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Lee AJB, Kittel TE, Kim RB, Bach TN, Zhang T, Mitchell CS. Comparing therapeutic modulators of the SOD1 G93A Amyotrophic Lateral Sclerosis mouse pathophysiology. Front Neurosci 2023; 16:1111763. [PMID: 36741054 PMCID: PMC9893287 DOI: 10.3389/fnins.2022.1111763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 12/28/2022] [Indexed: 01/20/2023] Open
Abstract
Introduction Amyotrophic Lateral Sclerosis (ALS) is a paralyzing, multifactorial neurodegenerative disease with limited therapeutics and no known cure. The study goal was to determine which pathophysiological treatment targets appear most beneficial. Methods A big data approach was used to analyze high copy SOD1 G93A experimental data. The secondary data set comprised 227 published studies and 4,296 data points. Treatments were classified by pathophysiological target: apoptosis, axonal transport, cellular chemistry, energetics, neuron excitability, inflammation, oxidative stress, proteomics, or systemic function. Outcome assessment modalities included onset delay, health status (rotarod performance, body weight, grip strength), and survival duration. Pairwise statistical analysis (two-tailed t-test with Bonferroni correction) of normalized fold change (treatment/control) assessed significant differences in treatment efficacy. Cohen's d quantified pathophysiological treatment category effect size compared to "all" (e.g., all pathophysiological treatment categories combined). Results Inflammation treatments were best at delaying onset (d = 0.42, p > 0.05). Oxidative stress treatments were significantly better for prolonging survival duration (d = 0.18, p < 0.05). Excitability treatments were significantly better for prolonging overall health status (d = 0.22, p < 0.05). However, the absolute best pathophysiological treatment category for prolonging health status varied with disease progression: oxidative stress was best for pre-onset health (d = 0.18, p > 0.05); excitability was best for prolonging function near onset (d = 0.34, p < 0.05); inflammation was best for prolonging post-onset function (d = 0.24, p > 0.05); and apoptosis was best for prolonging end-stage function (d = 0.49, p > 0.05). Finally, combination treatments simultaneously targeting multiple pathophysiological categories (e.g., polytherapy) performed significantly (p < 0.05) better than monotherapies at end-stage. Discussion In summary, the most effective pathophysiological treatments change as function of assessment modality and disease progression. Shifting pathophysiological treatment category efficacy with disease progression supports the homeostatic instability theory of ALS disease progression.
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Affiliation(s)
- Albert J. B. Lee
- Laboratory for Pathology Dynamics, Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, United States
- Center for Machine Learning, Georgia Institute of Technology, Atlanta, GA, United States
| | - Tyler E. Kittel
- Laboratory for Pathology Dynamics, Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, United States
| | - Renaid B. Kim
- Laboratory for Pathology Dynamics, Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, United States
- University of Michigan Medical School, Ann Arbor, MI, United States
| | - Thao-Nguyen Bach
- Laboratory for Pathology Dynamics, Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, United States
- University of Texas at Dallas, Dallas, TX, United States
| | - Tian Zhang
- Laboratory for Pathology Dynamics, Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, United States
| | - Cassie S. Mitchell
- Laboratory for Pathology Dynamics, Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, United States
- Center for Machine Learning, Georgia Institute of Technology, Atlanta, GA, United States
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Tandon R, Levey AI, Lah JJ, Seyfried NT, Mitchell CS. Machine Learning Selection of Most Predictive Brain Proteins Suggests Role of Sugar Metabolism in Alzheimer's Disease. J Alzheimers Dis 2023; 92:411-424. [PMID: 36776048 PMCID: PMC10041447 DOI: 10.3233/jad-220683] [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] [Accepted: 01/05/2023] [Indexed: 02/09/2023]
Abstract
BACKGROUND The complex and not yet fully understood etiology of Alzheimer's disease (AD) shows important proteopathic signs which are unlikely to be linked to a single protein. However, protein subsets from deep proteomic datasets can be useful in stratifying patient risk, identifying stage dependent disease markers, and suggesting possible disease mechanisms. OBJECTIVE The objective was to identify protein subsets that best classify subjects into control, asymptomatic Alzheimer's disease (AsymAD), and AD. METHODS Data comprised 6 cohorts; 620 subjects; 3,334 proteins. Brain tissue-derived predictive protein subsets for classifying AD, AsymAD, or control were identified and validated with label-free quantification and machine learning. RESULTS A 29-protein subset accurately classified AD (AUC = 0.94). However, an 88-protein subset best predicted AsymAD (AUC = 0.92) or Control (AUC = 0.92) from AD (AUC = 0.98). AD versus Control: APP, DHX15, NRXN1, PBXIP1, RABEP1, STOM, and VGF. AD versus AsymAD: ALDH1A1, BDH2, C4A, FABP7, GABBR2, GNAI3, PBXIP1, and PRKAR1B. AsymAD versus Control: APP, C4A, DMXL1, EXOC2, PITPNB, RABEP1, and VGF. Additional predictors: DNAJA3, PTBP2, SLC30A9, VAT1L, CROCC, PNP, SNCB, ENPP6, HAPLN2, PSMD4, and CMAS. CONCLUSION Biomarkers were dynamically separable across disease stages. Predictive proteins were significantly enriched to sugar metabolism.
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Affiliation(s)
- Raghav Tandon
- Laboratory for Pathology Dynamics, Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA
- Center for Machine Learning, Georgia Institute of Technology, Atlanta, GA, USA
| | - Allan I. Levey
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - James J. Lah
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Nicholas T. Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Cassie S. Mitchell
- Laboratory for Pathology Dynamics, Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA
- Center for Machine Learning, Georgia Institute of Technology, Atlanta, GA, USA
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Jordan K, Murphy J, Singh A, Mitchell CS. Astrocyte-Mediated Neuromodulatory Regulation in Preclinical ALS: A Metadata Analysis. Front Cell Neurosci 2018; 12:491. [PMID: 30618638 PMCID: PMC6305074 DOI: 10.3389/fncel.2018.00491] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 11/29/2018] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a neurodegenerative disease characterized by progressive degradation of motoneurons in the central nervous system (CNS). Astrocytes are key regulators for inflammation and neuromodulatory signaling, both of which contribute to ALS. The study goal was to ascertain potential temporal changes in astrocyte-mediated neuromodulatory regulation with transgenic ALS model progression: glutamate, GTL-1, GluR1, GluR2, GABA, ChAT activity, VGF, TNFα, aspartate, and IGF-1. We examine neuromodulatory changes in data aggregates from 42 peer-reviewed studies derived from transgenic ALS mixed cell cultures (neurons + astrocytes). For each corresponding experimental time point, the ratio of transgenic to wild type (WT) was found for each compound. ANOVA and a student's t-test were performed to compare disease stages (early, post-onset, and end stage). Glutamate in transgenic SOD1-G93A mixed cell cultures does not change over time (p > 0.05). GLT-1 levels were found to be decreased 23% over WT but only at end-stage (p < 0.05). Glutamate receptors (GluR1, GluR2) in SOD1-G93A were not substantially different from WT, although SOD1-G93A GluR1 decreased by 21% from post-onset to end-stage (p < 0.05). ChAT activity was insignificantly decreased. VGF is decreased throughout ALS (p < 0.05). Aspartate is elevated by 25% in SOD1-G93A but only during end-stage (p < 0.05). TNFα is increased by a dramatic 362% (p < 0.05). Furthermore, principal component analysis identified TNFα as contributing to 55% of the data variance in the first component. Thus, TNFα, which modulates astrocyte regulation via multiple pathways, could be a strategic treatment target. Overall results suggest changes in neuromodulator levels are subtle in SOD1-G93A ALS mixed cell cultures. If excitotoxicity is present as is often presumed, it could be due to ALS cells being more sensitive to small changes in neuromodulation. Hence, seemingly unsubstantial or oscillatory changes in neuromodulators could wreak havoc in ALS cells, resulting in failed microenvironment homeostasis whereby both hyperexcitability and hypoexcitability can coexist. Future work is needed to examine local, spatiotemporal neuromodulatory homeostasis and assess its functional impact in ALS.
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Affiliation(s)
- Kathleen Jordan
- Laboratory for Pathology Dynamics, Department of Biomedical Engineering, Georgia Institute of Technology, Emory University School of Medicine, Atlanta, GA, United States
| | - Joseph Murphy
- Laboratory for Pathology Dynamics, Department of Biomedical Engineering, Georgia Institute of Technology, Emory University School of Medicine, Atlanta, GA, United States
| | - Anjanya Singh
- Laboratory for Pathology Dynamics, Department of Biomedical Engineering, Georgia Institute of Technology, Emory University School of Medicine, Atlanta, GA, United States
- School of Medicine, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Cassie S. Mitchell
- Laboratory for Pathology Dynamics, Department of Biomedical Engineering, Georgia Institute of Technology, Emory University School of Medicine, Atlanta, GA, United States
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Huber CM, Yee C, May T, Dhanala A, Mitchell CS. Cognitive Decline in Preclinical Alzheimer's Disease: Amyloid-Beta versus Tauopathy. J Alzheimers Dis 2018; 61:265-281. [PMID: 29154274 PMCID: PMC5734131 DOI: 10.3233/jad-170490] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We perform a large-scale meta-analysis of 51 peer-reviewed 3xTg-AD mouse publications to compare Alzheimer’s disease (AD) quantitative clinical outcome measures, including amyloid-β (Aβ), total tau, and phosphorylated tau (pTau), with cognitive performance in Morris water maze (MWM) and Novel Object Recognition (NOR). “High” levels of Aβ (Aβ40, Aβ42) showed significant but weak trends with cognitive decline (MWM: slope = 0.336, R2 = 0.149, n = 259, p < 0.001; NOR: slope = 0.156, R2 = 0.064, n = 116, p < 0.05); only soluble Aβ or directly measured Aβ meaningfully contribute. Tau expression in 3xTg-AD mice was within 10–20% of wild type and not associated with cognitive decline. In contrast, increased pTau is directly and significantly correlated with cognitive decline in MWM (slope = 0.408, R2 = 0.275, n = 371, p < < 0.01) and NOR (slope = 0.319, R2 = 0.176, n = 113, p < 0.05). While a variety of pTau epitopes (AT8, AT270, AT180, PHF-1) were examined, AT8 correlated most strongly with cognition (slope = 0.586, R2 = 0.521, n = 185, p < < 0.001). Multiple linear regression confirmed pTau is a stronger predictor of MWM performance than Aβ. Despite pTau’s lower physical concentration than Aβ, pTau levels more directly and quantitatively correlate with 3xTg-AD cognitive decline. pTau’s contribution to neurofibrillary tangles well after Aβ levels plateau makes pTau a viable treatment target even in late-stage clinical AD. Principal component analysis, which included hyperphosphorylation induced by kinases (pGSK3β, GSK3β, CDK5), identified phosphorylated ser9 GSK3β as the primary contributor to MWM variance. In summary, meta-analysis of cognitive decline in preclinical AD finds tauopathy more impactful than Aβ. Nonetheless, complex AD interactions dictate successful therapeutics harness synergy between Aβ and pTau, possibly through the GSK3 pathway.
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Affiliation(s)
- Colin M Huber
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA.,Department of Bioengineering, University of Pennsylvania School of Engineering and Applied Sciences, Philadelphia, PA, USA
| | - Connor Yee
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA
| | - Taylor May
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA
| | - Apoorva Dhanala
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA
| | - Cassie S Mitchell
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA
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Bond L, Bernhardt K, Madria P, Sorrentino K, Scelsi H, Mitchell CS. A Metadata Analysis of Oxidative Stress Etiology in Preclinical Amyotrophic Lateral Sclerosis: Benefits of Antioxidant Therapy. Front Neurosci 2018; 12:10. [PMID: 29416499 PMCID: PMC5787557 DOI: 10.3389/fnins.2018.00010] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 01/08/2018] [Indexed: 12/13/2022] Open
Abstract
Oxidative stress, induced by an imbalance of free radicals, incites neurodegeneration in Amyotrophic Lateral Sclerosis (ALS). In fact, a mutation in antioxidant enzyme superoxide dismutase 1 (SOD1) accounts for 20% of familial ALS cases. However, the variance among individual studies examining ALS oxidative stress clouds corresponding conclusions. Therefore, we construct a comprehensive, temporal view of oxidative stress and corresponding antioxidant therapy in preclinical ALS by mining published quantitative experimental data and performing metadata analysis of 41 studies. In vitro aggregate analysis of innate oxidative stress inducers, glutamate and hydrogen peroxide, revealed 70–90% of cell death coincides to inducer exposure equivalent to 30–50% peak concentration (p < 0.05). A correlative plateau in cell death suggests oxidative stress impact is greatest in early-stage neurodegeneration. In vivo SOD1-G93A transgenic ALS mouse aggregate analysis of heat shock proteins (HSPs) revealed HSP levels are 30% lower in muscle than spine (p < 0.1). Overall spine HSP levels, including HSP70, are mildly upregulated in SOD1-G93A mice compared to wild type, but not significantly (p > 0.05). Thus, innate HSP compensatory responses to oxidative stress are simply insufficient, a result supportive of homeostatic system instability as central to ALS etiology. In vivo aggregate analysis of antioxidant therapy finds SOD1-G93A ALS mouse survival duration significantly increases by 11.2% (p << 0.001) but insignificantly decreases onset age by 2%. Thus, the aggregate antioxidant treatment effect on survival in preclinical ALS is not sufficient to overcome clinical heterogeneity, which explains the literature disparity between preclinical and clinical antioxidant survival benefit. The aggregate effect sizes on preclinical ALS survival and onset illustrate that present antioxidants, alone, are not sufficient to halt ALS, which underscores its multi-factorial nature. Nonetheless, antioxidant-treated SOD1-G93A ALS mice have significantly increased motor performance (p < 0.05) measured via rotarod. With a colossal aggregate preclinical effect size average of 59.6%, antioxidants are promising for increasing function/quality of life in clinical ALS patients, a premise worth exploration via low-risk nutritional supplements. Finally, more direct, quantitative measures of oxidative stress, antioxidant levels and bioavailability are key to developing powerful antioxidant therapeutics that can assert measurable impacts on redox homeostasis in the brain and spinal cord.
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Affiliation(s)
- Leila Bond
- Laboratory for Pathology Dynamics, Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, United States
| | - Kamren Bernhardt
- Laboratory for Pathology Dynamics, Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, United States
| | - Priyank Madria
- Laboratory for Pathology Dynamics, Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, United States
| | - Katherine Sorrentino
- Laboratory for Pathology Dynamics, Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, United States
| | - Hailee Scelsi
- Laboratory for Pathology Dynamics, Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, United States.,Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, United States
| | - Cassie S Mitchell
- Laboratory for Pathology Dynamics, Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, United States
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Lu Y, Gao H, Zhang M, Chen B, Yang H. Glial Cell Line-Derived Neurotrophic Factor-Transfected Placenta-Derived Versus Bone Marrow-Derived Mesenchymal Cells for Treating Spinal Cord Injury. Med Sci Monit 2017; 23:1800-1811. [PMID: 28408732 PMCID: PMC5400030 DOI: 10.12659/msm.902754] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Background Placenta-derived mesenchymal stem cells (PMSCs) were isolated from placenta and had differentiation and self-renewal potential. We transfected PMSCs with glial cell line-derived neurotrophic factor (GDNF) and compared their effect for repairing spinal cord injury (SCI) with that of GDNF-transfected bone marrow-derived mesenchymal stem cell (BMSC). Material/Methods The PMSCs were isolated from Sprague-Dawley rat placenta; BMSCs were isolated from Sprague-Dawley rat thigh bone marrow. Primary cultured BMSCs and PMSCs were uniformly spindle-shaped. Flow cytometry indicated that both cell types were CD29- and CD90-positive and CD34- and CD45-negative, confirming that they were MSCs. The PMSCs and BMSCs were transfected with recombinant lentivirus containing the GDNF gene in vitro. PMSC and BMSC viability was increased after transfection, and GDNF expression was increased until 10 d after transfection. SCI was created in the rats (n=64) and was repaired using transfected PMSCs and BMSCs or untransfected PMSCs and BMSCs. Results The transfected PMSCs and BMSCs repaired the SCI. Flow cytometry, histology, immunohistochemical, kinesiology properties, and Basso-Beattie-Bresnahan locomotion score measurements determined no significant difference between transfected PMSCs and BMSCs at 7, 14, and 21 d post-transplantation (P>0.05); the injury healed better in transfected PMSCs and BMSCs than in untransfected PMSCs and BMSCs (P<0.05). Conclusions MSCs have similar biology characteristics and capacity for SCI repair to BMSCs and can be used as a new resource for treating SCI.
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Affiliation(s)
- Yao Lu
- Department of Orthopedics, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China (mainland)
| | - Hui Gao
- Department of Dermatology, College of Clinical of Yangzhou University, Yangzhou, Jiangsu, China (mainland)
| | - Man Zhang
- Department of Dermatology, College of Clinical of Yangzhou University, Yangzhou, Jiangsu, China (mainland)
| | - Bing Chen
- Comparative Medicine Center, Yangzhou University, Yangzhou, Jiangsu, China (mainland)
| | - Huilin Yang
- Department of Orthopedics, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China (mainland)
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Jeyachandran A, Mertens B, McKissick EA, Mitchell CS. Type I Vs. Type II Cytokine Levels as a Function of SOD1 G93A Mouse Amyotrophic Lateral Sclerosis Disease Progression. Front Cell Neurosci 2015; 9:462. [PMID: 26648846 PMCID: PMC4664727 DOI: 10.3389/fncel.2015.00462] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 11/13/2015] [Indexed: 01/01/2023] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a fatal motoneuron disease that is characterized by the degradation of neurons throughout the central nervous system. Inflammation have been cited a key contributor to ALS neurodegeneration, but the timeline of cytokine upregulation remains unresolved. The goal of this study was to temporally examine the correlation between the varying levels of pro-inflammatory type I cytokines (IL-1β, IL-1α, IL-12, TNF-α, and GFAP) and anti-inflammatory type II cytokines (IL-4, IL-6, IL-10) throughout the progression of ALS in the SOD1 G93A mouse model. Cytokine level data from high copy SOD1 G93A transgenic mice was collected from 66 peer-reviewed studies. For each corresponding experimental time point, the ratio of transgenic to wild type (TG/WT) cytokine was calculated. One-way ANOVA and t-tests with Bonferonni correction were used to analyze the data. Meta-analysis was performed for four discrete stages: early, pre-onset, post-onset, and end stage. A significant increase in TG cytokine levels was found when compared to WT cytokine levels across the entire SOD1 G93A lifespan for majority of the cytokines. The rates of change of the individual cytokines, and type I and type II were not significantly different; however, the mean fold change of type I was expressed at significantly higher levels than type II levels across all stages with the difference between the means becoming more pronounced at the end stage. An overexpression of cytokines occurred both before and after the onset of ALS symptoms. The trend between pro-inflammatory type I and type II cytokine mean levels indicate a progressive instability of the dynamic balance between pro- and anti-inflammatory cytokines as anti-inflammatory cytokines fail to mediate the pronounced increase in pro-inflammatory cytokines. Very early immunoregulatory treatment is necessary to successfully interrupt ALS-induced neuroinflammation.
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Affiliation(s)
- Amilia Jeyachandran
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University Atlanta, GA, USA
| | - Benjamin Mertens
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University Atlanta, GA, USA
| | - Eric A McKissick
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University Atlanta, GA, USA
| | - Cassie S Mitchell
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University Atlanta, GA, USA
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Mitchell CS, Cates A, Kim RB, Hollinger SK. Undergraduate Biocuration: Developing Tomorrow's Researchers While Mining Today's Data. JOURNAL OF UNDERGRADUATE NEUROSCIENCE EDUCATION : JUNE : A PUBLICATION OF FUN, FACULTY FOR UNDERGRADUATE NEUROSCIENCE 2015; 14:A56-A65. [PMID: 26557796 PMCID: PMC4640483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 09/17/2015] [Accepted: 09/22/2015] [Indexed: 06/05/2023]
Abstract
Biocuration is a time-intensive process that involves extraction, transcription, and organization of biological or clinical data from disjointed data sets into a user-friendly database. Curated data is subsequently used primarily for text mining or informatics analysis (bioinformatics, neuroinformatics, health informatics, etc.) and secondarily as a researcher resource. Biocuration is traditionally considered a Ph.D. level task, but a massive shortage of curators to consolidate the ever-mounting biomedical "big data" opens the possibility of utilizing biocuration as a means to mine today's data while teaching students skill sets they can utilize in any career. By developing a biocuration assembly line of simplified and compartmentalized tasks, we have enabled biocuration to be effectively performed by a hierarchy of undergraduate students. We summarize the necessary physical resources, process for establishing a data path, biocuration workflow, and undergraduate hierarchy of curation, technical, information technology (IT), quality control and managerial positions. We detail the undergraduate application and training processes and give detailed job descriptions for each position on the assembly line. We present case studies of neuropathology curation performed entirely by undergraduates, namely the construction of experimental databases of Amyotrophic Lateral Sclerosis (ALS) transgenic mouse models and clinical data from ALS patient records. Our results reveal undergraduate biocuration is scalable for a group of 8-50+ with relatively minimal required resources. Moreover, with average accuracy rates greater than 98.8%, undergraduate biocurators are equivalently accurate to their professional counterparts. Initial training to be completely proficient at the entry-level takes about five weeks with a minimal student time commitment of four hours/week.
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Affiliation(s)
- Cassie S. Mitchell
- Address correspondence to: Dr. Cassie S. Mitchell, Biomedical Engineering, Georgia Insitute of Technology, 313 Ferst Drive, Atlanta, GA 30332.
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Coan G, Mitchell CS. An Assessment of Possible Neuropathology and Clinical Relationships in 46 Sporadic Amyotrophic Lateral Sclerosis Patient Autopsies. NEURODEGENER DIS 2015; 15:301-12. [PMID: 26183171 DOI: 10.1159/000433581] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 05/26/2015] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Recent studies have suggested overlapping pathological features among motor neuron, cognitive and neurodegenerative diseases. AIMS/METHODS Secondary analysis of 46 amyotrophic lateral sclerosis (ALS) patient autopsies was performed to independently assess pathological feature prevalence (e.g. percent of patients with any positive finding), degree of severity (e.g. mild, moderate, severe), and 2,200+ potential clinical/neuropathological correlations. The possible impact of gender, onset age, onset type (limb vs. bulbar), riluzole treatment, and severe TDP-43 pathology was assessed within patient subgroups. RESULTS Assessed features (prevalence, severity) include: lateral corticospinal tract degeneration (89%, moderate); Purkinje cell loss (85%, mild); localized neuronal loss (83%, mild to moderate); TDP-43 inclusions (80%, moderate); Betz cell loss (76%, mild); neurofibrillary tangles (78%, severe); anterior corticospinal tract degeneration (72%, moderate); spinal ventral root atrophy (65%, moderate); atherosclerosis (35%, mild); β-amyloid (35%, mild); tauopathy/tau inclusions (17%, mild); ventricular dilation (13%, mild); Lewy body formation (11%, mild); microinfarcts (7%, mild); and α-synuclein (4%, mild). Twenty-two percent of patients met criteria for Alzheimer's disease (AD) and 26% for frontotemporal lobar degeneration. Substantial differences were identified in the AD group and in the different onset age groups. CONCLUSION Our findings support the hypothesis that ALS and its variants could comprise a larger neuropathological continuum.
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Affiliation(s)
- Grant Coan
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Ga., USA
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Irvin CW, Kim RB, Mitchell CS. Seeking homeostasis: temporal trends in respiration, oxidation, and calcium in SOD1 G93A Amyotrophic Lateral Sclerosis mice. Front Cell Neurosci 2015; 9:248. [PMID: 26190973 PMCID: PMC4486844 DOI: 10.3389/fncel.2015.00248] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 06/18/2015] [Indexed: 12/12/2022] Open
Abstract
Impairments in mitochondria, oxidative regulation, and calcium homeostasis have been well documented in numerous Amyotrophic Lateral Sclerosis (ALS) experimental models, especially in the superoxide dismutase 1 glycine 93 to alanine (SOD1 G93A) transgenic mouse. However, the timing of these deficiencies has been debatable. In a systematic review of 45 articles, we examine experimental measurements of cellular respiration, mitochondrial mechanisms, oxidative markers, and calcium regulation. We evaluate the quantitative magnitude and statistical temporal trend of these aggregated assessments in high transgene copy SOD1 G93A mice compared to wild type mice. Analysis of overall trends reveals cellular respiration, intracellular adenosine triphosphate, and corresponding mitochondrial elements (Cox, cytochrome c, complex I, enzyme activity) are depressed for the entire lifespan of the SOD1 G93A mouse. Oxidant markers (H2O2, 8OH2'dG, MDA) are initially similar to wild type but are double that of wild type by the time of symptom onset despite early post-natal elevation of protective heat shock proteins. All aspects of calcium regulation show early disturbances, although a notable and likely compensatory convergence to near wild type levels appears to occur between 40 and 80 days (pre-onset), followed by a post-onset elevation in intracellular calcium. The identified temporal trends and compensatory fluctuations provide evidence that the "cause" of ALS may lay within failed homeostatic regulation, itself, rather than any one particular perturbing event or cellular mechanism. We discuss the vulnerabilities of motoneurons to regulatory instability and possible hypotheses regarding failed regulation and its potential treatment in ALS.
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Affiliation(s)
- Cameron W Irvin
- Department of Biomedical Engineering, Georgia Institute of Technology - Emory University, Atlanta, GA USA
| | - Renaid B Kim
- Department of Biomedical Engineering, Georgia Institute of Technology - Emory University, Atlanta, GA USA
| | - Cassie S Mitchell
- Department of Biomedical Engineering, Georgia Institute of Technology - Emory University, Atlanta, GA USA
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Pfohl SR, Halicek MT, Mitchell CS. Characterization of the Contribution of Genetic Background and Gender to Disease Progression in the SOD1 G93A Mouse Model of Amyotrophic Lateral Sclerosis: A Meta-Analysis. J Neuromuscul Dis 2015; 2:137-150. [PMID: 26594635 PMCID: PMC4652798 DOI: 10.3233/jnd-140068] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background: The SOD1 G93A mouse model of amyotrophic lateral sclerosis (ALS) is the most frequently used model to examine ALS pathophysiology. There is a lack of homogeneity in usage of the SOD1 G93A mouse, including differences in genetic background and gender, which could confound the field’s results. Objective: In an analysis of 97 studies, we characterized the ALS progression for the high transgene copy control SOD1 G93A mouse on the basis of disease onset, overall lifespan, and disease duration for male and female mice on the B6SJL and C57BL/6J genetic backgrounds and quantified magnitudes of differences between groups. Methods: Mean age at onset, onset assessment measure, disease duration, and overall lifespan data from each study were extracted and statistically modeled as the response of linear regression with the sex and genetic background factored as predictors. Additional examination was performed on differing experimental onset and endpoint assessment measures. Results: C57BL/6 background mice show delayed onset of symptoms, increased lifespan, and an extended disease duration compared to their sex-matched B6SJL counterparts. Female B6SJL generally experience extended lifespan and delayed onset compared to their male counterparts, while female mice on the C57BL/6 background show delayed onset but no difference in survival compared to their male counterparts. Finally, different experimental protocols (tremor, rotarod, etc.) for onset determination result in notably different onset means. Conclusions: Overall, the observed effect of sex on disease endpoints was smaller than that which can be attributed to the genetic background. The often-reported increase in lifespan for female mice was observed only for mice on the B6SJL background, implicating a strain-dependent effect of sex on disease progression that manifests despite identical mutant SOD1 expression.
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Affiliation(s)
- Stephen R Pfohl
- Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA
| | - Martin T Halicek
- Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA
| | - Cassie S Mitchell
- Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA
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Kim RB, Irvin CW, Tilva KR, Mitchell CS. State of the field: An informatics-based systematic review of the SOD1-G93A amyotrophic lateral sclerosis transgenic mouse model. Amyotroph Lateral Scler Frontotemporal Degener 2015; 17:1-14. [PMID: 25998063 PMCID: PMC4724331 DOI: 10.3109/21678421.2015.1047455] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Numerous sub-cellular through system-level disturbances have been identified in over 1300 articles examining the superoxide dismutase-1 guanine 93 to alanine (SOD1-G93A) transgenic mouse amyotrophic lateral sclerosis (ALS) pathophysiology. Manual assessment of such a broad literature base is daunting. We performed a comprehensive informatics-based systematic review or 'field analysis' to agnostically compute and map the current state of the field. Text mining of recaptured articles was used to quantify published data topic breadth and frequency. We constructed a nine-category pathophysiological function-based ontology to systematically organize and quantify the field's primary data. Results demonstrated that the distribution of primary research belonging to each category is: systemic measures an motor function, 59%; inflammation, 46%; cellular energetics, 37%; proteomics, 31%; neural excitability, 22%; apoptosis, 20%; oxidative stress, 18%; aberrant cellular chemistry, 14%; axonal transport, 10%. We constructed a SOD1-G93A field map that visually illustrates and categorizes the 85% most frequently assessed sub-topics. Finally, we present the literature-cited significance of frequently published terms and uncover thinly investigated areas. In conclusion, most articles individually examine at least two categories, which is indicative of the numerous underlying pathophysiological interrelationships. An essential future path is examination of cross-category pathophysiological interrelationships and their co-correspondence to homeostatic regulation and disease progression.
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Affiliation(s)
- Renaid B Kim
- a Department of Biomedical Engineering , Georgia Institute of Technology & Emory University , Atlanta , Georgia , USA
| | - Cameron W Irvin
- a Department of Biomedical Engineering , Georgia Institute of Technology & Emory University , Atlanta , Georgia , USA
| | - Keval R Tilva
- a Department of Biomedical Engineering , Georgia Institute of Technology & Emory University , Atlanta , Georgia , USA
| | - Cassie S Mitchell
- a Department of Biomedical Engineering , Georgia Institute of Technology & Emory University , Atlanta , Georgia , USA
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Mortazavi MM, Verma K, Harmon OA, Griessenauer CJ, Adeeb N, Theodore N, Tubbs RS. The microanatomy of spinal cord injury: A review. Clin Anat 2014; 28:27-36. [DOI: 10.1002/ca.22432] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Accepted: 06/23/2014] [Indexed: 01/08/2023]
Affiliation(s)
| | - Ketan Verma
- Pediatric Neurosurgery; Children's of Alabama
| | | | | | - Nimer Adeeb
- Pediatric Neurosurgery; Children's of Alabama
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14
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Li WT, Zhang XY, Xue H, Ni CP, Wang EG, An LB. Comparison of three different time points of starting treadmill training in spinal cord injured rats. Dev Neurorehabil 2013; 16:382-90. [PMID: 23477565 DOI: 10.3109/17518423.2012.762555] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
OBJECTIVE It has been widely acknowledged that early treadmill training plays an important role in rewiring neurons in a functionally meaningful manner in spinal cord injury (SCI) treatment. However, it is still unclear how early to start treadmill training to obtain the most efficacious results after SCI. The purpose of this study was to find the earliest time point when treadmill training was most effective in rewiring neurons. METHODS The rats were randomly divided into five groups: a sham group, control group, and three treadmill groups based on training start time post-injury: a 24 h group, 48 h group, and 72 h group. RESULTS The results revealed that in the 72 h group, Basso, Beattie, and Bresnaham scores increased and apoptotic cells decreased significantly compared to the other groups. There were no statistically differences in neuron counting and 5-bromo-2V-deoxyuridine assays between the groups. CONCLUSION These results indicated that the best start time for treadmill training is 72 h after SCI.
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Affiliation(s)
- Wen-Tao Li
- School of Nursing, Jilin University , Changchun , China
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Mladinic M, Nistri A, Taccola G. Acute Spinal Cord Injury In Vitro: Insight into Basic Mechanisms. ANIMAL MODELS OF SPINAL CORD REPAIR 2013. [DOI: 10.1007/978-1-62703-197-4_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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16
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Mitchell CS, Lee RH. Cargo distributions differentiate pathological axonal transport impairments. J Theor Biol 2012; 300:277-91. [PMID: 22285784 DOI: 10.1016/j.jtbi.2012.01.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Revised: 12/22/2011] [Accepted: 01/11/2012] [Indexed: 10/14/2022]
Abstract
Axonal transport is an essential process in neurons, analogous to shipping goods, by which energetic and cellular building supplies are carried downstream (anterogradely) and wastes are carried upstream (retrogradely) by molecular motors, which act as cargo porters. Impairments in axonal transport have been linked to devastating and often lethal neurodegenerative diseases, such as Amyotrophic Lateral Sclerosis, Huntington's, and Alzheimer's. Axonal transport impairment types include a decrease in available motors for cargo transport (motor depletion), the presence of defective or non-functional motors (motor dilution), and the presence of increased or larger cargos (protein aggregation). An impediment to potential treatment identification has been the inability to determine what type(s) of axonal transport impairment candidates that could be present in a given disease. In this study, we utilize a computational model and common axonal transport experimental metrics to reveal the axonal transport impairment general characteristics or "signatures" that result from three general defect types of motor depletion, motor dilution, and protein aggregation. Our results not only provide a means to discern these general impairments types, they also reveal key dynamic and emergent features of axonal transport, which potentially underlie multiple impairment types. The identified characteristics, as well as the analytical method, can be used to help elucidate the axonal transport impairments observed in experimental and clinical data. For example, using the model-predicted defect signatures, we identify the defect candidates, which are most likely to be responsible for the axonal transport impairments in the G93A SOD1 mouse model of ALS.
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Affiliation(s)
- Cassie S Mitchell
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332, USA.
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Ferguson AR, Stück ED, Nielson JL. Syndromics: a bioinformatics approach for neurotrauma research. Transl Stroke Res 2011; 2:438-54. [PMID: 22207883 PMCID: PMC3236294 DOI: 10.1007/s12975-011-0121-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Revised: 10/14/2011] [Accepted: 10/18/2011] [Indexed: 12/25/2022]
Abstract
Substantial scientific progress has been made in the past 50 years in delineating many of the biological mechanisms involved in the primary and secondary injuries following trauma to the spinal cord and brain. These advances have highlighted numerous potential therapeutic approaches that may help restore function after injury. Despite these advances, bench-to-bedside translation has remained elusive. Translational testing of novel therapies requires standardized measures of function for comparison across different laboratories, paradigms, and species. Although numerous functional assessments have been developed in animal models, it remains unclear how to best integrate this information to describe the complete translational "syndrome" produced by neurotrauma. The present paper describes a multivariate statistical framework for integrating diverse neurotrauma data and reviews the few papers to date that have taken an information-intensive approach for basic neurotrauma research. We argue that these papers can be described as the seminal works of a new field that we call "syndromics", which aim to apply informatics tools to disease models to characterize the full set of mechanistic inter-relationships from multi-scale data. In the future, centralized databases of raw neurotrauma data will enable better syndromic approaches and aid future translational research, leading to more efficient testing regimens and more clinically relevant findings.
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Affiliation(s)
- Adam R. Ferguson
- Brain and Spinal Injury Center (BASIC), Department of Neurological Surgery, University of California, 1001 Potrero Avenue, Building 1, Room 101, San Francisco, CA 94110 USA
| | - Ellen D. Stück
- Brain and Spinal Injury Center (BASIC), Department of Neurological Surgery, University of California, 1001 Potrero Avenue, Building 1, Room 101, San Francisco, CA 94110 USA
| | - Jessica L. Nielson
- Brain and Spinal Injury Center (BASIC), Department of Neurological Surgery, University of California, 1001 Potrero Avenue, Building 1, Room 101, San Francisco, CA 94110 USA
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Synaptic glutamate spillover increases NMDA receptor reliability at the cerebellar glomerulus. J Theor Biol 2011; 289:217-24. [PMID: 21884708 DOI: 10.1016/j.jtbi.2011.08.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 08/11/2011] [Accepted: 08/16/2011] [Indexed: 11/22/2022]
Abstract
Glutamate spillover in the mossy fiber to granule cell cerebellar glomeruli has been hypothesized to increase neurotransmission reliability. In this study, we evaluate this hypothesis using an experimentally based quantitative model of glutamate spillover on the N-methyl-d-aspartate receptors (NMDA-Rs) at the cerebellar glomerulus. The transient and steady-state responses of NMDA-Rs were examined over a physiological range of firing rates. Examined cases included direct glutamate release activation, glutamate spillover activation, and a combination of direct and spillover activation. Our results illustrate that the effects of spillover alone are equivalent to direct release and, notably, combined spillover and direct release effects on NMDA-Rs are not additive. Our results show that spillover does in fact provide a high degree of reliability given that the synaptic vesicle release rate must fall to approximately 15-25% of what is considered the normal baseline level in order to substantially alter neurotransmission across the examined range of frequencies. We suggest that the high reliability provided by activation due to glutamate spillover could be used to conserve energy by reducing the required overall glutamate load at higher frequencies.
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