Classification of Glioblastoma Associated with Immune Checkpoints and Tumor Microenvironment based on Immunogenomic Profiling.

BACKGROUND: Immune microenvironment is involved in tumor initiation and progression, and its effect on glioblastoma (GBM) is still unknown. OBJECT: We sought to investigate the association between immune status and GBM. METHODS: Transcriptome data and the relevant clinical data were downloaded from The Cancer Genome Atlas and Gene Expression Omnibus (GEO) databases, and we identified two immune subtypes based on 29 immune-associated gene sets. RESULTS: Through single-sample gene set enrichment analysis (ssGSEA), we found that the high-immunity subtype had the most tumor-infiltrating immune cells and immune checkpoint molecules in GBM patients. Furthermore, we could more effectively identify immune signature pathways in GBM. CONCLUSION: After validation with the GEO dataset, we conclude that the identified GBM high-immune subtypes may be amenable to the application of novel immune therapy for GBM.

Integrated analysis of single cell-RNA sequencing and Mendelian randomization identifies lactate dehydrogenase B as a target of melatonin in ischemic stroke.

AIMS: Despite the success of single-cell RNA sequencing in identifying cellular heterogeneity in ischemic stroke, clarifying the mechanisms underlying these associations of differently expressed genes remains challenging. Several studies that integrate gene expression and gene expression quantitative trait loci (eQTLs) with genome wide-association study (GWAS) data to determine their causal role have been proposed. METHODS: Here, we combined Mendelian randomization (MR) framework and single cell (sc) RNA sequencing to study how differently expressed genes (DEGs) mediating the effect of gene expression on ischemic stroke. The hub gene was further validated in the in vitro model. RESULTS: We identified 2339 DEGs in 10 cell clusters. Among these DEGs, 58 genes were associated with the risk of ischemic stroke. After external validation with eQTL dataset, lactate dehydrogenase B (LDHB) is identified to be positively associated with ischemic stroke. The expression of LDHB has also been validated in sc RNA-seq with dominant expression in microglia and astrocytes, and melatonin is able to reduce the LDHB expression and activity in vitro ischemic models. CONCLUSION: Our study identifies LDHB as a novel biomarker for ischemic stroke via combining the sc RNA-seq and MR analysis.

A novel classifier combining G protein-coupled receptors and the tumor microenvironment is associated with survival status in glioblastoma.

Background: Numerous studies have highlighted the crucial role of G protein-coupled receptors (GPCRs) in tumor microenvironment (TME) remodeling and their correlation with tumor progression. However, the association between GPCRs and the TME in glioblastoma (GBM) remains largely unexplored. Methods: In this study, we investigated the expression profile of GPCRs in GBM using integrated data from single-cell RNA sequencing and bulk sequencing. Surgical samples obtained from meningioma and GBM patients underwent single-cell RNA sequencing to examine GPCR levels and cell-cell interactions. Tumor microenvironment (TME) score is calculated by the infiltrated immune cells with CIBERSORT. Results: Our findings revealed a predominantly increased expression of GPCRs in GBM, and demonstrated that the classification of GPCRs and TME is an independent risk factor in GBM. Patients with high GPCR expression in the tumor tissue and low TME score exhibited the worst outcomes, suggesting a potentially aggressive tumor phenotype. On the other hand, patients with low GPCR expression in the tumor tissue and high TME score showed significantly better outcomes, indicating a potentially more favorable tumor microenvironment. Furthermore, the study found that T cells with high GPCR levels displayed extensive cell-cell connections with other tumor and immune cells in the single cell RNA analysis, indicating their potential involvement in immune escape. Conclusion: In conclusion, GPCRs in combination with TME classification can serve as prognostic markers for GBM. GPCRs play an essential role in tumor progression and the TME in GBM.

Integrated spatial transcriptome and metabolism study reveals metabolic heterogeneity in human injured brain.

Single-cell transcriptomics can provide quantitative molecular signatures for large, unbiased samples of the diverse cell types in the brain. With the advances of multi-omics datasets, a major challenge is to validate and integrate results into a biological understanding of spatial organization and functional orientation. Here, we generate spatial transcriptomes and metabolites from six patients with brain trauma with surgical samples. The resulting spatial marker gene, which is highly replicable across analysis methods, sequencing technologies, and modalities, is a comprehensive molecular marker of the diverse metabolic changes in human injured brains. The atlas includes an area of lipid peroxidation that resembles injured neurons in the brain. We further discover imbalanced myo-inositol and myo-inositol phosphate and related spatial markers. Our results highlight the complex transcriptomic regulation and metabolic alterations in the injured brain and will directly enable the design of reagents to target specific genes in the human brain for functional analysis.

Single-Cell Sequencing Reveals Necroptosis-Related Prognostic Genes of Glioblastoma.

Background: Glioblastoma (GBM) is one of the most malignant forms of brain cancer, with the extremely lower survival rate. Necroptosis (NCPS) is also one of the most wide types of cell death, and its clinical importance in GBM is not clear. Methods: We first identified necroptotic genes in GBM by single-cell RNA sequencing analysis of our surgical samples and weighted coexpression network analysis (WGNCA) from TCGA GBM data. The cox regression model with least absolute shrinkage and selection operator (LASSO) was used to construct the risk model. Then, KM plot and reactive operation curve (ROC) analysis were used to assess the prediction ability of the model. At last, the infiltrated immune cells and gene mutation profiling were investigated between the high- and low-NCPS groups as well. Result: The risk model including ten necroptosis-related genes was identified as an independent risk factor for the outcome. In addition, we found that the risk model is correlated with the infiltrated immune cells and tumor mutation burden in GBM. NDUFB2 is identified to be a risk gene in GBM with bioinformatical analysis and in vitro experiment validation. Conclusion: This risk model of necroptosis-related genes might provide clinical evidence for GBM interventions.

Novel Immune-Related LncRNA Pairs are Associated with Immunol Infiltration and Survival Status in Glioblastoma.

Background: Immune-related lncRNA is involved in tumor initiation and progression, while its effect in glioblastoma (GBM) is still unknown. Objective: We sought to investigate the association between immune-related lncRNA (ir-lncRNA) and GBM. Methods: Transcriptomic and clinical data were obtained from the TCGA dataset, and we found 2008 ir-lncRNA differentially expressed between GBM and adjacent brain tissues. Results: Appling the univariate Cox and Lasso regression model, we found 30 prognosis-related ir-lncRNA pairs to construct a Cox regression risk model to associate the outcome of GBM patients. Furthermore, with this risk model, we can identify the tumor immune infiltration status, the expression of immunosuppressive biomarkers, and chemical sensitivity in GBM patients. Conclusions: We constructed an immunologic risk model with lncRNA to associate the survival outcome of GBM patients, which can provide useful biomarkers.

Involvement of Autophagy in the Protective Effects of Ginsenoside Rb1 in a Rat Model of Traumatic Brain Injury.

BACKGROUND AND OBJECTIVES: No treatment modalities have been identified to prevent neuron damage induced by traumatic brain injury (TBI). The objective of this study was to investigate whether ginsenoside Rb1 (GS-Rb1) could be utilized to exert neuroprotective effects in TBI. METHODS: Lateral fluid percussion injury (LFPI) was used to induce an experimental TBI model. Lewis rats were divided into a GS-Rb1 group (5, 10, 20 mg/kg, intraperitoneally injected daily), a sham group, and a vehicle group. Neurological impairments were assessed with brain water content, Evans blue extravasation, neurological deficit scores, and Morris water maze test. TUNEL and NeuN staining were utilized to detect neuron apoptosis. The relative expression of apoptosis- and autophagy-relevant molecules were assayed with real-time PCR and western blot. RESULTS: GS-Rb1 inhibited TBI-induced brain edema and Evans blue extravasation in a dose-dependent manner. Furthermore, GS-Rb1 improved neurological impairments with diminished neurological deficit scores, decreased escape latencies, increased time in the target quadrant, and increased number of platform site crossings. GS-Rb1 protected against neuron apoptosis with downregulated Bax expression and upregulated Bcl-2 expression. It was worth noting that TBI increased the LC3II/LC3I ratio and upregulated the relative expression of Beclin-1, Atg-7, and Atg-3; moreover, TBI downregulated the relative expression of P62. The administration of GS-Rb1 further strengthened the relative expression of autophagy-related molecules. CONCLUSIONS: GS-Rb1 alleviates neurological impairments induced by TBI with upregulated autophagy.

RP11-552D4.1: a novel m6a-related LncRNA associated with immune status in glioblastoma.

Glioblastoma (GBM) is the most malignant form of brain cancer in the world. Nevertheless, the survival rate of patients with GBM is extremely low. N6-methyladenosine (m6A) and long noncoding RNAs (lncRNAs) conduct important biological functions in patients' survival status and the immunotherapeutic response. Here, m6A-related lncRNAs were identified by a co-expression method. Univariate and multivariate Cox regression together with LASSO were applied to establish the risk model. Kaplan-Meier and ROC analysis were applied to evaluate the prediction power of this risk model. Finally, the related immune profiling and chemical sensitivity targets were also investigated. The risk model holding three m6A-related lncRNAs was confirmed as an independent predictor for the prognosis. Furthermore, we found the risk model based on m6A-related lncRNAs is associated with the immune status, immunosuppressive biomarkers, and chemo-sensitivity in GBM patients. The RP11-552D4.1 is found to facilitate neuronal proliferation. This risk model consisted of m6A-related lncRNAs may be available for the clinical interventions in GBM patients.

DNA Methylation-Related circRNA_0116449 Is Involved in Lipid Peroxidation in Traumatic Brain Injury.

Circular ribonucleic acid (circRNA) has a critical effect in central nervous diseases; however, the exact role of circRNAs in human traumatic brain injury (TBI) remains elusive. Epigenetic modifications, such as DNA methylation, can modify the mRNA level of genes without changing their related DNA sequence in response to brain insults. We hypothesized that DNA methylation-related circRNAs may be implicated in the mechanisms of TBI. The methylation-related circ_0116449 was identified from differential methylation positions and shown to reduce the neuronal loss and lipid markers. Mechanical study indicated that circ_0116449 functions as a miR-142-3p sponge and increases the expression of its target gene: NR1D2, together with NR1D1 and RORA to suppress lipid peroxidation both in vitro and in vivo. Our study suggests that DNA methylation-related circ_0116449 may be a novel target for regulating lipid metabolism in TBI.

circHtra1/miR-3960/GRB10 Axis Promotes Neuronal Loss and Immune Deficiency in Traumatic Brain Injury.

Circular RNAs (circRNAs) are abundant in the brain and contribute to central nervous system diseases; however, the exact roles of circRNAs in human traumatic brain injury (TBI) have not been established. In this study, we used a competing endogenous RNA (ceRNA) chipset as well as in vitro and in vivo assays to characterize differentially expressed circRNAs in TBI. We detected 3035 differentially expressed circRNAs in the severe TBI group, 2362 in the moderate group, and 433 in the mild group. A ceRNA network was constructed. The circRNA has_circ_0020269 (circHtra1) was significantly upregulated after brain insults and was correlated with the severity of injury. circHtra1 inhibited cell proliferation and promoted apoptosis, and its knockdown reversed these effects. Further analyses revealed that circHtra1 functions as a miR-3960 sponge and increases the expression of GRB10, which is involved in NK cell infiltration after TBI. circHtra1 was identified as a target of the IGF-1/ADAR1 axis. Reduced expression of ADAR1 (involved in A-to-I editing) after brain insults upregulated circHtra1. Our results show that circHtra1 promotes neuronal loss by sponging miR-3960 and regulating GRB10 and apoptosis during brain insults. In addition, A-to-I editing could regulate circRNA expression profiles after TBI, and circHtra1 is a potential therapeutic target.

The role of Rho/ROCK in epileptic seizure-related neuronal damage.

Epilepsy is one of the most severe neurological disorders characterized by spontaneous recurrent seizures. Although more than two-thirds of patients can be cured with anti-epileptic drugs (AEDs), the rest one-third of epilepsy patients are resistant to AEDs. A series of studies have demonstrated Rho/Rho-associated kinase (ROCK) pathway might be involved in the pathogenesis of epilepsy in the recent twenty years. Several related pathway inhibitors of Rho/ROCK have been used in the treatment of epilepsy. We searched PubMed from Jan 1, 2000 to Dec 31, 2020, using the terms "epilepsy AND Rho AND ROCK" and "seizure AND Rho AND ROCK". We selected articles that characterized Rho/ROCK in animal models of epilepsy and patients. We then chose the most relevant research studies including in-vitro, in-vivo and clinical trials. The expression of Rho/ROCK could be a potential non-invasive biomarker to apply in treatment for patients with epilepsy. RhoA and ROCK show significant upregulation in the acute and chronic stage of epilepsy. ROCK inhibitors can reduce the epilepsy, epileptic seizure-related neuronal death and comorbidities. These findings demonstrate the novel development for diagnosis and treatment for patients with epilepsy. Rho/ROCK signaling pathway inhibitors may show more promising effects in epilepsy and related neurological diseases.

Neonatal microglia and proteinase inhibitors-treated adult microglia improve traumatic brain injury in rats by resolving the neuroinflammation.

Microglia participate in the regulation of neuroinflammation caused by traumatic brain injury (TBI). This research aimed to explore the repair effects of intracranial injection of neonatal microglia or protease-treated adult microglia on TBI in rat model. Lateral fluid percussion injury was used to establish rat brain injury model. E64 and serpinA3N were employed for the treatment of adult microglia. Cleaved caspase-3 level was analyzed through immunoblotting assay. Enzyme-linked immunosorbent assay was employed to analyze cytokine and chemokine levels. Astrocytosis and microgliosis were shown by immunofluorescence. The cognitive function of rats was analyzed by water maze. The injection of neonatal microglia inhibited cell apoptosis, reduced astrocytosis and microgliosis, decreased the level of chemokines and cytokines in cortex and ipsilateral hippocampus, and improved cognitive function of TBI rat model. The transplantation of peptidase inhibitors-treated adult microglia also inhibited cell apoptosis, reduced astrocytosis and microgliosis, and improved cognitive function of rats with TBI. The transplantation of either neonatal microglia or peptidase inhibitors-treated adult microglia significantly inhibited the pathogenesis of TBI in rat model, while untreated adult microglia showed no significant effect.

GJA1-20K Enhances Mitochondria Transfer from Astrocytes to Neurons via Cx43-TnTs After Traumatic Brain Injury.

Astrocytes are crucial in neural protection after traumatic brain injury (TBI), a global health problem causing severe brain tissue damage. Astrocytic connexin 43 (Cx43), encoded by GJA1 gene, has been demonstrated to facilitate the protection of astrocytes to neural damage with unclear mechanisms. This study aims to explore the role of GJA1-20K/Cx43 axis in the astrocyte-neuron interaction after TBI and the underlying mechanisms. Primarily cultured cortical neurons isolated from embryonic C57BL/6 mice were treated by compressed nitrogen-oxygen mixed gas to simulate TBI-like damage in vitro. The transwell astrocyte-neuron co-culture system were constructed to recapitulate the interaction between the two cell types. Quantitative PCR was applied to analyze mRNA level of target genes. Western blot and immunofluorescence were conducted to detect target proteins expression. GJA1-20K overexpression significantly down-regulated the expression of phosphorylated Cx43 (p-Cx43) without affecting the total Cx43 protein level. Besides, GJA1-20K overexpression obviously enhanced the dendrite length, as well as the expression levels of function and synthesis-related factors of mitochondria in damaged neurons. GJA1-20K up-regulated functional Cx43 expression in astrocytes, which promoted mitochondria transmission from astrocytes to neurons which might be responsible to the protection of astrocyte to neurons after TBI-like damage in vitro.

Integrated single-cell multiomics reveals novel immune candidate markers for post-traumatic coagulopathy.

Introduction: Post-traumatic coagulopathy (PTC) is a critical pathology in traumatic brain injury (TBI), however, its potential mechanism is not clear. To explore this in peripheral samples, we integrated single cell RNA-sequencing and T cell repertoire (TCR)-sequencing across a cohort of patients with TBI. Methods: Clinical samples from patients with more brain severity demonstrated overexpression of T cell receptor-encoding genes and less TCR diversity. Results: By mapping TCR clonality, we found patients with PTC have less TCR clones, and the TCR clones are mainly distributed in cytotoxic effector CD8+T cell. In addition, the counts of CD8+ T cell and natural killer (NK) cells are associated with the coagulation parameter by WGCNA, and the granzyme and lectin-like receptor profiles are also decreased in the peripheral blood from TBI patients, suggesting that reduced peripheral CD8+ clonality and cytotoxic profiles may be involved in PTC after TBI. Conclusion: Our work systematically revealed the critical immune status in PTC patients at the single-cell level.

Expression Profiles of Long Non-coding RNA and Messenger RNA in Human Traumatic Brain Injury.

Long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs) play an important role in central nervous diseases; however, the exact expression and co-expressed profiles in human traumatic brain injury (TBI) are still unknown. Therefore, we investigated whole blood in 12 patients with TBI and 4 healthy controls to observe expression characteristics with different severity. We identified 3,035 lncRNAs and 1,204 mRNAs differentially expressed in the severe TBI group, 2,362 lncRNAs and 656 mRNAs in the moderate group, and 433 lncRNAs and 100 mRNAs in the mild group. Enrichment analyses showed 30 signaling pathways such as inflammatory and immune response pathways. Subsequently, a lncRNA-gene co-expression network was generated for 717 lncRNA-mRNA pairs and most of them with a positive correlation. Based on GSEA analysis, we found that TBI caused severe immune abnormality reflected on Th1, Th2, and Th17 cell differentiation deficiency. Finally, the expression of one upregulated and one downregulated lncRNA was validated in all three TBI groups, which was consistent with the microarray results. In summary, our results show that expression profiles of lncRNAs and mRNAs are significantly different in bloods from different severity TBI especially in immune response, providing novel insight for lncRNAs in human TBI.

Synchrony in serum antibody response to conserved proteins of Moraxella catarrhalis in young children.

Conserved Moraxella catarrhalis (Mcat) proteins, oligopeptide permease (Opp)A, hemagglutinin (Hag), outer membrane protein (OMP) CD, Pilin A clade 2 (PilA2), and Moraxella surface protein (Msp) 22 have been studied as vaccine candidates. Children who experience frequent acute otitis media (AOM) confirmed with pathogen identification by tympanocentesis are referred to as stringently-defined otitis prone (sOP). Synchrony of serum antibody responses against 5 Mcat proteins, OppA, Hag, OMP CD, PilA2, and Msp22 resulting from nasopharyngeal colonization and AOM was studied for 85 non-otitis prone (NOP) children and 34 sOP children. Changes in serum IgG were quantitated with ELISA. Serum IgG antibody levels against OppA, Hag, OMP CD, and Msp22 rose in synchrony in NOP and sOP children; that is, the proteins appeared equally and highly immunogenic in children at age 6 to 22-25 months old and then leveled off in their rise at 22-25 to 30 months old. In contrast, rises of PilA2 were slow from 6 months old and kept constant and did not level off significantly before 30 months old. OppA, Hag, OMP CD, and Msp22 elicited a synchronous acquisition of naturally-induced serum antibody in young children. A multi-valent Mcat protein vaccine combining OppA, Hag, OMP CD, and Msp22 may exhibit less antigen competition when administered as a combination vaccine in young children.

Overexpression of Astrocytes-Specific GJA1-20k Enhances the Viability and Recovery of the Neurons in a Rat Model of Traumatic Brain Injury.

Traumatic brain injury (TBI) is a devastating actuality in clinics worldwide. It is estimated that approximately 10 million people among the world suffer from TBI each year, and a considerable number of patients will be temporarily or permanently disabled or even die due to this disease. Astrocytes play a very important role in the repair of brain tissue after TBI, including the formation of a neuroprotective barrier, inhibition of brain edema, and inhibition of normal nerve cell apoptosis. However, the detailed mechanism underlying this protective effect is still unclear. To investigate the regulatory factors of astrocytes to other neurons post-TBI, we established a TBI rat model and used the AAV to mediate the overexpression of GJA1-20k in astrocytes of rats. And functionally, the specific overexpression of GJA1-20k in astrocytes promoted the viability and recovery of neurons in TBI. Mechanistically, the astrocytes-specific upregulation of GJA1-20k protected the function of mitochondria in neurons of FPI rats, thus suppressing the apoptosis of the damaged neurons. We hereby reported that astrocytes-specific overexpression of GJA1-20k enhanced the viability and recovery of the neurons in TBI through regulating their mitochondrial function.

Astrocytes-derived exosomes induce neuronal recovery after traumatic brain injury via delivering gap junction alpha 1-20 k.

Astrocytes are more resistant to ischemia and hypoxia in the acute phase of brain injury after traumatic brain injury (TBI). Previous study showed that gap junction alpha 1 (GJA1) phosphorylation can increase the survival of damaged astrocytes. The GJA1-20 k expression in neurons co-culture with astrocytes was positively correlated with exosomes uptake. This study aims to explore the effect of exogenous GJA1-20 k carried by astrocyte-derived exosomes on neurons apoptosis and mitochondrial function after TBI. Astrocytes were co-cultured with the neuron with/without damage from air pressure. Exosomes were isolated, extracted from the culture medium by differential ultra-centrifugation, and verified by electron microscopy. Immunofluorescence staining, tunnel, western blot were employed to detect exosomes marker CD60, apoptosis, and mitochondrial function related protein expression and GJA1-20 k in cell culture. A rat model of hydraulic injury TBI was built, and exosomes was transferred. 2,3,5-Triphenyltetrazolium chloride (TTC) staining and immunohistochemistry staining of Nissl and microtubule associated protein 2 were used to detect the brain damage. A transwell stereo culture model of astrocytes and TBI-like injured neuron was constructed. The exosomes derived from astrocytes promoted the recovery of damaged neuron by in vitro exosome treatment. Compared with GJA1-20 k knockout exosome control group, GJA1-20 k exosomes were uptaken by neuron and downregulated the apoptosis rate and upregulated mitochondrial function to promote neuronal recovery. Finally, the results were validated by TTC staining and damaged tissue sections of rat TBI model. This study contributes to a better understanding of the astrocyte-neuron protection mechanism in TBI and provides a potential new target for the treatment of TBI.