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Huhe H, Shapley SM, Duong D, Wu F, Ha SK, Choi SH, Kofler J, Mou Y, Guimaraes TR, Thathiah A, Schaeffer LKH, Carter GW, Seyfried NT, Silva AC, Sukoff Rizzo SJ. Marmosets as model systems for the study of Alzheimer's disease and related dementias: substantiation of physiological Tau 3R and 4R isoform expression and phosphorylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.26.590453. [PMID: 38746277 PMCID: PMC11092449 DOI: 10.1101/2024.04.26.590453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
INTRODUCTION Marmosets have been shown to spontaneously develop pathological hallmarks of Alzheimer's disease (AD) during advanced age, including amyloid-beta plaques, positioning them as a model system to overcome the rodent-to-human translational gap for AD. However, Tau expression in the marmoset brain has been understudied. METHODS To comprehensively investigate Tau isoform expression in marmosets, brain tissue from eight unrelated marmosets across various ages was evaluated and compared to human postmortem AD tissue. Microtubule-associated protein tau ( MAPT ) mRNA expression and splicing were confirmed by RT-PCR. Tau isoforms in the marmoset brain were examined by western blot, mass spectrometry, immunofluorescence, and immunohistochemical staining. Synaptic Tau expression was analyzed from crude synaptosome extractions. RESULTS 3R and 4R Tau isoforms are expressed in marmoset brains at both transcript and protein levels across ages. Results from western blot analysis were confirmed by mass spectrometry, which revealed that Tau peptides in marmoset corresponded to the 3R and 4R peptides in the human AD brain. 3R Tau was primarily enriched in neonate brains, and 4R enhanced in adult and aged brains. Tau was widely distributed in neurons with localization in the soma and synaptic regions. Phosphorylation residues were observed on Thr-181, Thr-217, and Thr-231, Ser202/Thr205, Ser396/Ser404. Paired helical filament (PHF)-like aggregates were also detected in aged marmosets. DISCUSSION Our results confirm the expression of both 3R and 4R Tau isoforms and important phosphorylation residues in the marmoset brain. These data emphasize the significance of marmosets with natural expression of AD-related hallmarks as important translational models for the study of AD.
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Arar S, Haque MA, Bhatt N, Zhao Y, Kayed R. Effect of Natural Osmolytes on Recombinant Tau Monomer: Propensity of Oligomerization and Aggregation. ACS Chem Neurosci 2024; 15:1366-1377. [PMID: 38503425 PMCID: PMC10995947 DOI: 10.1021/acschemneuro.3c00614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 03/21/2024] Open
Abstract
The pathological misfolding and aggregation of the microtubule associated protein tau (MAPT), a full length Tau2N4R with 441aa, is considered the principal disease relevant constituent in tauopathies including Alzheimer's disease (AD) with an imbalanced ratio in 3R/4R isoforms. The exact cellular fluid composition, properties, and changes that coincide with tau misfolding, seed formation, and propagation events remain obscure. The proteostasis network, along with the associated osmolytes, is responsible for maintaining the presence of tau in its native structure or dealing with misfolding. In this study, for the first time, the roles of natural brain osmolytes are being investigated for their potential effects on regulating the conformational stability of the tau monomer (tauM) and its propensity to aggregate or disaggregate. Herein, the effects of physiological osmolytes myo-inositol, taurine, trimethyl amine oxide (TMAO), betaine, sorbitol, glycerophosphocholine (GPC), and citrulline on tau's aggregation state were investigated. The overall results indicate the ability of sorbitol and GPC to maintain the monomeric form and prevent aggregation of tau, whereas myo-inositol, taurine, TMAO, betaine, and citrulline promote tau aggregation to different degrees, as revealed by protein morphology in atomic force microscopy images. Biochemical and biophysical methods also revealed that tau proteins adopt different conformations under the influence of these osmolytes. TauM in the presence of all osmolytes expressed no toxicity when tested by a lactate dehydrogenase assay. Investigating the conformational stability of tau in the presence of osmolytes may provide a better understanding of the complex nature of tau aggregation in AD and the protective and/or chaotropic nature of osmolytes.
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Affiliation(s)
- Sharif Arar
- Mitchell
Center for Neurodegenerative Diseases, University
of Texas Medical Branch, Galveston, Texas 77555, United States
- Departments
of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas 77555, United States
- Department
of Chemistry, School of Science, The University
of Jordan, Amman 11942, Jordan
| | - Md Anzarul Haque
- Mitchell
Center for Neurodegenerative Diseases, University
of Texas Medical Branch, Galveston, Texas 77555, United States
- Departments
of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Nemil Bhatt
- Mitchell
Center for Neurodegenerative Diseases, University
of Texas Medical Branch, Galveston, Texas 77555, United States
- Departments
of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Yingxin Zhao
- Department
of Internal Medicine, University of Texas
Medical Branch, Galveston, Texas 77555, United States
- Institute
for Translational Sciences, University of
Texas Medical Branch, Galveston, Texas 77555, United States
| | - Rakez Kayed
- Mitchell
Center for Neurodegenerative Diseases, University
of Texas Medical Branch, Galveston, Texas 77555, United States
- Departments
of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas 77555, United States
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Umeda H, Sawazaki T, Furuta M, Suzuki T, Kawashima SA, Mitsunuma H, Hori Y, Tomita T, Sohma Y, Kanai M. Quantitative Assays for Catalytic Photo-Oxygenation of Alzheimer Disease-Related Tau Proteins. ACS Chem Neurosci 2023; 14:2710-2716. [PMID: 37470225 DOI: 10.1021/acschemneuro.3c00264] [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: 07/21/2023] Open
Abstract
Catalytic photo-oxygenation of tau amyloid is a potential therapeutic approach to tauopathies, including Alzheimer disease (AD). However, tau is a complex target containing great molecular size and heterogeneous isoforms/proteoforms. Although catalytic photo-oxygenation has been confirmed when using catalyst 1 and recombinant tau pretreated with heparin, its effects on tau from human patients have not yet been clarified. In this study, focusing on the histidine residues being oxygenated, we have constructed two assay systems capable of quantitatively evaluating the catalytic activity when used on human patient tau: (1) fluorescence labeling at oxygenated histidine sites and (2) LC-MS/MS analysis of histidine-containing fragments. Using these assays, we identified 2 as a promising catalyst for oxygenation of human tau. In addition, our results suggest that aggregated tau induced by heparin is different from actual AD patient tau in developing effective photo-oxygenation catalysts.
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Affiliation(s)
- Hiroki Umeda
- Laboratory of Synthetic Organic Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Taka Sawazaki
- School of Pharmaceutical Sciences, Wakayama Medical University, Wakayama 640-8156, Japan
| | - Masahiro Furuta
- Laboratory of Synthetic Organic Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Takanobu Suzuki
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Shigehiro A Kawashima
- Laboratory of Synthetic Organic Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Harunobu Mitsunuma
- Laboratory of Synthetic Organic Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
- JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Yukiko Hori
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Taisuke Tomita
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Youhei Sohma
- School of Pharmaceutical Sciences, Wakayama Medical University, Wakayama 640-8156, Japan
| | - Motomu Kanai
- Laboratory of Synthetic Organic Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
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Willis JA, Cheburkanov V, Yakovlev VV. High-Dose Photodynamic Therapy Increases Tau Protein Signals in Drosophila. IEEE JOURNAL OF SELECTED TOPICS IN QUANTUM ELECTRONICS : A PUBLICATION OF THE IEEE LASERS AND ELECTRO-OPTICS SOCIETY 2023; 29:7201108. [PMID: 38327699 PMCID: PMC10846862 DOI: 10.1109/jstqe.2023.3270403] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Amyloid-Detection and imaging of amyloid-β plaques (Aβ) has been a focus in the field of neurodegeneration (ND) due to the high correlation with Parkinson's and Alzheimer's diseases. Here, a novel approach is being proposed and developed to induce and assess those diseases. Photodynamic therapy (PDT) is applied to the fruit fly Drosophila melanogaster as a model of systemic oxidative stress to induce rapid Aβ accumulation. Excised brains are evaluated by Brillouin-Raman spectroscopy and microscopy with UV surface emissions (MUSE) to interrogate physical property changes due to fixation and high-dose PDT. MUSE reveals reasonable autofluorescence in the spectral range of Aβ, particularly for females, with increased signal once stained. A presence of significant mechanical changes in fresh brains treated with PDT compared to healthy controls is revealed using Brillouin spectroscopy. Aβ plaque presence was confirmed with confocal analysis, with female PDT flies yielding nearly four-fold the mean intensity of controls, thus marking PDT as a potential neurodegenerative disease model. MUSE may serve as a viable early screening method for Aβ presence and quantification in a research setting. This reduces the time for sample preparation and drastically decreases the cost of Aβ quantification.
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Affiliation(s)
- Jace A. Willis
- Department of Biomedical Engineering at Texas A&M University, TX 77840, USA
| | | | - Vladislav V. Yakovlev
- Departments of Biomedical Engineering and Physics at Texas A&M University, TX 77840, USA
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Hawksworth JI, Denolf L, Timmerman E, Gevaert K. Increasing the Overall Proteome Coverage by Combining Protein Digestion by Tryp-N and Trypsin. Methods Mol Biol 2023; 2718:1-10. [PMID: 37665451 DOI: 10.1007/978-1-0716-3457-8_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: 09/05/2023]
Abstract
Mass spectrometry-based proteomics combining more than one protease in parallel facilitates the identification of more peptides and proteins than when a single protease is used. Trypsin cleaves proteins C-terminally to arginine and lysine, while its mirroring protease Tryp-N cleaves N-terminally to the same amino acids. Here, we combine trypsin and Tryp-N with the commercially available S-Trap columns, which purify protein samples and catalyze digestion. Comparison of trypsin or Tryp-N coupled with S-Trap columns demonstrates plasma and cell lysate proteins unique to one protease. We thus suggest the use of both proteases in a complementary manner to obtain deeper proteome coverage.
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Affiliation(s)
- Jade I Hawksworth
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Lode Denolf
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Evy Timmerman
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB Proteomics Core, Ghent, Belgium
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
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6
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Guo Q, Dammer EB, Zhou M, Kundinger SR, Gearing M, Lah JJ, Levey AI, Shulman JM, Seyfried NT. Targeted Quantification of Detergent-Insoluble RNA-Binding Proteins in Human Brain Reveals Stage and Disease Specific Co-aggregation in Alzheimer's Disease. Front Mol Neurosci 2021; 14:623659. [PMID: 33815056 PMCID: PMC8014091 DOI: 10.3389/fnmol.2021.623659] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/12/2021] [Indexed: 01/02/2023] Open
Abstract
Core spliceosome and related RNA-binding proteins aggregate in Alzheimer’s disease (AD) brain even in early asymptomatic stages (AsymAD) of disease. To assess the specificity of RNA-binding protein aggregation in AD, we developed a targeted mass spectrometry approach to quantify broad classes of RNA-binding proteins with other pathological proteins including tau and amyloid beta (Aβ) in detergent insoluble fractions from control, AsymAD, AD and Parkinson’s disease (PD) brain. Relative levels of specific insoluble RNA-binding proteins across different disease groups correlated with accumulation of Aβ and tau aggregates. RNA-binding proteins, including splicing factors with homology to the basic-acidic dipeptide repeats of U1-70K, preferentially aggregated in AsymAD and AD. In contrast, PD brain aggregates were relatively depleted of many RNA-binding proteins compared to AsymAD and AD groups. Correlation network analyses resolved 29 distinct modules of co-aggregating proteins including modules linked to spliceosome assembly, nuclear speckles and RNA splicing. Modules related to spliceosome assembly and nuclear speckles showed stage-specific enrichment of insoluble RBPs from AsymAD and AD brains, whereas the RNA splicing module was reduced specifically in PD. Collectively, this work identifies classes of RNA-binding proteins that distinctly co-aggregate in detergent-insoluble fractions across the specific neurodegenerative diseases we examined.
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Affiliation(s)
- Qi Guo
- Department of Biochemistry, School of Medicine, Emory University, Atlanta, GA, United States
| | - Eric B Dammer
- Department of Biochemistry, School of Medicine, Emory University, Atlanta, GA, United States.,Goizueta Alzheimer's Disease Research Center, School of Medicine, Emory University, Atlanta, GA, United States
| | - Maotian Zhou
- Department of Biochemistry, School of Medicine, Emory University, Atlanta, GA, United States
| | - Sean R Kundinger
- Department of Biochemistry, School of Medicine, Emory University, Atlanta, GA, United States
| | - Marla Gearing
- Goizueta Alzheimer's Disease Research Center, School of Medicine, Emory University, Atlanta, GA, United States.,Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA, United States
| | - James J Lah
- Goizueta Alzheimer's Disease Research Center, School of Medicine, Emory University, Atlanta, GA, United States.,Department of Neurology, School of Medicine, Emory University, Atlanta, GA, United States
| | - Allan I Levey
- Goizueta Alzheimer's Disease Research Center, School of Medicine, Emory University, Atlanta, GA, United States.,Department of Neurology, School of Medicine, Emory University, Atlanta, GA, United States
| | - Joshua M Shulman
- Departments of Neurology, Neuroscience and Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, United States.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, United States
| | - Nicholas T Seyfried
- Department of Biochemistry, School of Medicine, Emory University, Atlanta, GA, United States.,Goizueta Alzheimer's Disease Research Center, School of Medicine, Emory University, Atlanta, GA, United States.,Department of Neurology, School of Medicine, Emory University, Atlanta, GA, United States
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7
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Jain AP, Sathe G. Proteomics Landscape of Alzheimer's Disease. Proteomes 2021; 9:proteomes9010013. [PMID: 33801961 PMCID: PMC8005944 DOI: 10.3390/proteomes9010013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/02/2021] [Accepted: 03/08/2021] [Indexed: 01/22/2023] Open
Abstract
Alzheimer’s disease (AD) is the most prevalent form of dementia, and the numbers of AD patients are expected to increase as human life expectancy improves. Deposition of β-amyloid protein (Aβ) in the extracellular matrix and intracellular neurofibrillary tangles are molecular hallmarks of the disease. Since the precise pathophysiology of AD has not been elucidated yet, effective treatment is not available. Thus, understanding the disease pathology, as well as identification and development of valid biomarkers, is imperative for early diagnosis as well as for monitoring disease progression and therapeutic responses. Keeping this goal in mind several studies using quantitative proteomics platform have been carried out on both clinical specimens including the brain, cerebrospinal fluid (CSF), plasma and on animal models of AD. In this review, we summarize the mass spectrometry (MS)-based proteomics studies on AD and discuss the discovery as well as validation stages in brief to identify candidate biomarkers.
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Affiliation(s)
- Ankit P. Jain
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India;
| | - Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India;
- Manipal Academy of Higher Education (MAHE), Manipal 576104, India
- Correspondence:
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8
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Higginbotham L, Ping L, Dammer EB, Duong DM, Zhou M, Gearing M, Hurst C, Glass JD, Factor SA, Johnson ECB, Hajjar I, Lah JJ, Levey AI, Seyfried NT. Integrated proteomics reveals brain-based cerebrospinal fluid biomarkers in asymptomatic and symptomatic Alzheimer's disease. SCIENCE ADVANCES 2020; 6:eaaz9360. [PMID: 33087358 PMCID: PMC7577712 DOI: 10.1126/sciadv.aaz9360] [Citation(s) in RCA: 176] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 09/03/2020] [Indexed: 05/02/2023]
Abstract
Alzheimer's disease (AD) lacks protein biomarkers reflective of its diverse underlying pathophysiology, hindering diagnostic and therapeutic advancements. Here, we used integrative proteomics to identify cerebrospinal fluid (CSF) biomarkers representing a wide spectrum of AD pathophysiology. Multiplex mass spectrometry identified ~3500 and ~12,000 proteins in AD CSF and brain, respectively. Network analysis of the brain proteome resolved 44 biologically diverse modules, 15 of which overlapped with the CSF proteome. CSF AD markers in these overlapping modules were collapsed into five protein panels representing distinct pathophysiological processes. Synaptic and metabolic panels were decreased in AD brain but increased in CSF, while glial-enriched myelination and immunity panels were increased in brain and CSF. The consistency and disease specificity of panel changes were confirmed in >500 additional CSF samples. These panels also identified biological subpopulations within asymptomatic AD. Overall, these results are a promising step toward a network-based biomarker tool for AD clinical applications.
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Affiliation(s)
- Lenora Higginbotham
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
- Goizueta Alzheimer's Disease Research Center, Emory University, Atlanta, GA, USA
| | - Lingyan Ping
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
- Goizueta Alzheimer's Disease Research Center, Emory University, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Eric B Dammer
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
- Goizueta Alzheimer's Disease Research Center, Emory University, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Duc M Duong
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
- Goizueta Alzheimer's Disease Research Center, Emory University, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Maotian Zhou
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
- Goizueta Alzheimer's Disease Research Center, Emory University, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Marla Gearing
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Goizueta Alzheimer's Disease Research Center, Emory University, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Cheyenne Hurst
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Jonathan D Glass
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
- Goizueta Alzheimer's Disease Research Center, Emory University, Atlanta, GA, USA
| | - Stewart A Factor
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Erik C B Johnson
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
- Goizueta Alzheimer's Disease Research Center, Emory University, Atlanta, GA, USA
| | - Ihab Hajjar
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Goizueta Alzheimer's Disease Research Center, Emory University, Atlanta, GA, USA
| | - James J Lah
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
- Goizueta Alzheimer's Disease Research Center, Emory University, Atlanta, GA, USA
| | - Allan I Levey
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA.
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
- Goizueta Alzheimer's Disease Research Center, Emory University, Atlanta, GA, USA
| | - Nicholas T Seyfried
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA.
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
- Goizueta Alzheimer's Disease Research Center, Emory University, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
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Zhou M, Haque RU, Dammer EB, Duong DM, Ping L, Johnson ECB, Lah JJ, Levey AI, Seyfried NT. Targeted mass spectrometry to quantify brain-derived cerebrospinal fluid biomarkers in Alzheimer's disease. Clin Proteomics 2020; 17:19. [PMID: 32514259 PMCID: PMC7257173 DOI: 10.1186/s12014-020-09285-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 05/19/2020] [Indexed: 12/14/2022] Open
Abstract
INTRODUCTION Alzheimer's disease (AD) is the most common cause of dementia, characterized by progressive cognitive decline. Protein biomarkers of AD brain pathology, including β-amyloid and Tau, are reflected in cerebrospinal fluid (CSF), yet the identification of additional biomarkers linked to other brain pathophysiologies remains elusive. We recently reported a multiplex tandem-mass tag (TMT) CSF proteomic analysis of nearly 3000 proteins, following depletion of highly abundant proteins and off-line fractionation, across control and AD cases. Of these, over 500 proteins were significantly increased or decreased in AD, including markers reflecting diverse biological functions in brain. Here, we use a targeted mass spectrometry (MS) approach, termed parallel reaction monitoring (PRM), to quantify select CSF biomarkers without pre-depletion or fractionation to assess the reproducibility of our findings and the specificity of changes for AD versus other causes of cognitive impairment. METHOD We nominated 41 proteins (94 peptides) from the TMT CSF discovery dataset, representing a variety of brain cell-types and biological functions, for label-free PRM analysis in a replication cohort of 88 individuals that included 20 normal controls, 37 clinically diagnosed AD cases and 31 cases with non-AD cognitive impairment. To control for technical variables, isotopically labeled synthetic heavy peptide standards were added into each of the 88 CSF tryptic digests. Furthermore, a peptide pool, representing an equivalent amount of peptide from all samples, was analyzed (n = 10) across each batch. Together, this approach enabled us to assess both the intra- and inter-sample differences in peptide signal response and retention time. RESULTS Despite differences in sample preparation, quantitative MS approaches and patient samples, 25 proteins, including Tau, had a consistent and significant change in AD in both the discovery and replication cohorts. Validated CSF markers with low coefficient of variation included the protein products for neuronal/synaptic (GDA, GAP43, SYN1, BASP1, YWHAB, YWHAZ, UCHL1, STMN1 and MAP1B), glial/inflammation (SMOC1, ITGAM, CHI3L1, SPP1, and CHIT1) and metabolic (PKM, ALDOA and FABP3) related genes. Logistical regression analyses revealed several proteins with high sensitivity and specificity for classifying AD cases from controls and other non-AD dementias. SMOC1, YWHAZ, ALDOA and MAP1B emerged as biomarker candidates that could best discriminate between individuals with AD and non-AD cognitive impairment as well as Tau/β-amyloid ratio. Notably, SMOC1 levels in postmortem brain are highly correlated with AD pathology even in the preclinical stage of disease, indicating that CSF SMOC1 levels reflect underlying brain pathology specific for AD. CONCLUSION Collectively these findings highlight the utility of targeted MS approaches to quantify biomarkers associated with AD that could be used for monitoring disease progression, stratifying patients for clinical trials and measuring therapeutic response.
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Affiliation(s)
- Maotian Zhou
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322 USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Rafi U. Haque
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Eric B. Dammer
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322 USA
| | - Duc M. Duong
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322 USA
| | - Lingyan Ping
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322 USA
| | - Erik C. B. Johnson
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - James J. Lah
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Allan I. Levey
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Nicholas T. Seyfried
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322 USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322 USA
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10
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Using the tools of proteomics to understand the pathogenesis of idiopathic inflammatory myopathies. Curr Opin Rheumatol 2019; 31:617-622. [PMID: 31385878 DOI: 10.1097/bor.0000000000000643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW One of the most important advances in medical research over the past 20 years has been the emergence of technologies to assess complex biological processes on a global scale. Although a great deal of attention has been given to genome-scale genetics and genomics technologies, the utility of studying the proteome in a comprehensive way is sometimes under-appreciated. In this review, we discuss recent advances in proteomics as applied to dermatomyositis/polymyositis as well as findings from other inflammatory diseases that may enlighten our understanding of dermatomyositis/polymyositis. RECENT FINDINGS Proteomic approaches have been used to investigate basic mechanisms contributing to lung and skin disease in dermatomyositis/polymyositis as well as to the muscle disease itself. In addition, proteomic approaches have been used to identify autoantibodies targeting the endothelium in juvenile dermatomyositis. Studies from other inflammatory diseases have shown the promise of using proteomics to characterize the composition of immune complexes and the protein cargoes of exosomes. SUMMARY There are many relevant scientific and clinical questions in dermatomyositis/polymyositis that can be addressed using proteomics approaches. Careful attention to both methodology and analytic approaches are required to obtain useful and reproducible data.
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