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Bogdan S, Puścion-Jakubik A, Klimiuk K, Socha K, Kochanowicz J, Gorodkiewicz E. The Levels of Leptin, Cystatin C, Neuropilin-1 and Tau Protein in Relation to Dietary Habits in Patients with Alzheimer's Disease. J Clin Med 2023; 12:6855. [PMID: 37959320 PMCID: PMC10650913 DOI: 10.3390/jcm12216855] [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: 09/15/2023] [Revised: 10/22/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
Alzheimer's disease (AD) is the most common form of dementia in older people. Its prevalence is expected to increase, and therefore it poses a serious challenge to the healthcare system. The aim of the study was to assess the concentration of leptin, cystatin C, neuropilin-1 and tau protein, as well as the influence of dietary habits on these parameters, in a group of AD patients (n = 110) compared to 60 healthy people (n = 60). It has been shown that AD patients, compared to healthy people, are characterized by significantly higher median concentrations of leptin (9.97 vs. 3.08), cystatin c (1.53 vs. 0.56) and tau protein (8.46 vs. 4.19), but significantly lower median neuropilin-1 (69.94 vs. 167.28). Multiple regression analyses showed that leptin levels could be explained by dietary habits in 27%, cystatin C in 51%, neuropilin-1 in 41% and tau protein in 25% of cases. Modification of eating habits may contribute to improving the values of the discussed parameters.
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Affiliation(s)
- Sylwia Bogdan
- Bioanalysis Laboratory, Faculty of Chemistry, University of Bialystok, Ciołkowskiego 1K, 15-245 Bialystok, Poland; (S.B.); (E.G.)
| | - Anna Puścion-Jakubik
- Department of Bromatology, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Białystok, Mickiewicza 2D Street, 15-222 Bialystok, Poland;
| | - Katarzyna Klimiuk
- Podlasie Center of Psychogeriatrics, Swobodna 38 Street, 15-756 Bialystok, Poland;
| | - Katarzyna Socha
- Department of Bromatology, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Białystok, Mickiewicza 2D Street, 15-222 Bialystok, Poland;
| | - Jan Kochanowicz
- Department of Neurology, Medical University of Białystok, M. Skłodowskiej-Curie 24a Street, 15-276 Bialystok, Poland;
| | - Ewa Gorodkiewicz
- Bioanalysis Laboratory, Faculty of Chemistry, University of Bialystok, Ciołkowskiego 1K, 15-245 Bialystok, Poland; (S.B.); (E.G.)
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2
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Zhang C, Tan G, Zhang Y, Zhong X, Zhao Z, Peng Y, Cheng Q, Xue K, Xu Y, Li X, Li F, Zhang Y. Comprehensive analyses of brain cell communications based on multiple scRNA-seq and snRNA-seq datasets for revealing novel mechanism in neurodegenerative diseases. CNS Neurosci Ther 2023; 29:2775-2786. [PMID: 37269061 PMCID: PMC10493674 DOI: 10.1111/cns.14280] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 04/24/2023] [Accepted: 05/16/2023] [Indexed: 06/04/2023] Open
Abstract
AIMS Complex cellular communications between glial cells and neurons are critical for brain normal function and disorders, and single-cell level RNA-sequencing datasets display more advantages for analyzing cell communications. Therefore, it is necessary to systematically explore brain cell communications when considering factors such as sex and brain region. METHODS We extracted a total of 1,039,459 cells derived from 28 brain single-cell RNA-sequencing (scRNA-seq) or single-nucleus RNA-sequencing (snRNA-seq) datasets from the GEO database, including 12 human and 16 mouse datasets. These datasets were further divided into 71 new sub-datasets when considering disease, sex, and region conditions. In the meanwhile, we integrated four methods to evaluate ligand-receptor interaction score among six major brain cell types (microglia, neuron, astrocyte, oligodendrocyte, OPC, and endothelial cell). RESULTS For Alzheimer's disease (AD), disease-specific ligand-receptor pairs when compared with normal sub-datasets, such as SEMA4A-NRP1, were identified. Furthermore, we explored the sex- and region-specific cell communications and identified that WNT5A-ROR1 among microglia cells displayed close communications in male, and SPP1-ITGAV displayed close communications in the meninges region from microglia to neurons. Furthermore, based on the AD-specific cell communications, we constructed a model for AD early prediction and confirmed the predictive performance using multiple independent datasets. Finally, we developed an online platform for researchers to explore brain condition-specific cell communications. CONCLUSION This research provided a comprehensive study to explore brain cell communications, which could reveal novel biological mechanisms involved in normal brain function and neurodegenerative diseases such as AD.
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Affiliation(s)
- Chunlong Zhang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinChina
| | - Guiyuan Tan
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinChina
| | - Yuxi Zhang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinChina
| | - Xiaoling Zhong
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinChina
| | - Ziyan Zhao
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinChina
| | - Yunyi Peng
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinChina
| | - Qian Cheng
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinChina
| | - Ke Xue
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinChina
| | - Yanjun Xu
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinChina
| | - Xia Li
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinChina
| | - Feng Li
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinChina
| | - Yunpeng Zhang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinChina
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3
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Schrader JM, Xu F, Lee H, Barlock B, Benveniste H, Van Nostrand WE. Emergent White Matter Degeneration in the rTg-DI Rat Model of Cerebral Amyloid Angiopathy Exhibits Unique Proteomic Changes. THE AMERICAN JOURNAL OF PATHOLOGY 2022; 192:426-440. [PMID: 34896071 PMCID: PMC8895424 DOI: 10.1016/j.ajpath.2021.11.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/16/2021] [Accepted: 11/23/2021] [Indexed: 12/23/2022]
Abstract
Cerebral amyloid angiopathy (CAA), characterized by cerebral vascular amyloid accumulation, neuroinflammation, microbleeds, and white matter (WM) degeneration, is a common comorbidity in Alzheimer disease and a prominent contributor to vascular cognitive impairment and dementia. WM loss was recently reported in the corpus callosum (CC) in the rTg-DI rat model of CAA. The current study shows that the CC exhibits a much lower CAA burden compared with the adjacent cortex. Sequential Window Acquisition of All Theoretical Mass Spectra tandem mass spectrometry was used to show specific proteomic changes in the CC with emerging WM loss and compare them with the proteome of adjacent cortical tissue in rTg-DI rats. In the CC, annexin A3, heat shock protein β1, and cystatin C were elevated at 4 months (M) before WM loss and at 12M with evident WM loss. Although annexin A3 and cystatin C were also enhanced in the cortex at 12M, annexin A5 and the leukodystrophy-associated astrocyte proteins megalencephalic leukoencephalopathy with subcortical cysts 1 and GlialCAM were distinctly elevated in the CC. Pathway analysis indicated neurodegeneration of axons, reflected by reduced expression of myelin and neurofilament proteins, was common to the CC and cortex; activation of Tgf-β1 and F2/thrombin was restricted to the CC. This study provides new insights into the proteomic changes that accompany WM loss in the CC of rTg-DI rats.
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Affiliation(s)
- Joseph M. Schrader
- George & Anne Ryan Institute for Neuroscience, University of Rhode Island, Kingston, Rhode Island,Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, Rhode Island
| | - Feng Xu
- George & Anne Ryan Institute for Neuroscience, University of Rhode Island, Kingston, Rhode Island,Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, Rhode Island
| | - Hedok Lee
- Department of Anesthesiology, Yale University, New Haven, Connecticut
| | - Benjamin Barlock
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, Rhode Island
| | - Helene Benveniste
- Department of Anesthesiology, Yale University, New Haven, Connecticut
| | - William E. Van Nostrand
- George & Anne Ryan Institute for Neuroscience, University of Rhode Island, Kingston, Rhode Island,Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, Rhode Island,Address correspondence to William E. Van Nostrand, Ph.D., Department of Biomedical and Pharmaceutical Sciences, George and Anne Ryan Institute for Neuroscience, University of Rhode Island, 130 Flagg Rd., Kingston, RI 02881.
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4
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A human tau seeded neuronal cell model recapitulates molecular responses associated with Alzheimer's disease. Sci Rep 2022; 12:2673. [PMID: 35177665 PMCID: PMC8854741 DOI: 10.1038/s41598-022-06411-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 01/18/2022] [Indexed: 11/08/2022] Open
Abstract
Cellular models recapitulating features of tauopathies are useful tools to investigate the causes and consequences of tau aggregation and the identification of novel treatments. We seeded rat primary cortical neurons with tau isolated from Alzheimer’s disease brains to induce a time-dependent increase in endogenous tau inclusions. Transcriptomics of seeded and control cells identified 1075 differentially expressed genes (including 26 altered at two time points). These were enriched for lipid/steroid metabolism and neuronal/glial cell development genes. 50 genes were correlated with tau inclusion formation at both transcriptomic and proteomic levels, including several microtubule and cytoskeleton-related proteins such as Tubb2a, Tubb4a, Nefl and Snca. Several genes (such as Fyn kinase and PTBP1, a tau exon 10 repressor) interact directly with or regulate tau. We conclude that this neuronal model may be a suitable platform for high-throughput screens for target or hit compound identification and validation.
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5
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No Association between Single Nucleotide Polymorphisms (SNPs) of the Interferon-Induced Transmembrane Protein 3 (IFITM3) Gene and the Susceptibility of Alzheimer’s Disease (AD). Medicina (B Aires) 2021; 58:medicina58010055. [PMID: 35056363 PMCID: PMC8778958 DOI: 10.3390/medicina58010055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/21/2021] [Accepted: 12/27/2021] [Indexed: 11/22/2022] Open
Abstract
Background and Objectives: Alzheimer’s disease (AD) is the most common progressive neurodegenerative disorder, characterized by the accumulation of amyloid-beta (Aβ) in the brain. A recent study reported that the interferon-induced transmembrane protein 3 (IFITM3) protein plays a pivotal role in Aβ processing by the γ-secretase complex. Since several single nucleotide polymorphisms (SNPs) of the IFITM3 gene are related to the function and expression levels of the IFITM3 gene, the relationship between genetic polymorphisms in the IFITM3 gene and susceptibility to AD needs to be investigated. Materials and Methods: We investigated the genotype and allele frequencies of IFITM3 polymorphisms in 177 AD patients and 233 matched healthy controls by amplicon sequencing. In addition, we compared the genotype, allele and haplotype frequencies between AD patients and matched controls and performed an association analysis. Results: There were no significant differences in the genotype, allele or haplotype frequency distributions of the IFITM3 polymorphisms between AD patients and matched controls. Conclusions: To the best of our knowledge, this is the first case-control association study of the IFITM3 gene in AD.
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Hark TJ, Savas JN. Using stable isotope labeling to advance our understanding of Alzheimer's disease etiology and pathology. J Neurochem 2021; 159:318-329. [PMID: 33434345 PMCID: PMC8273190 DOI: 10.1111/jnc.15298] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 12/18/2022]
Abstract
Stable isotope labeling with mass spectrometry (MS)-based proteomic analysis has become a powerful strategy to assess protein steady-state levels, protein turnover, and protein localization. Applying these analyses platforms to neurodegenerative disorders may uncover new aspects of the etiology of these devastating diseases. Recently, stable isotopes-MS has been used to investigate early pathological mechanisms of Alzheimer's disease (AD) with mouse models of AD-like pathology. In this review, we summarize these stable isotope-MS experimental designs and the recent application in the context of AD pathology. We also describe our current efforts aimed at using nuclear magnetic resonance (NMR) analysis of stable isotope-labeled amyloid fibrils from AD mouse model brains. Collectively, these methodologies offer new opportunities to study proteome changes in AD and other neurodegenerative diseases by elucidating mechanisms to target for treatment and prevention.
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Affiliation(s)
- Timothy J Hark
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Jeffrey N Savas
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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7
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Vavougios GD, Nday C, Pelidou SH, Gourgoulianis KI, Stamoulis G, Doskas T, Zarogiannis SG. Outside-in induction of the IFITM3 trafficking system by infections, including SARS-CoV-2, in the pathobiology of Alzheimer's disease. Brain Behav Immun Health 2021; 14:100243. [PMID: 33817671 PMCID: PMC7997139 DOI: 10.1016/j.bbih.2021.100243] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/13/2021] [Accepted: 03/17/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND IFITM3 is a viral restriction protein that enables sequestration of viral particles and subsequent trafficking to lysosomes. Recently, IFITM3 upregulation was found to induce gamma - secretase activity and the production of amyloid beta. The purpose of this study was to determine whether dysregulation of IFITM3-dependent pathways was present in neurons and peripheral immune cells donated by AD patients. As a secondary aim, we sought to determine whether these perturbations could be induced by viruses, including SARS-CoV-2. METHODS Gene set enrichment analyses (GSEA) previously performed on publicly available transcriptomic data from tissues donated by AD patients were screened for enriched pathways containing IFITM3. Subsequently, signature containing IFITM3, derived from entorhinal cortex (EC) neurons containing neurofibrillary tangles (NFT) was screened for overlap with curated, publicly available, viral infection-induced gene signatures (including SARS-CoV-2). RESULTS GSEA determined that IFITM3 gene networks are significantly enriched both in CNS sites (entorhinal and hippocampal cortices) and in peripheral blood mononuclear cells (PBMCs) donated by AD patients. Overlap screening revealed that IFITM3 signatures are induced by several viruses, including SARS-CoV, MERS-CoV, SARS-CoV-2 and HIV-1 (adjusted p-value <0.001; Enrichr Database). DISCUSSION A data-driven analysis of AD tissues revealed IFITM3 gene signatures both in the CNS and in peripheral immune cells. GSEA revealed that an IFITM3 derived gene signature extracted from EC/NFT neurons overlapped with those extracted from publicly available viral infection datasets, including SARS-CoV-2. Our results are in line with currently emerging evidence on IFITM3's role in AD, and SARS-CoV-2's potential contribution in the setting of an expanded antimicrobial protection hypothesis.
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Affiliation(s)
- George D. Vavougios
- Neuroimmunology Laboratory, Department of Neurology, Athens Naval Hospital, P.C., 115 21, Athens, Greece
- Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, Biopolis, P.C., 41500, Larissa, Greece
- Department of Computer Science and Telecommunications, University of Thessaly, Papasiopoulou 2 – 4, P.C., 35 131, Galaneika, Lamia, Greece
| | - Christiane Nday
- Laboratory of Medical Physics, Faculty of Health Sciences, School of Medicine, Aristotle University of Thessaloniki, P.C., 5414, Thessaloniki, Greece
| | | | - Konstantinos I. Gourgoulianis
- Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, Biopolis, P.C., 41500, Larissa, Greece
| | - George Stamoulis
- Department of Electrical and Computer Engineering, University of Thessaly, 37 Glavani – 28th October Str, Deligiorgi Building, 4th Floor, P.C., 382 21, Volos, Greece
- Department of Computer Science and Telecommunications, University of Thessaly, Papasiopoulou 2 – 4, P.C., 35 131, Galaneika, Lamia, Greece
| | - Triantafyllos Doskas
- Neuroimmunology Laboratory, Department of Neurology, Athens Naval Hospital, P.C., 115 21, Athens, Greece
| | - Sotirios G. Zarogiannis
- Department of Physiology, Faculty of Medicine, School of Health Sciences, University of Thessaly, BIOPOLIS, Larissa, 41500, Greece
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8
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Yu W, Yu W, Yang Y, Lü Y. Exploring the Key Genes and Identification of Potential Diagnosis Biomarkers in Alzheimer's Disease Using Bioinformatics Analysis. Front Aging Neurosci 2021; 13:602781. [PMID: 34194312 PMCID: PMC8236887 DOI: 10.3389/fnagi.2021.602781] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 05/06/2021] [Indexed: 12/30/2022] Open
Abstract
Background Alzheimer’s disease (AD) is one of the major threats of the twenty-first century and lacks available therapy. Identification of novel molecular markers for diagnosis and treatment of AD is urgently demanded, and genetic biomarkers show potential prospects. Method We identify and intersected differentially expressed genes (DEGs) from five microarray datasets to detect consensus DEGs. Based on these DEGs, we conducted Gene Ontology (GO), performed the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, constructed a protein—protein interaction (PPI) network, and utilized Cytoscape to identify hub genes. The least absolute shrinkage and selection operator (LASSO) logistic regression was applied to identify potential diagnostic biomarkers. Gene set enrichment analysis (GSEA) was performed to investigate the biological functions of the key genes. Result We identified 608 consensus DEGs, several dysregulated pathways, and 18 hub genes. Sixteen hub genes dysregulated as AD progressed. The diagnostic model of 35 genes was constructed, which has a high area under the curve (AUC) value in both the validation dataset and combined dataset (AUC = 0.992 and AUC = 0.985, respectively). The model can also differentiate mild cognitive impairment and AD patients from controls in two blood datasets. Brain-derived neurotrophic factor (BDNF) and WW domain-containing transcription regulator protein 1 (WWTR1), which are associated with the Braak stage, Aβ 42 levels, and β-secretase activity, were identified as critical genes of AD. Conclusion Our study identified 16 hub genes correlated to the neuropathological stage and 35 potential biomarkers for the diagnosis of AD. WWTR1 were identified as candidate genes for future studies. This study deepens our understanding of the transcriptomic and functional features and provides new potential diagnostic biomarkers and therapeutic targets for AD.
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Affiliation(s)
- Wuhan Yu
- Department of Geriatrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Weihua Yu
- Institutes of Neuroscience, Chongqing Medical University, Chongqing, China
| | - Yan Yang
- State Key Laboratory of Power Transmission Equipment and System Security and New Technology, College of Electrical Engineering, Chongqing University, Chongqing, China
| | - Yang Lü
- Department of Geriatrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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9
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Podvin S, Jones A, Liu Q, Aulston B, Mosier C, Ames J, Winston C, Lietz CB, Jiang Z, O’Donoghue AJ, Ikezu T, Rissman RA, Yuan SH, Hook V. Mutant Presenilin 1 Dysregulates Exosomal Proteome Cargo Produced by Human-Induced Pluripotent Stem Cell Neurons. ACS OMEGA 2021; 6:13033-13056. [PMID: 34056454 PMCID: PMC8158845 DOI: 10.1021/acsomega.1c00660] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/16/2021] [Indexed: 05/28/2023]
Abstract
The accumulation and propagation of hyperphosphorylated tau (p-Tau) is a neuropathological hallmark occurring with neurodegeneration of Alzheimer's disease (AD). Extracellular vesicles, exosomes, have been shown to initiate tau propagation in the brain. Notably, exosomes from human-induced pluripotent stem cell (iPSC) neurons expressing the AD familial A246E mutant form of presenilin 1 (mPS1) are capable of inducing tau deposits in the mouse brain after in vivo injection. To gain insights into the exosome proteome cargo that participates in propagating tau pathology, this study conducted proteomic analysis of exosomes produced by human iPSC neurons expressing A246E mPS1. Significantly, mPS1 altered the profile of exosome cargo proteins to result in (1) proteins present only in mPS1 exosomes and not in controls, (2) the absence of proteins in the mPS1 exosomes which were present only in controls, and (3) shared proteins which were upregulated or downregulated in the mPS1 exosomes compared to controls. These results show that mPS1 dysregulates the proteome cargo of exosomes to result in the acquisition of proteins involved in the extracellular matrix and protease functions, deletion of proteins involved in RNA and protein translation systems along with proteasome and related functions, combined with the upregulation and downregulation of shared proteins, including the upregulation of amyloid precursor protein. Notably, mPS1 neuron-derived exosomes displayed altered profiles of protein phosphatases and kinases involved in regulating the status of p-tau. The dysregulation of exosome cargo proteins by mPS1 may be associated with the ability of mPS1 neuron-derived exosomes to propagate tau pathology.
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Affiliation(s)
- Sonia Podvin
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California San Diego,
La Jolla, San Diego 92093, California, United States
| | - Alexander Jones
- Biomedical
Sciences Graduate Program, University of
California, San Diego, La Jolla, San Diego 92093, California, United States
| | - Qing Liu
- Department
of Neurosciences, School of Medicine, University
of California, San Diego, La Jolla, San Diego 92093, California, United States
| | - Brent Aulston
- Department
of Neurosciences, School of Medicine, University
of California, San Diego, La Jolla, San Diego 92093, California, United States
| | - Charles Mosier
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California San Diego,
La Jolla, San Diego 92093, California, United States
| | - Janneca Ames
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California San Diego,
La Jolla, San Diego 92093, California, United States
| | - Charisse Winston
- Department
of Neurosciences, School of Medicine, University
of California, San Diego, La Jolla, San Diego 92093, California, United States
| | - Christopher B. Lietz
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California San Diego,
La Jolla, San Diego 92093, California, United States
| | - Zhenze Jiang
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California San Diego,
La Jolla, San Diego 92093, California, United States
| | - Anthony J. O’Donoghue
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California San Diego,
La Jolla, San Diego 92093, California, United States
| | - Tsuneya Ikezu
- Department
of Pharmacology and Experimental Therapeutics, Department of Neurology,
Alzheimer’s Disease Research Center, Boston University, School of Medicine, Boston 02118, Massachusetts, United States
| | - Robert A. Rissman
- Department
of Neurosciences, School of Medicine, University
of California, San Diego, La Jolla, San Diego 92093, California, United States
- Veterans
Affairs San Diego Healthcare System,
La Jolla, San Diego 92161, California, United States
| | - Shauna H. Yuan
- Department
of Neurosciences, School of Medicine, University
of California, San Diego, La Jolla, San Diego 92093, California, United States
| | - Vivian Hook
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California San Diego,
La Jolla, San Diego 92093, California, United States
- Biomedical
Sciences Graduate Program, University of
California, San Diego, La Jolla, San Diego 92093, California, United States
- Department
of Neurosciences, School of Medicine, University
of California, San Diego, La Jolla, San Diego 92093, California, United States
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10
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Andrade-Navarro MA, Mühlenberg K, Spruth EJ, Mah N, González-López A, Andreani T, Russ J, Huska MR, Muro EM, Fontaine JF, Amstislavskiy V, Soldatov A, Nietfeld W, Wanker EE, Priller J. RNA Sequencing of Human Peripheral Blood Cells Indicates Upregulation of Immune-Related Genes in Huntington's Disease. Front Neurol 2020; 11:573560. [PMID: 33329316 PMCID: PMC7731869 DOI: 10.3389/fneur.2020.573560] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 11/06/2020] [Indexed: 11/13/2022] Open
Abstract
Huntington's disease (HD) is an autosomal dominantly inherited neurodegenerative disorder caused by a trinucleotide repeat expansion in the Huntingtin gene. As disease-modifying therapies for HD are being developed, peripheral blood cells may be used to indicate disease progression and to monitor treatment response. In order to investigate whether gene expression changes can be found in the blood of individuals with HD that distinguish them from healthy controls, we performed transcriptome analysis by next-generation sequencing (RNA-seq). We detected a gene expression signature consistent with dysregulation of immune-related functions and inflammatory response in peripheral blood from HD cases vs. controls, including induction of the interferon response genes, IFITM3, IFI6 and IRF7. Our results suggest that it is possible to detect gene expression changes in blood samples from individuals with HD, which may reflect the immune pathology associated with the disease.
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Affiliation(s)
- Miguel A Andrade-Navarro
- Faculty of Biology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Katja Mühlenberg
- Neuroproteomics, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Eike J Spruth
- Department of Neuropsychiatry, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Nancy Mah
- Charité-Universitätsmedizin Berlin, Virchow-Klinikum, Berlin-Brandenburger Centrum für Regenerative Therapien, Berlin, Germany
| | - Adrián González-López
- Klinik f. Anästhesiologie m.S. operative Intensivmedizin, Virchow Klinikum, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Tommaso Andreani
- Faculty of Biology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Jenny Russ
- German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Matthew R Huska
- Department for Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Enrique M Muro
- Faculty of Biology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Jean-Fred Fontaine
- Faculty of Biology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
| | | | - Alexei Soldatov
- Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | | | - Erich E Wanker
- Neuroproteomics, Max-Delbrück Center for Molecular Medicine, Berlin, Germany.,German Centre for Neurodegenerative Diseases, Berlin Institute of Health, Berlin, Germany
| | - Josef Priller
- Department of Neuropsychiatry, Charité-Universitätsmedizin Berlin, Berlin, Germany.,German Centre for Neurodegenerative Diseases, Berlin Institute of Health, Berlin, Germany.,Centre for Clinical Brain Sciences, UK Dementia Research Institute, University of Edinburgh, Edinburgh, United Kingdom
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11
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Podvin S, Jones A, Liu Q, Aulston B, Ransom L, Ames J, Shen G, Lietz CB, Jiang Z, O'Donoghue AJ, Winston C, Ikezu T, Rissman RA, Yuan S, Hook V. Dysregulation of Exosome Cargo by Mutant Tau Expressed in Human-induced Pluripotent Stem Cell (iPSC) Neurons Revealed by Proteomics Analyses. Mol Cell Proteomics 2020; 19:1017-1034. [PMID: 32295833 PMCID: PMC7261814 DOI: 10.1074/mcp.ra120.002079] [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: 04/07/2020] [Indexed: 12/22/2022] Open
Abstract
Accumulation and propagation of hyperphosphorylated Tau (p-Tau) is a common neuropathological hallmark associated with neurodegeneration of Alzheimer's disease (AD), frontotemporal dementia and parkinsonism linked to chromosome 17 (FTDP-17), and related tauopathies. Extracellular vesicles, specifically exosomes, have recently been demonstrated to participate in mediating Tau propagation in brain. Exosomes produced by human induced pluripotent stem cell (iPSC)-derived neurons expressing mutant Tau (mTau), containing the P301L and V337M Tau mutations of FTDP-17, possess the ability to propagate p-Tau pathology after injection into mouse brain. To gain an understanding of the mTau exosome cargo involved in Tau pathogenesis, these pathogenic exosomes were analyzed by proteomics and bioinformatics. The data showed that mTau expression dysregulates the exosome proteome to result in 1) proteins uniquely present only in mTau, and not control exosomes, 2) the absence of proteins in mTau exosomes, uniquely present in control exosomes, and 3) shared proteins which were significantly upregulated or downregulated in mTau compared with control exosomes. Notably, mTau exosomes (not control exosomes) contain ANP32A (also known as I1PP2A), an endogenous inhibitor of the PP2A phosphatase which regulates the phosphorylation state of p-Tau. Several of the mTau exosome-specific proteins have been shown to participate in AD mechanisms involving lysosomes, inflammation, secretases, and related processes. Furthermore, the mTau exosomes lacked a substantial portion of proteins present in control exosomes involved in pathways of localization, vesicle transport, and protein binding functions. The shared proteins present in both mTau and control exosomes represented exosome functions of vesicle-mediated transport, exocytosis, and secretion processes. These data illustrate mTau as a dynamic regulator of the biogenesis of exosomes to result in acquisition, deletion, and up- or downregulation of protein cargo to result in pathogenic mTau exosomes capable of in vivo propagation of p-Tau neuropathology in mouse brain.
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Affiliation(s)
- Sonia Podvin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California
| | - Alexander Jones
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, California
| | - Qing Liu
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, California
| | - Brent Aulston
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, California
| | - Linnea Ransom
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, California
| | - Janneca Ames
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California
| | - Gloria Shen
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California
| | - Christopher B Lietz
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California
| | - Zhenze Jiang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California
| | - Anthony J O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California
| | - Charisse Winston
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, California
| | - Tsuneya Ikezu
- Department of Pharmacology and Experimental Therapeutics, Department of Neurology, Alzheimer's Disease Research Center, Boston University, School of Medicine, Boston, Massachusetts
| | - Robert A Rissman
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, California; VA San Diego Healthcare System, La Jolla, California
| | - Shauna Yuan
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, California
| | - Vivian Hook
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California; Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, California.
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12
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Brisdelli F, Di Francesco L, Giorgi A, Lizzi AR, Luzi C, Mignogna G, Bozzi A, Schininà ME. Proteomic Analysis of Quercetin-Treated K562 Cells. Int J Mol Sci 2019; 21:ijms21010032. [PMID: 31861640 PMCID: PMC6981597 DOI: 10.3390/ijms21010032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 12/17/2019] [Indexed: 02/07/2023] Open
Abstract
Among natural products under investigation for their additive potential in cancer prevention and treatment, the flavonoid quercetin has received attention for its effects on the cell cycle arrest and apoptosis. In the past, we addressed this issue in K562 cells, a cellular model of the human chronic myeloid leukemia. Here, we applied stable isotope labeling by amino acids in cell culture (SILAC) proteomics with the aim to increase knowledge on the regulative and metabolic pathways modulated by quercetin in these cells. After 24 h of quercetin treatment, we observed that apoptosis was not completely established, thus we selected this time range to capture quantitative data. As a result, we were able to achieve a robust identification of 1703 proteins, and to measure fold changes between quercetin-treated and untreated cells for 1206 proteins. Through a bioinformatics functional analysis on a subset of 112 proteins, we propose that the apoptotic phenotype of K562 cells entails a significant modulation of the translational machinery, RNA metabolism, antioxidant defense systems, and enzymes involved in lipid metabolism. Finally, we selected eight differentially expressed proteins, validated their modulated expression in quercetin-treated K562 cells, and discussed their possible role in flavonoid cytotoxicity. This quantitative profiling, performed for the first time on this type of tumor cells upon treatment with a flavonoid, will contribute to revealing the molecular basis of the multiplicity of the effects selectively exerted by quercetin on K562 cells.
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Affiliation(s)
- Fabrizia Brisdelli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (F.B.); (A.R.L.); (C.L.); (A.B.)
| | - Laura Di Francesco
- Department of Biochemical Sciences, Sapienza, University of Rome, 00185 Rome, Italy; (L.D.F.); (A.G.); (G.M.)
| | - Alessandra Giorgi
- Department of Biochemical Sciences, Sapienza, University of Rome, 00185 Rome, Italy; (L.D.F.); (A.G.); (G.M.)
| | - Anna Rita Lizzi
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (F.B.); (A.R.L.); (C.L.); (A.B.)
| | - Carla Luzi
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (F.B.); (A.R.L.); (C.L.); (A.B.)
| | - Giuseppina Mignogna
- Department of Biochemical Sciences, Sapienza, University of Rome, 00185 Rome, Italy; (L.D.F.); (A.G.); (G.M.)
| | - Argante Bozzi
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (F.B.); (A.R.L.); (C.L.); (A.B.)
| | - M. Eugenia Schininà
- Department of Biochemical Sciences, Sapienza, University of Rome, 00185 Rome, Italy; (L.D.F.); (A.G.); (G.M.)
- Correspondence:
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Cheray M, Stratoulias V, Joseph B, Grabert K. The Rules of Engagement: Do Microglia Seal the Fate in the Inverse Relation of Glioma and Alzheimer's Disease? Front Cell Neurosci 2019; 13:522. [PMID: 31824268 PMCID: PMC6879422 DOI: 10.3389/fncel.2019.00522] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 11/07/2019] [Indexed: 12/30/2022] Open
Abstract
Microglia, the immune cells of the brain, play a major role in the maintenance of brain homeostasis and constantly screen the brain environment to detect any infection or damage. Once activated by a stimulus, microglial cells initiate an immune response followed by the resolution of brain inflammation. A failure or deviation in the housekeeping function of these guardian cells can lead to multiple diseases, including brain cancer and neurodegenerative diseases such as Alzheimer's disease (AD). A small number of studies have investigated the causal relation of both diseases, thereby revealing an inverse relationship where cancer patients have a reduced risk to develop AD and vice versa. In this review, we aim to shed light on the role of microglia in the fate to develop specifically glioma as one type of cancer or AD. We will examine the common and/or opposing genetic predisposition as well as associated pathways of these diseases to unravel a possible involvement of microglia in the occurrence of either disease. Lastly, a set of guidelines will be proposed for future research and diagnostics to clarify and improve the knowledge on the role of microglia in the decision toward one pathology or another.
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Affiliation(s)
- Mathilde Cheray
- Toxicology Unit, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Vassilis Stratoulias
- Toxicology Unit, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Bertrand Joseph
- Toxicology Unit, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Kathleen Grabert
- Toxicology Unit, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
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14
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Wang D, Ba H, Li C, Zhao Q, Li C. Proteomic Analysis of Plasma Membrane Proteins of Antler Stem Cells Using Label-Free LC⁻MS/MS. Int J Mol Sci 2018; 19:E3477. [PMID: 30400663 PMCID: PMC6275008 DOI: 10.3390/ijms19113477] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/31/2018] [Accepted: 11/03/2018] [Indexed: 12/16/2022] Open
Abstract
Deer antlers are unusual mammalian organs that can fully regenerate after annual shedding. Stem cells resident in the pedicle periosteum (PPCs) provide the main cell source for antler regeneration. Central to various cellular processes are plasma membrane proteins, but the expression of these proteins has not been well documented in antler regeneration. In the present study, plasma membrane proteins of PPCs and facial periosteal cells (FPCs) were analyzed using label-free liquid chromatography⁻mass spetrometry (LC⁻MS/MS). A total of 1739 proteins were identified. Of these proteins, 53 were found solely in the PPCs, 100 solely in the FPCs, and 1576 co-existed in both PPCs and FPCs; and 39 were significantly up-regulated in PPCs and 49 up-regulated in FPCs. In total, 226 gene ontology (GO) terms were significantly enriched from the differentially expressed proteins (DEPs). Five clusters of biological processes from these GO terms comprised responses to external stimuli, signal transduction, membrane transport, regulation of tissue regeneration, and protein modification processes. Further studies are required to demonstrate the relevancy of these DEPs in antler stem cell biology and antler regeneration.
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Affiliation(s)
- Datao Wang
- Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun 130112, China.
| | - Hengxing Ba
- Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun 130112, China.
| | - Chenguang Li
- Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun 130112, China.
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China.
| | - Quanmin Zhao
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China.
| | - Chunyi Li
- Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun 130112, China.
- Department of Biology, Changchun Sci-Tech University, Changchun 130600, China.
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15
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Mulcahy MJ, Paulo JA, Hawrot E. Proteomic Investigation of Murine Neuronal α7-Nicotinic Acetylcholine Receptor Interacting Proteins. J Proteome Res 2018; 17:3959-3975. [PMID: 30285449 DOI: 10.1021/acs.jproteome.8b00618] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The α7-nicotinic acetylcholine receptor (α7-nAChR) is a ligand-gated ion channel that is expressed widely in vertebrates and is the principal high-affinity α-bungarotoxin (α-bgtx) binding protein in the mammalian CNS. α7-nAChRs associate with proteins that can modulate its properties. The α7-nAChR interactome is the summation of proteins interacting or associating with α7-nAChRs in a protein complex. To identify an α7-nAChR interactome in neural tissue, we isolated α-bgtx-affinity protein complexes from wild-type and α7-nAChR knockout (α7 KO) mouse whole brain tissue homogenates using α-bgtx-affinity beads. Affinity precipitated proteins were trypsinized and analyzed with an Orbitrap Fusion mass spectrometer. Proteins isolated with the α7-nAChR specific ligand, α-bgtx, were determined to be α7-nAChR associated proteins. The α7-nAChR subunit and 120 additional proteins were identified. Additionally, 369 proteins were identified as binding to α-bgtx in the absence of α7-nAChR expression, thereby identifying nonspecific proteins for α7-nAChR investigations using α-bgtx enrichment. These results expand on our previous investigations of α7-nAChR interacting proteins using α-bgtx-affinity bead isolation by controlling for differences between α7-nAChR and α-bgtx-specific proteins, developing an improved protein isolation methodology, and incorporating the latest technology in mass spectrometry. The α7-nAChR interactome identified in this study includes proteins associated with the expression, localization, function, or modulation of α7-nAChRs, and it provides a foundation for future studies to elucidate how these interactions contribute to human disease.
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Affiliation(s)
- Matthew J Mulcahy
- Division of Biology and Biological Engineering , California Institute of Technology , 1200 East California Boulevard , Pasadena , California 91125-2900 , United States.,Department of Molecular Pharmacology, Physiology and Biotechnology , Brown University , Providence , Rhode Island 02912 , United States
| | - Joao A Paulo
- Department of Cell Biology , Harvard Medical School , 240 Longwood Avenue , Boston , Massachusetts 02115 , United States
| | - Edward Hawrot
- Department of Molecular Pharmacology, Physiology and Biotechnology , Brown University , Providence , Rhode Island 02912 , United States
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Comparative characterization of rat hippocampal plasma membrane and mitochondrial membrane proteomes based on a sequential digestion-centered combinative strategy. Anal Bioanal Chem 2018; 410:3119-3131. [DOI: 10.1007/s00216-018-0995-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 02/22/2018] [Accepted: 03/05/2018] [Indexed: 12/27/2022]
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