Syndromics: a bioinformatics approach for neurotrauma research

Microglia promote maladaptive plasticity in autonomic circuitry after spinal cord injury in mice

Robust structural remodeling and synaptic plasticity occurs within spinal autonomic circuitry after severe high-level spinal cord injury (SCI). As a result, normally innocuous visceral or somatic stimuli elicit uncontrolled activation of spinal sympathetic reflexes that contribute to systemic disease and organ-specific pathology. How hyperexcitable sympathetic circuitry forms is unknown, but local cues from neighboring glia likely help mold these maladaptive neuronal networks. Here, we used a mouse model of SCI to show that microglia surrounded active glutamatergic interneurons and subsequently coordinated multi-segmental excitatory synaptogenesis and expansion of sympathetic networks that control immune, neuroendocrine, and cardiovascular functions. Depleting microglia during critical periods of circuit remodeling after SCI prevented maladaptive synaptic and structural plasticity in autonomic networks, decreased the frequency and severity of autonomic dysreflexia, and prevented SCI-induced immunosuppression. Forced turnover of microglia in microglia-depleted mice restored structural and functional indices of pathological dysautonomia, providing further evidence that microglia are key effectors of autonomic plasticity. Additional data show that microglia-dependent autonomic plasticity required expression of triggering receptor expressed on myeloid cells 2 (Trem2) and α2δ-1-dependent synaptogenesis. These data suggest that microglia are primary effectors of autonomic neuroplasticity and dysautonomia after SCI in mice. Manipulating microglia may be a strategy to limit autonomic complications after SCI or other forms of neurologic disease.

Data-driven approach to integrating genomic and behavioral preclinical traumatic brain injury research

Understanding recovery from TBI is complex, involving multiple systems and modalities. The current study applied modern data science tools to manage this complexity and harmonize large-scale data to understand relationships between gene expression and behavioral outcomes in a preclinical model of chronic TBI (cTBI). Data collected by the Moody Project for Translational TBI Research included rats with no injury (naïve animals with similar amounts of anesthetic exposure to TBI and sham-injured animals), sham injury, or lateral fluid percussion TBI, followed by recovery periods up to 12 months. Behavioral measures included locomotor coordination (beam balance neuroscore) and memory and cognition assessments (Morris water maze: MWM) at multiple timepoints. Gene arrays were performed using hippocampal and cortical samples to probe 45,610 genes. To reduce the high dimensionality of molecular and behavioral domains and uncover gene-behavior associations, we performed non-linear principal components analyses (NL-PCA), which de-noised the data. Genomic NL-PCA unveiled three interpretable eigengene components (PC2, PC3, and PC4). Ingenuity pathway analysis (IPA) identified the PCs as an integrated stress response (PC2; EIF2-mTOR, corticotropin signaling, etc.), inflammatory factor translation (PC3; PI3K-p70S6K signaling), and neurite growth inhibition (PC4; Rho pathways). Behavioral PCA revealed three principal components reflecting the contribution of MWM overall speed and distance, neuroscore/beam walk, and MWM platform measures. Integrating the genomic and behavioral domains, we then performed a 'meta-PCA' on individual PC scores for each rat from genomic and behavioral PCAs. This meta-PCA uncovered three unique multimodal PCs, characterized by robust associations between inflammatory/stress response and neuroscore/beam walk performance (meta-PC1), stress response and MWM performance (meta-PC2), and stress response and neuroscore/beam walk performance (meta-PC3). Multivariate analysis of variance (MANOVA) on genomic-behavioral meta-PC scores tested separately on cortex and hippocampal samples revealed the main effects of TBI and recovery time. These findings are a proof of concept for the integration of disparate data domains for translational knowledge discovery, harnessing the full syndromic space of TBI.

Reflections on Data Sharing Practices in Spinal Cord Injury Research

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).

Excavating FAIR Data: the Case of the Multicenter Animal Spinal Cord Injury Study (MASCIS), Blood Pressure, and Neuro-Recovery

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.

Reproducible analysis of disease space via principal components using the novel R package syndRomics

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.

Acute post-injury blockade of α2δ-1 calcium channel subunits prevents pathological autonomic plasticity after spinal cord injury

After spinal cord injury (SCI), normally innocuous visceral or somatic stimuli can trigger uncontrolled reflex activation of sympathetic circuitry, causing pathological dysautonomia. We show that remarkable structural remodeling and plasticity occur within spinal autonomic circuitry, creating abnormal sympathetic reflexes that promote dysautonomia. However, when mice are treated early after SCI with human-equivalent doses of the US Food and Drug Administration (FDA)-approved drug gabapentin (GBP), it is possible to block multi-segmental excitatory synaptogenesis and abolish sprouting of autonomic neurons that innervate immune organs and sensory afferents that trigger pain and autonomic dysreflexia (AD). This “prophylactic GBP” regimen decreases the frequency and severity of AD and protects against SCI-induced immune suppression. These benefits persist even 1 month after stopping treatment. GBP could be repurposed to prevent dysautonomia in at-risk individuals with high-level SCI.

Brennan et al. show that α2δ−1 calcium channel subunits drive remarkable structural reorganization of autonomic circuitry and autonomic dysfunction after spinal cord injury. Early (prophylactic) post-injury treatment with gabapentin, an FDA-approved drug, prevents α2δ−1-dependent structural changes and autonomic dysfunction. Prophylactic gabapentin could be repurposed clinically for at-risk individuals.

Self-directed rehabilitation training intensity thresholds for efficient recovery of skilled forelimb function in rats with cervical spinal cord injury

Task specific rehabilitation training is commonly used to treat motor dysfunction after neurological injures such as spinal cord injury (SCI), yet the use of task specific training in preclinical animal studies of SCI is not common. This is due in part to the difficulty in training animals to perform specific motor tasks, but also due to the lack of knowledge about optimal rehabilitation training parameters to maximize recovery. The single pellet reaching, grasping and retrieval (SPRGR) task (a.k.a. single pellet reaching task or Whishaw task) is a skilled forelimb motor task used to provide rehabilitation training and test motor recovery in rodents with cervical SCI. However, the relationships between the amount, duration, intensity, and timing of training remain poorly understood. In this study, using automated robots that allow rats with cervical SCI ad libitum access to self-directed SPRGR rehabilitation training, we show clear relationships between the total amount of rehabilitation training, the intensity of training (i.e., number of attempts/h), and performance in the task. Specifically, we found that rats naturally segregate into High and Low performance groups based on training strategy and performance in the task. Analysis of the different training strategies showed that more training (i.e., increased number of attempts in the SPRGR task throughout rehabilitation training) at higher intensities (i.e., number of attempts per hour) increased performance in the task, and that improved performance in the SPRGR task was linked to differences in corticospinal tract axon collateral densities in the injured spinal cords. Importantly, however, our data also indicate that rehabilitation training becomes progressively less efficient (i.e., less recovery for each attempt) as both the amount and intensity of rehabilitation training increases. Finally, we found that Low performing animals could increase their training intensity and transition to High performing animals in chronic SCI. These results highlight the rehabilitation training strategies that are most effective to regain skilled forelimb motor function after SCI, which will facilitate pre-clinical rehabilitation studies using animal models and could be beneficial in the development of more efficient clinical rehabilitation training strategies.

Applying univariate vs. multivariate statistics to investigate therapeutic efficacy in (pre)clinical trials: A Monte Carlo simulation study on the example of a controlled preclinical neurotrauma trial

BACKGROUND

Small sample sizes combined with multiple correlated endpoints pose a major challenge in the statistical analysis of preclinical neurotrauma studies. The standard approach of applying univariate tests on individual response variables has the advantage of simplicity of interpretation, but it fails to account for the covariance/correlation in the data. In contrast, multivariate statistical techniques might more adequately capture the multi-dimensional pathophysiological pattern of neurotrauma and therefore provide increased sensitivity to detect treatment effects.

RESULTS

We systematically evaluated the performance of univariate ANOVA, Welch's ANOVA and linear mixed effects models versus the multivariate techniques, ANOVA on principal component scores and MANOVA tests by manipulating factors such as sample and effect size, normality and homogeneity of variance in computer simulations. Linear mixed effects models demonstrated the highest power when variance between groups was equal or variance ratio was 1:2. In contrast, Welch's ANOVA outperformed the remaining methods with extreme variance heterogeneity. However, power only reached acceptable levels of 80% in the case of large simulated effect sizes and at least 20 measurements per group or moderate effects with at least 40 replicates per group. In addition, we evaluated the capacity of the ordination techniques, principal component analysis (PCA), redundancy analysis (RDA), linear discriminant analysis (LDA), and partial least squares discriminant analysis (PLS-DA) to capture patterns of treatment effects without formal hypothesis testing. While LDA suffered from a high false positive rate due to multicollinearity, PCA, RDA, and PLS-DA were robust and PLS-DA outperformed PCA and RDA in capturing a true treatment effect pattern.

CONCLUSIONS

Multivariate tests do not provide an appreciable increase in power compared to univariate techniques to detect group differences in preclinical studies. However, PLS-DA seems to be a useful ordination technique to explore treatment effect patterns without formal hypothesis testing.

Refining rodent models of spinal cord injury

This report was produced by an Expert Working Group (EWG) consisting of UK-based researchers, veterinarians and regulators of animal experiments with specialist knowledge of the use of animal models of spinal cord injury (SCI). It aims to facilitate the implementation of the Three Rs (Replacement, Reduction and Refinement), with an emphasis on refinement. Specific animal welfare issues were identified and discussed, and practical measures proposed, with the aim of reducing animal use and suffering, reducing experimental variability, and increasing translatability within this critically important research field.

Sleep-disordered breathing is associated with brain vascular reactivity in spinal cord injury

OBJECTIVE

To determine the population-level odds of individuals with spinal cord injury (SCI) experiencing fatigue and sleep apnea, to elucidate relationships with level and severity of injury, and to examine associations with abnormal cerebrovascular responsiveness.

METHODS

We used population-level data, meta-analyses, and primary physiologic assessments to provide a large-scale integrated assessment of sleep-related complications after SCI. Population-level and meta-analyses included more than 60,000 able-bodied individuals and more than 1,800 individuals with SCI. Physiologic assessments were completed on a homogenous sample of individuals with cervical SCI and matched controls. We examined the prevalence of (1) self-reported chronic fatigue, (2) clinically identified sleep apnea, and 3) cerebrovascular responsiveness to changing CO₂.

RESULTS

Logistic regression revealed a 7-fold elevated odds of chronic fatigue after SCI (odds ratio [OR] 7.9, 95% confidence interval [CI] 3.5-16.2), and that fatigue and trouble sleeping are correlated with the level and severity of injury. We further show that those with SCI experience elevated risk of clinically defined sleep-disordered breathing in more than 600 individuals with SCI (pooled OR 3.1, 95% CI 1.3-7.5). We confirmed that individuals with SCI experience a high rate of clinically defined sleep apnea using primary polysomnography assessments. We then provide evidence using syndromic analysis that sleep-disordered breathing is a factor strongly associated with impaired cerebrovascular responsiveness to CO₂ in patients with SCI.

CONCLUSIONS

Individuals with SCI have an increased prevalence of sleep-disordered breathing, which may partially underpin their increased risk of stroke. There is thus a need to integrate sleep-related breathing examinations into routine care for individuals with SCI.

Exploration of surgical blood pressure management and expected motor recovery in individuals with traumatic spinal cord injury

STUDY DESIGN

Retrospective analysis.

OBJECTIVE

To assess the impact of mean arterial blood pressure (MAP) during surgical intervention for spinal cord injury (SCI) on motor recovery.

SETTING

Level-one Trauma Hospital and Acute Rehabilitation Hospital in San Jose, CA, USA.

METHODS

Twenty-five individuals with traumatic SCI who received surgical and acute rehabilitation care at a level-one trauma center were included in this study. The Surgical Information System captured intraoperative MAPs on a minute-by-minute basis and exposure was quantified at sequential thresholds from 50 to 104 mmHg. Change in International Standards for Neurological Classification of Spinal Cord Injury (ISNCSCI) motor score was calculated based on physiatry evaluations at the earliest postoperative time and at discharge from acute rehabilitation. Linear regression models were used to estimate the rate of recovery across the entire MAP range.

RESULTS

An exploratory analysis revealed that increased time within an intraoperative MAP range (70-94 mmHg) was associated with ISNCSCI motor score improvement. A significant regression equation was found for the MAP range 70-94 mmHg (F[1, 23] = 5.07, r² = 0.181, p = 0.034). ISNCSCI motor scores increased 0.039 for each minute of exposure to the MAP range 70-94 mmHg during the operative procedure; this represents a significant correlation between intraoperative time with MAP 70-94 and subsequent motor recovery. Blood pressure exposures above or below this range did not display a positive association with motor recovery.

CONCLUSIONS

Hypertension as well as hypotension during surgery may impact the trajectory of recovery in individuals with SCI, and there may be a direct relationship between intraoperative MAP and motor recovery.

Differential fracture response to traumatic brain injury suggests dominance of neuroinflammatory response in polytrauma

Polytraumatic injuries, specifically long bone fracture and traumatic brain injury (TBI), frequently occur together. Clinical observation has long held that TBI can accelerate fracture healing, yet the complexity and heterogeneity of these injuries has produced conflicting data with limited information on underlying mechanisms. We developed a murine polytrauma model with TBI and fracture to evaluate healing in a controlled system. Fractures were created both contralateral and ipsilateral to the TBI to test whether differential responses of humoral and/or neuronal systems drove altered healing patterns. Our results show increased bone formation after TBI when injuries occur contralateral to each other, rather than ipsilateral, suggesting a role of the nervous system based on the crossed neuroanatomy of motor and sensory systems. Analysis of the humoral system shows that blood cell counts and inflammatory markers are differentially modulated by polytrauma. A data-driven multivariate analysis integrating all outcome measures showed a distinct pathological state of polytrauma and co-variations between fracture, TBI and systemic markers. Taken together, our results suggest that a contralateral bone fracture and TBI alter the local neuroinflammatory state to accelerate early fracture healing. We believe applying a similar data-driven approach to clinical polytrauma may help to better understand the complicated pathophysiological mechanisms of healing.

Data Dissemination: Shortening the Long Tail of Traumatic Brain Injury Dark Data

Translation of traumatic brain injury (TBI) research findings from bench to bedside involves aligning multi-species data across diverse data types including imaging and molecular biomarkers, histopathology, behavior, and functional outcomes. In this review we argue that TBI translation should be acknowledged for what it is: a problem of big data that can be addressed using modern data science approaches. We review the history of the term big data, tracing its origins in Internet technology as data that are "big" according to the "4Vs" of volume, velocity, variety, veracity and discuss how the term has transitioned into the mainstream of biomedical research. We argue that the problem of TBI translation fundamentally centers around data variety and that solutions to this problem can be found in modern machine learning and other cutting-edge analytical approaches. Throughout our discussion we highlight the need to pull data from diverse sources including unpublished data ("dark data") and "long-tail data" (small, specialty TBI datasets undergirding the published literature). We review a few early examples of published articles in both the pre-clinical and clinical TBI research literature to demonstrate how data reuse can drive new discoveries leading into translational therapies. Making TBI data resources more Findable, Accessible, Interoperable, and Reusable (FAIR) through better data stewardship has great potential to accelerate discovery and translation for the silent epidemic of TBI.

Testing a Multivariate Proteomic Panel for Traumatic Brain Injury Biomarker Discovery: A TRACK-TBI Pilot Study

The complex and heterogeneous nature of traumatic brain injury (TBI) has rendered the identification of diagnostic and prognostic biomarkers elusive. A single acute biomarker may not be sufficient to categorize injury severity and/or predict outcome. Using multivariate dimension reduction analyses, we tested the sensitivity and specificity of a multi-analyte panel of proteins as an ensemble biomarker for TBI. Serum was collected within 24 h of injury in a cohort of 130 patients enrolled in the multi-center prospective Transforming Research and Clinical Knowledge in Traumatic Brain Injury Pilot (TRACK-TBI Pilot) study and run on an array that measured 72 proteins. Using unsupervised principal components analysis, we first identified the subset of protein changes accounting for the most variance across patients. This yielded a group of 21 proteins that reflected an inverse relationship between inflammatory cytokines and regulators of anti-inflammation, and generated an individual inflammatory profile score for each patient. We then tested the association between these scores and computed tomography (CT) findings at hospital admission, as well as their prognostic association with functional recovery at 3 and 6 months (Glasgow Outcome Scale-Extended), and cognitive recovery at 6 months (California Verbal Learning Test, Second Edition) after injury. Inflammatory signatures were significantly increased in patients with positive CT findings, as well as in those who showed poor or incomplete recovery. Inflammation biomarker scores also showed significant sensitivity and specificity as a discriminator of these outcome measures (all areas under the curve [AUCs] >0.62). This proof of concept for the feasibility of multivariate biomarker identification demonstrates the prognostic validity of using a proteomic panel as a potential biomarker for TBI.

Developing a data sharing community for spinal cord injury research

The rapid growth in data sharing presents new opportunities across the spectrum of biomedical research. Global efforts are underway to develop practical guidance for implementation of data sharing and open data resources. These include the recent recommendation of 'FAIR Data Principles', which assert that if data is to have broad scientific value, then digital representations of that data should be Findable, Accessible, Interoperable and Reusable (FAIR). The spinal cord injury (SCI) research field has a long history of collaborative initiatives that include sharing of preclinical research models and outcome measures. In addition, new tools and resources are being developed by the SCI research community to enhance opportunities for data sharing and access. With this in mind, the National Institute of Neurological Disorders and Stroke (NINDS) at the National Institutes of Health (NIH) hosted a workshop on October 5-6, 2016 in Bethesda, MD, in collaboration with the Open Data Commons for Spinal Cord Injury (ODC-SCI) titled "Preclinical SCI Data: Creating a FAIR Share Community". Workshop invitees were nominated by the workshop steering committee (co-chairs: ARF and VPL; members: AC, KDA, MSB, KF, LBJ, PGP, JMS), to bring together junior and senior level experts including preclinical and basic SCI researchers from academia and industry, data science and bioinformatics experts, investigators with expertise in other neurological disease fields, clinical researchers, members of the SCI community, and program staff representing federal and private funding agencies. The workshop and ODC-SCI efforts were sponsored by the International Spinal Research Trust (ISRT), the Rick Hansen Institute, Wings for Life, the Craig H. Neilsen Foundation and NINDS. The number of attendees was limited to ensure active participation and feedback in small groups. The goals were to examine the current landscape for data sharing in SCI research and provide a path to its future. Below are highlights from the workshop, including perspectives on the value of data sharing in SCI research, workshop participant perspectives and concerns, descriptions of existing resources and actionable directions for further engaging the SCI research community in a model that may be applicable to many other areas of neuroscience. This manuscript is intended to share these initial findings with the broader research community, and to provide talking points for continued feedback from the SCI field, as it continues to move forward in the age of data sharing.

Pulmonary outcomes following specialized respiratory management for acute cervical spinal cord injury: a retrospective analysis

Study Design

Retrospective analysis.

Objectives

To identify multivariate interactions of respiratory function that are sensitive to spinal cord injury level and pharmacological treatment to promote strategies that increases successful liberation from mechanical ventilation.

Setting

United States regional spinal cord injury (SCI) treatment center.

Methods

Retrospective chart review of patients consecutively admitted to Santa Clara Valley Medical Center (SCVMC) between May 2013 and December 2014 for ventilator weaning with C1-5 AIS A or B SCI, < 3 months from injury and who had a tracheostomy in place. A non-linear, categorical principal component analysis (NL-PCA) was performed to test the multivariate interaction of respiratory outcomes from patients (N=36) being weaned off ventilator support after acute SCI with (N=15) or without (N=21) theophylline treatment.

Results

36 patients met inclusion criteria (2 C1, 5 C2, 11 C3, 14 C4, 4 C5). The NL-PCA returned 3 independent components that accounted for 95% of the variance in the dataset. Multivariate general linear models (GLM) hypothesis tests revealed a significant syndromic interaction between theophylline treatment and SCI level (Wilks’ Lambda, p=0.028, F(12,64)=2.116, η2=0.256, 1−β=0.838), with post-hoc testing demonstrating a significant interaction on PC1, explained by a positive correlation between improved forced vital capacity and time it took to reach 16 hours of ventilator free breathing. Thirty-three patients (92%) achieved 16 hours ventilator-free breathing (VFB), 30 (83%) achieved 24 hours VFB.

Conclusions

We suspect that some portion of the high success rate of ventilator weaning may be attributable to theophylline use in higher cervical SCI; in addition to our aggressive regimen of high volume ventilation, medication optimization, and pulmonary toilet (positive pressure treatments and mechanical insufflation-exsufflation).

A data-driven approach for evaluating multi-modal therapy in traumatic brain injury

Combination therapies targeting multiple recovery mechanisms have the potential for additive or synergistic effects, but experimental design and analyses of multimodal therapeutic trials are challenging. To address this problem, we developed a data-driven approach to integrate and analyze raw source data from separate pre-clinical studies and evaluated interactions between four treatments following traumatic brain injury. Histologic and behavioral outcomes were measured in 202 rats treated with combinations of an anti-inflammatory agent (minocycline), a neurotrophic agent (LM11A-31), and physical therapy consisting of assisted exercise with or without botulinum toxin-induced limb constraint. Data was curated and analyzed in a linked workflow involving non-linear principal component analysis followed by hypothesis testing with a linear mixed model. Results revealed significant benefits of the neurotrophic agent LM11A-31 on learning and memory outcomes after traumatic brain injury. In addition, modulations of LM11A-31 effects by co-administration of minocycline and by the type of physical therapy applied reached statistical significance. These results suggest a combinatorial effect of drug and physical therapy interventions that was not evident by univariate analysis. The study designs and analytic techniques applied here form a structured, unbiased, internally validated workflow that may be applied to other combinatorial studies, both in animals and humans.

What Is Being Trained? How Divergent Forms of Plasticity Compete To Shape Locomotor Recovery after Spinal Cord Injury

Spinal cord injury (SCI) is a devastating syndrome that produces dysfunction in motor and sensory systems, manifesting as chronic paralysis, sensory changes, and pain disorders. The multi-faceted and heterogeneous nature of SCI has made effective rehabilitative strategies challenging. Work over the last 40 years has aimed to overcome these obstacles by harnessing the intrinsic plasticity of the spinal cord to improve functional locomotor recovery. Intensive training after SCI facilitates lower extremity function and has shown promise as a tool for retraining the spinal cord by engaging innate locomotor circuitry in the lumbar cord. As new training paradigms evolve, the importance of appropriate afferent input has emerged as a requirement for adaptive plasticity. The integration of kinematic, sensory, and loading force information must be closely monitored and carefully manipulated to optimize training outcomes. Inappropriate peripheral input may produce lasting maladaptive sensory and motor effects, such as central pain and spasticity. Thus, it is important to closely consider the type of afferent input the injured spinal cord receives. Here we review preclinical and clinical input parameters fostering adaptive plasticity, as well as those producing maladaptive plasticity that may undermine neurorehabilitative efforts. We differentiate between passive (hindlimb unloading [HU], limb immobilization) and active (peripheral nociception) forms of aberrant input. Furthermore, we discuss the timing of initiating exposure to afferent input after SCI for promoting functional locomotor recovery. We conclude by presenting a candidate rapid synaptic mechanism for maladaptive plasticity after SCI, offering a pharmacological target for restoring the capacity for adaptive spinal plasticity in real time.

The African clawed frog Xenopus laevis: A model organism to study regeneration of the central nervous system

While an injury to the central nervous system (CNS) in humans and mammals is irreversible, amphibians and teleost fish have the capacity to fully regenerate after severe injury to the CNS. Xenopus laevis has a high potential to regenerate the brain and spinal cord during larval stages (47-54), and loses this capacity during metamorphosis. The optic nerve has the capacity to regenerate throughout the frog's lifespan. Here, we review CNS regeneration in frogs, with a focus in X. laevis, but also provide some information about X. tropicalis and other frogs. We start with an overview of the anatomy of the Xenopus CNS, including the main supraspinal tracts that emerge from the brain stem, which play a key role in motor control and are highly conserved across vertebrates. We follow with the advantages of using Xenopus, a classical laboratory model organism, with increasing availability of genetic tools like transgenesis and genome editing, and genomic sequences for both X. laevis and X. tropicalis. Most importantly, Xenopus provides the possibility to perform intra-species comparative experiments between regenerative and non-regenerative stages that allow the identification of which factors are permissive for neural regeneration, and/or which are inhibitory. We aim to provide sufficient evidence supporting how useful Xenopus can be to obtain insights into our understanding of CNS regeneration, which, complemented with studies in mammalian vertebrate model systems, can provide a collaborative road towards finding novel therapeutic approaches for injuries to the CNS.

Leveraging biomedical informatics for assessing plasticity and repair in primate spinal cord injury

Recent preclinical advances highlight the therapeutic potential of treatments aimed at boosting regeneration and plasticity of spinal circuitry damaged by spinal cord injury (SCI). With several promising candidates being considered for translation into clinical trials, the SCI community has called for a non-human primate model as a crucial validation step to test efficacy and validity of these therapies prior to human testing. The present paper reviews the previous and ongoing efforts of the California Spinal Cord Consortium (CSCC), a multidisciplinary team of experts from 5 University of California medical and research centers, to develop this crucial translational SCI model. We focus on the growing volumes of high resolution data collected by the CSCC, and our efforts to develop a biomedical informatics framework aimed at leveraging multidimensional data to monitor plasticity and repair targeting recovery of hand and arm function. Although the main focus of many researchers is the restoration of voluntary motor control, we also describe our ongoing efforts to add assessments of sensory function, including pain, vital signs during surgery, and recovery of bladder and bowel function. By pooling our multidimensional data resources and building a unified database infrastructure for this clinically relevant translational model of SCI, we are now in a unique position to test promising therapeutic strategies' efficacy on the entire syndrome of SCI. We review analyses highlighting the intersection between motor, sensory, autonomic and pathological contributions to the overall restoration of function. This article is part of a Special Issue entitled SI: Spinal cord injury.

Development of a database for translational spinal cord injury research

Efforts to understand spinal cord injury (SCI) and other complex neurotrauma disorders at the pre-clinical level have shown progress in recent years. However, successful translation of basic research into clinical practice has been slow, partly because of the large, heterogeneous data sets involved. In this sense, translational neurological research represents a "big data" problem. In an effort to expedite translation of pre-clinical knowledge into standards of patient care for SCI, we describe the development of a novel database for translational neurotrauma research known as Visualized Syndromic Information and Outcomes for Neurotrauma-SCI (VISION-SCI). We present demographics, descriptive statistics, and translational syndromic outcomes derived from our ongoing efforts to build a multi-center, multi-species pre-clinical database for SCI models. We leveraged archived surgical records, postoperative care logs, behavioral outcome measures, and histopathology from approximately 3000 mice, rats, and monkeys from pre-clinical SCI studies published between 1993 and 2013. The majority of animals in the database have measures collected for health monitoring, such as weight loss/gain, heart rate, blood pressure, postoperative monitoring of bladder function and drug/fluid administration, behavioral outcome measures of locomotion, and tissue sparing postmortem. Attempts to align these variables with currently accepted common data elements highlighted the need for more translational outcomes to be identified as clinical endpoints for therapeutic testing. Last, we use syndromic analysis to identify conserved biological mechanisms of recovery after cervical SCI between rats and monkeys that will allow for more-efficient testing of therapeutics that will need to be translated toward future clinical trials.

Personalized neuroprosthetics

Decades of technological developments have populated the field of neuroprosthetics with myriad replacement strategies, neuromodulation therapies, and rehabilitation procedures to improve the quality of life for individuals with neuromotor disorders. Despite the few but impressive clinical successes, and multiple breakthroughs in animal models, neuroprosthetic technologies remain mainly confined to sophisticated laboratory environments. We summarize the core principles and latest achievements in neuroprosthetics, but also address the challenges that lie along the path toward clinical fruition. We propose a pragmatic framework to personalize neurotechnologies and rehabilitation for patient-specific impairments to achieve the timely dissemination of neuroprosthetic medicine.

The Irvine, Beatties, and Bresnahan (IBB) Forelimb Recovery Scale: An Assessment of Reliability and Validity

The IBB scale is a recently developed forelimb scale for the assessment of fine control of the forelimb and digits after cervical spinal cord injury [SCI; (1)]. The present paper describes the assessment of inter-rater reliability and face, concurrent and construct validity of this scale following SCI. It demonstrates that the IBB is a reliable and valid scale that is sensitive to severity of SCI and to recovery over time. In addition, the IBB correlates with other outcome measures and is highly predictive of biological measures of tissue pathology. Multivariate analysis using principal component analysis (PCA) demonstrates that the IBB is highly predictive of the syndromic outcome after SCI (2), and is among the best predictors of bio-behavioral function, based on strong construct validity. Altogether, the data suggest that the IBB, especially in concert with other measures, is a reliable and valid tool for assessing neurological deficits in fine motor control of the distal forelimb, and represents a powerful addition to multivariate outcome batteries aimed at documenting recovery of function after cervical SCI in rats.

Undirected compensatory plasticity contributes to neuronal dysfunction after severe spinal cord injury

Severe spinal cord injury in humans leads to a progressive neuronal dysfunction in the chronic stage of the injury. This dysfunction is characterized by premature exhaustion of muscle activity during assisted locomotion, which is associated with the emergence of abnormal reflex responses. Here, we hypothesize that undirected compensatory plasticity within neural systems caudal to a severe spinal cord injury contributes to the development of neuronal dysfunction in the chronic stage of the injury. We evaluated alterations in functional, electrophysiological and neuromorphological properties of lumbosacral circuitries in adult rats with a staggered thoracic hemisection injury. In the chronic stage of the injury, rats exhibited significant neuronal dysfunction, which was characterized by co-activation of antagonistic muscles, exhaustion of locomotor muscle activity, and deterioration of electrochemically-enabled gait patterns. As observed in humans, neuronal dysfunction was associated with the emergence of abnormal, long-latency reflex responses in leg muscles. Analyses of circuit, fibre and synapse density in segments caudal to the spinal cord injury revealed an extensive, lamina-specific remodelling of neuronal networks in response to the interruption of supraspinal input. These plastic changes restored a near-normal level of synaptic input within denervated spinal segments in the chronic stage of injury. Syndromic analysis uncovered significant correlations between the development of neuronal dysfunction, emergence of abnormal reflexes, and anatomical remodelling of lumbosacral circuitries. Together, these results suggest that spinal neurons deprived of supraspinal input strive to re-establish their synaptic environment. However, this undirected compensatory plasticity forms aberrant neuronal circuits, which may engage inappropriate combinations of sensorimotor networks during gait execution.

Derivation of multivariate syndromic outcome metrics for consistent testing across multiple models of cervical spinal cord injury in rats

Spinal cord injury (SCI) and other neurological disorders involve complex biological and functional changes. Well-characterized preclinical models provide a powerful tool for understanding mechanisms of disease; however managing information produced by experimental models represents a significant challenge for translating findings across research projects and presents a substantial hurdle for translation of novel therapies to humans. In the present work we demonstrate a novel ‘syndromic’ information-processing approach for capitalizing on heterogeneous data from diverse preclinical models of SCI to discover translational outcomes for therapeutic testing. We first built a large, detailed repository of preclinical outcome data from 10 years of basic research on cervical SCI in rats, and then applied multivariate pattern detection techniques to extract features that are conserved across different injury models. We then applied this translational knowledge to derive a data-driven multivariate metric that provides a common ‘ruler’ for comparisons of outcomes across different types of injury (NYU/MASCIS weight drop injuries, Infinite Horizons (IH) injuries, and hemisection injuries). The findings revealed that each individual endpoint provides a different view of the SCI syndrome, and that considering any single outcome measure in isolation provides a misleading, incomplete view of the SCI syndrome. This limitation was overcome by taking a novel multivariate integrative approach for leveraging complex data from preclinical models of neurological disease to identify therapies that target multiple outcomes. We suggest that applying this syndromic approach provides a roadmap for translating therapies for SCI and other complex neurological diseases.