A Combined Proteomics and Bioinformatics Approach Reveals Novel Signaling Pathways and Molecular Targets After Intracerebral Hemorrhage

Integrative transcriptomic and network pharmacology analysis reveals the neuroprotective role of BYHWD through enhancing autophagy by inhibiting Ctsb in intracerebral hemorrhage mice

BACKGROUND

In this study, we aimed to combine transcriptomic and network pharmacology to explore the crucial mRNAs and specific regulatory molecules of Buyang Huanwu Decoction (BYHWD) in intracerebral hemorrhage (ICH) treatment.

METHODS

C57BL/6 mice were randomly divided into three groups: sham, ICH, and BYHWD. BYHWD (43.29 g/kg) was administered once a day for 7 days. An equal volume of double-distilled water was used as a control. Behavioural and histopathological experiments were conducted to confirm the neuroprotective effects of BYHWD. Brain tissues were collected for transcriptomic detection. Bioinformatics analysis were performed to illustrate the target gene functions. Network pharmacology was used to predict potential targets for BYHWD. Next, transcriptomic assays were combined with network pharmacology to identify the potential differentially expressed mRNAs. Immunofluorescence staining, real-time polymerase chain reaction, western blotting, and transmission electron microscopy were performed to elucidate the underlying mechanisms.

RESULTS

BYHWD intervention in ICH reduced neurological deficits. Network pharmacology analysis identified 203 potential therapeutic targets for ICH, whereas transcriptomic assay revealed 109 differentially expressed mRNAs post-ICH. Among these, cathepsin B, ATP binding cassette subfamily B member 1, toll-like receptor 4, chemokine (C-C motif) ligand 12, and baculoviral IAP repeat-containing 5 were identified as potential target mRNAs through the integration of transcriptomics and network pharmacology approaches. Bioinformatics analysis suggested that the beneficial effects of BYHWD in ICH may be associated with apoptosis, animal autophagy signal pathways, and PI3K-Akt and mTOR biological processes. Furthermore, BYHWD intervention decreased Ctsb expression levels and increased autophagy levels in ICH.

CONCLUSIONS

Animal experiments in combination with bioinformatics analysis confirmed that BYHWD plays a neuroprotective role in ICH by regulating Ctsb to enhance autophagy.

Intracranial hemorrhage management in the multi-omics era

Intracranial hemorrhage (ICH) is a devastating disorder. Neuroprotective strategies that prevent tissue injury and improve functional outcomes have been identified in multiple animal models of ICH. However, these potential interventions in clinical trials produced generally disappointing results. With progress in omics, studies of omics data, including genomics, transcriptomics, epigenetics, proteomics, metabolomics, and the gut microbiome, may help promote precision medicine. In this review, we focused on introducing the applications of all omics in ICH and shed light on all of the considerable advantages to systematically analyze the necessity and importance of multiple omics technology in ICH.

Stroke Proteomics: From Discovery to Diagnostic and Therapeutic Applications

Stroke remains a leading cause of death and disability, with limited therapeutic options and suboptimal tools for diagnosis and prognosis. High throughput technologies such as proteomics generate large volumes of experimental data at once, thus providing an advanced opportunity to improve the status quo by facilitating identification of novel therapeutic targets and molecular biomarkers. Proteomics studies in animals are largely designed to decipher molecular pathways and targets altered in brain tissue after stroke, whereas studies in human patients primarily focus on biomarker discovery in biofluids and, more recently, in thrombi and extracellular vesicles. Here, we offer a comprehensive review of stroke proteomics studies conducted in both animal and human specimen and present our view on limitations, challenges, and future perspectives in the field. In addition, as a unique resource for the scientific community, we provide extensive lists of all proteins identified in proteomic studies as altered by stroke and perform postanalysis of animal data to reveal stroke-related cellular processes and pathways.

Succinylation profiles of brain injury after intracerebral hemorrhage

Protein posttranslational modifications (PTMs) regulate the biological processes of human diseases by genetic code expansion and cellular pathophysiology regulation; however, system-wide changes in PTM levels in the intracerebral hemorrhage (ICH) brain remain poorly understood. Succinylation refers to a major PTM during the regulation of multiple biological processes. In this study, according to the methods of quantitative succinyllysine proteomics based on high-resolution mass spectrometry, we investigated ICH-associated brain protein succinyllysine modifications and obtained 3,680 succinylated sites and quantified around 3,530 sites. Among them, 25 succinyllysine sites on 23 proteins were upregulated (hypersuccinylated), whereas 13 succinyllysine sites on 12 proteins were downregulated (hyposuccinylated) following ICH. The cell component enrichment analysis of these succinylproteins with significant changes showed that 58.3% of the hyposuccinylated proteins were observed in the mitochondria, while the hyper-succinylproteins located in mitochondria decreased in the percentage to about 35% in ICH brains with a concomitant increase in the percentage of cytoplasm to 30.4%. Further bioinformatic analysis showed that the succinylproteins were mostly mitochondria and synapse-related subcellular located and involved in many pathophysiological processes, like metabolism, synapse working, and ferroptosis. Moreover, the integrative analysis of our succinylproteomics data and previously published transcriptome data showed that the mRNAs matched by most differentially succinylated proteins were especially highly expressed in neurons, endothelial cells, and astrocytes. Our study uncovers some succinylation-affected processes and pathways in response to ICH brains and gives us novel insights into understanding pathophysiological processes of brain injury caused by ICH.

Temporal metabolomic alteration in rat brains of experimental intracerebral hemorrhage

BACKGROUND

Intracerebral hemorrhage (ICH) is the top lethal and disabling form of stroke. The pathophysiology of ICH is not fully understood yet. Metabolites are indicators and regulators of cellular processes. However, the overall brain metabolic pattern and the temporal alterations after ICH remain unknown.

METHODS

A total of 40 male rats were randomly assigned to sham group and ICH group. ICH was induced by collagenase Ⅶ. Body weight was assessed. Neurological deficits were evaluated by modified neurological severity score. Then, the perihematomal brain tissues were collected for metabolites detection using high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS). The metabolic profiles were displayed by principal component analysis (PCA), partial least-squares-discriminant analysis (PLS-DA) and cluster analysis. The significant differential metabolites were screened by fold change > 2.0, the false discovery rate (FDR) < 0.05 and Variable Importance of Projection (VIP) > 1. Next, the relevant metabolic pathways were discerned by MetaboAnalyst website. A metabolite-protein interaction network was subsequentially constructed to further annotate the function of differential metabolites.

RESULTS

Rats suffered from compromised body weight increasement and impaired neurological function. The metabolomics profiles of brain tissues in the post-ICH rats were markedly different from those in the sham group on days 3 and 14. Thirty-four metabolites (bilirubin, uric acid, 6-Methylnicotinamide et al.) were abnormally upregulated in the acute stage, while 27 metabolites were disturbed in the recovery stage, including bilirubin, uric acid, and histamine et al. Seven and three metabolic pathways altered in the acute and recovery stage, respectively. Metabolite-protein interaction analysis revealed that the disturbed metabolites may participate in ICH pathophysiology by altering amino acid metabolism, peroxisome proliferators-activated receptor signaling pathway, fatty acid metabolism and urea cycle in the acute stage, while influencing amino acid metabolism, urea cycle and peroxisome in the recovery stage.

CONCLUSIONS

Our study mapped the pathological metabolomics profiles of the post-ICH rat brains in the acute and recovery phases. This work will assist in discovering novel therapeutic targets and treatments for ICH.

Entinostat improves acute neurological outcomes and attenuates hematoma volume after Intracerebral Hemorrhage

Intracerebral hemorrhage (ICH) or hemorrhagic stroke is a major public health problem with no effective treatment. Given the emerging role of epigenetic mechanisms in the pathophysiology of ICH, we tested the hypothesis that a class 1 histone deacetylase inhibitor (HDACi), Entinostat, attenuates neurodegeneration and improves neurobehavioral outcomes after ICH. To address this, we employed a preclinical mouse model of ICH and Entinostat was administered intraperitoneally one-hour post induction of ICH. Entinostat treatment significantly reduced the number of degenerating neurons and TUNEL-positive cells after ICH in comparison to vehicle-treated controls. Moreover, Entinostat treatment significantly reduced hematoma volume, T2-weighted hemorrhagic lesion volume and improved acute neurological outcomes after ICH. Further, Entinostat significantly reduced the hemin-induced release of proinflammatory cytokines in vitro. Consistently, the expression of proinflammatory microglial/macrophage marker, CD16/32, was remarkably reduced in Entinostat treated group after ICH in comparison to control. Altogether, data implicates the potential of class 1 HDACi, Entinostat, in improving acute neurological function after ICH warranting further investigation.

Sex-Specific Differences in Extracellular Vesicle Protein Cargo in Synovial Fluid of Patients with Osteoarthritis

Women are at a significantly higher risk of developing osteoarthritis (OA) compared to males. The pathogenesis of osteoarthritis (OA) in women is poorly understood. Extracellular vesicles (EVs) have been shown to play an essential role in numerous signaling processes during the pathogenesis of age-related diseases via paracrine signaling. Molecular profiling of the synovial fluid-derived EVs cargo in women may help in the discovery of novel biomarkers and therapeutics for the treatment of OA in women. Previously, we reported that synovial fluid-derived EV miRNA cargo differs in a sex-specific manner. This study aims to characterize synovial fluid-derived EV protein cargo in OA patients. Our data showed sex-specific EVs protein content in OA. We found haptoglobin, orosomucoid, and ceruloplasmin significantly up-regulated, whereas apolipoprotein down-regulated in female OA EVs. In males, we discovered β-2-glycoprotein, and complement component 5 proteins significantly up-regulated and Spt-Ada-Gcn5 acetyltransferase (SAGA)-associated factor 29 down-regulated in male OA EVs. Database for Annotation, Visualization, and Integrated Discovery (DAVID) and QuickGO analysis revealed OA-specific protein involvement in several biological, molecular, and cellular pathways, specifically in inflammatory processes. In conclusion, synovial fluid EV protein content is altered in a sex-specific manner with OA, explaining the increased prevalence and severity of OA in women.