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Wojtas AM, Dammer EB, Guo Q, Ping L, Shantaraman A, Duong DM, Yin L, Fox EJ, Seifar F, Lee EB, Johnson ECB, Lah JJ, Levey AI, Levites Y, Rangaraju S, Golde TE, Seyfried NT. Proteomic changes in the human cerebrovasculature in Alzheimer's disease and related tauopathies linked to peripheral biomarkers in plasma and cerebrospinal fluid. Alzheimers Dement 2024. [PMID: 38713744 DOI: 10.1002/alz.13821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 02/21/2024] [Accepted: 03/02/2024] [Indexed: 05/09/2024]
Abstract
INTRODUCTION Cerebrovascular dysfunction is a pathological hallmark of Alzheimer's disease (AD). Nevertheless, detecting cerebrovascular changes within bulk tissues has limited our ability to characterize proteomic alterations from less abundant cell types. METHODS We conducted quantitative proteomics on bulk brain tissues and isolated cerebrovasculature from the same individuals, encompassing control (N = 28), progressive supranuclear palsy (PSP) (N = 18), and AD (N = 21) cases. RESULTS Protein co-expression network analysis identified unique cerebrovascular modules significantly correlated with amyloid plaques, cerebrovascular amyloid angiopathy (CAA), and/or tau pathology. The protein products within AD genetic risk loci were concentrated within cerebrovascular modules. The overlap between differentially abundant proteins in AD cerebrospinal fluid (CSF) and plasma with cerebrovascular network highlighted a significant increase of matrisome proteins, SMOC1 and SMOC2, in CSF, plasma, and brain. DISCUSSION These findings enhance our understanding of cerebrovascular deficits in AD, shedding light on potential biomarkers associated with CAA and vascular dysfunction in neurodegenerative diseases.
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Affiliation(s)
- Aleksandra M Wojtas
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Eric B Dammer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Qi Guo
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Lingyan Ping
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Ananth Shantaraman
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Duc M Duong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Luming Yin
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Edward J Fox
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Fatemeh Seifar
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Edward B Lee
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Pennsylvania, USA
| | - Erik C B Johnson
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - James J Lah
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Allan I Levey
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Yona Levites
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Srikant Rangaraju
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Todd E Golde
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, Georgia, USA
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Saloner R, Staffaroni A, Dammer E, Johnson ECB, Paolillo E, Wise A, Heuer H, Forsberg L, Lago AL, Webb J, Vogel J, Santillo A, Hansson O, Kramer J, Miller B, Li J, Loureiro J, Sivasankaran R, Worringer K, Seyfried N, Yokoyama J, Seeley W, Spina S, Grinberg L, VandeVrede L, Ljubenkov P, Bayram E, Bozoki A, Brushaber D, Considine C, Day G, Dickerson B, Domoto-Reilly K, Faber K, Galasko D, Geschwind D, Ghoshal N, Graff-Radford N, Hales C, Honig L, Hsiung GY, Huey E, Kornak J, Kremers W, Lapid M, Lee S, Litvan I, McMillan C, Mendez M, Miyagawa T, Pantelyat A, Pascual B, Paulson H, Petrucelli L, Pressman P, Ramos E, Rascovsky K, Roberson E, Savica R, Snyder A, Sullivan AC, Tartaglia C, Vandebergh M, Boeve B, Rosen H, Rojas J, Boxer A, Casaletto K. Large-scale network analysis of the cerebrospinal fluid proteome identifies molecular signatures of frontotemporal lobar degeneration. Res Sq 2024:rs.3.rs-4103685. [PMID: 38585969 PMCID: PMC10996789 DOI: 10.21203/rs.3.rs-4103685/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The pathophysiological mechanisms driving disease progression of frontotemporal lobar degeneration (FTLD) and corresponding biomarkers are not fully understood. We leveraged aptamer-based proteomics (> 4,000 proteins) to identify dysregulated communities of co-expressed cerebrospinal fluid proteins in 116 adults carrying autosomal dominant FTLD mutations (C9orf72, GRN, MAPT) compared to 39 noncarrier controls. Network analysis identified 31 protein co-expression modules. Proteomic signatures of genetic FTLD clinical severity included increased abundance of RNA splicing (particularly in C9orf72 and GRN) and extracellular matrix (particularly in MAPT) modules, as well as decreased abundance of synaptic/neuronal and autophagy modules. The generalizability of genetic FTLD proteomic signatures was tested and confirmed in independent cohorts of 1) sporadic progressive supranuclear palsy-Richardson syndrome and 2) frontotemporal dementia spectrum syndromes. Network-based proteomics hold promise for identifying replicable molecular pathways in adults living with FTLD. 'Hub' proteins driving co-expression of affected modules warrant further attention as candidate biomarkers and therapeutic targets.
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Affiliation(s)
| | | | | | | | | | - Amy Wise
- University of California, San Francisco
| | | | | | | | | | | | | | | | | | | | - Jingyao Li
- Novartis Institutes for Biomedical Research, Inc
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Suzee Lee
- University of California, San Francisco
| | | | - Corey McMillan
- Department of Neurology, University of Pennsylvania, Philadelphia, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Adam Boxer
- Memory and Aging Center, Department of Neurology, University of California, San Francisco
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Guo Q, Ping L, Dammer EB, Yin L, Xu K, Shantaraman A, Fox EJ, Golde TE, Johnson ECB, Roberts BR, Lah JJ, Levey AI, Seyfried NT. Heparin-enriched plasma proteome is significantly altered in Alzheimer's Disease. Res Sq 2024:rs.3.rs-3933136. [PMID: 38464223 PMCID: PMC10925398 DOI: 10.21203/rs.3.rs-3933136/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Introduction Heparin binding proteins (HBPs) with roles in extracellular matrix assembly are strongly correlated to β-amyloid (Aβ) and tau pathology in Alzheimer's disease (AD) brain and cerebrospinal fluid (CSF). However, it remains challenging to detect these proteins in plasma using standard mass spectrometry-based proteomic approaches. Methods We employed heparin affinity chromatography, followed by off-line fractionation and tandem mass tag mass spectrometry (TMT-MS), to capture and enrich HBPs in plasma obtained from AD (n=62) and control (n=47) samples. These profiles were then correlated to a consensus AD brain proteome, as well as with Aβ, tau and phosphorylated tau (pTau) CSF biomarkers from the same individuals. We then leveraged published human postmortem brain proteome datasets to assess the overlap with the heparin-enriched plasma proteome. Results Heparin-enrichment from plasma was highly reproducible, enriched well-known HBPs like APOE and thrombin, and depleted high-abundance proteins such as albumin. A total of 2865 proteins, spanning 10 orders of magnitude were detectable. Utilizing a consensus AD brain protein co-expression network, we observed that specific plasma HBPs exhibited consistent direction of change in both brain and plasma, whereas others displayed divergent changes highlighting the complex interplay between the two compartments. Elevated HBPs in AD plasma, when compared to controls, included members of the matrisome module in brain that accumulate within Aβ deposits, such as SMOC1, SMOC2, SPON1, MDK, OLFML3, FRZB, GPNMB, and APOE. Additionally, heparin enriched plasma proteins demonstrated significant correlations with conventional AD CSF biomarkers, including Aβ, total tau, pTau, and plasma pTau from the same individuals. Conclusion These findings support the utility of a heparin-affinity approach for enriching amyloid-associated proteins, as well as a wide spectrum of plasma biomarkers that reflect pathological changes in the AD brain.
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Affiliation(s)
- Qi Guo
- Emory University School of Medicine
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Shen Y, Ali M, Timsina J, Wang C, Do A, Western D, Liu M, Gorijala P, Budde J, Liu H, Gordon B, McDade E, Morris JC, Llibre-Guerra JJ, Bateman RJ, Joseph-Mathurin N, Perrin RJ, Maschi D, Wyss-Coray T, Pastor P, Goate A, Renton AE, Surace EI, Johnson ECB, Levey AI, Alvarez I, Levin J, Ringman JM, Allegri RF, Seyfried N, Day GS, Wu Q, Fernández MV, Ibanez L, Sung YJ, Cruchaga C. Systematic proteomics in Autosomal dominant Alzheimer's disease reveals decades-early changes of CSF proteins in neuronal death, and immune pathways. medRxiv 2024:2024.01.12.24301242. [PMID: 38260583 PMCID: PMC10802763 DOI: 10.1101/2024.01.12.24301242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Background To date, there is no high throughput proteomic study in the context of Autosomal Dominant Alzheimer's disease (ADAD). Here, we aimed to characterize early CSF proteome changes in ADAD and leverage them as potential biomarkers for disease monitoring and therapeutic strategies. Methods We utilized Somascan® 7K assay to quantify protein levels in the CSF from 291 mutation carriers (MCs) and 185 non-carriers (NCs). We employed a multi-layer regression model to identify proteins with different pseudo-trajectories between MCs and NCs. We replicated the results using publicly available ADAD datasets as well as proteomic data from sporadic Alzheimer's disease (sAD). To biologically contextualize the results, we performed network and pathway enrichment analyses. Machine learning was applied to create and validate predictive models. Findings We identified 125 proteins with significantly different pseudo-trajectories between MCs and NCs. Twelve proteins showed changes even before the traditional AD biomarkers (Aβ42, tau, ptau). These 125 proteins belong to three different modules that are associated with age at onset: 1) early stage module associated with stress response, glutamate metabolism, and mitochondria damage; 2) the middle stage module, enriched in neuronal death and apoptosis; and 3) the presymptomatic stage module was characterized by changes in microglia, and cell-to-cell communication processes, indicating an attempt of rebuilding and establishing new connections to maintain functionality. Machine learning identified a subset of nine proteins that can differentiate MCs from NCs better than traditional AD biomarkers (AUC>0.89). Interpretation Our findings comprehensively described early proteomic changes associated with ADAD and captured specific biological processes that happen in the early phases of the disease, fifteen to five years before clinical onset. We identified a small subset of proteins with the potentials to become therapy-monitoring biomarkers of ADAD MCs. Funding Proteomic data generation was supported by NIH: RF1AG044546.
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Wojtas AM, Dammer EB, Guo Q, Ping L, Shantaraman A, Duong DM, Yin L, Fox EJ, Seifar F, Lee EB, Johnson ECB, Lah JJ, Levey AI, Levites Y, Rangaraju S, Golde TE, Seyfried NT. Proteomic Changes in the Human Cerebrovasculature in Alzheimer's Disease and Related Tauopathies Linked to Peripheral Biomarkers in Plasma and Cerebrospinal Fluid. medRxiv 2024:2024.01.10.24301099. [PMID: 38260316 PMCID: PMC10802758 DOI: 10.1101/2024.01.10.24301099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Dysfunction of the neurovascular unit stands as a significant pathological hallmark of Alzheimer's disease (AD) and age-related neurodegenerative diseases. Nevertheless, detecting vascular changes in the brain within bulk tissues has proven challenging, limiting our ability to characterize proteomic alterations from less abundant cell types. To address this challenge, we conducted quantitative proteomic analyses on both bulk brain tissues and cerebrovascular-enriched fractions from the same individuals, encompassing cognitively unimpaired control, progressive supranuclear palsy (PSP), and AD cases. Protein co-expression network analysis identified modules unique to the cerebrovascular fractions, specifically enriched with pericytes, endothelial cells, and smooth muscle cells. Many of these modules also exhibited significant correlations with amyloid plaques, cerebral amyloid angiopathy (CAA), and/or tau pathology in the brain. Notably, the protein products within AD genetic risk loci were found concentrated within modules unique to the vascular fractions, consistent with a role of cerebrovascular deficits in the etiology of AD. To prioritize peripheral AD biomarkers associated with vascular dysfunction, we assessed the overlap between differentially abundant proteins in AD cerebrospinal fluid (CSF) and plasma with a vascular-enriched network modules in the brain. This analysis highlighted matrisome proteins, SMOC1 and SMOC2, as being increased in CSF, plasma, and brain. Immunohistochemical analysis revealed SMOC1 deposition in both parenchymal plaques and CAA in the AD brain, whereas SMOC2 was predominantly localized to CAA. Collectively, these findings significantly enhance our understanding of the involvement of cerebrovascular abnormalities in AD, shedding light on potential biomarkers and molecular pathways associated with CAA and vascular dysfunction in neurodegenerative diseases.
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Affiliation(s)
- Aleksandra M. Wojtas
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Eric B. Dammer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Qi Guo
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Lingyan Ping
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Ananth Shantaraman
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Duc M. Duong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Luming Yin
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Edward J. Fox
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Fatemeh Seifar
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Edward B. Lee
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, PA, 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
| | - 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
| | - Allan I. Levey
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Yona Levites
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Srikant Rangaraju
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Todd E. Golde
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Nicholas T. Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
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Gudmundsdottir V, Frick E, Emilsson V, Jonmundsson T, Steindorsdottir A, Johnson ECB, Puerta R, Dammer E, Shantaraman A, Cano A, Boada M, Valero S, Garcia-Gonzalez P, Gudmundsson E, Gudjonsson A, Pitts R, Qiu X, Finkel N, Loureiro J, Orth A, Seyfried N, Levey A, Ruiz A, Aspelund T, Jennings L, Launer L, Gudnason V. Serum proteomics reveals APOE dependent and independent protein signatures in Alzheimer's disease. Res Sq 2024:rs.3.rs-3706206. [PMID: 38260284 PMCID: PMC10802738 DOI: 10.21203/rs.3.rs-3706206/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The current demand for early intervention, prevention, and treatment of late onset Alzheimer's disease (LOAD) warrants deeper understanding of the underlying molecular processes which could contribute to biomarker and drug target discovery. Utilizing high-throughput proteomic measurements in serum from a prospective population-based cohort of older adults (n = 5,294), we identified 303 unique proteins associated with incident LOAD (median follow-up 12.8 years). Over 40% of these proteins were associated with LOAD independently of APOE-ε4 carrier status. These proteins were implicated in neuronal processes and overlapped with protein signatures of LOAD in brain and cerebrospinal fluid. We found 17 proteins which LOAD-association was strongly dependent on APOE-ε4 carrier status. Most of them showed consistent associations with LOAD in cerebrospinal fluid and a third had brain-specific gene expression. Remarkably, four proteins in this group (TBCA, ARL2, S100A13 and IRF6) were downregulated by APOE-ε4 yet upregulated as a consequence of LOAD as determined in a bi-directional Mendelian randomization analysis, reflecting a potential response to the disease onset. Accordingly, the direct association of these proteins to LOAD was reversed upon APOE-ε4 genotype adjustment, a finding which we replicate in an external cohort (n = 719). Our findings provide an insight into the dysregulated pathways that may lead to the development and early detection of LOAD, including those both independent and dependent on APOE-ε4. Importantly, many of the LOAD-associated proteins we find in the circulation have been found to be expressed - and have a direct link with AD - in brain tissue. Thus, the proteins identified here, and their upstream modulating pathways, provide a new source of circulating biomarker and therapeutic target candidates for LOAD.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Merce Boada
- Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades-UIC, Barcelona
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Lenore Launer
- National Institute on Aging, National Institutes of Health
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7
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Frick EA, Emilsson V, Jonmundsson T, Steindorsdottir AE, Johnson ECB, Puerta R, Dammer EB, Shantaraman A, Cano A, Boada M, Valero S, García-González P, Gudmundsson EF, Gudjonsson A, Loureiro JJ, Orth AP, Seyfried NT, Levey AI, Ruiz A, Aspelund T, Jennings LL, Launer LJ, Gudmundsdottir V, Gudnason V. Serum proteomics reveals APOE dependent and independent protein signatures in Alzheimer's disease. medRxiv 2023:2023.11.08.23298251. [PMID: 37986771 PMCID: PMC10659486 DOI: 10.1101/2023.11.08.23298251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The current demand for early intervention, prevention, and treatment of late onset Alzheimer's disease (LOAD) warrants deeper understanding of the underlying molecular processes which could contribute to biomarker and drug target discovery. Utilizing high-throughput proteomic measurements in serum from a prospective population-based cohort of older adults (n=5,294), we identified 303 unique proteins associated with incident LOAD (median follow-up 12.8 years). Over 40% of these proteins were associated with LOAD independently of APOE-ε4 carrier status. These proteins were implicated in neuronal processes and overlapped with protein signatures of LOAD in brain and cerebrospinal fluid. We found 17 proteins which LOAD-association was strongly dependent on APOE-ε4 carrier status. Most of them showed consistent associations with LOAD in cerebrospinal fluid and a third had brain-specific gene expression. Remarkably, four proteins in this group (TBCA, ARL2, S100A13 and IRF6) were downregulated by APOE-ε4 yet upregulated as a consequence of LOAD as determined in a bi-directional Mendelian randomization analysis, reflecting a potential response to the disease onset. Accordingly, the direct association of these proteins to LOAD was reversed upon APOE-ε4 genotype adjustment, a finding which we replicate in an external cohort (n=719). Our findings provide an insight into the dysregulated pathways that may lead to the development and early detection of LOAD, including those both independent and dependent on APOE-ε4. Importantly, many of the LOAD-associated proteins we find in the circulation have been found to be expressed - and have a direct link with AD - in brain tissue. Thus, the proteins identified here, and their upstream modulating pathways, provide a new source of circulating biomarker and therapeutic target candidates for LOAD.
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Affiliation(s)
| | - Valur Emilsson
- Icelandic Heart Association, Kopavogur, 200, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
| | | | | | - Erik C B Johnson
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, 30329, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, 30329, GA, USA
| | - Raquel Puerta
- Research Center and Memory Clinic. Ace Alzheimer Center Barcelona - Universitat Internacional de Catalunya, Barcelona, 08028, Spain, Barcelona
| | - Eric B Dammer
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, 30329, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, 30329, GA, USA
| | - Anantharaman Shantaraman
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, 30329, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, 30329, GA, USA
| | - Amanda Cano
- Research Center and Memory Clinic. Ace Alzheimer Center Barcelona - Universitat Internacional de Catalunya, Barcelona, 08028, Spain, Barcelona
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, 28029, Spain
| | - Mercè Boada
- Research Center and Memory Clinic. Ace Alzheimer Center Barcelona - Universitat Internacional de Catalunya, Barcelona, 08028, Spain, Barcelona
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, 28029, Spain
| | - Sergi Valero
- Research Center and Memory Clinic. Ace Alzheimer Center Barcelona - Universitat Internacional de Catalunya, Barcelona, 08028, Spain, Barcelona
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, 28029, Spain
| | - Pablo García-González
- Research Center and Memory Clinic. Ace Alzheimer Center Barcelona - Universitat Internacional de Catalunya, Barcelona, 08028, Spain, Barcelona
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, 28029, Spain
| | | | | | | | | | - Nicholas T Seyfried
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, 30329, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, 30329, GA, USA
| | - Allan I Levey
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, 30329, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, 30329, GA, USA
| | - Agustin Ruiz
- Research Center and Memory Clinic. Ace Alzheimer Center Barcelona - Universitat Internacional de Catalunya, Barcelona, 08028, Spain, Barcelona
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, 28029, Spain
| | - Thor Aspelund
- Icelandic Heart Association, Kopavogur, 200, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
| | | | - Lenore J Launer
- Laboratory of Epidemiology and Population Sciences, Intramural Research Program, National Institute on Aging, Bethesda, 20892, MD, USA
| | - Valborg Gudmundsdottir
- Icelandic Heart Association, Kopavogur, 200, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, 200, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
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Hurst CD, Dunn AR, Dammer EB, Duong DM, Shapley SM, Seyfried NT, Kaczorowski CC, Johnson ECB. Genetic background influences the 5XFAD Alzheimer's disease mouse model brain proteome. Front Aging Neurosci 2023; 15:1239116. [PMID: 37901791 PMCID: PMC10602695 DOI: 10.3389/fnagi.2023.1239116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/12/2023] [Indexed: 10/31/2023] Open
Abstract
There is an urgent need to improve the translational validity of Alzheimer's disease (AD) mouse models. Introducing genetic background diversity in AD mouse models has been proposed as a way to increase validity and enable the discovery of previously uncharacterized genetic contributions to AD susceptibility or resilience. However, the extent to which genetic background influences the mouse brain proteome and its perturbation in AD mouse models is unknown. In this study, we crossed the 5XFAD AD mouse model on a C57BL/6J (B6) inbred background with the DBA/2J (D2) inbred background and analyzed the effects of genetic background variation on the brain proteome in F1 progeny. Both genetic background and 5XFAD transgene insertion strongly affected protein variance in the hippocampus and cortex (n = 3,368 proteins). Protein co-expression network analysis identified 16 modules of highly co-expressed proteins common across the hippocampus and cortex in 5XFAD and non-transgenic mice. Among the modules strongly influenced by genetic background were those related to small molecule metabolism and ion transport. Modules strongly influenced by the 5XFAD transgene were related to lysosome/stress responses and neuronal synapse/signaling. The modules with the strongest relationship to human disease-neuronal synapse/signaling and lysosome/stress response-were not significantly influenced by genetic background. However, other modules in 5XFAD that were related to human disease, such as GABA synaptic signaling and mitochondrial membrane modules, were influenced by genetic background. Most disease-related modules were more strongly correlated with AD genotype in the hippocampus compared with the cortex. Our findings suggest that the genetic diversity introduced by crossing B6 and D2 inbred backgrounds influences proteomic changes related to disease in the 5XFAD model, and that proteomic analysis of other genetic backgrounds in transgenic and knock-in AD mouse models is warranted to capture the full range of molecular heterogeneity in genetically diverse models of AD.
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Affiliation(s)
- Cheyenne D. Hurst
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, United States
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, United States
| | - Amy R. Dunn
- Department of Mammalian Genetics, The Jackson Laboratory, Bar Harbor, ME, United States
| | - Eric B. Dammer
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, United States
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, United States
| | - Duc M. Duong
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, United States
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, United States
| | - Sarah M. Shapley
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, United States
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, United States
| | - Nicholas T. Seyfried
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, United States
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, United States
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, United States
| | - Catherine C. Kaczorowski
- Department of Mammalian Genetics, The Jackson Laboratory, Bar Harbor, ME, United States
- Department of Neurology, The University of Michigan, Ann Arbor, MI, United States
| | - Erik C. B. Johnson
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, United States
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, United States
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9
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Higginbotham L, Carter EK, Dammer EB, Haque RU, Johnson ECB, Duong DM, Yin L, De Jager PL, Bennett DA, Felsky D, Tio ES, Lah JJ, Levey AI, Seyfried NT. Unbiased classification of the elderly human brain proteome resolves distinct clinical and pathophysiological subtypes of cognitive impairment. Neurobiol Dis 2023; 186:106286. [PMID: 37689213 PMCID: PMC10750427 DOI: 10.1016/j.nbd.2023.106286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/24/2023] [Accepted: 09/06/2023] [Indexed: 09/11/2023] Open
Abstract
Cognitive impairment in the elderly features complex molecular pathophysiology extending beyond the hallmark pathologies of traditional disease classification. Molecular subtyping using large-scale -omic strategies can help resolve this biological heterogeneity. Using quantitative mass spectrometry, we measured ∼8000 proteins across >600 dorsolateral prefrontal cortex tissues with clinical diagnoses of no cognitive impairment (NCI), mild cognitive impairment (MCI), and Alzheimer's disease (AD) dementia. Unbiased classification of MCI and AD cases based on individual proteomic profiles resolved three classes with expression differences across numerous cell types and biological ontologies. Two classes displayed molecular signatures atypical of AD neurodegeneration, such as elevated synaptic and decreased inflammatory markers. In one class, these atypical proteomic features were associated with clinical and pathological hallmarks of cognitive resilience. We were able to replicate these classes and their clinicopathological phenotypes across two additional tissue cohorts. These results promise to better define the molecular heterogeneity of cognitive impairment and meaningfully impact its diagnostic and therapeutic precision.
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Affiliation(s)
- Lenora Higginbotham
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA.
| | - E Kathleen Carter
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA; Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Eric B Dammer
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Rafi U Haque
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Erik C B Johnson
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Duc M Duong
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Luming Yin
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Philip L De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Taub Institute, Columbia University Irving Medical Center, New York Presbyterian Hospital, New York, NY, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Daniel Felsky
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada; Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Earvin S Tio
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada; Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - James J Lah
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Allan I Levey
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Nicholas T Seyfried
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA; Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA.
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10
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Johnson ECB, Bian S, Haque RU, Carter EK, Watson CM, Gordon BA, Ping L, Duong DM, Epstein MP, McDade E, Barthélemy NR, Karch CM, Xiong C, Cruchaga C, Perrin RJ, Wingo AP, Wingo TS, Chhatwal JP, Day GS, Noble JM, Berman SB, Martins R, Graff-Radford NR, Schofield PR, Ikeuchi T, Mori H, Levin J, Farlow M, Lah JJ, Haass C, Jucker M, Morris JC, Benzinger TLS, Roberts BR, Bateman RJ, Fagan AM, Seyfried NT, Levey AI. Cerebrospinal fluid proteomics define the natural history of autosomal dominant Alzheimer's disease. Nat Med 2023; 29:1979-1988. [PMID: 37550416 PMCID: PMC10427428 DOI: 10.1038/s41591-023-02476-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 06/27/2023] [Indexed: 08/09/2023]
Abstract
Alzheimer's disease (AD) pathology develops many years before the onset of cognitive symptoms. Two pathological processes-aggregation of the amyloid-β (Aβ) peptide into plaques and the microtubule protein tau into neurofibrillary tangles (NFTs)-are hallmarks of the disease. However, other pathological brain processes are thought to be key disease mediators of Aβ plaque and NFT pathology. How these additional pathologies evolve over the course of the disease is currently unknown. Here we show that proteomic measurements in autosomal dominant AD cerebrospinal fluid (CSF) linked to brain protein coexpression can be used to characterize the evolution of AD pathology over a timescale spanning six decades. SMOC1 and SPON1 proteins associated with Aβ plaques were elevated in AD CSF nearly 30 years before the onset of symptoms, followed by changes in synaptic proteins, metabolic proteins, axonal proteins, inflammatory proteins and finally decreases in neurosecretory proteins. The proteome discriminated mutation carriers from noncarriers before symptom onset as well or better than Aβ and tau measures. Our results highlight the multifaceted landscape of AD pathophysiology and its temporal evolution. Such knowledge will be critical for developing precision therapeutic interventions and biomarkers for AD beyond those associated with Aβ and tau.
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Affiliation(s)
- Erik C B Johnson
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA.
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA.
| | - Shijia Bian
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Rafi U Haque
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
| | - E Kathleen Carter
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Caroline M Watson
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Brian A Gordon
- Mallinckrodt Institute of Radiology, Washington University in St Louis, St Louis, MO, USA
| | - Lingyan Ping
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Duc M Duong
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Michael P Epstein
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Eric McDade
- Department of Neurology, Washington University in St Louis, St Louis, MO, USA
| | | | - Celeste M Karch
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA
| | - Chengjie Xiong
- Department of Neurology, Washington University in St Louis, St Louis, MO, USA
- Division of Biostatistics, Washington University in St Louis, St Louis, MO, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA
| | - Richard J Perrin
- Department of Neurology, Washington University in St Louis, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University in St Louis, St Louis, MO, USA
| | - Aliza P Wingo
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Psychiatry, Emory University School of Medicine, Atlanta, GA, USA
- Division of Mental Health, Atlanta VA Medical Center, Atlanta, GA, USA
| | - Thomas S Wingo
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Jasmeer P Chhatwal
- Massachusetts General and Brigham & Women's Hospitals, Harvard Medical School, Boston, MA, USA
| | - Gregory S Day
- Department of Neurology, Mayo Clinic, Jacksonville, FL, USA
| | - James M Noble
- Department of Neurology, Taub Institute for Research on Alzheimer's Disease and the Aging Brain, and GH Sergievsky Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Sarah B Berman
- Departments of Neurology and Clinical and Translational Science, Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ralph Martins
- Edith Cowan University, Perth, Western Australia, Australia
| | | | - Peter R Schofield
- Neuroscience Research Australia, Sydney, New South Wales, Australia
- School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Takeshi Ikeuchi
- Department of Molecular Genetics, Brain Research Institute, Niigata University, Niigata, Japan
| | - Hiroshi Mori
- Osaka Metropolitan University Medical School, Nagaoka Sutoku University, Nagaoka, Japan
| | - Johannes Levin
- Department of Neurology, Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - James J Lah
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Christian Haass
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Metabolic Biochemistry, Biomedical Center (BMC), Ludwig-Maximilians University, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Mathias Jucker
- Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - John C Morris
- Department of Neurology, Washington University in St Louis, St Louis, MO, USA
| | - Tammie L S Benzinger
- Mallinckrodt Institute of Radiology, Washington University in St Louis, St Louis, MO, USA
| | - Blaine R Roberts
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Randall J Bateman
- Department of Neurology, Washington University in St Louis, St Louis, MO, USA
| | - Anne M Fagan
- Department of Neurology, Washington University in St Louis, St Louis, MO, USA
| | - Nicholas T Seyfried
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Allan I Levey
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
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11
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Modeste ES, Ping L, Watson CM, Duong DM, Dammer EB, Johnson ECB, Roberts BR, Lah JJ, Levey AI, Seyfried NT. Quantitative proteomics of cerebrospinal fluid from African Americans and Caucasians reveals shared and divergent changes in Alzheimer's disease. Mol Neurodegener 2023; 18:48. [PMID: 37468915 PMCID: PMC10355042 DOI: 10.1186/s13024-023-00638-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 06/21/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND Despite being twice as likely to get Alzheimer's disease (AD), African Americans have been grossly underrepresented in AD research. While emerging evidence indicates that African Americans with AD have lower cerebrospinal fluid (CSF) levels of Tau compared to Caucasians, other differences in AD CSF biomarkers have not been fully elucidated. Here, we performed unbiased proteomic profiling of CSF from African Americans and Caucasians with and without AD to identify both common and divergent AD CSF biomarkers. METHODS Multiplex tandem mass tag-based mass spectrometry (TMT-MS) quantified 1,840 proteins from 105 control and 98 AD patients of which 100 identified as Caucasian while 103 identified as African American. We used differential protein expression and co-expression approaches to assess how changes in the CSF proteome are related to race and AD. Co-expression network analysis organized the CSF proteome into 14 modules associated with brain cell-types and biological pathways. A targeted mass spectrometry method, selected reaction monitoring (SRM), with heavy labeled internal standards was used to measure a panel of CSF module proteins across a subset of African Americans and Caucasians with or without AD. A receiver operating characteristic (ROC) curve analysis assessed the performance of each protein biomarker in differentiating controls and AD by race. RESULTS Consistent with previous findings, the increase of Tau levels in AD was greater in Caucasians than in African Americans by both immunoassay and TMT-MS measurements. CSF modules which included 14-3-3 proteins (YWHAZ and YWHAG) demonstrated equivalent disease-related elevations in both African Americans and Caucasians with AD, whereas other modules demonstrated more profound disease changes within race. Modules enriched with proteins involved with glycolysis and neuronal/cytoskeletal proteins, including Tau, were more increased in Caucasians than in African Americans with AD. In contrast, a module enriched with synaptic proteins including VGF, SCG2, and NPTX2 was significantly lower in African Americans than Caucasians with AD. Following SRM and ROC analysis, VGF, SCG2, and NPTX2 were significantly better at classifying African Americans than Caucasians with AD. CONCLUSIONS Our findings provide insight into additional protein biomarkers and pathways reflecting underlying brain pathology that are shared or differ by race.
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Affiliation(s)
- Erica S. Modeste
- School of Medicine, Department of Biochemistry, Emory University, Atlanta, GA USA
| | - Lingyan Ping
- School of Medicine, Department of Biochemistry, Emory University, Atlanta, GA USA
| | - Caroline M. Watson
- School of Medicine, Department of Neurology, Emory University, Atlanta, GA USA
| | - Duc M. Duong
- School of Medicine, Department of Biochemistry, Emory University, Atlanta, GA USA
| | - Eric B. Dammer
- School of Medicine, Department of Biochemistry, Emory University, Atlanta, GA USA
| | - Erik C. B. Johnson
- School of Medicine, Department of Neurology, Emory University, Atlanta, GA USA
| | - Blaine R. Roberts
- School of Medicine, Department of Biochemistry, Emory University, Atlanta, GA USA
| | - James J. Lah
- School of Medicine, Department of Neurology, Emory University, Atlanta, GA USA
| | - Allan I. Levey
- School of Medicine, Department of Neurology, Emory University, Atlanta, GA USA
| | - Nicholas T. Seyfried
- School of Medicine, Department of Biochemistry, Emory University, Atlanta, GA USA
- School of Medicine, Department of Neurology, Emory University, Atlanta, GA USA
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12
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Hurst CD, Dunn AR, Dammer EB, Duong DM, Seyfried NT, Kaczorowski CC, Johnson ECB. Genetic background influences the 5XFAD Alzheimer's disease mouse model brain proteome. bioRxiv 2023:2023.06.12.544646. [PMID: 37398142 PMCID: PMC10312637 DOI: 10.1101/2023.06.12.544646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
There is a pressing need to improve the translational validity of Alzheimer's disease (AD) mouse models. Introducing genetic background diversity in AD mouse models has been proposed as a way to increase validity and enable discovery of previously uncharacterized genetic contributions to AD susceptibility or resilience. However, the extent to which genetic background influences the mouse brain proteome and its perturbation in AD mouse models is unknown. Here we crossed the 5XFAD AD mouse model on a C57BL/6J (B6) inbred background with the DBA/2J (D2) inbred background and analyzed the effects of genetic background variation on the brain proteome in F1 progeny. Both genetic background and 5XFAD transgene insertion strongly affected protein variance in hippocampus and cortex (n=3,368 proteins). Protein co-expression network analysis identified 16 modules of highly co-expressed proteins common across hippocampus and cortex in 5XFAD and non-transgenic mice. Among the modules strongly influenced by genetic background were those related to small molecule metabolism and ion transport. Modules strongly influenced by the 5XFAD transgene were related to lysosome/stress response and neuronal synapse/signaling. The modules with the strongest relationship to human disease-neuronal synapse/signaling and lysosome/stress response-were not significantly influenced by genetic background. However, other modules in 5XFAD that were related to human disease, such as GABA synaptic signaling and mitochondrial membrane modules, were influenced by genetic background. Most disease-related modules were more strongly correlated to AD genotype in hippocampus compared to cortex. Our findings suggest that genetic diversity introduced by crossing B6 and D2 inbred backgrounds influences proteomic changes related to disease in the 5XFAD model, and that proteomic analysis of other genetic backgrounds in transgenic and knock-in AD mouse models is warranted to capture the full range of molecular heterogeneity in genetically diverse models of AD.
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Affiliation(s)
- Cheyenne D. Hurst
- Goizueta Alzheimer’s Disease Research Center, Emory University School of Medicine, Atlanta, GA 30322 USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Amy R. Dunn
- The Jackson Laboratory, Bar Harbor, ME 04609 USA
| | - Eric B. Dammer
- Goizueta Alzheimer’s Disease Research Center, Emory University School of Medicine, Atlanta, GA 30322 USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Duc M. Duong
- Goizueta Alzheimer’s Disease Research Center, Emory University School of Medicine, Atlanta, GA 30322 USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Nicholas T. Seyfried
- Goizueta Alzheimer’s Disease Research Center, Emory University School of Medicine, Atlanta, GA 30322 USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322 USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Catherine C. Kaczorowski
- The Jackson Laboratory, Bar Harbor, ME 04609 USA
- The University of Michigan, Ann Arbor, MI 48105 USA
| | - Erik C. B. Johnson
- Goizueta Alzheimer’s Disease Research Center, Emory University School of Medicine, Atlanta, GA 30322 USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322 USA
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13
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Watson CM, Dammer EB, Ping L, Duong DM, Modeste E, Carter EK, Johnson ECB, Levey AI, Lah JJ, Roberts BR, Seyfried NT. Quantitative Mass Spectrometry Analysis of Cerebrospinal Fluid Protein Biomarkers in Alzheimer's Disease. Sci Data 2023; 10:261. [PMID: 37160957 PMCID: PMC10170100 DOI: 10.1038/s41597-023-02158-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/17/2023] [Indexed: 05/11/2023] Open
Abstract
Alzheimer's disease (AD) is the most common form of dementia, with cerebrospinal fluid (CSF) β-amyloid (Aβ), total Tau, and phosphorylated Tau (pTau) providing the most sensitive and specific biomarkers for diagnosis. However, these diagnostic biomarkers do not reflect the complex changes in AD brain beyond amyloid (A) and Tau (T) pathologies. Here, we report a selected reaction monitoring mass spectrometry (SRM-MS) method with isotopically labeled standards for relative protein quantification in CSF. Biomarker positive (AT+) and negative (AT-) CSF pools were used as quality controls (QCs) to assess assay precision. We detected 62 peptides (51 proteins) with an average coefficient of variation (CV) of ~13% across 30 QCs and 133 controls (cognitively normal, AT-), 127 asymptomatic (cognitively normal, AT+) and 130 symptomatic AD (cognitively impaired, AT+). Proteins that could distinguish AT+ from AT- individuals included SMOC1, GDA, 14-3-3 proteins, and those involved in glycolysis. Proteins that could distinguish cognitive impairment were mainly neuronal proteins (VGF, NPTX2, NPTXR, and SCG2). This demonstrates the utility of SRM-MS to quantify CSF protein biomarkers across stages of AD.
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Affiliation(s)
- Caroline M Watson
- Department of Neurology, Emory University School of Medicine, Atlanta, USA
| | - Eric B Dammer
- Department of Neurology, Emory University School of Medicine, Atlanta, USA
| | - Lingyan Ping
- Department of Neurology, Emory University School of Medicine, Atlanta, USA
| | - Duc M Duong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, USA
| | - Erica Modeste
- Department of Neurology, Emory University School of Medicine, Atlanta, USA
| | - E Kathleen Carter
- Department of Biochemistry, Emory University School of Medicine, Atlanta, USA
| | - Erik C B Johnson
- Department of Neurology, Emory University School of Medicine, Atlanta, USA
| | - Allan I Levey
- Department of Neurology, Emory University School of Medicine, Atlanta, USA.
| | - James J Lah
- Department of Neurology, Emory University School of Medicine, Atlanta, USA.
| | - Blaine R Roberts
- Department of Neurology, Emory University School of Medicine, Atlanta, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, USA
| | - Nicholas T Seyfried
- Department of Neurology, Emory University School of Medicine, Atlanta, USA.
- Department of Biochemistry, Emory University School of Medicine, Atlanta, USA.
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14
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Dammer EB, Seyfried NT, Johnson ECB. Batch Correction and Harmonization of -Omics Datasets with a Tunable Median Polish of Ratio. Front Syst Biol 2023; 3:1092341. [PMID: 37122388 PMCID: PMC10137904 DOI: 10.3389/fsysb.2023.1092341] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Large scale -omics datasets can provide new insights into normal and disease-related biology when analyzed through a systems biology framework. However, technical artefacts present in most -omics datasets due to variations in sample preparation, batching, platform settings, personnel, and other experimental procedures prevent useful analyses of such data without prior adjustment for these technical factors. Here, we demonstrate a tunable median polish of ratio (TAMPOR) approach for batch effect correction and agglomeration of multiple, multi-batch, site-specific cohorts into a single analyte abundance data matrix that is suitable for systems biology analyses. We illustrate the utility and versatility of TAMPOR through four distinct use cases where the method has been applied to different proteomic datasets, some of which contain a specific defect that must be addressed prior to analysis. We compare quality control metrics and sources of variance before and after application of TAMPOR to show that TAMPOR is effective at removing batch effects and other unwanted sources of variance in -omics data. We also show how TAMPOR can be used to harmonize -omics datasets even when the data are acquired using different analytical approaches. TAMPOR is a powerful and flexible approach for cleaning and harmonization of -omics data prior to downstream systems biology analysis.
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Affiliation(s)
- Eric B Dammer
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Nicholas T Seyfried
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Erik C B Johnson
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
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15
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Dammer EB, Ping L, Duong DM, Modeste ES, Seyfried NT, Lah JJ, Levey AI, Johnson ECB. Multi-platform proteomic analysis of Alzheimer’s disease cerebrospinal fluid and plasma reveals network biomarkers associated with proteostasis and the matrisome. Alzheimers Res Ther 2022; 14:174. [DOI: 10.1186/s13195-022-01113-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 10/31/2022] [Indexed: 11/18/2022]
Abstract
AbstractRobust and accessible biomarkers that can capture the heterogeneity of Alzheimer’s disease and its diverse pathological processes are urgently needed. Here, we undertook an investigation of Alzheimer’s disease cerebrospinal fluid (CSF) and plasma from the same subjects (n=18 control, n=18 AD) using three different proteomic platforms—SomaLogic SomaScan, Olink proximity extension assay, and tandem mass tag-based mass spectrometry—to assess which protein markers in these two biofluids may serve as reliable biomarkers of AD pathophysiology observed from unbiased brain proteomics studies. Median correlation of overlapping protein measurements across platforms in CSF (r~0.7) and plasma (r~0.6) was good, with more variability in plasma. The SomaScan technology provided the most measurements in plasma. Surprisingly, many proteins altered in AD CSF were found to be altered in the opposite direction in plasma, including important members of AD brain co-expression modules. An exception was SMOC1, a key member of the brain matrisome module associated with amyloid-β deposition in AD, which was found to be elevated in both CSF and plasma. Protein co-expression analysis on greater than 7000 protein measurements in CSF and 9500 protein measurements in plasma across all proteomic platforms revealed strong changes in modules related to autophagy, ubiquitination, and sugar metabolism in CSF, and endocytosis and the matrisome in plasma. Cross-platform and cross-biofluid proteomics represents a promising approach for AD biomarker development.
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16
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Del Campo M, Peeters CFW, Johnson ECB, Vermunt L, Hok-A-Hin YS, van Nee M, Chen-Plotkin A, Irwin DJ, Hu WT, Lah JJ, Seyfried NT, Dammer EB, Herradon G, Meeter LH, van Swieten J, Alcolea D, Lleó A, Levey AI, Lemstra AW, Pijnenburg YAL, Visser PJ, Tijms BM, van der Flier WM, Teunissen CE. CSF proteome profiling across the Alzheimer's disease spectrum reflects the multifactorial nature of the disease and identifies specific biomarker panels. Nat Aging 2022; 2:1040-1053. [PMID: 37118088 PMCID: PMC10292920 DOI: 10.1038/s43587-022-00300-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 09/28/2022] [Indexed: 04/30/2023]
Abstract
Development of disease-modifying therapies against Alzheimer's disease (AD) requires biomarkers reflecting the diverse pathological pathways specific for AD. We measured 665 proteins in 797 cerebrospinal fluid (CSF) samples from patients with mild cognitive impairment with abnormal amyloid (MCI(Aβ+): n = 50), AD-dementia (n = 230), non-AD dementias (n = 322) and cognitively unimpaired controls (n = 195) using proximity ligation-based immunoassays. Here we identified >100 CSF proteins dysregulated in MCI(Aβ+) or AD compared to controls or non-AD dementias. Proteins dysregulated in MCI(Aβ+) were primarily related to protein catabolism, energy metabolism and oxidative stress, whereas those specifically dysregulated in AD dementia were related to cell remodeling, vascular function and immune system. Classification modeling unveiled biomarker panels discriminating clinical groups with high accuracies (area under the curve (AUC): 0.85-0.99), which were translated into custom multiplex assays and validated in external and independent cohorts (AUC: 0.8-0.99). Overall, this study provides novel pathophysiological leads delineating the multifactorial nature of AD and potential biomarker tools for diagnostic settings or clinical trials.
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Affiliation(s)
- Marta Del Campo
- Neurochemistry Laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location VUmc, Amsterdam, The Netherlands.
- Departamento de Ciencias Farmacéuticas y de la Salud, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Spain.
- Barcelonaβeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona, Spain.
| | - Carel F W Peeters
- Department of Epidemiology & Data Science, Amsterdam Public Health research institute, Amsterdam University Medical Centers, Location VUmc, Amsterdam, The Netherlands
- Mathematical & Statistical Methods group (Biometris), Wageningen University & Research, Wageningen, The Netherlands
| | - Erik C B Johnson
- Goizueta Alzheimer's Disease Research Center, Emory University, Atlanta, GA, USA
| | - Lisa Vermunt
- Neurochemistry Laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location VUmc, Amsterdam, The Netherlands
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location VUmc, Amsterdam, The Netherlands
| | - Yanaika S Hok-A-Hin
- Neurochemistry Laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location VUmc, Amsterdam, The Netherlands
| | - Mirrelijn van Nee
- Department of Epidemiology & Data Science, Amsterdam Public Health research institute, Amsterdam University Medical Centers, Location VUmc, Amsterdam, The Netherlands
| | - Alice Chen-Plotkin
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - David J Irwin
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - William T Hu
- Rutgers-RWJ Medical School, Institute for Health, Health Care Policy, and Aging Research, Rutgers Biomedical and Health Sciences, New Brunswick, NJ, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - James J Lah
- Goizueta Alzheimer's Disease Research Center, Emory University, Atlanta, GA, USA
| | - Nicholas T Seyfried
- 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
- Goizueta Alzheimer's Disease Research Center, Emory University, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Gonzalo Herradon
- Departamento de Ciencias Farmacéuticas y de la Salud, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Spain
| | - Lieke H Meeter
- Department of Neurology and Alzheimer Center, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
| | - John van Swieten
- Department of Neurology and Alzheimer Center, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Daniel Alcolea
- Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau - Hospital de Sant Pau, Universitat Autònoma de Barcelona, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Alberto Lleó
- Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau - Hospital de Sant Pau, Universitat Autònoma de Barcelona, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Allan I Levey
- Goizueta Alzheimer's Disease Research Center, Emory University, Atlanta, GA, USA
| | - Afina W Lemstra
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location VUmc, Amsterdam, The Netherlands
| | - Yolande A L Pijnenburg
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location VUmc, Amsterdam, The Netherlands
| | - Pieter J Visser
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location VUmc, Amsterdam, The Netherlands
- Alzheimer Center Limburg, School for Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, Stockholm, Sweden
| | - Betty M Tijms
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location VUmc, Amsterdam, The Netherlands
| | - Wiesje M van der Flier
- Department of Epidemiology & Data Science, Amsterdam Public Health research institute, Amsterdam University Medical Centers, Location VUmc, Amsterdam, The Netherlands
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location VUmc, Amsterdam, The Netherlands
| | - Charlotte E Teunissen
- Neurochemistry Laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location VUmc, Amsterdam, The Netherlands
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17
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Johnson ECB, Carter EK, Dammer EB, Duong DM, Gerasimov ES, Liu Y, Liu J, Betarbet R, Ping L, Yin L, Serrano GE, Beach TG, Peng J, De Jager PL, Haroutunian V, Zhang B, Gaiteri C, Bennett DA, Gearing M, Wingo TS, Wingo AP, Lah JJ, Levey AI, Seyfried NT. Large-scale deep multi-layer analysis of Alzheimer's disease brain reveals strong proteomic disease-related changes not observed at the RNA level. Nat Neurosci 2022; 25:213-225. [PMID: 35115731 PMCID: PMC8825285 DOI: 10.1038/s41593-021-00999-y] [Citation(s) in RCA: 171] [Impact Index Per Article: 85.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 12/08/2021] [Indexed: 12/16/2022]
Abstract
The biological processes that are disrupted in the Alzheimer's disease (AD) brain remain incompletely understood. In this study, we analyzed the proteomes of more than 1,000 brain tissues to reveal new AD-related protein co-expression modules that were highly preserved across cohorts and brain regions. Nearly half of the protein co-expression modules, including modules significantly altered in AD, were not observed in RNA networks from the same cohorts and brain regions, highlighting the proteopathic nature of AD. Two such AD-associated modules unique to the proteomic network included a module related to MAPK signaling and metabolism and a module related to the matrisome. The matrisome module was influenced by the APOE ε4 allele but was not related to the rate of cognitive decline after adjustment for neuropathology. By contrast, the MAPK/metabolism module was strongly associated with the rate of cognitive decline. Disease-associated modules unique to the proteome are sources of promising therapeutic targets and biomarkers for AD.
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Affiliation(s)
- Erik C B Johnson
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA.
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA.
| | - E Kathleen Carter
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Eric B Dammer
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Duc M Duong
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Yue Liu
- Department of Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Jiaqi Liu
- Department of Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Ranjita Betarbet
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Lingyan Ping
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Luming Yin
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | | | | | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Philip L De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Taub Institute, Columbia University Irving Medical Center, New York Presbyterian Hospital, New York, NY, USA
| | - Vahram Haroutunian
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- James J. Peters VA Medical Center MIRECC, Bronx, NY, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Chris Gaiteri
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Marla Gearing
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Thomas S Wingo
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Aliza P Wingo
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Psychiatry, Emory University School of Medicine, Atlanta, GA, USA
- Division of Mental Health, Atlanta VA Medical Center, Atlanta, GA, USA
| | - James J Lah
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Allan I Levey
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA.
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA.
| | - Nicholas T Seyfried
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA.
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA.
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA.
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18
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Haytural H, Benfeitas R, Schedin-Weiss S, Bereczki E, Rezeli M, Unwin RD, Wang X, Dammer EB, Johnson ECB, Seyfried NT, Winblad B, Tijms BM, Visser PJ, Frykman S, Tjernberg LO. Insights into the changes in the proteome of Alzheimer disease elucidated by a meta-analysis. Sci Data 2021; 8:312. [PMID: 34862388 PMCID: PMC8642431 DOI: 10.1038/s41597-021-01090-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 10/21/2021] [Indexed: 11/10/2022] Open
Abstract
Mass spectrometry (MS)-based proteomics is a powerful tool to explore pathogenic changes of a disease in an unbiased manner and has been used extensively in Alzheimer disease (AD) research. Here, by performing a meta-analysis of high-quality proteomic studies, we address which pathological changes are observed consistently and therefore most likely are of great importance for AD pathogenesis. We retrieved datasets, comprising a total of 21,588 distinct proteins identified across 857 postmortem human samples, from ten studies using labeled or label-free MS approaches. Our meta-analysis findings showed significant alterations of 757 and 1,195 proteins in AD in the labeled and label-free datasets, respectively. Only 33 proteins, some of which were associated with synaptic signaling, had the same directional change across the individual studies. However, despite alterations in individual proteins being different between the labeled and the label-free datasets, several pathways related to synaptic signaling, oxidative phosphorylation, immune response and extracellular matrix were commonly dysregulated in AD. These pathways represent robust changes in the human AD brain and warrant further investigation.
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Affiliation(s)
- Hazal Haytural
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Solna, Sweden.
| | - Rui Benfeitas
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, S-10691, Stockholm, Sweden
| | - Sophia Schedin-Weiss
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Solna, Sweden
| | - Erika Bereczki
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Solna, Sweden
| | - Melinda Rezeli
- Division of Clinical Protein Science & Imaging, Department of Clinical Sciences (Lund) and Department of Biomedical Engineering, Lund University, Lund, Sweden
| | - Richard D Unwin
- Stoller Biomarker Discovery Centre, and Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Sciences Centre, CityLabs 1.0, Nelson Street, Manchester, M13 9NQ, UK
| | - Xusheng Wang
- Department of Biology, University of North Dakota, Grand Forks, ND, USA
| | - Eric B Dammer
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Erik C B Johnson
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Nicholas T Seyfried
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Bengt Winblad
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Solna, Sweden
- Karolinska University Hospital, Theme of Inflammation and Aging, Huddinge, Sweden
| | - Betty M Tijms
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Pieter Jelle Visser
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Solna, Sweden
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
- Alzheimer Center Limburg, School for Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Susanne Frykman
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Solna, Sweden
| | - Lars O Tjernberg
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Solna, Sweden.
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19
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Swarup V, Chang TS, Duong DM, Dammer EB, Dai J, Lah JJ, Johnson ECB, Seyfried NT, Levey AI, Geschwind DH. Identification of Conserved Proteomic Networks in Neurodegenerative Dementia. Cell Rep 2021; 31:107807. [PMID: 32579933 PMCID: PMC8221021 DOI: 10.1016/j.celrep.2020.107807] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 04/27/2020] [Accepted: 06/03/2020] [Indexed: 12/11/2022] Open
Abstract
Data-driven analyses are increasingly valued in modern medicine. We integrate quantitative proteomics and transcriptomics from over 1,000 post-mortem brains from six cohorts representing Alzheimer’s disease (AD), asymptomatic AD, progressive supranuclear palsy (PSP), and control patients from the Accelerating Medicines Partnership – Alzheimer’s Disease consortium. We define robust co-expression trajectories related to disease progression, including early neuronal, microglial, astrocyte, and immune response modules, and later mRNA splicing and mitochondrial modules. The majority of, but not all, modules are conserved at the transcriptomic level, including module C3, which is only observed in proteome networks and enriched in mitogen-activated protein kinase (MAPK) signaling. Genetic risk enriches in modules changing early in disease and indicates that AD and PSP have distinct causal biological drivers at the pathway level, despite aspects of similar pathology, including synaptic loss and glial inflammatory changes. The conserved, high-confidence proteomic changes enriched in genetic risk represent targets for drug discovery. Swarup et al. use a multi-omic, multi-cohort approach to identify robust early and late proteomic changes in AD and other neurodegenerative dementias and find that genetic risk is differentially enriched across disorders. Shared co-expression modules showing consistent molecular alterations at multi-omic levels are ripe for future investigation as drug targets.
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Affiliation(s)
- Vivek Swarup
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Timothy S Chang
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Duc M Duong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Eric B Dammer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jingting Dai
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Neurology, Second Xiangya Hospital, Central South University, Changsha, China
| | - James J Lah
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Erik C B Johnson
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA; 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
| | - Daniel H Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute of Precision Health, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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20
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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. Sci Adv 2020; 6:eaaz9360. [PMID: 33087358 PMCID: PMC7577712 DOI: 10.1126/sciadv.aaz9360] [Citation(s) in RCA: 158] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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21
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Johnson ECB, Ho K, Yu GQ, Das M, Sanchez PE, Djukic B, Lopez I, Yu X, Gill M, Zhang W, Paz JT, Palop JJ, Mucke L. Behavioral and neural network abnormalities in human APP transgenic mice resemble those of App knock-in mice and are modulated by familial Alzheimer's disease mutations but not by inhibition of BACE1. Mol Neurodegener 2020; 15:53. [PMID: 32921309 PMCID: PMC7489007 DOI: 10.1186/s13024-020-00393-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 07/08/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is the most frequent and costly neurodegenerative disorder. Although diverse lines of evidence suggest that the amyloid precursor protein (APP) is involved in its causation, the precise mechanisms remain unknown and no treatments are available to prevent or halt the disease. A favorite hypothesis has been that APP contributes to AD pathogenesis through the cerebral accumulation of the amyloid-β peptide (Aβ), which is derived from APP through sequential proteolytic cleavage by BACE1 and γ-secretase. However, inhibitors of these enzymes have failed in clinical trials despite clear evidence for target engagement. METHODS To further elucidate the roles of APP and its metabolites in AD pathogenesis, we analyzed transgenic mice overexpressing wildtype human APP (hAPP) or hAPP carrying mutations that cause autosomal dominant familial AD (FAD), as well as App knock-in mice that do not overexpress hAPP but have two mouse App alleles with FAD mutations and a humanized Aβ sequence. RESULTS Although these lines of mice had marked differences in cortical and hippocampal levels of APP, APP C-terminal fragments, soluble Aβ, Aβ oligomers and age-dependent amyloid deposition, they all developed cognitive deficits as well as non-convulsive epileptiform activity, a type of network dysfunction that also occurs in a substantive proportion of humans with AD. Pharmacological inhibition of BACE1 effectively reduced levels of amyloidogenic APP C-terminal fragments (C99), soluble Aβ, Aβ oligomers, and amyloid deposits in transgenic mice expressing FAD-mutant hAPP, but did not improve their network dysfunction and behavioral abnormalities, even when initiated at early stages before amyloid deposits were detectable. CONCLUSIONS hAPP transgenic and App knock-in mice develop similar pathophysiological alterations. APP and its metabolites contribute to AD-related functional alterations through complex combinatorial mechanisms that may be difficult to block with BACE inhibitors and, possibly, also with other anti-Aβ treatments.
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Affiliation(s)
- Erik C. B. Johnson
- Gladstone Institute of Neurological Disease, 1650 Owens Street, San Francisco, CA 94158 USA
- Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158 USA
| | - Kaitlyn Ho
- Gladstone Institute of Neurological Disease, 1650 Owens Street, San Francisco, CA 94158 USA
| | - Gui-Qiu Yu
- Gladstone Institute of Neurological Disease, 1650 Owens Street, San Francisco, CA 94158 USA
| | - Melanie Das
- Gladstone Institute of Neurological Disease, 1650 Owens Street, San Francisco, CA 94158 USA
| | - Pascal E. Sanchez
- Gladstone Institute of Neurological Disease, 1650 Owens Street, San Francisco, CA 94158 USA
| | - Biljana Djukic
- Gladstone Institute of Neurological Disease, 1650 Owens Street, San Francisco, CA 94158 USA
| | - Isabel Lopez
- Gladstone Institute of Neurological Disease, 1650 Owens Street, San Francisco, CA 94158 USA
| | - Xinxing Yu
- Gladstone Institute of Neurological Disease, 1650 Owens Street, San Francisco, CA 94158 USA
| | - Michael Gill
- Gladstone Institute of Neurological Disease, 1650 Owens Street, San Francisco, CA 94158 USA
| | - Weiping Zhang
- NHC Key Laboratory of Hormones and Development, Tianjin Institute of Endocrinology, Tianjin Medical University Metabolic Diseases Hospital, Tianjin, China
| | - Jeanne T. Paz
- Gladstone Institute of Neurological Disease, 1650 Owens Street, San Francisco, CA 94158 USA
- Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158 USA
| | - Jorge J. Palop
- Gladstone Institute of Neurological Disease, 1650 Owens Street, San Francisco, CA 94158 USA
- Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158 USA
| | - Lennart Mucke
- Gladstone Institute of Neurological Disease, 1650 Owens Street, San Francisco, CA 94158 USA
- Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158 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] [What about the content of this article? (0)] [Affiliation(s)] [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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23
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Johnson ECB, Dammer EB, Duong DM, Ping L, Zhou M, Yin L, Higginbotham LA, Guajardo A, White B, Troncoso JC, Thambisetty M, Montine TJ, Lee EB, Trojanowski JQ, Beach TG, Reiman EM, Haroutunian V, Wang M, Schadt E, Zhang B, Dickson DW, Ertekin-Taner N, Golde TE, Petyuk VA, De Jager PL, Bennett DA, Wingo TS, Rangaraju S, Hajjar I, Shulman JM, Lah JJ, Levey AI, Seyfried NT. Large-scale proteomic analysis of Alzheimer's disease brain and cerebrospinal fluid reveals early changes in energy metabolism associated with microglia and astrocyte activation. Nat Med 2020; 26:769-780. [PMID: 32284590 PMCID: PMC7405761 DOI: 10.1038/s41591-020-0815-6] [Citation(s) in RCA: 464] [Impact Index Per Article: 116.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 02/27/2020] [Indexed: 12/12/2022]
Abstract
Our understanding of Alzheimer's disease (AD) pathophysiology remains incomplete. Here we used quantitative mass spectrometry and coexpression network analysis to conduct the largest proteomic study thus far on AD. A protein network module linked to sugar metabolism emerged as one of the modules most significantly associated with AD pathology and cognitive impairment. This module was enriched in AD genetic risk factors and in microglia and astrocyte protein markers associated with an anti-inflammatory state, suggesting that the biological functions it represents serve a protective role in AD. Proteins from this module were elevated in cerebrospinal fluid in early stages of the disease. In this study of >2,000 brains and nearly 400 cerebrospinal fluid samples by quantitative proteomics, we identify proteins and biological processes in AD brains that may serve as therapeutic targets and fluid biomarkers for the disease.
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Affiliation(s)
- Erik C B Johnson
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA.
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA.
| | - Eric B Dammer
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Duc M Duong
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Lingyan Ping
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Maotian Zhou
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Luming Yin
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | | | | | | | | | - Madhav Thambisetty
- Clinical and Translational Neuroscience Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Thomas J Montine
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Edward B Lee
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - John Q Trojanowski
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Thomas G Beach
- Department of Pathology, Banner Sun Health Research Institute, Sun City, AZ, USA
| | - Eric M Reiman
- Banner Alzheimer's Institute, Arizona State University and University of Arizona, Phoenix, AZ, USA
| | - Vahram Haroutunian
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- JJ Peters VA Medical Center MIRECC, Bronx, NY, USA
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric Schadt
- Department of Genetics and Genomic Sciences, Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Department of Neurology, Mayo Clinic, Jacksonville, FL, USA
| | - Todd E Golde
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Philip L De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Taub Institute, Columbia University Irving Medical Center, New York Presbyterian Hospital, New York, NY, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Thomas S Wingo
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Srikant Rangaraju
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Ihab Hajjar
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Joshua M Shulman
- Departments of Neurology, Neuroscience and Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurologic Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - James J Lah
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Allan I Levey
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA.
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA.
| | - Nicholas T Seyfried
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA.
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA.
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA.
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Zhou M, Duong DM, Johnson ECB, Dai J, Lah JJ, Levey AI, Seyfried NT. Mass Spectrometry-Based Quantification of Tau in Human Cerebrospinal Fluid Using a Complementary Tryptic Peptide Standard. J Proteome Res 2019; 18:2422-2432. [PMID: 30983353 DOI: 10.1021/acs.jproteome.8b00920] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Here, we report a method for the generation of complementary tryptic (CompTryp) isotope-labeled peptide standards for the relative and absolute quantification of proteins by mass spectrometry (MS). These standards can be digested in parallel with either trypsin (Tryp-C) or trypsin-N (Tryp-N), to generate peptides that significantly overlap in primary sequence having C- and N-terminal arginine and lysine residues, respectively. As a proof of concept, an isotope-labeled CompTryp standard was synthesized for Tau, a well-established biomarker in Alzheimer's disease (AD), which included both N- and C-terminal heavy isotope-labeled (15N and 13C) arginine residues and flanking amino acid sequences to monitor proteolytic digestion. Despite having the exact same mass, the N- and C-terminal heavy Tau peptides are distinguishable by retention time and MS/MS fragmentation profiles. The isotope-labeled Tau CompTryp standard was added to human cerebrospinal fluid (CSF) followed by parallel digestion with Tryp-N and Tryp-C. The native and isotope-labeled peptide pairs were quantified by parallel reaction monitoring (PRM) in a single assay. Notably, both tryptic peptides were effective at quantifying Tau in human CSF, and both showed a significant difference in CSF Tau levels between AD and controls. Treating these CompTryp Tau peptide measurements as independent replicates also improved the coefficient of variation and correlation with Tau immunoassays. More broadly, we propose that CompTryp standards can be generated for any protein of interest, providing an efficient method to improve the robustness and reproducibility for MS analysis of clinical and research samples.
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Affiliation(s)
| | | | | | - Jingting Dai
- Department of Neurology, Second Xiangya Hospital , Central South University , Changsha , Hunan 410078 , China
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25
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Dai J, Johnson ECB, Dammer EB, Duong DM, Gearing M, Lah JJ, Levey AI, Wingo TS, Seyfried NT. Effects of APOE Genotype on Brain Proteomic Network and Cell Type Changes in Alzheimer's Disease. Front Mol Neurosci 2018; 11:454. [PMID: 30618606 PMCID: PMC6305300 DOI: 10.3389/fnmol.2018.00454] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 11/23/2018] [Indexed: 12/12/2022] Open
Abstract
Polymorphic alleles in the apolipoprotein E (APOE) gene are the main genetic determinants of late-onset Alzheimer's disease (AD) risk. Individuals carrying the APOE E4 allele are at increased risk to develop AD compared to those carrying the more common E3 allele, whereas those carrying the E2 allele are at decreased risk for developing AD. How ApoE isoforms influence risk for AD remains unclear. To help fill this gap in knowledge, we performed a comparative unbiased mass spectrometry-based proteomic analysis of post-mortem brain cortical tissues from pathologically-defined AD or control cases of different APOE genotypes. Control cases (n = 10) were homozygous for the common E3 allele, whereas AD cases (n = 24) were equally distributed among E2/3, E3/3, and E4/4 genotypes. We used differential protein expression and co-expression analytical approaches to assess how changes in the brain proteome are related to APOE genotype. We observed similar levels of amyloid-β, but reduced levels of neurofibrillary tau, in E2/3 brains compared to E3/3 and E4/4 AD brains. Weighted co-expression network analysis revealed 33 modules of co-expressed proteins, 12 of which were significantly different by APOE genotype in AD. The modules that were significantly different by APOE genotype were associated with synaptic transmission and inflammation, among other biological processes. Deconvolution and analysis of brain cell type changes revealed that the E2 allele suppressed homeostatic and disease-associated cell type changes in astrocytes, microglia, oligodendroglia, and endothelia. The E2 allele-specific effect on brain cell type changes was validated in a separate cohort of 130 brains. Our systems-level proteomic analyses of AD brain reveal alterations in the brain proteome and brain cell types associated with allelic variants in APOE, and suggest further areas for investigation into the upstream mechanisms that drive ApoE-associated risk for AD.
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Affiliation(s)
- Jingting Dai
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, United States.,Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, United States.,Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA, United States.,Department of Neurology, Second Xiangya Hospital, Central South University, Changsha, China
| | - Erik C B Johnson
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, United States.,Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA, United States
| | - Eric B Dammer
- Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA, United States
| | - Duc M Duong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, United States.,Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA, United States
| | - Marla Gearing
- Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA, United States.,Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
| | - James J Lah
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, United States.,Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA, United States
| | - Allan I Levey
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, United States.,Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA, United States
| | - Thomas S Wingo
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, United States.,Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA, United States.,Division of Neurology, Atlanta VA Medical Center, Decatur, GA, United States.,Department of Human Genetics, Emory University School of Medicine,Atlanta, GA, United States
| | - Nicholas T Seyfried
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, United States.,Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, United States.,Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA, United States
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26
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Johnson ECB, Dammer EB, Duong DM, Yin L, Thambisetty M, Troncoso JC, Lah JJ, Levey AI, Seyfried NT. Deep proteomic network analysis of Alzheimer's disease brain reveals alterations in RNA binding proteins and RNA splicing associated with disease. Mol Neurodegener 2018; 13:52. [PMID: 30286791 PMCID: PMC6172707 DOI: 10.1186/s13024-018-0282-4] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/07/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The complicated cellular and biochemical changes that occur in brain during Alzheimer's disease are poorly understood. In a previous study we used an unbiased label-free quantitative mass spectrometry-based proteomic approach to analyze these changes at a systems level in post-mortem cortical tissue from patients with Alzheimer's disease (AD), asymptomatic Alzheimer's disease (AsymAD), and controls. We found modules of co-expressed proteins that correlated with AD phenotypes, some of which were enriched in proteins identified as risk factors for AD by genetic studies. METHODS The amount of information that can be obtained from such systems-level proteomic analyses is critically dependent upon the number of proteins that can be quantified across a cohort. We report here a new proteomic systems-level analysis of AD brain based on 6,533 proteins measured across AD, AsymAD, and controls using an analysis pipeline consisting of isobaric tandem mass tag (TMT) mass spectrometry and offline prefractionation. RESULTS Our new TMT pipeline allowed us to more than double the depth of brain proteome coverage. This increased depth of coverage greatly expanded the brain protein network to reveal new protein modules that correlated with disease and were unrelated to those identified in our previous network. Differential protein abundance analysis identified 350 proteins that had altered levels between AsymAD and AD not caused by changes in specific cell type abundance, potentially reflecting biochemical changes that are associated with cognitive decline in AD. RNA binding proteins emerged as a class of proteins altered between AsymAD and AD, and were enriched in network modules that correlated with AD pathology. We developed a proteogenomic approach to investigate RNA splicing events that may be altered by RNA binding protein changes in AD. The increased proteome depth afforded by our TMT pipeline allowed us to identify and quantify a large number of alternatively spliced protein isoforms in brain, including AD risk factors such as BIN1, PICALM, PTK2B, and FERMT2. Many of the new AD protein network modules were enriched in alternatively spliced proteins and correlated with molecular markers of AD pathology and cognition. CONCLUSIONS Further analysis of the AD brain proteome will continue to yield new insights into the biological basis of AD.
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Affiliation(s)
- Erik C. B. Johnson
- Department of Neurology, Emory University School of Medicine, Whitehead Building—Suite 505C, 615 Michael Street, Atlanta, GA 30322 USA
| | - Eric B. Dammer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Duc M. Duong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Luming Yin
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Madhav Thambisetty
- National Institute on Aging, National Institutes of Health, Bethesda, MD 20892 USA
| | | | - James J. Lah
- Department of Neurology, Emory University School of Medicine, Whitehead Building—Suite 505C, 615 Michael Street, Atlanta, GA 30322 USA
| | - Allan I. Levey
- Department of Neurology, Emory University School of Medicine, Whitehead Building—Suite 505C, 615 Michael Street, Atlanta, GA 30322 USA
| | - Nicholas T. Seyfried
- Department of Neurology, Emory University School of Medicine, Whitehead Building—Suite 505C, 615 Michael Street, Atlanta, GA 30322 USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322 USA
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27
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Johnson ECB, Kang J. A small molecule targeting protein translation does not rescue spatial learning and memory deficits in the hAPP-J20 mouse model of Alzheimer's disease. PeerJ 2016; 4:e2565. [PMID: 27781164 PMCID: PMC5075699 DOI: 10.7717/peerj.2565] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 09/14/2016] [Indexed: 01/04/2023] Open
Abstract
A small molecule named ISRIB has recently been described to enhance memory in rodents. In this study we aimed to test whether ISRIB would reverse learning and memory deficits in the J20 mouse model of human amyloid precursor protein (hAPP) overexpression, a model that simulates many aspects of Alzheimer’s disease in which memory deficits are a hallmark feature. We did not observe a significant rescue effect with ISRIB treatment on spatial learning and memory as assessed in the Morris water maze in J20 mice. We also did not observe a significant enhancement of spatial learning or memory in nontransgenic mice with ISRIB treatment, although a trend emerged for memory enhancement in one cohort of mice. Future preclinical studies with ISRIB would benefit from additional robust markers of target engagement in the brain.
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Affiliation(s)
- Erik C B Johnson
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, United States; Department of Neurology, University of California -San Francisco, San Francisco, CA, United States
| | - Jing Kang
- Gladstone Institute of Neurological Disease, Gladstone Institutes , San Francisco , CA , United States
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28
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Johnson ECB, Lanning JD, Meredith SC. Peptide backbone modification in the bend region of amyloid-β inhibits fibrillogenesis but not oligomer formation. J Pept Sci 2016; 22:368-73. [PMID: 27114096 DOI: 10.1002/psc.2879] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 02/16/2016] [Accepted: 03/02/2016] [Indexed: 12/20/2022]
Abstract
Current evidence suggests that oligomers of the amyloid-β (Aβ) peptide are involved in the cellular toxicity of Alzheimer's disease, yet their biophysical characterization remains difficult because of lack of experimental control over the aggregation process under relevant physiologic conditions. Here, we show that modification of the Aβ peptide backbone at Gly29 allows for the formation of oligomers but inhibits fibril formation at physiologic temperature and pH. Our results suggest that the putative bend region in Aβ is important for higher-order aggregate formation. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
- Erik C B Johnson
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA.,Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
| | - Jennifer D Lanning
- Department of Pathology, The University of Chicago, Chicago, IL, 60637, USA
| | - Stephen C Meredith
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA.,Department of Pathology, The University of Chicago, Chicago, IL, 60637, USA
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29
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Affiliation(s)
- Kenneth L Tyler
- Department of Neurology, University of Colorado-Denver, Denver, CO, USA
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30
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Affiliation(s)
- Erik C. B. Johnson
- Department of Neurology, University of California−San Francisco, CA, USA
| | - Timothy W. West
- Department of Neurology, University of California−San Francisco, CA, USA
| | - Nerissa U. Ko
- Department of Neurology, University of California−San Francisco, CA, USA
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Abstract
Native chemical ligation of unprotected peptide segments involves reaction between a peptide-alpha-thioester and a cysteine-peptide, to yield a product with a native amide bond at the ligation site. Peptide-alpha-thioalkyl esters are commonly used because of their ease of preparation. These thioalkyl esters are rather unreactive so the ligation reaction is catalyzed by in situ transthioesterification with thiol additives. The most common thiol catalysts used to date have been either a mixture of thiophenol/benzyl mercaptan, or the alkanethiol MESNA. Despite the use of these thiol catalysts, ligation reactions typically take 24-48 h. To gain insight into the mechanism of native chemical ligaton and in order to find a better catalyst, we investigated the use of a number of thiol compounds. Substituted thiophenols with pK(a) > 6 were found to best combine the ability to exchange rapidly and completely with thioalkyl esters, and to then act as effective leaving groups in reaction of the peptide-thioester with the thiol side chain of a cysteine-peptide. A highly effective and practical catalyst was (4-carboxylmethyl)thiophenol ('MPAA'), a nonmalodorous, water-soluble thiol. Use of MPAA gave an order of magnitude faster reaction in model studies of native chemical ligation and in the synthesis of a small protein, turkey ovomucoid third domain (OMTKY3). MPAA should find broad use in native chemical ligation and in the total synthesis of proteins.
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Affiliation(s)
- Erik C B Johnson
- Department of Biochemistry and Molecular Biology, The University of Chicago, Illinois 60637, USA
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Johnson ECB, Malito E, Shen Y, Rich D, Tang WJ, Kent SBH. Modular total chemical synthesis of a human immunodeficiency virus type 1 protease. J Am Chem Soc 2007; 129:11480-90. [PMID: 17705484 DOI: 10.1021/ja072870n] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
As part of our ongoing studies of the human immunodeficiency virus type 1 (HIV-1) protease enzyme, we set out to develop a modular chemical synthesis of the protein from multiple peptide segments. Our initial attempts were frustrated by the insolubility of intermediate peptide products. To overcome this problem, we designed a synthetic strategy combining the solubility-enhancing properties of C-terminal (Arg)n tags and the biological phenomenon of autoprocessing of the Gag-Pol polyprotein that occurs during maturation of the HIV-1 virus in vivo. Synthesis of a 119-residue peptide chain containing 10 residues of the reverse transcriptase (RT) open reading frame plus an (Arg)(10) tag at the C-terminus was straightforward by native chemical ligation followed by conversion of the Cys residues to Ala by Raney nickel desulfurization. The product polypeptide itself completed the final synthetic step by removing the C-terminal modification under folding conditions, to give the mature 99-residue polypeptide. High-purity homodimeric HIV-1 protease protein was obtained in excellent yield and had full enzymatic activity; the structure of the synthetic enzyme was confirmed by X-ray crystallography to a resolution of 1.07 A. This efficient modular synthesis by a biomimetic autoprocessing strategy will enable the facile synthesis of unique chemical analogues of the HIV-1 protease to further elucidate the molecular basis of enzyme catalysis.
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Affiliation(s)
- Erik C B Johnson
- Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Ben-May Department for Cancer Research, The University of Chicago, Chicago, Illinois 60637, USA
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Johnson ECB, Kent SBH. Exploratory synthesis of peptide-alpha-thioester segments spanning the polypeptide sequence of the delta-opioid receptor, a G protein-coupled receptor. Biopolymers 2006; 88:340-9. [PMID: 17120238 DOI: 10.1002/bip.20639] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We have decided to use the delta-opioid receptor (372 residues) as a model system to develop methods for the total chemical synthesis of G protein-coupled receptors. The most important feature of this receptor from a chemical synthesis perspective is the wealth of cysteines spread throughout its sequence, which are required for native chemical ligation. A total of 13 cysteines are located in the the delta-opioid receptor polypetide chain in both loop and putative transmembrane (TM) regions. We envisioned a synthesis of the polypeptide that would make use of peptide-alpha-thioesters ranging from 37 to 63 residues in length. Here, we report data from an exploratory synthesis of such a set of peptide-alpha-thioesters. For all seven peptides, the crude material approximately 30 residues into the synthesis was sufficiently homogeneous to make isolation and purification straightforward. Extension of the peptides to between 40 and 50 residues in length generally produced a significant decrease in the quality of the crude products, although in most cases, we judged that high purity peptides could probably be isolated. By 60 residues, however, the crude peptide product mixtures are probably too heterogeneous to purify to homogeneity by reversed-phase HPLC. In general, delta-opioid receptor peptides with a single predicted TM domain were sufficiently soluble to handle postcleavage and to analyze by reversed-phase HPLC, whereas 1.5 TM domains rendered the peptides too hydrophobic to handle or analyze by standard protocols. Given the challenges of chain assembly, handling, and purification of these peptides, a synthetic strategy that uses approximately 12 or 13 shorter peptide segments of 20-40 residues each is probably a more feasible approach.
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Affiliation(s)
- Erik C B Johnson
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
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Abstract
We have undertaken fundamental studies on the solubility properties of a peptide derived from the fourth transmembrane (TM) domain of signal peptide peptidase, a 7-TM intramembrane-cleaving protease. We have found that by disfavoring secondary structure formation we are able to greatly improve the solubility, handling, and purification properties of this peptide. Our findings suggest that preventing secondary structure formation by reversible modification of the polypeptide backbone of hydrophobic transmembrane peptides may be a useful strategy for the total chemical protein synthesis of integral membrane proteins.
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Affiliation(s)
- Erik C B Johnson
- Institute for Biophysical Dynamics, Department of Biochemistry and Molecular Biology, The University of Chicago, 920 East 58th Street, Chicago, Illinois 60637, USA
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Johnson ECB, Durek T, Kent SBH. Total Chemical Synthesis, Folding, and Assay of a Small Protein on a Water-Compatible Solid Support. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200600381] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Affiliation(s)
- Erik C B Johnson
- Institute for Biophysical Dynamics, Department of Biochemistry, University of Chicago, IL 60637, USA
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Abstract
We demonstrate the potential of 4-methoxy-2-nitrobenzyl as a Boc chemistry-compatible fully reversible backbone modification for synthetic peptides.
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Affiliation(s)
- Erik C B Johnson
- Institute for Biophysical Dynamics, Department of Biochemistry and Molecular Biology,The University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA
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