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Shi C, Gottschalk WK, Colton CA, Mukherjee S, Lutz MW. Alzheimer's Disease Protein Relevance Analysis Using Human and Mouse Model Proteomics Data. FRONTIERS IN SYSTEMS BIOLOGY 2023; 3:1085577. [PMID: 37650081 PMCID: PMC10467016 DOI: 10.3389/fsysb.2023.1085577] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
The principles governing genotype-phenotype relationships are still emerging(1-3), and detailed translational as well as transcriptomic information is required to understand complex phenotypes, such as the pathogenesis of Alzheimer's disease. For this reason, the proteomics of Alzheimer disease (AD) continues to be studied extensively. Although comparisons between data obtained from humans and mouse models have been reported, approaches that specifically address the between-species statistical comparisons are understudied. Our study investigated the performance of two statistical methods for identification of proteins and biological pathways associated with Alzheimer's disease for cross-species comparisons, taking specific data analysis challenges into account, including collinearity, dimensionality reduction and cross-species protein matching. We used a human dataset from a well-characterized cohort followed for over 22 years with proteomic data available. For the mouse model, we generated proteomic data from whole brains of CVN-AD and matching control mouse models. We used these analyses to determine the reliability of a mouse model to forecast significant proteomic-based pathological changes in the brain that may mimic pathology in human Alzheimer's disease. Compared with LASSO regression, partial least squares discriminant analysis provided better statistical performance for the proteomics analysis. The major biological finding of the study was that extracellular matrix proteins and integrin-related pathways were dysregulated in both the human and mouse data. This approach may help inform the development of mouse models that are more relevant to the study of human late-onset Alzheimer's disease.
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Affiliation(s)
- Cathy Shi
- Department of Statistical Science, Duke University, Durham, NC 27708, USA
| | - W. Kirby Gottschalk
- Division of Translational Brain Sciences, Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Carol A. Colton
- Division of Translational Brain Sciences, Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sayan Mukherjee
- Department of Statistical Science, Duke University, Durham, NC 27708, USA
- Departments of Mathematics, Computer Science, and Biostatistics & Bioinformatics Duke University, Durham, NC 27708, USA
| | - Michael W. Lutz
- Division of Translational Brain Sciences, Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA
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Degan S, Feng Y, Hoffmann U, Turner DA. Placement of Extracranial Stimulating Electrodes and Measurement of Cerebral Blood Flow and Intracranial Electrical Fields in Anesthetized Mice. J Vis Exp 2023:10.3791/65195. [PMID: 37335103 PMCID: PMC10476879 DOI: 10.3791/65195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023] Open
Abstract
The detection of cerebral blood flow (CBF) responses to various forms of neuronal activation is critical for understanding dynamic brain function and variations in the substrate supply to the brain. This paper describes a protocol for measuring CBF responses to transcranial alternating current stimulation (tACS). Dose-response curves are estimated both from the CBF change occurring with tACS (mA) and from the intracranial electric field (mV/mm). We estimate the intracranial electrical field based on the different amplitudes measured by glass microelectrodes within each side of the brain. In this paper, we describe the experimental setup, which involves using either bilateral laser Doppler (LD) probes or laser speckle imaging (LSI) to measure the CBF; as a result, this setup requires anesthesia for the electrode placement and stability. We present a correlation between the CBF response and the current as a function of age, showing a significantly larger response at higher currents (1.5 mA and 2.0 mA) in young control animals (12-14 weeks) compared to older animals (28-32 weeks) (p < 0.005 difference). We also demonstrate a significant CBF response at electrical field strengths <5 mV/mm, which is an important consideration for eventual human studies. These CBF responses are also strongly influenced by the use of anesthesia compared to awake animals, the respiration control (i.e., intubated vs. spontaneous breathing), systemic factors (i.e., CO2), and local conduction within the blood vessels, which is mediated by pericytes and endothelial cells. Likewise, more detailed imaging/recording techniques may limit the field size from the entire brain to only a small region. We describe the use of extracranial electrodes for applying tACS stimulation, including both homemade and commercial electrode designs for rodents, the concurrent measurement of the CBF and intracranial electrical field using bilateral glass DC recording electrodes, and the imaging approaches. We are currently applying these techniques to implement a closed-loop format for augmenting the CBF in animal models of Alzheimer's disease and stroke.
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Affiliation(s)
- Simone Degan
- Department of Neurosurgery, Duke University Medical Center
| | - Yu Feng
- Department of Neurosurgery, Duke University Medical Center
| | - Ulrike Hoffmann
- Department of Anesthesiology and Pain Management, University Texas Southwestern Medical School
| | - Dennis A Turner
- Department of Neurosurgery, Duke University Medical Center; Department of Neurobiology, Duke University Medical Center; Department of Biomedical Engineering, Duke University; Research and Surgery Services, Durham VA Medical Center;
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Zhang Y, Xiang J, Tang L, Yang J, Li J. PGAGP: Predicting pathogenic genes based on adaptive network embedding algorithm. Front Genet 2023; 13:1087784. [PMID: 36744177 PMCID: PMC9895109 DOI: 10.3389/fgene.2022.1087784] [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: 11/03/2022] [Accepted: 12/09/2022] [Indexed: 01/21/2023] Open
Abstract
The study of disease-gene associations is an important topic in the field of computational biology. The accumulation of massive amounts of biomedical data provides new possibilities for exploring potential relations between diseases and genes through computational strategy, but how to extract valuable information from the data to predict pathogenic genes accurately and rapidly is currently a challenging and meaningful task. Therefore, we present a novel computational method called PGAGP for inferring potential pathogenic genes based on an adaptive network embedding algorithm. The PGAGP algorithm is to first extract initial features of nodes from a heterogeneous network of diseases and genes efficiently and effectively by Gaussian random projection and then optimize the features of nodes by an adaptive refining process. These low-dimensional features are used to improve the disease-gene heterogenous network, and we apply network propagation to the improved heterogenous network to predict pathogenic genes more effectively. By a series of experiments, we study the effect of PGAGP's parameters and integrated strategies on predictive performance and confirm that PGAGP is better than the state-of-the-art algorithms. Case studies show that many of the predicted candidate genes for specific diseases have been implied to be related to these diseases by literature verification and enrichment analysis, which further verifies the effectiveness of PGAGP. Overall, this work provides a useful solution for mining disease-gene heterogeneous network to predict pathogenic genes more effectively.
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Affiliation(s)
- Yan Zhang
- School of Computer Science and Engineering, Central South University, Changsha, China
- School of Information Science and Engineering, Changsha Medical University, Changsha, China
- Academician Workstation, Changsha Medical University, Changsha, China
| | - Ju Xiang
- School of Computer Science and Engineering, Central South University, Changsha, China
- School of Information Science and Engineering, Changsha Medical University, Changsha, China
- Academician Workstation, Changsha Medical University, Changsha, China
- School of Computer and Communication Engineering, Changsha University of Science and Technology, Changsha, China
- Department of Basic Medical Sciences and Neuroscience Research Center, Changsha Medical University, Changsha, China
| | - Liang Tang
- Academician Workstation, Changsha Medical University, Changsha, China
- Department of Basic Medical Sciences and Neuroscience Research Center, Changsha Medical University, Changsha, China
| | - Jialiang Yang
- Academician Workstation, Changsha Medical University, Changsha, China
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
- Geneis Beijing Co., Ltd, Beijing, China
| | - Jianming Li
- Academician Workstation, Changsha Medical University, Changsha, China
- Department of Basic Medical Sciences and Neuroscience Research Center, Changsha Medical University, Changsha, China
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4
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Evans EE, Mishra V, Mallow C, Gersz EM, Balch L, Howell A, Reilly C, Smith ES, Fisher TL, Zauderer M. Semaphorin 4D is upregulated in neurons of diseased brains and triggers astrocyte reactivity. J Neuroinflammation 2022; 19:200. [PMID: 35933420 PMCID: PMC9356477 DOI: 10.1186/s12974-022-02509-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 06/01/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The close interaction and interdependence of astrocytes and neurons allows for the possibility that astrocyte dysfunction contributes to and amplifies neurodegenerative pathology. Molecular pathways that trigger reactive astrocytes may represent important targets to preserve normal homeostatic maintenance and modify disease progression. METHODS Semaphorin 4D (SEMA4D) expression in the context of disease-associated neuropathology was assessed in postmortem brain sections of patients with Huntington's (HD) and Alzheimer's disease (AD), as well as in mouse models of HD (zQ175) and AD (CVN; APPSwDI/NOS2-/-) by immunohistochemistry. Effects of SEMA4D antibody blockade were assessed in purified astrocyte cultures and in the CVN mouse AD model. CVN mice were treated weekly from 26 to 38 weeks of age; thereafter mice underwent cognitive assessment and brains were collected for histopathology. RESULTS We report here that SEMA4D is upregulated in neurons during progression of neurodegenerative diseases and is a trigger of reactive astrocytes. Evidence of reactive astrocytes in close proximity to neurons expressing SEMA4D is detected in brain sections of patients and mouse models of HD and AD. We further report that SEMA4D-blockade prevents characteristic loss of GABAergic synapses and restores spatial memory and learning in CVN mice, a disease model that appears to reproduce many features of AD-like pathology including neuroinflammation. In vitro mechanistic studies demonstrate that astrocytes express cognate receptors for SEMA4D and that ligand binding triggers morphological variations, and changes in expression of key membrane receptors and enzymes characteristic of reactive astrocytes. These changes include reductions in EAAT-2 glutamate transporter and glutamine synthetase, key enzymes in neurotransmitter recycling, as well as reduced GLUT-1 glucose and MCT-4 lactate transporters, that allow astrocytes to couple energy metabolism with synaptic activity. Antibody blockade of SEMA4D prevented these changes and reversed functional deficits in glucose uptake. CONCLUSIONS Collectively, these results suggest that SEMA4D blockade may ameliorate disease pathology by preserving normal astrocyte function and reducing the negative consequences of reactive astrogliosis.
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Affiliation(s)
| | | | | | | | | | - Alan Howell
- Vaccinex, Inc., Research, Rochester, NY, USA
| | | | | | | | - Maurice Zauderer
- Vaccinex, Inc., Research, Rochester, NY, USA.
- Department of Neurology, Center for Health and Technology (SMD), University of Rochester Medical Center, Rochester, NY, USA.
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Whitson HE, Colton C, El Khoury J, Gate D, Goate A, Heneka MT, Kaddurah-Daouk R, Klein RS, Shinohara ML, Sisodia S, Spudich SS, Stevens B, Tanzi R, Ting JP, Garden G. Infection and inflammation: New perspectives on Alzheimer's disease. Brain Behav Immun Health 2022; 22:100462. [PMID: 36118272 PMCID: PMC9475126 DOI: 10.1016/j.bbih.2022.100462] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 04/10/2022] [Indexed: 11/24/2022] Open
Abstract
Neuroinflammation has been recognized as a component of Alzheimer's Disease (AD) pathology since the original descriptions by Alois Alzheimer and a role for infections in AD pathogenesis has long been hypothesized. More recently, this hypothesis has gained strength as human genetics and experimental data suggest key roles for inflammatory cells in AD pathogenesis. To review this topic, Duke/University of North Carolina (Duke/UNC) Alzheimer's Disease Research Center hosted a virtual symposium: "Infection and Inflammation: New Perspectives on Alzheimer's Disease (AD)." Participants considered current evidence for and against the hypothesis that AD could be caused or exacerbated by infection or commensal microbes. Discussion focused on connecting microglial transcriptional states to functional states, mouse models that better mimic human immunity, the potential involvement of inflammasome signaling, metabolic alterations, self-reactive T cells, gut microbes and fungal infections, and lessons learned from Covid-19 patients with neurologic symptoms. The content presented in the symposium, and major topics raised in discussions are reviewed in this summary of the proceedings.
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Affiliation(s)
- Heather E. Whitson
- Duke Center for the Study of Aging and Human Development, Duke University School of Medicine, Busse Bldg Rm 3502, Durham, NC, 27710, USA
- Durham VA Medical Center, Geriatric Research Education and Clinical Center, 508 Fulton Street, Durham, NC, 27705, USA
| | - Carol Colton
- Department of Neurology, Duke University School of Medicine, 3116 N Duke St, Durham, NM, 27704, USA
| | - Joseph El Khoury
- Center for Immunology & Inflammatory Diseases, Division of Infectious Diseases, Massachusetts General Hospital, 55 Fruit St, Boston, MA, 02114, USA
| | - David Gate
- The Ken & Ruth Davee Dept of Neurology, Northwestern University Feinberg School of Medicine, 303 E Chicago Ave, Ward 12-140, Chicago, IL 60611, USA
| | - Alison Goate
- Dept of Genetics and Genomic Sciences, Icahn School of Medicine at Mt. Sinai, One Gustave L. Levy Place, Box 1498, New York, NY, 10029-6574, USA
| | - Michael T. Heneka
- Dept of Neurodegenerative Disease and Geriatric Psychiatry/Neurology, University of Bonn Medical Center, Sigmund-Freud Str. 25, 53127, Bonn, Germany
| | - Rima Kaddurah-Daouk
- Dept of Psychiatry and Behavioral Sciences, Dept of Medicine, Duke Institute of Brain Sciences, Duke University School of Medicine, DUMC Box 3903, Blue Zone, South, Durham, NC, 27710, USA
| | - Robyn S. Klein
- Center for Neuroimmunology & Neuroinfectious Diseases, Depts of Medicine, Pathology & Immunology, and Neuroscience, Washington University School of Medicine, 660 S Euclid Ave, Box 8015, St. Louis, MO, 63110, USA
| | - Mari L. Shinohara
- Dept of Immunology, Duke University School of Medicine, 207 Research Dr, Box 3010, Durham, NC, 27710, USA
| | - Sangram Sisodia
- Dept of Neurobiology, University of Chicago, Abbott Memorial Hall, 947 East 58th St, MC 0928, Chicago, IL, 60637, USA
| | - Serena S. Spudich
- Dept of Neurology, Yale School of Medicine, PO Box 208018, New Haven, CT, 06520, USA
| | - Beth Stevens
- F.M. Kirby Neurobiology Center, Children's Hospital Boston, 300 Longwood Ave, Center for Life Sciences 12th Floor, Boston, MA, 02115, USA
| | - Rudolph Tanzi
- McCance Center for Brain Health, Massachusetts General Hospital, 114 16th St, Charlestown, MA, 02129, USA
| | - Jenny P. Ting
- Depts of Genetics, Microbiology and Immunology, Lineberger Comprehensive Cancer Center, Center for Translational Immunology, UNC School of Medicine, 125 Mason Farm Road, 6th Floor Marsico Hall, Chapel Hill, NC, 27599-7290, USA
| | - Gwenn Garden
- Dept of Neurology, UNC School of Medicine, Physicians Office Building, 170 Manning Drive, Campus Box 7025, Chapel Hill, NC, 27599-7025, USA
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7
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Brown KM, Nair JK, Janas MM, Anglero-Rodriguez YI, Dang LTH, Peng H, Theile CS, Castellanos-Rizaldos E, Brown C, Foster D, Kurz J, Allen J, Maganti R, Li J, Matsuda S, Stricos M, Chickering T, Jung M, Wassarman K, Rollins J, Woods L, Kelin A, Guenther DC, Mobley MW, Petrulis J, McDougall R, Racie T, Bombardier J, Cha D, Agarwal S, Johnson L, Jiang Y, Lentini S, Gilbert J, Nguyen T, Chigas S, LeBlanc S, Poreci U, Kasper A, Rogers AB, Chong S, Davis W, Sutherland JE, Castoreno A, Milstein S, Schlegel MK, Zlatev I, Charisse K, Keating M, Manoharan M, Fitzgerald K, Wu JT, Maier MA, Jadhav V. Expanding RNAi therapeutics to extrahepatic tissues with lipophilic conjugates. Nat Biotechnol 2022; 40:1500-1508. [PMID: 35654979 DOI: 10.1038/s41587-022-01334-x] [Citation(s) in RCA: 95] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 04/22/2022] [Indexed: 01/03/2023]
Abstract
Therapeutics based on short interfering RNAs (siRNAs) delivered to hepatocytes have been approved, but new delivery solutions are needed to target additional organs. Here we show that conjugation of 2'-O-hexadecyl (C16) to siRNAs enables safe, potent and durable silencing in the central nervous system (CNS), eye and lung in rodents and non-human primates with broad cell type specificity. We show that intrathecally or intracerebroventricularly delivered C16-siRNAs were active across CNS regions and cell types, with sustained RNA interference (RNAi) activity for at least 3 months. Similarly, intravitreal administration to the eye or intranasal administration to the lung resulted in a potent and durable knockdown. The preclinical efficacy of an siRNA targeting the amyloid precursor protein was evaluated through intracerebroventricular dosing in a mouse model of Alzheimer's disease, resulting in amelioration of physiological and behavioral deficits. Altogether, C16 conjugation of siRNAs has the potential for safe therapeutic silencing of target genes outside the liver with infrequent dosing.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Jing Li
- Alnylam Pharmaceuticals, Cambridge, MA, USA
| | | | | | | | | | | | | | | | - Alex Kelin
- Alnylam Pharmaceuticals, Cambridge, MA, USA
| | | | | | | | | | | | | | - Diana Cha
- Alnylam Pharmaceuticals, Cambridge, MA, USA
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8
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Miller-Rhodes P, Li H, Velagapudi R, Chiang W, Terrando N, Gelbard HA. URMC-099 prophylaxis prevents hippocampal vascular vulnerability and synaptic damage in an orthopedic model of delirium superimposed on dementia. FASEB J 2022; 36:e22343. [PMID: 35535564 PMCID: PMC9175136 DOI: 10.1096/fj.202200184rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 04/21/2022] [Accepted: 04/25/2022] [Indexed: 11/11/2022]
Abstract
Systemic perturbations can drive a neuroimmune cascade after surgical trauma, including affecting the blood-brain barrier (BBB), activating microglia, and contributing to cognitive deficits such as delirium. Delirium superimposed on dementia (DSD) is a particularly debilitating complication that renders the brain further vulnerable to neuroinflammation and neurodegeneration, albeit these molecular mechanisms remain poorly understood. Here, we have used an orthopedic model of tibial fracture/fixation in APPSwDI/mNos2-/- AD (CVN-AD) mice to investigate relevant pathogenetic mechanisms underlying DSD. We conducted the present study in 6-month-old CVN-AD mice, an age at which we speculated amyloid-β pathology had not saturated BBB and neuroimmune functioning. We found that URMC-099, our brain-penetrant anti-inflammatory neuroprotective drug, prevented inflammatory endothelial activation, breakdown of the BBB, synapse loss, and microglial activation in our DSD model. Taken together, our data link post-surgical endothelial activation, microglial MafB immunoreactivity, and synapse loss as key substrates for DSD, all of which can be prevented by URMC-099.
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Affiliation(s)
- Patrick Miller-Rhodes
- Center for Neurotherapeutics Discovery, Department of Neurology, University of Rochester Medical Center, Rochester, New York, USA.,Neuroscience Graduate Program, University of Rochester Medical Center, Rochester, New York, USA
| | - Herman Li
- Center for Neurotherapeutics Discovery, Department of Neurology, University of Rochester Medical Center, Rochester, New York, USA
| | - Ravikanth Velagapudi
- Department of Anesthesiology, Center for Translational Pain Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Wesley Chiang
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York, USA
| | - Niccolò Terrando
- Department of Anesthesiology, Center for Translational Pain Medicine, Duke University Medical Center, Durham, North Carolina, USA.,Department of Cell Biology, Duke University Medical Center, Durham, North Carolina, USA.,Department of Immunology, Duke University Medical Center, Durham, North Carolina, USA
| | - Harris A Gelbard
- Center for Neurotherapeutics Discovery, Department of Neurology, University of Rochester Medical Center, Rochester, New York, USA.,Department of Neurology, University of Rochester Medical Center, Rochester, New York, USA.,Department of Neuroscience, University of Rochester Medical Center, Rochester, New York, USA.,Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, USA.,Department of Microbiology & Immunology, University of Rochester Medical Center, Rochester, New York, USA
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Turner DA. Contrasting Metabolic Insufficiency in Aging and Dementia. Aging Dis 2021; 12:1081-1096. [PMID: 34221551 PMCID: PMC8219502 DOI: 10.14336/ad.2021.0104] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 01/04/2021] [Indexed: 12/14/2022] Open
Abstract
Metabolic insufficiency and neuronal dysfunction occur in normal aging but is exaggerated in dementia and Alzheimer's disease (AD). Metabolic insufficiency includes factors important for both substrate supply and utilization in the brain. Metabolic insufficiency occurs through a number of serial mechanisms, particularly changes in cerebrovascular supply through blood vessel abnormalities (ie, small and large vessel vasculopathy, stroke), alterations in neurovascular coupling providing dynamic blood flow supply in relation to neuronal demand, abnormalities in blood brain barrier including decreased glucose and amino acid transport, altered glymphatic flow in terms of substrate supply across the extracellular space to cells and drainage into CSF of metabolites, impaired transport into cells, and abnormal intracellular metabolism with more reliance on glycolysis and less on mitochondrial function. Recent studies have confirmed abnormal neurovascular coupling in a mouse model of AD in response to metabolic challenges, but the supply chain from the vascular system into neurons is disrupted much earlier in dementia than in equivalently aged individuals, contributing to the progressive neuronal degeneration and cognitive dysfunction associated with dementia. We discuss several metabolic treatment approaches, but these depend on characterizing patients as to who would benefit the most. Surrogate biomarkers of metabolism are being developed to include dynamic estimates of neuronal demand, sufficiency of neurovascular coupling, and glymphatic flow to supplement traditional static measurements. These surrogate biomarkers could be used to gauge efficacy of metabolic treatments in slowing down or modifying dementia time course.
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Affiliation(s)
- Dennis A Turner
- Neurosurgery, Neurobiology, and Biomedical Engineering, Duke University Medical Center, Durham, NC 27710, USA.
- Research and Surgery Services, Durham Veterans Affairs Medical Center, Durham, NC 27705, USA.
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Bryan J, Mandan A, Kamat G, Gottschalk WK, Badea A, Adams KJ, Thompson JW, Colton CA, Mukherjee S, Lutz MW. Likelihood ratio statistics for gene set enrichment in Alzheimer's disease pathways. Alzheimers Dement 2021; 17:561-573. [PMID: 33480182 PMCID: PMC8044005 DOI: 10.1002/alz.12223] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION The study of Alzheimer's disease (AD) has revealed biological pathways with implications for disease neuropathology and pathophysiology. These pathway-level effects may also be mediated by individual characteristics or covariates such as age or sex. Evaluation of AD biological pathways in the context of interactions with these covariates is critical to the understanding of AD as well as the development of model systems used to study the disease. METHODS Gene set enrichment methods are powerful tools used to interpret gene-level statistics at the level of biological pathways. We introduce a method for quantifying gene set enrichment using likelihood ratio-derived test statistics (gsLRT), which accounts for sample covariates like age and sex. We then use our method to test for age and sex interactions with protein expression levels in AD and to compare the pathway results between human and mouse species. RESULTS Our method, based on nested logistic regressions is competitive with the existing standard for gene set testing in the context of linear models and complex experimental design. The gene sets we identify as having a significant association with AD-both with and without additional covariate interactions-are validated by previous studies. Differences between gsLRT results on mouse and human datasets are observed. DISCUSSION Characterizing biological pathways involved in AD builds on the important work involving single gene drivers. Our gene set enrichment method finds pathways that are significantly related to AD while accounting for covariates that may be relevant to disease development. The method highlights commonalities and differences between human AD and mouse models, which may inform the development of higher fidelity models for the study of AD.
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Affiliation(s)
- Jordan Bryan
- Department of Statistical Science, Duke University, Durham, NC 27708, USA
| | - Arpita Mandan
- Department of Statistical Science, Duke University, Durham, NC 27708, USA
| | - Gauri Kamat
- Department of Statistical Science, Duke University, Durham, NC 27708, USA
| | | | - Alexandra Badea
- Department of Neurology, Duke University, Durham, NC 27708, USA
| | - Kendra J. Adams
- Department of Neurology, Duke University, Durham, NC 27708, USA
| | | | - Carol A. Colton
- Department of Neurology, Duke University, Durham, NC 27708, USA
| | - Sayan Mukherjee
- Department of Statistical Science, Duke University, Durham, NC 27708, USA
- Departments of Mathematics, Computer Science, and Biostatistics & Bioinformatics, Duke University, Durham, NC 27708, USA
| | - Michael W. Lutz
- Department of Neurology, Duke University, Durham, NC 27708, USA
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11
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Turner DA, Degan S, Hoffmann U, Galeffi F, Colton CA. CVN-AD Alzheimer's mice show premature reduction in neurovascular coupling in response to spreading depression and anoxia compared to aged controls. Alzheimers Dement 2021; 17:1109-1120. [PMID: 33656270 PMCID: PMC8277667 DOI: 10.1002/alz.12289] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 12/06/2020] [Accepted: 12/07/2020] [Indexed: 12/19/2022]
Abstract
We compared the efficacy of neurovascular coupling and substrate supply in cerebral cortex during severe metabolic challenges in transgenic Alzheimer's [CVN-AD] and control [C57Bl/6] mice, to evaluate the hypothesis that metabolic insufficiency is a critical component of degeneration leading to dementia. We analyzed cerebral blood flow and metabolic responses to spreading depression (induced by K+ applied to the cortex) and anoxia across aging in CVN-AD + C57Bl/6 genotypes. In the CVN-AD genotype progression to histological and cognitive hallmarks of dementia is a stereotyped function of age. We correlated physiology and imaging of the cortex with the blood flow responses measured with laser doppler probes. The results show that spreading depression resulted in a hyperemic blood flow response that was dramatically reduced (24% in amplitude, 70% in area) in both middle-aged and aged CVN-AD mice compared to C57Bl/6 age-matched controls. However, spreading depression amplitude and conduction velocity (≈6 mm/min) did not differ among groups. Anoxia (100% N2 ) showed significantly decreased (by 62%) reactive blood flow and autoregulation in aged AD-CVN mice compared to aged control animals. Significantly reduced neurovascular coupling occurred prematurely with aging in CVN-AD mice. Abbreviated physiological hyperemia and decreased resilience to anoxia may enhance early-onset metabolic deficiency through decreased substrate supply to the brain. Metabolic deficiency may contribute significantly to the degeneration associated with dementia as a function of aging and regions of the brain involved.
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Affiliation(s)
- Dennis A Turner
- Neurosurgery, Box 3807, Duke University Medical Center, Durham, North Carolina, 27710, USA.,Neurobiology, Box 3209, Duke University Medical Center, Durham, North Carolina, 27710, USA.,Biomedical Engineering, Box 90281, Duke University, Durham, North Carolina, 27708, USA.,Research and Surgery Services, Durham VA Medical Center, 508 Fulton Street, Durham, North Carolina, 27705, USA
| | - Simone Degan
- Neurosurgery, Box 3807, Duke University Medical Center, Durham, North Carolina, 27710, USA.,Research and Surgery Services, Durham VA Medical Center, 508 Fulton Street, Durham, North Carolina, 27705, USA
| | - Ulrike Hoffmann
- Anesthesiology, Box 3094, Duke University Medical Center, Durham, North Carolina, 27710, USA
| | - Francesca Galeffi
- Neurosurgery, Box 3807, Duke University Medical Center, Durham, North Carolina, 27710, USA.,Research and Surgery Services, Durham VA Medical Center, 508 Fulton Street, Durham, North Carolina, 27705, USA
| | - Carol A Colton
- Neurology, Box 2900, Duke University Medical Center, Durham, North Carolina, 27710, USA
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12
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Vitek MP, Araujo JA, Fossel M, Greenberg BD, Howell GR, Rizzo SJS, Seyfried NT, Tenner AJ, Territo PR, Windisch M, Bain LJ, Ross A, Carrillo MC, Lamb BT, Edelmayer RM. Translational animal models for Alzheimer's disease: An Alzheimer's Association Business Consortium Think Tank. ALZHEIMER'S & DEMENTIA (NEW YORK, N. Y.) 2021; 6:e12114. [PMID: 33457489 PMCID: PMC7798310 DOI: 10.1002/trc2.12114] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 07/04/2020] [Accepted: 07/09/2020] [Indexed: 12/12/2022]
Abstract
Over 5 million Americans and 50 million individuals worldwide are living with Alzheimer's disease (AD). The progressive dementia associated with AD currently has no cure. Although clinical trials in patients are ultimately required to find safe and effective drugs, animal models of AD permit the integration of brain pathologies with learning and memory deficits that are the first step in developing these new drugs. The purpose of the Alzheimer's Association Business Consortium Think Tank meeting was to address the unmet need to improve the discovery and successful development of Alzheimer's therapies. We hypothesize that positive responses to new therapies observed in validated models of AD will provide predictive evidence for positive responses to these same therapies in AD patients. To achieve this goal, we convened a meeting of experts to explore the current state of AD animal models, identify knowledge gaps, and recommend actions for development of next-generation models with better predictability. Among our findings, we all recognize that models reflecting only single aspects of AD pathogenesis do not mimic AD. Models or combinations of new models are needed that incorporate genetics with environmental interactions, timing of disease development, heterogeneous mechanisms and pathways, comorbidities, and other pathologies that lead to AD and related dementias. Selection of the best models requires us to address the following: (1) which animal species, strains, and genetic backgrounds are most appropriate; (2) which models permit efficient use throughout the drug development pipeline; (3) the translatability of behavioral-cognitive assays from animals to patients; and (4) how to match potential AD therapeutics with particular models. Best practice guidelines to improve reproducibility also need to be developed for consistent use of these models in different research settings. To enhance translational predictability, we discuss a multi-model evaluation strategy to de-risk the successful transition of pre-clinical drug assets to the clinic.
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Affiliation(s)
| | | | | | | | | | | | - Nicholas T. Seyfried
- Departments of Biochemistry and NeurologyEmory School of MedicineAtlantaGeorgiaUSA
| | - Andrea J. Tenner
- Department of Molecular Biology and BiochemistryUniversity of CaliforniaIrvineCaliforniaUSA
| | | | | | - Lisa J. Bain
- Independent Science and Medical WriterElversonPennsylvaniaUSA
| | - April Ross
- Former Alzheimer's Association EmployeeChicagoIllinoisUSA
| | | | - Bruce T. Lamb
- Indiana University School of MedicineStark Neurosciences Research InstituteIndianapolisIndianaUSA
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13
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Nwafor DC, Chakraborty S, Jun S, Brichacek AL, Dransfeld M, Gemoets DE, Dakhlallah D, Brown CM. Disruption of metabolic, sleep, and sensorimotor functional outcomes in a female transgenic mouse model of Alzheimer's disease. Behav Brain Res 2020; 398:112983. [PMID: 33137399 DOI: 10.1016/j.bbr.2020.112983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 10/05/2020] [Accepted: 10/26/2020] [Indexed: 12/17/2022]
Abstract
Alzheimer's Disease (AD) is the most prevalent form of dementia globally, and the number of individuals with AD diagnosis is expected to double by 2050. Numerous preclinical AD studies have shown that AD neuropathology accompanies alteration in learning and memory. However, less attention has been given to alterations in metabolism, sleep, and sensorimotor functional outcomes during AD pathogenesis. The objective of this study was to elucidate the extent to which metabolic activity, sleep-wake cycle, and sensorimotor function is impaired in APPSwDI/Nos2-/- (CVN-AD) transgenic mice. Female mice were used in this study because AD is more prevalent in women compared to men. We hypothesized that the presence of AD neuropathology in CVN-AD mice would accompany alterations in metabolic activity, sleep, and sensorimotor function. Our results showed that CVN-AD mice had significantly decreased energy expenditure compared to wild-type (WT) mice. An examination of associated functional outcome parameters showed that sleep activity was elevated during the awake (dark) cycle and as well as an overall decrease in spontaneous locomotor activity. An additional functional parameter, the nociceptive response to thermal stimuli, was also impaired in CVN-AD mice. Collectively, our results demonstrate CVN-AD mice exhibit alterations in functional parameters that resemble human-AD clinical progression.
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Affiliation(s)
- Divine C Nwafor
- Department of Neuroscience, School of Medicine, West Virginia University, Morgantown, WV 26506, USA
| | - Sreeparna Chakraborty
- Department of Microbiology, Immunology, and Cell Biology, School of Medicine, West Virginia University, Morgantown, WV 26506, USA
| | - Sujung Jun
- Department of Physiology and Pharmacology, School of Medicine, West Virginia University, Morgantown, WV 26506, USA
| | - Allison L Brichacek
- Department of Microbiology, Immunology, and Cell Biology, School of Medicine, West Virginia University, Morgantown, WV 26506, USA
| | - Margaret Dransfeld
- Department of Neuroscience, School of Medicine, West Virginia University, Morgantown, WV 26506, USA
| | - Darren E Gemoets
- Department of Biostatistics, School of Public Health, West Virginia University, Morgantown, WV 26506 USA
| | - Duaa Dakhlallah
- Department of Neuroscience, School of Medicine, West Virginia University, Morgantown, WV 26506, USA; Cancer Institute, West Virginia University Health Science Center, Morgantown, WV 26506, USA
| | - Candice M Brown
- Department of Neuroscience, School of Medicine, West Virginia University, Morgantown, WV 26506, USA; Department of Microbiology, Immunology, and Cell Biology, School of Medicine, West Virginia University, Morgantown, WV 26506, USA; Rockefeller Neuroscience Institute, West Virginia University, Morgantown, WV 26506, USA.
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14
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Nwafor DC, Chakraborty S, Brichacek AL, Jun S, Gambill CA, Wang W, Engler-Chiurazzi EB, Dakhlallah D, Pinkerton AB, Millán JL, Benkovic SA, Brown CM. Loss of tissue-nonspecific alkaline phosphatase (TNAP) enzyme activity in cerebral microvessels is coupled to persistent neuroinflammation and behavioral deficits in late sepsis. Brain Behav Immun 2020; 84:115-131. [PMID: 31778743 PMCID: PMC7010562 DOI: 10.1016/j.bbi.2019.11.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 11/12/2019] [Accepted: 11/20/2019] [Indexed: 12/13/2022] Open
Abstract
Sepsis is a host response to systemic inflammation and infection that may lead to multi-organ dysfunction and eventual death. While acute brain dysfunction is common among all sepsis patients, chronic neurological impairment is prevalent among sepsis survivors. The brain microvasculature has emerged as a major determinant of sepsis-associated brain dysfunction, yet the mechanisms that underlie its associated neuroimmune perturbations and behavioral deficits are not well understood. An emerging body of data suggests that inhibition of tissue-nonspecific alkaline phosphatase (TNAP) enzyme activity in cerebral microvessels may be associated with changes in endothelial cell barrier integrity. The objective of this study was to elucidate the connection between alterations in cerebrovascular TNAP enzyme activity and brain microvascular dysfunction in late sepsis. We hypothesized that the disruption of TNAP enzymatic activity in cerebral microvessels would be coupled to the sustained loss of brain microvascular integrity, elevated neuroinflammatory responses, and behavioral deficits. Male mice were subjected to cecal ligation and puncture (CLP), a model of experimental sepsis, and assessed up to seven days post-sepsis. All mice were observed daily for sickness behavior and underwent behavioral testing. Our results showed a significant decrease in brain microvascular TNAP enzyme activity in the somatosensory cortex and spinal cord of septic mice but not in the CA1 and CA3 hippocampal regions. Furthermore, we showed that loss of cerebrovascular TNAP enzyme activity was coupled to a loss of claudin-5 and increased perivascular IgG infiltration in the somatosensory cortex. Analyses of whole brain myeloid and T-lymphoid cell populations also revealed a persistent elevation of infiltrating leukocytes, which included both neutrophil and monocyte myeloid derived suppressor cells (MDSCs). Regional analyses of the somatosensory cortex, hippocampus, and spinal cord revealed significant astrogliosis and microgliosis in the cortex and spinal cord of septic mice that was accompanied by significant microgliosis in the CA1 and CA3 hippocampal regions. Assessment of behavioral deficits revealed no changes in learning and memory or evoked locomotion. However, the hot plate test uncovered a novel anti-nociceptive phenotype in our septic mice, and we speculate that this phenotype may be a consequence of sustained GFAP astrogliosis and loss of TNAP activity in the somatosensory cortex and spinal cord of septic mice. Taken together, these results demonstrate that the loss of TNAP enzyme activity in cerebral microvessels during late sepsis is coupled to sustained neuroimmune dysfunction which may underlie, in part, the chronic neurological impairments observed in sepsis survivors.
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Affiliation(s)
- Divine C. Nwafor
- Department of Neuroscience, West Virginia University Health Science Center, Morgantown, WV 26506, USA
| | - Sreeparna Chakraborty
- Department of Microbiology, Immunology, and Cell Biology, School of Medicine, West Virginia University Health Science Center, Morgantown, WV 26506, USA
| | - Allison L. Brichacek
- Department of Microbiology, Immunology, and Cell Biology, School of Medicine, West Virginia University Health Science Center, Morgantown, WV 26506, USA
| | - Sujung Jun
- Wilmer Eye Institute, John Hopkins University School of Medicine, Baltimore, MD 21231, USA.
| | - Catheryne A. Gambill
- Department of Microbiology, Immunology, and Cell Biology, School of Medicine, West Virginia University Health Science Center, Morgantown, WV 26506, USA
| | - Wei Wang
- Department of Neuroscience, West Virginia University Health Science Center, Morgantown, WV 26506, USA.
| | | | - Duaa Dakhlallah
- Department of Neuroscience, West Virginia University Health Science Center, Morgantown, WV 26506, USA; Cancer Institute, West Virginia University Health Science Center, Morgantown, WV 26506, USA.
| | | | - José Luis Millán
- Sanford-Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
| | - Stanley A. Benkovic
- Department of Neuroscience, West Virginia University Health Science Center, Morgantown, WV 26506, USA
| | - Candice M. Brown
- Department of Neuroscience, West Virginia University Health Science Center, Morgantown, WV 26506, USA,Department of Microbiology, Immunology, and Cell Biology, School of Medicine, West Virginia University Health Science Center, Morgantown, WV 26506, USA,Corresponding Author: Candice M. Brown, Ph.D., Assistant Professor, Neuroscience, 108 Biomedical Road, Box 9303, Center for Basic and Translational Stroke Research, Rockefeller Neuroscience Institute, West Virginia University Health Sciences, Morgantown, WV 26506, Phone: 304-293-0589,
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15
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Badea A, Wu W, Shuff J, Wang M, Anderson RJ, Qi Y, Johnson GA, Wilson JG, Koudoro S, Garyfallidis E, Colton CA, Dunson DB. Identifying Vulnerable Brain Networks in Mouse Models of Genetic Risk Factors for Late Onset Alzheimer's Disease. Front Neuroinform 2019; 13:72. [PMID: 31920610 PMCID: PMC6914731 DOI: 10.3389/fninf.2019.00072] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 11/13/2019] [Indexed: 12/18/2022] Open
Abstract
The major genetic risk for late onset Alzheimer’s disease has been associated with the presence of APOE4 alleles. However, the impact of different APOE alleles on the brain aging trajectory, and how they interact with the brain local environment in a sex specific manner is not entirely clear. We sought to identify vulnerable brain circuits in novel mouse models with homozygous targeted replacement of the mouse ApoE gene with either human APOE3 or APOE4 gene alleles. These genes are expressed in mice that also model the human immune response to age and disease-associated challenges by expressing the human NOS2 gene in place of the mouse mNos2 gene. These mice had impaired learning and memory when assessed with the Morris water maze (MWM) and novel object recognition (NOR) tests. Ex vivo MRI-DTI analyses revealed global and local atrophy, and areas of reduced fractional anisotropy (FA). Using tensor network principal component analyses for structural connectomes, we inferred the pairwise connections which best separate APOE4 from APOE3 carriers. These involved primarily interhemispheric connections among regions of olfactory areas, the hippocampus, and the cerebellum. Our results also suggest that pairwise connections may be subdivided and clustered spatially to reveal local changes on a finer scale. These analyses revealed not just genotype, but also sex specific differences. Identifying vulnerable networks may provide targets for interventions, and a means to stratify patients.
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Affiliation(s)
- Alexandra Badea
- Department of Radiology, Duke University, Durham, NC, United States.,Department of Neurology, Duke University School of Medicine, Durham, NC, United States.,Brain Imaging and Analysis Center, Duke University, Durham, NC, United States
| | - Wenlin Wu
- Pratt School of Engineering, Duke University, Durham, NC, United States
| | - Jordan Shuff
- Department of Biomedical Engineering, University of Delaware, Newark, NJ, United States
| | - Michele Wang
- Department of Psychology and Neuroscience, Trinity College of Arts & Sciences, Duke University, Durham, NC, United States
| | | | - Yi Qi
- Department of Radiology, Duke University, Durham, NC, United States
| | - G Allan Johnson
- Department of Radiology, Duke University, Durham, NC, United States
| | - Joan G Wilson
- Department of Neurology, Duke University School of Medicine, Durham, NC, United States
| | - Serge Koudoro
- School of Informatics, Computing, and Engineering, Indiana University Bloomington, Bloomington, IN, United States
| | - Eleftherios Garyfallidis
- School of Informatics, Computing, and Engineering, Indiana University Bloomington, Bloomington, IN, United States
| | - Carol A Colton
- Department of Neurology, Duke University School of Medicine, Durham, NC, United States
| | - David B Dunson
- Department of Statistical Science, Trinity College of Arts & Sciences, Duke University, Durham, NC, United States
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16
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Badea A, Delpratt NA, Anderson RJ, Dibb R, Qi Y, Wei H, Liu C, Wetsel WC, Avants BB, Colton C. Multivariate MR biomarkers better predict cognitive dysfunction in mouse models of Alzheimer's disease. Magn Reson Imaging 2019; 60:52-67. [PMID: 30940494 DOI: 10.1016/j.mri.2019.03.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 12/15/2022]
Abstract
To understand multifactorial conditions such as Alzheimer's disease (AD) we need brain signatures that predict the impact of multiple pathologies and their interactions. To help uncover the relationships between pathology affected brain circuits and cognitive markers we have used mouse models that represent, at least in part, the complex interactions altered in AD, while being raised in uniform environments and with known genotype alterations. In particular, we aimed to understand the relationship between vulnerable brain circuits and memory deficits measured in the Morris water maze, and we tested several predictive modeling approaches. We used in vivo manganese enhanced MRI traditional voxel based analyses to reveal regional differences in volume (morphometry), signal intensity (activity), and magnetic susceptibility (iron deposition, demyelination). These regions included hippocampus, olfactory areas, entorhinal cortex and cerebellum, as well as the frontal association area. The properties of these regions, extracted from each of the imaging markers, were used to predict spatial memory. We next used eigenanatomy, which reduces dimensionality to produce sets of regions that explain the variance in the data. For each imaging marker, eigenanatomy revealed networks underpinning a range of cognitive functions including memory, motor function, and associative learning, allowing the detection of associations between context, location, and responses. Finally, the integration of multivariate markers in a supervised sparse canonical correlation approach outperformed single predictor models and had significant correlates to spatial memory. Among a priori selected regions, expected to play a role in memory dysfunction, the fornix also provided good predictors, raising the possibility of investigating how disease propagation within brain networks leads to cognitive deterioration. Our cross-sectional results support that modeling approaches integrating multivariate imaging markers provide sensitive predictors of AD-like behaviors. Such strategies for mapping brain circuits responsible for behaviors may help in the future predict disease progression, or response to interventions.
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Affiliation(s)
- Alexandra Badea
- Center for In Vivo Microscopy, Department of Radiology, Duke University Medical Center, Durham, NC, USA; Department of Neurology, Duke University Medical Center, Durham, NC, USA; Brain Imaging and Analysis Center, Duke University, Durham, NC, USA.
| | - Natalie A Delpratt
- Center for In Vivo Microscopy, Department of Radiology, Duke University Medical Center, Durham, NC, USA
| | - R J Anderson
- Center for In Vivo Microscopy, Department of Radiology, Duke University Medical Center, Durham, NC, USA
| | - Russell Dibb
- Center for In Vivo Microscopy, Department of Radiology, Duke University Medical Center, Durham, NC, USA
| | - Yi Qi
- Center for In Vivo Microscopy, Department of Radiology, Duke University Medical Center, Durham, NC, USA
| | - Hongjiang Wei
- Institute for Medical Imaging Technology, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.
| | - Chunlei Liu
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, CA, USA
| | - William C Wetsel
- Department of Psychiatry and Behavioral Sciences, Cell Biology, Neurobiology, Duke University Medical Center, Durham, NC, USA
| | - Brian B Avants
- Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, VA, USA
| | - Carol Colton
- Department of Neurology, Duke University Medical Center, Durham, NC, USA
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17
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Alber J, McGarry K, Noto RB, Snyder PJ. Use of Eflornithine (DFMO) in the Treatment of Early Alzheimer's Disease: A Compassionate Use, Single-Case Study. Front Aging Neurosci 2018; 10:60. [PMID: 29559907 PMCID: PMC5845715 DOI: 10.3389/fnagi.2018.00060] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 02/20/2018] [Indexed: 01/22/2023] Open
Abstract
Background: Recent genome-wide association screening (GWAS) studies have linked Alzheimer's disease (AD) neuropathology to gene networks that regulate immune function. Kan et al. recently reported that Arg1 (an anti-inflammatory gene that codes for arginase-1) is expressed in parts of the brain associated with amyloidosis prior to the onset of neuronal loss, suggesting that chronic brain arginine deprivation promotes AD-related neuropathology. They blocked arginine catabolism in their mouse AD model by administration of eflornithine (DFMO) to juvenile animals, effectively blocking the expression of AD-related amyloid pathology as the mice aged. We report results from a single-case study in which DFMO was administered, for the first time, in an attempt to slow progression of AD in a single woman with multi-domain, amnestic MCI who was unable to tolerate an acetylcholinesterase inhibitor. Methods: Patient C.S. is a 74-year old female with a 5-year history of cognitive decline who was placed on DFMO (500 mg b.i.d.) for 12 months, with amyloid PET scans (baseline and 12-months), APOE genotyping and neuropsychological exams at baseline, 3, 9, and 12 months. Results: C.S. suffered continued cognitive decline over 12 months, including progressive worsening of orientation, social functions and ability to engage in IADL's. She also showed progressive decline on measures of episodic memory and executive function. Florbetapir PET imaging yielded elevated total neocortical SUVr scores at both baseline (SUVr = 1.55) and at 12 months (SUVr = 1.69). Conclusions: We report a first attempt at using DFMO to slow AD progression. This 12-month single-case trial did not halt continued amyloidosis nor cognitive decline. Although this trial was predicated on data reported by Kan et al. (2015) showing that DFMO administered to juvenile AD-prone mice led to diminished amyloid aggregation, this attempt to treat an older mild AD patient may not be a fair test of Kan et al.'s model and results. A future trial might seek to block amyloidosis in young adults who are autosomal gene carriers for early onset AD, or perhaps in adults who are very clearly in the pre-clinical disease stage. Trial Registration: This trial was registered as a Compassionate Use IND #128888 with the United States Food and Drug Administration (FDA).
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Affiliation(s)
- Jessica Alber
- Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University & Rhode Island Hospital, Providence, RI, United States
- Department of Neurology, Warren Alpert Medical School of Brown University, Providence, RI, United States
| | - Kelly McGarry
- Division of General Internal Medicine, Department of Medicine, Warren Alpert Medical School of Brown University & Rhode Island Hospital, Providence, RI, United States
| | - Richard B. Noto
- Department of Radiology, Warren Alpert Medical School of Brown University & Rhode Island Hospital, Providence, RI, United States
| | - Peter J. Snyder
- Department of Neurology, Warren Alpert Medical School of Brown University, Providence, RI, United States
- Interdisciplinary Neuroscience Program, University of Rhode Island, Kingston, RI, United States
- Ryan Institute for Neurosciences, University of Rhode Island, Kingston, RI, United States
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18
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Piiponniemi TO, Bragge T, Vauhkonen EE, Vartiainen P, Puoliväli JT, Sweeney PJ, Kopanitsa MV. Acquisition and reversal of visual discrimination learning in APPSwDI/Nos2−/− (CVN) mice. Neurosci Lett 2017; 650:126-133. [DOI: 10.1016/j.neulet.2017.04.049] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 04/23/2017] [Accepted: 04/24/2017] [Indexed: 11/26/2022]
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19
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Fiala M, Kooij G, Wagner K, Hammock B, Pellegrini M. Modulation of innate immunity of patients with Alzheimer's disease by omega-3 fatty acids. FASEB J 2017; 31:3229-3239. [PMID: 28420693 DOI: 10.1096/fj.201700065r] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 04/05/2017] [Indexed: 02/06/2023]
Abstract
The innate immune system of patients with Alzheimer's disease and mild cognitive impairment (MCI) is deregulated with highly increased or decreased transcription of inflammatory genes and consistently depressed phagocytosis of amyloid-β1-42 (Aβ) by monocytes and macrophages. Current immune therapies target single mechanisms in the adaptive immune system but not innate immunity. Here, we summarize recent advances in therapy by ω-3, ω-6, and epoxy fatty acids; specialized proresolving mediators; and vitamin D3 that have proven immune effects and emerging cognitive effects in patients with MCI. The hypothesis of this approach is that macrophages of normal participants, but not those of patients with Alzheimer's disease and MCI, possess effective phagocytosis for Aβ and protect homeostasis of the brain and, furthermore, that defective MCI macrophages recover phagocytic function via ω-3. Recent studies of fish-derived ω-3 supplementation in patients with MCI have shown polarization of Apoε3/ε3 patients' macrophages to an intermediate M1-M2 phenotype that is optimal for Aβ phagocytosis and the stabilization of cognitive decline. Therefore, accumulating preclinical and preliminary clinical evidence indicates that ω-3 supplementation should be tested in a randomized controlled clinical trial and that the analysis should involve the apolipoprotein E genotype and intervening conditions during trial.-Fiala, M., Kooij, G., Wagner, K., Hammock, B., Pellegrini, M. Modulation of innate immunity of patients with Alzheimer's disease by omega-3 fatty acids.
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Affiliation(s)
- Milan Fiala
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, California, USA;
| | - Gijs Kooij
- Department of Molecular Cell Biology and Immunology, Vrije Universiteit (VU) Medical Center, Multiple Sclerosis Center Amsterdam, Amsterdam, The Netherlands.,Perioperative and Pain Medicine, Center for Experimental Therapeutics and Reperfusion Injury, Harvard Institutes of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Karen Wagner
- Department of Entomology, University of California, Davis, Davis, California, USA
| | - Bruce Hammock
- Department of Entomology, University of California, Davis, Davis, California, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, California, USA
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20
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Ali R, Goubran M, Choudhri O, Zeineh MM. Seven-Tesla MRI and neuroimaging biomarkers for Alzheimer's disease. Neurosurg Focus 2016; 39:E4. [PMID: 26646928 DOI: 10.3171/2015.9.focus15326] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The goal of this paper was to review the effectiveness of using 7-T MRI to study neuroimaging biomarkers for Alzheimer's disease (AD). The authors reviewed the literature for articles published to date on the use of 7-T MRI to study AD. Thus far, there are 3 neuroimaging biomarkers for AD that have been studied using 7-T MRI in AD tissue: 1) neuroanatomical atrophy; 2) molecular characterization of hypointensities; and 3) microinfarcts. Seven-Tesla MRI has had mixed results when used to study the 3 aforementioned neuroimaging biomarkers for AD. First, in the detection of neuroanatomical atrophy, 7-T MRI has exciting potential. Historically, noninvasive imaging of neuroanatomical atrophy during AD has been limited by suboptimal resolution. However, now there is compelling evidence that the high resolution of 7-T MRI may help overcome this hurdle. Second, in detecting the characterization of hypointensities, 7-T MRI has had varied success. PET scans will most likely continue to lead in the noninvasive imaging of amyloid plaques; however, there is emerging evidence that 7-T MRI can accurately detect iron deposits within activated microglia, which may help shed light on the role of the immune system in AD pathogenesis. Finally, in the detection of microinfarcts, 7-T MRI may also play a promising role, which may help further elucidate the relationship between cerebrovascular health and AD progression.
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Affiliation(s)
| | - Maged Goubran
- Radiology, Stanford University School of Medicine, Stanford, California
| | | | - Michael M Zeineh
- Radiology, Stanford University School of Medicine, Stanford, California
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21
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Badea A, Kane L, Anderson RJ, Qi Y, Foster M, Cofer GP, Medvitz N, Buckley AF, Badea AK, Wetsel WC, Colton CA. The fornix provides multiple biomarkers to characterize circuit disruption in a mouse model of Alzheimer's disease. Neuroimage 2016; 142:498-511. [PMID: 27521741 DOI: 10.1016/j.neuroimage.2016.08.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 06/23/2016] [Accepted: 08/09/2016] [Indexed: 12/19/2022] Open
Abstract
Multivariate biomarkers are needed for detecting Alzheimer's disease (AD), understanding its etiology, and quantifying the effect of therapies. Mouse models provide opportunities to study characteristics of AD in well-controlled environments that can help facilitate development of early interventions. The CVN-AD mouse model replicates multiple AD hallmark pathologies, and we identified multivariate biomarkers characterizing a brain circuit disruption predictive of cognitive decline. In vivo and ex vivo magnetic resonance imaging (MRI) revealed that CVN-AD mice replicate the hippocampal atrophy (6%), characteristic of humans with AD, and also present changes in subcortical areas. The largest effect was in the fornix (23% smaller), which connects the septum, hippocampus, and hypothalamus. In characterizing the fornix with diffusion tensor imaging, fractional anisotropy was most sensitive (20% reduction), followed by radial (15%) and axial diffusivity (2%), in detecting pathological changes. These findings were strengthened by optical microscopy and ultrastructural analyses. Ultrastructual analysis provided estimates of axonal density, diameters, and myelination-through the g-ratio, defined as the ratio between the axonal diameter, and the diameter of the axon plus the myelin sheath. The fornix had reduced axonal density (47% fewer), axonal degeneration (13% larger axons), and abnormal myelination (1.5% smaller g-ratios). CD68 staining showed that white matter pathology could be secondary to neuronal degeneration, or due to direct microglial attack. In conclusion, these findings strengthen the hypothesis that the fornix plays a role in AD, and can be used as a disease biomarker and as a target for therapy.
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Affiliation(s)
- Alexandra Badea
- Center for In Vivo Microscopy, Duke University Medical Center, Department of Radiology, Durham, NC 27710, USA.
| | - Lauren Kane
- Trinity College of Arts & Sciences, Duke University, Durham, NC 27710, USA
| | - Robert J Anderson
- Center for In Vivo Microscopy, Duke University Medical Center, Department of Radiology, Durham, NC 27710, USA
| | - Yi Qi
- Center for In Vivo Microscopy, Duke University Medical Center, Department of Radiology, Durham, NC 27710, USA
| | - Mark Foster
- Center for In Vivo Microscopy, Duke University Medical Center, Department of Radiology, Durham, NC 27710, USA
| | - Gary P Cofer
- Center for In Vivo Microscopy, Duke University Medical Center, Department of Radiology, Durham, NC 27710, USA
| | - Neil Medvitz
- Department of Pathology, and Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC 27710, USA
| | - Anne F Buckley
- Department of Pathology, and Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC 27710, USA
| | - Andreas K Badea
- Center for In Vivo Microscopy, Duke University Medical Center, Department of Radiology, Durham, NC 27710, USA
| | - William C Wetsel
- Departments of Psychiatry and Behavioral Sciences, Cell Biology, and Neurobiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Carol A Colton
- Department of Neurology, Duke University Medical Center, Durham, NC 27710, USA
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22
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Abstract
The pathogenesis of Alzheimer's disease (AD) is a critical unsolved question; and although recent studies have demonstrated a strong association between altered brain immune responses and disease progression, the mechanistic cause of neuronal dysfunction and death is unknown. We have previously described the unique CVN-AD mouse model of AD, in which immune-mediated nitric oxide is lowered to mimic human levels, resulting in a mouse model that demonstrates the cardinal features of AD, including amyloid deposition, hyperphosphorylated and aggregated tau, behavioral changes, and age-dependent hippocampal neuronal loss. Using this mouse model, we studied longitudinal changes in brain immunity in relation to neuronal loss and, contrary to the predominant view that AD pathology is driven by proinflammatory factors, we find that the pathology in CVN-AD mice is driven by local immune suppression. Areas of hippocampal neuronal death are associated with the presence of immunosuppressive CD11c(+) microglia and extracellular arginase, resulting in arginine catabolism and reduced levels of total brain arginine. Pharmacologic disruption of the arginine utilization pathway by an inhibitor of arginase and ornithine decarboxylase protected the mice from AD-like pathology and significantly decreased CD11c expression. Our findings strongly implicate local immune-mediated amino acid catabolism as a novel and potentially critical mechanism mediating the age-dependent and regional loss of neurons in humans with AD.
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Zeineh MM, Chen Y, Kitzler HH, Hammond R, Vogel H, Rutt BK. Activated iron-containing microglia in the human hippocampus identified by magnetic resonance imaging in Alzheimer disease. Neurobiol Aging 2015; 36:2483-500. [PMID: 26190634 DOI: 10.1016/j.neurobiolaging.2015.05.022] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 05/27/2015] [Accepted: 05/30/2015] [Indexed: 01/02/2023]
Abstract
Although amyloid plaques and neurofibrillary pathology play important roles in Alzheimer disease (AD), our understanding of AD is incomplete, and the contribution of microglia and iron to neurodegeneration is unknown. High-field magnetic resonance imaging (MRI) is exquisitely sensitive to microscopic iron. To explore iron-associated neuroinflammatory AD pathology, we studied AD and control human brain specimens by (1) performing ultra-high resolution ex vivo 7 Tesla MRI, (2) coregistering the MRI with successive histologic staining for iron, microglia, amyloid beta, and tau, and (3) quantifying the relationship between magnetic resonance signal intensity and histological staining. In AD, we identified numerous small MR hypointensities primarily within the subiculum that were best explained by the combination of microscopic iron and activated microglia (p = 0.025), in contradistinction to the relatively lesser contribution of tau or amyloid. Neuropathologically, this suggests that microglial-mediated neurodegeneration may occur in the hippocampal formation in AD and is detectable by ultra-high resolution MRI.
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Affiliation(s)
- Michael M Zeineh
- Department of Radiology, Lucas Center for Imaging, Stanford University, Stanford, CA, USA.
| | - Yuanxin Chen
- Imaging Research Laboratories, Robarts Research Institute, Western University, London, Ontario, Canada
| | - Hagen H Kitzler
- Department of Neuroradiology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Robert Hammond
- Department of Pathology and Clinical Neurological Sciences, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Hannes Vogel
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Brian K Rutt
- Department of Radiology, Lucas Center for Imaging, Stanford University, Stanford, CA, USA
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Hoos MD, Vitek MP, Ridnour LA, Wilson J, Jansen M, Everhart A, Wink DA, Colton CA. The impact of human and mouse differences in NOS2 gene expression on the brain's redox and immune environment. Mol Neurodegener 2014; 9:50. [PMID: 25403885 PMCID: PMC4247207 DOI: 10.1186/1750-1326-9-50] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 10/10/2014] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Mouse models are used in the study of human disease. Despite well-known homologies, the difference in immune response between mice and humans impacts the application of data derived from mice to human disease outcomes. Nitric oxide synthase-2 (NOS2) is a key gene that displays species-specific outcomes via altered regulation of the gene promoter and via post-transcriptional mechanisms in humans that are not found in mice. The resulting levels of NO produced by activation of human NOS2 are different from the levels of NO produced by mouse Nos2. Since both tissue redox environment and immune responsiveness are regulated by the level of NO and its interactions, we investigated the significance of mouse and human differences on brain oxidative stress and on immune activation in HuNOS2tg/mNos2-/- mice that express the entire human NOS2 gene and that lack a functional mNos2 compared to wild type (WT) mice that express normal mNos2. METHODS/RESULTS Similarly to human, brain tissue from HuNOS2tg/mNos2-/- mice showed the presence of a NOS2 gene 3'UTR binding site. We also identified miRNA-939, the binding partner for this site, in mouse brain lysates and further demonstrated reduced levels of nitric oxide (NO) typical of the human immune response on injection with lipopolysaccharide (LPS). HuNOS2tg/mNos2-/- brain samples were probed for characteristic differences in redox and immune gene profiles compared to WT mice using gene arrays. Selected genes were also compared against mNos2-/- brain lysates. Reconstitution of the human NOS2 gene significantly altered genes that encode multiple anti-oxidant proteins, oxidases, DNA repair, mitochondrial proteins and redox regulated immune proteins. Expression levels of typical pro-inflammatory, anti-inflammatory and chemokine genes were not significantly different with the exception of increased TNFα and Ccr1 mRNA expression in the HuNOS2tg/mNos2-/- mice compared to WT or mNos2-/- mice. CONCLUSIONS NO is a principle factor in establishing the tissue redox environment and changes in NO levels impact oxidative stress and immunity, both of which are primary characteristics of neurodegenerative diseases. The HuNOS2tg/mNos2-/- mice provide a potentially useful mechanism to address critical species- specific immune differences that can impact the study of human diseases.
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Affiliation(s)
- Michael D Hoos
- />Department of Neurosurgery, Stonybrook Health Sciences, Stony Brook, NY 11794 USA
| | - Michael P Vitek
- />Department of Neurology, Duke University Medical Center, Durham, NC 27710 USA
| | - Lisa A Ridnour
- />Radiation Biology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Joan Wilson
- />Department of Neurology, Duke University Medical Center, Durham, NC 27710 USA
| | - Marilyn Jansen
- />Department of Neurology, Duke University Medical Center, Durham, NC 27710 USA
| | - Angela Everhart
- />Department of Neurology, Duke University Medical Center, Durham, NC 27710 USA
| | - David A Wink
- />Radiation Biology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Carol A Colton
- />Department of Neurology, Duke University Medical Center, Durham, NC 27710 USA
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