controls 33 peptides were found, of which 14 could be sequenced using a non-lytic single-pot proteomic detection method, CE/MS. ALS deregulated peptides vs. controls included Integral membrane protein 2B, Neurosecretory protein VGF, Osteopontin, Neuroendocrine protein 7B2 (Secretogranin-V), EGF-containing fibulin-like extracellular matrix protein 1, Xylosyltransferase 1 XT-1, Chromogranin-A, Superoxide dismutase SOD-1, Secretogranin-1 (Chromogranin B), NR2F2 Nuclear Receptor Subfamily 2 Group F Member 2 and Collagen alpha-1(VII) chain. INTERPRETATION Most striking deregulations in CSF from ALS patients were found in VGF, Osteopontin, SOD-1 and EFEMP1 peptides. No associations of disease severity, duration and region of onset with sequenced peptides were found.
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Affiliation(s)
- Rea Lumi
- Department of Neurology, Hannover University Medical School, Hannover, Germany
| | - Susanne Petri
- Department of Neurology, Hannover University Medical School, Hannover, Germany
| | | | | | - Julia Raad
- Mosaiques Diagnostics GmbH, Hannover, Germany
| | | | - Thomas Skripuletz
- Department of Neurology, Hannover University Medical School, Hannover, Germany
| | | | - Joachim Beige
- Kuratorium for Dialysis and Kidney Transplantation, Neu-Isenburg, Germany
- Martin-Luther-University Halle/Wittenberg, Halle/Saale, Germany
- Hospital Sankt Georg gGmbH, Leipzig, Germany
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2
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Schrader M. Origins, Technological Advancement, and Applications of Peptidomics. Methods Mol Biol 2024; 2758:3-47. [PMID: 38549006 DOI: 10.1007/978-1-0716-3646-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Peptidomics is the comprehensive characterization of peptides from biological sources instead of heading for a few single peptides in former peptide research. Mass spectrometry allows to detect a multitude of peptides in complex mixtures and thus enables new strategies leading to peptidomics. The term was established in the year 2001, and up to now, this new field has grown to over 3000 publications. Analytical techniques originally developed for fast and comprehensive analysis of peptides in proteomics were specifically adjusted for peptidomics. Although it is thus closely linked to proteomics, there are fundamental differences with conventional bottom-up proteomics. Fundamental technological advancements of peptidomics since have occurred in mass spectrometry and data processing, including quantification, and more slightly in separation technology. Different strategies and diverse sources of peptidomes are mentioned by numerous applications, such as discovery of neuropeptides and other bioactive peptides, including the use of biochemical assays. Furthermore, food and plant peptidomics are introduced similarly. Additionally, applications with a clinical focus are included, comprising biomarker discovery as well as immunopeptidomics. This overview extensively reviews recent methods, strategies, and applications including links to all other chapters of this book.
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Affiliation(s)
- Michael Schrader
- Department of Bioengineering Sciences, Weihenstephan-Tr. University of Applied Sciences, Freising, Germany.
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3
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Gutierrez-Merino C. Brain Hydrophobic Peptides Antagonists of Neurotoxic Amyloid β Peptide Monomers/Oligomers-Protein Interactions. Int J Mol Sci 2023; 24:13846. [PMID: 37762148 PMCID: PMC10531495 DOI: 10.3390/ijms241813846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/02/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Amyloid β (Aβ) oligomers have been linked to Alzheimer's disease (AD) pathogenesis and are the main neurotoxic forms of Aβ. This review focuses on the following: (i) the Aβ(1-42):calmodulin interface as a model for the design of antagonist Aβ peptides and its limitations; (ii) proteolytic degradation as the major source of highly hydrophobic peptides in brain cells; and (iii) brain peptides that have been experimentally demonstrated to bind to Aβ monomers or oligomers, Aβ fibrils, or Aβ plaques. It is highlighted that the hydrophobic amino acid residues of the COOH-terminal segment of Aβ(1-42) play a key role in its interaction with intracellular protein partners linked to its neurotoxicity. The major source of highly hydrophobic endogenous peptides of 8-10 amino acids in neurons is the proteasome activity. Many canonical antigen peptides bound to the major histocompatibility complex class 1 are of this type. These highly hydrophobic peptides bind to Aβ and are likely to be efficient antagonists of the binding of Aβ monomers/oligomers concentrations in the nanomolar range with intracellular proteins. Also, their complexation with Aβ will protect them against endopeptidases, suggesting a putative chaperon-like physiological function for Aβ that has been overlooked until now. Remarkably, the hydrophobic amino acid residues of Aβ responsible for the binding of several neuropeptides partially overlap with those playing a key role in its interaction with intracellular protein partners that mediates its neurotoxicity. Therefore, these latter neuropeptides are also potential candidates to antagonize Aβ peptides binding to target proteins. In conclusion, the analysis performed in this review points out that hydrophobic endogenous brain neuropeptides could be valuable biomarkers to evaluate the risk of the onset of sporadic AD, as well as for the prognosis of AD.
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Affiliation(s)
- Carlos Gutierrez-Merino
- Instituto de Biomarcadores de Patologías Moleculares, Universidad de Extremadura, 06006 Badajoz, Spain
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4
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Behzad M, Zirak N, Madani GH, Baidoo L, Rezaei A, Karbasi S, Sadeghi M, Shafie M, Mayeli M, Alzheimer's Disease Neuroimaging Initiative. CSF-Targeted Proteomics Indicate Amyloid-Beta Ratios in Patients with Alzheimer's Dementia Spectrum. Int J Alzheimers Dis 2023; 2023:5336273. [PMID: 36793451 PMCID: PMC9925239 DOI: 10.1155/2023/5336273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 12/01/2022] [Accepted: 12/07/2022] [Indexed: 02/08/2023] Open
Abstract
Background According to recent studies, amyloid-β (Aβ) isoforms as cerebrospinal fluid (CSF) biomarkers have remarkable predictive value for cognitive decline in the early stages of Alzheimer's disease (AD). Herein, we aimed to investigate the correlations between several targeted proteomics in CSF samples with Aβ ratios and cognitive scores in patients in AD spectrum to search for potential early diagnostic utility. Methods A total of 719 participants were found eligible for inclusion. Patients were then categorized into cognitively normal (CN), mild cognitive impairment (MCI), and AD and underwent an assessment of Aβ and proteomics. Clinical Dementia Rating (CDR), Alzheimer's Disease Assessment Scale (ADAS), and Mini Mental State Exam (MMSE) were used for further cognitive assessment. The Aβ42, Aβ42/Aβ40, and Aβ42/38 ratios were considered as means of comparison to identify those peptides corresponding significantly to these established biomarkers and cognitive scores. The diagnostic utility of the IASNTQSR, VAELEDEK, VVSSIEQK, GDSVVYGLR, EPVAGDAVPGPK, and QETLPSK was assessed. Results All investigated peptides corresponded significantly to Aβ42 in controls. In those with MCI, VAELEDEK and EPVAGDAVPGPK were significantly correlated with Aβ42 (p value < 0.001). Additionally, IASNTQSR, VVSSIEQK, GDSVVYGLR, and QETLPSK were significantly correlated with Aβ42/Aβ40 and Aβ42/38 (p value < 0.001) in this group. This group of peptides similarly corresponded to Aβ ratios in those with AD. Eventually, IASNTQSR, VAELEDEK, and VVSSIEQK were significantly associated with CDR, ADAS-11, and ADAS-13, particularly in MCI group. Conclusion Our research suggests potential early diagnostic and prognostic utilities for certain peptides extracted from CSF-targeted proteomics research. The ethical approval of ADNI is available at ClinicalTrials.gov with Identifier: NCT00106899.
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Affiliation(s)
- Maryam Behzad
- NeuroTRACT Association, Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
- Department of Chemistery, University of Tehran, Iran
| | - Negin Zirak
- NeuroTRACT Association, Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
- Department of Educational Science and Psychology, University of Tabriz, Tabriz, Iran
| | - Ghazal Hamidi Madani
- NeuroTRACT Association, Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
- Department of Biology, Faculty of Sciences, University of Guilan, Iran
| | - Linda Baidoo
- NeuroTRACT Association, Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Rezaei
- NeuroTRACT Association, Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Shima Karbasi
- NeuroTRACT Association, Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
- Department of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Sadeghi
- NeuroTRACT Association, Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahan Shafie
- NeuroTRACT Association, Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahsa Mayeli
- NeuroTRACT Association, Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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Llano DA, Devanarayan P, Devanarayan V. CSF peptides from VGF and other markers enhance prediction of MCI to AD progression using the ATN framework. Neurobiol Aging 2023; 121:15-27. [PMID: 36368195 DOI: 10.1016/j.neurobiolaging.2022.07.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 07/15/2022] [Accepted: 07/23/2022] [Indexed: 12/14/2022]
Abstract
The amyloid beta, tau, neurodegenerative markers framework has been proposed to serve as a system to classify and combine biomarkers for Alzheimer's Disease (AD). Although cerebrospinal (CSF) fluid AT (amyloid beta and tau)-based biomarkers have a well-established track record to distinguish AD from control subjects and to predict conversion from mild cognitive impairment (MCI) to AD, there is not an established non-tau based neurodegenerative ("N") marker from CSF. Here, we examine the ability of several candidate peptides in the CSF to serve as "N" markers to both classify disease state and predict MCI to AD conversion. We observed that although many putative N markers involved in synaptic processing and neuroinflammation were able to, when examined in isolation, distinguish MCI converters from non-converters, a derivative from VGF, when combined with AT markers, most strongly enhanced prediction of MCI to AD conversion. Low CSF VGF levels were also predictive of MCI to dementia conversion in the setting of normal AT markers, suggesting that it may serve as a very early predictor of dementia conversion. Other markers derived from neuronal pentraxin 2, GAP-43 and a 14-3-3 protein were also able to enhance MCI to AD prediction when used as a marker of neurodegeneration, but VGF had the highest predictive capacity. Thus, we propose that low levels of VGF in CSF may serve as "N" in the amyloid beta, tau, neurodegenerative markers framework to enhance the prediction of MCI to AD conversion.
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Affiliation(s)
- Daniel A Llano
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, Urbana, IL, USA; Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL, USA; Beckman Institute for Advanced Science and Technology, Urbana, IL, USA; Carle Neuroscience Institute, Urbana, IL, USA.
| | - Priya Devanarayan
- Department of Biology and Schreyer Honors College, Pennsylvania State University, University Park, PA, USA
| | - Viswanath Devanarayan
- Eisai, Inc., Nutley, NJ, USA; Department of Mathematics, Statistics and Computer Science, University of Illinois at Chicago, Chicago, IL, USA
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6
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Laszlo ZI, Hindley N, Sanchez Avila A, Kline RA, Eaton SL, Lamont DJ, Smith C, Spires-Jones TL, Wishart TM, Henstridge CM. Synaptic proteomics reveal distinct molecular signatures of cognitive change and C9ORF72 repeat expansion in the human ALS cortex. Acta Neuropathol Commun 2022; 10:156. [DOI: 10.1186/s40478-022-01455-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/10/2022] Open
Abstract
AbstractIncreasing evidence suggests synaptic dysfunction is a central and possibly triggering factor in Amyotrophic Lateral Sclerosis (ALS). Despite this, we still know very little about the molecular profile of an ALS synapse. To address this gap, we designed a synaptic proteomics experiment to perform an unbiased assessment of the synaptic proteome in the ALS brain. We isolated synaptoneurosomes from fresh-frozen post-mortem human cortex (11 controls and 18 ALS) and stratified the ALS group based on cognitive profile (Edinburgh Cognitive and Behavioural ALS Screen (ECAS score)) and presence of a C9ORF72 hexanucleotide repeat expansion (C9ORF72-RE). This allowed us to assess regional differences and the impact of phenotype and genotype on the synaptic proteome, using Tandem Mass Tagging-based proteomics. We identified over 6000 proteins in our synaptoneurosomes and using robust bioinformatics analysis we validated the strong enrichment of synapses. We found more than 30 ALS-associated proteins in synaptoneurosomes, including TDP-43, FUS, SOD1 and C9ORF72. We identified almost 500 proteins with altered expression levels in ALS, with region-specific changes highlighting proteins and pathways with intriguing links to neurophysiology and pathology. Stratifying the ALS cohort by cognitive status revealed almost 150 specific alterations in cognitively impaired ALS synaptic preparations. Stratifying by C9ORF72-RE status revealed 330 protein alterations in the C9ORF72-RE +ve group, with KEGG pathway analysis highlighting strong enrichment for postsynaptic dysfunction, related to glutamatergic receptor signalling. We have validated some of these changes by western blot and at a single synapse level using array tomography imaging. In summary, we have generated the first unbiased map of the human ALS synaptic proteome, revealing novel insight into this key compartment in ALS pathophysiology and highlighting the influence of cognitive decline and C9ORF72-RE on synaptic composition.
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7
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Blasco Tavares Pereira Lopes F, Schlatzer D, Wang R, Li X, Feng E, Koyutürk M, Qi X, Chance MR. Temporal and Sex-Linked Protein Expression Dynamics in a Familial Model of Alzheimer's Disease. Mol Cell Proteomics 2022; 21:100280. [PMID: 35944844 PMCID: PMC9483563 DOI: 10.1016/j.mcpro.2022.100280] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 07/27/2022] [Accepted: 08/03/2022] [Indexed: 12/03/2022] Open
Abstract
Mouse models of Alzheimer's disease (AD) show progression through stages reflective of human pathology. Proteomics identification of temporal and sex-linked factors driving AD-related pathways can be used to dissect initiating and propagating events of AD stages to develop biomarkers or design interventions. In the present study, we conducted label-free proteome measurements of mouse hippocampus tissue with variables of time (3, 6, and 9 months), genetic background (5XFAD versus WT), and sex (equal males and females). These time points are associated with well-defined phenotypes with respect to the following: Aβ42 plaque deposition, memory deficits, and neuronal loss, allowing correlation of proteome-based molecular signatures with the mouse model stages. Our data show 5XFAD mice exhibit increases in known human AD biomarkers as amyloid-beta peptide, APOE, GFAP, and ITM2B are upregulated across all time points/stages. At the same time, 23 proteins are here newly associated with Alzheimer's pathology as they are also dysregulated in 5XFAD mice. At a pathways level, the 5XFAD-specific upregulated proteins are significantly enriched for DNA damage and stress-induced senescence at 3-month only, while at 6-month, the AD-specific proteome signature is altered and significantly enriched for membrane trafficking and vesicle-mediated transport protein annotations. By 9-month, AD-specific dysregulation is also characterized by significant neuroinflammation with innate immune system, platelet activation, and hyper-reactive astrocyte-related enrichments. Aside from these temporal changes, analysis of sex-linked differences in proteome signatures uncovered novel sex and AD-associated proteins. Pathway analysis revealed sex-linked differences in the 5XFAD model to be involved in the regulation of well-known human AD-related processes of amyloid fibril formation, wound healing, lysosome biogenesis, and DNA damage. Verification of the discovery results by Western blot and parallel reaction monitoring confirm the fundamental conclusions of the study and poise the 5XFAD model for further use as a molecular tool for understanding AD.
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Affiliation(s)
- Filipa Blasco Tavares Pereira Lopes
- Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA; Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Daniela Schlatzer
- Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA; Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Rihua Wang
- Department of Physiology & Biophysics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA; Center for Mitochondrial Diseases, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Xiaolin Li
- Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA; Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Emily Feng
- Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA; Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Mehmet Koyutürk
- Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA; Department of Computer and Data Sciences, Case School of Engineering, Case Western Reserve University, Cleveland, Ohio, USA
| | - Xin Qi
- Department of Physiology & Biophysics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA; Center for Mitochondrial Diseases, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Mark R Chance
- Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA; Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.
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Proteomic Discovery and Validation of Novel Fluid Biomarkers for Improved Patient Selection and Prediction of Clinical Outcomes in Alzheimer’s Disease Patient Cohorts. Proteomes 2022; 10:proteomes10030026. [PMID: 35997438 PMCID: PMC9397030 DOI: 10.3390/proteomes10030026] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/13/2022] [Accepted: 07/23/2022] [Indexed: 01/25/2023] Open
Abstract
Alzheimer’s disease (AD) is an irreversible neurodegenerative disease characterized by progressive cognitive decline. The two cardinal neuropathological hallmarks of AD include the buildup of cerebral β amyloid (Aβ) plaques and neurofibrillary tangles of hyperphosphorylated tau. The current disease-modifying treatments are still not effective enough to lower the rate of cognitive decline. There is an urgent need to identify early detection and disease progression biomarkers that can facilitate AD drug development. The current established readouts based on the expression levels of amyloid beta, tau, and phospho-tau have shown many discrepancies in patient samples when linked to disease progression. There is an urgent need to identify diagnostic and disease progression biomarkers from blood, cerebrospinal fluid (CSF), or other biofluids that can facilitate the early detection of the disease and provide pharmacodynamic readouts for new drugs being tested in clinical trials. Advances in proteomic approaches using state-of-the-art mass spectrometry are now being increasingly applied to study AD disease mechanisms and identify drug targets and novel disease biomarkers. In this report, we describe the application of quantitative proteomic approaches for understanding AD pathophysiology, summarize the current knowledge gained from proteomic investigations of AD, and discuss the development and validation of new predictive and diagnostic disease biomarkers.
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Joshi R, Salton SRJ. Neurotrophin Crosstalk in the Etiology and Treatment of Neuropsychiatric and Neurodegenerative Disease. Front Mol Neurosci 2022; 15:932497. [PMID: 35909451 PMCID: PMC9335126 DOI: 10.3389/fnmol.2022.932497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/23/2022] [Indexed: 12/27/2022] Open
Abstract
This article reviews the current progress in our understanding of the mechanisms by which growth factors, including brain-derived neurotrophic factor (BDNF) and vascular endothelial growth factor (VEGF), and select neurotrophin-regulated gene products, such as VGF (non-acronymic) and VGF-derived neuropeptides, function in the central nervous system (CNS) to modulate neuropsychiatric and neurodegenerative disorders, with a discussion of the possible therapeutic applications of these growth factors to major depressive disorder (MDD) and Alzheimer’s disease (AD). BDNF and VEGF levels are generally decreased regionally in the brains of MDD subjects and in preclinical animal models of depression, changes that are associated with neuronal atrophy and reduced neurogenesis, and are reversed by conventional monoaminergic and novel ketamine-like antidepressants. Downstream of neurotrophins and their receptors, VGF was identified as a nerve growth factor (NGF)- and BDNF-inducible secreted protein and neuropeptide precursor that is produced and trafficked throughout the CNS, where its expression is greatly influenced by neuronal activity and exercise, and where several VGF-derived peptides modulate neuronal activity, function, proliferation, differentiation, and survival. Moreover, levels of VGF are reduced in the CSF of AD subjects, where it has been repetitively identified as a disease biomarker, and in the hippocampi of subjects with MDD, suggesting possible shared mechanisms by which reduced levels of VGF and other proteins that are similarly regulated by neurotrophin signaling pathways contribute to and potentially drive the pathogenesis and progression of co-morbid neuropsychiatric and neurodegenerative disorders, particularly MDD and AD, opening possible therapeutic windows.
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Affiliation(s)
- Rajeev Joshi
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Stephen R. J. Salton
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Icahn School of Medicine at Mount Sinai, Friedman Brain Institute, New York, NY, United States
- Brookdale Department of Geriatrics and Palliative Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- *Correspondence: Stephen R. J. Salton,
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Wang Y, Qin X, Han Y, Li B. VGF: A prospective biomarker and therapeutic target for neuroendocrine and nervous system disorders. Biomed Pharmacother 2022; 151:113099. [PMID: 35594706 DOI: 10.1016/j.biopha.2022.113099] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/04/2022] [Accepted: 05/10/2022] [Indexed: 11/28/2022] Open
Abstract
Neuroendocrine regulatory polypeptide VGF (nerve growth factor inducible) was firstly found in the rapid induction of nerve growth factor on PC12 cells. It was selectively distributed in neurons and many neuroendocrine tissues. This paper reviewed the latest literatures on the gene structure, transcriptional regulation, protein processing, distribution and potential receptors of VGF. The neuroendocrine roles of VGF and its derived polypeptides in regulating energy, water electrolyte balance, circadian rhythm and reproductive activities were also summarized. Furthermore, based on the experimental evidence in vivo and in vitro, dysregulation of VGF in different neuroendocrine diseases and the possible mechanism mediated by VGF polypeptides were discussed. We next discussed the potential as the clinical diagnosis and therapy for VGF related diseases in the future.
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Affiliation(s)
- Yibei Wang
- Department of Thoracic Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province, China; Department of Developmental Cell Biology, Key Laboratory of Medical Cell Biology, China Medical University, Shenyang, Liaoning Province, China.
| | - Xiaoxue Qin
- Department of Developmental Cell Biology, Key Laboratory of Medical Cell Biology, China Medical University, Shenyang, Liaoning Province, China.
| | - Yun Han
- Department of Thoracic Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province, China.
| | - Bo Li
- Department of Developmental Cell Biology, Key Laboratory of Medical Cell Biology, China Medical University, Shenyang, Liaoning Province, China.
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Muqaku B, Oeckl P. Peptidomic Approaches and Observations in Neurodegenerative Diseases. Int J Mol Sci 2022; 23:ijms23137332. [PMID: 35806335 PMCID: PMC9266836 DOI: 10.3390/ijms23137332] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/16/2022] [Accepted: 06/28/2022] [Indexed: 02/04/2023] Open
Abstract
Mass spectrometry (MS), with its immense technological developments over the last two decades, has emerged as an unavoidable technique in analyzing biomolecules such as proteins and peptides. Its multiplexing capability and explorative approach make it a valuable tool for analyzing complex clinical samples concerning biomarker research and investigating pathophysiological mechanisms. Peptides regulate various biological processes, and several of them play a critical role in many disease-related pathological conditions. One important example in neurodegenerative diseases is the accumulation of amyloid-beta peptides (Aβ) in the brain of Alzheimer’s disease (AD) patients. When investigating brain function and brain-related pathologies, such as neurodegenerative diseases, cerebrospinal fluid (CSF) represents the most suitable sample because of its direct contact with the brain. In this review, we evaluate publications applying peptidomics analysis to CSF samples, focusing on neurodegenerative diseases. We describe the methodology of peptidomics analysis and give an overview of the achievements of CSF peptidomics over the years. Finally, publications reporting peptides regulated in AD are discussed.
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Affiliation(s)
- Besnik Muqaku
- German Center for Neurodegenerative Diseases (DZNE e.V.), 89081 Ulm, Germany;
| | - Patrick Oeckl
- German Center for Neurodegenerative Diseases (DZNE e.V.), 89081 Ulm, Germany;
- Department of Neurology, Ulm University Hospital, 89081 Ulm, Germany
- Correspondence: ; Tel.: +49-731-500-63143
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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] [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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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] [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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14
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Martín-de-Saavedra MD, Santos MD, Penzes P. Intercellular signaling by ectodomain shedding at the synapse. Trends Neurosci 2022; 45:483-498. [DOI: 10.1016/j.tins.2022.03.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 01/21/2022] [Accepted: 03/11/2022] [Indexed: 12/21/2022]
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15
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Abstract
Peptides play a crucial role in many vitally important functions of living organisms. The goal of peptidomics is the identification of the "peptidome," the whole peptide content of a cell, organ, tissue, body fluid, or organism. In peptidomic or proteomic studies, capillary electrophoresis (CE) is an alternative technique for liquid chromatography. It is a highly efficient and fast separation method requiring extremely low amounts of sample. In peptidomic approaches, CE is commonly combined with mass spectrometric (MS) detection. Most often, CE is coupled with electrospray ionization MS and less frequently with matrix-assisted laser desorption/ionization MS. CE-MS has been employed in numerous studies dealing with determination of peptide biomarkers in different body fluids for various diseases, or in food peptidomic research for the analysis and identification of peptides with special biological activities. In addition to the above topics, sample preparation techniques commonly applied in peptidomics before CE separation and possibilities for peptide identification and quantification by CE-MS or CE-MS/MS methods are discussed in this chapter.
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16
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Fluid Biomarkers of Frontotemporal Lobar Degeneration. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1281:123-139. [PMID: 33433873 DOI: 10.1007/978-3-030-51140-1_9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A timely diagnosis of frontotemporal degeneration (FTD) is frequently challenging due to the heterogeneous symptomatology and poor phenotype-pathological correlation. Fluid biomarkers that reflect FTD pathophysiology could be instrumental in both clinical practice and pharmaceutical trials. In recent years, significant progress has been made in developing biomarkers of neurodegenerative diseases: amyloid-β and tau in cerebrospinal fluid (CSF) can be used to exclude Alzheimer's disease, while neurofilament light chain (NfL) is emerging as a promising, albeit nonspecific, marker of neurodegeneration in both CSF and blood. Gene-specific biomarkers such as PGRN in GRN mutation carriers and dipeptide repeat proteins in C9orf72 mutation carriers are potential target engagement markers in genetic FTD trials. Novel techniques capable of measuring very low concentrations of brain-derived proteins in peripheral fluids are facilitating studies of blood biomarkers as a minimally invasive alternative to CSF. A major remaining challenge is the identification of a biomarker that can be used to predict the neuropathological substrate in sporadic FTD patients.
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17
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Thomas SL, Thacker JB, Schug KA, Maráková K. Sample preparation and fractionation techniques for intact proteins for mass spectrometric analysis. J Sep Sci 2020; 44:211-246. [DOI: 10.1002/jssc.202000936] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Shannon L. Thomas
- Department of Chemistry & Biochemistry The University of Texas Arlington Arlington Texas USA
| | - Jonathan B. Thacker
- Department of Chemistry & Biochemistry The University of Texas Arlington Arlington Texas USA
| | - Kevin A. Schug
- Department of Chemistry & Biochemistry The University of Texas Arlington Arlington Texas USA
| | - Katarína Maráková
- Department of Pharmaceutical Analysis and Nuclear Pharmacy Faculty of Pharmacy Comenius University in Bratislava Bratislava Slovakia
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18
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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] [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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19
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Ma QL, Zhu C, Morselli M, Su T, Pelligrini M, Lu Z, Jones M, Denver P, Castro D, Gu X, Relampagos F, Caoili K, Teter B, Frautschy SA, Cole GM. The Novel Omega-6 Fatty Acid Docosapentaenoic Acid Positively Modulates Brain Innate Immune Response for Resolving Neuroinflammation at Early and Late Stages of Humanized APOE-Based Alzheimer's Disease Models. Front Immunol 2020; 11:558036. [PMID: 33178186 PMCID: PMC7596305 DOI: 10.3389/fimmu.2020.558036] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 08/27/2020] [Indexed: 12/21/2022] Open
Abstract
Neuroinflammation plays a crucial role in the development and progression of Alzheimer's disease (AD), in which activated microglia are found to be associated with neurodegeneration. However, there is limited evidence showing how neuroinflammation and activated microglia are directly linked to neurodegeneration in vivo. Besides, there are currently no effective anti-inflammatory drugs for AD. In this study, we report on an effective anti-inflammatory lipid, linoleic acid (LA) metabolite docosapentaenoic acid (DPAn-6) treatment of aged humanized EFAD mice with advanced AD pathology. We also report the associations of neuroinflammatory and/or activated microglial markers with neurodegeneration in vivo. First, we found that dietary LA reduced proinflammatory cytokines of IL1-β, IL-6, as well as mRNA expression of COX2 toward resolving neuroinflammation with an increase of IL-10 in adult AD models E3FAD and E4FAD mice. Brain fatty acid assays showed a five to six-fold increase in DPAn-6 by dietary LA, especially more in E4FAD mice, when compared to standard diet. Thus, we tested DPAn-6 in aged E4FAD mice. After DPAn-6 was administered to the E4FAD mice by oral gavage for three weeks, we found that DPAn-6 reduced microgliosis and mRNA expressions of inflammatory, microglial, and caspase markers. Further, DPAn-6 increased mRNA expressions of ADCYAP1, VGF, and neuronal pentraxin 2 in parallel, all of which were inversely correlated with inflammatory and microglial markers. Finally, both LA and DPAn-6 directly reduced mRNA expression of COX2 in amyloid-beta42 oligomer-challenged BV2 microglial cells. Together, these data indicated that DPAn-6 modulated neuroinflammatory responses toward resolution and improvement of neurodegeneration in the late stages of AD models.
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Affiliation(s)
- Qiu-Lan Ma
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA, United States.,Geriatric Research and Clinical Center, Greater Los Angeles Veterans Affairs Healthcare System, West Los Angeles VA Medical Center, Los Angeles, CA, United States
| | - Cansheng Zhu
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA, United States.,Geriatric Research and Clinical Center, Greater Los Angeles Veterans Affairs Healthcare System, West Los Angeles VA Medical Center, Los Angeles, CA, United States.,Department of Neurology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Marco Morselli
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States.,Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA, United States.,Institute for Quantitative and Computational Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Trent Su
- Institute for Quantitative and Computational Biology, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - Matteo Pelligrini
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States.,Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA, United States.,Institute for Quantitative and Computational Biology, University of California, Los Angeles, Los Angeles, CA, United States.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Zhengqi Lu
- Department of Neurology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Mychica Jones
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA, United States.,Geriatric Research and Clinical Center, Greater Los Angeles Veterans Affairs Healthcare System, West Los Angeles VA Medical Center, Los Angeles, CA, United States
| | - Paul Denver
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA, United States.,Geriatric Research and Clinical Center, Greater Los Angeles Veterans Affairs Healthcare System, West Los Angeles VA Medical Center, Los Angeles, CA, United States
| | - Daniel Castro
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA, United States.,Geriatric Research and Clinical Center, Greater Los Angeles Veterans Affairs Healthcare System, West Los Angeles VA Medical Center, Los Angeles, CA, United States
| | - Xuelin Gu
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA, United States.,Geriatric Research and Clinical Center, Greater Los Angeles Veterans Affairs Healthcare System, West Los Angeles VA Medical Center, Los Angeles, CA, United States
| | - Frances Relampagos
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA, United States.,Geriatric Research and Clinical Center, Greater Los Angeles Veterans Affairs Healthcare System, West Los Angeles VA Medical Center, Los Angeles, CA, United States
| | - Kaitlin Caoili
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA, United States.,Geriatric Research and Clinical Center, Greater Los Angeles Veterans Affairs Healthcare System, West Los Angeles VA Medical Center, Los Angeles, CA, United States
| | - Bruce Teter
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA, United States.,Geriatric Research and Clinical Center, Greater Los Angeles Veterans Affairs Healthcare System, West Los Angeles VA Medical Center, Los Angeles, CA, United States
| | - Sally A Frautschy
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA, United States.,Geriatric Research and Clinical Center, Greater Los Angeles Veterans Affairs Healthcare System, West Los Angeles VA Medical Center, Los Angeles, CA, United States.,Department of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Gregory M Cole
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA, United States.,Geriatric Research and Clinical Center, Greater Los Angeles Veterans Affairs Healthcare System, West Los Angeles VA Medical Center, Los Angeles, CA, United States.,Department of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
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20
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Zhao Q, Bai Y, Liu D, Zhao N, Gao H, Zhang X. Quinetides: diverse posttranslational modified peptides of ribonuclease-like storage protein from Panax quinquefolius as markers for differentiating ginseng species. J Ginseng Res 2020; 44:680-689. [PMID: 32913397 PMCID: PMC7471211 DOI: 10.1016/j.jgr.2019.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 05/13/2019] [Accepted: 05/23/2019] [Indexed: 10/27/2022] Open
Abstract
Background Peptides have diverse and important physiological roles in plants and are ideal markers for species identification. It is unclear whether there are specific peptides in Panax quinquefolius L. (PQ). The aims of this study were to identify Quinetides, a series of diverse posttranslational modified native peptides of the ribonuclease-like storage protein (ginseng major protein), from PQ to explore novel peptide markers and develop a new method to distinguish PQ from Panax ginseng. Methods We used different fragmentation modes in the LTQ Orbitrap analysis to identify the enriched Quinetide targets of PQ, and we discovered Quinetide markers of PQ and P. ginseng using ultrahigh-performance liquid chromatography-quadrupole time-of-flight mass spectrometry analysis. These "peptide markers" were validated by simultaneously monitoring Rf and F11 as standard ginsenosides. Results We discovered 100 Quinetides of PQ with various post-translational modifications (PTMs), including a series of glycopeptides, all of which originated from the protein ginseng major protein. We effectively distinguished PQ from P. ginseng using new "peptide markers." Four unique peptides (Quinetides TP6 and TP7 as markers of PQ and Quinetides TP8 and TP9 as markers of P. ginseng) and their associated glycosylation products were discovered in PQ and P. ginseng. Conclusion We provide specific information on PQ peptides and propose the clinical application of peptide markers to distinguish PQ from P. ginseng.
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Affiliation(s)
- Qiang Zhao
- KeyLaboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China.,CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Yunpeng Bai
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Dan Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Nan Zhao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Huiyuan Gao
- KeyLaboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Xiaozhe Zhang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
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21
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Chaplot K, Jarvela TS, Lindberg I. Secreted Chaperones in Neurodegeneration. Front Aging Neurosci 2020; 12:268. [PMID: 33192447 PMCID: PMC7481362 DOI: 10.3389/fnagi.2020.00268] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/03/2020] [Indexed: 12/11/2022] Open
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)
| | | | - 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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22
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Beckmann ND, Lin WJ, Wang M, Cohain AT, Charney AW, Wang P, Ma W, Wang YC, Jiang C, Audrain M, Comella PH, Fakira AK, Hariharan SP, Belbin GM, Girdhar K, Levey AI, Seyfried NT, Dammer EB, Duong D, Lah JJ, Haure-Mirande JV, Shackleton B, Fanutza T, Blitzer R, Kenny E, Zhu J, Haroutunian V, Katsel P, Gandy S, Tu Z, Ehrlich ME, Zhang B, Salton SR, Schadt EE. Multiscale causal networks identify VGF as a key regulator of Alzheimer's disease. Nat Commun 2020; 11:3942. [PMID: 32770063 PMCID: PMC7414858 DOI: 10.1038/s41467-020-17405-z] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 06/15/2020] [Indexed: 12/31/2022] Open
Abstract
Though discovered over 100 years ago, the molecular foundation of sporadic Alzheimer's disease (AD) remains elusive. To better characterize the complex nature of AD, we constructed multiscale causal networks on a large human AD multi-omics dataset, integrating clinical features of AD, DNA variation, and gene- and protein-expression. These probabilistic causal models enabled detection, prioritization and replication of high-confidence master regulators of AD-associated networks, including the top predicted regulator, VGF. Overexpression of neuropeptide precursor VGF in 5xFAD mice partially rescued beta-amyloid-mediated memory impairment and neuropathology. Molecular validation of network predictions downstream of VGF was also achieved in this AD model, with significant enrichment for homologous genes identified as differentially expressed in 5xFAD brains overexpressing VGF. Our findings support a causal role for VGF in protecting against AD pathogenesis and progression.
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Affiliation(s)
- Noam D Beckmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Wei-Jye Lin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 510120, Guangzhou, China
- Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Ariella T Cohain
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexander W Charney
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Center for Statistical Genetics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Weiping Ma
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Ying-Chih Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Cheng Jiang
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Mickael Audrain
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Phillip H Comella
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Amanda K Fakira
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Siddharth P Hariharan
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Gillian M Belbin
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kiran Girdhar
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Allan I Levey
- Department of Neurology and Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Nicholas T Seyfried
- Department of Neurology and Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Eric B Dammer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Duc Duong
- Department of Neurology and Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - James J Lah
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Jean-Vianney Haure-Mirande
- Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Alzheimer's Disease Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ben Shackleton
- Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Tomas Fanutza
- Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Alzheimer's Disease Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Robert Blitzer
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Eimear Kenny
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Jun Zhu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Sema4, Stamford, CT, 06902, USA
| | - Vahram Haroutunian
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Alzheimer's Disease Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Department of Psychiatry, JJ Peters VA Medical Center, 130 West Kingsbridge Road, Bronx, NY, 10468, USA
| | - Pavel Katsel
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Department of Psychiatry, JJ Peters VA Medical Center, 130 West Kingsbridge Road, Bronx, NY, 10468, USA
| | - Sam Gandy
- Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Alzheimer's Disease Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, JJ Peters VA Medical Center, 130 West Kingsbridge Road, Bronx, NY, 10468, USA
| | - Zhidong Tu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Michelle E Ehrlich
- Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Stephen R Salton
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.
- Sema4, Stamford, CT, 06902, USA.
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23
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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] [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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24
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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] [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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25
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SWATH-MS analysis of cerebrospinal fluid to generate a robust battery of biomarkers for Alzheimer's disease. Sci Rep 2020; 10:7423. [PMID: 32366888 PMCID: PMC7198522 DOI: 10.1038/s41598-020-64461-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 04/16/2020] [Indexed: 12/14/2022] Open
Abstract
Cerebrospinal fluid (CSF) Aβ42 and tau protein levels are established diagnostic biomarkers of Alzheimer's disease (AD). However, their inadequacy to represent clinical efficacy in drug trials indicates the need for new biomarkers. Sequential window acquisition of all theoretical fragment ion spectra (SWATH)-based mass spectrometry (MS) is an advanced proteomic tool for large-scale, high-quality quantification. In this study, SWATH-MS showed that VGF, chromogranin-A, secretogranin-1, and opioid-binding protein/cell adhesion molecule were significantly decreased in 42 AD patients compared to 39 controls, whereas 14-3-3ζ was increased (FDR < 0.05). In addition, 16 other proteins showed substantial changes (FDR < 0.2). The expressions of the top 21 analytes were closely interconnected, but were poorly correlated with CSF Aβ42, tTau, and pTau181 levels. Logistic regression analysis and data mining were used to establish the best algorithm for AD, which created novel biomarker panels with high diagnostic value (AUC = 0.889 and 0.924) and a strong correlation with clinical severity (all p < 0.001). Targeted proteomics was used to validate their usefulness in a different cohort (n = 36) that included patients with other brain disorders (all p < 0.05). This study provides a list of proteins (and combinations thereof) that could serve as new AD biomarkers.
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26
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Khoonsari PE, Shevchenko G, Herman S, Remnestål J, Giedraitis V, Brundin R, Degerman Gunnarsson M, Kilander L, Zetterberg H, Nilsson P, Lannfelt L, Ingelsson M, Kultima K. Improved Differential Diagnosis of Alzheimer's Disease by Integrating ELISA and Mass Spectrometry-Based Cerebrospinal Fluid Biomarkers. J Alzheimers Dis 2020; 67:639-651. [PMID: 30614806 PMCID: PMC6398544 DOI: 10.3233/jad-180855] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Background: Alzheimer’s disease (AD) is diagnosed based on a clinical evaluation as well as analyses of classical biomarkers: Aβ42, total tau (t-tau), and phosphorylated tau (p-tau) in cerebrospinal fluid (CSF). Although the sensitivities and specificities of the classical biomarkers are fairly good for detection of AD, there is still a need to develop novel biochemical markers for early detection of AD. Objective: We explored if integration of novel proteins with classical biomarkers in CSF can better discriminate AD from non-AD subjects. Methods: We applied ELISA, mass spectrometry, and multivariate modeling to investigate classical biomarkers and the CSF proteome in subjects (n = 206) with 76 AD patients, 74 mild cognitive impairment (MCI) patients, 11 frontotemporal dementia (FTD) patients, and 45 non-dementia controls. The MCI patients were followed for 4–9 years and 21 of these converted to AD, whereas 53 remained stable. Results: By combining classical CSF biomarkers with twelve novel markers, the area of the ROC curves (AUROCS) of distinguishing AD and MCI/AD converters from non-AD were 93% and 96%, respectively. The FTDs and non-dementia controls were identified versus all other groups with AUROCS of 96% and 87%, respectively. Conclusions: Integration of new and classical CSF biomarkers in a model-based approach can improve the identification of AD, FTD, and non-dementia control subjects.
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Affiliation(s)
- Payam Emami Khoonsari
- Department of Medical Sciences, Clinical Chemistry, Uppsala University, Uppsala, Sweden
| | - Ganna Shevchenko
- Department of Chemistry-BMC, Analytical Chemistry, Uppsala University, Uppsala, Sweden
| | - Stephanie Herman
- Department of Medical Sciences, Clinical Chemistry, Uppsala University, Uppsala, Sweden
| | - Julia Remnestål
- Division of Affinity Proteomics, SciLifeLab, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Vilmantas Giedraitis
- Department of Public Health and Caring Sciences/Geriatrics, Uppsala University, Uppsala, Sweden
| | - RoseMarie Brundin
- Department of Public Health and Caring Sciences/Geriatrics, Uppsala University, Uppsala, Sweden
| | | | - Lena Kilander
- Department of Public Health and Caring Sciences/Geriatrics, Uppsala University, Uppsala, Sweden
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.,UK Dementia Research Institute at UCL, London, United Kingdom.,Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, United Kingdom
| | - Peter Nilsson
- Division of Affinity Proteomics, SciLifeLab, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Lars Lannfelt
- Department of Public Health and Caring Sciences/Geriatrics, Uppsala University, Uppsala, Sweden
| | - Martin Ingelsson
- Department of Public Health and Caring Sciences/Geriatrics, Uppsala University, Uppsala, Sweden
| | - Kim Kultima
- Department of Medical Sciences, Clinical Chemistry, Uppsala University, Uppsala, Sweden
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27
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El Gaamouch F, Audrain M, Lin WJ, Beckmann N, Jiang C, Hariharan S, Heeger PS, Schadt EE, Gandy S, Ehrlich ME, Salton SR. VGF-derived peptide TLQP-21 modulates microglial function through C3aR1 signaling pathways and reduces neuropathology in 5xFAD mice. Mol Neurodegener 2020; 15:4. [PMID: 31924226 PMCID: PMC6954537 DOI: 10.1186/s13024-020-0357-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 12/31/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Multiomic studies by several groups in the NIH Accelerating Medicines Partnership for Alzheimer's Disease (AMP-AD) identified VGF as a major driver of Alzheimer's disease (AD), also finding that reduced VGF levels correlate with mean amyloid plaque density, Clinical Dementia Rating (CDR) and Braak scores. VGF-derived peptide TLQP-21 activates the complement C3a receptor-1 (C3aR1), predominantly expressed in the brain on microglia. However, it is unclear how mouse or human TLQP-21, which are not identical, modulate microglial function and/or AD progression. METHODS We performed phagocytic/migration assays and RNA sequencing on BV2 microglial cells and primary microglia isolated from wild-type or C3aR1-null mice following treatment with TLQP-21 or C3a super agonist (C3aSA). Effects of intracerebroventricular TLQP-21 delivery were evaluated in 5xFAD mice, a mouse amyloidosis model of AD. Finally, the human HMC3 microglial cell line was treated with human TLQP-21 to determine whether specific peptide functions are conserved from mouse to human. RESULTS We demonstrate that TLQP-21 increases motility and phagocytic capacity in murine BV2 microglial cells, and in primary wild-type but not in C3aR1-null murine microglia, which under basal conditions have impaired phagocytic function compared to wild-type. RNA sequencing of primary microglia revealed overlapping transcriptomic changes induced by treatment with TLQP-21 or C3a super agonist (C3aSA). There were no transcriptomic changes in C3aR1-null or wild-type microglia exposed to the mutant peptide TLQP-R21A, which does not activate C3aR1. Most of the C3aSA- and TLQP-21-induced differentially expressed genes were linked to cell migration and proliferation. Intracerebroventricular TLQP-21 administration for 28 days via implanted osmotic pump resulted in a reduction of amyloid plaques and associated dystrophic neurites and restored expression of subsets of Alzheimer-associated microglial genes. Finally, we found that human TLQP-21 activates human microglia in a fashion similar to activation of murine microglia by mouse TLQP-21. CONCLUSIONS These data provide molecular and functional evidence suggesting that mouse and human TLQP-21 modulate microglial function, with potential implications for the progression of AD-related neuropathology.
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Affiliation(s)
- Farida El Gaamouch
- Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
| | - Mickael Audrain
- Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
| | - Wei-Jye Lin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong China
- Medical Research Center of Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong China
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
| | - Noam Beckmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
| | - Cheng Jiang
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
| | - Siddharth Hariharan
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
| | - Peter S. Heeger
- Department of Medicine, Translational Transplant Research Center, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Eric E. Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
- Sema4, Stamford, CT 06902 USA
| | - Sam Gandy
- Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
- Department of Psychiatry and Alzheimer’s Disease Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
| | - Michelle E. Ehrlich
- Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Stephen R. Salton
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
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28
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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: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [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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VGF in Cerebrospinal Fluid Combined With Conventional Biomarkers Enhances Prediction of Conversion From MCI to AD. Alzheimer Dis Assoc Disord 2019; 33:307-314. [PMID: 31305322 DOI: 10.1097/wad.0000000000000328] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND Previous work has suggested that the brain and cerebrospinal fluid (CSF) levels of a neural protein involved in synaptic transmission, VGF (a noninitialism), may be altered in mild cognitive impairment (MCI) and Alzheimer Disease (AD). The objective of the current work is to examine the potential of CSF levels of a peptide derived from VGF to predict conversion from MCI to AD. MATERIALS AND METHODS Using multivariate analytical approaches, the performance of the conventional biomarkers (CSF Aβ1-42 and phosphorylated tau +/- hippocampal volume) was compared with the same biomarkers combined with CSF VGF peptide levels in a large publicly available data set from human subjects. RESULTS It was observed that VGF peptides are lowered in CSF of patients with AD compared with controls and that combinations of CSF Aβ1-42 and phosphorylated tau, hippocampal volume, and VGF peptide levels outperformed conventional biomarkers alone (hazard ratio=2.2 vs. 3.9), for predicting MCI to AD conversion. CONCLUSIONS CSF VGF enhances the ability of conventional biomarkers to predict MCI to AD conversion. Future work will be needed to determine the specificity of VGF for AD versus other neurodegenerative diseases.
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VGF Peptides in Cerebrospinal Fluid of Patients with Dementia with Lewy Bodies. Int J Mol Sci 2019; 20:ijms20194674. [PMID: 31547145 PMCID: PMC6801397 DOI: 10.3390/ijms20194674] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/10/2019] [Accepted: 09/16/2019] [Indexed: 12/13/2022] Open
Abstract
In a previous proteomic study, we identified the neurosecretory protein VGF (VGF) as a potential biomarker for dementia with Lewy bodies (DLB). Here, we extended the study of VGF by comparing levels in cerebrospinal fluid (CSF) from 44 DLB patients, 20 Alzheimer’s disease (AD) patients, and 22 cognitively normal controls selected from the Amsterdam Dementia Cohort. CSF was analyzed using two orthogonal analytical methods: (1) In-house-developed quantitative ELISA and (2) selected reaction monitoring (SRM). We further addressed associations of VGF with other CSF biomarkers and cognition. VGF levels were lower in CSF from patients with DLB compared to either AD patients or controls. VGF was positively correlated with CSF tau and α-synuclein (0.55 < r < 0.75), but not with Aβ1-42. In DLB patients, low VGF levels were related to a more advanced cognitive decline at time of first presentation, whereas high levels of VGF were associated with steeper subsequent longitudinal cognitive decline. Hence, CSF VGF levels were lower in DLB compared to both AD and controls across different analytical methods. The strong associations with cognitive decline further points out VGF as a possible disease stage or prognostic marker for DLB.
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31
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Latosinska A, Siwy J, Mischak H, Frantzi M. Peptidomics and proteomics based on CE‐MS as a robust tool in clinical application: The past, the present, and the future. Electrophoresis 2019; 40:2294-2308. [DOI: 10.1002/elps.201900091] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/16/2019] [Accepted: 04/16/2019] [Indexed: 12/23/2022]
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Mack SM, Gomes I, Devi LA. Neuropeptide PEN and Its Receptor GPR83: Distribution, Signaling, and Regulation. ACS Chem Neurosci 2019; 10:1884-1891. [PMID: 30726666 DOI: 10.1021/acschemneuro.8b00559] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Neuropeptides are chemical messengers that act to regulate a number of physiological processes, including feeding, reward, pain, and memory, among others. PEN is one of the most abundant hypothalamic neuropeptides; however, until recently, its target receptor remained unknown. In this Review, we summarize recent developments in research focusing on PEN and its receptor GPR83. We describe the studies leading to the deorphanization of GPR83 as the receptor for PEN. We also describe the signaling mediated by the PEN-GPR83 system, as well as the physiological roles in which PEN-GPR83 has been implicated. As studies have suggested a role for the PEN-GPR83 system in food intake and body weight regulation, as well as in drug addiction and reward disorders, a thorough understanding of this novel neuropeptide-receptor system will help identify novel therapeutic targets to treat pathophysiological conditions involving PEN-GPR83.
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Affiliation(s)
- Seshat M. Mack
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Ivone Gomes
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Lakshmi A. Devi
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
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Jarvela TS, Womack T, Georgiou P, Gould TD, Eriksen JL, Lindberg I. 7B2 chaperone knockout in APP model mice results in reduced plaque burden. Sci Rep 2018; 8:9813. [PMID: 29955078 PMCID: PMC6023903 DOI: 10.1038/s41598-018-28031-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 06/08/2018] [Indexed: 01/18/2023] Open
Abstract
Impairment of neuronal proteostasis is a hallmark of Alzheimer's and other neurodegenerative diseases. However, the underlying molecular mechanisms leading to pathogenic protein aggregation, and the role of secretory chaperone proteins in this process, are poorly understood. We have previously shown that the neural-and endocrine-specific secretory chaperone 7B2 potently blocks in vitro fibrillation of Aβ42. To determine whether 7B2 can function as a chaperone in vivo, we measured plaque formation and performed behavioral assays in 7B2-deficient mice in an hAPPswe/PS1dE9 Alzheimer's model mouse background. Surprisingly, immunocytochemical analysis of cortical levels of thioflavin S- and Aβ-reactive plaques showed that APP mice with a partial or complete lack of 7B2 expression exhibited a significantly lower number and burden of thioflavin S-reactive, as well as Aβ-immunoreactive, plaques. However, 7B2 knockout did not affect total brain levels of either soluble or insoluble Aβ. While hAPP model mice performed poorly in the Morris water maze, their brain 7B2 levels did not impact performance. Since 7B2 loss reduced amyloid plaque burden, we conclude that brain 7B2 can impact Aβ disposition in a manner that facilitates plaque formation. These results are reminiscent of prior findings in hAPP model mice lacking the ubiquitous secretory chaperone clusterin.
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Affiliation(s)
- Timothy S Jarvela
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Tasha Womack
- Department of Pharmacology, College of Pharmacy, University of Houston, Houston, TX, USA
| | - Polymnia Georgiou
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Todd D Gould
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jason L Eriksen
- Department of Pharmacology, College of Pharmacy, University of Houston, Houston, TX, USA
| | - Iris Lindberg
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA.
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Ross JA, Reyes BAS, Van Bockstaele EJ. Amyloid beta peptides, locus coeruleus-norepinephrine system and dense core vesicles. Brain Res 2018; 1702:46-53. [PMID: 29577889 DOI: 10.1016/j.brainres.2018.03.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/06/2018] [Accepted: 03/07/2018] [Indexed: 10/17/2022]
Abstract
The evolution of peptidergic signaling systems in the central nervous system serves a distinct and crucial role in brain processes and function. The diversity of physiological peptides and the complexity of their regulation and secretion from the dense core vesicles (DCV) throughout the brain is a topic greatly in need of investigation, though recent years have shed light on cellular and molecular mechanisms that are summarized in this review. Here, we focus on the convergence of peptidergic systems onto the Locus Coeruleus (LC), the sole provider of norepinephrine (NE) to the cortex and hippocampus, via large DCV. As the LC-NE system is one of the first regions of the brain to undergo degeneration in Alzheimer's Disease (AD), and markers of DCV have consistently been demonstrated to have biomarker potential for AD progression, here we summarize the current literature linking the LC-NE system with DCV dysregulation and Aβ peptides. We also include neuroanatomical data suggesting that the building blocks of senile plaques, Aβ monomers, may be localized to DCV of the LC and noradrenergic axon terminals of the prefrontal cortex. Finally, we explore the putative consequences of chronic stress on Aβ production and the role that DCV may play in LC degeneration. Clinical data of immunological markers of DCV in AD patients are discussed.
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Affiliation(s)
- Jennifer A Ross
- Department of Pharmacology and Physiology, College of Medicine, Drexel University, Philadelphia, PA 19102, United States.
| | - Beverly A S Reyes
- Department of Pharmacology and Physiology, College of Medicine, Drexel University, Philadelphia, PA 19102, United States
| | - Elisabeth J Van Bockstaele
- Department of Pharmacology and Physiology, College of Medicine, Drexel University, Philadelphia, PA 19102, United States
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35
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Duits FH, Brinkmalm G, Teunissen CE, Brinkmalm A, Scheltens P, Van der Flier WM, Zetterberg H, Blennow K. Synaptic proteins in CSF as potential novel biomarkers for prognosis in prodromal Alzheimer's disease. ALZHEIMERS RESEARCH & THERAPY 2018; 10:5. [PMID: 29370833 PMCID: PMC6389073 DOI: 10.1186/s13195-017-0335-x] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 12/20/2017] [Indexed: 12/30/2022]
Abstract
BACKGROUND We investigated whether a panel of 12 potential novel biomarkers consisting of proteins involved in synapse functioning and immunity would be able to distinguish patients with Alzheimer's disease (AD) and patients with mild cognitive impairment (MCI) from control subjects. METHODS We included 40 control subjects, 40 subjects with MCI, and 40 subjects with AD from the Amsterdam Dementia Cohort who were matched for age and sex (age 65 ± 5 years, 19 [48%] women). The mean follow-up of patients with MCI was 3 years. Two or three tryptic peptides per protein were analyzed in cerebrospinal fluid using parallel reaction monitoring mass spectrometry. Corresponding stable isotope-labeled peptides were added and used as reference peptides. Multilevel generalized estimating equations (GEEs) with peptides clustered per subject and per protein (as within-subject variables) were used to assess differences between diagnostic groups. To assess differential effects of individual proteins, we included the diagnosis × protein interaction in the model. Separate GEE analyses were performed to assess differences between stable patients and patients with progressive MCI (MCI-AD). RESULTS There was a main effect for diagnosis (p < 0.01) and an interaction between diagnosis and protein (p < 0.01). Analysis stratified according to protein showed higher levels in patients with MCI for most proteins, especially in patients with MCI-AD. Chromogranin A, secretogranin II, neurexin 3, and neuropentraxin 1 showed the largest effect sizes; β values ranged from 0.53 to 0.78 for patients with MCI versus control subjects or patients with AD, and from 0.67 to 0.98 for patients with MCI-AD versus patients with stable MCI. In contrast, neurosecretory protein VGF was lower in patients with AD than in patients with MCI (ß = -0.93 [SE 0.22]) and control subjects (ß = 0.46 [SE 0.19]). CONCLUSIONS Our results suggest that several proteins involved in vesicular transport and synaptic stability are elevated in patients with MCI, especially in patients with MCI progressing to AD dementia. This may reflect early events in the AD pathophysiological cascade. These proteins may be valuable as disease stage or prognostic markers in an early symptomatic stage of the disease.
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Affiliation(s)
- Flora H Duits
- Alzheimer Center and Department of Neurology, Amsterdam Neuroscience, VU University Medical Center, P.O. Box 7057, 1007MB, Amsterdam, The Netherlands.
| | - Gunnar Brinkmalm
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Charlotte E Teunissen
- Alzheimer Center and Department of Neurology, Amsterdam Neuroscience, VU University Medical Center, P.O. Box 7057, 1007MB, Amsterdam, The Netherlands.,Neurochemistry Laboratory and Biobank, Department of Clinical Chemistry, Amsterdam Neuroscience, VU University Medical Center, Amsterdam, The Netherlands
| | - Ann Brinkmalm
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Philip Scheltens
- Alzheimer Center and Department of Neurology, Amsterdam Neuroscience, VU University Medical Center, P.O. Box 7057, 1007MB, Amsterdam, The Netherlands
| | - Wiesje M Van der Flier
- Alzheimer Center and Department of Neurology, Amsterdam Neuroscience, VU University Medical Center, P.O. Box 7057, 1007MB, Amsterdam, The Netherlands.,Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands
| | - Henrik Zetterberg
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.,Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, UK.,UK Dementia Research Institute at UCL, University College London, London, UK
| | - Kaj Blennow
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
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Abstract
Peptidomics is the comprehensive characterization of peptides from biological sources mainly by HPLC and mass spectrometry. Mass spectrometry allows the detection of a multitude of single peptides in complex mixtures. The term first appeared in full papers in the year 2001, after over 100 years of peptide research with a main focus on one or a few specific peptides. Within the last 15 years, this new field has grown to over 1200 publications. Mass spectrometry techniques, in combination with other analytical methods, were developed for the fast and comprehensive analysis of peptides in proteomics and specifically adjusted to implement peptidomics technologies. Although peptidomics is closely linked to proteomics, there are fundamental differences with conventional bottom-up proteomics. The development of peptidomics is described, including the most important implementations for its technological basis. Different strategies are covered which are applied to several important applications, such as neuropeptidomics and discovery of bioactive peptides or biomarkers. This overview includes links to all other chapters in the book as well as recent developments of separation, mass spectrometric, and data processing technologies. Additionally, some new applications in food and plant peptidomics as well as immunopeptidomics are introduced.
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Brinkmalm G, Sjödin S, Simonsen AH, Hasselbalch SG, Zetterberg H, Brinkmalm A, Blennow K. A Parallel Reaction Monitoring Mass Spectrometric Method for Analysis of Potential CSF Biomarkers for Alzheimer's Disease. Proteomics Clin Appl 2017; 12. [PMID: 29028155 DOI: 10.1002/prca.201700131] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Indexed: 01/04/2023]
Abstract
SCOPE The aim of this study was to develop and evaluate a parallel reaction monitoring mass spectrometry (PRM-MS) assay consisting of a panel of potential protein biomarkers in cerebrospinal fluid (CSF). EXPERIMENTAL DESIGN Thirteen proteins were selected based on their association with neurodegenerative diseases and involvement in synaptic function, secretory vesicle function, or innate immune system. CSF samples were digested and two to three peptides per protein were quantified using stable isotope-labeled peptide standards. RESULTS Coefficients of variation were generally below 15%. Clinical evaluation was performed on a cohort of 10 patients with Alzheimer's disease (AD) and 15 healthy subjects. Investigated proteins of the granin family exhibited the largest difference between the patient groups. Secretogranin-2 (p<0.005) and neurosecretory protein VGF (p<0.001) concentrations were lowered in AD. For chromogranin A, two of three peptides had significantly lowered AD concentrations (p<0.01). The concentrations of the synaptic proteins neurexin-1 and neuronal pentraxin-1, as well as neurofascin were also significantly lowered in AD (p<0.05). The other investigated proteins, β2-microglobulin, cystatin C, amyloid precursor protein, lysozyme C, neurexin-2, neurexin-3, and neurocan core protein, were not significantly altered. CONCLUSION AND CLINICAL RELEVANCE PRM-MS of protein panels is a valuable tool to evaluate biomarker candidates for neurodegenerative disorders.
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Affiliation(s)
- 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
| | - Simon Sjödin
- 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
| | - Anja Hviid Simonsen
- Danish Dementia Research Centre, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | | | - 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.,Department of Molecular Neuroscience, University College London Institute of Neurology, Queen Square, London, UK.,UK Dementia Research Institute, London, UK
| | - 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
| | - 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
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Llano DA, Bundela S, Mudar RA, Devanarayan V. A multivariate predictive modeling approach reveals a novel CSF peptide signature for both Alzheimer's Disease state classification and for predicting future disease progression. PLoS One 2017; 12:e0182098. [PMID: 28771542 PMCID: PMC5542644 DOI: 10.1371/journal.pone.0182098] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 07/12/2017] [Indexed: 11/19/2022] Open
Abstract
To determine if a multi-analyte cerebrospinal fluid (CSF) peptide signature can be used to differentiate Alzheimer’s Disease (AD) and normal aged controls (NL), and to determine if this signature can also predict progression from mild cognitive impairment (MCI) to AD, analysis of CSF samples was done on the Alzheimer’s Disease Neuroimaging Initiative (ADNI) dataset. The profiles of 320 peptides from baseline CSF samples of 287 subjects over a 3–6 year period were analyzed. As expected, the peptide most able to differentiate between AD vs. NL was found to be Apolipoprotein E. Other peptides, some of which are not classically associated with AD, such as heart fatty acid binding protein, and the neuronal pentraxin receptor, also differentiated disease states. A sixteen-analyte signature was identified which differentiated AD vs. NL with an area under the receiver operating characteristic curve of 0.89, which was better than any combination of amyloid beta (1–42), tau, and phospho-181 tau. This same signature, when applied to a new and independent data set, also strongly predicted both probability and rate of future progression of MCI subjects to AD, better than traditional markers. These data suggest that multivariate peptide signatures from CSF predict MCI to AD progression, and point to potentially new roles for certain proteins not typically associated with AD.
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Affiliation(s)
- Daniel A. Llano
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, United States of America
- * E-mail:
| | - Saurabh Bundela
- Exploratory Statistics, AbbVie, Inc., North Chicago, IL, United States of America
| | - Raksha A. Mudar
- Department of Speech and Hearing Science, University of Illinois at Urbana-Champaign, United States of America
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Majerova P, Barath P, Michalicova A, Katina S, Novak M, Kovac A. Changes of Cerebrospinal Fluid Peptides due to Tauopathy. J Alzheimers Dis 2017; 58:507-520. [DOI: 10.3233/jad-170110] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Petra Majerova
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovak Republic
- AXON Neuroscience R&D, Bratislava, Slovak Republic
| | - Peter Barath
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Alena Michalicova
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovak Republic
- AXON Neuroscience R&D, Bratislava, Slovak Republic
| | - Stanislav Katina
- AXON Neuroscience R&D, Bratislava, Slovak Republic
- Institute of Mathematics and Statistics, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Michal Novak
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovak Republic
- AXON Neuroscience R&D, Bratislava, Slovak Republic
| | - Andrej Kovac
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovak Republic
- AXON Neuroscience R&D, Bratislava, Slovak Republic
- Department of Pharmacology and Toxicology, The University of Veterinary Medicine and Pharmacy, Kosice, Slovak Republic
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Bastos P, Ferreira R, Manadas B, Moreira PI, Vitorino R. Insights into the human brain proteome: Disclosing the biological meaning of protein networks in cerebrospinal fluid. Crit Rev Clin Lab Sci 2017; 54:185-204. [PMID: 28393582 DOI: 10.1080/10408363.2017.1299682] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cerebrospinal fluid (CSF) is an excellent source of biological information regarding the nervous system, once it is in close contact and accurately reflects alterations in this system. Several studies have analyzed differential protein profiles of CSF samples between healthy and diseased human subjects. However, the pathophysiological mechanisms and how CSF proteins relate to diseases are still poorly known. By applying bioinformatics tools, we attempted to provide new insights on the biological and functional meaning of proteomics data envisioning the identification of putative disease biomarkers. Bioinformatics analysis of data retrieved from 99 mass spectrometry (MS)-based studies on CSF profiling highlighted 1985 differentially expressed proteins across 49 diseases. A large percentage of the modulated proteins originate from exosome vesicles, and the majority are involved in either neuronal cell growth, development, maturation, migration, or neurotransmitter-mediated cellular communication. Nevertheless, some diseases present a unique CSF proteome profile, which were critically analyzed in the present study. For instance, 48 proteins were found exclusively upregulated in the CSF of patients with Alzheimer's disease and are mainly involved in steroid esterification and protein activation cascade processes. A higher number of exclusively upregulated proteins were found in the CSF of patients with multiple sclerosis (76 proteins) and with bacterial meningitis (70 proteins). Whereas in multiple sclerosis, these proteins are mostly involved in the regulation of RNA metabolism and apoptosis, in bacterial meningitis the exclusively upregulated proteins participate in inflammation and antibacterial humoral response, reflecting disease pathogenesis. The exploration of the contribution of exclusively upregulated proteins to disease pathogenesis will certainly help to envision potential biomarkers in the CSF for the clinical management of nervous system diseases.
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Affiliation(s)
- Paulo Bastos
- a Department of Chemistry , University of Aveiro , Aveiro , Portugal.,b Department of Medical Sciences , Institute for Biomedicine - iBiMED, University of Aveiro , Aveiro , Portugal
| | - Rita Ferreira
- c QOPNA, Department of Chemistry , University of Aveiro , Aveiro , Portugal
| | - Bruno Manadas
- d CNC, Center for Neuroscience and Cell Biology, University of Coimbra , Coimbra , Portugal
| | - Paula I Moreira
- d CNC, Center for Neuroscience and Cell Biology, University of Coimbra , Coimbra , Portugal.,e Laboratory of Physiology, Faculty of Medicine , University of Coimbra , Coimbra , Portugal
| | - Rui Vitorino
- b Department of Medical Sciences , Institute for Biomedicine - iBiMED, University of Aveiro , Aveiro , Portugal.,f Departmento de Cirurgia e Fisiologia, Faculdade de Medicina , Unidade de Investigação Cardiovascular, Universidade do Porto , Porto , Portugal
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Latina V, Caioli S, Zona C, Ciotti MT, Amadoro G, Calissano P. Impaired NGF/TrkA Signaling Causes Early AD-Linked Presynaptic Dysfunction in Cholinergic Primary Neurons. Front Cell Neurosci 2017; 11:68. [PMID: 28360840 PMCID: PMC5350152 DOI: 10.3389/fncel.2017.00068] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 02/24/2017] [Indexed: 12/31/2022] Open
Abstract
Alterations in NGF/TrkA signaling have been suggested to underlie the selective degeneration of the cholinergic basal forebrain neurons occurring in vivo in AD (Counts and Mufson, 2005; Mufson et al., 2008; Niewiadomska et al., 2011) and significant reduction of cognitive decline along with an improvement of cholinergic hypofunction have been found in phase I clinical trial in humans affected from mild AD following therapeutic NGF gene therapy (Tuszynski et al., 2005, 2015). Here, we show that the chronic (10–12 D.I.V.) in vitro treatment with NGF (100 ng/ml) under conditions of low supplementation (0.2%) with the culturing serum-substitute B27 selectively enriches the basal forebrain cholinergic neurons (+36.36%) at the expense of other non-cholinergic, mainly GABAergic (−38.45%) and glutamatergic (−56.25%), populations. By taking advantage of this newly-developed septo-hippocampal neuronal cultures, our biochemical and electrophysiological investigations demonstrate that the early failure in excitatory neurotransmission following NGF withdrawal is paralleled by concomitant and progressive loss in selected presynaptic and vesicles trafficking proteins including synapsin I, SNAP-25 and α-synuclein. This rapid presynaptic dysfunction: (i) precedes the commitment to cell death and is reversible in a time-dependent manner, being suppressed by de novo external administration of NGF within 6 hr from its initial withdrawal; (ii) is specific because it is not accompanied by contextual changes in expression levels of non-synaptic proteins from other subcellular compartments; (ii) is not secondary to axonal degeneration because it is insensible to pharmacological treatment with known microtubule-stabilizing drug such paclitaxel; (iv) involves TrkA-dependent mechanisms because the effects of NGF reapplication are blocked by acute exposure to specific and cell-permeable inhibitor of its high-affinity receptor. Taken together, this study may have important clinical implications in the field of AD neurodegeneration because it: (i) provides new insights on the earliest molecular mechanisms underlying the loss of synaptic/trafficking proteins and, then, of synapes integrity which occurs in vulnerable basal forebrain population at preclinical stages of neuropathology; (ii) offers prime presynaptic-based molecular target to extend the therapeutic time-window of NGF action in the strategy of improving its neuroprotective in vivo intervention in affected patients.
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Affiliation(s)
- Valentina Latina
- Institute of Translational Pharmacology, National Research Council (CNR) Rome, Italy
| | | | - Cristina Zona
- IRCCS Santa Lucia FoundationRome, Italy; Department of Systems Medicine, University of Rome Tor VergataRome, Italy
| | - Maria T Ciotti
- NGF and Molecular Mechanisms of Neurodegenerative Diseases, European Brain Research Institute (EBRI) Rome, Italy
| | - Giuseppina Amadoro
- Institute of Translational Pharmacology, National Research Council (CNR)Rome, Italy; NGF and Molecular Mechanisms of Neurodegenerative Diseases, European Brain Research Institute (EBRI)Rome, Italy
| | - Pietro Calissano
- NGF and Molecular Mechanisms of Neurodegenerative Diseases, European Brain Research Institute (EBRI) Rome, Italy
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Neuropeptide VGF Promotes Maturation of Hippocampal Dendrites That Is Reduced by Single Nucleotide Polymorphisms. Int J Mol Sci 2017; 18:ijms18030612. [PMID: 28287464 PMCID: PMC5372628 DOI: 10.3390/ijms18030612] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/03/2017] [Accepted: 03/08/2017] [Indexed: 12/13/2022] Open
Abstract
The neuropeptide VGF (non-acronymic) is induced by brain-derived neurotrophic factor and promotes hippocampal neurogenesis, as well as synaptic activity. However, morphological changes induced by VGF have not been elucidated. Developing hippocampal neurons were exposed to VGF through bath application or virus-mediated expression in vitro. VGF-derived peptide, TLQP-62, enhanced dendritic branching, and outgrowth. Furthermore, VGF increased dendritic spine density and the proportion of immature spines. Spine formation was associated with increased synaptic protein expression and co-localization of pre- and postsynaptic markers. Three non-synonymous single nucleotide polymorphisms (SNPs) were selected in human VGF gene. Transfection of N2a cells with plasmids containing these SNPs revealed no relative change in protein expression levels and normal protein size, except for a truncated protein from the premature stop codon, E525X. All three SNPs resulted in a lower proportion of N2a cells bearing neurites relative to wild-type VGF. Furthermore, all three mutations reduced the total length of dendrites in developing hippocampal neurons. Taken together, our results suggest VGF enhances dendritic maturation and that these effects can be altered by common mutations in the VGF gene. The findings may have implications for people suffering from psychiatric disease or other conditions who may have altered VGF levels.
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Ganief T, Gqamana P, Garnett S, Hoare J, Stein DJ, Joska J, Soares N, Blackburn JM. Quantitative proteomic analysis of HIV-1 Tat-induced dysregulation in SH-SY5Y neuroblastoma cells. Proteomics 2017; 17. [PMID: 28101920 DOI: 10.1002/pmic.201600236] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 12/23/2016] [Accepted: 01/12/2017] [Indexed: 11/11/2022]
Abstract
Despite affecting up to 70% of HIV-positive patients and being the leading cause of dementia in patients under 40 years, the molecular mechanisms involved in the onset of HIV-associated neurocognitive disorders (HAND) are not well understood. To address this, we performed SILAC-based quantitative proteomic analysis on HIV-Tat treated SH-SY5Y neuroblastoma cells. Isolated protein was fractionated by SDS-PAGE and analyzed by nLC-MS/MS on an Orbitrap Velos. Using MaxQuant, we identified and quantified 3077 unique protein groups, of which 407 were differentially regulated. After applying an additional standard deviation-based cutoff, 29 of these were identified as highly significantly and stably dysregulated. GO term analysis shows dysregulation in both protein translation machinery as well as cytoskeletal regulation that have both been implicated in other dementias. In addition, several key cytoskeletal regulatory proteins such as ARHGEF17, the Rho GTPase, SHROOM3, and CMRP1 are downregulated. Together, these data demonstrate that HIV-Tat can dysregulate neuronal cytoskeletal regulatory proteins that could lead to the major HAND clinical manifestation-synapse loss.
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Affiliation(s)
- Tariq Ganief
- Department of Integrative Biomedical Sciences, University of Cape Town, South Africa
| | - Putuma Gqamana
- Department of Integrative Biomedical Sciences, University of Cape Town, South Africa
| | - Shaun Garnett
- Department of Integrative Biomedical Sciences, University of Cape Town, South Africa
| | - Jackie Hoare
- Department of Psychiatry, University of Cape Town, South Africa
| | - Dan J Stein
- Department of Psychiatry, University of Cape Town, South Africa.,MRC Unit on Anxiety and Stress Disorders, University of Cape Town, South Africa
| | - John Joska
- Department of Psychiatry, University of Cape Town, South Africa
| | - Nelson Soares
- Department of Integrative Biomedical Sciences, University of Cape Town, South Africa
| | - Jonathan M Blackburn
- Department of Integrative Biomedical Sciences, University of Cape Town, South Africa.,Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
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Robinson RAS, Amin B, Guest PC. Multiplexing Biomarker Methods, Proteomics and Considerations for Alzheimer’s Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 974:21-48. [DOI: 10.1007/978-3-319-52479-5_2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Barrera-Ocampo A, Arlt S, Matschke J, Hartmann U, Puig B, Ferrer I, Zürbig P, Glatzel M, Sepulveda-Falla D, Jahn H. Amyloid-β Precursor Protein Modulates the Sorting of Testican-1 and Contributes to Its Accumulation in Brain Tissue and Cerebrospinal Fluid from Patients with Alzheimer Disease. J Neuropathol Exp Neurol 2016; 75:903-16. [PMID: 27486134 PMCID: PMC5015660 DOI: 10.1093/jnen/nlw065] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The mechanisms leading to amyloid-β (Aβ) accumulation in sporadic Alzheimer disease (AD) are unknown but both increased production or impaired clearance likely contribute to aggregation. To understand the potential roles of the extracellular matrix proteoglycan Testican-1 in the pathophysiology of AD, we used samples from AD patients and controls and an in vitro approach. Protein expression analysis showed increased levels of Testican-1 in frontal and temporal cortex of AD patients; histological analysis showed that Testican-1 accumulates and co-aggregates with Aβ plaques in the frontal, temporal and entorhinal cortices of AD patients. Proteomic analysis identified 10 fragments of Testican-1 in cerebrospinal fluid (CSF) from AD patients. HEK293T cells expressing human wild type or mutant Aβ precursor protein (APP) were transfected with Testican-1. The co-expression of both proteins modified the sorting of Testican-1 into the endocytic pathway leading to its transient accumulation in Golgi, which seemed to affect APP processing, as indicated by reduced Aβ40 and Aβ42 levels in APP mutant cells. In conclusion, patient data reflect a clearance impairment that may favor Aβ accumulation in AD brains and our in vitro model supports the notion that the interaction between APP and Testican-1 may be a key step in the production and aggregation of Aβ species.
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Affiliation(s)
- Alvaro Barrera-Ocampo
- From the Institute of Neuropathology (AB-O, JM, BP, MG, DS-F), Department of Psychiatry and Psychotherapy (SA, HJ), University Medical Center Hamburg-Eppendorf, Hamburg, Germany, Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany (UH), Institute of Neuropathology, Bellvitge University Hospital, CIBERNED, Hospitalet de Llobregat, University of Barcelona, Spain (IF), Mosaiques Diagnostics and Therapeutics AG, Hannover, Germany (PZ), and Department of Pharmaceutical Sciences, Natura Research Group, Faculty of Natural Sciences, ICESI University, Cali, Colombia (AB-O)
| | - Sönke Arlt
- From the Institute of Neuropathology (AB-O, JM, BP, MG, DS-F), Department of Psychiatry and Psychotherapy (SA, HJ), University Medical Center Hamburg-Eppendorf, Hamburg, Germany, Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany (UH), Institute of Neuropathology, Bellvitge University Hospital, CIBERNED, Hospitalet de Llobregat, University of Barcelona, Spain (IF), Mosaiques Diagnostics and Therapeutics AG, Hannover, Germany (PZ), and Department of Pharmaceutical Sciences, Natura Research Group, Faculty of Natural Sciences, ICESI University, Cali, Colombia (AB-O)
| | - Jakob Matschke
- From the Institute of Neuropathology (AB-O, JM, BP, MG, DS-F), Department of Psychiatry and Psychotherapy (SA, HJ), University Medical Center Hamburg-Eppendorf, Hamburg, Germany, Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany (UH), Institute of Neuropathology, Bellvitge University Hospital, CIBERNED, Hospitalet de Llobregat, University of Barcelona, Spain (IF), Mosaiques Diagnostics and Therapeutics AG, Hannover, Germany (PZ), and Department of Pharmaceutical Sciences, Natura Research Group, Faculty of Natural Sciences, ICESI University, Cali, Colombia (AB-O)
| | - Ursula Hartmann
- From the Institute of Neuropathology (AB-O, JM, BP, MG, DS-F), Department of Psychiatry and Psychotherapy (SA, HJ), University Medical Center Hamburg-Eppendorf, Hamburg, Germany, Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany (UH), Institute of Neuropathology, Bellvitge University Hospital, CIBERNED, Hospitalet de Llobregat, University of Barcelona, Spain (IF), Mosaiques Diagnostics and Therapeutics AG, Hannover, Germany (PZ), and Department of Pharmaceutical Sciences, Natura Research Group, Faculty of Natural Sciences, ICESI University, Cali, Colombia (AB-O)
| | - Berta Puig
- From the Institute of Neuropathology (AB-O, JM, BP, MG, DS-F), Department of Psychiatry and Psychotherapy (SA, HJ), University Medical Center Hamburg-Eppendorf, Hamburg, Germany, Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany (UH), Institute of Neuropathology, Bellvitge University Hospital, CIBERNED, Hospitalet de Llobregat, University of Barcelona, Spain (IF), Mosaiques Diagnostics and Therapeutics AG, Hannover, Germany (PZ), and Department of Pharmaceutical Sciences, Natura Research Group, Faculty of Natural Sciences, ICESI University, Cali, Colombia (AB-O)
| | - Isidre Ferrer
- From the Institute of Neuropathology (AB-O, JM, BP, MG, DS-F), Department of Psychiatry and Psychotherapy (SA, HJ), University Medical Center Hamburg-Eppendorf, Hamburg, Germany, Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany (UH), Institute of Neuropathology, Bellvitge University Hospital, CIBERNED, Hospitalet de Llobregat, University of Barcelona, Spain (IF), Mosaiques Diagnostics and Therapeutics AG, Hannover, Germany (PZ), and Department of Pharmaceutical Sciences, Natura Research Group, Faculty of Natural Sciences, ICESI University, Cali, Colombia (AB-O)
| | - Petra Zürbig
- From the Institute of Neuropathology (AB-O, JM, BP, MG, DS-F), Department of Psychiatry and Psychotherapy (SA, HJ), University Medical Center Hamburg-Eppendorf, Hamburg, Germany, Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany (UH), Institute of Neuropathology, Bellvitge University Hospital, CIBERNED, Hospitalet de Llobregat, University of Barcelona, Spain (IF), Mosaiques Diagnostics and Therapeutics AG, Hannover, Germany (PZ), and Department of Pharmaceutical Sciences, Natura Research Group, Faculty of Natural Sciences, ICESI University, Cali, Colombia (AB-O)
| | - Markus Glatzel
- From the Institute of Neuropathology (AB-O, JM, BP, MG, DS-F), Department of Psychiatry and Psychotherapy (SA, HJ), University Medical Center Hamburg-Eppendorf, Hamburg, Germany, Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany (UH), Institute of Neuropathology, Bellvitge University Hospital, CIBERNED, Hospitalet de Llobregat, University of Barcelona, Spain (IF), Mosaiques Diagnostics and Therapeutics AG, Hannover, Germany (PZ), and Department of Pharmaceutical Sciences, Natura Research Group, Faculty of Natural Sciences, ICESI University, Cali, Colombia (AB-O)
| | - Diego Sepulveda-Falla
- From the Institute of Neuropathology (AB-O, JM, BP, MG, DS-F), Department of Psychiatry and Psychotherapy (SA, HJ), University Medical Center Hamburg-Eppendorf, Hamburg, Germany, Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany (UH), Institute of Neuropathology, Bellvitge University Hospital, CIBERNED, Hospitalet de Llobregat, University of Barcelona, Spain (IF), Mosaiques Diagnostics and Therapeutics AG, Hannover, Germany (PZ), and Department of Pharmaceutical Sciences, Natura Research Group, Faculty of Natural Sciences, ICESI University, Cali, Colombia (AB-O)
| | - Holger Jahn
- From the Institute of Neuropathology (AB-O, JM, BP, MG, DS-F), Department of Psychiatry and Psychotherapy (SA, HJ), University Medical Center Hamburg-Eppendorf, Hamburg, Germany, Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany (UH), Institute of Neuropathology, Bellvitge University Hospital, CIBERNED, Hospitalet de Llobregat, University of Barcelona, Spain (IF), Mosaiques Diagnostics and Therapeutics AG, Hannover, Germany (PZ), and Department of Pharmaceutical Sciences, Natura Research Group, Faculty of Natural Sciences, ICESI University, Cali, Colombia (AB-O)
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The neural chaperone proSAAS blocks α-synuclein fibrillation and neurotoxicity. Proc Natl Acad Sci U S A 2016; 113:E4708-15. [PMID: 27457957 DOI: 10.1073/pnas.1601091113] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Emerging evidence strongly suggests that chaperone proteins are cytoprotective in neurodegenerative proteinopathies involving protein aggregation; for example, in the accumulation of aggregated α-synuclein into the Lewy bodies present in Parkinson's disease. Of the various chaperones known to be associated with neurodegenerative disease, the small secretory chaperone known as proSAAS (named after four residues in the amino terminal region) has many attractive properties. We show here that proSAAS, widely expressed in neurons throughout the brain, is associated with aggregated synuclein deposits in the substantia nigra of patients with Parkinson's disease. Recombinant proSAAS potently inhibits the fibrillation of α-synuclein in an in vitro assay; residues 158-180, containing a largely conserved element, are critical to this bioactivity. ProSAAS also exhibits a neuroprotective function; proSAAS-encoding lentivirus blocks α-synuclein-induced cytotoxicity in primary cultures of nigral dopaminergic neurons, and recombinant proSAAS blocks α-synuclein-induced cytotoxicity in SH-SY5Y cells. Four independent proteomics studies have previously identified proSAAS as a potential cerebrospinal fluid biomarker in various neurodegenerative diseases. Coupled with prior work showing that proSAAS blocks β-amyloid aggregation into fibrils, this study supports the idea that neuronal proSAAS plays an important role in proteostatic processes. ProSAAS thus represents a possible therapeutic target in neurodegenerative disease.
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Hölttä M, Dean RA, Siemers E, Mawuenyega KG, Sigurdson W, May PC, Holtzman DM, Portelius E, Zetterberg H, Bateman RJ, Blennow K, Gobom J. A single dose of the γ-secretase inhibitor semagacestat alters the cerebrospinal fluid peptidome in humans. Alzheimers Res Ther 2016; 8:11. [PMID: 26948580 PMCID: PMC4780148 DOI: 10.1186/s13195-016-0178-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 01/29/2016] [Indexed: 01/09/2023]
Abstract
BACKGROUND In Alzheimer's disease, beta-amyloid peptides in the brain aggregate into toxic oligomers and plaques, a process which is associated with neuronal degeneration, memory loss, and cognitive decline. One therapeutic strategy is to decrease the production of potentially toxic beta-amyloid species by the use of inhibitors or modulators of the enzymes that produce beta-amyloid from amyloid precursor protein (APP). The failures of several such drug candidates by lack of effect or undesired side-effects underscore the importance to monitor the drug effects in the brain on a molecular level. Here we evaluate if peptidomic analysis in cerebrospinal fluid (CSF) can be used for this purpose. METHODS Fifteen human healthy volunteers, divided into three groups, received a single dose of placebo or either 140 mg or 280 mg of the γ-secretase inhibitor semagacestat (LY450139). Endogenous peptides in CSF, sampled prior to administration of the drug and at six subsequent time points, were analyzed by liquid chromatography coupled to mass spectrometry, using isobaric labeling based on the tandem mass tag approach for relative quantification. RESULTS Out of 302 reproducibly detected peptides, 11 were affected by the treatment. Among these, one was derived from APP and one from amyloid precursor-like protein 1. Nine peptides were derived from proteins that may not be γ-secretase substrates per se, but that are regulated in a γ-secretase-dependent manner. CONCLUSIONS These results indicate that a CSF peptidomic approach may be a valuable tool both to verify target engagement and to identify other pharmacodynamic effects of the drug. Data are available via ProteomeXchange with identifier PXD003075. TRIAL REGISTRATION NCT00765115 , registered 30/09/2008.
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Affiliation(s)
- Mikko Hölttä
- Department of Psychiatry and Neurochemistry, Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, SU/Mölndal Hospital, 431 80, Mölndal, Sweden.
| | - Robert A Dean
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Headquarters, Indianapolis, IN, 46285, USA.
| | - Eric Siemers
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Headquarters, Indianapolis, IN, 46285, USA.
| | - Kwasi G Mawuenyega
- Department of Neurology, Washington University School of Medicine, 660 South Euclid, Campus Box 8111, St. Louis, MO, 63110, USA.
| | - Wendy Sigurdson
- Department of Neurology, Washington University School of Medicine, 660 South Euclid, Campus Box 8111, St. Louis, MO, 63110, USA.
- Alzheimer's Disease Research Center, Washington University School of Medicine, 660 South Euclid, Campus Box 8111, St. Louis, MO, 63110, USA.
| | - Patrick C May
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Headquarters, Indianapolis, IN, 46285, USA.
| | - David M Holtzman
- Department of Neurology, Washington University School of Medicine, 660 South Euclid, Campus Box 8111, St. Louis, MO, 63110, USA.
- Alzheimer's Disease Research Center, Washington University School of Medicine, 660 South Euclid, Campus Box 8111, St. Louis, MO, 63110, USA.
- Hope Center for Neurological Disorders, Washington University School of Medicine, 660 South Euclid, Campus Box 8111, St. Louis, MO, 63110, USA.
| | - Erik Portelius
- Department of Psychiatry and Neurochemistry, Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, SU/Mölndal Hospital, 431 80, Mölndal, Sweden.
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, SU/Mölndal Hospital, 431 80, Mölndal, Sweden.
- UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK.
| | - Randall J Bateman
- Department of Neurology, Washington University School of Medicine, 660 South Euclid, Campus Box 8111, St. Louis, MO, 63110, USA.
- Alzheimer's Disease Research Center, Washington University School of Medicine, 660 South Euclid, Campus Box 8111, St. Louis, MO, 63110, USA.
- Hope Center for Neurological Disorders, Washington University School of Medicine, 660 South Euclid, Campus Box 8111, St. Louis, MO, 63110, USA.
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, SU/Mölndal Hospital, 431 80, Mölndal, Sweden.
| | - Johan Gobom
- Department of Psychiatry and Neurochemistry, Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, SU/Mölndal Hospital, 431 80, Mölndal, Sweden.
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Khoonsari PE, Häggmark A, Lönnberg M, Mikus M, Kilander L, Lannfelt L, Bergquist J, Ingelsson M, Nilsson P, Kultima K, Shevchenko G. Analysis of the Cerebrospinal Fluid Proteome in Alzheimer's Disease. PLoS One 2016; 11:e0150672. [PMID: 26950848 PMCID: PMC4780771 DOI: 10.1371/journal.pone.0150672] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 02/16/2016] [Indexed: 12/24/2022] Open
Abstract
Alzheimer’s disease is a neurodegenerative disorder accounting for more than 50% of cases of dementia. Diagnosis of Alzheimer’s disease relies on cognitive tests and analysis of amyloid beta, protein tau, and hyperphosphorylated tau in cerebrospinal fluid. Although these markers provide relatively high sensitivity and specificity for early disease detection, they are not suitable for monitor of disease progression. In the present study, we used label-free shotgun mass spectrometry to analyse the cerebrospinal fluid proteome of Alzheimer’s disease patients and non-demented controls to identify potential biomarkers for Alzheimer’s disease. We processed the data using five programs (DecyderMS, Maxquant, OpenMS, PEAKS, and Sieve) and compared their results by means of reproducibility and peptide identification, including three different normalization methods. After depletion of high abundant proteins we found that Alzheimer’s disease patients had lower fraction of low-abundance proteins in cerebrospinal fluid compared to healthy controls (p<0.05). Consequently, global normalization was found to be less accurate compared to using spiked-in chicken ovalbumin for normalization. In addition, we determined that Sieve and OpenMS resulted in the highest reproducibility and PEAKS was the programs with the highest identification performance. Finally, we successfully verified significantly lower levels (p<0.05) of eight proteins (A2GL, APOM, C1QB, C1QC, C1S, FBLN3, PTPRZ, and SEZ6) in Alzheimer’s disease compared to controls using an antibody-based detection method. These proteins are involved in different biological roles spanning from cell adhesion and migration, to regulation of the synapse and the immune system.
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Affiliation(s)
- Payam Emami Khoonsari
- Department of Medical Sciences, Cancer Pharmacology and Computational Medicine, Uppsala University, Uppsala, Sweden
| | - Anna Häggmark
- Affinity Proteomics, Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Maria Lönnberg
- Analytical Chemistry, Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden
| | - Maria Mikus
- Affinity Proteomics, Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Lena Kilander
- Department of Public Health/Geriatrics, Uppsala University, Uppsala, Sweden
| | - Lars Lannfelt
- Department of Public Health/Geriatrics, Uppsala University, Uppsala, Sweden
| | - Jonas Bergquist
- Analytical Chemistry, Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden
| | - Martin Ingelsson
- Department of Public Health/Geriatrics, Uppsala University, Uppsala, Sweden
| | - Peter Nilsson
- Affinity Proteomics, Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Kim Kultima
- Department of Medical Sciences, Cancer Pharmacology and Computational Medicine, Uppsala University, Uppsala, Sweden
- * E-mail:
| | - Ganna Shevchenko
- Analytical Chemistry, Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden
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Heemskerk AAM, Deelder AM, Mayboroda OA. CE-ESI-MS for bottom-up proteomics: Advances in separation, interfacing and applications. MASS SPECTROMETRY REVIEWS 2016; 35:259-271. [PMID: 24852088 DOI: 10.1002/mas.21432] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 03/27/2014] [Indexed: 06/03/2023]
Abstract
With the development of more sensitive hyphenation strategies for capillary electrophoresis-electrospray-mass spectrometry the technique has reemerged as technique with high separation power combined with high sensitivity in the analysis of peptides and protein digests. This review will discuss the newly developed hyphenation strategies for CE-ESI-MS and their application in bottom-up proteomics as well as the applications in the same time span, 2009 to present, using co-axial sheathliquid. Subsequently all separate aspects in the development of a CE-ESI-MS method for bottom-up proteomics shall be discussed, highlighting certain applications and discussing pros and cons of the various choices. The separation of peptides in a capillary electrophoresis system is discussed including the great potential for modeling of this migration of peptides due to the simple electrophoretic separation process. Furthermore, the technical aspects of method development are discussed, namely; background electrolyte choice, coating of the separation capillary and chosen loading method. Finally, conclusions and an outlook on future developments in the field of bottom-up proteomics by CE-ESI-MS will be provided.
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Affiliation(s)
- Anthonius A M Heemskerk
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2300, RC, Leiden, The Netherlands
| | - André M Deelder
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2300, RC, Leiden, The Netherlands
| | - Oleg A Mayboroda
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2300, RC, Leiden, The Netherlands
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