1
|
Molière A, Park JYC, Goyala A, Vayndorf EM, Zhang B, Hsiung KC, Jung Y, Kwon S, Statzer C, Meyer D, Nguyen R, Chadwick J, Thompson MA, Schumacher B, Lee SJV, Essmann CL, MacArthur MR, Kaeberlein M, David D, Gems D, Ewald CY. Improved resilience and proteostasis mediate longevity upon DAF-2 degradation in old age. GeroScience 2024; 46:5015-5036. [PMID: 38900346 PMCID: PMC11335714 DOI: 10.1007/s11357-024-01232-x] [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: 12/14/2023] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
Little is known about the possibility of reversing age-related biological changes when they have already occurred. To explore this, we have characterized the effects of reducing insulin/IGF-1 signaling (IIS) during old age. Reduction of IIS throughout life slows age-related decline in diverse species, most strikingly in the nematode Caenorhabditis elegans. Here we show that even at advanced ages, auxin-induced degradation of DAF-2 in single tissues, including neurons and the intestine, is still able to markedly increase C. elegans lifespan. We describe how reversibility varies among senescent changes. While senescent pathologies that develop in mid-life were not reversed, there was a rejuvenation of the proteostasis network, manifesting as a restoration of the capacity to eliminate otherwise intractable protein aggregates that accumulate with age. Moreover, resistance to several stressors was restored. These results support several new conclusions. (1) Loss of resilience is not solely a consequence of pathologies that develop in earlier life. (2) Restoration of proteostasis and resilience by inhibiting IIS is a plausible cause of the increase in lifespan. And (3), most interestingly, some aspects of the age-related transition from resilience to frailty can be reversed to a certain extent. This raises the possibility that the effect of IIS and related pathways on resilience and frailty during aging in higher animals might possess some degree of reversibility.
Collapse
Affiliation(s)
- Adrian Molière
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, CH-8603, Schwerzenbach, Switzerland
| | - Ji Young Cecilia Park
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, CH-8603, Schwerzenbach, Switzerland
| | - Anita Goyala
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, CH-8603, Schwerzenbach, Switzerland
| | - Elena M Vayndorf
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195-7470, USA
| | - Bruce Zhang
- Institute of Healthy Ageing, and Research Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Kuei Ching Hsiung
- Institute of Healthy Ageing, and Research Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Yoonji Jung
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, South Korea
| | - Sujeong Kwon
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, South Korea
| | - Cyril Statzer
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, CH-8603, Schwerzenbach, Switzerland
| | - David Meyer
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University Hospital and University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
| | - Richard Nguyen
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195-7470, USA
| | | | | | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University Hospital and University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
| | - Seung-Jae V Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, South Korea
| | - Clara L Essmann
- Bioinformatics and Molecular Genetics, Institute of Biology III, Faculty of Biology, Albert-Ludwigs-University Freiburg, 79108, Freiburg, Germany
| | - Michael R MacArthur
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08540, USA
| | - Matt Kaeberlein
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195-7470, USA
| | | | - David Gems
- Institute of Healthy Ageing, and Research Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Collin Y Ewald
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, CH-8603, Schwerzenbach, Switzerland.
| |
Collapse
|
2
|
Basile S, Parisi C, Bellia F, Zimbone S, Arrabito G, Gulli D, Pignataro B, Giuffrida ML, Sortino S, Copani A. Red-Light-Photosensitized Tyrosine 10 Nitration of β-Amyloid 1-42 Diverts the Protein from Forming Toxic Aggregates. ACS Chem Neurosci 2024; 15:2916-2924. [PMID: 39036818 DOI: 10.1021/acschemneuro.4c00284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024] Open
Abstract
Several studies have highlighted the presence of nitration damage following neuroinflammation in Alzheimer's disease (AD). Accordingly, post-transcriptional modifications of β-amyloid (Aβ), including peptide nitration, have been explored as a marker of the disease. However, the implications of Aβ nitration in terms of aggregation propensity and neurotoxicity are still debated. Here, we show new data obtained using a photoactivatable peroxynitrite generator (BPT-NO) to overcome the limitations associated with chemical nitration methods. We found that the photoactivation of BPT-NO with the highly biocompatible red light selectively induces the nitration of tyrosine 10 of freshly solubilized full-length Aβ1-42. Photonitrated Aβ1-42 was, therefore, investigated for aggregation states and functions. It resulted that photonitrated Aβ1-42 did not aggregate into small oligomers but rather self-assembled into large amorphous aggregates. When tested on neuronal-like SH-SY5Y cells and microglial C57BL/6 BV2 cells, photonitrated Aβ1-42 showed to be free of neurotoxicity and able to induce phagocytic microglia cells. We propose that light-controlled nitration of the multiple forms in which Aβ occurs (i.e., monomers, oligomers, fibrils) could be a tool to assess in real-time the impact of tyrosine nitration on the amyloidogenic and toxic properties of Aβ1-42.
Collapse
Affiliation(s)
- Sarah Basile
- Department of Drug and Health Sciences (DSFS), University of Catania, 95125 Catania, Italy
| | - Cristina Parisi
- Department of Drug and Health Sciences (DSFS), University of Catania, 95125 Catania, Italy
| | - Francesco Bellia
- Institute of Crystallography (IC), National Research Council, 95126 Catania, Italy
| | - Stefania Zimbone
- Institute of Crystallography (IC), National Research Council, 95126 Catania, Italy
| | - Giuseppe Arrabito
- Department of Physics and Chemistry (DiFC) Emilio Segrè, University of Palermo, 90128 Palermo, Italy
- ATeN Center, University of Palermo, 90128 Palermo, Italy
| | - Daniele Gulli
- ATeN Center, University of Palermo, 90128 Palermo, Italy
| | - Bruno Pignataro
- Department of Physics and Chemistry (DiFC) Emilio Segrè, University of Palermo, 90128 Palermo, Italy
- ATeN Center, University of Palermo, 90128 Palermo, Italy
| | | | - Salvatore Sortino
- Department of Drug and Health Sciences (DSFS), University of Catania, 95125 Catania, Italy
| | - Agata Copani
- Department of Drug and Health Sciences (DSFS), University of Catania, 95125 Catania, Italy
- Institute of Crystallography (IC), National Research Council, 95126 Catania, Italy
| |
Collapse
|
3
|
Ganne A, Mainali N, Balasubramaniam M, Atluri R, Pahal S, Asante J, Nagel C, Vallurupalli S, Shmookler Reis RJ, Ayyadevara S. Ezetimibe Lowers Risk of Alzheimer's and Related Dementias over Sevenfold, Reducing Aggregation in Model Systems by Inhibiting 14-3-3G::Hexokinase Interaction. AGING BIOLOGY 2024; 2:20240028. [PMID: 39263528 PMCID: PMC11389752 DOI: 10.59368/agingbio.20240028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
Numerous factors predispose to progression of cognitive impairment to Alzheimer's disease and related dementias (ADRD), most notably age, APOE(ε4) alleles, traumatic brain injury, heart disease, hypertension, obesity/diabetes, and Down's syndrome. Protein aggregation is diagnostic for neurodegenerative diseases, and may be causal through promotion of chronic neuroinflammation. We isolated aggregates from postmortem hippocampi of ADRD patients, heart-disease patients, and age-matched controls. Aggregates, characterized by high-resolution proteomics (with or without crosslinking), were significantly elevated in heart-disease and ADRD hippocampi. Hexokinase-1 (HK1) and 14-3-3G/γ proteins, previously implicated in neuronal signaling and neurodegeneration, are especially enriched in ADRD and heart-disease aggregates vs. controls (each P<0.008), and their interaction was implied by extensive crosslinking in both disease groups. Screening the hexokinase-1::14-3-3G interface with FDA-approved drug structures predicted strong affinity for ezetimibe, a benign cholesterol-lowering medication. Diverse cultured human-cell and whole-nematode models of ADRD aggregation showed that this drug potently disrupts HK1::14-3-3G adhesion, reduces disease-associated aggregation, and activates autophagy. Mining clinical databases supports drug reduction of ADRD risk, decreasing it to 0.14 overall (P<0.0001; 95% C.I. 0.06-0.34), and <0.12 in high-risk heart-disease subjects (P<0.006). These results suggest that drug disruption of the 14-3-3G::HK1 interface blocks an early "lynchpin" adhesion, prospectively reducing aggregate accrual and progression of ADRD.
Collapse
Affiliation(s)
- Akshatha Ganne
- Department of Geriatrics and Institute on Aging, University of Arkansas for Medical Sciences, Little Rock AR 72205
| | - Nirjal Mainali
- Bioinformatics Program, University of Arkansas at Little Rock and University of Arkansas for Medical Sciences, Little Rock AR 72205
- Department of Geriatrics and Institute on Aging, University of Arkansas for Medical Sciences, Little Rock AR 72205
| | | | - Ramani Atluri
- Department of Geriatrics and Institute on Aging, University of Arkansas for Medical Sciences, Little Rock AR 72205
| | - Sonu Pahal
- Bioinformatics Program, University of Arkansas at Little Rock and University of Arkansas for Medical Sciences, Little Rock AR 72205
- Department of Geriatrics and Institute on Aging, University of Arkansas for Medical Sciences, Little Rock AR 72205
| | - Joseph Asante
- Bioinformatics Program, University of Arkansas at Little Rock and University of Arkansas for Medical Sciences, Little Rock AR 72205
- Department of Geriatrics and Institute on Aging, University of Arkansas for Medical Sciences, Little Rock AR 72205
| | - Corey Nagel
- College of Nursing, University of Arkansas for Medical Sciences, Little Rock AR 72205
| | - Srikanth Vallurupalli
- Central Arkansas Veterans Healthcare System, Little Rock AR 72205
- Department of Internal Medicine, Division of Cardiology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Robert J Shmookler Reis
- Bioinformatics Program, University of Arkansas at Little Rock and University of Arkansas for Medical Sciences, Little Rock AR 72205
- Department of Geriatrics and Institute on Aging, University of Arkansas for Medical Sciences, Little Rock AR 72205
- Central Arkansas Veterans Healthcare System, Little Rock AR 72205
| | - Srinivas Ayyadevara
- Bioinformatics Program, University of Arkansas at Little Rock and University of Arkansas for Medical Sciences, Little Rock AR 72205
- Department of Geriatrics and Institute on Aging, University of Arkansas for Medical Sciences, Little Rock AR 72205
- Central Arkansas Veterans Healthcare System, Little Rock AR 72205
| |
Collapse
|
4
|
Hole KL, Zhu B, Huggon L, Brown JT, Mason JM, Williams RJ. Tau P301L disengages from the proteosome core complex and neurogranin coincident with enhanced neuronal network excitability. Cell Death Dis 2024; 15:429. [PMID: 38890273 PMCID: PMC11189525 DOI: 10.1038/s41419-024-06815-2] [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: 10/30/2023] [Revised: 06/04/2024] [Accepted: 06/07/2024] [Indexed: 06/20/2024]
Abstract
Tauopathies are characterised by the pathological accumulation of misfolded tau. The emerging view is that toxic tau species drive synaptic dysfunction and potentially tau propagation before measurable neurodegeneration is evident, but the underlying molecular events are not well defined. Human non-mutated 0N4R tau (tauWT) and P301L mutant 0N4R tau (tauP301L) were expressed in mouse primary cortical neurons using adeno-associated viruses to monitor early molecular changes and synaptic function before the onset of neuronal loss. In this model tauP301L was differentially phosphorylated relative to tauwt with a notable increase in phosphorylation at ser262. Affinity purification - mass spectrometry combined with tandem mass tagging was used to quantitatively compare the tauWT and tauP301L interactomes. This revealed an enrichment of tauP301L with ribosomal proteins but a decreased interaction with the proteasome core complex and reduced tauP301L degradation. Differences in the interaction of tauP301L with members of a key synaptic calcium-calmodulin signalling pathway were also identified, most notably, increased association with CaMKII but reduced association with calcineurin and the candidate AD biomarker neurogranin. Decreased association of neurogranin to tauP301L corresponded with the appearance of enhanced levels of extracellular neurogranin suggestive of potential release or leakage from synapses. Finally, analysis of neuronal network activity using micro-electrode arrays showed that overexpression of tauP301L promoted basal hyperexcitability coincident with these changes in the tau interactome and implicating tau in specific early alterations in synaptic function.
Collapse
Affiliation(s)
- Katriona L Hole
- Department of Life Sciences, University of Bath, Bath, UK
- The Francis Crick Institute, London, UK
| | - Bangfu Zhu
- Department of Life Sciences, University of Bath, Bath, UK
| | - Laura Huggon
- Department of Life Sciences, University of Bath, Bath, UK
- UK Dementia Research Institute at King's College London, London, UK
| | - Jon T Brown
- Department of Clinical and Biomedical Sciences, University of Exeter, Exeter, UK
| | - Jody M Mason
- Department of Life Sciences, University of Bath, Bath, UK
| | | |
Collapse
|
5
|
Thierry M, Ponce J, Martà-Ariza M, Askenazi M, Faustin A, Leitner D, Pires G, Kanshin E, Drummond E, Ueberheide B, Wisniewski T. The influence of APOE ε4 on the pTau interactome in sporadic Alzheimer's disease. Acta Neuropathol 2024; 147:91. [PMID: 38772917 PMCID: PMC11108952 DOI: 10.1007/s00401-024-02744-8] [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: 03/11/2024] [Revised: 04/12/2024] [Accepted: 05/12/2024] [Indexed: 05/23/2024]
Abstract
APOEε4 is the major genetic risk factor for sporadic Alzheimer's disease (AD). Although APOEε4 is known to promote Aβ pathology, recent data also support an effect of APOE polymorphism on phosphorylated Tau (pTau) pathology. To elucidate these potential effects, the pTau interactome was analyzed across APOE genotypes in the frontal cortex of 10 advanced AD cases (n = 5 APOEε3/ε3 and n = 5 APOEε4/ε4), using a combination of anti-pTau pS396/pS404 (PHF1) immunoprecipitation (IP) and mass spectrometry (MS). This proteomic approach was complemented by an analysis of anti-pTau PHF1 and anti-Aβ 4G8 immunohistochemistry, performed in the frontal cortex of 21 advanced AD cases (n = 11 APOEε3/ε3 and n = 10 APOEε4/ε4). Our dataset includes 1130 and 1330 proteins enriched in IPPHF1 samples from APOEε3/ε3 and APOEε4/ε4 groups (fold change ≥ 1.50, IPPHF1 vs IPIgG ctrl). We identified 80 and 68 proteins as probable pTau interactors in APOEε3/ε3 and APOEε4/ε4 groups, respectively (SAINT score ≥ 0.80; false discovery rate (FDR) ≤ 5%). A total of 47/80 proteins were identified as more likely to interact with pTau in APOEε3/ε3 vs APOEε4/ε4 cases. Functional enrichment analyses showed that they were significantly associated with the nucleoplasm compartment and involved in RNA processing. In contrast, 35/68 proteins were identified as more likely to interact with pTau in APOEε4/ε4 vs APOEε3/ε3 cases. They were significantly associated with the synaptic compartment and involved in cellular transport. A characterization of Tau pathology in the frontal cortex showed a higher density of plaque-associated neuritic crowns, made of dystrophic axons and synapses, in APOEε4 carriers. Cerebral amyloid angiopathy was more frequent and severe in APOEε4/ε4 cases. Our study supports an influence of APOE genotype on pTau-subcellular location in AD. These results suggest a facilitation of pTau progression to Aβ-affected brain regions in APOEε4 carriers, paving the way to the identification of new therapeutic targets.
Collapse
Affiliation(s)
- Manon Thierry
- Department of Neurology, Center for Cognitive Neurology, Grossman School of Medicine, New York University, Science Building, Rm 1023J, 435 East 30th Street, New York, NY, USA.
| | - Jackeline Ponce
- Department of Biochemistry and Molecular Pharmacology, Proteomics Laboratory, Grossman School of Medicine, New York University, New York, NY, USA
| | - Mitchell Martà-Ariza
- Department of Neurology, Center for Cognitive Neurology, Grossman School of Medicine, New York University, Science Building, Rm 1023J, 435 East 30th Street, New York, NY, USA
- Institut de Neurociències, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Arline Faustin
- Department of Neurology, Center for Cognitive Neurology, Grossman School of Medicine, New York University, Science Building, Rm 1023J, 435 East 30th Street, New York, NY, USA
| | - Dominique Leitner
- Department of Neurology, Center for Cognitive Neurology, Grossman School of Medicine, New York University, Science Building, Rm 1023J, 435 East 30th Street, New York, NY, USA
- Department of Neurology, Comprehensive Epilepsy Center, Grossman School of Medicine, New York University, New York, NY, USA
| | - Geoffrey Pires
- Department of Neurology, Center for Cognitive Neurology, Grossman School of Medicine, New York University, Science Building, Rm 1023J, 435 East 30th Street, New York, NY, USA
| | - Evgeny Kanshin
- Department of Biochemistry and Molecular Pharmacology, Proteomics Laboratory, Grossman School of Medicine, New York University, New York, NY, USA
| | - Eleanor Drummond
- Brain and Mind Centre, School of Medical Science, University of Sydney, Sydney, Australia
| | - Beatrix Ueberheide
- Department of Biochemistry and Molecular Pharmacology, Proteomics Laboratory, Grossman School of Medicine, New York University, New York, NY, USA
| | - Thomas Wisniewski
- Department of Neurology, Center for Cognitive Neurology, Grossman School of Medicine, New York University, Science Building, Rm 1023J, 435 East 30th Street, New York, NY, USA.
- Departments of Pathology and Psychiatry, Grossman School of Medicine, New York University, Science Building, Rm 1017, 435 East 30 Street, New York, NY, 10016, USA.
| |
Collapse
|
6
|
Buchholz S, Zempel H. The six brain-specific TAU isoforms and their role in Alzheimer's disease and related neurodegenerative dementia syndromes. Alzheimers Dement 2024; 20:3606-3628. [PMID: 38556838 PMCID: PMC11095451 DOI: 10.1002/alz.13784] [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: 12/08/2023] [Revised: 02/08/2024] [Accepted: 02/12/2024] [Indexed: 04/02/2024]
Abstract
INTRODUCTION Alternative splicing of the human MAPT gene generates six brain-specific TAU isoforms. Imbalances in the TAU isoform ratio can lead to neurodegenerative diseases, underscoring the need for precise control over TAU isoform balance. Tauopathies, characterized by intracellular aggregates of hyperphosphorylated TAU, exhibit extensive neurodegeneration and can be classified by the TAU isoforms present in pathological accumulations. METHODS A comprehensive review of TAU and related dementia syndromes literature was conducted using PubMed, Google Scholar, and preprint server. RESULTS While TAU is recognized as key driver of neurodegeneration in specific tauopathies, the contribution of the isoforms to neuronal function and disease development remains largely elusive. DISCUSSION In this review we describe the role of TAU isoforms in health and disease, and stress the importance of comprehending and studying TAU isoforms in both, physiological and pathological context, in order to develop targeted therapeutic interventions for TAU-associated diseases. HIGHLIGHTS MAPT splicing is tightly regulated during neuronal maturation and throughout life. TAU isoform expression is development-, cell-type and brain region specific. The contribution of TAU to neurodegeneration might be isoform-specific. Ineffective TAU-based therapies highlight the need for specific targeting strategies.
Collapse
Affiliation(s)
- Sarah Buchholz
- Institute of Human GeneticsFaculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Center for Molecular Medicine Cologne (CMMC)University of CologneCologneGermany
- Present address:
Department Schaefer, Neurobiology of AgeingMax Planck Institute for Biology of AgeingCologneGermany
| | - Hans Zempel
- Institute of Human GeneticsFaculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Center for Molecular Medicine Cologne (CMMC)University of CologneCologneGermany
| |
Collapse
|
7
|
Morderer D, Wren MC, Liu F, Kouri N, Maistrenko A, Khalil B, Pobitzer N, Salemi M, Phinney BS, Dickson DW, Murray ME, Rossoll W. Probe-dependent Proximity Profiling (ProPPr) Uncovers Similarities and Differences in Phospho-Tau-Associated Proteomes Between Tauopathies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.25.585597. [PMID: 38585836 PMCID: PMC10996607 DOI: 10.1101/2024.03.25.585597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Tauopathies represent a diverse group of neurodegenerative disorders characterized by the abnormal aggregation of the microtubule-associated protein tau. Despite extensive research, the precise mechanisms underlying the complexity of different types of tau pathology remain incompletely understood. Here we describe an approach for proteomic profiling of aggregate-associated proteomes on slides with formalin-fixed, paraffin-embedded (FFPE) tissue that utilizes proximity labelling upon high preservation of aggregate morphology, which permits the profiling of pathological aggregates regardless of their size. To comprehensively investigate the common and unique protein interactors associated with the variety of tau lesions present across different human tauopathies, Alzheimer's disease (AD), corticobasal degeneration (CBD), Pick's disease (PiD), and progressive supranuclear palsy (PSP), were selected to represent the major tauopathy diseases. Implementation of our widely applicable Probe-dependent Proximity Profiling (ProPPr) strategy, using the AT8 antibody, permitted identification and quantification of proteins associated with phospho-tau lesions in well-characterized human post-mortem tissue. The analysis revealed both common and disease-specific proteins associated with phospho-tau aggregates, highlighting potential targets for therapeutic intervention and biomarker development. Candidate validation through high-resolution co-immunofluorescence of distinct aggregates across disease and control cases, confirmed the association of retromer complex protein VPS35 with phospho-tau lesions across the studied tauopathies. Furthermore, we discovered disease-specific associations of proteins including ferritin light chain (FTL) and the neuropeptide precursor VGF within distinct pathological lesions. Notably, examination of FTL-positive microglia in CBD astrocytic plaques indicate a potential role for microglial involvement in the pathogenesis of these tau lesions. Our findings provide valuable insights into the proteomic landscape of tauopathies, shedding light on the molecular mechanisms underlying tau pathology. This first comprehensive characterization of tau-associated proteomes across different tauopathies enhances our understanding of disease heterogeneity and provides a resource for future functional investigation, as well as development of targeted therapies and diagnostic biomarkers.
Collapse
|
8
|
Younas A, Younas N, Iqbal MJ, Ferrer I, Zerr I. Comparative interactome mapping of Tau-protein in classical and rapidly progressive Alzheimer's disease identifies subtype-specific pathways. Neuropathol Appl Neurobiol 2024; 50:e12964. [PMID: 38374702 DOI: 10.1111/nan.12964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 12/27/2023] [Accepted: 01/16/2024] [Indexed: 02/21/2024]
Abstract
AIMS Tau is a key player in Alzheimer's disease (AD) and other Tauopathies. Tau pathology in the brain directly correlates with neurodegeneration in AD. The recent identification of a rapid variant of AD demands an urgent need to uncover underlying mechanisms leading to differential progression in AD. Accordingly, we aimed to dissect the underlying differential mechanisms of toxicity associated with the Tau protein in AD subtypes and to find out subtype-dependent biomarkers and therapeutic targets. METHODS To identify and characterise subtype-specific Tau-associated mechanisms of pathology, we performed comparative interactome mapping of Tau protein in classical AD (cAD) and rapidly progressive AD (rpAD) cases using co-immunoprecipitation coupled with quantitative mass spectrometry. The mass spectrometry data were extensively analysed using several bioinformatics approaches. RESULTS The comparative interactome mapping of Tau protein revealed distinct and unique interactors (DPYSL4, ARHGEF2, TUBA4A and UQCRC2) in subtypes of AD. Interestingly, an analysis of the Tau-interacting proteins indicated enrichment of mitochondrial organisation processes, including negative regulation of mitochondrion organisation, mitochondrial outer membrane permeabilisation involved in programmed cell death, regulation of autophagy of mitochondrion and necroptotic processes, specifically in the rpAD interactome. While, in cAD, the top enriched processes were related to oxidation-reduction process, transport and monocarboxylic acid metabolism. CONCLUSIONS Overall, our results provide a comprehensive map of Tau-interacting protein networks in a subtype-dependent manner and shed light on differential functions/pathways in AD subtypes. This comprehensive map of the Tau-interactome has provided subsets of disease-related proteins that can serve as novel biomarkers/biomarker panels and new drug targets.
Collapse
Affiliation(s)
- Abrar Younas
- National Reference Center for Surveillance of TSE, Department of Neurology, University Medical Center Göttingen, Göttingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
- Department of Biological Sciences, Faculty of Sciences, University of Sialkot, Sialkot, Pakistan
| | - Neelam Younas
- National Reference Center for Surveillance of TSE, Department of Neurology, University Medical Center Göttingen, Göttingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Muhammad Javed Iqbal
- Department of Biotechnology, Faculty of Sciences, University of Sialkot, Sialkot, Pakistan
| | - Isidre Ferrer
- Department of Pathology and Experimental Therapeutics, University of Barcelona, Hospitalet de Llobregat, Spain
| | - Inga Zerr
- National Reference Center for Surveillance of TSE, Department of Neurology, University Medical Center Göttingen, Göttingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| |
Collapse
|
9
|
Balasubramaniam M, Ganne A, Mainali N, Pahal S, Ayyadevara S, Shmookler Reis RJ. Alzheimer's-specific brain amyloid interactome: Neural-network analysis of intra-aggregate crosslinking identifies novel drug targets. iScience 2024; 27:108745. [PMID: 38274404 PMCID: PMC10809092 DOI: 10.1016/j.isci.2023.108745] [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: 08/15/2023] [Revised: 11/15/2023] [Accepted: 12/12/2023] [Indexed: 01/27/2024] Open
Abstract
Alzheimer's disease (AD) is characterized by peri-neuronal amyloid plaque and intra-neuronal neurofibrillary tangles. These aggregates are identified by the immunodetection of "seed" proteins (Aβ1-42 and hyperphosphorylated tau, respectively), but include many other proteins incorporated nonrandomly. Using click-chemistry intra-aggregate crosslinking, we previously modeled amyloid "contactomes" in SY5Y-APPSw neuroblastoma cells, revealing that aspirin impedes aggregate growth and complexity. By an analogous strategy, we now construct amyloid-specific aggregate interactomes of AD and age-matched-control hippocampi. Comparing these interactomes reveals AD-specific interactions, from which neural-network (NN) analyses predict proteins with the highest impact on pathogenic aggregate formation and/or stability. RNAi knockdowns of implicated proteins, in C. elegans and human-cell-culture models of AD, validated those predictions. Gene-Ontology meta-analysis of AD-enriched influential proteins highlighted the involvement of mitochondrial and cytoplasmic compartments in AD-specific aggregation. This approach derives dynamic consensus models of aggregate growth and architecture, implicating highly influential proteins as new targets to disrupt amyloid accrual in the AD brain.
Collapse
Affiliation(s)
| | - Akshatha Ganne
- Department of Geriatrics, Reynolds Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Nirjal Mainali
- Bioinformatics Program, University of Arkansas for Medical Sciences and University of Arkansas at Little Rock, Little Rock, AR 72205, USA
| | - Sonu Pahal
- Bioinformatics Program, University of Arkansas for Medical Sciences and University of Arkansas at Little Rock, Little Rock, AR 72205, USA
| | - Srinivas Ayyadevara
- Department of Geriatrics, Reynolds Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- McClellan Veterans Medical Center, Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA
| | - Robert J. Shmookler Reis
- Department of Geriatrics, Reynolds Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- McClellan Veterans Medical Center, Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA
| |
Collapse
|
10
|
Mainali N, Li X, Wang X, Balasubramaniam M, Ganne A, Kore R, Shmookler Reis RJ, Mehta JL, Ayyadevara S. Myocardial infarction elevates endoplasmic reticulum stress and protein aggregation in heart as well as brain. Mol Cell Biochem 2023:10.1007/s11010-023-04856-3. [PMID: 37922111 DOI: 10.1007/s11010-023-04856-3] [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: 07/10/2023] [Accepted: 09/09/2023] [Indexed: 11/05/2023]
Abstract
Cardiovascular diseases, including myocardial infarction (MI), constitute the leading cause of morbidity and mortality worldwide. Protein-aggregate deposition is a hallmark of aging and neurodegeneration. Our previous study reported that aggregation is strikingly elevated in hearts of hypertensive and aged mice; however, no prior study has addressed MI effects on aggregation in heart or brain. Here, we present novel data on heart and brain aggregation in mice following experimental MI, induced by left coronary artery (LCA) ligation. Infarcted and peri-infarcted heart tissue, and whole cerebra, were isolated from mice at sacrifice, 7 days following LCA ligation. Sham-MI mice (identical surgery without ligation) served as controls. We purified detergent-insoluble aggregates from these tissues, and quantified key protein constituents by high-resolution mass spectrometry (LC-MS/MS). Infarct heart tissue had 2.5- to 10-fold more aggregates than non-infarct or sham-MI heart tissue (each P = 0.001). Protein constituents from MI cerebral aggregates overlapped substantially with those from human Alzheimer's disease brain. Prior injection of mice with mesenchymal stem cell (MSC) exosomes, shown to limit infarct size after LCA ligation, reduced cardiac aggregation ~ 60%, and attenuated markers of endoplasmic reticulum (ER) stress in heart and brain (GRP78, ATF6, P-PERK) by 50-75%. MI also elevated aggregate constituents enriched in Alzheimer's disease (AD) aggregates, such as proteasomal subunits, heat-shock proteins, complement C3, clusterin/ApoJ, and other apolipoproteins. These data provide novel evidence that aggregation is elevated in mouse hearts and brains after myocardial ischemia, leading to cognitive impairment resembling AD, but can be attenuated by exosomes or drug (CDN1163) interventions that oppose ER stress.
Collapse
Affiliation(s)
- Nirjal Mainali
- Bioinformatics Program, University of Arkansas at Little Rock and University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
- Department of Geriatrics and Reynolds Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Xiao Li
- Henan Key Laboratory of Medical Tissue Regeneration, Xinxiang Medical University, Xinxiang, 453003, China
| | - Xianwei Wang
- Henan Key Laboratory of Medical Tissue Regeneration, Xinxiang Medical University, Xinxiang, 453003, China
| | | | - Akshatha Ganne
- Department of Geriatrics and Reynolds Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Rajshekhar Kore
- Central Arkansas Veterans Healthcare Service, Little Rock, AR, 72205, USA
- Division of Cardiology, University of Arkansas for Medical Sciences and Central Arkansas Veterans Healthcare System, Little Rock, AR, USA
| | - Robert J Shmookler Reis
- Bioinformatics Program, University of Arkansas at Little Rock and University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA.
- Department of Geriatrics and Reynolds Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA.
- Central Arkansas Veterans Healthcare Service, Little Rock, AR, 72205, USA.
| | - Jawahar L Mehta
- Central Arkansas Veterans Healthcare Service, Little Rock, AR, 72205, USA.
- Division of Cardiology, University of Arkansas for Medical Sciences and Central Arkansas Veterans Healthcare System, Little Rock, AR, USA.
- Department of Cardiology, University of Arkansas for Medical Sciences and Central Arkansas Veterans Healthcare System, Little Rock, AR, USA.
| | - Srinivas Ayyadevara
- Bioinformatics Program, University of Arkansas at Little Rock and University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA.
- Department of Geriatrics and Reynolds Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA.
- Central Arkansas Veterans Healthcare Service, Little Rock, AR, 72205, USA.
| |
Collapse
|
11
|
Li X, Gao Y, Li B, Zhao W, Cai Q, Yin W, Zeng S, Li X, Gao H, Cheng M. Integrated proteomics and metabolomics analysis of D-pinitol function during hippocampal damage in streptozocin-induced aging-accelerated mice. Front Mol Neurosci 2023; 16:1251513. [PMID: 38025258 PMCID: PMC10664147 DOI: 10.3389/fnmol.2023.1251513] [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: 07/12/2023] [Accepted: 10/09/2023] [Indexed: 12/01/2023] Open
Abstract
Purpose Diabetes can cause hippocampal damage and lead to cognitive impairment. Diabetic cognitive impairment (DCI) is a chronic complication of diabetes associated with a high disability rate; however, its pathogenesis and therapeutic targets are unclear. We aimed to explore the mechanism of hippocampal damage during diabetes and evaluate the potential role of D-pinitol (DP) in protecting hippocampal tissue and improving cognitive dysfunction. Methods DP (150 mg/kg/day) was administered intragastrically to streptozocin-induced aging-accelerated mice for 8 weeks. Hippocampal tissues were examined using tandem mass tag (TMT)-based proteomics and liquid chromatography-mass spectrometry (LC-MS)/MS-based non-targeted metabolomic analysis. Differentially expressed proteins (DEPs) and differentially regulated metabolites (DRMs) were screened for further analysis, and some DEPs were verified using western blotting. Results Our results showed that 329 proteins had significantly altered hippocampal expression in untreated diabetic mice (DM), which was restored to normal after DP treatment in 72 cases. In total, 207 DRMs were identified in the DM group, and the expression of 32 DRMs was restored to normal post-DP treatment. These proteins and metabolites are involved in metabolic pathways (purine metabolism, arginine and proline metabolism, and histidine metabolism), actin cytoskeleton regulation, oxidative phosphorylation, and Rap1-mediated signaling. Conclusions Our study may help to better understand the mechanism of diabetic hippocampal damage and cognitive impairment and suggest a potential therapeutic target.
Collapse
Affiliation(s)
- Xiaoxia Li
- Department of Geriatric Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Key Laboratory of Cardiovascular Proteomics of Shandong Province, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Jinan Clinical Research Center for Geriatric Medicine, Jinan, China
- Department of Diabetes, The Third People's Hospital of Gansu Province, Lanzhou, China
| | - Yuan Gao
- Department of Geriatric Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Key Laboratory of Cardiovascular Proteomics of Shandong Province, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Jinan Clinical Research Center for Geriatric Medicine, Jinan, China
| | - Baoying Li
- Key Laboratory of Cardiovascular Proteomics of Shandong Province, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Health Management Center (East Area), Qilu Hospital of Shandong University, Jinan, China
| | - Wenqian Zhao
- Department of Geriatric Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Key Laboratory of Cardiovascular Proteomics of Shandong Province, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Jinan Clinical Research Center for Geriatric Medicine, Jinan, China
| | - Qian Cai
- Department of Geriatric Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Key Laboratory of Cardiovascular Proteomics of Shandong Province, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Jinan Clinical Research Center for Geriatric Medicine, Jinan, China
| | - Wenbin Yin
- Department of Geriatric Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Key Laboratory of Cardiovascular Proteomics of Shandong Province, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Jinan Clinical Research Center for Geriatric Medicine, Jinan, China
| | - Shudong Zeng
- Department of Geriatric Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Key Laboratory of Cardiovascular Proteomics of Shandong Province, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Jinan Clinical Research Center for Geriatric Medicine, Jinan, China
| | - Xiaoli Li
- Department of Pharmacy, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Haiqing Gao
- Department of Geriatric Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Key Laboratory of Cardiovascular Proteomics of Shandong Province, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Jinan Clinical Research Center for Geriatric Medicine, Jinan, China
| | - Mei Cheng
- Department of Geriatric Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Key Laboratory of Cardiovascular Proteomics of Shandong Province, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Jinan Clinical Research Center for Geriatric Medicine, Jinan, China
| |
Collapse
|
12
|
Kakraba S, Ayyadevara S, Mainali N, Balasubramaniam M, Bowroju S, Penthala NR, Atluri R, Barger SW, Griffin ST, Crooks PA, Shmookler Reis RJ. Thiadiazolidinone (TDZD) Analogs Inhibit Aggregation-Mediated Pathology in Diverse Neurodegeneration Models, and Extend C. elegans Life- and Healthspan. Pharmaceuticals (Basel) 2023; 16:1498. [PMID: 37895969 PMCID: PMC10610358 DOI: 10.3390/ph16101498] [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: 08/25/2023] [Revised: 09/29/2023] [Accepted: 10/02/2023] [Indexed: 10/29/2023] Open
Abstract
Chronic, low-grade inflammation has been implicated in aging and age-dependent conditions, including Alzheimer's disease, cardiomyopathy, and cancer. One of the age-associated processes underlying chronic inflammation is protein aggregation, which is implicated in neuroinflammation and a broad spectrum of neurodegenerative diseases such as Alzheimer's, Huntington's, and Parkinson's diseases. We screened a panel of bioactive thiadiazolidinones (TDZDs) from our in-house library for rescue of protein aggregation in human-cell and C. elegans models of neurodegeneration. Among the tested TDZD analogs, PNR886 and PNR962 were most effective, significantly reducing both the number and intensity of Alzheimer-like tau and amyloid aggregates in human cell-culture models of pathogenic aggregation. A C. elegans strain expressing human Aβ1-42 in muscle, leading to AD-like amyloidopathy, developed fewer and smaller aggregates after PNR886 or PNR962 treatment. Moreover, age-progressive paralysis was reduced 90% by PNR886 and 75% by PNR962, and "healthspan" (the median duration of spontaneous motility) was extended 29% and 62%, respectively. These TDZD analogs also extended wild-type C. elegans lifespan by 15-30% (p < 0.001), placing them among the most effective life-extension drugs. Because the lead drug in this family, TDZD-8, inhibits GSK3β, we used molecular-dynamic tools to assess whether these analogs may also target GSK3β. In silico modeling predicted that PNR886 or PNR962 would bind to the same allosteric pocket of inactive GSK3β as TDZD-8, employing the same pharmacophore but attaching with greater avidity. PNR886 and PNR962 are thus compelling candidate drugs for treatment of tau- and amyloid-associated neurodegenerative diseases such as AD, potentially also reducing all-cause mortality.
Collapse
Affiliation(s)
- Samuel Kakraba
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (N.M.); (M.B.); (R.A.); (S.W.B.); (S.T.G.)
| | - Srinivas Ayyadevara
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (N.M.); (M.B.); (R.A.); (S.W.B.); (S.T.G.)
- Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA
| | - Nirjal Mainali
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (N.M.); (M.B.); (R.A.); (S.W.B.); (S.T.G.)
| | - Meenakshisundaram Balasubramaniam
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (N.M.); (M.B.); (R.A.); (S.W.B.); (S.T.G.)
| | - Suresh Bowroju
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (S.B.); (N.R.P.); (P.A.C.)
| | - Narsimha Reddy Penthala
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (S.B.); (N.R.P.); (P.A.C.)
| | - Ramani Atluri
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (N.M.); (M.B.); (R.A.); (S.W.B.); (S.T.G.)
| | - Steven W. Barger
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (N.M.); (M.B.); (R.A.); (S.W.B.); (S.T.G.)
- Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA
| | - Sue T. Griffin
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (N.M.); (M.B.); (R.A.); (S.W.B.); (S.T.G.)
- Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA
| | - Peter A. Crooks
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (S.B.); (N.R.P.); (P.A.C.)
| | - Robert J. Shmookler Reis
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (N.M.); (M.B.); (R.A.); (S.W.B.); (S.T.G.)
- Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA
| |
Collapse
|
13
|
Weiner S, Sauer M, Brinkmalm G, Constantinescu J, Constantinescu R, Gomes BF, Becker B, Nellgård B, Dalla K, Galasko D, Zetterberg H, Blennow K, Gobom J. SCRN1: A cerebrospinal fluid biomarker correlating with tau in Alzheimer's disease. Alzheimers Dement 2023; 19:4609-4618. [PMID: 36946611 DOI: 10.1002/alz.13042] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/29/2022] [Accepted: 01/04/2023] [Indexed: 03/23/2023]
Abstract
INTRODUCTION Secernin-1 (SCRN1) is a neuronal protein that co-localizes with neurofibrillary tangles in Alzheimer's disease (AD), but not with tau inclusions in corticobasal degeneration (CBD), progressive supranuclear palsy (PSP), or Pick's disease. METHODS We measured SCRN1 concentration in cerebrospinal fluid (CSF) using a novel mass spectrometric parallel reaction monitoring method in three clinical cohorts comprising patients with neurochemically characterized AD (n = 25) and controls (n = 28), clinically diagnosed Parkinson's disease (PD; n = 38), multiple system atrophy (MSA; n = 31), PSP (n = 20), CBD (n = 8), healthy controls (n = 37), and neuropathology-confirmed AD (n = 47). RESULTS CSF SCRN1 was significantly increased in AD (P < 0.01, fold change = 1.4) compared to controls (receiver operating characteristic area under the curve = 0.78) but not in CBD, PSP, PD, or MSA. CSF SCRN1 positively correlated with CSF total tau (R = 0.78, P = 1.1 × 10-13 ), phosphorylated tau181 (R = 0.64, P = 3.2 × 10-8 ), and Braak stage and negatively correlated with Mini-Mental State Examination score. DISCUSSION CSF SCRN1 is a candidate biomarker of AD, reflecting tau pathology. HIGHLIGHTS We developed a parallel reaction monitoring assay to measure secernin-1 (SCRN1) in cerebrospinal fluid (CSF). CSF SCRN1 was increased in Alzheimer's disease compared to healthy controls. CSF SCRN1 remained unchanged in Parkinson's disease, multiple system atrophy, progressive supranuclear palsy, or corticobasal degeneration compared to controls. CSF SCRN1 correlated strongly with CSF phosphorylated tau and total tau. CSF SCRN1 increased across Braak stages and negatively correlated with Mini-Mental State Examination score.
Collapse
Affiliation(s)
- Sophia Weiner
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, University of Gothenburg, Mölndal, Sweden
| | - Mathias Sauer
- Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Gunnar Brinkmalm
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, University of Gothenburg, Mölndal, Sweden
| | - Julius Constantinescu
- Department of Neurology, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Radu Constantinescu
- Department of Neurology, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Bárbara Fernandes Gomes
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, University of Gothenburg, Mölndal, Sweden
| | - Bruno Becker
- Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Bengt Nellgård
- Department of Anesthesiology and Intensive Care Medicine, Institute of Clinical Sciences, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Keti Dalla
- Department of Anesthesiology and Intensive Care Medicine, Institute of Clinical Sciences, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Douglas Galasko
- Department of Neurosciences, University of California, San Diego, La Jolla, California, USA
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK
- UK Dementia Research Institute, London, UK
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong, China
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Johan Gobom
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, Sahlgrenska University Hospital, Mölndal, Sweden
| |
Collapse
|
14
|
Singh R, Hussain J, Kaur A, Jamdare BG, Pathak D, Garg K, Kaur R, Shankar S, Sunkaria A. The hidden players: Shedding light on the significance of post-translational modifications and miRNAs in Alzheimer's disease development. Ageing Res Rev 2023; 90:102002. [PMID: 37423542 DOI: 10.1016/j.arr.2023.102002] [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: 05/26/2023] [Revised: 06/29/2023] [Accepted: 07/03/2023] [Indexed: 07/11/2023]
Abstract
Alzheimer's disease (AD) is the most prevalent, expensive, lethal, and burdening neurodegenerative disease of this century. The initial stages of this disease are characterized by a reduced ability to encode and store new memories. Subsequent cognitive and behavioral deterioration occurs during the later stages. Abnormal cleavage of amyloid precursor protein (APP) resulting in amyloid-beta (Aβ) accumulation along with hyperphosphorylation of tau protein are the two characteristic hallmarks of AD. Recently, several post-translational modifications (PTMs) have been identified on both Aβ as well as tau proteins. However, a complete understanding of how different PTMs influence the structure and function of proteins in both healthy and diseased conditions is still lacking. It has been speculated that these PTMs might play vital roles in the progression of AD. In addition, several short non-coding microRNA (miRNA) sequences have been found to be deregulated in the peripheral blood of Alzheimer patients. The miRNAs are single-stranded RNAs that control gene expression by causing mRNA degradation, deadenylation, or translational repression and have been implicated in the regulation of several neuronal and glial activities. The lack of comprehensive understanding regarding disease mechanisms, biomarkers, and therapeutic targets greatly hampers the development of effective strategies for early diagnosis and the identification of viable therapeutic targets. Moreover, existing treatment options for managing the disease have proven to be ineffective and provide only temporary relief. Therefore, understanding the role of miRNAs and PTMs in AD can provide valuable insights into disease mechanisms, aid in the identification of biomarkers, facilitate the discovery of novel therapeutic targets, and inspire innovative treatments for this challenging condition.
Collapse
Affiliation(s)
- Ravinder Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Julfequar Hussain
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Amandeep Kaur
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Balaji Gokul Jamdare
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Deepti Pathak
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Kanchan Garg
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Ramanpreet Kaur
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Shivani Shankar
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Aditya Sunkaria
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India.
| |
Collapse
|
15
|
Romero-Fernandez W, Carvajal-Tapia C, Prusky A, Katdare KA, Wang E, Shostak A, Ventura-Antunes L, Harmsen HJ, Lippmann ES, Fuxe K, MacGurn JA, Borroto-Escuela DO, Schrag MS. Detection, visualization and quantification of protein complexes in human Alzheimer's disease brains using proximity ligation assay. Sci Rep 2023; 13:11948. [PMID: 37488165 PMCID: PMC10366145 DOI: 10.1038/s41598-023-38000-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/30/2023] [Indexed: 07/26/2023] Open
Abstract
Examination of healthy and diseased human brain is essential to translational neuroscience. Protein-protein interactions play a pivotal role in physiological and pathological processes, but their detection is difficult, especially in aged and fixed human brain tissue. We used the in-situ proximity ligation assay (PLA) to broaden the range of molecular interactions assessable in-situ in the human neuropathology. We adapted fluorescent in-situ PLA to detect ubiquitin-modified proteins in human brains with Alzheimer's disease (AD), including approaches for the management of autofluorescence and quantification using a high-content image analysis system. We confirmed that phosphorylated microtubule-associated protein tau (Serine202, Threonine205) aggregates were modified by ubiquitin and that phospho-tau-ubiquitin complexes were increased in hippocampal and frontal cortex regions in AD compared to non-AD brains. Overall, we refined PLA for use in human neuropathology, which has revealed a profound change in the distribution of ubiquitin in AD brain and its association with characteristic tau pathologies.
Collapse
Affiliation(s)
- Wilber Romero-Fernandez
- Department of Neurology, Vanderbilt University Medical Center, MRBIII 465 21St Avenue S, Suite 6158, Nashville, TN, 37240, USA.
| | - Cristian Carvajal-Tapia
- Department of Neurology, Vanderbilt University Medical Center, MRBIII 465 21St Avenue S, Suite 6158, Nashville, TN, 37240, USA
| | - Alex Prusky
- Department of Neurology, Vanderbilt University Medical Center, MRBIII 465 21St Avenue S, Suite 6158, Nashville, TN, 37240, USA
| | - Ketaki A Katdare
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, 37232, USA
| | - Emmeline Wang
- Department of Neurology, Vanderbilt University Medical Center, MRBIII 465 21St Avenue S, Suite 6158, Nashville, TN, 37240, USA
| | - Alena Shostak
- Department of Neurology, Vanderbilt University Medical Center, MRBIII 465 21St Avenue S, Suite 6158, Nashville, TN, 37240, USA
| | - Lissa Ventura-Antunes
- Department of Neurology, Vanderbilt University Medical Center, MRBIII 465 21St Avenue S, Suite 6158, Nashville, TN, 37240, USA
| | - Hannah J Harmsen
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37240, USA
| | - Ethan S Lippmann
- Department of Neurology, Vanderbilt University Medical Center, MRBIII 465 21St Avenue S, Suite 6158, Nashville, TN, 37240, USA
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, 37235, USA
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University, Nashville, TN, 37235, USA
| | - Kjell Fuxe
- Department of Neuroscience, Karolinska Institute, Solna, 17177, Stockholm, Sweden
| | - Jason A MacGurn
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, 37240, USA
| | - Dasiel O Borroto-Escuela
- Department of Neuroscience, Karolinska Institute, Solna, 17177, Stockholm, Sweden
- Receptomics and Brain Disorders Lab, Department of Human Physiology, Sport and Exercise, Faculty of Medicine, University of Malaga, Edificio Lopez-Penalver, Jimenez Fraud 10, 29071, Málaga, Spain
| | - Matthew S Schrag
- Department of Neurology, Vanderbilt University Medical Center, MRBIII 465 21St Avenue S, Suite 6158, Nashville, TN, 37240, USA.
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, 37232, USA.
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University, Nashville, TN, 37235, USA.
| |
Collapse
|
16
|
Radford RAW, Rayner SL, Szwaja P, Morsch M, Cheng F, Zhu T, Widagdo J, Anggono V, Pountney DL, Chung R, Lee A. Identification of phosphorylated tau protein interactors in progressive supranuclear palsy (PSP) reveals networks involved in protein degradation, stress response, cytoskeletal dynamics, metabolic processes, and neurotransmission. J Neurochem 2023; 165:563-586. [PMID: 36847488 PMCID: PMC10953353 DOI: 10.1111/jnc.15796] [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: 11/23/2022] [Revised: 01/27/2023] [Accepted: 02/21/2023] [Indexed: 03/01/2023]
Abstract
Progressive supranuclear palsy (PSP) is a late-onset neurodegenerative disease defined pathologically by the presence of insoluble phosphorylated-Tau (p-Tau) in neurons and glia. Identifying co-aggregating proteins within p-Tau inclusions may reveal important insights into processes affected by the aggregation of Tau. We used a proteomic approach, which combines antibody-mediated biotinylation and mass spectrometry (MS) to identify proteins proximal to p-Tau in PSP. Using this proof-of-concept workflow for identifying interacting proteins of interest, we characterized proteins proximal to p-Tau in PSP cases, identifying >84% of previously identified interaction partners of Tau and known modifiers of Tau aggregation, while 19 novel proteins not previously found associated with Tau were identified. Furthermore, our data also identified confidently assigned phosphorylation sites that have been previously reported on p-Tau. Additionally, using ingenuity pathway analysis (IPA) and human RNA-seq datasets, we identified proteins previously associated with neurological disorders and pathways involved in protein degradation, stress responses, cytoskeletal dynamics, metabolism, and neurotransmission. Together, our study demonstrates the utility of biotinylation by antibody recognition (BAR) approach to answer a fundamental question to rapidly identify proteins in proximity to p-Tau from post-mortem tissue. The application of this workflow opens up the opportunity to identify novel protein targets to give us insight into the biological process at the onset and progression of tauopathies.
Collapse
Affiliation(s)
- Rowan A. W. Radford
- Centre for Motor Neuron Disease ResearchMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversityNew South WalesNorth RydeAustralia
| | - Stephanie L. Rayner
- Centre for Motor Neuron Disease ResearchMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversityNew South WalesNorth RydeAustralia
| | - Paulina Szwaja
- Centre for Motor Neuron Disease ResearchMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversityNew South WalesNorth RydeAustralia
| | - Marco Morsch
- Centre for Motor Neuron Disease ResearchMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversityNew South WalesNorth RydeAustralia
| | - Flora Cheng
- Centre for Motor Neuron Disease ResearchMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversityNew South WalesNorth RydeAustralia
| | - Tianyi Zhu
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain InstituteThe University of QueenslandQueenslandBrisbaneAustralia
| | - Jocelyn Widagdo
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain InstituteThe University of QueenslandQueenslandBrisbaneAustralia
| | - Victor Anggono
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain InstituteThe University of QueenslandQueenslandBrisbaneAustralia
| | - Dean L. Pountney
- School of Pharmacy and Medical SciencesGriffith UniversityQueenslandGold CoastAustralia
| | - Roger Chung
- Centre for Motor Neuron Disease ResearchMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversityNew South WalesNorth RydeAustralia
| | - Albert Lee
- Centre for Motor Neuron Disease ResearchMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversityNew South WalesNorth RydeAustralia
| |
Collapse
|
17
|
Ramirez LM, Zweckstetter M. Molecular-level interplay between intrinsically disordered clients and Hsp90. Curr Opin Chem Biol 2023; 74:102304. [PMID: 37068388 DOI: 10.1016/j.cbpa.2023.102304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/13/2023] [Accepted: 03/15/2023] [Indexed: 04/19/2023]
Abstract
Proteostasis is maintained by a network of molecular chaperones, a prominent member of which is the 90-kilodalton heat shock protein Hsp90. The chaperone function of Hsp90 has been extensively reviewed previously, emphasizing its ATPase activity and remodeling of folded client proteins. Experimental evidence implicating Hsp90 in neurodegenerative diseases has bolstered interest in the noncanonical chaperoning of intrinsically disordered protein (IDPs), however the interplay between Hsp90 and its disordered clients remains poorly understood. In this review we describe recent advances that have contributed to our understanding of the intricate mechanisms characterizing Hsp90-mediated chaperoning of the IDPs tau and α-synuclein and survey emerging insights into the modulation of the chaperone-client interplay in the context of neurodegeneration.
Collapse
Affiliation(s)
- Lisa Marie Ramirez
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075 Gӧttingen, Germany
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075 Gӧttingen, Germany; Department for NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Gӧttingen, Germany.
| |
Collapse
|
18
|
Light, Water, and Melatonin: The Synergistic Regulation of Phase Separation in Dementia. Int J Mol Sci 2023; 24:ijms24065835. [PMID: 36982909 PMCID: PMC10054283 DOI: 10.3390/ijms24065835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/17/2023] [Indexed: 03/22/2023] Open
Abstract
The swift rise in acceptance of molecular principles defining phase separation by a broad array of scientific disciplines is shadowed by increasing discoveries linking phase separation to pathological aggregations associated with numerous neurodegenerative disorders, including Alzheimer’s disease, that contribute to dementia. Phase separation is powered by multivalent macromolecular interactions. Importantly, the release of water molecules from protein hydration shells into bulk creates entropic gains that promote phase separation and the subsequent generation of insoluble cytotoxic aggregates that drive healthy brain cells into diseased states. Higher viscosity in interfacial waters and limited hydration in interiors of biomolecular condensates facilitate phase separation. Light, water, and melatonin constitute an ancient synergy that ensures adequate protein hydration to prevent aberrant phase separation. The 670 nm visible red wavelength found in sunlight and employed in photobiomodulation reduces interfacial and mitochondrial matrix viscosity to enhance ATP production via increasing ATP synthase motor efficiency. Melatonin is a potent antioxidant that lowers viscosity to increase ATP by scavenging excess reactive oxygen species and free radicals. Reduced viscosity by light and melatonin elevates the availability of free water molecules that allow melatonin to adopt favorable conformations that enhance intrinsic features, including binding interactions with adenosine that reinforces the adenosine moiety effect of ATP responsible for preventing water removal that causes hydrophobic collapse and aggregation in phase separation. Precise recalibration of interspecies melatonin dosages that account for differences in metabolic rates and bioavailability will ensure the efficacious reinstatement of the once-powerful ancient synergy between light, water, and melatonin in a modern world.
Collapse
|
19
|
Romero-Fernandez W, Carvajal-Tapia C, Prusky A, Katdare K, Wang E, Shostak A, Ventura-Antunes L, Harmsen H, Lippmann E, Borroto-Escuela D, MacGurn J, Fuxe K, Schrag M. Detection, Visualization and Quantification of Protein Complexes in Human Alzheimer's Disease Brains using Proximity Ligation Assay. RESEARCH SQUARE 2023:rs.3.rs-2570335. [PMID: 36824944 PMCID: PMC9949263 DOI: 10.21203/rs.3.rs-2570335/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Examination of healthy and diseased human brain is essential to translational neuroscience. Protein-protein interactions play a pivotal role in physiological and pathological processes, but their detection is difficult, especially in aged and fixed human brain tissue. We used the proximity ligation assay (PLA) to broaden the range of molecular interactions assessable in-situ in human neuropathology. We adapted fluorescent in-situ PLA to detect ubiquitin-modified proteins in human brains with Alzheimer's disease (AD), including approaches for the management of autofluorescence and quantification using a high-content image analysis system. We confirmed that hyperphosphorylated microtubule-associated protein tau (Serine202, Threonine205) aggregates were modified by ubiquitin and that phospho-tau-ubiquitin complexes were increased in hippocampal and frontal cortex regions in AD compared to non-AD brains. Overall, we refined PLA for use in human neuropathology, which has revealed a profound change in the distribution of ubiquitin in AD brain and its association with characteristic tau pathologies.
Collapse
|
20
|
Ganne A, Balasubramaniam M, Ayyadevara H, Kiaei L, Shmookler Reis RJ, Varughese KI, Kiaei M. In silico analysis of TUBA4A mutations in Amyotrophic Lateral Sclerosis to define mechanisms of microtubule disintegration. Sci Rep 2023; 13:2096. [PMID: 36747013 PMCID: PMC9902468 DOI: 10.1038/s41598-023-28381-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 01/18/2023] [Indexed: 02/08/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is an inexorably progressive and degenerative disorder of motor neurons with no currently-known cure. Studies to determine the mechanism of neurotoxicity and the impact of ALS-linked mutations (SOD1, FUS, TARDP, C9ORF72, PFN1, TUBA4A and others) have greatly expanded our knowledge of ALS disease mechanisms and have helped to identify potential targets for ALS therapy. Cellular pathologies (e.g., aggregation of mutant forms of SOD1, TDP43, FUS, Ubiqulin2, PFN1, and C9ORF72), mitochondrial dysfunction, neuroinflammation, and oxidative damage are major pathways implicated in ALS. Nevertheless, the selective vulnerability of motor neurons remains unexplained. The importance of tubulins for long-axon infrastructure, and the special morphology and function of motor neurons, underscore the central role of the cytoskeleton. The recent linkage of mutations to the tubulin α chain, TUBA4A, to familial and sporadic cases of ALS provides a new investigative opportunity to shed light on both mechanisms of ALS and the vulnerability of motor neurons. In the current study we investigate TUBA4A, a structural microtubule protein with mutations causal to familial ALS, using molecular-dynamic (MD) modeling of protein structure to predict the effects of each mutation and its overall impact on GTP binding, chain stability, tubulin assembly, and aggregation propensity. These studies predict that each of the reported mutations will cause notable structural changes to the TUBA4A (α chain) tertiary protein structure, adversely affecting its physical properties and functions. Molecular docking and MD simulations indicate certain α chain mutations (e.g. K430N, R215C, and W407X) may cause structural deviations that impair GTP binding, and plausibly prevent or destabilize tubulin polymerization. Furthermore, several mutations (including R320C and K430N) confer a significant increase in predicted aggregation propensity of TUBA4A mutants relative to wild-type. Taken together, these in silico modeling studies predict structural perturbations and disruption of GTP binding, culminating in failure to form a stable tubulin heterocomplex, which may furnish an important pathogenic mechanism to trigger motor neuron degeneration in ALS.
Collapse
Affiliation(s)
- Akshatha Ganne
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Meenakshisundaram Balasubramaniam
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA.,Central Arkansas Veterans Healthcare Service, McClellan Veterans Medical Center, Little Rock, AR, 72205, USA.,SiBioLead, LLC, Little Rock, AR, 72207, USA
| | | | - Lily Kiaei
- University of California, Los Angeles, Los Angeles, CA, 90095, USA.,RockGen Therapeutics, LLC, Little Rock, AR, 72205, USA
| | - Robert J Shmookler Reis
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA.,Central Arkansas Veterans Healthcare Service, McClellan Veterans Medical Center, Little Rock, AR, 72205, USA.,SiBioLead, LLC, Little Rock, AR, 72207, USA
| | - Kottayil I Varughese
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Mahmoud Kiaei
- RockGen Therapeutics, LLC, Little Rock, AR, 72205, USA. .,Department of Pharmacology and Toxicology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA. .,Department of Neurology, University of Arkansas for Medical Sciences, 4301 W. Markham St., Slot 611 (BioMed 1, Rm B-306A), Little Rock, AR, 72205, USA.
| |
Collapse
|
21
|
Khayat E, Delfing BM, Laracuente X, Olson A, Lockhart C, Klimov DK. Lysine Acetylation Changes the Mechanism of Aβ25-35 Peptide Binding and Dimerization in the DMPC Bilayer. ACS Chem Neurosci 2023; 14:494-505. [PMID: 36656569 DOI: 10.1021/acschemneuro.2c00722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The impact of Lys28 acetylation on Alzheimer's Aβ peptide binding to the lipid bilayer has not been previously studied, either experimentally or computationally. To probe this common post-translational modification, we performed all-atom replica exchange molecular dynamics simulations targeting binding and aggregation of acetylated acAβ25-35 peptide within the DMPC bilayer. Using the unmodified Aβ25-35 studied previously as a reference, our results can be summarized as follows. First, Lys28 acetylation strengthens the Aβ25-35 hydrophobic moment and consequently promotes the helical structure across the peptide extending it into the N-terminus. Second, because Lys28 acetylation disrupts electrostatic contact between Lys28 and lipid phosphate groups, it reduces the binding affinity of acAβ25-35 peptides to the DMPC bilayer. Accordingly, although acetylation preserves the bimodal binding featuring a preferred inserted state and a less probable surface bound state, it decreases the stability of the former. Third, acetylation promotes acAβ25-35 aggregation and eliminates monomers as thermodynamically viable species. More importantly, acAβ25-35 retains as the most thermodynamically stable the inserted dimer with unique head-to-tail helical aggregation interface. However, due to enhanced helix structure, this dimer state becomes less stable and is less likely to propagate into higher order aggregates. Thus, acetylation is predicted to facilitate the formation of low-molecular-weight oligomers. Other post-translational modifications, including phosphorylation and oxidation, reduce helical propensity and have divergent impact on aggregation. Consequently, acetylation, when considered in its totality, has distinct consequences on Aβ25-35 binding and aggregation in the lipid bilayer.
Collapse
Affiliation(s)
- Elias Khayat
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
| | - Bryan M Delfing
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
| | - Xavier Laracuente
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
| | - Audrey Olson
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
| | - Christopher Lockhart
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
| | - Dmitri K Klimov
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
| |
Collapse
|
22
|
Direct and Indirect Effects of Filamin A on Tau Pathology in Neuronal Cells. Mol Neurobiol 2023; 60:1021-1039. [PMID: 36399251 PMCID: PMC9849303 DOI: 10.1007/s12035-022-03121-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/04/2022] [Indexed: 11/19/2022]
Abstract
In Alzheimer disease (AD), Tau, an axonal microtubule-associated protein, becomes hyperphosphorylated, detaches from microtubules, accumulates, and self-aggregates in the somatodendritic (SD) compartment. The accumulation of hyperphosphorylated and aggregated Tau is also seen in other neurodegenerative diseases such as frontotemporal lobar degeneration (FTLD-Tau). Previous studies reported a link between filamin A (FLNA), an actin-binding protein found in the SD compartment, and Tau pathology. In the present study, we further explored this link. We confirmed the interaction of Tau with FLNA in neuroblastoma 2a (N2a) cells. This interaction was mediated by a domain located between the 157 and 383 amino acids (a.a.) of Tau. Our results also revealed that the overexpression of FLNA resulted in an intracellular accumulation of wild-type Tau and Tau mutants (P301L, V337M, and R406W) in N2a cells. Tau phosphorylation and cleavage by caspase-3 but not its aggregation were increased upon FLNA overexpression in N2a cells. In the parietal cortex of AD brain, insoluble FLNA was increased compared to control brain, but it did not correlate with Tau pathology. Interestingly, Tau binding to microtubules and F-actin was preserved upon FLNA overexpression in N2a cells. Lastly, our results revealed that FLNA also induced the accumulation of annexin A2, a Tau interacting partner involved in its axonal localization. Collectively, our data indicated that in Tauopathies, FLNA could contribute to Tau pathology by acting on Tau and annexin A2.
Collapse
|
23
|
Pires G, Ueberheide B, Wisniewski T, Drummond E. Use of Affinity Purification-Mass Spectrometry to Identify Phosphorylated Tau Interactors in Alzheimer's Disease. Methods Mol Biol 2023; 2561:263-277. [PMID: 36399275 DOI: 10.1007/978-1-0716-2655-9_14] [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] [Indexed: 11/19/2022]
Abstract
Phosphorylated tau is the main protein present in neurofibrillary tangles, the presence of which is a key neuropathological hallmark of Alzheimer's disease (AD). The toxic effects of phosphorylated tau are likely mediated by interacting proteins; however, methods to identify these interacting proteins comprehensively in human brain tissue are limited. Here, we describe a method that enables the efficient identification of hundreds of proteins that interact with phosphorylated tau (pTau), using affinity purification-mass spectrometry (AP-MS) on human, fresh-frozen brain tissue from donors with AD. Tissue is homogenized using a gentle technique that preserves protein-protein interactions, and co-immunoprecipitation of pTau and its interacting proteins is performed using the PHF1 antibody. The resulting protein interactors are then identified using label-free quantitative liquid chromatography-mass spectrometry (LC-MS)/MS. The Significance Analysis of INTeractome (SAINT) algorithm is used to determine which proteins significantly interact with pTau. This approach enables the detection of an abundance of all 6 isoforms of tau, 23 phosphorylated residues on tau, and 125 significant pTau protein interactors, in human AD brain tissue.
Collapse
Affiliation(s)
- Geoffrey Pires
- Center for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, New York, NY, USA
- Alzheimer's and Prion Diseases Team, Paris Brain Institute, CNRS, UMR 7225, INSERM 1127, Sorbonne University UM75, Paris, France
| | - Beatrix Ueberheide
- Center for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, New York, NY, 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, New York University Grossman School of Medicine, New York, NY, USA
| | - Thomas Wisniewski
- Center for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, New York, NY, USA
- Departments of Pathology and Psychiatry, New York University Grossman School of Medicine, New York, NY, USA
| | - Eleanor Drummond
- Center for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, New York, NY, USA.
- Brain & Mind Center and School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, Australia.
| |
Collapse
|
24
|
Physiological Consequences of Targeting 14-3-3 and Its Interacting Partners in Neurodegenerative Diseases. Int J Mol Sci 2022; 23:ijms232415457. [PMID: 36555098 PMCID: PMC9779020 DOI: 10.3390/ijms232415457] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
The mammalian 14-3-3 family comprises seven intrinsically unstructured, evolutionarily conserved proteins that bind >200 protein targets, thereby modulating cell-signaling pathways. The presence of 14-3-3 proteins in cerebrospinal fluid provides a sensitive and specific biomarker of neuronal damage associated with Alzheimer’s disease (AD), Creutzfeldt−Jakob disease (CJD), spongiform encephalitis, brain cancers, and stroke. We observed significant enrichment of 14-3-3 paralogs G, S, and Z in human brain aggregates diagnostic of AD. We used intra-aggregate crosslinking to identify 14-3-3 interaction partners, all of which were significantly enriched in AD brain aggregates relative to controls. We screened FDA-approved drugs in silico for structures that could target the 14-3-3G/hexokinase interface, an interaction specific to aggregates and AD. C. elegans possesses only two 14-3-3 orthologs, which bind diverse proteins including DAF-16 (a FOXO transcription factor) and SIR-2.1 (a sensor of nutrients and stress), influencing lifespan. Top drug candidates were tested in C. elegans models of neurodegeneration-associated aggregation and in a human neuroblastoma cell-culture model of AD-like amyloidosis. Several drugs opposed aggregation in all models assessed and rescued behavioral deficits in C. elegans AD-like neuropathy models, suggesting that 14-3-3 proteins are instrumental in aggregate accrual and supporting the advancement of drugs targeting 14-3-3 protein complexes with their partners.
Collapse
|
25
|
Kavanagh T, Halder A, Drummond E. Tau interactome and RNA binding proteins in neurodegenerative diseases. Mol Neurodegener 2022; 17:66. [PMID: 36253823 PMCID: PMC9575286 DOI: 10.1186/s13024-022-00572-6] [Citation(s) in RCA: 15] [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: 05/20/2022] [Accepted: 09/30/2022] [Indexed: 11/19/2022] Open
Abstract
Pathological tau aggregation is a primary neuropathological feature of many neurodegenerative diseases. Intriguingly, despite the common presence of tau aggregates in these diseases the affected brain regions, clinical symptoms, and morphology, conformation, and isoform ratio present in tau aggregates varies widely. The tau-mediated disease mechanisms that drive neurodegenerative disease are still unknown. Tau interactome studies are critically important for understanding tauopathy. They reveal the interacting partners that define disease pathways, and the tau interactions present in neuropathological aggregates provide potential insight into the cellular environment and protein interactions present during pathological tau aggregation. Here we provide a combined analysis of 12 tau interactome studies of human brain tissue, human cell culture models and rodent models of disease. Together, these studies identified 2084 proteins that interact with tau in human tissue and 1152 proteins that interact with tau in rodent models of disease. Our combined analysis of the tau interactome revealed consistent enrichment of interactions between tau and proteins involved in RNA binding, ribosome, and proteasome function. Comparison of human and rodent tau interactome studies revealed substantial differences between the two species. We also performed a second analysis to identify the tau interacting proteins that are enriched in neurons containing granulovacuolar degeneration or neurofibrillary tangle pathology. These results revealed a timed dysregulation of tau interactions as pathology develops. RNA binding proteins, particularly HNRNPs, emerged as early disease-associated tau interactors and therefore may have an important role in driving tau pathology.
Collapse
Affiliation(s)
- Tomas Kavanagh
- Brain and Mind Centre and School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, 94 Mallett Street, Sydney, NSW Australia
| | - Aditi Halder
- Brain and Mind Centre and School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, 94 Mallett Street, Sydney, NSW Australia
| | - Eleanor Drummond
- Brain and Mind Centre and School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, 94 Mallett Street, Sydney, NSW Australia
| |
Collapse
|
26
|
Ganne A, Balasubramaniam M, Ayyadevara S, Shmookler Reis RJ. Machine-learning analysis of intrinsically disordered proteins identifies key factors that contribute to neurodegeneration-related aggregation. Front Aging Neurosci 2022; 14:938117. [PMID: 35992603 PMCID: PMC9382113 DOI: 10.3389/fnagi.2022.938117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
Protein structure is determined by the amino acid sequence and a variety of post-translational modifications, and provides the basis for physiological properties. Not all proteins in the proteome attain a stable conformation; roughly one third of human proteins are unstructured or contain intrinsically disordered regions exceeding 40% of their length. Proteins comprising or containing extensive unstructured regions are termed intrinsically disordered proteins (IDPs). IDPs are known to be overrepresented in protein aggregates of diverse neurodegenerative diseases. We evaluated the importance of disordered proteins in the nematode Caenorhabditis elegans, by RNAi-mediated knockdown of IDPs in disease-model strains that mimic aggregation associated with neurodegenerative pathologies. Not all disordered proteins are sequestered into aggregates, and most of the tested aggregate-protein IDPs contribute to important physiological functions such as stress resistance or reproduction. Despite decades of research, we still do not understand what properties of a disordered protein determine its entry into aggregates. We have employed machine-learning models to identify factors that predict whether a disordered protein is found in sarkosyl-insoluble aggregates isolated from neurodegenerative-disease brains (both AD and PD). Machine-learning predictions, coupled with principal component analysis (PCA), enabled us to identify the physiochemical properties that determine whether a disordered protein will be enriched in neuropathic aggregates.
Collapse
Affiliation(s)
- Akshatha Ganne
- Bioinformatics Program, University of Arkansas for Medical Sciences and University of Arkansas at Little Rock, Little Rock, AR, United States
| | | | - Srinivas Ayyadevara
- Bioinformatics Program, University of Arkansas for Medical Sciences and University of Arkansas at Little Rock, Little Rock, AR, United States
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
- Central Arkansas Veterans Healthcare System, Little Rock, AR, United States
- *Correspondence: Srinivas Ayyadevara,
| | - Robert J. Shmookler Reis
- Bioinformatics Program, University of Arkansas for Medical Sciences and University of Arkansas at Little Rock, Little Rock, AR, United States
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
- Central Arkansas Veterans Healthcare System, Little Rock, AR, United States
- Robert J. Shmookler Reis,
| |
Collapse
|
27
|
Ganne A, Balasubramaniam M, Griffin WST, Shmookler Reis RJ, Ayyadevara S. Glial Fibrillary Acidic Protein: A Biomarker and Drug Target for Alzheimer’s Disease. Pharmaceutics 2022; 14:pharmaceutics14071354. [PMID: 35890250 PMCID: PMC9322874 DOI: 10.3390/pharmaceutics14071354] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 02/05/2023] Open
Abstract
Glial fibrillary acidic protein (GFAP) is an intermediate filament structural protein involved in cytoskeleton assembly and integrity, expressed in high abundance in activated glial cells. GFAP is neuroprotective, as knockout mice are hypersensitive to traumatic brain injury. GFAP in cerebrospinal fluid is a biomarker of Alzheimer’s disease (AD), dementia with Lewy bodies, and frontotemporal dementia (FTD). Here, we present novel evidence that GFAP is markedly overexpressed and differentially phosphorylated in AD hippocampus, especially in AD with the apolipoprotein E [ε4, ε4] genotype, relative to age-matched controls (AMCs). Kinases that phosphorylate GFAP are upregulated in AD relative to AMC. A knockdown of these kinases in SH-SY5Y-APPSw human neuroblastoma cells reduced amyloid accrual and lowered protein aggregation and associated behavioral traits in C. elegans models of polyglutamine aggregation (as observed in Huntington’s disease) and of Alzheimer’s-like amyloid formation. In silico screening of the ChemBridge structural library identified a small molecule, MSR1, with stable and specific binding to GFAP. Both MSR1 exposure and GF AP-specific RNAi knockdown reduce aggregation with remarkably high concordance of aggregate proteins depleted. These data imply that GFAP and its phosphorylation play key roles in neuropathic aggregate accrual and provide valuable new biomarkers, as well as novel therapeutic targets to alleviate, delay, or prevent AD.
Collapse
Affiliation(s)
- Akshatha Ganne
- Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA; (A.G.); (M.B.); (W.S.T.G.)
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | | | - W. Sue T. Griffin
- Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA; (A.G.); (M.B.); (W.S.T.G.)
- BioInformatics Program, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Robert J. Shmookler Reis
- Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA; (A.G.); (M.B.); (W.S.T.G.)
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- BioInformatics Program, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Department of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Correspondence: (R.J.S.R.); (S.A.); Tel.: +1-501-526-5820 (R.J.S.R.); +1-501-526-7282 (S.A.)
| | - Srinivas Ayyadevara
- Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA; (A.G.); (M.B.); (W.S.T.G.)
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- BioInformatics Program, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Correspondence: (R.J.S.R.); (S.A.); Tel.: +1-501-526-5820 (R.J.S.R.); +1-501-526-7282 (S.A.)
| |
Collapse
|
28
|
Ferrer I, Andrés-Benito P, Ausín K, Cartas-Cejudo P, Lachén-Montes M, del Rio JA, Fernández-Irigoyen J, Santamaría E. Dysregulated Brain Protein Phosphorylation Linked to Increased Human Tau Expression in the hTau Transgenic Mouse Model. Int J Mol Sci 2022; 23:6427. [PMID: 35742871 PMCID: PMC9223516 DOI: 10.3390/ijms23126427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/02/2022] [Accepted: 06/07/2022] [Indexed: 11/17/2022] Open
Abstract
Altered protein phosphorylation is a major pathologic modification in tauopathies and Alzheimer's disease (AD) linked to abnormal tau fibrillar deposits in neurofibrillary tangles (NFTs) and pre-tangles and β-amyloid deposits in AD. hTau transgenic mice, which express 3R and less 4R human tau with no mutations in a murine knock-out background, show increased tau deposition in neurons but not NFTs and pre-tangles at the age of nine months. Label-free (phospho)proteomics and SWATH-MS identified 2065 proteins in hTau and wild-type (WT) mice. Only six proteins showed increased levels in hTau; no proteins were down-regulated. Increased tau phosphorylation in hTau was detected at Ser199, Ser202, Ser214, Ser396, Ser400, Thr403, Ser404, Ser413, Ser416, Ser422, Ser491, and Ser494, in addition to Thr181, Thr231, Ser396/Ser404, but not at Ser202/Thr205. In addition, 4578 phosphopeptides (corresponding to 1622 phosphoproteins) were identified in hTau and WT mice; 64 proteins were differentially phosphorylated in hTau. Sixty proteins were grouped into components of membranes, membrane signaling, synapses, vesicles, cytoskeleton, DNA/RNA/protein metabolism, ubiquitin/proteasome system, cholesterol and lipid metabolism, and cell signaling. These results showed that over-expression of human tau without pre-tangle and NFT formation preferentially triggers an imbalance in the phosphorylation profile of specific proteins involved in the cytoskeletal-membrane-signaling axis.
Collapse
Affiliation(s)
- Isidro Ferrer
- Department of Pathology and Experimental Therapeutics, Network Centre of Biomedical Research of Neurodegenerative Diseases (CIBERNED), Institute of Health Carlos III, University of Barcelona, 08907 Barcelona, Spain;
- Bellvitge University Hospital, Bellvitge Biomedical Research Institute (IDIBELL), Calle Feixa Llarga sn, 08907 Barcelona, Spain
| | - Pol Andrés-Benito
- Department of Pathology and Experimental Therapeutics, Network Centre of Biomedical Research of Neurodegenerative Diseases (CIBERNED), Institute of Health Carlos III, University of Barcelona, 08907 Barcelona, Spain;
- Bellvitge University Hospital, Bellvitge Biomedical Research Institute (IDIBELL), Calle Feixa Llarga sn, 08907 Barcelona, Spain
| | - Karina Ausín
- Proteomics Platform, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, 31192 Pamplona, Spain; (K.A.); (J.F.-I.)
| | - Paz Cartas-Cejudo
- Clinical Neuroproteomics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Irunlarrea Street, 31192 Pamplona, Spain; (P.C.-C.); (M.L.-M.); (E.S.)
| | - Mercedes Lachén-Montes
- Clinical Neuroproteomics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Irunlarrea Street, 31192 Pamplona, Spain; (P.C.-C.); (M.L.-M.); (E.S.)
| | - José Antonio del Rio
- Molecular and Cellular Neurobiotechnology, Institute of Bioengineering of Catalonia (IBEC), Barcelona Institute for Science and Technology, Science Park Barcelona (PCB), 08028 Barcelona, Spain;
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Carrer Baldiri Reixac, 08028 Barcelona, Spain
| | - Joaquín Fernández-Irigoyen
- Proteomics Platform, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, 31192 Pamplona, Spain; (K.A.); (J.F.-I.)
| | - Enrique Santamaría
- Clinical Neuroproteomics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Irunlarrea Street, 31192 Pamplona, Spain; (P.C.-C.); (M.L.-M.); (E.S.)
| |
Collapse
|
29
|
Wang JY, Zhang W, Roehrl VB, Roehrl MW, Roehrl MH. An Autoantigen Atlas From Human Lung HFL1 Cells Offers Clues to Neurological and Diverse Autoimmune Manifestations of COVID-19. Front Immunol 2022; 13:831849. [PMID: 35401574 PMCID: PMC8987778 DOI: 10.3389/fimmu.2022.831849] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/21/2022] [Indexed: 12/27/2022] Open
Abstract
COVID-19 is accompanied by a myriad of both transient and long-lasting autoimmune responses. Dermatan sulfate (DS), a glycosaminoglycan crucial for wound healing, has unique affinity for autoantigens (autoAgs) from apoptotic cells. DS-autoAg complexes are capable of stimulating autoreactive B cells and autoantibody production. We used DS-affinity proteomics to define the autoantigen-ome of lung fibroblasts and bioinformatics analyses to study the relationship between autoantigenic proteins and COVID-induced alterations. Using DS-affinity, we identified an autoantigen-ome of 408 proteins from human HFL1 cells, at least 231 of which are known autoAgs. Comparing with available COVID data, 352 proteins of the autoantigen-ome have thus far been found to be altered at protein or RNA levels in SARS-CoV-2 infection, 210 of which are known autoAgs. The COVID-altered proteins are significantly associated with RNA metabolism, translation, vesicles and vesicle transport, cell death, supramolecular fibrils, cytoskeleton, extracellular matrix, and interleukin signaling. They offer clues to neurological problems, fibrosis, smooth muscle dysfunction, and thrombosis. In particular, 150 altered proteins are related to the nervous system, including axon, myelin sheath, neuron projection, neuronal cell body, and olfactory bulb. An association with the melanosome is also identified. The findings from our study illustrate a connection between COVID infection and autoimmunity. The vast number of COVID-altered proteins with high intrinsic propensity to become autoAgs offers an explanation for the diverse autoimmune complications in COVID patients. The variety of autoAgs related to mRNA metabolism, translation, and vesicles suggests a need for long-term monitoring of autoimmunity in COVID. The COVID autoantigen atlas we are establishing provides a detailed molecular map for further investigation of autoimmune sequelae of the pandemic, such as "long COVID" syndrome. Summary Sentence An autoantigen-ome by dermatan sulfate affinity from human lung HFL1 cells may explain neurological and autoimmune manifestations of COVID-19.
Collapse
Affiliation(s)
| | - Wei Zhang
- Department of Gastroenterology, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | | | | | - Michael H. Roehrl
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| |
Collapse
|
30
|
Gal J, Katsumata Y, Zhu H, Srinivasan S, Chen J, Johnson LA, Wang WX, Golden LR, Wilcock DM, Jicha GA, Cykowski MD, Nelson PT. Apolipoprotein E Proteinopathy Is a Major Dementia-Associated Pathologic Biomarker in Individuals with or without the APOE Epsilon 4 Allele. THE AMERICAN JOURNAL OF PATHOLOGY 2022; 192:564-578. [PMID: 34954207 PMCID: PMC8895423 DOI: 10.1016/j.ajpath.2021.11.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 10/27/2021] [Accepted: 11/24/2021] [Indexed: 12/14/2022]
Abstract
The amygdala is vulnerable to multiple or "mixed" mis-aggregated proteins associated with neurodegenerative conditions that can manifest clinically with amnestic dementia; the amygdala region is often affected even at earliest disease stages. With the original intent of identifying novel dementia-associated proteins, the detergent-insoluble proteome was characterized from the amygdalae of 40 participants from the University of Kentucky Alzheimer's Disease Center autopsy cohort. These individuals encompassed a spectrum of clinical conditions (cognitively normal to severe amnestic dementia). Polypeptides from the detergent-insoluble fraction were interrogated using liquid chromatography-electrospray ionization-tandem mass spectrometry. As anticipated, portions of peptides previously associated with neurologic diseases were enriched from subjects with dementia. Among all detected peptides, Apolipoprotein E (ApoE) stood out: even more than the expected Tau, APP/Aβ, and α-Synuclein peptides, ApoE peptides were strongly enriched in dementia cases, including from individuals lacking the APOE ε4 genotype. The amount of ApoE protein detected in detergent-insoluble fractions was robustly associated with levels of complement proteins C3 and C4. Immunohistochemical staining of APOE ε3/ε3 subjects' amygdalae confirmed ApoE co-localization with C4 in amyloid plaques. Thus, analyses of human amygdala proteomics indicate that rather than being only an "upstream" genetic risk factor, ApoE is an aberrantly aggregated protein in its own right, and show that the ApoE protein may play active disease-driving mechanistic roles in persons lacking the APOE ε4 allele.
Collapse
Affiliation(s)
- Jozsef Gal
- Spinal Cord and Brain Injury Research Center (SCoBIRC), University of Kentucky, Lexington, Kentucky,Department of Neuroscience, University of Kentucky, Lexington, Kentucky
| | - Yuriko Katsumata
- Department of Biostatistics, University of Kentucky, Lexington, Kentucky,Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky
| | - Haining Zhu
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky,Research & Development, Lexington VA Medical Center, Lexington, Kentucky
| | - Sukanya Srinivasan
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky
| | - Jing Chen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky
| | - Lance Allen Johnson
- Department of Neuroscience, University of Kentucky, Lexington, Kentucky,Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky
| | - Wang-Xia Wang
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky,Department of Pathology, University of Kentucky, Lexington, Kentucky
| | | | - Donna M. Wilcock
- Department of Neuroscience, University of Kentucky, Lexington, Kentucky,Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky,Department of Physiology, University of Kentucky, Lexington, Kentucky
| | - Gregory A. Jicha
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky,Department of Neurology, University of Kentucky, Lexington, Kentucky
| | | | - Peter Tobias Nelson
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky; Department of Pathology, University of Kentucky, Lexington, Kentucky.
| |
Collapse
|
31
|
Walker JM, Kazempour Dehkordi S, Fracassi A, Vanschoiack A, Pavenko A, Taglialatela G, Woltjer R, Richardson TE, Zare H, Orr ME. Differential protein expression in the hippocampi of resilient individuals identified by digital spatial profiling. Acta Neuropathol Commun 2022; 10:23. [PMID: 35164877 PMCID: PMC8842950 DOI: 10.1186/s40478-022-01324-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/30/2022] [Indexed: 02/04/2023] Open
Abstract
Clinical symptoms correlate with underlying neurodegenerative changes in the vast majority of people. However, an intriguing group of individuals demonstrate neuropathologic changes consistent with Alzheimer disease (AD) yet remain cognitively normal (termed "resilient"). Previous studies have reported less overall neuronal loss, less gliosis, and fewer comorbidities in these individuals. Herein, NanoString GeoMx™ Digital Spatial Profiler (DSP) technology was utilized to investigate protein expression differences comparing individuals with dementia and AD neuropathologic change to resilient individuals. DSP allows for spatial analysis of protein expression in multiple regions of interest (ROIs) on formalin-fixed paraffin-embedded sections. ROIs in this analysis were hippocampal neurofibrillary tangle (NFT)-bearing neurons, non-NFT-bearing neurons, and their immediate neuronal microenvironments. Analyses of 86 proteins associated with CNS cell-typing or known neurodegenerative changes in 168 ROIs from 14 individuals identified 11 proteins displaying differential expression in NFT-bearing neurons of the resilient when compared to the demented (including APP, IDH1, CD68, GFAP, SYP and Histone H3). In addition, IDH1, CD68, and SYP were differentially expressed in the environment of NFT-bearing neurons when comparing resilient to demented. IDH1 (which is upregulated under energetic and oxidative stress) and PINK1 (which is upregulated in response to mitochondrial dysfunction and oxidative stress) both displayed lower expression in the environment of NFT-bearing neurons in the resilient. Therefore, the resilient display less evidence of energetic and oxidative stress. Synaptophysin (SYP) was increased in the resilient, which likely indicates better maintenance of synapses and synaptic connections. Furthermore, neurofilament light chain (NEFL) and ubiquitin c-terminal hydrolase (Park5) were higher in the resilient in the environment of NFTs. These differences all suggest healthier intact axons, dendrites and synapses in the resilient. In conclusion, resilient individuals display protein expression patterns suggestive of an environment containing less energetic and oxidative stress, which in turn results in maintenance of neurons and their synaptic connections.
Collapse
Affiliation(s)
- Jamie M. Walker
- Department of Pathology and Laboratory Medicine, University of Texas Health Science Center, San Antonio, TX USA
- Department of Pathology, Glenn Biggs Institute for Alzheimer’s & Neurodegenerative Diseases, University of Texas Health Science Center, 7703 Floyd Curl Dr., MC 8070, San Antonio, TX 78229-3900 USA
| | - Shiva Kazempour Dehkordi
- Department of Pathology, Glenn Biggs Institute for Alzheimer’s & Neurodegenerative Diseases, University of Texas Health Science Center, 7703 Floyd Curl Dr., MC 8070, San Antonio, TX 78229-3900 USA
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, TX USA
| | - Anna Fracassi
- Mitchell Center for Neurodegenerative Diseases, Department of Neurology, UTMB, Galveston, TX USA
| | | | | | - Giulio Taglialatela
- Mitchell Center for Neurodegenerative Diseases, Department of Neurology, UTMB, Galveston, TX USA
| | - Randall Woltjer
- Department of Pathology & Laboratory Medicine, Oregon Health and Science University, Portland, OR USA
| | - Timothy E. Richardson
- Department of Pathology and Laboratory Medicine, University of Texas Health Science Center, San Antonio, TX USA
- Department of Pathology, Glenn Biggs Institute for Alzheimer’s & Neurodegenerative Diseases, University of Texas Health Science Center, 7703 Floyd Curl Dr., MC 8070, San Antonio, TX 78229-3900 USA
| | - Habil Zare
- Department of Pathology, Glenn Biggs Institute for Alzheimer’s & Neurodegenerative Diseases, University of Texas Health Science Center, 7703 Floyd Curl Dr., MC 8070, San Antonio, TX 78229-3900 USA
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, TX USA
| | - Miranda E. Orr
- Section of Gerontology and Geriatric Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
- Sticht Center for Healthy Aging and Alzheimer’s Prevention, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
- Salisbury VA Medical Center, Salisbury, NC 28144 USA
- Department of Internal Medicine, Wake Forest School of Medicine, 575 Patterson Ave, Winston-Salem, NC 27101 USA
| |
Collapse
|
32
|
Ayyadevara S, Ganne A, Balasubramaniam M, Shmookler Reis RJ. Intrinsically disordered proteins identified in the aggregate proteome serve as biomarkers of neurodegeneration. Metab Brain Dis 2022; 37:147-152. [PMID: 34347206 PMCID: PMC8748380 DOI: 10.1007/s11011-021-00791-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/04/2021] [Indexed: 11/26/2022]
Abstract
A protein's structure is determined by its amino acid sequence and post-translational modifications, and provides the basis for its physiological functions. Across all organisms, roughly a third of the proteome comprises proteins that contain highly unstructured or intrinsically disordered regions. Proteins comprising or containing extensive unstructured regions are referred to as intrinsically disordered proteins (IDPs). IDPs are believed to participate in complex physiological processes through refolding of IDP regions, dependent on their binding to a diverse array of potential protein partners. They thus play critical roles in the assembly and function of protein complexes. Recent advances in experimental and computational analyses predicted multiple interacting partners for the disordered regions of proteins, implying critical roles in signal transduction and regulation of biological processes. Numerous disordered proteins are sequestered into aggregates in neurodegenerative diseases such as Alzheimer's disease (AD) where they are enriched even in serum, making them good candidates for serum biomarkers to enable early detection of AD.
Collapse
Affiliation(s)
- Srinivas Ayyadevara
- Central Arkansas Veterans Healthcare Service, Little Rock, AR, 72205, USA.
- Reynolds Institute on Aging, Department of Geriatrics, University of Arkansas for Medical Sciences, 629 Jack Stephens Drive, Little Rock, AR, 72205, USA.
- BioInformatics Program, University of Arkansas at Little Rock and University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA.
| | - Akshatha Ganne
- BioInformatics Program, University of Arkansas at Little Rock and University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Meenakshisundaram Balasubramaniam
- Reynolds Institute on Aging, Department of Geriatrics, University of Arkansas for Medical Sciences, 629 Jack Stephens Drive, Little Rock, AR, 72205, USA
| | - Robert J Shmookler Reis
- Central Arkansas Veterans Healthcare Service, Little Rock, AR, 72205, USA.
- Reynolds Institute on Aging, Department of Geriatrics, University of Arkansas for Medical Sciences, 629 Jack Stephens Drive, Little Rock, AR, 72205, USA.
- BioInformatics Program, University of Arkansas at Little Rock and University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA.
| |
Collapse
|
33
|
Label-free photothermal disruption of cytotoxic aggregates rescues pathology in a C. elegans model of Huntington's disease. Sci Rep 2021; 11:19732. [PMID: 34611196 PMCID: PMC8492664 DOI: 10.1038/s41598-021-98661-x] [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: 01/30/2021] [Accepted: 08/26/2021] [Indexed: 11/25/2022] Open
Abstract
Aggregation of proteins is a prominent hallmark of virtually all neurodegenerative disorders including Alzheimer’s, Parkinson’s and Huntington’s diseases. Little progress has been made in their treatment to slow or prevent the formation of aggregates by post-translational modification and regulation of cellular responses to misfolded proteins. Here, we introduce a label-free, laser-based photothermal treatment of polyglutamine (polyQ) aggregates in a C. elegans nematode model of huntingtin-like polyQ aggregation. As a proof of principle, we demonstrated that nanosecond laser pulse-induced local photothermal heating can directly disrupt the aggregates so as to delay their accumulation, maintain motility, and extend the lifespan of treated nematodes. These beneficial effects were validated by confocal photothermal, fluorescence, and video imaging. The results obtained demonstrate that our theranostics platform, integrating photothermal therapy without drugs or other chemicals, combined with advanced imaging to monitor photothermal ablation of aggregates, initiates systemic recovery and thus validates the concept of aggregate-disruption treatments for neurodegenerative diseases in humans.
Collapse
|
34
|
Shmookler Reis RJ, Atluri R, Balasubramaniam M, Johnson J, Ganne A, Ayyadevara S. "Protein aggregates" contain RNA and DNA, entrapped by misfolded proteins but largely rescued by slowing translational elongation. Aging Cell 2021; 20:e13326. [PMID: 33788386 PMCID: PMC8135009 DOI: 10.1111/acel.13326] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/12/2021] [Accepted: 02/01/2021] [Indexed: 01/03/2023] Open
Abstract
All neurodegenerative diseases feature aggregates, which usually contain disease-specific diagnostic proteins; non-protein constituents, however, have rarely been explored. Aggregates from SY5Y-APPSw neuroblastoma, a cell model of familial Alzheimer's disease, were crosslinked and sequences of linked peptides identified. We constructed a normalized "contactome" comprising 11 subnetworks, centered on 24 high-connectivity hubs. Remarkably, all 24 are nucleic acid-binding proteins. This led us to isolate and sequence RNA and DNA from Alzheimer's and control aggregates. RNA fragments were mapped to the human genome by RNA-seq and DNA by ChIP-seq. Nearly all aggregate RNA sequences mapped to specific genes, whereas DNA fragments were predominantly intergenic. These nucleic acid mappings are all significantly nonrandom, making an artifactual origin extremely unlikely. RNA (mostly cytoplasmic) exceeded DNA (chiefly nuclear) by twofold to fivefold. RNA fragments recovered from AD tissue were ~1.5-to 2.5-fold more abundant than those recovered from control tissue, similar to the increase in protein. Aggregate abundances of specific RNA sequences were strikingly differential between cultured SY5Y-APPSw glioblastoma cells expressing APOE3 vs. APOE4, consistent with APOE4 competition for E-box/CLEAR motifs. We identified many G-quadruplex and viral sequences within RNA and DNA of aggregates, suggesting that sequestration of viral genomes may have driven the evolution of disordered nucleic acid-binding proteins. After RNA-interference knockdown of the translational-procession factor EEF2 to suppress translation in SY5Y-APPSw cells, the RNA content of aggregates declined by >90%, while reducing protein content by only 30% and altering DNA content by ≤10%. This implies that cotranslational misfolding of nascent proteins may ensnare polysomes into aggregates, accounting for most of their RNA content.
Collapse
Affiliation(s)
- Robert J. Shmookler Reis
- Central Arkansas Veterans Healthcare System Little Rock AR USA
- Department of Geriatrics University of Arkansas for Medical Sciences Little Rock AR USA
- BioInformatics Program University of Arkansas for Medical Sciences and University of Arkansas at Little Rock Little Rock AR USA
| | - Ramani Atluri
- Department of Geriatrics University of Arkansas for Medical Sciences Little Rock AR USA
| | | | - Jay Johnson
- BioInformatics Program University of Arkansas for Medical Sciences and University of Arkansas at Little Rock Little Rock AR USA
| | - Akshatha Ganne
- BioInformatics Program University of Arkansas for Medical Sciences and University of Arkansas at Little Rock Little Rock AR USA
| | - Srinivas Ayyadevara
- Central Arkansas Veterans Healthcare System Little Rock AR USA
- Department of Geriatrics University of Arkansas for Medical Sciences Little Rock AR USA
| |
Collapse
|
35
|
Jin Y, Vadukul DM, Gialama D, Ge Y, Thrush R, White JT, Aprile FA. The Diagnostic Potential of Amyloidogenic Proteins. Int J Mol Sci 2021; 22:4128. [PMID: 33923609 PMCID: PMC8074075 DOI: 10.3390/ijms22084128] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 12/12/2022] Open
Abstract
Neurodegenerative disorders are a highly prevalent class of diseases, whose pathological mechanisms start before the appearance of any clear symptoms. This fact has prompted scientists to search for biomarkers that could aid early treatment. These currently incurable pathologies share the presence of aberrant aggregates called amyloids in the nervous system, which are composed of specific proteins. In this review, we discuss how these proteins, their conformations and modifications could be exploited as biomarkers for diagnostic purposes. We focus on proteins that are associated with the most prevalent neurodegenerative disorders, including Alzheimer's and Parkinson's diseases, amyotrophic lateral sclerosis, and frontotemporal dementia. We also describe current challenges in detection, the most recent techniques with diagnostic potentials and possible future developments in diagnosis.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Francesco Antonio Aprile
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK; (Y.J.); (D.M.V.); (D.G.); (Y.G.); (R.T.); (J.T.W.)
| |
Collapse
|
36
|
Wang JY, Zhang W, Roehrl MW, Roehrl VB, Roehrl MH. An Autoantigen Atlas from Human Lung HFL1 Cells Offers Clues to Neurological and Diverse Autoimmune Manifestations of COVID-19. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.01.24.427965. [PMID: 33501444 PMCID: PMC7836114 DOI: 10.1101/2021.01.24.427965] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
COVID-19 is accompanied by a myriad of both transient and long-lasting autoimmune responses. Dermatan sulfate (DS), a glycosaminoglycan crucial for wound healing, has unique affinity for autoantigens (autoAgs) from apoptotic cells. DS-autoAg complexes are capable of stimulating autoreactive B cells and autoantibody production. Using DS affinity, we identified an autoantigenome of 408 proteins from human fetal lung fibroblast HFL11 cells, at least 231 of which are known autoAgs. Comparing with available COVID data, 352 proteins of the autoantigenome have thus far been found to be altered at protein or RNA levels in SARS-Cov-2 infection, 210 of which are known autoAgs. The COVID-altered proteins are significantly associated with RNA metabolism, translation, vesicles and vesicle transport, cell death, supramolecular fibrils, cytoskeleton, extracellular matrix, and interleukin signaling. They offer clues to neurological problems, fibrosis, smooth muscle dysfunction, and thrombosis. In particular, 150 altered proteins are related to the nervous system, including axon, myelin sheath, neuron projection, neuronal cell body, and olfactory bulb. An association with the melanosome is also identified. The findings from our study illustrate a strong connection between viral infection and autoimmunity. The vast number of COVID-altered proteins with propensity to become autoAgs offers an explanation for the diverse autoimmune complications in COVID patients. The variety of autoAgs related to mRNA metabolism, translation, and vesicles raises concerns about potential adverse effects of mRNA vaccines. The COVID autoantigen atlas we are establishing provides a detailed molecular map for further investigation of autoimmune sequelae of the pandemic.
Collapse
Affiliation(s)
| | - Wei Zhang
- Department of Gastroenterology, Affiliated Hospital of Guizhou Medical University, Guizhou, China
| | | | | | - Michael H. Roehrl
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA
| |
Collapse
|
37
|
Konstantoulea K, Louros N, Rousseau F, Schymkowitz J. Heterotypic interactions in amyloid function and disease. FEBS J 2021; 289:2025-2046. [PMID: 33460517 DOI: 10.1111/febs.15719] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/07/2021] [Accepted: 01/15/2021] [Indexed: 11/27/2022]
Abstract
Amyloid aggregation results from the self-assembly of identical aggregation-prone sequences into cross-beta-sheet structures. The process is best known for its association with a wide range of human pathologies but also as a functional mechanism in all kingdoms of life. Less well elucidated is the role of heterotypic interactions between amyloids and other proteins and macromolecules and how this contributes to disease. We here review current data with a focus on neurodegenerative amyloid-associated diseases. Evidence indicates that heterotypic interactions occur in a wide range of amyloid processes and that these interactions modify fundamental aspects of amyloid aggregation including seeding, aggregation rates and toxicity. More work is required to understand the mechanistic origin of these interactions, but current understanding suggests that both supersaturation and sequence-specific binding can contribute to heterotypic amyloid interactions. Further unravelling these mechanisms may help to answer outstanding questions in the field including the selective vulnerability of cells types and tissues and the stereotypical spreading patterns of amyloids in disease.
Collapse
Affiliation(s)
- Katerina Konstantoulea
- VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Nikolaos Louros
- VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Frederic Rousseau
- VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Joost Schymkowitz
- VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| |
Collapse
|
38
|
Caldwell KA, Willicott CW, Caldwell GA. Modeling neurodegeneration in Caenorhabditis elegans. Dis Model Mech 2020; 13:13/10/dmm046110. [PMID: 33106318 PMCID: PMC7648605 DOI: 10.1242/dmm.046110] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The global burden of neurodegenerative diseases underscores the urgent need for innovative strategies to define new drug targets and disease-modifying factors. The nematode Caenorhabditis elegans has served as the experimental subject for multiple transformative discoveries that have redefined our understanding of biology for ∼60 years. More recently, the considerable attributes of C. elegans have been applied to neurodegenerative diseases, including amyotrophic lateral sclerosis, Alzheimer's disease, Parkinson's disease and Huntington's disease. Transgenic nematodes with genes encoding normal and disease variants of proteins at the single- or multi-copy level under neuronal-specific promoters limits expression to select neuronal subtypes. The anatomical transparency of C. elegans affords the use of co-expressed fluorescent proteins to follow the progression of neurodegeneration as the animals age. Significantly, a completely defined connectome facilitates detailed understanding of the impact of neurodegeneration on organismal health and offers a unique capacity to accurately link cell death with behavioral dysfunction or phenotypic variation in vivo. Moreover, chemical treatments, as well as forward and reverse genetic screening, hasten the identification of modifiers that alter neurodegeneration. When combined, these chemical-genetic analyses establish critical threshold states to enhance or reduce cellular stress for dissecting associated pathways. Furthermore, C. elegans can rapidly reveal whether lifespan or healthspan factor into neurodegenerative processes. Here, we outline the methodologies employed to investigate neurodegeneration in C. elegans and highlight numerous studies that exemplify its utility as a pre-clinical intermediary to expedite and inform mammalian translational research. Summary: While unsurpassed as an experimental system for fundamental biology, Caenorhabditis elegans remains undervalued for its translational potential. Here, we highlight significant outcomes from, and resources available for, C. elegans-based research into neurodegenerative disorders.
Collapse
Affiliation(s)
- Kim A Caldwell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA .,Departments of Neurobiology, Neurology, Center for Neurodegeneration and Experimental Therapeutics, and Nathan Shock Center of Excellence in the Basic Biology of Aging, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Corey W Willicott
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Guy A Caldwell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA.,Departments of Neurobiology, Neurology, Center for Neurodegeneration and Experimental Therapeutics, and Nathan Shock Center of Excellence in the Basic Biology of Aging, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| |
Collapse
|
39
|
Drummond E, Pires G, MacMurray C, Askenazi M, Nayak S, Bourdon M, Safar J, Ueberheide B, Wisniewski T. Phosphorylated tau interactome in the human Alzheimer's disease brain. Brain 2020; 143:2803-2817. [PMID: 32812023 PMCID: PMC7526722 DOI: 10.1093/brain/awaa223] [Citation(s) in RCA: 177] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 05/05/2020] [Accepted: 05/22/2020] [Indexed: 01/07/2023] Open
Abstract
Accumulation of phosphorylated tau is a key pathological feature of Alzheimer's disease. Phosphorylated tau accumulation causes synaptic impairment, neuronal dysfunction and formation of neurofibrillary tangles. The pathological actions of phosphorylated tau are mediated by surrounding neuronal proteins; however, a comprehensive understanding of the proteins that phosphorylated tau interacts with in Alzheimer's disease is surprisingly limited. Therefore, the aim of this study was to determine the phosphorylated tau interactome. To this end, we used two complementary proteomics approaches: (i) quantitative proteomics was performed on neurofibrillary tangles microdissected from patients with advanced Alzheimer's disease; and (ii) affinity purification-mass spectrometry was used to identify which of these proteins specifically bound to phosphorylated tau. We identified 542 proteins in neurofibrillary tangles. This included the abundant detection of many proteins known to be present in neurofibrillary tangles such as tau, ubiquitin, neurofilament proteins and apolipoprotein E. Affinity purification-mass spectrometry confirmed that 75 proteins present in neurofibrillary tangles interacted with PHF1-immunoreactive phosphorylated tau. Twenty-nine of these proteins have been previously associated with phosphorylated tau, therefore validating our proteomic approach. More importantly, 34 proteins had previously been associated with total tau, but not yet linked directly to phosphorylated tau (e.g. synaptic protein VAMP2, vacuolar-ATPase subunit ATP6V0D1); therefore, we provide new evidence that they directly interact with phosphorylated tau in Alzheimer's disease. In addition, we also identified 12 novel proteins, not previously known to be physiologically or pathologically associated with tau (e.g. RNA binding protein HNRNPA1). Network analysis showed that the phosphorylated tau interactome was enriched in proteins involved in the protein ubiquitination pathway and phagosome maturation. Importantly, we were able to pinpoint specific proteins that phosphorylated tau interacts with in these pathways for the first time, therefore providing novel potential pathogenic mechanisms that can be explored in future studies. Combined, our results reveal new potential drug targets for the treatment of tauopathies and provide insight into how phosphorylated tau mediates its toxicity in Alzheimer's disease.
Collapse
Affiliation(s)
- Eleanor Drummond
- Brain and Mind Centre and Central Clinical School, Faculty of Medicine and Health, University of Sydney, Australia
- Centre for Cognitive Neurology, Department of Neurology, New York University School of Medicine, New York, NY, USA
| | - Geoffrey Pires
- Centre for Cognitive Neurology, Department of Neurology, New York University School of Medicine, New York, NY, USA
- Alzheimer’s and Prion Diseases Team, Paris Brain Institute, CNRS, UMR 7225, INSERM 1127, Sorbonne University UM75, Paris, France
| | - Claire MacMurray
- Centre for Cognitive Neurology, Department of Neurology, New York University School of Medicine, New York, NY, USA
| | | | - Shruti Nayak
- Proteomics Laboratory, Division of Advanced Research Technologies, NYU School of Medicine, New York, NY, USA
| | - Marie Bourdon
- Centre for Cognitive Neurology, Department of Neurology, New York University School of Medicine, New York, NY, USA
| | - Jiri Safar
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
- Department of Neurology, Case Western Reserve University, Cleveland, OH, USA
| | - Beatrix Ueberheide
- Biomedical Hosting LLC, USA
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Thomas Wisniewski
- Centre for Cognitive Neurology, Department of Neurology, New York University School of Medicine, New York, NY, USA
- Department of Psychiatry, New York University School of Medicine, New York, NY, USA
| |
Collapse
|
40
|
Adhikari R, Yang M, Saikia N, Dutta C, Alharbi WFA, Shan Z, Pandey R, Tiwari A. Acetylation of Aβ42 at Lysine 16 Disrupts Amyloid Formation. ACS Chem Neurosci 2020; 11:1178-1191. [PMID: 32207962 PMCID: PMC7605495 DOI: 10.1021/acschemneuro.0c00069] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The residue lysine 28 (K28) is known to form an important salt bridge that stabilizes the Aβ amyloid structure, and acetylation of lysine 28 (K28Ac) slows the Aβ42 fibrillization rate but does not affect fibril morphology. On the other hand, acetylation of lysine 16 (K16Ac) residue greatly diminishes the fibrillization property of Aβ42 peptide and also affects its toxicity. This is due to the fact that lysine 16 acetylated amyloid beta peptide forms amorphous aggregates instead of amyloid fibrils. This is likely a result of increased hydrophobicity of the K16-A21 region due to K16 acetylation, as confirmed by molecular dynamic simulation studies. The calculated results show that the hydrophobic patches of aggregates from acetylated peptides were different when compared to wild-type (WT) peptide. K16Ac and double acetylated (KKAc) peptide aggregates show significantly higher cytotoxicity compared to the WT or K28Ac peptide aggregates alone. However, the heterogeneous mixture of WT and acetylated Aβ42 peptide aggregates exhibited higher free radical formation as well as cytotoxicity, suggesting dynamic interactions between different species could be a critical contributor to Aβ pathology.
Collapse
Affiliation(s)
- Rashmi Adhikari
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Mu Yang
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Nabanita Saikia
- Department of Physics, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Colina Dutta
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Wafa F A Alharbi
- Department of Biological Sciences, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Zhiying Shan
- Department of Kinesiology and Integrative Physiology, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Ravindra Pandey
- Department of Physics, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Ashutosh Tiwari
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| |
Collapse
|
41
|
Grantham J. The Molecular Chaperone CCT/TRiC: An Essential Component of Proteostasis and a Potential Modulator of Protein Aggregation. Front Genet 2020; 11:172. [PMID: 32265978 PMCID: PMC7096549 DOI: 10.3389/fgene.2020.00172] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 02/13/2020] [Indexed: 12/15/2022] Open
Abstract
Chaperonin containing tailless complex polypeptide 1 (CCT) or tailless complex polypeptide 1 ring complex (TRiC) is an essential eukaryotic molecular chaperone. It is a multi-subunit oligomer of two rings of eight individual protein subunits. When assembled, each of the eight CCT subunits occupies a specific position within each chaperonin ring. Thus a geometrically defined binding interface is formed from the divergent sequences within the CCT subunit substrate binding domains. CCT is required for the folding of the abundant cytoskeletal proteins actin and tubulin, which in turn form assemblies of microfilaments and microtubules. CCT is also involved in the folding of some additional protein substrates and some CCT subunits have been shown to have functions when monomeric. Since observations were made in worms over a decade ago using an RNAi screen, which connected CCT subunits to the aggregation of polyglutamine tracts, a role for CCT as a potential modulator of protein aggregation has started to emerge. Here there will be a focus on how mechanistically CCT may be able to achieve this and if this potential function of CCT provides any insights and directions for developing future treatments for protein aggregation driven neurodegenerative diseases generally, many of which are associated with aging.
Collapse
Affiliation(s)
- Julie Grantham
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| |
Collapse
|
42
|
Kakraba S, Ayyadevara S, Penthala NR, Balasubramaniam M, Ganne A, Liu L, Alla R, Bommagani SB, Barger SW, Griffin WST, Crooks PA, Shmookler Reis RJ. A Novel Microtubule-Binding Drug Attenuates and Reverses Protein Aggregation in Animal Models of Alzheimer's Disease. Front Mol Neurosci 2020; 12:310. [PMID: 31920540 PMCID: PMC6920216 DOI: 10.3389/fnmol.2019.00310] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 11/29/2019] [Indexed: 11/14/2022] Open
Abstract
Age-progressive neurodegenerative pathologies, including Alzheimer’s disease (AD), are distinguished and diagnosed by disease-specific components of intra- or extra-cellular aggregates. Increasing evidence suggests that neuroinflammation promotes protein aggregation, and is involved in the etiology of neurological diseases. We synthesized and tested analogs of the naturally occurring tubulin-binding compound, combretastatin A-4. One such analog, PNR502, markedly reduced the quantity of Alzheimer-associated amyloid aggregates in the BRI-Aβ1–42 mouse model of AD, while blunting the ability of the pro-inflammatory cytokine IL-1β to raise levels of amyloid plaque and its protein precursors in a neuronal cell-culture model. In transgenic Caenorhabditis elegans (C. elegans) strains that express human Aβ1–42 in muscle or neurons, PNR502 rescued Aβ-induced disruption of motility (3.8-fold, P < 0.0001) or chemotaxis (1.8-fold, P < 0.05), respectively. Moreover, in C. elegans with neuronal expression of Aβ1–42, a single day of PNR502 exposure reverses the chemotaxis deficit by 54% (P < 0.01), actually exceeding the protection from longer exposure. Moreover, continuous PNR502 treatment extends nematode lifespan 23% (P ≤ 0.001). Given that PNR502 can slow, prevent, or reverse Alzheimer-like protein aggregation in human-cell-culture and animal models, and that its principal predicted and observed binding targets are proteins previously implicated in Alzheimer’s, we propose that PNR502 has therapeutic potential to inhibit cerebral Aβ1–42 aggregation and prevent or reverse neurodegeneration.
Collapse
Affiliation(s)
- Samuel Kakraba
- BioInformatics Program, University of Arkansas for Medical Sciences and University of Arkansas at Little Rock, Little Rock, AR, United States
| | - Srinivas Ayyadevara
- Central Arkansas Veterans Healthcare Service, Little Rock, AR, United States.,Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Narsimha Reddy Penthala
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | | | - Akshatha Ganne
- BioInformatics Program, University of Arkansas for Medical Sciences and University of Arkansas at Little Rock, Little Rock, AR, United States
| | - Ling Liu
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Ramani Alla
- Central Arkansas Veterans Healthcare Service, Little Rock, AR, United States.,Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Shoban Babu Bommagani
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Steven W Barger
- Central Arkansas Veterans Healthcare Service, Little Rock, AR, United States.,Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - W Sue T Griffin
- Central Arkansas Veterans Healthcare Service, Little Rock, AR, United States.,Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Peter A Crooks
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Robert J Shmookler Reis
- BioInformatics Program, University of Arkansas for Medical Sciences and University of Arkansas at Little Rock, Little Rock, AR, United States.,Central Arkansas Veterans Healthcare Service, Little Rock, AR, United States.,Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| |
Collapse
|
43
|
Pires G, McElligott S, Drusinsky S, Halliday G, Potier MC, Wisniewski T, Drummond E. Secernin-1 is a novel phosphorylated tau binding protein that accumulates in Alzheimer's disease and not in other tauopathies. Acta Neuropathol Commun 2019; 7:195. [PMID: 31796108 PMCID: PMC6892024 DOI: 10.1186/s40478-019-0848-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 11/14/2019] [Indexed: 12/13/2022] Open
Abstract
We recently identified Secernin-1 (SCRN1) as a novel amyloid plaque associated protein using localized proteomics. Immunohistochemistry studies confirmed that SCRN1 was present in plaque-associated dystrophic neurites and also revealed distinct and abundant co-localization with neurofibrillary tangles (NFTs). Little is known about the physiological function of SCRN1 and its role in Alzheimer's disease (AD) and other neurodegenerative diseases has not been studied. Therefore, we performed a comprehensive study of SCRN1 distribution in neurodegenerative diseases. Immunohistochemistry was used to map SCRN1 accumulation throughout the progression of AD in a cohort of 58 patients with a range of NFT pathology (Abundant NFT, n = 21; Moderate NFT, n = 22; Low/No NFT, n = 15), who were clinically diagnosed as having AD, mild cognitive impairment or normal cognition. SCRN1 accumulation was also examined in two cases with both Frontotemporal Lobar Degeneration (FTLD)-Tau and AD-related neuropathology, cases of Down Syndrome (DS) with AD (n = 5), one case of hereditary cerebral hemorrhage with amyloidosis - Dutch type (HCHWA-D) and other non-AD tauopathies including: primary age-related tauopathy (PART, [n = 5]), Corticobasal Degeneration (CBD, [n = 5]), Progressive Supranuclear Palsy (PSP, [n = 5]) and Pick's disease (PiD, [n = 4]). Immunohistochemistry showed that SCRN1 was a neuronal protein that abundantly accumulated in NFTs and plaque-associated dystrophic neurites throughout the progression of AD. Quantification of SCRN1 immunohistochemistry confirmed that SCRN1 preferentially accumulated in NFTs in comparison to surrounding non-tangle containing neurons at both early and late stages of AD. Similar results were observed in DS with AD and PART. However, SCRN1 did not co-localize with phosphorylated tau inclusions in CBD, PSP or PiD. Co-immunoprecipitation revealed that SCRN1 interacted with phosphorylated tau in human AD brain tissue. Together, these results suggest that SCRN1 is uniquely associated with tau pathology in AD, DS and PART. As such, SCRN1 has potential as a novel therapeutic target and could serve as a useful biomarker to distinguish AD from other tauopathies.
Collapse
Affiliation(s)
- Geoffrey Pires
- Center for Cognitive Neurology and Department of Neurology, New York University School of Medicine, 435 East 30th Street, Rm 1017, New York, NY, 10016, USA
| | - Sacha McElligott
- Center for Cognitive Neurology and Department of Neurology, New York University School of Medicine, 435 East 30th Street, Rm 1017, New York, NY, 10016, USA
| | - Shiron Drusinsky
- Center for Cognitive Neurology and Department of Neurology, New York University School of Medicine, 435 East 30th Street, Rm 1017, New York, NY, 10016, USA
| | - Glenda Halliday
- Brain & Mind Centre and Central Clinical School, Faculty of Medicine and Health, University of Sydney, 94 Mallett Street, Camperdown, NSW, 2050, Australia
| | - Marie-Claude Potier
- Institut du Cerveau et de la Moelle épinière, CNRS UMR7225, INSERM U1127, UPMC, Hôpital de la Pitié-Salpêtrière, 47 Bd de l'Hôpital, Paris, France
| | - Thomas Wisniewski
- Center for Cognitive Neurology and Department of Neurology, New York University School of Medicine, 435 East 30th Street, Rm 1017, New York, NY, 10016, USA.
- Departments of Pathology and Psychiatry, New York University School of Medicine, 435 East 30th Street, Rm 1017, New York, NY, 10016, USA.
| | - Eleanor Drummond
- Center for Cognitive Neurology and Department of Neurology, New York University School of Medicine, 435 East 30th Street, Rm 1017, New York, NY, 10016, USA.
- Brain & Mind Centre and Central Clinical School, Faculty of Medicine and Health, University of Sydney, 94 Mallett Street, Camperdown, NSW, 2050, Australia.
| |
Collapse
|
44
|
Balasubramaniam M, Ayyadevara S, Ganne A, Kakraba S, Penthala NR, Du X, Crooks PA, Griffin ST, Shmookler Reis RJ. Aggregate Interactome Based on Protein Cross-linking Interfaces Predicts Drug Targets to Limit Aggregation in Neurodegenerative Diseases. iScience 2019; 20:248-264. [PMID: 31593839 PMCID: PMC6817627 DOI: 10.1016/j.isci.2019.09.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 06/20/2019] [Accepted: 09/17/2019] [Indexed: 01/02/2023] Open
Abstract
Diagnosis of neurodegenerative diseases hinges on “seed” proteins detected in disease-specific aggregates. These inclusions contain diverse constituents, adhering through aberrant interactions that our prior data indicate are nonrandom. To define preferential protein-protein contacts mediating aggregate coalescence, we created click-chemistry reagents that cross-link neighboring proteins within human, APPSw-driven, neuroblastoma-cell aggregates. These reagents incorporate a biotinyl group to efficiently recover linked tryptic-peptide pairs. Mass-spectroscopy outputs were screened for all possible peptide pairs in the aggregate proteome. These empirical linkages, ranked by abundance, implicate a protein-adherence network termed the “aggregate contactome.” Critical hubs and hub-hub interactions were assessed by RNAi-mediated rescue of chemotaxis in aging nematodes, and aggregation-driving properties were inferred by multivariate regression and neural-network approaches. Aspirin, while disrupting aggregation, greatly simplified the aggregate contactome. This approach, and the dynamic model of aggregate accrual it implies, reveals the architecture of insoluble-aggregate networks and may reveal targets susceptible to interventions to ameliorate protein-aggregation diseases. Cross-link data support a preferred hierarchy of protein accrual into aggregates Contact networks can predict proteins that contribute functionally to aggregation RNAi knockdowns of key hubs and hub connectors imply functional roles in accrual Aspirin opposes protein aggregation by reducing contactome interactions >5-fold
Collapse
Affiliation(s)
- Meenakshisundaram Balasubramaniam
- McClellan Veterans Medical Ctr., Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA; Department of Geriatrics, Reynolds Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Srinivas Ayyadevara
- McClellan Veterans Medical Ctr., Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA; Department of Geriatrics, Reynolds Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Akshatha Ganne
- Bioinformatics Program, University of Arkansas for Medical Sciences, University of Arkansas at Little Rock, Little Rock, AR 72205, USA
| | - Samuel Kakraba
- Bioinformatics Program, University of Arkansas for Medical Sciences, University of Arkansas at Little Rock, Little Rock, AR 72205, USA
| | - Narsimha Reddy Penthala
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Xiuxia Du
- Department of Bioinformatics & Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Peter A Crooks
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Sue T Griffin
- McClellan Veterans Medical Ctr., Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA; Department of Geriatrics, Reynolds Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Robert J Shmookler Reis
- McClellan Veterans Medical Ctr., Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA; Department of Geriatrics, Reynolds Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| |
Collapse
|
45
|
Pace MC, Xu G, Fromholt S, Howard J, Crosby K, Giasson BI, Lewis J, Borchelt DR. Changes in proteome solubility indicate widespread proteostatic disruption in mouse models of neurodegenerative disease. Acta Neuropathol 2018; 136:919-938. [PMID: 30140941 DOI: 10.1007/s00401-018-1895-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 08/02/2018] [Indexed: 12/17/2022]
Abstract
The deposition of pathologic misfolded proteins in neurodegenerative disorders such as Alzheimer's disease, Parkinson's disease, frontotemporal dementia and amyotrophic lateral sclerosis is hypothesized to burden protein homeostatic (proteostatic) machinery, potentially leading to insufficient capacity to maintain the proteome. This hypothesis has been supported by previous work in our laboratory, as evidenced by the perturbation of cytosolic protein solubility in response to amyloid plaques in a mouse model of Alzheimer's amyloidosis. In the current study, we demonstrate changes in proteome solubility are a common pathology to mouse models of neurodegenerative disease. Pathological accumulations of misfolded tau, α-synuclein and mutant superoxide dismutase 1 in CNS tissues of transgenic mice were associated with changes in the solubility of hundreds of CNS proteins in each model. We observed that changes in proteome solubility were progressive and, using the rTg4510 model of inducible tau pathology, demonstrated that these changes were dependent upon sustained expression of the primary pathologic protein. In all of the models examined, changes in proteome solubility were robust, easily detected, and provided a sensitive indicator of proteostatic disruption. Interestingly, a subset of the proteins that display a shift towards insolubility were common between these different models, suggesting that a specific subset of the proteome is vulnerable to proteostatic disruption. Overall, our data suggest that neurodegenerative proteinopathies modeled in mice impose a burden on the proteostatic network that diminishes the ability of neural cells to prevent aberrant conformational changes that alter the solubility of hundreds of abundant cellular proteins.
Collapse
Affiliation(s)
- Michael C Pace
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, University of Florida, Gainesville, FL, 32610-0244, USA
| | - Guilian Xu
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, University of Florida, Gainesville, FL, 32610-0244, USA
| | - Susan Fromholt
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, University of Florida, Gainesville, FL, 32610-0244, USA
| | - John Howard
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, University of Florida, Gainesville, FL, 32610-0244, USA
| | - Keith Crosby
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, University of Florida, Gainesville, FL, 32610-0244, USA
| | - Benoit I Giasson
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, University of Florida, Gainesville, FL, 32610-0244, USA
| | - Jada Lewis
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, University of Florida, Gainesville, FL, 32610-0244, USA.
| | - David R Borchelt
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, University of Florida, Gainesville, FL, 32610-0244, USA.
- SantaFe Healthcare Alzheimer's Disease Research Center, Gainesville, FL, USA.
| |
Collapse
|
46
|
Ayyadevara S, Ganne A, Hendrix RD, Balasubramaniam M, Shmookler Reis RJ, Barger SW. Functional assessments through novel proteomics approaches: Application to insulin/IGF signaling in neurodegenerative disease'. J Neurosci Methods 2018; 319:40-46. [PMID: 30412730 DOI: 10.1016/j.jneumeth.2018.11.005] [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] [Received: 08/02/2018] [Revised: 11/04/2018] [Accepted: 11/05/2018] [Indexed: 11/26/2022]
Abstract
BACKGROUND Events that instigate disease may involve biochemical events distinct from changes in the steady-state levels of proteins. Even chronic degenerative disorders appear to involve changes such as post-translational modifications. NEW METHOD We have begun a series of proteomics analyses on proteins that have been fractionated by functional status. Because Alzheimer's disease (AD) is associated with metabolic perturbations such as Type-2 diabetes, fractionation hinged on binding to phosphatidylinositol trisphosphate (PIP3), key to insulin/insulin-like growth factor signaling. We compared mice on normal chow to counterparts subjected to diet-induced obesity (DIO) or to mice expressing human Aβ1-42 from a transgene. RESULTS The prevailing phenotypic finding in either experimental group was loss of PIP3 binding. Of the 1228 proteins that showed valid PIP3 binding in any group of mice, 55% exhibited a significant quantitative difference in the number of spectral counts as a function of DIO, 63% as function of the Aβ transgene, and 79% as a function of either variable. There was remarkable overlap among the proteins altered in the two experimental groups, and pathway analysis indicated effects on proteostasis, apoptosis, and synaptic vesicles. COMPARISON WITH EXISTING METHODS Most proteomics approaches only identify differences in the steady-state levels of proteins. Our overlay of a functional distinction permits new levels of discovery that may achieve novel insights into physiology in an unbiased and inclusive manner. CONCLUSIONS Proteomics analyses have revolutionized the discovery phase of biomedical research but are conventionally limited in scope. The creative use of fractionation prior to proteomic discovery is likely to provide important insights into AD and related disorders.
Collapse
Affiliation(s)
- Srinivas Ayyadevara
- Central Arkansas Veterans Healthcare System, Little Rock, AR, 72205, United States; Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States.
| | - Akshatha Ganne
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States; BioInformatics Program, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States
| | - Rachel D Hendrix
- Department of Neurobiology & Developmental Sciences, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, United States
| | | | - Robert J Shmookler Reis
- Central Arkansas Veterans Healthcare System, Little Rock, AR, 72205, United States; Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States; BioInformatics Program, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States; Department of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, United States
| | - Steven W Barger
- Central Arkansas Veterans Healthcare System, Little Rock, AR, 72205, United States; Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States; Department of Neurobiology & Developmental Sciences, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, United States.
| |
Collapse
|
47
|
Structural insights into pro-aggregation effects of C. elegans CRAM-1 and its human ortholog SERF2. Sci Rep 2018; 8:14891. [PMID: 30291272 PMCID: PMC6173753 DOI: 10.1038/s41598-018-33143-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 09/19/2018] [Indexed: 12/20/2022] Open
Abstract
Toxic protein aggregates are key features of progressive neurodegenerative diseases. In addition to “seed” proteins diagnostic for each neuropathy (e.g., Aβ1–42 and tau in Alzheimer’s disease), aggregates contain numerous other proteins, many of which are common to aggregates from diverse diseases. We reported that CRAM-1, discovered in insoluble aggregates of C. elegans expressing Q40::YFP, blocks proteasomal degradation of ubiquitinated proteins and thus promotes aggregation. We now show that CRAM-1 contains three α-helical segments forming a UBA-like domain, structurally similar to those of mammalian adaptor proteins (e.g. RAD23, SQSTM1/p62) that shuttle ubiquitinated cargos to proteasomes or autophagosomes for degradation. Molecular modeling indicates that CRAM-1, through this UBA-like domain, can form tight complexes with mono- and di-ubiquitin and may thus prevent tagged proteins from interacting with adaptor/shuttle proteins required for degradation. A human ortholog of CRAM-1, SERF2 (also largely disordered), promotes aggregation in SH-SY5Y-APPSw human neuroblastoma cells, since SERF2 knockdown protects these cells from amyloid formation. Atomistic molecular-dynamic simulations predict spontaneous unfolding of SERF2, and computational large-scale protein-protein interactions predict its stable binding to ubiquitins. SERF2 is also predicted to bind to most proteins screened at random, although with lower average stability than to ubiquitins, suggesting roles in aggregation initiation and/or progression.
Collapse
|
48
|
Bondarev SA, Antonets KS, Kajava AV, Nizhnikov AA, Zhouravleva GA. Protein Co-Aggregation Related to Amyloids: Methods of Investigation, Diversity, and Classification. Int J Mol Sci 2018; 19:ijms19082292. [PMID: 30081572 PMCID: PMC6121665 DOI: 10.3390/ijms19082292] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 07/29/2018] [Accepted: 08/02/2018] [Indexed: 01/04/2023] Open
Abstract
Amyloids are unbranched protein fibrils with a characteristic spatial structure. Although the amyloids were first described as protein deposits that are associated with the diseases, today it is becoming clear that these protein fibrils play multiple biological roles that are essential for different organisms, from archaea and bacteria to humans. The appearance of amyloid, first of all, causes changes in the intracellular quantity of the corresponding soluble protein(s), and at the same time the aggregate can include other proteins due to different molecular mechanisms. The co-aggregation may have different consequences even though usually this process leads to the depletion of a functional protein that may be associated with different diseases. The protein co-aggregation that is related to functional amyloids may mediate important biological processes and change of protein functions. In this review, we survey the known examples of the amyloid-related co-aggregation of proteins, discuss their pathogenic and functional roles, and analyze methods of their studies from bacteria and yeast to mammals. Such analysis allow for us to propose the following co-aggregation classes: (i) titration: deposition of soluble proteins on the amyloids formed by their functional partners, with such interactions mediated by a specific binding site; (ii) sequestration: interaction of amyloids with certain proteins lacking a specific binding site; (iii) axial co-aggregation of different proteins within the same amyloid fibril; and, (iv) lateral co-aggregation of amyloid fibrils, each formed by different proteins.
Collapse
Affiliation(s)
- Stanislav A Bondarev
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab., 7/9, St. Petersburg 199034, Russia.
- Laboratory of Amyloid Biology, St. Petersburg State University, Russia, Universitetskaya nab., 7/9, St. Petersburg 199034, Russia.
| | - Kirill S Antonets
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab., 7/9, St. Petersburg 199034, Russia.
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, Podbelskogo sh., 3, Pushkin, St. Petersburg 196608, Russia.
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier 1919 Route de Mende, CEDEX 5, 34293 Montpellier, France.
- Institut de Biologie Computationnelle (IBC), 34095 Montpellier, France.
- University ITMO, Institute of Bioengineering, Kronverksky Pr. 49, St. Petersburg 197101, Russia.
| | - Anton A Nizhnikov
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab., 7/9, St. Petersburg 199034, Russia.
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, Podbelskogo sh., 3, Pushkin, St. Petersburg 196608, Russia.
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab., 7/9, St. Petersburg 199034, Russia.
- Laboratory of Amyloid Biology, St. Petersburg State University, Russia, Universitetskaya nab., 7/9, St. Petersburg 199034, Russia.
| |
Collapse
|
49
|
Adiutori R, Aarum J, Zubiri I, Bremang M, Jung S, Sheer D, Pike I, Malaspina A. The proteome of neurofilament-containing protein aggregates in blood. Biochem Biophys Rep 2018; 14:168-177. [PMID: 29872749 PMCID: PMC5986704 DOI: 10.1016/j.bbrep.2018.04.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/15/2018] [Accepted: 04/26/2018] [Indexed: 11/24/2022] Open
Abstract
Protein aggregation in biofluids is a poorly understood phenomenon. Under normal physiological conditions, fluid-borne aggregates may contain plasma or cell proteins prone to aggregation. Recent observations suggest that neurofilaments (Nf), the building blocks of neurons and a biomarker of neurodegeneration, are included in high molecular weight complexes in circulation. The composition of these Nf-containing hetero-aggregates (NCH) may change in systemic or organ-specific pathologies, providing the basis to develop novel disease biomarkers. We have tested ultracentrifugation (UC) and a commercially available protein aggregate binder, Seprion PAD-Beads (SEP), for the enrichment of NCH from plasma of healthy individuals, and then characterised the Nf content of the aggregate fractions using gel electrophoresis and their proteome by mass spectrometry (MS). Western blot analysis of fractions obtained by UC showed that among Nf isoforms, neurofilament heavy chain (NfH) was found within SDS-stable high molecular weight aggregates. Shotgun proteomics of aggregates obtained with both extraction techniques identified mostly cell structural and to a lesser extent extra-cellular matrix proteins, while functional analysis revealed pathways involved in inflammatory response, phagosome and prion-like protein behaviour. UC aggregates were specifically enriched with proteins involved in endocrine, metabolic and cell-signalling regulation. We describe the proteome of neurofilament-containing aggregates isolated from healthy individuals biofluids using different extraction methods.
Collapse
Affiliation(s)
- Rocco Adiutori
- Centre for Neuroscience and Trauma, Queen Mary University of London, Blizard Institute, Barts and The School of Medicine and Dentistry, London, United Kingdom
| | - Johan Aarum
- Centre for Genomics and Child Health, Queen Mary University of London, Blizard Institute, Barts and The London School of Medicine and Dentistry, London, United Kingdom
| | - Irene Zubiri
- Centre for Neuroscience and Trauma, Queen Mary University of London, Blizard Institute, Barts and The School of Medicine and Dentistry, London, United Kingdom
| | - Michael Bremang
- Proteome Sciences Plc, Hamilton House, Mabledon Place, London, United Kingdom
| | - Stephan Jung
- ProteomeSciencesR&DGmbH&Co.KG, Frankfurt, Germany
| | - Denise Sheer
- Centre for Genomics and Child Health, Queen Mary University of London, Blizard Institute, Barts and The London School of Medicine and Dentistry, London, United Kingdom
| | - Ian Pike
- Proteome Sciences Plc, Hamilton House, Mabledon Place, London, United Kingdom
| | - Andrea Malaspina
- Centre for Neuroscience and Trauma, Queen Mary University of London, Blizard Institute, Barts and The School of Medicine and Dentistry, London, United Kingdom
| |
Collapse
|
50
|
Gal J, Chen J, Katsumata Y, Fardo DW, Wang WX, Artiushin S, Price D, Anderson S, Patel E, Zhu H, Nelson PT. Detergent Insoluble Proteins and Inclusion Body-Like Structures Immunoreactive for PRKDC/DNA-PK/DNA-PKcs, FTL, NNT, and AIFM1 in the Amygdala of Cognitively Impaired Elderly Persons. J Neuropathol Exp Neurol 2018; 77:21-39. [PMID: 29186589 DOI: 10.1093/jnen/nlx097] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 10/15/2017] [Indexed: 12/21/2022] Open
Abstract
Misfolded protein in the amygdala is a neuropathologic feature of Alzheimer disease and many other neurodegenerative disorders. We examined extracts from human amygdala (snap-frozen at autopsy) to investigate whether novel and as yet uncharacterized misfolded proteins would be detectable. Polypeptides from the detergent-insoluble, urea-soluble protein fractions of amygdala were interrogated using liquid chromatography-electrospray ionization-tandem mass spectrometry. Among the detergent-insoluble proteins identified in amygdala of demented subjects but not controls were Tau, TDP-43, Aβ, α-synuclein, and ApoE. Additional detergent-insoluble proteins from demented subjects in the high-molecular weight portion of SDS gels included NNT, TNIK, PRKDC (DNA-PK, or DNA-PKcs), ferritin light chain (FTL), AIFM1, SYT11, STX1B, EAA1, COL25A1, M4K4, CLH1, SQSTM, SYNJ1, C3, and C4. In follow-up immunohistochemical experiments, NNT, TNIK, PRKDC, AIFM1, and FTL were observed in inclusion body-like structures in cognitively impaired subjects' amygdalae. Double-label immunofluorescence revealed that FTL and phospho-PRKDC immunoreactivity colocalized partially with TDP-43 and/or Tau inclusion bodies. Western blots showed high-molecular weight "smears", particularly for NNT and PRKDC. A preliminary genetic association study indicated that rare NNT, TNIK, and PRKDC gene variants had nominally significant association with Alzheimer-type dementia risk. In summary, novel detergent-insoluble proteins, with evidence of proteinaceous deposits, were found in amygdalae of elderly, cognitively impaired subjects.
Collapse
Affiliation(s)
- Jozsef Gal
- Department of Molecular and Cellular Biochemistry; Department of Biostatistics; Sanders-Brown Center on Aging; Department of Pathology, University of Kentucky, Lexington, Kentucky; and Research and Development, Lexington VA Medical Center, Lexington, Kentucky
| | - Jing Chen
- Department of Molecular and Cellular Biochemistry; Department of Biostatistics; Sanders-Brown Center on Aging; Department of Pathology, University of Kentucky, Lexington, Kentucky; and Research and Development, Lexington VA Medical Center, Lexington, Kentucky
| | - Yuriko Katsumata
- Department of Molecular and Cellular Biochemistry; Department of Biostatistics; Sanders-Brown Center on Aging; Department of Pathology, University of Kentucky, Lexington, Kentucky; and Research and Development, Lexington VA Medical Center, Lexington, Kentucky
| | - David W Fardo
- Department of Molecular and Cellular Biochemistry; Department of Biostatistics; Sanders-Brown Center on Aging; Department of Pathology, University of Kentucky, Lexington, Kentucky; and Research and Development, Lexington VA Medical Center, Lexington, Kentucky
| | - Wang-Xia Wang
- Department of Molecular and Cellular Biochemistry; Department of Biostatistics; Sanders-Brown Center on Aging; Department of Pathology, University of Kentucky, Lexington, Kentucky; and Research and Development, Lexington VA Medical Center, Lexington, Kentucky
| | - Sergey Artiushin
- Department of Molecular and Cellular Biochemistry; Department of Biostatistics; Sanders-Brown Center on Aging; Department of Pathology, University of Kentucky, Lexington, Kentucky; and Research and Development, Lexington VA Medical Center, Lexington, Kentucky
| | - Douglas Price
- Department of Molecular and Cellular Biochemistry; Department of Biostatistics; Sanders-Brown Center on Aging; Department of Pathology, University of Kentucky, Lexington, Kentucky; and Research and Development, Lexington VA Medical Center, Lexington, Kentucky
| | - Sonya Anderson
- Department of Molecular and Cellular Biochemistry; Department of Biostatistics; Sanders-Brown Center on Aging; Department of Pathology, University of Kentucky, Lexington, Kentucky; and Research and Development, Lexington VA Medical Center, Lexington, Kentucky
| | - Ela Patel
- Department of Molecular and Cellular Biochemistry; Department of Biostatistics; Sanders-Brown Center on Aging; Department of Pathology, University of Kentucky, Lexington, Kentucky; and Research and Development, Lexington VA Medical Center, Lexington, Kentucky
| | - Haining Zhu
- Department of Molecular and Cellular Biochemistry; Department of Biostatistics; Sanders-Brown Center on Aging; Department of Pathology, University of Kentucky, Lexington, Kentucky; and Research and Development, Lexington VA Medical Center, Lexington, Kentucky
| | - Peter T Nelson
- Department of Molecular and Cellular Biochemistry; Department of Biostatistics; Sanders-Brown Center on Aging; Department of Pathology, University of Kentucky, Lexington, Kentucky; and Research and Development, Lexington VA Medical Center, Lexington, Kentucky
| |
Collapse
|