Proteomic changes in traumatic brain injury: experimental approaches

Acute-Phase Neurofilament Light and Glial Fibrillary Acidic Proteins in Cerebrospinal Fluid Predict Long-Term Outcome After Severe Traumatic Brain Injury

BACKGROUND

This study investigated trajectory profiles and the association of concentrations of the biomarkers neurofilament light (NfL) and glial fibrillary acidic protein (GFAP) in ventricular cerebrospinal fluid (CSF) with clinical outcome at 1 year and 10-15 years after a severe traumatic brain injury (sTBI).

METHODS

This study included patients with sTBI at the Neurointensive Care Unit at Sahlgrenska University Hospital, Gothenburg, Sweden. The injury was regarded as severe if patients had a Glasgow Coma Scale ≤ 8 corresponding to Reaction Level Scale ≥ 4. CSF was collected from a ventricular catheter during a 2-week period. Concentrations of NfL and GFAP in CSF were analyzed with enzyme-linked immunosorbent assay. The Glasgow Outcome Scale (GOS) was used to assess the 1-year and 10-15-year outcomes. After adjustment for age and previous neurological diseases, logistic regression was performed for the outcomes GOS 1 (dead) or GOS 2-5 (alive) and GOS 1-3 (poor) or GOS 4-5 (good) versus the independent continuous variables (NfL and GFAP).

RESULTS

Fifty-three patients with sTBI were investigated; forty-seven adults are presented in the article, and six children (aged 7-18 years) are described in Supplement 1. The CSF concentrations of NfL gradually increased over 2 weeks post trauma, whereas GFAP concentrations peaked on days 3-4. Increasing NfL and GFAP CSF concentrations increased the odds of GOS 1-3 outcome 1 year after trauma (odds ratio [OR] 1.73, 95% confidence interval [CI] 1.07-2.80, p = 0.025; and OR 1.61, 95% CI 1.09-2.37, p = 0.016, respectively). Similarly, increasing CSF concentrations of NfL and GFAP increased the odds for GOS 1-3 outcome 10-15 years after trauma (OR 2.04, 95% CI 1.05-3.96, p = 0.035; and OR 1.60, 95% CI 1.02-2.00, p = 0.040).

CONCLUSIONS

This study shows that initial high concentrations of NfL and GFAP in CSF are both associated with higher odds for GOS 1-3 outcome 1 year and 10-15 years after an sTBI, implicating its potential usage as a prognostic marker in the future.

Mapping dynamic molecular changes in hippocampal subregions after traumatic brain injury through spatial proteomics

BACKGROUND

Traumatic brain injury (TBI) often results in diverse molecular responses, challenging traditional proteomic studies that measure average changes at tissue levels and fail to capture the complexity and heterogeneity of the affected tissues. Spatial proteomics offers a solution by providing insights into sub-region-specific alterations within tissues. This study focuses on the hippocampal sub-regions, analyzing proteomic expression profiles in mice at the acute (1 day) and subacute (7 days) phases of post-TBI to understand subregion-specific vulnerabilities and long-term consequences.

METHODS

Three mice brains were collected from each group, including Sham, 1-day post-TBI and 7-day post-TBI. Hippocampal subregions were extracted using Laser Microdissection (LMD) and subsequently analyzed by label-free quantitative proteomics.

RESULTS

The spatial analysis reveals region-specific protein abundance changes, highlighting the elevation of FN1, LGALS3BP, HP, and MUG-1 in the stratum moleculare (SM), suggesting potential immune cell enrichment post-TBI. Notably, established markers of chronic traumatic encephalopathy, IGHM and B2M, exhibit specific upregulation in the dentate gyrus bottom (DG2) independent of direct mechanical injury. Metabolic pathway analysis identifies disturbances in glucose and lipid metabolism, coupled with activated cholesterol synthesis pathways enriched in SM at 7-Day post-TBI and subsequently in deeper DG1 and DG2 suggesting a role in neurogenesis and the onset of recovery. Coordinated activation of neuroglia and microtubule dynamics in DG2 suggest recovery mechanisms in less affected regions. Cluster analysis revealed spatial variations post-TBI, indicative of dysregulated neuronal plasticity and neurogenesis and further predisposition to neurological disorders. TBI-induced protein upregulation (MUG-1, PZP, GFAP, TJP, STAT-1, and CD44) across hippocampal sub-regions indicates shared molecular responses and links to neurological disorders. Spatial variations were demonstrated by proteins dysregulated in both or either of the time-points exclusively in each subregion (ELAVL2, CLIC1 in PL, CD44 and MUG-1 in SM, and SHOC2, LGALS3 in DG).

CONCLUSIONS

Utilizing advanced spatial proteomics techniques, the study unveils the dynamic molecular responses in distinct hippocampal subregions post-TBI. It uncovers region-specific vulnerabilities and dysregulated neuronal processes, and potential recovery-related pathways that contribute to our understanding of TBI's neurological consequences and provides valuable insights for biomarker discovery and therapeutic targets.

Gut dysbiosis and neurological modalities: An engineering approach via proteomic analysis of gut-brain axis

The human gut microbiota is a complex and dynamic community of microorganisms, that influence metabolic, neurodevelopmental, and immune pathways. Microbial dysbiosis, characterized by changes in microbial diversity and relative abundances, is implicated in the development of various chronic neurological and neurodegenerative disorders. These disorders are marked by the accumulation of pathological protein aggregates, leading to the progressive loss of neurons and behavioural functions. Dysregulations in protein-protein interaction networks and signalling complexes, critical for normal brain function, are common in neurological disorders but challenging to unravel, particularly at the neuron and synapse-specific levels. To advance therapeutic strategies, a deeper understanding of neuropathogenesis, especially during the progressive disease phase, is needed. Biomarkers play a crucial role in identifying disease pathophysiology and monitoring disease progression. Proteomics, a powerful technology, shows promise in accelerating biomarker discovery and aiding in the development of novel treatments. In this chapter, we provide an in-depth overview of how proteomic techniques, utilizing various biofluid samples from patients with neurological conditions and diverse animal models, have contributed valuable insights into the pathogenesis of numerous neurological disorders. We also discuss the current state of research, potential challenges, and future directions in proteomic approaches to unravel neuro-pathological conditions.

Quantitative proteomic and phosphoproteomic analyses of the hippocampus reveal the involvement of NMDAR1 signaling in repetitive mild traumatic brain injury

The cumulative damage caused by repetitive mild traumatic brain injury can cause long-term neurodegeneration leading to cognitive impairment. This cognitive impairment is thought to result specifically from damage to the hippocampus. In this study, we detected cognitive impairment in mice 6 weeks after repetitive mild traumatic brain injury using the novel object recognition test and the Morris water maze test. Immunofluorescence staining showed that p-tau expression was increased in the hippocampus after repetitive mild traumatic brain injury. Golgi staining showed a significant decrease in the total density of neuronal dendritic spines in the hippocampus, as well as in the density of mature dendritic spines. To investigate the specific molecular mechanisms underlying cognitive impairment due to hippocampal damage, we performed proteomic and phosphoproteomic analyses of the hippocampus with and without repetitive mild traumatic brain injury. The differentially expressed proteins were mainly enriched in inflammation, immunity, and coagulation, suggesting that non-neuronal cells are involved in the pathological changes that occur in the hippocampus in the chronic stage after repetitive mild traumatic brain injury. In contrast, differentially expressed phosphorylated proteins were mainly enriched in pathways related to neuronal function and structure, which is more consistent with neurodegeneration. We identified N-methyl-D-aspartate receptor 1 as a hub molecule involved in the response to repetitive mild traumatic brain injury , and western blotting showed that, while N-methyl-D-aspartate receptor 1 expression was not altered in the hippocampus after repetitive mild traumatic brain injury, its phosphorylation level was significantly increased, which is consistent with the omics results. Administration of GRP78608, an N-methyl-D-aspartate receptor 1 antagonist, to the hippocampus markedly improved repetitive mild traumatic brain injury-induced cognitive impairment. In conclusion, our findings suggest that N-methyl-D-aspartate receptor 1 signaling in the hippocampus is involved in cognitive impairment in the chronic stage after repetitive mild traumatic brain injury and may be a potential target for intervention and treatment.

Neuroanatomical zones of human traumatic brain injury reveal significant differences in protein profile and protein oxidation: Implications for secondary injury events

Traumatic brain injury (TBI) causes significant neurological deficits and long-term degenerative changes. Primary injury in TBI entails distinct neuroanatomical zones, i.e., contusion (Ct) and pericontusion (PC). Their dynamic expansion could contribute to unpredictable neurological deterioration in patients. Molecular characterization of these zones compared with away from contusion (AC) zone is invaluable for TBI management. Using proteomics-based approach, we were able to distinguish Ct, PC and AC zones in human TBI brains. Ct was associated with structural changes (blood-brain barrier (BBB) disruption, neuroinflammation, axonal injury, demyelination and ferroptosis), while PC was associated with initial events of secondary injury (glutamate excitotoxicity, glial activation, accumulation of cytoskeleton proteins, oxidative stress, endocytosis) and AC displayed mitochondrial dysfunction that could contribute to secondary injury events and trigger long-term degenerative changes. Phosphoproteome analysis in these zones revealed that certain differentially phosphorylated proteins synergistically contribute to the injury events along with the differentially expressed proteins. Non-synaptic mitochondria (ns-mito) was associated with relatively more differentially expressed proteins (DEPs) compared to synaptosomes (Syn), while the latter displayed increased protein oxidation including tryptophan (Trp) oxidation. Proteomic analysis of immunocaptured complex I (CI) from Syn revealed increased Trp oxidation in Ct > PC > AC (vs. control). Oxidized W272 in the ND1 subunit of CI, revealed local conformational changes in ND1 and the neighboring subunits, as indicated by molecular dynamics simulation (MDS). Taken together, neuroanatomical zones in TBI show distinct protein profile and protein oxidation representing different primary and secondary injury events with potential implications for TBI pathology and neurological status of the patients.

Traumatic brain injury recapitulates developmental changes of axons

During development, half of brain white matter axons are maintained for growth, while the remainder undergo developmental axon degeneration. After traumatic brain injury (TBI), injured axons also appear to follow pathways leading to either degeneration or repair. These observations raise the intriguing, but unexamined possibility that TBI recapitulates developmental axonal programs. Here, we examined axonal changes in the developing brain in young rats and after TBI in adult rat. Multiple shared changes in axonal microtubule (MT) through tubulin post-translational modifications and MT associated proteins (MAPs), tau and MAP6, were found in both development and TBI. Specifically, degenerating axons in both development and TBI underwent phosphorylation of tau and excessive tubulin tyrosination, suggesting MT instability and depolyermization. Conversely, nearby axons without degenerating morphologies, had increased MAP6 expression and maintenance of tubulin acetylation, suggesting enhanced MT stabilization, thereby supporting survival or repair. Quantitative proteomics revealed similar signaling pathways of axon degeneration and growth/repair, including protein clusters and networks. This comparison approach demonstrates how focused evaluation of developmental processes may provide insight into pathways initiated by TBI. In particular, the data suggest that TBI may reawaken dormant axonal programs that direct axons towards either degeneration or growth/repair, supporting further study in this area.

Subacute and chronic proteomic and phosphoproteomic analyses of a mouse model of traumatic brain injury at two timepoints and comparison with chronic traumatic encephalopathy in human samples

Repetitive mild traumatic brain injury (r-mTBI) is the most widespread type of brain trauma worldwide. The cumulative injury effect triggers long-lasting pathological and molecular changes that may increase risk of chronic neurodegenerative diseases. R-mTBI is also characterized by changes in the brain proteome, where the majority of molecules altered early post-TBI are different from those altered at more chronic phases. This differentiation may contribute to the heterogeneity of available data on potential therapeutic targets and may present an obstacle in developing effective treatments. Here, we aimed to characterize a proteome profile of r-mTBI in a mouse model at two time points – 3 and 24 weeks post last TBI, as this may be a more relevant therapeutic window for individuals suffering negative consequences of r-mTBI. We identified a great number of proteins and phosphoproteins that remain continuously dysregulated from 3 to 24 weeks. These proteins may serve as effective therapeutic targets for sub-acute and chronic stages of post r-mTBI. We also compared canonical pathway activation associated with either total proteins or phosphoproteins and revealed that they both are upregulated at 24 weeks. However, at 3 weeks post-TBI, only pathways associated with total proteins are upregulated, while pathways driven by phosphoproteins are downregulated. Finally, to assess the translatability of our data, we compared proteomic changes in our mouse model with those reported in autopsied human samples of Chronic Traumatic Encephalopathy (CTE) patients compared to controls. We observed 39 common proteins that were upregulated in both species and 24 common pathways associated with these proteins. These findings support the translational relevance of our mouse model of r-mTBI for successful identification and translation of therapeutic targets.

Pro-resolving lipid mediators in traumatic brain injury: emerging concepts and translational approach

Despite the high mortality and disability associated with traumatic brain injury (TBI), effective pharmacologic treatments are lacking. Of emerging interest, bioactive lipids, including specialized pro-resolving lipid mediators of inflammation (SPMs), act to attenuate inflammation after injury resolution. The SPM lipidome may serve as a biomarker of disease and predictor of clinical outcomes, and the use of exogenous SPM administration represents a novel therapeutic strategy for TBI. This review article provides a comprehensive discussion of the current pre-clinical and clinical literature supporting the importance of bioactive lipids, including SPMs, in TBI recovery. We additionally propose a translational approach to answer important clinical and scientific questions to advance the study of bioactive lipids and SPMs towards clinical research. Given the morbidity and mortality associated with TBI with limited treatment options, novel approaches are needed.

Experimental model for the study of traumatic brain injury

Traumatic brain injury (TBI) represents a public healthcare problem and a major economic burden, all over the world. It is estimated that every year, on the globe, there occur about two million severe TBI and over 42 million mild TBI. The main causes of TBI in civil population are fallings, followed by car accidents. In the last decades, the accelerated development of car industry and the poor development of traffic infrastructure in low- and average-income countries led to an increasing number of brain injuries, this becoming a major problem for medical health systems. According to some studies, approximately 1.35 million people die every year because of car accidents. In the last four decades, these types of injuries started to be studied in order to understand the lesion mechanisms for developing new safety equipment that may be installed on vehicles. The device presented by us for causing a TBI in a lab rat (mechanical pendulum) allows the performance of several major types of TBI, according to the kinetic energy, exposure area, contact surface, etc. The impact energies obtained by the device we presented may vary on a large scale, from less than 1 J up to 10 J, according to its weight, launching angle and impact head shape, thus being obtained minor, moderate or severe TBI.

Lessons learned from proteome analysis of perinatal neurovascular pathologies

INTRODUCTION

Perinatal and pediatric diseases related to neurovascular disorders cause significant problems during life, affecting a population with a long life expectancy. Early diagnosis and assessment of the severity of these diseases are crucial to establish an appropriate neuroprotective treatment. Currently, physical examination, neuroimaging and clinical judgment are the main tools for diagnosis, although these tests have certain limitations. There is growing interest in the potential value of noninvasive biomarkers that can be used to monitor child patients at risk of brain damage, allowing accurate, and reproducible measurements.

AREAS COVERED

This review describes potential biomarkers for the diagnosis of perinatal neurovascular diseases and discusses the possibilities they open for the classification and treatment of neonatal neurovascular diseases.

EXPERT OPINION

Although high rates of ischemic and hemorrhagic stroke exist in pediatric populations, most studies have focused on biomarkers of hypoxic-ischemic encephalopathy. Inflammatory and neuronal biomarkers such as S-100B and GFAP, in combination with others yet to be discovered, could be considered as part of multiplex panels to diagnose these diseases and potentially for monitoring response to treatments. Ideally, noninvasive biofluids would be the best source for evaluating these biomarkers in proteomic assays in perinatal patients.

TMT-based proteomics analysis reveals the protective effects of Xuefu Zhuyu decoction in a rat model of traumatic brain injury

ETHNOPHARMACOLOGICAL RELEVANCE

Xuefu Zhuyu decoction (XFZYD) is a traditional Chinese herbal prescription. It is effective in treating traumatic brain injury (TBI). However, the underlying molecular mechanisms remain unclear.

AIM OF THE STUDY

This study aimed to reveal the possible mechanisms of XFZYD in treating acute TBI through proteomics clues.

MATERIALS AND METHODS

Controlled Cortical Impact (CCI) rats were given gavage administration of XFZYD (9 g/kg/d) or distilled water (equal volume) for three days. The Modified Neurological Severity Score (mNSS), brain water content, HE staining, Nissl staining and immunohistochemistry were performed to assess the effects of XFZYD for TBI treatment. Additionally, tandem mass tag-based (TMT) quantitative proteomics technology was applied to detect proteins of brain cortex. Bioinformatics analysis including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and Protein-protein interaction (PPI) networks were used to analyze differentially expressed proteins (DEPs). Bioinformatics Analysis Tool for Molecular mechanism of TCM (BATMAN-TCM) was conducted to anchor diseases and pathways. Besides, western blotting and immunofluorescence were exerted to verify related proteins.

RESULTS

XFZYD improved neurologic functions, reduced encephaledema and ameliorated cell morphology around the injured area in CCI rats. A total of 6099 proteins were identified with false discovery rate (FDR) < 1%. Overlapping DEPs (105 DEPs) were identified (295 DEPs and 804 DEPs in CCI/Sham or XFZYD/CCI group, respectively). Of these DEPs, 17 were regulated by XFZYD. Bioinformatics analysis showed that the 17 DEPs were predominantly related to platelet activation and PI3K-Akt signaling pathway. Next, PLG and CD34 were verified with molecular biotechnology.

CONCLUSIONS

XFZYD exerts therapeutic effects through multi-pathways regulation in the treatment of TBI. This work may provide proteomics clues for the continuation of research on TBI treatment with XFZYD.

The 'Omics' of Epigenetic Modulation by Valproic Acid Treatment in Traumatic Brain Injury-What We Know and What the Future Holds

Traumatic brain injury (TBI) is a heterogeneous injury that is a major cause of morbidity and mortality worldwide. Epigenetic modulation through the alteration of cellular acetylation by valproic acid (VPA) administration has shown promise as a novel pharmacological treatment for TBI. It improves clinical outcomes through multiple mechanisms, many of which are still poorly understood. In recent years, omics technologies have emerged as a promising strategy to detect molecular changes at the cellular level. This review highlights the use of these high throughput technologies in advancing the understanding of epigenetic modulation by VPA in TBI. It also describes the future role of omics techniques in developing a point of care test to guide patient selection for VPA administration.