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Moresis A, Restivo L, Bromilow S, Flik G, Rosati G, Scorrano F, Tsoory M, O'Connor EC, Gaburro S, Bannach-Brown A. A minimal metadata set (MNMS) to repurpose nonclinical in vivo data for biomedical research. Lab Anim (NY) 2024; 53:67-79. [PMID: 38438748 PMCID: PMC10912024 DOI: 10.1038/s41684-024-01335-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 01/31/2024] [Indexed: 03/06/2024]
Abstract
Although biomedical research is experiencing a data explosion, the accumulation of vast quantities of data alone does not guarantee a primary objective for science: building upon existing knowledge. Data collected that lack appropriate metadata cannot be fully interrogated or integrated into new research projects, leading to wasted resources and missed opportunities for data repurposing. This issue is particularly acute for research using animals, where concerns regarding data reproducibility and ensuring animal welfare are paramount. Here, to address this problem, we propose a minimal metadata set (MNMS) designed to enable the repurposing of in vivo data. MNMS aligns with an existing validated guideline for reporting in vivo data (ARRIVE 2.0) and contributes to making in vivo data FAIR-compliant. Scenarios where MNMS should be implemented in diverse research environments are presented, highlighting opportunities and challenges for data repurposing at different scales. We conclude with a 'call for action' to key stakeholders in biomedical research to adopt and apply MNMS to accelerate both the advancement of knowledge and the betterment of animal welfare.
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Affiliation(s)
- Anastasios Moresis
- Roche Pharma Research and Early Development, Data & Analytics, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Leonardo Restivo
- Neuro-Behavioral Analysis Unit, Faculty of Biology & Medicine, University of Lausanne, Lausanne, Switzerland
| | - Sophie Bromilow
- Group Legal Department, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Gunnar Flik
- Discovery, Charles River Laboratories, Groningen, the Netherlands
| | | | - Fabrizio Scorrano
- Emerging Technologies, Comparative Medicine, Novartis International AG, Basel, Switzerland
| | - Michael Tsoory
- Behavioral and Physiological Phenotyping Unit, Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Eoin C O'Connor
- Roche Pharma Research and Early Development, Neuroscience & Rare Diseases, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland.
| | | | - Alexandra Bannach-Brown
- QUEST Center for Responsible Research, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany.
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Musselman KE, Craven BC. Inclusivity and Engagement: The Canadian Spinal Cord Injury - Rehabilitation Association Welcomes You to the 10th National Spinal Cord Injury Conference. Top Spinal Cord Inj Rehabil 2023; 29:ii-iii. [PMID: 38174136 PMCID: PMC10759843 DOI: 10.46292/1945-5763-29.suppl.ii] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
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3
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Warner FM, Tong B, McDougall J, Martin Ginis KA, Rabchevsky AG, Cragg JJ, Kramer JL. Perspectives on Data Sharing in Persons With Spinal Cord Injury. Neurotrauma Rep 2023; 4:781-789. [PMID: 38028277 PMCID: PMC10659015 DOI: 10.1089/neur.2023.0035] [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] [Indexed: 12/01/2023] Open
Abstract
Open data sharing of clinical research aims to improve transparency and support novel scientific discoveries. There are also risks, including participant identification and the potential for stigmatization. The perspectives of persons participating in research are needed to inform open data-sharing policies. The aim of the current study was to determine perspectives on data sharing in persons with spinal cord injury (SCI), including risks and benefits, and types of data people are most willing to share. A secondary aim was to examine predictors of willingness to share data. Persons with SCIs in the United States and Canada completed a survey developed and disseminated through various channels, including our community partner, the North American Spinal Cord Injury Consortium. The study collected data from 232 participants, with 52.2% from Canada and 42.2% from the United States, and the majority completed the survey in English. Most participants had previously participated in research and had been living with an SCI for ≥5 years. Overall, most participants reported that the potential benefits of data sharing outweighed the negatives, with persons with SCI seen as the most trustworthy partners for data sharing. The highest levels of concern were that information could be stolen and companies might use the information for marketing purposes. Persons with SCI were generally supportive of data sharing for research purposes. Clinical trials should consider including a statement on open data sharing in informed consents to better acknowledge the contribution of research participants in future studies.
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Affiliation(s)
- Freda M. Warner
- International Collaboration on Repair Discoveries (ICORD), Blusson Spinal Cord Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Bobo Tong
- International Collaboration on Repair Discoveries (ICORD), Blusson Spinal Cord Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jessie McDougall
- International Collaboration on Repair Discoveries (ICORD), Blusson Spinal Cord Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Rehabilitation Sciences, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kathleen A. Martin Ginis
- International Collaboration on Repair Discoveries (ICORD), Blusson Spinal Cord Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Division of Physical Medicine and Rehabilitation, Department of Medicine, University of British Columbia, Kelowna, British Columbia, Canada
- School of Health and Exercise Sciences, Faculty of Health and Social Development, University of British Columbia, Kelowna, British Columbia, Canada
| | - Alexander G. Rabchevsky
- Department of Physiology and Spinal Cord and Brain Injury Research Center (SCoBIRC), University of Kentucky, Lexington, Kentucky, USA
| | - Jacquelyn J. Cragg
- International Collaboration on Repair Discoveries (ICORD), Blusson Spinal Cord Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - John L.K. Kramer
- International Collaboration on Repair Discoveries (ICORD), Blusson Spinal Cord Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Anesthesiology, Pharmacology, and Therapeutics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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4
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Radabaugh HL, Ferguson AR, Bramlett HM, Dietrich WD. Increasing Rigor of Preclinical Research to Maximize Opportunities for Translation. Neurotherapeutics 2023; 20:1433-1445. [PMID: 37525025 PMCID: PMC10684440 DOI: 10.1007/s13311-023-01400-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/09/2023] [Indexed: 08/02/2023] Open
Abstract
The use of animal models in pre-clinical research has significantly broadened our understanding of the pathologies that underlie traumatic brain injury (TBI)-induced damage and deficits. However, despite numerous pre-clinical studies reporting the identification of promising neurotherapeutics, translation of these therapies to clinical application has so far eluded the TBI research field. A concerted effort to address this lack of translatability is long overdue. Given the inherent heterogeneity of TBI and the replication crisis that continues to plague biomedical research, this is a complex task that will require a multifaceted approach centered around rigor and reproducibility. Here, we discuss the role of three primary focus areas for better aligning pre-clinical research with clinical TBI management. These focus areas are (1) reporting and standardization of protocols, (2) replication of prior knowledge including the confirmation of expected pharmacodynamics, and (3) the broad application of open science through inter-center collaboration and data sharing. We further discuss current efforts that are establishing the core framework needed for successfully addressing the translatability crisis of TBI.
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Affiliation(s)
- Hannah L Radabaugh
- Brain and Spinal Injury Center, Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Adam R Ferguson
- Brain and Spinal Injury Center, Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- San Francisco Veterans Affairs Healthcare System, San Francisco, CA, USA
| | - Helen M Bramlett
- Department of Neurological Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - W Dalton Dietrich
- Department of Neurological Surgery, University of Miami Miller School of Medicine, Miami, FL, USA.
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5
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Dietz VA, Roberts N, Knox K, Moore S, Pitonak M, Barr C, Centeno J, Leininger S, New KC, Nowell P, Rodreick M, Geoffroy CG, Stampas A, Dulin JN. Fighting for recovery on multiple fronts: The past, present, and future of clinical trials for spinal cord injury. Front Cell Neurosci 2022; 16:977679. [PMID: 36212690 PMCID: PMC9533868 DOI: 10.3389/fncel.2022.977679] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022] Open
Abstract
Through many decades of preclinical research, great progress has been achieved in understanding the complex nature of spinal cord injury (SCI). Preclinical research efforts have guided and shaped clinical trials, which are growing in number by the year. Currently, 1,149 clinical trials focused on improving outcomes after SCI are registered in the U.S. National Library of Medicine at ClinicalTrials.gov. We conducted a systematic analysis of these SCI clinical trials, using publicly accessible data downloaded from ClinicalTrials.gov. After extracting all available data for these trials, we categorized each trial according to the types of interventions being tested and the types of outcomes assessed. We then evaluated clinical trial characteristics, both globally and by year, in order to understand the areas of growth and change over time. With regard to clinical trial attributes, we found that most trials have low enrollment, only test single interventions, and have limited numbers of primary outcomes. Some gaps in reporting are apparent; for instance, over 75% of clinical trials with "Completed" status do not have results posted, and the Phase of some trials is incorrectly classified as "Not applicable" despite testing a drug or biological compound. When analyzing trials based on types of interventions assessed, we identified the largest representation in trials testing rehab/training/exercise, neuromodulation, and behavioral modifications. Most highly represented primary outcomes include motor function of the upper and lower extremities, safety, and pain. The most highly represented secondary outcomes include quality of life and pain. Over the past 15 years, we identified increased representation of neuromodulation and rehabilitation trials, and decreased representation of drug trials. Overall, the number of new clinical trials initiated each year continues to grow, signifying a hopeful future for the clinical treatment of SCI. Together, our work provides a comprehensive glimpse into the past, present, and future of SCI clinical trials, and suggests areas for improvement in clinical trial reporting.
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Affiliation(s)
- Valerie A. Dietz
- Department of Biology, Texas A&M University, College Station, TX, United States
| | - Nolan Roberts
- Department of Biology, Texas A&M University, College Station, TX, United States
| | - Katelyn Knox
- Department of Biology, Texas A&M University, College Station, TX, United States
| | - Sherilynne Moore
- Department of Biology, Texas A&M University, College Station, TX, United States
| | - Michael Pitonak
- Department of Biology, Texas A&M University, College Station, TX, United States
| | - Chris Barr
- Unite 2 Fight Paralysis, Minneapolis, MN, United States
| | - Jesus Centeno
- Unite 2 Fight Paralysis, Minneapolis, MN, United States
| | | | - Kent C. New
- Unite 2 Fight Paralysis, Minneapolis, MN, United States
| | - Peter Nowell
- Unite 2 Fight Paralysis, Minneapolis, MN, United States
| | | | - Cedric G. Geoffroy
- Department of Neuroscience and Experimental Therapeutics, Texas A&M University, College Station, TX, United States
- Texas A&M Institute for Neuroscience, Texas A&M University, College Station, TX, United States
| | - Argyrios Stampas
- Department of Physical Medicine and Rehabilitation, UTHealth Houston McGovern Medical School, Houston, TX, United States
| | - Jennifer N. Dulin
- Department of Biology, Texas A&M University, College Station, TX, United States
- Texas A&M Institute for Neuroscience, Texas A&M University, College Station, TX, United States
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6
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Torres-Espín A, Ferguson AR. Harmonization-Information Trade-Offs for Sharing Individual Participant Data in Biomedicine. HARVARD DATA SCIENCE REVIEW 2022; 4:10.1162/99608f92.a9717b34. [PMID: 36420049 PMCID: PMC9681014 DOI: 10.1162/99608f92.a9717b34] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024] Open
Abstract
Biomedical practice is evidence-based. Peer-reviewed papers are the primary medium to present evidence and data-supported results to drive clinical practice. However, it could be argued that scientific literature does not contain data, but rather narratives about and summaries of data. Meta-analyses of published literature may produce biased conclusions due to the lack of transparency in data collection, publication bias, and inaccessibility to the data underlying a publication ('dark data'). Co-analysis of pooled data at the level of individual research participants can offer higher levels of evidence, but this requires that researchers share raw individual participant data (IPD). FAIR (findable, accessible, interoperable, and reusable) data governance principles aim to guide data lifecycle management by providing a framework for actionable data sharing. Here we discuss the implications of FAIR for data harmonization, an essential step for pooling data for IPD analysis. We describe the harmonization-information trade-off, which states that the level of granularity in harmonizing data determines the amount of information lost. Finally, we discuss a framework for managing the trade-off and the levels of harmonization. In the coming era of funder mandates for data sharing, research communities that effectively manage data harmonization will be empowered to harness big data and advanced analytics such as machine learning and artificial intelligence tools, leading to stunning new discoveries that augment our understanding of diseases and their treatments. By elevating scientific data to the status of a first-class citizen of the scientific enterprise, there is strong potential for biomedicine to transition from a narrative publication product orientation to a modern data-driven enterprise where data itself is viewed as a primary work product of biomedical research.
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Affiliation(s)
- Abel Torres-Espín
- Brain and Spinal Injury Center (BASIC), Department of Neurological Surgery, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, California, United States of America
| | - Adam R Ferguson
- Brain and Spinal Injury Center (BASIC), Department of Neurological Surgery, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, California, United States of America
- San Francisco Veterans Affairs Health Care System, San Francisco, California, United States of America
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7
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Chou A, Torres-Espín A, Huie JR, Krukowski K, Lee S, Nolan A, Guglielmetti C, Hawkins BE, Chaumeil MM, Manley GT, Beattie MS, Bresnahan JC, Martone ME, Grethe JS, Rosi S, Ferguson AR. Empowering Data Sharing and Analytics through the Open Data Commons for Traumatic Brain Injury Research. Neurotrauma Rep 2022; 3:139-157. [PMID: 35403104 PMCID: PMC8985540 DOI: 10.1089/neur.2021.0061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Traumatic brain injury (TBI) is a major public health problem. Despite considerable research deciphering injury pathophysiology, precision therapies remain elusive. Here, we present large-scale data sharing and machine intelligence approaches to leverage TBI complexity. The Open Data Commons for TBI (ODC-TBI) is a community-centered repository emphasizing Findable, Accessible, Interoperable, and Reusable data sharing and publication with persistent identifiers. Importantly, the ODC-TBI implements data sharing of individual subject data, enabling pooling for high-sample-size, feature-rich data sets for machine learning analytics. We demonstrate pooled ODC-TBI data analyses, starting with descriptive analytics of subject-level data from 11 previously published articles (N = 1250 subjects) representing six distinct pre-clinical TBI models. Second, we perform unsupervised machine learning on multi-cohort data to identify persistent inflammatory patterns across different studies, improving experimental sensitivity for pro- versus anti-inflammation effects. As funders and journals increasingly mandate open data practices, ODC-TBI will create new scientific opportunities for researchers and facilitate multi-data-set, multi-dimensional analytics toward effective translation.
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Affiliation(s)
- Austin Chou
- Brain and Spinal Injury Center, University of California San Francisco, San Francisco, California, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Abel Torres-Espín
- Brain and Spinal Injury Center, University of California San Francisco, San Francisco, California, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - J Russell Huie
- Brain and Spinal Injury Center, University of California San Francisco, San Francisco, California, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
- San Francisco Veterans Affairs Healthcare System, San Francisco, California, USA
| | - Karen Krukowski
- Brain and Spinal Injury Center, University of California San Francisco, San Francisco, California, USA
- Department of Physical Therapy and Rehabilitation Science, University of California San Francisco, San Francisco, California, USA
| | - Sangmi Lee
- Brain and Spinal Injury Center, University of California San Francisco, San Francisco, California, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Amber Nolan
- Brain and Spinal Injury Center, University of California San Francisco, San Francisco, California, USA
- Department of Physical Therapy and Rehabilitation Science, University of California San Francisco, San Francisco, California, USA
| | - Caroline Guglielmetti
- Department of Physical Therapy and Rehabilitation Science, University of California San Francisco, San Francisco, California, USA
- Department of Radiology & Biomedical Imaging, University of California San Francisco, San Francisco, California, USA
| | - Bridget E Hawkins
- Department of Anesthesiology, University of Texas Medical Branch at Galveston, Galveston, Texas, USA
- Moody Project for Traumatic Brain Injury Research, University of Texas Medical Branch at Galveston, Galveston, Texas, USA
| | - Myriam M Chaumeil
- Department of Physical Therapy and Rehabilitation Science, University of California San Francisco, San Francisco, California, USA
- Department of Radiology & Biomedical Imaging, University of California San Francisco, San Francisco, California, USA
| | - Geoffrey T Manley
- Brain and Spinal Injury Center, University of California San Francisco, San Francisco, California, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Michael S Beattie
- Brain and Spinal Injury Center, University of California San Francisco, San Francisco, California, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
- San Francisco Veterans Affairs Healthcare System, San Francisco, California, USA
- Weill Institute for Neuroscience, University of California San Francisco, San Francisco, California, USA
| | - Jacqueline C Bresnahan
- Brain and Spinal Injury Center, University of California San Francisco, San Francisco, California, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
- Weill Institute for Neuroscience, University of California San Francisco, San Francisco, California, USA
| | - Maryann E Martone
- Department of Neuroscience, University of California San Diego, San Diego, California, USA
| | - Jeffrey S Grethe
- Department of Neuroscience, University of California San Diego, San Diego, California, USA
| | - Susanna Rosi
- Brain and Spinal Injury Center, University of California San Francisco, San Francisco, California, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
- Department of Physical Therapy and Rehabilitation Science, University of California San Francisco, San Francisco, California, USA
- Weill Institute for Neuroscience, University of California San Francisco, San Francisco, California, USA
- Kavli Institute of Fundamental Neuroscience, University of California San Francisco, San Francisco, California, USA
| | - Adam R Ferguson
- Brain and Spinal Injury Center, University of California San Francisco, San Francisco, California, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
- San Francisco Veterans Affairs Healthcare System, San Francisco, California, USA
- Weill Institute for Neuroscience, University of California San Francisco, San Francisco, California, USA
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8
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Estrada V, Oldenburg E, Popa O, Muller HW. Mapping the long rocky road to effective spinal cord injury therapy - A meta-review of pre-clinical and clinical research. J Neurotrauma 2022; 39:591-612. [PMID: 35196894 DOI: 10.1089/neu.2021.0298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Spinal cord injury (SCI) is a rare condition, which even after decades of research, to date still presents an incurable condition with a complex symptomatology. SCI can result in paralysis, pain, loss of sensation, bladder and sexual dysfunction, and muscle degeneration to name but a few. The large number of publications makes it difficult to keep track of current progress in the field and of the many treatment options, which have been suggested and are being proposed with increasing frequency. Scientific databases with user-oriented search options will offer possible solutions, but they are still mostly in the development phase. In this meta-analysis, we summarize and narrow down SCI therapeutic approaches applied in pre-clinical and clinical research. Statistical analyses of treatment clusters - assorted after counting annual publication numbers in PubMed and ClinicalTrials.gov databases - were performed to allow the comparison of research foci and of their translation efficacy into clinical therapy. Using the example of SCI research, our findings demonstrate the challenges that come with the accelerating research progress - an issue, which many research fields are faced with today. The analyses point out similarities and differences in the prioritization of SCI research in pre-clinical versus clinical therapy strategies. Moreover, the results demonstrate the rapidly growing importance of modern (bio-)engineering technologies.
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Affiliation(s)
- Veronica Estrada
- Heinrich Heine University Düsseldorf, 9170, Neurology, Molecular Neurobiology Laboratory, Düsseldorf, Germany;
| | - Ellen Oldenburg
- Heinrich Heine University Düsseldorf, 9170, Institute of Quantitative and Theoretical Biology, Düsseldorf, Germany;
| | - Ovidiu Popa
- Heinrich Heine University Düsseldorf, 9170, Institute of Quantitative and Theoretical Biology, Düsseldorf, Germany;
| | - Hans W Muller
- Heinrich Heine University Düsseldorf, 9170, Neurology, Düsseldorf, Germany;
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9
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Gensel JC, Orr MB. Reflections on Data Sharing Practices in Spinal Cord Injury Research. Neuroinformatics 2022; 20:3-6. [PMID: 33454872 PMCID: PMC8282785 DOI: 10.1007/s12021-020-09498-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2020] [Indexed: 01/05/2023]
Abstract
There are few pharmacological therapeutics available for spinal cord injury despite years of preclinical and clinical research. This brief editorial discusses some of the shortcomings of translational research efforts. In addition, we comment on our previous experiences with data curation and highlight evolving efforts by the spinal cord injury research community to improve prospects for future therapeutic development, especially pertaining to preclinical data sharing through the Open Data Commons for Spinal Cord Injury (ODC-SCI).
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Affiliation(s)
- John C. Gensel
- Spinal Cord and Brain Injury Research Center, Department of Physiology, University of Kentucky Medical School, Lexington, KY, United States,corresponding author:
| | - Michael B. Orr
- Spinal Cord and Brain Injury Research Center, Department of Physiology, University of Kentucky Medical School, Lexington, KY, United States,Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, United States
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10
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Torres-Espín A, Almeida CA, Chou A, Huie JR, Chiu M, Vavrek R, Sacramento J, Orr MB, Gensel JC, Grethe JS, Martone ME, Fouad K, Ferguson AR. Promoting FAIR Data Through Community-driven Agile Design: the Open Data Commons for Spinal Cord Injury (odc-sci.org). Neuroinformatics 2022; 20:203-219. [PMID: 34347243 PMCID: PMC9537193 DOI: 10.1007/s12021-021-09533-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2021] [Indexed: 01/07/2023]
Abstract
The past decade has seen accelerating movement from data protectionism in publishing toward open data sharing to improve reproducibility and translation of biomedical research. Developing data sharing infrastructures to meet these new demands remains a challenge. One model for data sharing involves simply attaching data, irrespective of its type, to publisher websites or general use repositories. However, some argue this creates a 'data dump' that does not promote the goals of making data Findable, Accessible, Interoperable and Reusable (FAIR). Specialized data sharing communities offer an alternative model where data are curated by domain experts to make it both open and FAIR. We report on our experiences developing one such data-sharing ecosystem focusing on 'long-tail' preclinical data, the Open Data Commons for Spinal Cord Injury (odc-sci.org). ODC-SCI was developed with community-based agile design requirements directly pulled from a series of workshops with multiple stakeholders (researchers, consumers, non-profit funders, governmental agencies, journals, and industry members). ODC-SCI focuses on heterogeneous tabular data collected by preclinical researchers including bio-behaviour, histopathology findings and molecular endpoints. This has led to an example of a specialized neurocommons that is well-embraced by the community it aims to serve. In the present paper, we provide a review of the community-based design template and describe the adoption by the community including a high-level review of current data assets, publicly released datasets, and web analytics. Although odc-sci.org is in its late beta stage of development, it represents a successful example of a specialized data commons that may serve as a model for other fields.
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Affiliation(s)
- Abel Torres-Espín
- Weill Institute for Neurosciences, Brain and Spinal Injury Center, Department of Neurological Surgery, University of California San Francisco, San Francisco, CA USA
| | - Carlos A. Almeida
- Weill Institute for Neurosciences, Brain and Spinal Injury Center, Department of Neurological Surgery, University of California San Francisco, San Francisco, CA USA
| | - Austin Chou
- Weill Institute for Neurosciences, Brain and Spinal Injury Center, Department of Neurological Surgery, University of California San Francisco, San Francisco, CA USA
| | - J. Russell Huie
- Weill Institute for Neurosciences, Brain and Spinal Injury Center, Department of Neurological Surgery, University of California San Francisco, San Francisco, CA USA
| | - Michael Chiu
- Department of Neuroscience, University of California, San Diego, San Diego, CA USA
| | - Romana Vavrek
- Faculty of Rehabilitation Medicine and the Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB Canada
| | - Jeff Sacramento
- Weill Institute for Neurosciences, Brain and Spinal Injury Center, Department of Neurological Surgery, University of California San Francisco, San Francisco, CA USA
| | - Michael B. Orr
- Spinal Cord and Brain Injury Research Center, Department of Physiology, University of Kentucky College of Medicine, Lexington, KY USA
| | - John C. Gensel
- Spinal Cord and Brain Injury Research Center, Department of Physiology, University of Kentucky College of Medicine, Lexington, KY USA
| | - Jeffery S. Grethe
- Department of Neuroscience, University of California, San Diego, San Diego, CA USA
| | - Maryann E. Martone
- Department of Neuroscience, University of California, San Diego, San Diego, CA USA
| | - Karim Fouad
- Faculty of Rehabilitation Medicine and the Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB Canada
| | - Adam R. Ferguson
- Weill Institute for Neurosciences, Brain and Spinal Injury Center, Department of Neurological Surgery, University of California San Francisco, San Francisco, CA USA ,San Francisco Veterans Affairs Health Care System, San Francisco, CA USA
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11
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Almeida CA, Torres-Espin A, Huie JR, Sun D, Noble-Haeusslein LJ, Young W, Beattie MS, Bresnahan JC, Nielson JL, Ferguson AR. Excavating FAIR Data: the Case of the Multicenter Animal Spinal Cord Injury Study (MASCIS), Blood Pressure, and Neuro-Recovery. Neuroinformatics 2022; 20:39-52. [PMID: 33651310 PMCID: PMC9015816 DOI: 10.1007/s12021-021-09512-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2021] [Indexed: 01/07/2023]
Abstract
Meta-analyses suggest that the published literature represents only a small minority of the total data collected in biomedical research, with most becoming 'dark data' unreported in the literature. Dark data is due to publication bias toward novel results that confirm investigator hypotheses and omission of data that do not. Publication bias contributes to scientific irreproducibility and failures in bench-to-bedside translation. Sharing dark data by making it Findable, Accessible, Interoperable, and Reusable (FAIR) may reduce the burden of irreproducible science by increasing transparency and support data-driven discoveries beyond the lifecycle of the original study. We illustrate feasibility of dark data sharing by recovering original raw data from the Multicenter Animal Spinal Cord Injury Study (MASCIS), an NIH-funded multi-site preclinical drug trial conducted in the 1990s that tested efficacy of several therapies after a spinal cord injury (SCI). The original drug treatments did not produce clear positive results and MASCIS data were stored in boxes for more than two decades. The goal of the present study was to independently confirm published machine learning findings that perioperative blood pressure is a major predictor of SCI neuromotor outcome (Nielson et al., 2015). We recovered, digitized, and curated the data from 1125 rats from MASCIS. Analyses indicated that high perioperative blood pressure at the time of SCI is associated with poorer health and worse neuromotor outcomes in more severe SCI, whereas low perioperative blood pressure is associated with poorer health and worse neuromotor outcome in moderate SCI. These findings confirm and expand prior results that a narrow window of blood-pressure control optimizes outcome, and demonstrate the value of recovering dark data for assessing reproducibility of findings with implications for precision therapeutic approaches.
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Affiliation(s)
- Carlos A Almeida
- Department of Neurological Surgery, Weill Institute for Neurosciences, Brain and Spinal Injury Center, University of California San Francisco, San Francisco, CA, USA
| | - Abel Torres-Espin
- Department of Neurological Surgery, Weill Institute for Neurosciences, Brain and Spinal Injury Center, University of California San Francisco, San Francisco, CA, USA
| | - J Russell Huie
- Department of Neurological Surgery, Weill Institute for Neurosciences, Brain and Spinal Injury Center, University of California San Francisco, San Francisco, CA, USA
| | - Dongming Sun
- W.M. Keck Center for Collaborative Neuroscience, Rutgers University, New Brunswick, NJ, USA
| | - Linda J Noble-Haeusslein
- Department of Neurology, University of Texas, Austin, TX, USA
- Department of Psychology, University of Texas, Austin, TX, USA
| | - Wise Young
- W.M. Keck Center for Collaborative Neuroscience, Rutgers University, New Brunswick, NJ, USA
| | - Michael S Beattie
- Department of Neurological Surgery, Weill Institute for Neurosciences, Brain and Spinal Injury Center, University of California San Francisco, San Francisco, CA, USA
| | - Jacqueline C Bresnahan
- Department of Neurological Surgery, Weill Institute for Neurosciences, Brain and Spinal Injury Center, University of California San Francisco, San Francisco, CA, USA
| | - Jessica L Nielson
- Department of Psychiatry and Behavioral Sciences, University of Minnesota, Minneapolis, MN, USA.
- Institute for Health Informatics, University of Minnesota, Minneapolis, MN, USA.
| | - Adam R Ferguson
- Department of Neurological Surgery, Weill Institute for Neurosciences, Brain and Spinal Injury Center, University of California San Francisco, San Francisco, CA, USA.
- San Francisco Veterans Affairs Health Care System, San Francisco, CA, USA.
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12
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Sutherland TC, Sefiani A, Horvat D, Huntington TE, Lei Y, West AP, Geoffroy CG. Age-Dependent Decline in Neuron Growth Potential and Mitochondria Functions in Cortical Neurons. Cells 2021; 10:1625. [PMID: 34209640 PMCID: PMC8306398 DOI: 10.3390/cells10071625] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 12/23/2022] Open
Abstract
The age of incidence of spinal cord injury (SCI) and the average age of people living with SCI is continuously increasing. However, SCI is extensively modeled in young adult animals, hampering translation of research to clinical applications. While there has been significant progress in manipulating axon growth after injury, the impact of aging is still unknown. Mitochondria are essential to successful neurite and axon growth, while aging is associated with a decline in mitochondrial functions. Using isolation and culture of adult cortical neurons, we analyzed mitochondrial changes in 2-, 6-, 12- and 18-month-old mice. We observed reduced neurite growth in older neurons. Older neurons also showed dysfunctional respiration, reduced membrane potential, and altered mitochondrial membrane transport proteins; however, mitochondrial DNA (mtDNA) abundance and cellular ATP were increased. Taken together, these data suggest that dysfunctional mitochondria in older neurons may be associated with the age-dependent reduction in neurite growth. Both normal aging and traumatic injury are associated with mitochondrial dysfunction, posing a challenge for an aging SCI population as the two elements can combine to worsen injury outcomes. The results of this study highlight this as an area of great interest in CNS trauma.
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Affiliation(s)
- Theresa C. Sutherland
- Department of Neuroscience and Experimental Therapeutics, Texas A&M Health Science Center, Bryan, TX 77807, USA; (T.C.S.); (A.S.); (D.H.); (T.E.H.)
| | - Arthur Sefiani
- Department of Neuroscience and Experimental Therapeutics, Texas A&M Health Science Center, Bryan, TX 77807, USA; (T.C.S.); (A.S.); (D.H.); (T.E.H.)
| | - Darijana Horvat
- Department of Neuroscience and Experimental Therapeutics, Texas A&M Health Science Center, Bryan, TX 77807, USA; (T.C.S.); (A.S.); (D.H.); (T.E.H.)
| | - Taylor E. Huntington
- Department of Neuroscience and Experimental Therapeutics, Texas A&M Health Science Center, Bryan, TX 77807, USA; (T.C.S.); (A.S.); (D.H.); (T.E.H.)
| | - Yuanjiu Lei
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX 77807, USA; (Y.L.); (A.P.W.)
| | - A. Phillip West
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX 77807, USA; (Y.L.); (A.P.W.)
| | - Cédric G. Geoffroy
- Department of Neuroscience and Experimental Therapeutics, Texas A&M Health Science Center, Bryan, TX 77807, USA; (T.C.S.); (A.S.); (D.H.); (T.E.H.)
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13
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LaPlaca MC, Huie JR, Alam HB, Bachstetter AD, Bayir H, Bellgowan PF, Cummings D, Dixon CE, Ferguson AR, Ferland-Beckham C, Floyd CL, Friess SH, Galanopoulou AS, Hall ED, Harris NG, Hawkins BE, Hicks RR, Hulbert LE, Johnson VE, Kabitzke PA, Lafrenaye AD, Lemmon VP, Lifshitz CW, Lifshitz J, Loane DJ, Misquitta L, Nikolian VC, Noble-Haeusslein LJ, Smith DH, Taylor-Burds C, Umoh N, Vovk O, Williams AM, Young M, Zai LJ. Pre-Clinical Common Data Elements for Traumatic Brain Injury Research: Progress and Use Cases. J Neurotrauma 2021; 38:1399-1410. [PMID: 33297844 PMCID: PMC8082734 DOI: 10.1089/neu.2020.7328] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Traumatic brain injury (TBI) is an extremely complex condition due to heterogeneity in injury mechanism, underlying conditions, and secondary injury. Pre-clinical and clinical researchers face challenges with reproducibility that negatively impact translation and therapeutic development for improved TBI patient outcomes. To address this challenge, TBI Pre-clinical Working Groups expanded upon previous efforts and developed common data elements (CDEs) to describe the most frequently used experimental parameters. The working groups created 913 CDEs to describe study metadata, animal characteristics, animal history, injury models, and behavioral tests. Use cases applied a set of commonly used CDEs to address and evaluate the degree of missing data resulting from combining legacy data from different laboratories for two different outcome measures (Morris water maze [MWM]; RotorRod/Rotarod). Data were cleaned and harmonized to Form Structures containing the relevant CDEs and subjected to missing value analysis. For the MWM dataset (358 animals from five studies, 44 CDEs), 50% of the CDEs contained at least one missing value, while for the Rotarod dataset (97 animals from three studies, 48 CDEs), over 60% of CDEs contained at least one missing value. Overall, 35% of values were missing across the MWM dataset, and 33% of values were missing for the Rotarod dataset, demonstrating both the feasibility and the challenge of combining legacy datasets using CDEs. The CDEs and the associated forms created here are available to the broader pre-clinical research community to promote consistent and comprehensive data acquisition, as well as to facilitate data sharing and formation of data repositories. In addition to addressing the challenge of standardization in TBI pre-clinical studies, this effort is intended to bring attention to the discrepancies in assessment and outcome metrics among pre-clinical laboratories and ultimately accelerate translation to clinical research.
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Affiliation(s)
- Michelle C. LaPlaca
- Department of Biomedical Engineering, Georgia Institute of Technology/Emory University, Atlanta, Georgia, USA
- San Francisco Veterans Affairs Health Care System, San Francisco, California, USA
| | - J. Russell Huie
- Brain and Spinal Injury Center, Department of Neurological Surgery, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California, USA
| | - Hasan B. Alam
- Department of Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Adam D. Bachstetter
- Department of Neuroscience, University of Kentucky, Lexington, Kentucky, USA
| | - Hűlya Bayir
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | | | - C. Edward Dixon
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Adam R. Ferguson
- Brain and Spinal Injury Center, Department of Neurological Surgery, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California, USA
| | | | - Candace L. Floyd
- Department of Physical Medicine and Rehabilitation, University of Utah, Salt Lake City, Utah, USA
| | - Stuart H. Friess
- Division of Critical Care Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | | | - Edward D. Hall
- Department of Neuroscience, University of Kentucky, Lexington, Kentucky, USA
| | - Neil G. Harris
- Department of Neurosurgery, University of California, Los Angeles, Los Angeles, California, USA
| | - Bridget E. Hawkins
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, Texas, USA
| | | | - Lindsey E. Hulbert
- Department of Animal Sciences and Industry, Kansas State University, Manhattan, Kansas, USA
| | - Victoria E. Johnson
- Department of Neurosurgery, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Audrey D. Lafrenaye
- Department of Anatomy and Neurobiology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Vance P. Lemmon
- Department of Neurological Surgery, University of Miami, Miami, Florida, USA
| | - Carrie W. Lifshitz
- Department of Child Health, University of Arizona College of Medicine Phoenix, Phoenix, Arizona, USA
| | - Jonathan Lifshitz
- Department of Child Health, University of Arizona College of Medicine Phoenix, Phoenix, Arizona, USA
| | - David J. Loane
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | | | | | | | - Douglas H. Smith
- Department of Neurosurgery, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Nsini Umoh
- Department of Defense, U.S. Army Medical Research and Materiel Command, Fort Detrick, Frederick, Maryland, USA
| | - Olga Vovk
- National Institutes of Health, Bethesda, Maryland, USA
| | - Aaron M. Williams
- Department of Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Margaret Young
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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14
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The Life of a Trailing Spouse. J Neurosci 2021; 41:3-10. [PMID: 33408132 DOI: 10.1523/jneurosci.2874-20.2020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 11/22/2020] [Accepted: 11/24/2020] [Indexed: 11/21/2022] Open
Abstract
In 1981, I published a paper in the first issue of the Journal of Neuroscience with my postdoctoral mentor, Alan Pearlman. It reported a quantitative analysis of the receptive field properties of neurons in reeler mouse visual cortex and the surprising conclusion that although the neuronal somas were strikingly malpositioned, their receptive fields were unchanged. This suggested that in mouse cortex at least, neuronal circuits have very robust systems in place to ensure the proper formation of connections. This had the unintended consequence of transforming me from an electrophysiologist into a cellular and molecular neuroscientist who studied cell adhesion molecules and the molecular mechanisms they use to regulate axon growth. It took me a surprisingly long time to appreciate that your science is driven by the people around you and by the technologies that are locally available. As a professional puzzler, I like all different kinds of puzzles, but the most fun puzzles involve playing with other puzzlers. This is my story of learning how to find like-minded puzzlers to solve riddles about axon growth and regeneration.
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15
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Torres-Espín A, Chou A, Huie JR, Kyritsis N, Upadhyayula PS, Ferguson AR. Reproducible analysis of disease space via principal components using the novel R package syndRomics. eLife 2021; 10:61812. [PMID: 33443012 PMCID: PMC7857733 DOI: 10.7554/elife.61812] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/13/2021] [Indexed: 01/12/2023] Open
Abstract
Biomedical data are usually analyzed at the univariate level, focused on a single primary outcome measure to provide insight into systems biology, complex disease states, and precision medicine opportunities. More broadly, these complex biological and disease states can be detected as common factors emerging from the relationships among measured variables using multivariate approaches. ‘Syndromics’ refers to an analytical framework for measuring disease states using principal component analysis and related multivariate statistics as primary tools for extracting underlying disease patterns. A key part of the syndromic workflow is the interpretation, the visualization, and the study of robustness of the main components that characterize the disease space. We present a new software package, syndRomics, an open-source R package with utility for component visualization, interpretation, and stability for syndromic analysis. We document the implementation of syndRomics and illustrate the use of the package in case studies of neurological trauma data.
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Affiliation(s)
- Abel Torres-Espín
- Weill Institute for Neurosciences, Brain and Spinal Injury Center (BASIC), University of California, San Francisco (UCSF), San Francisco, United States.,Department of Neurological Surgery, University of California San Francisco (UCSF), San Francisco, United States.,Zuckerberg San Francisco General Hospital and Trauma Center, San Francisco, United States
| | - Austin Chou
- Weill Institute for Neurosciences, Brain and Spinal Injury Center (BASIC), University of California, San Francisco (UCSF), San Francisco, United States.,Department of Neurological Surgery, University of California San Francisco (UCSF), San Francisco, United States.,Zuckerberg San Francisco General Hospital and Trauma Center, San Francisco, United States
| | - J Russell Huie
- Weill Institute for Neurosciences, Brain and Spinal Injury Center (BASIC), University of California, San Francisco (UCSF), San Francisco, United States.,Department of Neurological Surgery, University of California San Francisco (UCSF), San Francisco, United States.,Zuckerberg San Francisco General Hospital and Trauma Center, San Francisco, United States
| | - Nikos Kyritsis
- Weill Institute for Neurosciences, Brain and Spinal Injury Center (BASIC), University of California, San Francisco (UCSF), San Francisco, United States.,Department of Neurological Surgery, University of California San Francisco (UCSF), San Francisco, United States.,Zuckerberg San Francisco General Hospital and Trauma Center, San Francisco, United States
| | - Pavan S Upadhyayula
- School of Medicine, University of California San Diego (UCSD), San Diego, United States
| | - Adam R Ferguson
- Weill Institute for Neurosciences, Brain and Spinal Injury Center (BASIC), University of California, San Francisco (UCSF), San Francisco, United States.,Department of Neurological Surgery, University of California San Francisco (UCSF), San Francisco, United States.,Zuckerberg San Francisco General Hospital and Trauma Center, San Francisco, United States.,San Francisco VA Health Care System, San Francisco, United States
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16
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Fouad K, Popovich PG, Kopp MA, Schwab JM. The neuroanatomical-functional paradox in spinal cord injury. Nat Rev Neurol 2021; 17:53-62. [PMID: 33311711 PMCID: PMC9012488 DOI: 10.1038/s41582-020-00436-x] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2020] [Indexed: 12/13/2022]
Abstract
Although lesion size is widely considered to be the most reliable predictor of outcome after CNS injury, lesions of comparable size can produce vastly different magnitudes of functional impairment and subsequent recovery. This neuroanatomical-functional paradox is likely to contribute to the many failed attempts to independently replicate findings from animal models of neurotrauma. In humans, the analogous clinical-radiological paradox could explain why individuals with similar injuries can respond differently to rehabilitation. We describe the neuroanatomical-functional paradox in the context of traumatic spinal cord injury (SCI) and discuss the underlying mechanisms of the paradox, including the concepts of lesion-affected and recovery-related networks. We also consider the various secondary complications that further limit the accuracy of outcome prediction in SCI and provide suggestions for how to increase the predictive, translational value of preclinical SCI models.
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Affiliation(s)
- Karim Fouad
- Department of Physical Therapy, Faculty of Rehabilitation Medicine, University of Alberta, Edmonton, AB, Canada
- Institute for Neuroscience and Mental Health, University of Alberta, Edmonton, AB, Canada
| | - Phillip G Popovich
- Belford Center for Spinal Cord Injury, The Ohio State University, Wexner Medical Center, Columbus, OH, USA
- Center for Brain and Spinal Cord Repair, The Ohio State University, Wexner Medical Center, Columbus, OH, USA
- Department of Neuroscience, The Ohio State University, Wexner Medical Center, Columbus, OH, USA
- The Neurological Institute, The Ohio State University, Wexner Medical Center, Columbus, OH, USA
| | - Marcel A Kopp
- Clinical & Experimental Spinal Cord Injury Research, Department of Neurology with Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health (QUEST-Center for Transforming Biomedical Research), Berlin, Germany
| | - Jan M Schwab
- Belford Center for Spinal Cord Injury, The Ohio State University, Wexner Medical Center, Columbus, OH, USA.
- Center for Brain and Spinal Cord Repair, The Ohio State University, Wexner Medical Center, Columbus, OH, USA.
- Department of Neuroscience, The Ohio State University, Wexner Medical Center, Columbus, OH, USA.
- The Neurological Institute, The Ohio State University, Wexner Medical Center, Columbus, OH, USA.
- Clinical & Experimental Spinal Cord Injury Research, Department of Neurology with Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.
- Spinal Cord Injury Medicine (Neuroplegiology), Department of Neurology, The Ohio State University, Wexner Medical Center, Columbus, OH, USA.
- Department of Physical Medicine and Rehabilitation, The Ohio State University, Wexner Medical Center, Columbus, OH, USA.
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17
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Sutherland TC, Geoffroy CG. Are mitochondria the key to reduce the age-dependent decline in axon growth after spinal cord injury? Neural Regen Res 2021; 16:1444-1445. [PMID: 33318447 PMCID: PMC8284276 DOI: 10.4103/1673-5374.301016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Theresa C Sutherland
- Department of Neuroscience and Experimental Therapeutics, Texas A&M Health Science Center, Bryan, TX, USA
| | - Cédric G Geoffroy
- Department of Neuroscience and Experimental Therapeutics, Texas A&M Health Science Center, Bryan, TX, USA
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18
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Maas AIR, Peul W, Thomé C. Surgical decompression in acute spinal cord injury: earlier is better. Lancet Neurol 2020; 20:84-86. [PMID: 33357515 DOI: 10.1016/s1474-4422(20)30478-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 12/03/2020] [Indexed: 11/29/2022]
Affiliation(s)
- Andrew I R Maas
- Department of Neurosurgery, Antwerp University Hospital and University of Antwerp, Edegem 2650, Belgium.
| | - Wilco Peul
- Department of Neurosurgery, Leiden University Medical Centre, Leiden, Netherlands; Department of Neurosurgery, Haaglanden Medical Centre, The Hague, Netherlands
| | - Claudius Thomé
- Department of Neurosurgery, Medical University Innsbruck, Innsbruck, Austria
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19
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Fouad K, Ng C, Basso DM. Behavioral testing in animal models of spinal cord injury. Exp Neurol 2020; 333:113410. [PMID: 32735871 PMCID: PMC8325780 DOI: 10.1016/j.expneurol.2020.113410] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/13/2020] [Accepted: 07/17/2020] [Indexed: 01/08/2023]
Abstract
This review is based on a lecture presented at the Craig H. Neilsen Foundation sponsored Spinal Cord Injury Training Program at Ohio State University. We discuss the advantages and challenges of injury models in rodents and theory relation to various behavioral outcome measures. We offer strategies and advice on experimental design, behavioral testing, and on the challenges, one will encounter with animal testing. This review is designed to guide those entering the field of spinal cord injury and/or involved with in vivo animal testing.
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Affiliation(s)
- K Fouad
- University of Alberta, Faculty of Rehabilitation Medicine, Dept of Physical Therapy, 3-48 Corbett Hall, Edmonton T6G 2G4, Canada; University of Alberta, Neuroscience and Mental Health Institute, 2-132 Li Ka Shing, Edmonton T6G 2E1, Canada.
| | - C Ng
- University of Alberta, Neuroscience and Mental Health Institute, 2-132 Li Ka Shing, Edmonton T6G 2E1, Canada
| | - D M Basso
- Ohio State University, College of Medicine, School of Health and Rehabilitation Sciences, 106A Atwell Hall, 453 W. 10th Ave, Columbus, OH 43210, USA
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20
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Stewart AN, MacLean SM, Stromberg AJ, Whelan JP, Bailey WM, Gensel JC, Wilson ME. Considerations for Studying Sex as a Biological Variable in Spinal Cord Injury. Front Neurol 2020; 11:802. [PMID: 32849242 PMCID: PMC7419700 DOI: 10.3389/fneur.2020.00802] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/26/2020] [Indexed: 12/13/2022] Open
Abstract
In response to NIH initiatives to investigate sex as a biological variable in preclinical animal studies, researchers have increased their focus on male and female differences in neurotrauma. Inclusion of both sexes when modeling neurotrauma is leading to the identification of novel areas for therapeutic and scientific exploitation. Here, we review the organizational and activational effects of sex hormones on recovery from injury and how these changes impact the long-term health of spinal cord injury (SCI) patients. When determining how sex affects SCI it remains imperative to expand outcomes beyond locomotor recovery and consider other complications plaguing the quality of life of patients with SCI. Interestingly, the SCI field predominately utilizes female rodents for basic science research which contrasts most other male-biased research fields. We discuss the unique caveats this creates to the translatability of preclinical research in the SCI field. We also review current clinical and preclinical data examining sex as biological variable in SCI. Further, we report how technical considerations such as housing, size, care management, and age, confound the interpretation of sex-specific effects in animal studies of SCI. We have uncovered novel findings regarding how age differentially affects mortality and injury-induced anemia in males and females after SCI, and further identified estrus cycle dysfunction in mice after injury. Emerging concepts underlying sexually dimorphic responses to therapy are also discussed. Through a combination of literature review and primary research observations we present a practical guide for considering and incorporating sex as biological variable in preclinical neurotrauma studies.
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Affiliation(s)
- Andrew N Stewart
- Department of Physiology, University of Kentucky, Lexington, KY, United States.,Spinal Cord and Brain Injury Research Center, College of Medicine, University of Kentucky, Lexington, KY, United States
| | - Steven M MacLean
- Department of Physiology, University of Kentucky, Lexington, KY, United States.,Spinal Cord and Brain Injury Research Center, College of Medicine, University of Kentucky, Lexington, KY, United States
| | - Arnold J Stromberg
- Department of Statistics, College of Arts and Sciences, University of Kentucky, Lexington, KY, United States
| | - Jessica P Whelan
- Department of Physiology, University of Kentucky, Lexington, KY, United States.,Spinal Cord and Brain Injury Research Center, College of Medicine, University of Kentucky, Lexington, KY, United States
| | - William M Bailey
- Department of Physiology, University of Kentucky, Lexington, KY, United States.,Spinal Cord and Brain Injury Research Center, College of Medicine, University of Kentucky, Lexington, KY, United States
| | - John C Gensel
- Department of Physiology, University of Kentucky, Lexington, KY, United States.,Spinal Cord and Brain Injury Research Center, College of Medicine, University of Kentucky, Lexington, KY, United States
| | - Melinda E Wilson
- Department of Physiology, University of Kentucky, Lexington, KY, United States
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21
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Sutherland TC, Geoffroy CG. The Influence of Neuron-Extrinsic Factors and Aging on Injury Progression and Axonal Repair in the Central Nervous System. Front Cell Dev Biol 2020; 8:190. [PMID: 32269994 PMCID: PMC7109259 DOI: 10.3389/fcell.2020.00190] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/06/2020] [Indexed: 12/21/2022] Open
Abstract
In the aging western population, the average age of incidence for spinal cord injury (SCI) has increased, as has the length of survival of SCI patients. This places great importance on understanding SCI in middle-aged and aging patients. Axon regeneration after injury is an area of study that has received substantial attention and made important experimental progress, however, our understanding of how aging affects this process, and any therapeutic effort to modulate repair, is incomplete. The growth and regeneration of axons is mediated by both neuron intrinsic and extrinsic factors. In this review we explore some of the key extrinsic influences on axon regeneration in the literature, focusing on inflammation and astrogliosis, other cellular responses, components of the extracellular matrix, and myelin proteins. We will describe how each element supports the contention that axonal growth after injury in the central nervous system shows an age-dependent decline, and how this may affect outcomes after a SCI.
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Affiliation(s)
- Theresa C Sutherland
- Department of Neuroscience and Experimental Therapeutics, Texas A&M Health Science Center, Bryan, TX, United States
| | - Cédric G Geoffroy
- Department of Neuroscience and Experimental Therapeutics, Texas A&M Health Science Center, Bryan, TX, United States
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