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Liang Z, Zhuang H, Cao X, Ma G, Shen L. Subcellular proteomics insights into Alzheimer's disease development. Proteomics Clin Appl 2024; 18:e2200112. [PMID: 37650321 DOI: 10.1002/prca.202200112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 07/27/2023] [Accepted: 08/12/2023] [Indexed: 09/01/2023]
Abstract
Alzheimer's disease (AD), one of the most common dementias, is a neurodegenerative disease characterized by cognitive impairment and decreased judgment function. The expected number of AD patient is increasing in the context of the world's advancing medical care and increasing human life expectancy. Since current molecular mechanism studies on AD pathogenesis are incomplete, there is no specific and effective therapeutic agent. Mass spectrometry (MS)-based unbiased proteomics studies provide an effective and comprehensive approach. Many advances have been made in the study of the mechanism, diagnostic markers, and drug targets of AD using proteomics. This paper focus on subcellular level studies, reviews studies using proteomics to study AD-associated mitochondrial dysfunction, synaptic, and myelin damage, the protein composition of amyloid plaques (APs) and neurofibrillary tangles (NFTs), changes in tissue extracellular vehicles (EVs) and exosome proteome, and the protein changes in ribosomes and lysosomes. The methods of sample separation and preparation and proteomic analysis as well as the main findings of these studies are involved. The results of these proteomics studies provide insights into the pathogenesis of AD and provide theoretical resource and direction for future research in AD, helping to identify new biomarkers and drugs targets for AD.
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Affiliation(s)
- Zhiyuan Liang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, P. R. China
| | - Hongbin Zhuang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, P. R. China
| | - Xueshan Cao
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, P. R. China
- College of Physics and Optoelectronics Engineering, Shenzhen University, Shenzhen, P. R. China
| | - Guanwei Ma
- School of Public Health, the key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, P. R. China
| | - Liming Shen
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, P. R. China
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, P. R. China
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2
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Yang LH, Wang GZ, Gao C. SEPT3 as a Potential Molecular Target of Triple-Negative Breast Cancer. Int J Gen Med 2024; 17:1605-1613. [PMID: 38686040 PMCID: PMC11057513 DOI: 10.2147/ijgm.s462541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/22/2024] [Indexed: 05/02/2024] Open
Abstract
Background The survival rate for triple-negative breast cancer (TNBC) is very low due to its advanced metastatic and aggressive nature, and there is no specific target to improve the survival rate. The expression and clinical signature of neuronal-specific septin-3 (Septin3, SEPT3) in TNBC remain undetermined. Methods SEPT3 differential expression in TNBC was detected with the use of bioinformatic approaches based on TCGA and GEO database, which was verified with immunohistochemistry in TNBC tissues. Next, the effect of SEPT3 on survival and the association between SEPT3 expression and clinical characteristics were assessed for TNBC patients. We performed Cox analysis to evaluate whether SEPT3 is an independent predictor for TNBC patients. Results SEPT3 was identified as a key differentially expressed gene. SEPT3 was observed to be elevated in 112 TNBC significantly. Increased expression of SEPT3 contributed to an unfavorable prognosis in patients with TNBC. Additionally, SEPT3 was associated with several factors including TNM stage, lymph node metastasis, Ki67 level and histological grade. SEPT3 was determined to be an independent risk factor for TNBC patients through Cox regression analysis. Conclusion This study demonstrated that SEPT3 could be a potential disease marker for TNBC patients by bioinformatics analysis and validation in clinical samples.
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Affiliation(s)
- Li-Hua Yang
- Department of Breast Tumor Surgery, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Edong Healthcare Group, Huangshi, Hubei, People’s Republic of China
| | - Guo-Zhou Wang
- Department of Breast Tumor Surgery, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Edong Healthcare Group, Huangshi, Hubei, People’s Republic of China
| | - Chao Gao
- Department of General Practitioner, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Edong Healthcare Group, Huangshi, Hubei, People’s Republic of China
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3
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Mansouri Z, Khodagholi F, Zaringhalam J, Abbaszadeh F, Ghasemi R, Maghsoudi N. Intranasal CEPO-FC prevents attention deficits in streptozotocin-induced rat model of Alzheimer's disease: Focus on synaptic plasticity-related factors. EXCLI JOURNAL 2024; 23:491-508. [PMID: 38741725 PMCID: PMC11089095 DOI: 10.17179/excli2023-6818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 04/17/2024] [Indexed: 05/16/2024]
Abstract
Alzheimer's disease remains an issue of great controversy due to its pathology. It is characterized by cognitive impairments and neuropsychiatric symptoms. The FDA approved medications for this disease, can only mitigate the symptoms. One reason for the lack of effective medications is the inaccessibility of the brain which is encompassed by the blood-brain barrier, making intranasal (IN) route of administration potentially advantageous. Male Wistar rats underwent stereotaxic surgery to induce an Alzheimer's disease model via intracerebroventricular (ICV) streptozotocin injection, and Carbamylated Erythropoietin-Fc (CEPO-FC), a derivative of Erythropoietin without its harmful characteristics, was administered intranasally for ten consecutive days. Cognition performance for memory and attention was assessed using the Novel Object Recognition Test and the Object-Based Attention Test respectively. Depression like behavior was evaluated using the Forced Swim Test. Western blotting was done on the extracted hippocampus to quantify STIM proteins. Calbindin, PSD-95, Neuroplastin, Synaptophysin and GAP-43 genes were assessed by Realtime PCR. Behavioral tests demonstrated that IN CEPO-FC could halt cognition deficits and molecular investigations showed that, STIM proteins were decreased in Alzheimer's model, and increased after IN CEPO-FC treatment. Calbindin and PSD-95 were downregulated in our disease model and upregulated when treated with IN CEPO-FC. While Neuroplastin, and GAP-43 expressions remained unchanged. This study suggests that IN CEPO-FC in low doses could be promising for improving cognition and synaptic plasticity deficits in Alzheimer's disease and since IN route of administration is a convenient way, choosing IN CEPO-FC for clinical trial might worth consideration. See also the graphical abstract(Fig. 1).
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Affiliation(s)
- Zahra Mansouri
- Neuroscience Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fariba Khodagholi
- Neuroscience Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jalal Zaringhalam
- Neurophysiology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Physiology, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Abbaszadeh
- Neurobiology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Rasoul Ghasemi
- Neurophysiology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Physiology, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Nader Maghsoudi
- Neuroscience Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Verma H, Kaur S, Kaur S, Gangwar P, Dhiman M, Mantha AK. Role of Cytoskeletal Elements in Regulation of Synaptic Functions: Implications Toward Alzheimer's Disease and Phytochemicals-Based Interventions. Mol Neurobiol 2024:10.1007/s12035-024-04053-3. [PMID: 38491338 DOI: 10.1007/s12035-024-04053-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 02/13/2024] [Indexed: 03/18/2024]
Abstract
Alzheimer's disease (AD), a multifactorial disease, is characterized by the accumulation of neurofibrillary tangles (NFTs) and amyloid beta (Aβ) plaques. AD is triggered via several factors like alteration in cytoskeletal proteins, a mutation in presenilin 1 (PSEN1), presenilin 2 (PSEN2), amyloid precursor protein (APP), and post-translational modifications (PTMs) in the cytoskeletal elements. Owing to the major structural and functional role of cytoskeletal elements, like the organization of axon initial segmentation, dendritic spines, synaptic regulation, and delivery of cargo at the synapse; modulation of these elements plays an important role in AD pathogenesis; like Tau is a microtubule-associated protein that stabilizes the microtubules, and it also causes inhibition of nucleo-cytoplasmic transportation by disrupting the integrity of nuclear pore complex. One of the major cytoskeletal elements, actin and its dynamics, regulate the dendritic spine structure and functions; impairments have been documented towards learning and memory defects. The second major constituent of these cytoskeletal elements, microtubules, are necessary for the delivery of the cargo, like ion channels and receptors at the synaptic membranes, whereas actin-binding protein, i.e., Cofilin's activation form rod-like structures, is involved in the formation of paired helical filaments (PHFs) observed in AD. Also, the glial cells rely on their cytoskeleton to maintain synaptic functionality. Thus, making cytoskeletal elements and their regulation in synaptic structure and function as an important aspect to be focused for better management and targeting AD pathology. This review advocates exploring phytochemicals and Ayurvedic plant extracts against AD by elucidating their neuroprotective mechanisms involving cytoskeletal modulation and enhancing synaptic plasticity. However, challenges include their limited bioavailability due to the poor solubility and the limited potential to cross the blood-brain barrier (BBB), emphasizing the need for targeted strategies to improve therapeutic efficacy.
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Affiliation(s)
- Harkomal Verma
- Department of Zoology, School of Basic Sciences, Central University of Punjab, Village Ghudda, VPO - Ghudda, Bathinda, 151 401, Punjab, India
| | - Sharanjot Kaur
- Department of Microbiology, School of Basic Sciences, Central University of Punjab, Village Ghudda, Bathinda, Punjab, India
| | - Sukhchain Kaur
- Department of Microbiology, School of Basic Sciences, Central University of Punjab, Village Ghudda, Bathinda, Punjab, India
| | - Prabhakar Gangwar
- Department of Zoology, School of Basic Sciences, Central University of Punjab, Village Ghudda, VPO - Ghudda, Bathinda, 151 401, Punjab, India
| | - Monisha Dhiman
- Department of Microbiology, School of Basic Sciences, Central University of Punjab, Village Ghudda, Bathinda, Punjab, India
| | - Anil Kumar Mantha
- Department of Zoology, School of Basic Sciences, Central University of Punjab, Village Ghudda, VPO - Ghudda, Bathinda, 151 401, Punjab, India.
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Lista S, González-Domínguez R, López-Ortiz S, González-Domínguez Á, Menéndez H, Martín-Hernández J, Lucia A, Emanuele E, Centonze D, Imbimbo BP, Triaca V, Lionetto L, Simmaco M, Cuperlovic-Culf M, Mill J, Li L, Mapstone M, Santos-Lozano A, Nisticò R. Integrative metabolomics science in Alzheimer's disease: Relevance and future perspectives. Ageing Res Rev 2023; 89:101987. [PMID: 37343679 DOI: 10.1016/j.arr.2023.101987] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 06/23/2023]
Abstract
Alzheimer's disease (AD) is determined by various pathophysiological mechanisms starting 10-25 years before the onset of clinical symptoms. As multiple functionally interconnected molecular/cellular pathways appear disrupted in AD, the exploitation of high-throughput unbiased omics sciences is critical to elucidating the precise pathogenesis of AD. Among different omics, metabolomics is a fast-growing discipline allowing for the simultaneous detection and quantification of hundreds/thousands of perturbed metabolites in tissues or biofluids, reproducing the fluctuations of multiple networks affected by a disease. Here, we seek to critically depict the main metabolomics methodologies with the aim of identifying new potential AD biomarkers and further elucidating AD pathophysiological mechanisms. From a systems biology perspective, as metabolic alterations can occur before the development of clinical signs, metabolomics - coupled with existing accessible biomarkers used for AD screening and diagnosis - can support early disease diagnosis and help develop individualized treatment plans. Presently, the majority of metabolomic analyses emphasized that lipid metabolism is the most consistently altered pathway in AD pathogenesis. The possibility that metabolomics may reveal crucial steps in AD pathogenesis is undermined by the difficulty in discriminating between the causal or epiphenomenal or compensatory nature of metabolic findings.
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Affiliation(s)
- Simone Lista
- i+HeALTH Strategic Research Group, Department of Health Sciences, Miguel de Cervantes European University (UEMC), Valladolid, Spain.
| | - Raúl González-Domínguez
- Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Hospital Universitario Puerta del Mar, Universidad de Cádiz, Cádiz, Spain
| | - Susana López-Ortiz
- i+HeALTH Strategic Research Group, Department of Health Sciences, Miguel de Cervantes European University (UEMC), Valladolid, Spain
| | - Álvaro González-Domínguez
- Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Hospital Universitario Puerta del Mar, Universidad de Cádiz, Cádiz, Spain
| | - Héctor Menéndez
- i+HeALTH Strategic Research Group, Department of Health Sciences, Miguel de Cervantes European University (UEMC), Valladolid, Spain
| | - Juan Martín-Hernández
- i+HeALTH Strategic Research Group, Department of Health Sciences, Miguel de Cervantes European University (UEMC), Valladolid, Spain
| | - Alejandro Lucia
- Research Institute of the Hospital 12 de Octubre ('imas12'), Madrid, Spain; Faculty of Sport Sciences, European University of Madrid, Villaviciosa de Odón, Madrid, Spain; CIBER of Frailty and Healthy Ageing (CIBERFES), Madrid, Spain
| | | | - Diego Centonze
- Department of Systems Medicine, Tor Vergata University, Rome, Italy; Unit of Neurology, IRCCS Neuromed, Pozzilli, IS, Italy
| | - Bruno P Imbimbo
- Department of Research and Development, Chiesi Farmaceutici, Parma, Italy
| | - Viviana Triaca
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), Rome, Italy
| | - Luana Lionetto
- Clinical Biochemistry, Mass Spectrometry Section, Sant'Andrea University Hospital, Rome, Italy; Department of Neuroscience, Mental Health and Sensory Organs, Faculty of Medicine and Psychology, Sapienza University of Rome, Rome, Italy
| | - Maurizio Simmaco
- Clinical Biochemistry, Mass Spectrometry Section, Sant'Andrea University Hospital, Rome, Italy; Department of Neuroscience, Mental Health and Sensory Organs, Faculty of Medicine and Psychology, Sapienza University of Rome, Rome, Italy
| | - Miroslava Cuperlovic-Culf
- Digital Technologies Research Center, National Research Council, Ottawa, Canada; Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Jericha Mill
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA; School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | - Mark Mapstone
- Department of Neurology, Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, CA, USA
| | - Alejandro Santos-Lozano
- i+HeALTH Strategic Research Group, Department of Health Sciences, Miguel de Cervantes European University (UEMC), Valladolid, Spain; Research Institute of the Hospital 12 de Octubre ('imas12'), Madrid, Spain
| | - Robert Nisticò
- School of Pharmacy, University of Rome "Tor Vergata", Rome, Italy; Laboratory of Pharmacology of Synaptic Plasticity, EBRI Rita Levi-Montalcini Foundation, Rome, Italy
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Askenazi M, Kavanagh T, Pires G, Ueberheide B, Wisniewski T, Drummond E. Compilation of reported protein changes in the brain in Alzheimer's disease. Nat Commun 2023; 14:4466. [PMID: 37491476 PMCID: PMC10368642 DOI: 10.1038/s41467-023-40208-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 07/14/2023] [Indexed: 07/27/2023] Open
Abstract
Proteomic studies of human Alzheimer's disease brain tissue have potential to identify protein changes that drive disease, and to identify new drug targets. Here, we analyse 38 published Alzheimer's disease proteomic studies, generating a map of protein changes in human brain tissue across thirteen brain regions, three disease stages (preclinical Alzheimer's disease, mild cognitive impairment, advanced Alzheimer's disease), and proteins enriched in amyloid plaques, neurofibrillary tangles, and cerebral amyloid angiopathy. Our dataset is compiled into a searchable database (NeuroPro). We found 848 proteins were consistently altered in 5 or more studies. Comparison of protein changes in early-stage and advanced Alzheimer's disease revealed proteins associated with synapse, vesicle, and lysosomal pathways show change early in disease, but widespread changes in mitochondrial associated protein expression change are only seen in advanced Alzheimer's disease. Protein changes were similar for brain regions considered vulnerable and regions considered resistant. This resource provides insight into Alzheimer's disease brain protein changes and highlights proteins of interest for further study.
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Affiliation(s)
| | - Tomas Kavanagh
- Brain and Mind Centre and School of Medical Sciences, University of Sydney, Camperdown, NSW, 2050, Australia
| | - Geoffrey Pires
- Center for Cognitive Neurology, Department of Neurology, Grossman School of Medicine, New York University, New York, NY, 10016, USA
| | - Beatrix Ueberheide
- Center for Cognitive Neurology, Department of Neurology, Grossman School of Medicine, New York University, New York, NY, 10016, USA
- Proteomics Laboratory, Division of Advanced Research Technologies, Grossman School of Medicine, New York University, New York, NY, 10016, USA
- Biochemistry and Molecular Pharmacology, Grossman School of Medicine, New York University, New York, NY, 10016, USA
| | - Thomas Wisniewski
- Center for Cognitive Neurology, Department of Neurology, Grossman School of Medicine, New York University, New York, NY, 10016, USA
| | - Eleanor Drummond
- Brain and Mind Centre and School of Medical Sciences, University of Sydney, Camperdown, NSW, 2050, Australia.
- Center for Cognitive Neurology, Department of Neurology, Grossman School of Medicine, New York University, New York, NY, 10016, USA.
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Dawson T, Rentia U, Sanford J, Cruchaga C, Kauwe JSK, Crandall KA. Locus specific endogenous retroviral expression associated with Alzheimer's disease. Front Aging Neurosci 2023; 15:1186470. [PMID: 37484691 PMCID: PMC10359044 DOI: 10.3389/fnagi.2023.1186470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/13/2023] [Indexed: 07/25/2023] Open
Abstract
Introduction Human endogenous retroviruses (HERVs) are transcriptionally-active remnants of ancient retroviral infections that may play a role in Alzheimer's disease. Methods We combined two, publicly available RNA-Seq datasets with a third, novel dataset for a total cohort of 103 patients with Alzheimer's disease and 45 healthy controls. We use telescope to perform HERV quantification for these samples and simultaneously perform gene expression analysis. Results We identify differentially expressed genes and differentially expressed HERVs in Alzheimer's disease patients. Differentially expressed HERVs are scattered throughout the genome; many of them are members of the HERV-K superfamily. A number of HERVs are correlated with the expression of dysregulated genes in Alzheimer's and are physically proximal to genes which drive disease pathways. Discussion Dysregulated expression of ancient retroviral insertions in the human genome are present in Alzheimer's disease and show localization patterns that may explain how these elements drive pathogenic gene expression.
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Affiliation(s)
- Tyson Dawson
- Computational Biology Institute, The George Washington University, Washington, DC, United States
- Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States
| | - Uzma Rentia
- Computational Biology Institute, The George Washington University, Washington, DC, United States
| | - Jessie Sanford
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States
| | - John S. K. Kauwe
- Department of Biology, Brigham Young University, Provo, UT, United States
| | - Keith A. Crandall
- Computational Biology Institute, The George Washington University, Washington, DC, United States
- Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States
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Andrés-Benito P, Íñigo-Marco I, Brullas M, Carmona M, del Rio JA, Fernández-Irigoyen J, Santamaría E, Povedano M, Ferrer I. Proteostatic modulation in brain aging without associated Alzheimer's disease-and age-related neuropathological changes. Aging (Albany NY) 2023; 15:3295-3330. [PMID: 37179123 PMCID: PMC10449282 DOI: 10.18632/aging.204698] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/17/2023] [Indexed: 05/15/2023]
Abstract
AIMS (Phospho)proteomics of old-aged subjects without cognitive or behavioral symptoms, and without AD-neuropathological changes and lacking any other neurodegenerative alteration will increase understanding about the physiological state of human brain aging without associate neurological deficits and neuropathological lesions. METHODS (Phospho)proteomics using conventional label-free- and SWATH-MS (Sequential window acquisition of all theoretical fragment ion spectra mass spectrometry) has been assessed in the frontal cortex (FC) of individuals without NFTs, senile plaques (SPs) and age-related co-morbidities classified by age (years) in four groups; group 1 (young, 30-44); group 2 (middle-aged: MA, 45-52); group 3 (early-elderly, 64-70); and group 4 (late-elderly, 75-85). RESULTS Protein levels and deregulated protein phosphorylation linked to similar biological terms/functions, but involving different individual proteins, are found in FC with age. The modified expression occurs in cytoskeleton proteins, membranes, synapses, vesicles, myelin, membrane transport and ion channels, DNA and RNA metabolism, ubiquitin-proteasome-system (UPS), kinases and phosphatases, fatty acid metabolism, and mitochondria. Dysregulated phosphoproteins are associated with the cytoskeleton, including microfilaments, actin-binding proteins, intermediate filaments of neurons and glial cells, and microtubules; membrane proteins, synapses, and dense core vesicles; kinases and phosphatases; proteins linked to DNA and RNA; members of the UPS; GTPase regulation; inflammation; and lipid metabolism. Noteworthy, protein levels of large clusters of hierarchically-related protein expression levels are stable until 70. However, protein levels of components of cell membranes, vesicles and synapses, RNA modulation, and cellular structures (including tau and tubulin filaments) are markedly altered from the age of 75. Similarly, marked modifications occur in the larger phosphoprotein clusters involving cytoskeleton and neuronal structures, membrane stabilization, and kinase regulation in the late elderly. CONCLUSIONS Present findings may increase understanding of human brain proteostasis modifications in the elderly in the subpopulation of individuals not having AD neuropathological change and any other neurodegenerative change in any telencephalon region.
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Affiliation(s)
- Pol Andrés-Benito
- Neurologic Diseases and Neurogenetics Group - Bellvitge Institute for Biomedical Research (IDIBE LL), L’Hospitalet de Llobregat, Barcelona 08907, Spain
- CIBERNED (Network Centre of Biomedical Research of Neurodegenerative Diseases), Institute of Health Carlos III, L’Hospitalet de Llobregat, Barcelona 08907, Spain
| | - Ignacio Íñigo-Marco
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), diSNA, Pamplona 31008, Spain
| | - Marta Brullas
- CIBERNED (Network Centre of Biomedical Research of Neurodegenerative Diseases), Institute of Health Carlos III, L’Hospitalet de Llobregat, Barcelona 08907, Spain
- Neuropathology Group, Institute of Biomedical Research, IDIBELL, L’Hospitalet de Llobregat, Barcelona 08907, Spain
| | - Margarita Carmona
- CIBERNED (Network Centre of Biomedical Research of Neurodegenerative Diseases), Institute of Health Carlos III, L’Hospitalet de Llobregat, Barcelona 08907, Spain
- Neuropathology Group, Institute of Biomedical Research, IDIBELL, L’Hospitalet de Llobregat, Barcelona 08907, Spain
| | - José Antonio del Rio
- CIBERNED (Network Centre of Biomedical Research of Neurodegenerative Diseases), Institute of Health Carlos III, L’Hospitalet de Llobregat, Barcelona 08907, Spain
- Molecular and Cellular Neurobiotechnology Group, Institute of Bioengineering of Catalonia (IBEC), Barcelona Institute for Science and Technology, Science Park Barcelona (PCB), Barcelona 08028, Spain
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona 08007, Spain
| | - Joaquín Fernández-Irigoyen
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), diSNA, Pamplona 31008, Spain
| | - Enrique Santamaría
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), diSNA, Pamplona 31008, Spain
| | - Mónica Povedano
- Neurologic Diseases and Neurogenetics Group - Bellvitge Institute for Biomedical Research (IDIBE LL), L’Hospitalet de Llobregat, Barcelona 08907, Spain
- CIBERNED (Network Centre of Biomedical Research of Neurodegenerative Diseases), Institute of Health Carlos III, L’Hospitalet de Llobregat, Barcelona 08907, Spain
| | - Isidro Ferrer
- CIBERNED (Network Centre of Biomedical Research of Neurodegenerative Diseases), Institute of Health Carlos III, L’Hospitalet de Llobregat, Barcelona 08907, Spain
- Neuropathology Group, Institute of Biomedical Research, IDIBELL, L’Hospitalet de Llobregat, Barcelona 08907, Spain
- Department of Pathology and Experimental Therapeutics, University of Barcelona, L’Hospitalet de Llobregat, Barcelona 08907, Spain
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I F. The unique neuropathological vulnerability of the human brain to aging. Ageing Res Rev 2023; 87:101916. [PMID: 36990284 DOI: 10.1016/j.arr.2023.101916] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/19/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023]
Abstract
Alzheimer's disease (AD)-related neurofibrillary tangles (NFT), argyrophilic grain disease (AGD), aging-related tau astrogliopathy (ARTAG), limbic predominant TDP-43 proteinopathy (LATE), and amygdala-predominant Lewy body disease (LBD) are proteinopathies that, together with hippocampal sclerosis, progressively appear in the elderly affecting from 50% to 99% of individuals aged 80 years, depending on the disease. These disorders usually converge on the same subject and associate with additive cognitive impairment. Abnormal Tau, TDP-43, and α-synuclein pathologies progress following a pattern consistent with an active cell-to-cell transmission and abnormal protein processing in the host cell. However, cell vulnerability and transmission pathways are specific for each disorder, albeit abnormal proteins may co-localize in particular neurons. All these alterations are unique or highly prevalent in humans. They all affect, at first, the archicortex and paleocortex to extend at later stages to the neocortex and other regions of the telencephalon. These observations show that the phylogenetically oldest areas of the human cerebral cortex and amygdala are not designed to cope with the lifespan of actual humans. New strategies aimed at reducing the functional overload of the human telencephalon, including optimization of dream repair mechanisms and implementation of artificial circuit devices to surrogate specific brain functions, appear promising.
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Affiliation(s)
- Ferrer I
- Department of Pathology and Experimental Therapeutics, University of Barcelona, Barcelona, Spain; Emeritus Researcher of the Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain; Biomedical Research Network of Neurodegenerative Diseases (CIBERNED), Barcelona, Spain; Institute of Neurosciences, University of Barcelona, Barcelona, Spain; Hospitalet de Llobregat, Barcelona, Spain.
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10
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Patil G, Kulsange S, Kazi R, Chirmade T, Kale V, Mote C, Aswar M, Koratkar S, Agawane S, Kulkarni M. Behavioral and Proteomic Studies Reveal Methylglyoxal Activate Pathways Associated with Alzheimer's Disease. ACS Pharmacol Transl Sci 2023; 6:65-75. [PMID: 36654748 PMCID: PMC9841776 DOI: 10.1021/acsptsci.2c00143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Indexed: 12/29/2022]
Abstract
Diabetes is one of the major risk factors for Alzheimer's disease (AD) development. The role of elevated levels of glucose, methylglyoxal (MGO), and advanced glycation end products (AGEs) in the pathogenesis of AD is not well understood. In this pursuit, we studied the role of methylglyoxal in the pathogenesis of AD in rat models. The elevated plus-maze (EPM) behavioral study indicated that MGO induces anxiety. Treatment of telmisartan (RAGE expression inhibitor) and aminoguanidine (MGO quencher) attenuated MGO induced anxiety. Further, hippocampal proteomics demonstrated that MGO treated rats differentially regulate proteins involved in calcium homeostasis, mitochondrial functioning, and apoptosis, which may affect neurotransmission and neuronal plasticity. The hippocampal tau phosphorylation level was increased in MGO treated rats, which was reduced in the presence of aminoguanidine and telmisartan. The plasma fructosamine level was increased upon MGO treatment. Hippocampal histochemistry showed vascular degeneration and neuronal loss upon MGO treatment. This study provides mechanistic insight into the role of MGO in the diabetes-associated development of AD.
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Affiliation(s)
- Gouri Patil
- Biochemical
Sciences Division, CSIR-National Chemical
Laboratory, Pune 411008, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Shabda Kulsange
- Biochemical
Sciences Division, CSIR-National Chemical
Laboratory, Pune 411008, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Rubina Kazi
- Biochemical
Sciences Division, CSIR-National Chemical
Laboratory, Pune 411008, India
| | - Tejas Chirmade
- Biochemical
Sciences Division, CSIR-National Chemical
Laboratory, Pune 411008, India
| | - Vaikhari Kale
- Biochemical
Sciences Division, CSIR-National Chemical
Laboratory, Pune 411008, India
| | - Chandrashekhar Mote
- Department
of Veterinary Pathology, KNP College of Veterinary Science, Shirwal Satara (Maharashtra Animal and Fishery Sciences
University Nagpur), Satara 412801, Maharashtra, India
| | - Manoj Aswar
- Department
of Pharmacology, Sinhgad Institute of Pharmacy,
Narhe, Pune 411041, Maharashtra, India
| | - Santosh Koratkar
- Symbiosis
School of Biological Sciences, Symbiosis
International (Deemed University), Pune 412115, Maharashtra, India
| | - Sachin Agawane
- Biochemical
Sciences Division, CSIR-National Chemical
Laboratory, Pune 411008, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mahesh Kulkarni
- Biochemical
Sciences Division, CSIR-National Chemical
Laboratory, Pune 411008, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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11
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Neuronal-specific septin-3 binds Atg8/LC3B, accumulates and localizes to autophagosomes during induced autophagy. Cell Mol Life Sci 2022; 79:471. [PMID: 35932293 PMCID: PMC9356936 DOI: 10.1007/s00018-022-04488-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 06/27/2022] [Accepted: 07/13/2022] [Indexed: 11/03/2022]
Abstract
In synapses that show signs of local apoptosis and mitochondrial stress and undergo neuro-immunological synapse pruning, an increase in the levels of the presynaptic protein, neuronal-specific septin-3 can be observed. Septin-3 is a member of the septin GTPase family with the ability to form multimers and contribute to the cytoskeleton. However, the function of septin-3 remains elusive. Here, we provide evidence that septin-3 is capable of binding the most-studied autophagy protein Atg8 homolog microtubule-associated protein 1 light chain 3B (LC3B), besides another homolog, GABA receptor-associated protein-like 2 (GABARAPL2). Moreover, we demonstrate that colocalization of septin-3 and LC3B increases upon chemical autophagy induction in primary neuronal cells. Septin-3 is accumulated in primary neurons upon autophagy enhancement or blockade, similar to autophagy proteins. Using electron microscopy, we also show that septin-3 localizes to LC3B positive membranes and can be found at mitochondria. However, colocalization results of septin-3 and the early mitophagy marker PTEN-induced kinase 1 (PINK1) do not support that binding of septin-3 to mitochondria is mitophagy related. We conclude that septin-3 correlates with synaptic/neuronal autophagy, binds Atg8 and localizes to autophagic membranes that can be enhanced with chemical autophagy induction. Based on our results, elevated septin-3 levels might indicate enhanced or impeded autophagy in neurons.
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12
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Jordan KL, Koss DJ, Outeiro TF, Giorgini F. Therapeutic Targeting of Rab GTPases: Relevance for Alzheimer’s Disease. Biomedicines 2022; 10:biomedicines10051141. [PMID: 35625878 PMCID: PMC9138223 DOI: 10.3390/biomedicines10051141] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/22/2022] [Accepted: 04/18/2022] [Indexed: 11/16/2022] Open
Abstract
Rab GTPases (Rabs) are small proteins that play crucial roles in vesicle transport and membrane trafficking. Owing to their widespread functions in several steps of vesicle trafficking, Rabs have been implicated in the pathogenesis of several disorders, including cancer, diabetes, and multiple neurodegenerative diseases. As treatments for neurodegenerative conditions are currently rather limited, the identification and validation of novel therapeutic targets, such as Rabs, is of great importance. This review summarises proof-of-concept studies, demonstrating that modulation of Rab GTPases in the context of Alzheimer’s disease (AD) can ameliorate disease-related phenotypes, and provides an overview of the current state of the art for the pharmacological targeting of Rabs. Finally, we also discuss the barriers and challenges of therapeutically targeting these small proteins in humans, especially in the context of AD.
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Affiliation(s)
- Kate L. Jordan
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK;
| | - David J. Koss
- Faculty of Medical Sciences, Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne NE2 4HH, UK; (D.J.K.); (T.F.O.)
| | - Tiago F. Outeiro
- Faculty of Medical Sciences, Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne NE2 4HH, UK; (D.J.K.); (T.F.O.)
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, 37075 Göttingen, Germany
- Max Planck Institute for Natural Sciences, 37075 Göttingen, Germany
- Scientific Employee with a Honorary Contract at Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 37075 Göttingen, Germany
| | - Flaviano Giorgini
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK;
- Correspondence:
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13
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Drummond E, Kavanagh T, Pires G, Marta-Ariza M, Kanshin E, Nayak S, Faustin A, Berdah V, Ueberheide B, Wisniewski T. The amyloid plaque proteome in early onset Alzheimer's disease and Down syndrome. Acta Neuropathol Commun 2022; 10:53. [PMID: 35418158 PMCID: PMC9008934 DOI: 10.1186/s40478-022-01356-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/28/2022] [Indexed: 11/17/2022] Open
Abstract
Amyloid plaques contain many proteins in addition to beta amyloid (Aβ). Previous studies examining plaque-associated proteins have shown these additional proteins are important; they provide insight into the factors that drive amyloid plaque development and are potential biomarkers or therapeutic targets for Alzheimer's disease (AD). The aim of this study was to comprehensively identify proteins that are enriched in amyloid plaques using unbiased proteomics in two subtypes of early onset AD: sporadic early onset AD (EOAD) and Down Syndrome (DS) with AD. We focused our study on early onset AD as the drivers of the more aggressive pathology development in these cases is unknown and it is unclear whether amyloid-plaque enriched proteins differ between subtypes of early onset AD. Amyloid plaques and neighbouring non-plaque tissue were microdissected from human brain sections using laser capture microdissection and label-free LC-MS was used to quantify the proteins present. 48 proteins were consistently enriched in amyloid plaques in EOAD and DS. Many of these proteins were more significantly enriched in amyloid plaques than Aβ. The most enriched proteins in amyloid plaques in both EOAD and DS were: COL25A1, SMOC1, MDK, NTN1, OLFML3 and HTRA1. Endosomal/lysosomal proteins were particularly highly enriched in amyloid plaques. Fluorescent immunohistochemistry was used to validate the enrichment of four proteins in amyloid plaques (moesin, ezrin, ARL8B and SMOC1) and to compare the amount of total Aβ, Aβ40, Aβ42, phosphorylated Aβ, pyroglutamate Aβ species and oligomeric species in EOAD and DS. These studies showed that phosphorylated Aβ, pyroglutamate Aβ species and SMOC1 were significantly higher in DS plaques, while oligomers were significantly higher in EOAD. Overall, we observed that amyloid plaques in EOAD and DS largely contained the same proteins, however the amount of enrichment of some proteins was different in EOAD and DS. Our study highlights the significant enrichment of many proteins in amyloid plaques, many of which may be potential therapeutic targets and/or biomarkers for AD.
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Affiliation(s)
- Eleanor Drummond
- Brain and Mind Centre and School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, 94 Mallett Street, Camperdown, NSW, Australia.
- Centre for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, Science Building, Rm 1017, 435 East 30th Street, New York, NY, 10016, USA.
| | - Tomas Kavanagh
- Brain and Mind Centre and School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, 94 Mallett Street, Camperdown, NSW, Australia
| | - Geoffrey Pires
- Centre for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, Science Building, Rm 1017, 435 East 30th Street, New York, NY, 10016, USA
| | - Mitchell Marta-Ariza
- Centre for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, Science Building, Rm 1017, 435 East 30th Street, New York, NY, 10016, USA
| | - Evgeny Kanshin
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY, USA
| | - Shruti Nayak
- Merck & Co., Inc, Computational & Structural Chemistry, Kenilworth, NJ, USA
| | - Arline Faustin
- Centre for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, Science Building, Rm 1017, 435 East 30th Street, New York, NY, 10016, USA
| | - Valentin Berdah
- Centre for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, Science Building, Rm 1017, 435 East 30th Street, New York, NY, 10016, USA
| | - Beatrix Ueberheide
- Centre for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, Science Building, Rm 1017, 435 East 30th Street, New York, NY, 10016, USA
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Thomas Wisniewski
- Centre for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, Science Building, Rm 1017, 435 East 30th Street, New York, NY, 10016, USA.
- Departments of Pathology and Psychiatry, Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, USA.
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14
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Recent Advances in Understanding of Alzheimer's Disease Progression through Mass Spectrometry-Based Metabolomics. PHENOMICS (CHAM, SWITZERLAND) 2022; 2:1-17. [PMID: 35656096 PMCID: PMC9159642 DOI: 10.1007/s43657-021-00036-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Alzheimer's disease (AD) is the leading cause of dementia in the aging population, but despite extensive research, there is no consensus on the biological cause of AD. While AD research is dominated by protein/peptide-centric research based on the amyloid hypothesis, a theory that designates dysfunction in beta-amyloid production, accumulation, or disposal as the primary cause of AD, many studies focus on metabolomics as a means of understanding the biological processes behind AD progression. In this review, we discuss mass spectrometry (MS)-based AD metabolomics studies, including sample type and preparation, mass spectrometry specifications, and data analysis, as well as biological insights gleaned from these studies, with the hope of informing future AD metabolomic studies.
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15
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Haytural H, Jordà-Siquier T, Winblad B, Mulle C, Tjernberg LO, Granholm AC, Frykman S, Barthet G. Distinctive alteration of presynaptic proteins in the outer molecular layer of the dentate gyrus in Alzheimer's disease. Brain Commun 2021; 3:fcab079. [PMID: 34013204 PMCID: PMC8117432 DOI: 10.1093/braincomms/fcab079] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/15/2021] [Accepted: 03/05/2021] [Indexed: 12/11/2022] Open
Abstract
Synaptic degeneration has been reported as one of the best pathological correlates of cognitive deficits in Alzheimer’s disease. However, the location of these synaptic alterations within hippocampal sub-regions, the vulnerability of the presynaptic versus postsynaptic compartments, and the biological mechanisms for these impairments remain unknown. Here, we performed immunofluorescence labelling of different synaptic proteins in fixed and paraffin-embedded human hippocampal sections and report reduced levels of several presynaptic proteins of the neurotransmitter release machinery (complexin-1, syntaxin-1A, synaptotagmin-1 and synaptogyrin-1) in Alzheimer’s disease cases. The deficit was restricted to the outer molecular layer of the dentate gyrus, whereas other hippocampal sub-fields were preserved. Interestingly, standard markers of postsynaptic densities (SH3 and multiple ankyrin repeat domains protein 2) and dendrites (microtubule-associated protein 2) were unaltered, as well as the relative number of granule cells in the dentate gyrus, indicating that the deficit is preferentially presynaptic. Notably, staining for the axonal components, myelin basic protein, SMI-312 and Tau, was unaffected, suggesting that the local presynaptic impairment does not result from axonal loss or alterations of structural proteins of axons. There was no correlation between the reduction in presynaptic proteins in the outer molecular layer and the extent of the amyloid load or of the dystrophic neurites expressing phosphorylated forms of Tau. Altogether, this study highlights the distinctive vulnerability of the outer molecular layer of the dentate gyrus and supports the notion of presynaptic failure in Alzheimer’s disease.
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Affiliation(s)
- Hazal Haytural
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Karolinska Institutet, 171 64 Solna, Sweden
| | - Tomàs Jordà-Siquier
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, F-33000 Bordeaux, France
| | - Bengt Winblad
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Karolinska Institutet, 171 64 Solna, Sweden.,Karolinska University Hospital, Theme Aging, 141 86 Huddinge, Sweden
| | - Christophe Mulle
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, F-33000 Bordeaux, France
| | - Lars O Tjernberg
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Karolinska Institutet, 171 64 Solna, Sweden
| | - Ann-Charlotte Granholm
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Karolinska Institutet, 171 64 Solna, Sweden.,Knoebel Institute for Healthy Aging, University of Denver, Denver 80208, CO, USA
| | - Susanne Frykman
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Karolinska Institutet, 171 64 Solna, Sweden
| | - Gaël Barthet
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, F-33000 Bordeaux, France
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16
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Li X, Tsolis KC, Koper MJ, Ronisz A, Ospitalieri S, von Arnim CAF, Vandenberghe R, Tousseyn T, Scheuerle A, Economou A, Carpentier S, Otto M, Thal DR. Sequence of proteome profiles in preclinical and symptomatic Alzheimer's disease. Alzheimers Dement 2021; 17:946-958. [PMID: 33871169 DOI: 10.1002/alz.12345] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 03/03/2021] [Accepted: 03/11/2021] [Indexed: 12/15/2022]
Abstract
Proteome profile changes in Alzheimer's disease (AD) brains have been reported. However, it is unclear whether they represent a continuous process, or whether there is a sequential involvement of distinct proteins. To address this question, we used mass spectrometry. We analyzed soluble, dispersible, sodium dodecyl sulfate, and formic acid fractions of neocortex homogenates (mainly Brodmann area 17-19) from 18 pathologically diagnosed preclinical AD, 17 symptomatic AD, and 18 cases without signs of neurodegeneration. By doing so, we identified four groups of AD-related proteins being changed in levels in preclinical and symptomatic AD cases: early-responding, late-responding, gradually-changing, and fraction-shifting proteins. Gene ontology analysis of these proteins and all known AD-risk/causative genes identified vesicle endocytosis and the secretory pathway-related processes as an early-involved AD component. In conclusion, our findings suggest that subtle changes involving the secretory pathway and endocytosis precede severe proteome changes in symptomatic AD as part of the preclinical phase of AD. The respective early-responding proteins may also contribute to synaptic vesicle cycle alterations in symptomatic AD.
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Affiliation(s)
- Xiaohang Li
- Laboratory for Neuropathology, Department of Imaging and Pathology, KU Leuven (University of Leuven), Leuven, Belgium.,Leuven Brain Institute (LBI), KU Leuven (University of Leuven), Leuven, Belgium
| | - Konstantinos C Tsolis
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology, KU Leuven (University of Leuven), Leuven, Belgium
| | - Marta J Koper
- Laboratory for Neuropathology, Department of Imaging and Pathology, KU Leuven (University of Leuven), Leuven, Belgium.,Leuven Brain Institute (LBI), KU Leuven (University of Leuven), Leuven, Belgium.,Laboratory for the Research of Neurodegenerative Diseases, Department of Neurosciences, KU Leuven (University of Leuven), Leuven, Belgium.,Center for Brain and Disease Research, VIB, Leuven, Belgium
| | - Alicja Ronisz
- Laboratory for Neuropathology, Department of Imaging and Pathology, KU Leuven (University of Leuven), Leuven, Belgium.,Leuven Brain Institute (LBI), KU Leuven (University of Leuven), Leuven, Belgium
| | - Simona Ospitalieri
- Laboratory for Neuropathology, Department of Imaging and Pathology, KU Leuven (University of Leuven), Leuven, Belgium.,Leuven Brain Institute (LBI), KU Leuven (University of Leuven), Leuven, Belgium
| | - Christine A F von Arnim
- Department of Neurology, University of Ulm, Ulm, Germany.,Department of Geriatrics, University Medical Center Göttingen, Göttingen, Germany
| | - Rik Vandenberghe
- Department of Neurology, UZ Leuven (University Hospitals Leuven), Leuven, Belgium.,Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven (University of Leuven), Leuven, Belgium
| | - Thomas Tousseyn
- Department of Pathology, UZ Leuven (University Hospitals Leuven), Leuven, Belgium
| | | | - Anastassios Economou
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology, KU Leuven (University of Leuven), Leuven, Belgium
| | - Sebastien Carpentier
- BIOMED facility for SYstems BIOlogy based MAss spectrometry, KU Leuven (University of Leuven), Leuven, Belgium
| | - Markus Otto
- Department of Neurology, University of Ulm, Ulm, Germany
| | - Dietmar Rudolf Thal
- Laboratory for Neuropathology, Department of Imaging and Pathology, KU Leuven (University of Leuven), Leuven, Belgium.,Leuven Brain Institute (LBI), KU Leuven (University of Leuven), Leuven, Belgium.,Department of Pathology, UZ Leuven (University Hospitals Leuven), Leuven, Belgium
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17
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Jain AP, Sathe G. Proteomics Landscape of Alzheimer's Disease. Proteomes 2021; 9:proteomes9010013. [PMID: 33801961 PMCID: PMC8005944 DOI: 10.3390/proteomes9010013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/02/2021] [Accepted: 03/08/2021] [Indexed: 01/22/2023] Open
Abstract
Alzheimer’s disease (AD) is the most prevalent form of dementia, and the numbers of AD patients are expected to increase as human life expectancy improves. Deposition of β-amyloid protein (Aβ) in the extracellular matrix and intracellular neurofibrillary tangles are molecular hallmarks of the disease. Since the precise pathophysiology of AD has not been elucidated yet, effective treatment is not available. Thus, understanding the disease pathology, as well as identification and development of valid biomarkers, is imperative for early diagnosis as well as for monitoring disease progression and therapeutic responses. Keeping this goal in mind several studies using quantitative proteomics platform have been carried out on both clinical specimens including the brain, cerebrospinal fluid (CSF), plasma and on animal models of AD. In this review, we summarize the mass spectrometry (MS)-based proteomics studies on AD and discuss the discovery as well as validation stages in brief to identify candidate biomarkers.
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Affiliation(s)
- Ankit P. Jain
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India;
| | - Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India;
- Manipal Academy of Higher Education (MAHE), Manipal 576104, India
- Correspondence:
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18
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Shulgin AA, Lebedev TD, Prassolov VS, Spirin PV. Plasmolipin and Its Role in Cell Processes. Mol Biol 2021; 55:773-785. [PMID: 34955555 PMCID: PMC8682038 DOI: 10.1134/s0026893321050113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/26/2021] [Accepted: 04/05/2021] [Indexed: 12/04/2022]
Abstract
The mechanisms involved in the origin and development of malignant and neurodegenerative diseases are an important area of modern biomedicine. A crucial task is to identify new molecular markers that are associated with rearrangements of intracellular signaling and can be used for prognosis and the development of effective treatment approaches. The proteolipid plasmolipin (PLLP) is a possible marker. PLLP is a main component of the myelin sheath and plays an important role in the development and normal function of the nervous system. PLLP is involved in intracellular transport, lipid raft formation, and Notch signaling. PLLP is presumably involved in various disorders, such as cancer, schizophrenia, Alzheimer's disease, and type 2 diabetes mellitus. PLLP and its homologs were identified as possible virus entry receptors. The review summarizes the data on the PLLP structure, normal functions, and role in diseases.
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Affiliation(s)
- A. A. Shulgin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia ,Moscow Institute of Physics and Technology (State University), 141701 Dolgoprudny, Moscow oblast Russia
| | - T. D. Lebedev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - V. S. Prassolov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - P. V. Spirin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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19
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Györffy BA, Tóth V, Török G, Gulyássy P, Kovács RÁ, Vadászi H, Micsonai A, Tóth ME, Sántha M, Homolya L, Drahos L, Juhász G, Kékesi KA, Kardos J. Synaptic mitochondrial dysfunction and septin accumulation are linked to complement-mediated synapse loss in an Alzheimer's disease animal model. Cell Mol Life Sci 2020; 77:5243-5258. [PMID: 32034429 PMCID: PMC7671981 DOI: 10.1007/s00018-020-03468-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 12/25/2019] [Accepted: 01/21/2020] [Indexed: 12/21/2022]
Abstract
Synaptic functional disturbances with concomitant synapse loss represent central pathological hallmarks of Alzheimer's disease. Excessive accumulation of cytotoxic amyloid oligomers is widely recognized as a key event that underlies neurodegeneration. Certain complement components are crucial instruments of widespread synapse loss because they can tag synapses with functional impairments leading to their engulfment by microglia. However, an exact understanding of the affected synaptic functions that predispose to complement-mediated synapse elimination is lacking. Therefore, we conducted systematic proteomic examinations on synaptosomes prepared from an amyloidogenic mouse model of Alzheimer's disease (APP/PS1). Synaptic fractions were separated according to the presence of the C1q-tag using fluorescence-activated synaptosome sorting and subjected to proteomic comparisons. The results raised the decline of mitochondrial functions in the C1q-tagged synapses of APP/PS1 mice based on enrichment analyses, which was verified using flow cytometry. Additionally, proteomics results revealed extensive alterations in the level of septin protein family members, which are known to dynamically form highly organized pre- and postsynaptic supramolecular structures, thereby affecting synaptic transmission. High-resolution microscopy investigations demonstrated that synapses with considerable amounts of septin-3 and septin-5 show increased accumulation of C1q in APP/PS1 mice compared to the wild-type ones. Moreover, a strong positive correlation was apparent between synaptic septin-3 levels and C1q deposition as revealed via flow cytometry and confocal microscopy examinations. In sum, our results imply that deterioration of synaptic mitochondrial functions and alterations in the organization of synaptic septins are associated with complement-dependent synapse loss in Alzheimer's disease.
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Affiliation(s)
- Balázs A Györffy
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
- Laboratory of Proteomics, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Vilmos Tóth
- Laboratory of Proteomics, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
- Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - György Török
- Molecular Cell Biology Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences Centre of Excellence, Budapest, Hungary
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Péter Gulyássy
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Réka Á Kovács
- Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Henrietta Vadászi
- Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - András Micsonai
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
- Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Melinda E Tóth
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Miklós Sántha
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - László Homolya
- Molecular Cell Biology Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences Centre of Excellence, Budapest, Hungary
| | - László Drahos
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Gábor Juhász
- Laboratory of Proteomics, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
- CRU Hungary Ltd., Göd, Hungary
| | - Katalin A Kékesi
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
- Laboratory of Proteomics, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
- Department of Physiology and Neurobiology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - József Kardos
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary.
- Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary.
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20
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Stepler KE, Mahoney ER, Kofler J, Hohman TJ, Lopez OL, Robinson RAS. Inclusion of African American/Black adults in a pilot brain proteomics study of Alzheimer's disease. Neurobiol Dis 2020; 146:105129. [PMID: 33049317 PMCID: PMC7990397 DOI: 10.1016/j.nbd.2020.105129] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/02/2020] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease (AD) disproportionately affects certain racial and ethnic subgroups, such as African American/Black and Hispanic adults. Genetic, comorbid, and socioeconomic risk factors contribute to this disparity; however, the molecular contributions have been largely unexplored. Herein, we conducted a pilot proteomics study of postmortem brains from African American/Black and non-Hispanic White adults neuropathologically diagnosed with AD compared to closely-matched cognitively normal individuals. Examination of hippocampus, inferior parietal lobule, and globus pallidus regions using quantitative proteomics resulted in 568 differentially-expressed proteins in AD. These proteins were consistent with the literature and included glial fibrillary acidic protein, peroxiredoxin-1, and annexin A5. In addition, 351 novel proteins in AD were identified, which could partially be due to cohort diversity. From linear regression analyses, we identified 185 proteins with significant race x diagnosis interactions across various brain regions. These differences generally were reflective of differential expression of proteins in AD that occurred in only a single racial/ethnic group. Overall, this pilot study suggests that disease understanding can be furthered by including diversity in racial/ethnic groups; however, this must be done on a larger scale.
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Affiliation(s)
- Kaitlyn E Stepler
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, United States of America
| | - Emily R Mahoney
- Vanderbilt Memory & Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN 37212, United States of America; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, United States of America
| | - Julia Kofler
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, United States of America
| | - Timothy J Hohman
- Vanderbilt Memory & Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN 37212, United States of America; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, United States of America; Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232, United States of America; Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, TN 37232, United States of America
| | - Oscar L Lopez
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA 15213, United States of America; Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, United States of America
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, United States of America; Vanderbilt Memory & Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN 37212, United States of America; Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232, United States of America; Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, TN 37232, United States of America; Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37232, United States of America.
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21
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Chung D, Shum A, Caraveo G. GAP-43 and BASP1 in Axon Regeneration: Implications for the Treatment of Neurodegenerative Diseases. Front Cell Dev Biol 2020; 8:567537. [PMID: 33015061 PMCID: PMC7494789 DOI: 10.3389/fcell.2020.567537] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/14/2020] [Indexed: 01/06/2023] Open
Abstract
Growth-associated protein-43 (GAP-43) and brain acid-soluble protein 1 (BASP1) regulate actin dynamics and presynaptic vesicle cycling at axon terminals, thereby facilitating axonal growth, regeneration, and plasticity. These functions highly depend on changes in GAP-43 and BASP1 expression levels and post-translational modifications such as phosphorylation. Interestingly, examinations of GAP-43 and BASP1 in neurodegenerative diseases reveal alterations in their expression and phosphorylation profiles. This review provides an overview of the structural properties, regulations, and functions of GAP-43 and BASP1, highlighting their involvement in neural injury response and regeneration. By discussing GAP-43 and BASP1 in the context of neurodegenerative diseases, we also explore the therapeutic potential of modulating their activities to compensate for neuron loss in neurodegenerative diseases.
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Affiliation(s)
- Daayun Chung
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Andrew Shum
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Gabriela Caraveo
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
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22
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Rahman MA, Hossain S, Abdullah N, Aminudin N. Brain proteomics links oxidative stress with metabolic and cellular stress response proteins in behavioural alteration of Alzheimer's disease model rats. AIMS Neurosci 2020; 6:299-315. [PMID: 32341985 PMCID: PMC7179348 DOI: 10.3934/neuroscience.2019.4.299] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/28/2019] [Indexed: 11/18/2022] Open
Abstract
Alzheimer's disease (AD) impairs memory and learning related behavioural performances of the affected person. Compared with the controls, memory and learning related behavioural performances of the AD model rats followed by hippocampal proteomics had been observed in the present study. In the eight armed radial maze, altered performance of the AD rats had been observed. Using liquid chromatography coupled tandem mass spectrometry (LC-MS/MS), 822 proteins had been identified with protein threshold at 95.0%, minimum peptide of 2 and peptide threshold at 0.1% FDR. Among them, 329 proteins were differentially expressed with statistical significance (P < 0.05). Among the significantly regulated (P < 0.05) 329 proteins, 289 met the criteria of fold change (LogFC of 1.5) cut off value. Number of proteins linked with AD, oxidative stress (OS) and hypercholesterolemia was 59, 20 and 12, respectively. Number of commonly expressed proteins was 361. The highest amount of proteins differentially expressed in the AD rats were those involved in metabolic processes followed by those linked with OS. Most notable was the perturbed state of the cholesterol metabolizing proteins in the AD group. Current findings suggest that proteins associated with oxidative stress, glucose and cholesterol metabolism and cellular stress response are among the mostly affected proteins in AD subjects. Thus, novel therapeutic approaches targeting these proteins could be strategized to withstand the ever increasing global AD burden.
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Affiliation(s)
- Mohammad Azizur Rahman
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka, Bangladesh.,Mushroom Research Centre, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Shahdat Hossain
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Noorlidah Abdullah
- Mushroom Research Centre, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Norhaniza Aminudin
- Mushroom Research Centre, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia.,University of Malaya Centre for Proteomics Research, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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23
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Tremblay C, François A, Delay C, Freland L, Vandal M, Bennett DA, Calon F. Association of Neuropathological Markers in the Parietal Cortex With Antemortem Cognitive Function in Persons With Mild Cognitive Impairment and Alzheimer Disease. J Neuropathol Exp Neurol 2020; 76:70-88. [PMID: 28158844 PMCID: PMC7526851 DOI: 10.1093/jnen/nlw109] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The associations between cognitive function and neuropathological markers in patients with mild cognitive impairment (MCI) and Alzheimer disease (AD) remain only partly defined. We investigated relationships between antemortem global cognitive scores and β-amyloid (Aβ), tau, TDP-43, synaptic proteins and other key AD neuropathological markers assessed by biochemical approaches in postmortem anterior parietal cortex samples from 36 subjects (12 MCI, 12 AD and 12 not cognitively impaired) from the Religious Orders Study. Overall, the strongest negative correlation coefficients associated with global cognitive scores were obtained for insoluble phosphorylated tau (r2 = -0.484), insoluble Aβ42 (r2 = -0.389) and neurofibrillary tangle counts (r2 = -0.494) (all p < 0.001). Robust inverse associations with cognition scores were also established for TDP-43-positive cytoplasmic inclusions (r2 = -0.476), total insoluble tau (r2 = -0.385) and Aβ plaque counts (r2 = -0.426). Sarkosyl (SK)- or formic acid (FA)-extracted tau showed similar interrelations. On the other hand, synaptophysin (r2 = +0.335), pS403/404 TDP-43 (r2 = +0.265) and septin-3 (r2 = +0.257) proteins positively correlated with cognitive scores. This study suggests that tau and Aβ42 in their insoluble aggregated forms, synaptic proteins and TDP-43 are the markers in the parietal cortex that are most strongly associated with cognitive function. This further substantiates the relevance of investigating these markers to understand the pathogenesis of AD and develop therapeutic tools.
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Affiliation(s)
- Cyntia Tremblay
- From the Faculté de pharmacie, Université Laval, Québec, QC, Canada (CT, AF, LF, MV, FC); Centre Hospitalier Universitaire de Québec (CHU-Q) Research Center, Neuroscience Axis, Québec, QC, Canada (CT, AF, LF, MV, FC); "Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement" (RID-AGE) Research Group, University of Lille, INSERM U1167, Lille University Medical Center, Institut Pasteur de Lille, Lille, France (CD); and Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL (DAB)
| | - Arnaud François
- From the Faculté de pharmacie, Université Laval, Québec, QC, Canada (CT, AF, LF, MV, FC); Centre Hospitalier Universitaire de Québec (CHU-Q) Research Center, Neuroscience Axis, Québec, QC, Canada (CT, AF, LF, MV, FC); "Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement" (RID-AGE) Research Group, University of Lille, INSERM U1167, Lille University Medical Center, Institut Pasteur de Lille, Lille, France (CD); and Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL (DAB)
| | - Charlotte Delay
- From the Faculté de pharmacie, Université Laval, Québec, QC, Canada (CT, AF, LF, MV, FC); Centre Hospitalier Universitaire de Québec (CHU-Q) Research Center, Neuroscience Axis, Québec, QC, Canada (CT, AF, LF, MV, FC); "Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement" (RID-AGE) Research Group, University of Lille, INSERM U1167, Lille University Medical Center, Institut Pasteur de Lille, Lille, France (CD); and Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL (DAB)
| | - Laure Freland
- From the Faculté de pharmacie, Université Laval, Québec, QC, Canada (CT, AF, LF, MV, FC); Centre Hospitalier Universitaire de Québec (CHU-Q) Research Center, Neuroscience Axis, Québec, QC, Canada (CT, AF, LF, MV, FC); "Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement" (RID-AGE) Research Group, University of Lille, INSERM U1167, Lille University Medical Center, Institut Pasteur de Lille, Lille, France (CD); and Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL (DAB)
| | - Milène Vandal
- From the Faculté de pharmacie, Université Laval, Québec, QC, Canada (CT, AF, LF, MV, FC); Centre Hospitalier Universitaire de Québec (CHU-Q) Research Center, Neuroscience Axis, Québec, QC, Canada (CT, AF, LF, MV, FC); "Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement" (RID-AGE) Research Group, University of Lille, INSERM U1167, Lille University Medical Center, Institut Pasteur de Lille, Lille, France (CD); and Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL (DAB)
| | - David A Bennett
- From the Faculté de pharmacie, Université Laval, Québec, QC, Canada (CT, AF, LF, MV, FC); Centre Hospitalier Universitaire de Québec (CHU-Q) Research Center, Neuroscience Axis, Québec, QC, Canada (CT, AF, LF, MV, FC); "Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement" (RID-AGE) Research Group, University of Lille, INSERM U1167, Lille University Medical Center, Institut Pasteur de Lille, Lille, France (CD); and Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL (DAB)
| | - Frédéric Calon
- From the Faculté de pharmacie, Université Laval, Québec, QC, Canada (CT, AF, LF, MV, FC); Centre Hospitalier Universitaire de Québec (CHU-Q) Research Center, Neuroscience Axis, Québec, QC, Canada (CT, AF, LF, MV, FC); "Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement" (RID-AGE) Research Group, University of Lille, INSERM U1167, Lille University Medical Center, Institut Pasteur de Lille, Lille, France (CD); and Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL (DAB)
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24
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Haytural H, Mermelekas G, Emre C, Nigam SM, Carroll SL, Winblad B, Bogdanovic N, Barthet G, Granholm AC, Orre LM, Tjernberg LO, Frykman S. The Proteome of the Dentate Terminal Zone of the Perforant Path Indicates Presynaptic Impairment in Alzheimer Disease. Mol Cell Proteomics 2020; 19:128-141. [PMID: 31699905 PMCID: PMC6944231 DOI: 10.1074/mcp.ra119.001737] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/05/2019] [Indexed: 01/13/2023] Open
Abstract
Synaptic dysfunction is an early pathogenic event in Alzheimer disease (AD) that contributes to network disturbances and cognitive decline. Some synapses are more vulnerable than others, including the synapses of the perforant path, which provides the main excitatory input to the hippocampus. To elucidate the molecular mechanisms underlying the dysfunction of these synapses, we performed an explorative proteomic study of the dentate terminal zone of the perforant path. The outer two-thirds of the molecular layer of the dentate gyrus, where the perforant path synapses are located, was microdissected from five subjects with AD and five controls. The microdissected tissues were dissolved and digested by trypsin. Peptides from each sample were labeled with different isobaric tags, pooled together and pre-fractionated into 72 fractions by high-resolution isoelectric focusing. Each fraction was then analyzed by liquid chromatography-mass spectrometry. We quantified the relative expression levels of 7322 proteins, whereof 724 showed significantly altered levels in AD. Our comprehensive data analysis using enrichment and pathway analyses strongly indicated that presynaptic signaling, such as exocytosis and synaptic vesicle cycle processes, is severely disturbed in this area in AD, whereas postsynaptic proteins remained unchanged. Among the significantly altered proteins, we selected three of the most downregulated synaptic proteins; complexin-1, complexin-2 and synaptogyrin-1, for further validation, using a new cohort consisting of six AD and eight control cases. Semi-quantitative analysis of immunohistochemical staining confirmed decreased levels of complexin-1, complexin-2 and synaptogyrin-1 in the outer two-thirds of the molecular layer of the dentate gyrus in AD. Our in-depth proteomic analysis provides extensive knowledge on the potential molecular mechanism underlying synaptic dysfunction related to AD and supports that presynaptic alterations are more important than postsynaptic changes in early stages of the disease. The specific synaptic proteins identified could potentially be targeted to halt synaptic dysfunction in AD.
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Affiliation(s)
- Hazal Haytural
- Division of Neurogeriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Solna, Sweden.
| | - Georgios Mermelekas
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Ceren Emre
- Division of Neurogeriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Solna, Sweden
| | | | - Steven L Carroll
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Bengt Winblad
- Division of Neurogeriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Solna, Sweden; Karolinska University Hospital, Theme Aging, Stockholm, Sweden
| | - Nenad Bogdanovic
- Karolinska University Hospital, Theme Aging, Stockholm, Sweden; Division of Clinical geriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Huddinge, Sweden
| | - Gaël Barthet
- Interdisciplinary Institute for Neuroscience, CNRS UMR, Bordeaux, France; University of Bordeaux, Bordeaux, France
| | - Ann-Charlotte Granholm
- Division of Neurogeriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Solna, Sweden; Knoebel Institute for Healthy Aging, University of Denver, Denver, Colorado
| | - Lukas M Orre
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Lars O Tjernberg
- Division of Neurogeriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Solna, Sweden
| | - Susanne Frykman
- Division of Neurogeriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Solna, Sweden
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25
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Hesse R, Hurtado ML, Jackson RJ, Eaton SL, Herrmann AG, Colom-Cadena M, Tzioras M, King D, Rose J, Tulloch J, McKenzie CA, Smith C, Henstridge CM, Lamont D, Wishart TM, Spires-Jones TL. Comparative profiling of the synaptic proteome from Alzheimer's disease patients with focus on the APOE genotype. Acta Neuropathol Commun 2019; 7:214. [PMID: 31862015 PMCID: PMC6925519 DOI: 10.1186/s40478-019-0847-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 11/13/2019] [Indexed: 12/13/2022] Open
Abstract
Degeneration of synapses in Alzheimer's disease (AD) strongly correlates with cognitive decline, and synaptic pathology contributes to disease pathophysiology. We recently observed that the strongest genetic risk factor for sporadic AD, apolipoprotein E epsilon 4 (APOE4), is associated with exacerbated synapse loss and synaptic accumulation of oligomeric amyloid beta in human AD brain. To begin to understand the molecular cascades involved in synapse loss in AD and how this is mediated by APOE, and to generate a resource of knowledge of changes in the synaptic proteome in AD, we conducted a proteomic screen and systematic in silico analysis of synaptoneurosome preparations from temporal and occipital cortices of human AD and control subjects with known APOE gene status. We examined brain tissue from 33 subjects (7-10 per group). We pooled tissue from all subjects in each group for unbiased proteomic analyses followed by validation with individual case samples. Our analysis identified over 5500 proteins in human synaptoneurosomes and highlighted disease, brain region, and APOE-associated changes in multiple molecular pathways including a decreased abundance in AD of proteins important for synaptic and mitochondrial function and an increased abundance of proteins involved in neuroimmune interactions and intracellular signaling.
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26
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Gomez L, Odom GJ, Young JI, Martin ER, Liu L, Chen X, Griswold AJ, Gao Z, Zhang L, Wang L. coMethDMR: accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies with continuous phenotypes. Nucleic Acids Res 2019; 47:e98. [PMID: 31291459 PMCID: PMC6753499 DOI: 10.1093/nar/gkz590] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 06/09/2019] [Accepted: 07/08/2019] [Indexed: 12/12/2022] Open
Abstract
Recent technology has made it possible to measure DNA methylation profiles in a cost-effective and comprehensive genome-wide manner using array-based technology for epigenome-wide association studies. However, identifying differentially methylated regions (DMRs) remains a challenging task because of the complexities in DNA methylation data. Supervised methods typically focus on the regions that contain consecutive highly significantly differentially methylated CpGs in the genome, but may lack power for detecting small but consistent changes when few CpGs pass stringent significance threshold after multiple comparison. Unsupervised methods group CpGs based on genomic annotations first and then test them against phenotype, but may lack specificity because the regional boundaries of methylation are often not well defined. We present coMethDMR, a flexible, powerful, and accurate tool for identifying DMRs. Instead of testing all CpGs within a genomic region, coMethDMR carries out an additional step that selects co-methylated sub-regions first. Next, coMethDMR tests association between methylation levels within the sub-region and phenotype via a random coefficient mixed effects model that models both variations between CpG sites within the region and differential methylation simultaneously. coMethDMR offers well-controlled Type I error rate, improved specificity, focused testing of targeted genomic regions, and is available as an open-source R package.
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Affiliation(s)
- Lissette Gomez
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Gabriel J Odom
- Division of Biostatistics, Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Juan I Young
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA.,Dr. John T. Macdonald Foundation, Department of Human Genetics, University of Miami, Miami, FL 33136, USA
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA.,Dr. John T. Macdonald Foundation, Department of Human Genetics, University of Miami, Miami, FL 33136, USA
| | - Lizhong Liu
- Division of Biostatistics, Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Xi Chen
- Division of Biostatistics, Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA.,Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Anthony J Griswold
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA.,Dr. John T. Macdonald Foundation, Department of Human Genetics, University of Miami, Miami, FL 33136, USA
| | - Zhen Gao
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Lanyu Zhang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Lily Wang
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA.,Division of Biostatistics, Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA.,Dr. John T. Macdonald Foundation, Department of Human Genetics, University of Miami, Miami, FL 33136, USA.,Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
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27
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Kim DK, Han D, Park J, Choi H, Park JC, Cha MY, Woo J, Byun MS, Lee DY, Kim Y, Mook-Jung I. Deep proteome profiling of the hippocampus in the 5XFAD mouse model reveals biological process alterations and a novel biomarker of Alzheimer's disease. Exp Mol Med 2019; 51:1-17. [PMID: 31727875 PMCID: PMC6856180 DOI: 10.1038/s12276-019-0326-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 06/20/2019] [Accepted: 07/24/2019] [Indexed: 12/12/2022] Open
Abstract
Alzheimer’s disease (AD), which is the most common type of dementia, is characterized by the deposition of extracellular amyloid plaques. To understand the pathophysiology of the AD brain, the assessment of global proteomic dynamics is required. Since the hippocampus is a major region affected in the AD brain, we performed hippocampal analysis and identified proteins that are differentially expressed between wild-type and 5XFAD model mice via LC-MS methods. To reveal the relationship between proteomic changes and the progression of amyloid plaque deposition in the hippocampus, we analyzed the hippocampal proteome at two ages (5 and 10 months). We identified 9,313 total proteins and 1411 differentially expressed proteins (DEPs) in 5- and 10-month-old wild-type and 5XFAD mice. We designated a group of proteins showing the same pattern of changes as amyloid beta (Aβ) as the Aβ-responsive proteome. In addition, we examined potential biomarkers by investigating secretory proteins from the Aβ-responsive proteome. Consequently, we identified vitamin K-dependent protein S (PROS1) as a novel microglia-derived biomarker candidate in the hippocampus of 5XFAD mice. Moreover, we confirmed that the PROS1 level in the serum of 5XFAD mice increases as the disease progresses. An increase in PROS1 is also observed in the sera of AD patients and shows a close correlation with AD neuroimaging markers in humans. Therefore, our quantitative proteome data obtained from 5XFAD model mice successfully predicted AD-related biological alterations and suggested a novel protein biomarker for AD. A protein newly implicated in Alzheimer’s disease could serve as a diagnostic biomarker or therapeutic target. A team led by Youngsoo Kim and Inhee Mook-Jung from Seoul National University, South Korea, analyzed all the proteins expressed in the hippocampus, the brain’s memory center, in mice with and without Alzheimer’s-like disease. They identified more than 1,400 proteins differentially expressed between the mouse model of Alzheimer’s and the normal mice. Among these were 36 secretory proteins that tended to increase their levels along with build-up of amyloid-beta, the protein found in clumps in the brains of people with Alzheimer’s. Many already had known links to Alzheimer’s, but the researchers also identified a novel protein called PROS1. Blood samples from Alzheimer’s patients also showed an increase in PROS1 levels, with a close correlation with amyloid-beta build-up in the brain.
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Affiliation(s)
- Dong Kyu Kim
- Department of Biomedical Sciences, Seoul National University, College of Medicine, Seoul, Korea
| | - Dohyun Han
- Proteomics Core Facility, Transdisciplinary Research and Collaboration, Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Joonho Park
- Interdisciplinary Program for Bioengineering, Seoul National University, College of Engineering, Seoul, Korea
| | - Hyunjung Choi
- Interdisciplinary Graduate Program in Genetic Engineering, Seoul National University, Seoul, Korea
| | - Jong-Chan Park
- Department of Biomedical Sciences, Seoul National University, College of Medicine, Seoul, Korea
| | - Moon-Yong Cha
- LG Chem Life Science R&D Campus, Drug Discovery Center, Seoul, Korea
| | - Jongmin Woo
- Department of Biomedical Sciences, Seoul National University, College of Medicine, Seoul, Korea
| | - Min Soo Byun
- Institute of Human Behavioral Medicine, Medical Research Center, Seoul National University, Seoul, Korea
| | - Dong Young Lee
- Department of Psychiatry, Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Neuropsychiatry, Seoul National University Hospital, Seoul, Korea
| | - Youngsoo Kim
- Department of Biomedical Sciences, Seoul National University, College of Medicine, Seoul, Korea. .,Interdisciplinary Program for Bioengineering, Seoul National University, College of Engineering, Seoul, Korea.
| | - Inhee Mook-Jung
- Department of Biomedical Sciences, Seoul National University, College of Medicine, Seoul, Korea.
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28
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Li KW, Ganz AB, Smit AB. Proteomics of neurodegenerative diseases: analysis of human post-mortem brain. J Neurochem 2019; 151:435-445. [PMID: 30289976 PMCID: PMC6899881 DOI: 10.1111/jnc.14603] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/15/2018] [Accepted: 10/01/2018] [Indexed: 12/12/2022]
Abstract
Dementias are prevalent brain disorders in the aged population. Dementias pose major socio-medical burden, but currently there is no cure available. Novel proteomics approaches hold promise to identify alterations of the brain proteome that could provide clues on disease etiology, and identify candidate proteins to develop further as a biomarker. In this review, we focus on recent proteomics findings from brains affected with Alzheimer's Disease, Parkinson Disease Dementia, Frontotemporal Dementia, and Amyotrophic Lateral Sclerosis. These studies confirmed known cellular changes, and in addition identified novel proteins that may underlie distinct aspects of the diseases. This article is part of the special issue "Proteomics".
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Affiliation(s)
- K. W. Li
- Department of Molecular and Cellular NeurobiologyCenter for Neurogenomics and Cognitive ResearchAmsterdam NeuroscienceVrije UniversiteitAmsterdamThe Netherlands
| | - Andrea B. Ganz
- Department of Molecular and Cellular NeurobiologyCenter for Neurogenomics and Cognitive ResearchAmsterdam NeuroscienceVrije UniversiteitAmsterdamThe Netherlands
| | - August B. Smit
- Department of Molecular and Cellular NeurobiologyCenter for Neurogenomics and Cognitive ResearchAmsterdam NeuroscienceVrije UniversiteitAmsterdamThe Netherlands
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29
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Huang M, Darvas M, Keene CD, Wang Y. Targeted Quantitative Proteomic Approach for High-Throughput Quantitative Profiling of Small GTPases in Brain Tissues of Alzheimer's Disease Patients. Anal Chem 2019; 91:12307-12314. [PMID: 31460748 PMCID: PMC6939614 DOI: 10.1021/acs.analchem.9b02485] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Neurodegenerative disorders, including Alzheimer's disease (AD), are prevalent among the elderly. Small GTPases of the Ras superfamily are essential regulators of intracellular trafficking and signal transduction. In this study, we develop a targeted quantification method for small GTPase proteins, where the method involves scheduled multiple-reaction monitoring analysis and the use of synthetic stable isotope-labeled peptides as internal standards or surrogate standards. We further applied this method to examine the altered expression of small GTPase proteins in post-mortem frontal cortex tissues from AD patients with different degrees of disease severity. We were able to achieve sensitive and reproducible quantifications of 80 small GTPases in brain tissue samples from 15 patients. Our results revealed substantial up-regulations of several synaptic GTPases, i.e., RAB3A/C, RAB4A/B, and RAB27B, in tissues from patients with higher degrees of AD pathology, suggesting that aberrant synaptic trafficking may modulate the progression of AD. The method should be generally applicable for high-throughput targeted quantification of small GTPase proteins in other tissue and cellular samples.
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Affiliation(s)
- Ming Huang
- Environmental Toxicology Graduate Program and Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Martin Darvas
- Department of Pathology, University of Washington, Seattle, Washington 98104, United States
| | - C. Dirk Keene
- Department of Pathology, University of Washington, Seattle, Washington 98104, United States
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program and Department of Chemistry, University of California, Riverside, California 92521, United States
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30
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Sjödin S, Brinkmalm G, Öhrfelt A, Parnetti L, Paciotti S, Hansson O, Hardy J, Blennow K, Zetterberg H, Brinkmalm A. Endo-lysosomal proteins and ubiquitin CSF concentrations in Alzheimer's and Parkinson's disease. ALZHEIMERS RESEARCH & THERAPY 2019; 11:82. [PMID: 31521194 PMCID: PMC6745076 DOI: 10.1186/s13195-019-0533-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 08/22/2019] [Indexed: 01/17/2023]
Abstract
BACKGROUND Increasing evidence implicates dysfunctional proteostasis and the involvement of the autophagic and endo-lysosomal system and the ubiquitin-proteasome system in neurodegenerative diseases. In Alzheimer's disease (AD), there is an accumulation of autophagic vacuoles within the neurons. In Parkinson's disease (PD), susceptibility has been linked to genes encoding proteins involved in autophagy and lysosomal function, as well as mutations causing lysosomal disorders. Furthermore, both diseases are characterized by the accumulation of protein aggregates. METHODS Proteins associated with endocytosis, lysosomal function, and the ubiquitin-proteasome system were identified in the cerebrospinal fluid (CSF) and targeted by combining solid-phase extraction and parallel reaction monitoring mass spectrometry. In total, 50 peptides from 18 proteins were quantified in three cross-sectional cohorts including AD (N = 61), PD (N = 21), prodromal AD (N = 10), stable mild cognitive impairment (N = 15), and controls (N = 68). RESULTS A pilot study, including subjects selected based on their AD CSF core biomarker concentrations, showed increased concentrations of several targeted proteins in subjects with core biomarker levels indicating AD pathology compared to controls. Next, in a clinically characterized cohort, lower concentrations in CSF of proteins in PD were found compared to subjects with prodromal AD. Further investigation in an additional clinical study again revealed lower concentrations in CSF of proteins in PD compared to controls and AD. CONCLUSION In summary, significantly different peptide CSF concentrations were identified from proteins AP2B1, C9, CTSB, CTSF, GM2A, LAMP1, LAMP2, TCN2, and ubiquitin. Proteins found to have altered concentrations in more than one study were AP2B1, CTSB, CTSF, GM2A, LAMP2, and ubiquitin. Interestingly, given the genetic implication of lysosomal function in PD, we did identify the CSF concentrations of CTSB, CTSF, GM2A, and LAMP2 to be altered. However, we also found differences in proteins associated with endocytosis (AP2B1) and the ubiquitin-proteasome system (ubiquitin). No difference in any peptide CSF concentration was found in clinically characterized subjects with AD compared to controls. In conclusion, CSF analyses of subjects with PD suggest a general lysosomal dysfunction, which resonates well with recent genetic findings, while such changes are minor or absent in AD.
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Affiliation(s)
- Simon Sjödin
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, House V3, SU/Mölndal, SE-43180, Mölndal, Sweden. .,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.
| | - Gunnar Brinkmalm
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, House V3, SU/Mölndal, SE-43180, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Annika Öhrfelt
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, House V3, SU/Mölndal, SE-43180, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Lucilla Parnetti
- Laboratory of Clinical Neurochemistry, Neurology Clinic, University of Perugia, Perugia, Italy
| | - Silvia Paciotti
- Department of Experimental Medicine, University of Perugia, Perugia, Italy.,Laboratory of Clinical Neurochemistry, Department of Medicine, University of Perugia, Perugia, Italy
| | - Oskar Hansson
- Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Lund University, Lund, Sweden.,Memory Clinic, Skåne University Hospital, Malmö, Sweden
| | - John Hardy
- Department of Molecular Neuroscience, University College London Institute of Neurology, Queen Square, London, UK.,UK Dementia Research Institute at UCL, London, UK
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, House V3, SU/Mölndal, SE-43180, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, House V3, SU/Mölndal, SE-43180, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.,Department of Molecular Neuroscience, University College London Institute of Neurology, Queen Square, London, UK.,UK Dementia Research Institute at UCL, London, UK
| | - Ann Brinkmalm
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, House V3, SU/Mölndal, SE-43180, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
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31
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Kannaian B, Sharma B, Phillips M, Chowdhury A, Manimekalai MSS, Adav SS, Ng JTY, Kumar A, Lim S, Mu Y, Sze SK, Grüber G, Pervushin K. Abundant neuroprotective chaperone Lipocalin-type prostaglandin D synthase (L-PGDS) disassembles the Amyloid-β fibrils. Sci Rep 2019; 9:12579. [PMID: 31467325 PMCID: PMC6715741 DOI: 10.1038/s41598-019-48819-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/06/2019] [Indexed: 01/08/2023] Open
Abstract
Misfolding of Amyloid β (Aβ) peptides leads to the formation of extracellular amyloid plaques. Molecular chaperones can facilitate the refolding or degradation of such misfolded proteins. Here, for the first time, we report the unique ability of Lipocalin-type Prostaglandin D synthase (L-PGDS) protein to act as a disaggregase on the pre-formed fibrils of Aβ(1-40), abbreviated as Aβ40, and Aβ(25-35) peptides, in addition to inhibiting the aggregation of Aβ monomers. Furthermore, our proteomics results indicate that L-PGDS can facilitate extraction of several other proteins from the insoluble aggregates extracted from the brain of an Alzheimer's disease patient. In this study, we have established the mode of binding of L-PGDS with monomeric and fibrillar Aβ using Nuclear Magnetic Resonance (NMR) Spectroscopy, Small Angle X-ray Scattering (SAXS), and Transmission Electron Microscopy (TEM). Our results confirm a direct interaction between L-PGDS and monomeric Aβ40 and Aβ(25-35), thereby inhibiting their spontaneous aggregation. The monomeric unstructured Aβ40 binds to L-PGDS via its C-terminus, while the N-terminus remains free which is observed as a new domain in the L-PGDS-Aβ40 complex model.
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Affiliation(s)
- Bhuvaneswari Kannaian
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Bhargy Sharma
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Margaret Phillips
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Anup Chowdhury
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Malathy S S Manimekalai
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Sunil S Adav
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
- Singapore Phenome Centre, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
| | - Justin T Y Ng
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Ambrish Kumar
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, 637459, Singapore
| | - Sierin Lim
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, 637459, Singapore
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Siu K Sze
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Konstantin Pervushin
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
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32
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Yagensky O, Kohansal-Nodehi M, Gunaseelan S, Rabe T, Zafar S, Zerr I, Härtig W, Urlaub H, Chua JJ. Increased expression of heme-binding protein 1 early in Alzheimer's disease is linked to neurotoxicity. eLife 2019; 8:47498. [PMID: 31453805 PMCID: PMC6739868 DOI: 10.7554/elife.47498] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 08/25/2019] [Indexed: 12/15/2022] Open
Abstract
Alzheimer’s disease is the most prevalent neurodegenerative disorder leading to progressive cognitive decline. Despite decades of research, understanding AD progression at the molecular level, especially at its early stages, remains elusive. Here, we identified several presymptomatic AD markers by investigating brain proteome changes over the course of neurodegeneration in a transgenic mouse model of AD (3×Tg-AD). We show that one of these markers, heme-binding protein 1 (Hebp1), is elevated in the brains of both 3×Tg-AD mice and patients affected by rapidly-progressing forms of AD. Hebp1, predominantly expressed in neurons, interacts with the mitochondrial contact site complex (MICOS) and exhibits a perimitochondrial localization. Strikingly, wildtype, but not Hebp1-deficient, neurons showed elevated cytotoxicity in response to heme-induced apoptosis. Increased survivability in Hebp1-deficient neurons is conferred by blocking the activation of the mitochondrial-associated caspase signaling pathway. Taken together, our data highlight a role of Hebp1 in progressive neuronal loss during AD progression.
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Affiliation(s)
- Oleksandr Yagensky
- Research Group Protein Trafficking in Synaptic Development and Function, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | | | - Saravanan Gunaseelan
- Interactomics and Intracellular Trafficking Laboratory, Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Tamara Rabe
- Department of Genes and Behavior, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Saima Zafar
- Biomedical Engineering and Sciences Department, School of Mechanical and Manufacturing Engineering (SMME), National University of Sciences and Technology (NUST), Islamabad, Pakistan.,Clinical Dementia Center, Department of Neurology, German Center for Neurodegenerative Diseases, University Medical Center Göttingen, Göttingen, Germany
| | - Inga Zerr
- Clinical Dementia Center, Department of Neurology, German Center for Neurodegenerative Diseases, University Medical Center Göttingen, Göttingen, Germany
| | - Wolfgang Härtig
- Paul Flechsig Institute for Brain Research, University of Leipzig, Leipzig, Germany
| | - Henning Urlaub
- Research Group Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - John Je Chua
- Research Group Protein Trafficking in Synaptic Development and Function, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Interactomics and Intracellular Trafficking Laboratory, Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,LSI Neurobiology Programme, National University of Singapore, Singapore, Singapore.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
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33
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Bergau N, Maul S, Rujescu D, Simm A, Navarrete Santos A. Reduction of Glycolysis Intermediate Concentrations in the Cerebrospinal Fluid of Alzheimer's Disease Patients. Front Neurosci 2019; 13:871. [PMID: 31496932 PMCID: PMC6713159 DOI: 10.3389/fnins.2019.00871] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 08/02/2019] [Indexed: 12/22/2022] Open
Abstract
The profile of 122 metabolites in the cerebrospinal fluid (CSF) of patients suffering from Alzheimer's disease (AD) and controls was studied. Among the 122 metabolites analyzed, 61 could be detected. Statistically significant differences between the AD and control group were only detected for metabolites of the glycolysis. Thus, accurate quantification of 11 glycolytic metabolites was done. We detected a significant reduction of five of them, namely phosphoenolpyruvate, 2-phosphoglycerate, 3-phosphoglycerate, pyruvate and dihydroxyacetone phosphate in the AD CSF compared to controls. These results correlate with the known reduction of glucose metabolism in the brain of patients with AD and indicate that metabolic analysis of the central carbon metabolism can be a potential tool in AD diagnostic. Although the Receiver operating characteristic (ROC) analyses of the metabolites do not reach the level of the diagnostic informativity of AD biomarkers, the combination of specific glycolysis metabolites with the established biomarkers may lead to an improvement in sensitivity and specificity.
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Affiliation(s)
- Nick Bergau
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Stephan Maul
- Department of Psychiatry, Psychotherapy and Psychosomatics, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Dan Rujescu
- Department of Psychiatry, Psychotherapy and Psychosomatics, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Andreas Simm
- Center for Basic Medical Research, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany.,Clinic for Cardiac Surgery, University Hospital, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Alexander Navarrete Santos
- Center for Basic Medical Research, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany.,Clinic for Cardiac Surgery, University Hospital, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
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34
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Adler P, Mayne J, Walker K, Ning Z, Figeys D. Therapeutic Targeting of Casein Kinase 1δ/ε in an Alzheimer’s Disease Mouse Model. J Proteome Res 2019; 18:3383-3393. [DOI: 10.1021/acs.jproteome.9b00312] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Paula Adler
- Shanghai Institute of Materia Medica−University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Janice Mayne
- Shanghai Institute of Materia Medica−University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Krystal Walker
- Shanghai Institute of Materia Medica−University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Zhibin Ning
- Shanghai Institute of Materia Medica−University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Daniel Figeys
- Shanghai Institute of Materia Medica−University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada
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35
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Drummond E, Goñi F, Liu S, Prelli F, Scholtzova H, Wisniewski T. Potential Novel Approaches to Understand the Pathogenesis and Treat Alzheimer's Disease. J Alzheimers Dis 2019; 64:S299-S312. [PMID: 29562516 DOI: 10.3233/jad-179909] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
There is growing genetic and proteomic data highlighting the complexity of Alzheimer's disease (AD) pathogenesis. Greater use of unbiased "omics" approaches is being increasingly recognized as essential for the future development of effective AD research, that need to better reflect the multiple distinct pathway abnormalities that can drive AD pathology. The track record of success in AD clinical trials thus far has been very poor. In part, this high failure rate has been related to the premature translation of highly successful results in animal models that mirror only limited aspects of AD pathology to humans. We highlight our recent efforts to increase use of human tissue to gain a better understanding of the AD pathogenesis subtype variety and to develop several distinct therapeutic approaches tailored to address this diversity. These therapeutic approaches include the blocking of the Aβ/apoE interaction, stimulation of innate immunity, and the simultaneous blocking of Aβ/tau oligomer toxicity. We believe that future successful therapeutic approaches will need to be combined to better reflect the complexity of the abnormal pathways triggered in AD pathogenesis.
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Affiliation(s)
- Eleanor Drummond
- Department of Neurology, Center for Cognitive Neurology, NYU School of Medicine, New York, NY, USA
| | - Fernando Goñi
- Department of Neurology, Center for Cognitive Neurology, NYU School of Medicine, New York, NY, USA
| | - Shan Liu
- Department of Neurology, Center for Cognitive Neurology, NYU School of Medicine, New York, NY, USA
| | - Frances Prelli
- Department of Neurology, Center for Cognitive Neurology, NYU School of Medicine, New York, NY, USA
| | - Henrieta Scholtzova
- Department of Neurology, Center for Cognitive Neurology, NYU School of Medicine, New York, NY, USA
| | - Thomas Wisniewski
- Departments of Neurology, Pathology and Psychiatry, Center for Cognitive Neurology, NYU School of Medicine, New York, NY, USA
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36
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San Segundo-Acosta P, Montero-Calle A, Fuentes M, Rábano A, Villalba M, Barderas R. Identification of Alzheimer's Disease Autoantibodies and Their Target Biomarkers by Phage Microarrays. J Proteome Res 2019; 18:2940-2953. [PMID: 31136180 DOI: 10.1021/acs.jproteome.9b00258] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The characterization of the humoral response in Alzheimer's disease (AD) patients might aid in detecting the disease at early stages. We have combined phage display and protein microarrays to identify AD autoantibodies and their target biomarkers. After enrichment of the T7 phage display libraries from AD and healthy brain tissue mRNA in AD-specific phages, 1536 monoclonal phages were printed on microarrays to probe them with 8 AD and 8 healthy control sera. A total of 57 phages showed higher seroreactivity in AD. In total, 13 out of the 44 unique sequences displayed on the phages were selected for validation using 68 AD and 52 healthy control sera. Peptides from Anthrax toxin receptor 1, Nuclear protein 1, Glycogen phosphorylase, and Olfactory receptor 8J1 expressed in bacteria as HaloTag fusion proteins showed a statistically significant ability to discriminate between AD patients and controls. The identified panel of AD autoantibodies might provide new insights into the blood-based diagnosis of the disease.
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Affiliation(s)
- Pablo San Segundo-Acosta
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas , Universidad Complutense de Madrid , E-28040 Madrid , Spain.,Chronic Disease Programme (UFIEC) , Instituto de Salud Carlos III , Majadahonda, E-28220 , Madrid , Spain
| | - Ana Montero-Calle
- Chronic Disease Programme (UFIEC) , Instituto de Salud Carlos III , Majadahonda, E-28220 , Madrid , Spain
| | - Manuel Fuentes
- Proteomics Unit , Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL) , 37007 Salamanca , Spain.,Department of Medicine and General Cytometry Service-Nucleus, CIBERONC CB16/12/00400 , Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL) , 37007 Salamanca , Spain
| | - Alberto Rábano
- Alzheimer Disease Research Unit, CIEN Foundation , Queen Sofia Foundation Alzheimer Center , 28031 Madrid , Spain
| | - Mayte Villalba
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas , Universidad Complutense de Madrid , E-28040 Madrid , Spain
| | - Rodrigo Barderas
- Chronic Disease Programme (UFIEC) , Instituto de Salud Carlos III , Majadahonda, E-28220 , Madrid , Spain
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37
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Feasibility of Utilizing Stable-Isotope Dimethyl Labeling in Liquid Chromatography⁻Tandem Mass Spectrometry-Based Determination for Food Allergens-Case of Kiwifruit. Molecules 2019; 24:molecules24101920. [PMID: 31109069 PMCID: PMC6571768 DOI: 10.3390/molecules24101920] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/17/2019] [Accepted: 05/17/2019] [Indexed: 12/28/2022] Open
Abstract
Stable-isotope dimethyl labeling is a highly reactive and cost-effective derivatization procedure that could be utilized in proteomics analysis. In this study, a liquid chromatography- tandem mass spectrometry in multiple reaction monitoring mode (LC-MS-MRM) platform for the quantification of kiwi allergens was first developed using this strategy. Three signature peptides for target allergens Act d 1, Act d 5, and Act d 11 were determined and were derivatized with normal and deuterated formaldehyde as external calibrants and internal standards, respectively. The results showed that sample preparation with the phenol method provided comprehensive protein populations. Recoveries at four different levels ranging from 72.5-109.3% were achieved for the H-labeled signature peptides of Act d 1 (SPA1-H) and Act d 5 (SPA5-H) with precision ranging from 1.86-9.92%. The limit of quantification (LOQ) was set at 8 pg mL-1 for SPA1-H and at 8 ng mL-1 for SPA5-H. The developed procedure was utilized to analyze seven kinds of hand-made kiwi foods containing 0.0175-0.0515 mg g-1 of Act d 1 and 0.0252-0.0556 mg g-1 of Act d 5. This study extended the applicability of stable-isotope dimethyl labeling to the economical and precise determination of food allergens and peptides.
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38
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Lysosomotropic challenge of mast cells causes intra-granular reactive oxygen species production. Cell Death Discov 2019; 5:95. [PMID: 31123601 PMCID: PMC6520368 DOI: 10.1038/s41420-019-0177-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 04/12/2019] [Indexed: 12/15/2022] Open
Abstract
Mast cells contribute to the pathology of allergic and other disorders. Strategies to interfere with harmful mast cell-related activities are therefore warranted. Previously we established a principle for inducing selective apoptosis of mast cells, by the use of lysosomotropic agents that cause secretory granule permeabilization, leading to production of reactive oxygen species (ROS). However, the mechanism of ROS production has not been known. Here we addressed this issue. Live microscopy analysis showed that the secretory granules comprise major subcellular compartments for ROS production in response to mefloquine. As further signs for the primary involvement of secretory granules, both ROS production and cell death was blunted in mast cells lacking serglycin, a secretory granule-restricted proteoglycan. Inhibition of granule acidification caused an essentially complete blockade of granule permeabilization, ROS production and cell death in response to mefloquine. ROS production was also attenuated in the presence of an iron chelator, and after inhibition of either granzyme B or the ERK1/2 MAP kinase signaling pathway. Together, our findings reveal that the mast cell secretory granules constitute major sites for ROS production in mast cells subjected to lysosomotropic challenge. Moreover, this study reveals a central role for granule acidification in ROS generation and the pro-apoptotic response triggered downstream of secretory granule permeabilization.
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39
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McKetney J, Runde R, Hebert AS, Salamat S, Roy S, Coon JJ. Proteomic Atlas of the Human Brain in Alzheimer's Disease. J Proteome Res 2019; 18:1380-1391. [PMID: 30735395 PMCID: PMC6480317 DOI: 10.1021/acs.jproteome.9b00004] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The brain represents one of the most divergent and critical organs in the human body. Yet, it can be afflicted by a variety of neurodegenerative diseases specifically linked to aging, about which we lack a full biomolecular understanding of onset and progression, such as Alzheimer's disease (AD). Here we provide a proteomic resource comprising nine anatomically distinct sections from three aged individuals, across a spectrum of disease progression, categorized by quantity of neurofibrillary tangles. Using state-of-the-art mass spectrometry, we identify a core brain proteome that exhibits only small variance in expression, accompanied by a group of proteins that are highly differentially expressed in individual sections and broader regions. AD affected tissue exhibited slightly elevated levels of tau protein with similar relative expression to factors associated with the AD pathology. Substantial differences were identified between previous proteomic studies of mature adult brains and our aged cohort. Our findings suggest considerable value in examining specifically the brain proteome of aged human populations from a multiregional perspective. This resource can serve as a guide, as well as a point of reference for how specific regions of the brain are affected by aging and neurodegeneration.
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Affiliation(s)
- Justin McKetney
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Rosie Runde
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison
- Department of Neuroscience, University of Wisconsin–Madison, 1111 Highland Avenue, Madison, Wisconsin 53705
| | - Alexander S Hebert
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706
| | - Shahriar Salamat
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison
- Department of Neuroscience, University of Wisconsin–Madison, 1111 Highland Avenue, Madison, Wisconsin 53705
| | - Subhojit Roy
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison
- Department of Neuroscience, University of Wisconsin–Madison, 1111 Highland Avenue, Madison, Wisconsin 53705
| | - Joshua J. Coon
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
- Morgridge Institute for Research, Madison, WI 53706
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Xu J, Patassini S, Rustogi N, Riba-Garcia I, Hale BD, Phillips AM, Waldvogel H, Haines R, Bradbury P, Stevens A, Faull RLM, Dowsey AW, Cooper GJS, Unwin RD. Regional protein expression in human Alzheimer's brain correlates with disease severity. Commun Biol 2019; 2:43. [PMID: 30729181 PMCID: PMC6361956 DOI: 10.1038/s42003-018-0254-9] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 12/03/2018] [Indexed: 01/18/2023] Open
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder that currently affects 36 million people worldwide with no effective treatment available. Development of AD follows a distinctive pattern in the brain and is poorly modelled in animals. Therefore, it is vital to widen the spatial scope of the study of AD and prioritise the study of human brains. Here we show that functionally distinct human brain regions display varying and region-specific changes in protein expression. These changes provide insights into the progression of disease, novel AD-related pathways, the presence of a gradient of protein expression change from less to more affected regions and a possibly protective protein expression profile in the cerebellum. This spatial proteomics analysis provides a framework which can underpin current research and open new avenues to enhance molecular understanding of AD pathophysiology, provide new targets for intervention and broaden the conceptual frameworks for future AD research.
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Affiliation(s)
- Jingshu Xu
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Sciences Centre, Core Technology Facility (3rd Floor), 46 Grafton Street, Manchester, M13 9NT UK
- School of Biological Sciences, and Maurice Wilkins Centre for Molecular Biodiscovery, Faculty of Science, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand
| | - Stefano Patassini
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Sciences Centre, Core Technology Facility (3rd Floor), 46 Grafton Street, Manchester, M13 9NT UK
- School of Biological Sciences, and Maurice Wilkins Centre for Molecular Biodiscovery, Faculty of Science, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand
| | - Nitin Rustogi
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Sciences Centre, Core Technology Facility (3rd Floor), 46 Grafton Street, Manchester, M13 9NT UK
| | - Isabel Riba-Garcia
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Sciences Centre, Core Technology Facility (3rd Floor), 46 Grafton Street, Manchester, M13 9NT UK
| | - Benjamin D. Hale
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Sciences Centre, Core Technology Facility (3rd Floor), 46 Grafton Street, Manchester, M13 9NT UK
| | - Alexander M Phillips
- Department of Electrical Engineering and Electronics, University of Liverpool, Liverpool, L69 3GJ UK
| | - Henry Waldvogel
- Centre for Brain Research, Faculty of Medical and Health Sciences, University of Auckland, Auckland, 1142 New Zealand
| | - Robert Haines
- Research IT, The University of Manchester, Manchester, M13 9PL UK
| | - Phil Bradbury
- Research IT, The University of Manchester, Manchester, M13 9PL UK
| | - Adam Stevens
- Division of Developmental Biology & Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, M13 9PL UK
| | - Richard L. M. Faull
- Centre for Brain Research, Faculty of Medical and Health Sciences, University of Auckland, Auckland, 1142 New Zealand
| | - Andrew W. Dowsey
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Sciences Centre, Core Technology Facility (3rd Floor), 46 Grafton Street, Manchester, M13 9NT UK
- Department of Population Health Sciences and Bristol Veterinary School, Faculty of Health Sciences, University of Bristol, Bristol, BS8 2BN UK
| | - Garth J. S. Cooper
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Sciences Centre, Core Technology Facility (3rd Floor), 46 Grafton Street, Manchester, M13 9NT UK
- School of Biological Sciences, and Maurice Wilkins Centre for Molecular Biodiscovery, Faculty of Science, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand
- Centre for Brain Research, Faculty of Medical and Health Sciences, University of Auckland, Auckland, 1142 New Zealand
| | - Richard D. Unwin
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Sciences Centre, Core Technology Facility (3rd Floor), 46 Grafton Street, Manchester, M13 9NT UK
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Kappel S, Borgström A, Stokłosa P, Dörr K, Peinelt C. Store-operated calcium entry in disease: Beyond STIM/Orai expression levels. Semin Cell Dev Biol 2019; 94:66-73. [PMID: 30630032 DOI: 10.1016/j.semcdb.2019.01.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 11/29/2018] [Accepted: 01/05/2019] [Indexed: 12/19/2022]
Abstract
Precise intracellular calcium signaling is crucial to numerous cellular functions. In non-excitable cells, store-operated calcium entry (SOCE) is a key step in the generation of intracellular calcium signals. Tight regulation of SOCE is important, and dysregulation is involved in several pathophysiological cellular malfunctions. The current underlying SOCE, calcium release-activated calcium current (ICRAC), was first discovered almost three decades ago. Since its discovery, the molecular components of ICRAC, Orai1 and stromal interaction molecule 1 (STIM1), have been extensively investigated. Several regulatory mechanisms and proteins contribute to alterations in SOCE and cellular malfunctions in cancer, immune and neurodegenerative diseases, inflammation, and neuronal disorders. This review summarizes these regulatory mechanisms, including glycosylation, pH sensing, and the regulatory proteins golli, α-SNAP, SARAF, ORMDL3, CRACR2A, and TRPM4 channels.
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Affiliation(s)
- Sven Kappel
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCure, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
| | - Anna Borgström
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCure, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
| | - Paulina Stokłosa
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCure, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
| | | | - Christine Peinelt
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCure, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.
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Quantitative proteomics reveals distinct composition of amyloid plaques in Alzheimer's disease. Alzheimers Dement 2019; 15:429-440. [PMID: 30502339 DOI: 10.1016/j.jalz.2018.10.006] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 10/29/2018] [Indexed: 11/22/2022]
Abstract
INTRODUCTION We investigated the proteomic profiles of amyloid plaques (APs) from Alzheimer's disease (AD) and age-matched non-AD brains and APP/PS1 transgenic model mice. METHODS APs and adjacent control regions were collected from fresh-frozen brain sections using laser capture dissection. Proteins were quantitated using tag-labeling coupled high-throughput mass spectra. RESULTS Over 4000 proteins were accurately quantified, and more than 40 were identified as highly enriched in both AD and non-AD APs, including apoE, midkine, VGFR1, and complement C4. Intriguingly, proteins including synaptic structural proteins and complement C1r, C5, and C9 were found to be upregulated in AD APs but not non-AD APs. Moreover, the proteomic pattern of AD APs was distinct from APP/PS1 APs and exhibited correlation with aging hippocampus. DISCUSSION Our results provide new insight into AP composition. We demonstrate unexpected differences between AD, non-AD, and APP/PS1 mouse APs, which may relate to different pathological processes.
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Stepler KE, Robinson RAS. The Potential of ‘Omics to Link Lipid Metabolism and Genetic and Comorbidity Risk Factors of Alzheimer’s Disease in African Americans. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1118:1-28. [DOI: 10.1007/978-3-030-05542-4_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Grasso G. Mass spectrometry is a multifaceted weapon to be used in the battle against Alzheimer's disease: Amyloid beta peptides and beyond. MASS SPECTROMETRY REVIEWS 2019; 38:34-48. [PMID: 29905953 DOI: 10.1002/mas.21566] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 03/09/2018] [Indexed: 06/08/2023]
Abstract
Amyloid-β peptide (Aβ) accumulation and aggregation have been considered for many years the main cause of Alzheimer's disease (AD), and therefore have been the principal target of investigation as well as of the proposed therapeutic approaches (Grasso [2011] Mass Spectrom Rev. 30: 347-365). However, the amyloid cascade hypothesis, which considers Aβ accumulation the only causative agent of the disease, has proven to be incomplete if not wrong. In recent years, actors such as metal ions, oxidative stress, and other cofactors have been proposed as possible co-agents or, in some cases, main causative factors of AD. In this scenario, MS investigation has proven to be fundamental to design possible diagnostic strategies of this elusive disease, as well as to understand the biomolecular mechanisms involved, in the attempt to find a possible therapeutic solution. We review the current applications of MS in the search for possible Aβ biomarkers of AD to help the diagnosis of the disease. Recent examples of the important contributions that MS has given to prove or build theories on the molecular pathways involved with such terrible disease are also reviewed.
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Affiliation(s)
- Giuseppe Grasso
- Department of Chemical Sciences, University of Catania, Catania, Italy
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45
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Dayon L, Núñez Galindo A, Wojcik J, Cominetti O, Corthésy J, Oikonomidi A, Henry H, Kussmann M, Migliavacca E, Severin I, Bowman GL, Popp J. Alzheimer disease pathology and the cerebrospinal fluid proteome. Alzheimers Res Ther 2018; 10:66. [PMID: 30021611 PMCID: PMC6052524 DOI: 10.1186/s13195-018-0397-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 06/11/2018] [Indexed: 12/18/2022]
Abstract
BACKGROUND Altered proteome profiles have been reported in both postmortem brain tissues and body fluids of subjects with Alzheimer disease (AD), but their broad relationships with AD pathology, amyloid pathology, and tau-related neurodegeneration have not yet been fully explored. Using a robust automated MS-based proteomic biomarker discovery workflow, we measured cerebrospinal fluid (CSF) proteomes to explore their association with well-established markers of core AD pathology. METHODS Cross-sectional analysis was performed on CSF collected from 120 older community-dwelling adults with normal (n = 48) or impaired cognition (n = 72). LC-MS quantified hundreds of proteins in the CSF. CSF concentrations of β-amyloid 1-42 (Aβ1-42), tau, and tau phosphorylated at threonine 181 (P-tau181) were determined with immunoassays. First, we explored proteins relevant to biomarker-defined AD. Then, correlation analysis of CSF proteins with CSF markers of amyloid pathology, neuronal injury, and tau hyperphosphorylation (i.e., Aβ1-42, tau, P-tau181) was performed using Pearson's correlation coefficient and Bonferroni correction for multiple comparisons. RESULTS We quantified 790 proteins in CSF samples with MS. Four CSF proteins showed an association with CSF Aβ1-42 levels (p value ≤ 0.05 with correlation coefficient (R) ≥ 0.38). We identified 50 additional CSF proteins associated with CSF tau and 46 proteins associated with CSF P-tau181 (p value ≤ 0.05 with R ≥ 0.37). The majority of those proteins that showed such associations were brain-enriched proteins. Gene Ontology annotation revealed an enrichment for synaptic proteins and proteins originating from reelin-producing cells and the myelin sheath. CONCLUSIONS We used an MS-based proteomic workflow to profile the CSF proteome in relation to cerebral AD pathology. We report strong evidence of previously reported CSF proteins and several novel CSF proteins specifically associated with amyloid pathology or neuronal injury and tau hyperphosphorylation.
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Affiliation(s)
- Loïc Dayon
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | | | | | | | - John Corthésy
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | | | - Hugues Henry
- Department of Laboratories, CHUV, Lausanne, Switzerland
| | - Martin Kussmann
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
- Present address: Liggins Institute, University of Auckland, Auckland, New Zealand
| | | | - India Severin
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Gene L. Bowman
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Julius Popp
- Old Age Psychiatry, Department of Psychiatry, CHUV, Lausanne, Switzerland
- Geriatric Psychiatry, Department of Mental Health and Psychiatry, HUG, Geneva, Switzerland
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46
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Swanson A, Wolf T, Sitzmann A, Willette AA. Neuroinflammation in Alzheimer's disease: Pleiotropic roles for cytokines and neuronal pentraxins. Behav Brain Res 2018; 347:49-56. [PMID: 29462653 PMCID: PMC5988985 DOI: 10.1016/j.bbr.2018.02.015] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 01/30/2018] [Accepted: 02/13/2018] [Indexed: 12/14/2022]
Abstract
Neuroinflammation is a potential factor speculated to underlie Alzheimer's disease (AD) etiopathogenesis and progression. The overwhelming focus in this area of research to date has been on the chronic upregulation of pro-inflammatory cytokines to understand how neuroinflammatory mechanisms contribute to neurodegeneration. Yet, it is important to understand the pleiotropic roles of these cytokines in modulating neuroinflammation in which they cannot be labeled as a strictly "good" or "bad" biomarker phenotype. As such, biomarkers with more precise functions are needed to better understand how neuroinflammation impacts the brain in AD. Neuronal pentraxins are a concentration- dependent group of pro- or anti- inflammatory cytokines. There is contradictory evidence of these pentraxins as being both neuroprotective and potentially detrimental in AD. Potential neuroprotective examples include their ability to predict AD-related outcomes such as cognition, memory function and synaptic refinement. This review will briefly outline the basis of AD and subsequently summarize findings for neuropathological mechanisms of neuroinflammation, roles for traditional pro-and anti-inflammatory cytokines, and data found thus far on the neuronal pentraxins.
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Affiliation(s)
- Ashley Swanson
- Department of Food Science and Human Nutrition, Iowa State University, 2312 Food Sciences Building, 536 Farm House Lane, Ames, IA 50011, United States.
| | - Tovah Wolf
- Department of Food Science and Human Nutrition, Iowa State University, 2312 Food Sciences Building, 536 Farm House Lane, Ames, IA 50011, United States.
| | - Alli Sitzmann
- Department of Psychology, Iowa State University, W112 Lagomarcino Hall, 901 Stange Road, Ames, IA 50011, United States.
| | - Auriel A Willette
- Department of Food Science and Human Nutrition, Iowa State University, 2312 Food Sciences Building, 536 Farm House Lane, Ames, IA 50011, United States; Department of Psychology, Iowa State University, W112 Lagomarcino Hall, 901 Stange Road, Ames, IA 50011, United States; Department of Biomedical Sciences, Iowa State University, 2008 Veterinary Medicine, Ames, IA 50011, United States; Department of Neurology, University of Iowa, 2007 Roy Carver Pavilion, 200 Hawkins Drive, Iowa City, IA 52242, United States.
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Wang L, Shi FX, Xu WQ, Cao Y, Li N, Li M, Wang Q, Wang JZ, Tian Q, Yu LK, Zhou XW. The Down-Expression of ACE and IDE Exacerbates Exogenous Amyloid-β Neurotoxicity in CB2R–/– Mice. J Alzheimers Dis 2018; 64:957-971. [DOI: 10.3233/jad-180142] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Lin Wang
- Department of Pathophysiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Neurological Disease of National Education Ministry and Hubei Province, Institute for Brain Research, Huazhong University of Science and Technology, Wuhan, China
| | - Fang-Xiao Shi
- Department of Pathophysiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Neurological Disease of National Education Ministry and Hubei Province, Institute for Brain Research, Huazhong University of Science and Technology, Wuhan, China
| | - Wei-Qi Xu
- Department of Pathophysiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Neurological Disease of National Education Ministry and Hubei Province, Institute for Brain Research, Huazhong University of Science and Technology, Wuhan, China
| | - Yun Cao
- Department of Pathophysiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Neurological Disease of National Education Ministry and Hubei Province, Institute for Brain Research, Huazhong University of Science and Technology, Wuhan, China
| | - Na Li
- Department of Pathophysiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Neurological Disease of National Education Ministry and Hubei Province, Institute for Brain Research, Huazhong University of Science and Technology, Wuhan, China
| | - Man Li
- Key Laboratory of Neurological Disease of National Education Ministry and Hubei Province, Institute for Brain Research, Huazhong University of Science and Technology, Wuhan, China
| | - Qun Wang
- Department of Pathophysiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Neurological Disease of National Education Ministry and Hubei Province, Institute for Brain Research, Huazhong University of Science and Technology, Wuhan, China
| | - Jian-Zhi Wang
- Department of Pathophysiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Neurological Disease of National Education Ministry and Hubei Province, Institute for Brain Research, Huazhong University of Science and Technology, Wuhan, China
| | - Qing Tian
- Department of Pathophysiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Neurological Disease of National Education Ministry and Hubei Province, Institute for Brain Research, Huazhong University of Science and Technology, Wuhan, China
| | - Li-Kai Yu
- Department of Rheumatology and Immunology, Union Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xin-Wen Zhou
- Department of Pathophysiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Neurological Disease of National Education Ministry and Hubei Province, Institute for Brain Research, Huazhong University of Science and Technology, Wuhan, China
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Jeong A, Suazo KF, Wood WG, Distefano MD, Li L. Isoprenoids and protein prenylation: implications in the pathogenesis and therapeutic intervention of Alzheimer's disease. Crit Rev Biochem Mol Biol 2018; 53:279-310. [PMID: 29718780 PMCID: PMC6101676 DOI: 10.1080/10409238.2018.1458070] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The mevalonate-isoprenoid-cholesterol biosynthesis pathway plays a key role in human health and disease. The importance of this pathway is underscored by the discovery that two major isoprenoids, farnesyl and geranylgeranyl pyrophosphate, are required to modify an array of proteins through a process known as protein prenylation, catalyzed by prenyltransferases. The lipophilic prenyl group facilitates the anchoring of proteins in cell membranes, mediating protein-protein interactions and signal transduction. Numerous essential intracellular proteins undergo prenylation, including most members of the small GTPase superfamily as well as heterotrimeric G proteins and nuclear lamins, and are involved in regulating a plethora of cellular processes and functions. Dysregulation of isoprenoids and protein prenylation is implicated in various disorders, including cardiovascular and cerebrovascular diseases, cancers, bone diseases, infectious diseases, progeria, and neurodegenerative diseases including Alzheimer's disease (AD). Therefore, isoprenoids and/or prenyltransferases have emerged as attractive targets for developing therapeutic agents. Here, we provide a general overview of isoprenoid synthesis, the process of protein prenylation and the complexity of prenylated proteins, and pharmacological agents that regulate isoprenoids and protein prenylation. Recent findings that connect isoprenoids/protein prenylation with AD are summarized and potential applications of new prenylomic technologies for uncovering the role of prenylated proteins in the pathogenesis of AD are discussed.
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Affiliation(s)
- Angela Jeong
- Departments of Experimental and Clinical Pharmacolog,University of Minnesota, Minneapolis, MN 55455
| | | | - W. Gibson Wood
- Departments of Pharmacology, University of Minnesota, Minneapolis, MN 55455
| | - Mark D. Distefano
- Departments of Chemistry,University of Minnesota, Minneapolis, MN 55455
| | - Ling Li
- Departments of Experimental and Clinical Pharmacolog,University of Minnesota, Minneapolis, MN 55455
- Departments of Pharmacology, University of Minnesota, Minneapolis, MN 55455
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Abreu CM, Soares-Dos-Reis R, Melo PN, Relvas JB, Guimarães J, Sá MJ, Cruz AP, Mendes Pinto I. Emerging Biosensing Technologies for Neuroinflammatory and Neurodegenerative Disease Diagnostics. Front Mol Neurosci 2018; 11:164. [PMID: 29867354 PMCID: PMC5964192 DOI: 10.3389/fnmol.2018.00164] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 04/30/2018] [Indexed: 01/02/2023] Open
Abstract
Neuroinflammation plays a critical role in the onset and progression of many neurological disorders, including Multiple Sclerosis, Alzheimer's and Parkinson's diseases. In these clinical conditions the underlying neuroinflammatory processes are significantly heterogeneous. Nevertheless, a common link is the chronic activation of innate immune responses and imbalanced secretion of pro and anti-inflammatory mediators. In light of this, the discovery of robust biomarkers is crucial for screening, early diagnosis, and monitoring of neurological diseases. However, the difficulty to investigate biochemical processes directly in the central nervous system (CNS) is challenging. In recent years, biomarkers of CNS inflammatory responses have been identified in different body fluids, such as blood, cerebrospinal fluid, and tears. In addition, progress in micro and nanotechnology has enabled the development of biosensing platforms capable of detecting in real-time, multiple biomarkers in clinically relevant samples. Biosensing technologies are approaching maturity where they will become deployed in community settings, at which point screening programs and personalized medicine will become a reality. In this multidisciplinary review, our goal is to highlight both clinical and recent technological advances toward the development of multiplex-based solutions for effective neuroinflammatory and neurodegenerative disease diagnostics and monitoring.
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Affiliation(s)
- Catarina M Abreu
- International Iberian Nanotechnology Laboratory, Braga, Portugal.,Medical School, Swansea University, Swansea, United Kingdom
| | - Ricardo Soares-Dos-Reis
- Neurology Department, Centro Hospitalar de São João, Porto, Portugal.,Department of Clinical Neurosciences and Mental Health, Faculdade de Medicina, Universidade do Porto, Porto, Portugal.,Department of Biomedicine, Faculdade de Medicina, Universidade do Porto, Porto, Portugal
| | - Pedro N Melo
- Graduate Programme in Areas of Basic and Applied Biology, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - João B Relvas
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Joana Guimarães
- Neurology Department, Centro Hospitalar de São João, Porto, Portugal.,Department of Clinical Neurosciences and Mental Health, Faculdade de Medicina, Universidade do Porto, Porto, Portugal.,Center for Drug Discovery and Innovative Medicines (MedInUP), Universidade do Porto, Porto, Portugal
| | - Maria José Sá
- Neurology Department, Centro Hospitalar de São João, Porto, Portugal.,Energy, Environment and Health Research Unit (FP-ENAS), University Fernando Pessoa, Porto, Portugal.,Faculty of Health Sciences, University Fernando Pessoa, Porto, Portugal
| | - Andrea P Cruz
- International Iberian Nanotechnology Laboratory, Braga, Portugal
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IonStar enables high-precision, low-missing-data proteomics quantification in large biological cohorts. Proc Natl Acad Sci U S A 2018; 115:E4767-E4776. [PMID: 29743190 DOI: 10.1073/pnas.1800541115] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Reproducible quantification of large biological cohorts is critical for clinical/pharmaceutical proteomics yet remains challenging because most prevalent methods suffer from drastically declined commonly quantified proteins and substantially deteriorated quantitative quality as cohort size expands. MS2-based data-independent acquisition approaches represent tremendous advancements in reproducible protein measurement, but often with limited depth. We developed IonStar, an MS1-based quantitative approach enabling in-depth, high-quality quantification of large cohorts by combining efficient/reproducible experimental procedures with unique data-processing components, such as efficient 3D chromatographic alignment, sensitive and selective direct ion current extraction, and stringent postfeature generation quality control. Compared with several popular label-free methods, IonStar exhibited far lower missing data (0.1%), superior quantitative accuracy/precision [∼5% intragroup coefficient of variation (CV)], the widest protein abundance range, and the highest sensitivity/specificity for identifying protein changes (<5% false altered-protein discovery) in a benchmark sample set (n = 20). We demonstrated the usage of IonStar by a large-scale investigation of traumatic injuries and pharmacological treatments in rat brains (n = 100), quantifying >7,000 unique protein groups (>99.8% without missing data across the 100 samples) with a low false discovery rate (FDR), two or more unique peptides per protein, and high quantitative precision. IonStar represents a reliable and robust solution for precise and reproducible protein measurement in large cohorts.
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