DNMT3A promotes glioma growth and malignancy via TNF-α/NF-κB signaling pathway.

Background: DNMT3A is the main molecule responsible for DNA methylation in cells. DNMT3A affects the progression of inflammation, degenerative diseases, and malignant tumors, and exhibits significant aberrantly expression in tumor tissues. Methods: Transcriptome data and relevant clinical information were downloaded from The Cancer Genome Atlas (TCGA), Chinese Glioma Genome Atlas (CGGA), and Gene Expression Omnibus (GEO) datasets. Differential expression analysis and prognostic analysis were conducted based on above statistics. We constructed a clinical prognostic model and identified DNMT3A as an independent prognostic factor to accurately predict patient prognosis. Differential gene enrichment analysis revealed that DNMT3A affects the progression of glioma through multiple pathways, among which the tumor necrosis factor-α (TNF-α)/nuclear factor-kappa B (NF-κB) pathway shows a strong correlation. Immunological analysis also revealed a certain correlation between DNMT3A and tumor immunity. We demonstrated through gene editing that DNMT3A can affect the release of TNF-α in cells, thereby affecting the progression of glioma. Functional experiments have also demonstrated that DNMT3A plays a crucial role in tumors. Results: RNA-sequencing and survival analyses of lower-grade glioma (LGG) patients in TCGA, CGGA, and GEO cohorts showed that high DNMT3A expression correlated with poor prognosis of LGG patients. Univariate and multivariate Cox regression analyses showed that DNMT3A expression was an independent prognostic indicator in LGG. The prognosis prediction nomogram with age, World Health Organization (WHO) grading, and DNMT3A expression showed reliable performance in predicting the 1-, 3-, and 5-year overall survival (OS) of LGG patients. Functional enrichment analysis, gene set enrichment analysis (GSEA), and ESTIMATE algorithm analyses showed that DNMT3A expression was associated with the tumor infiltration of immune cells and predicted response to immunotherapy in two immunotherapy cohorts of pan-cancer patients. Furthermore, short hairpin RNA (shRNA)-mediated knockdown of DNMT3A in the LGG cell lines suppressed proliferation, migration, and invasion of LGG cells by downregulating the TNF-α/NF-κB signaling pathway. Conclusions: Our data showed that DNMT3A was a potential prognostic biomarker in glioma. DNMT3A promoted proliferation and malignancy of LGG cells through the TNF-α/NF-κB signaling pathway. DNMT3A is a promising therapeutic target for treating patients with LGG.

WTAP regulates the production of reactive oxygen species, promotes malignant progression, and is closely related to the tumor microenvironment in glioblastoma.

RNA modifications have been substantiated to regulate the majority of physiological activities in the organism, including the metabolism of reactive oxygen species (ROS), which plays an important role in cells. As for the effect of RNA modification genes on ROS metabolism in glioblastoma (GBM), it has not been studied yet. Therefore, this study aims to screen the RNA modification genes that are most related to ROS metabolism and explore their effects on the biological behavior of GBM in vitro. Here, an association between WTAP and ROS metabolism was identified by bioinformatics analysis, and WTAP was highly expressed in GBM tissue compared with normal brain tissue, which was confirmed by western blotting and immunohistochemical staining. When using a ROS inducer to stimulate GBM cells in the WTAP overexpression group, the ROS level increased more significantly and the expression levels of superoxide dismutase 1 (SOD1) and catalase (CAT) also increased. Next, colony formation assay, wound healing assay, and transwell assay were performed to investigate the proliferation, migration, and invasion of GBM cells. The results showed that WTAP, as an oncogene, promoted the malignant progression of GBM cells. Functional enrichment analysis predicted that WTAP was involved in the regulation of tumor/immune-related functional pathways. Western blotting was used to identify that WTAP had a regulatory effect on the phosphorylation of PI3K/Akt signaling. Finally, based on functional enrichment analysis, we further performed immune-related analysis on WTAP. In conclusion, this study analyzed WTAP from three aspects, which provided new ideas for the treatment of GBM.

Pan-cancer analysis: predictive role of TAP1 in cancer prognosis and response to immunotherapy.

BACKGROUND: Transporter associated with antigen processing 1 (TAP1) is a molecule involved in processing and presentation of major histocompatibility complex class I restricted antigens, including tumor-associated antigens. TAP1 participates in tumor immunity, and is aberrantly expressed in multiple cancer types; METHODS: Transcriptome profiles were obtained from The Cancer Genome Atlas and Genotype-Tissue Expression databases. Genetic alterations, protein distribution, and interaction information for TAP1 were downloaded from cBioPortal, Human Protein Atlas and Compartmentalized Protein-Protein Interaction, respectively. Single-cell analyses of TAP1 across cancers were conducted via the Tumor Immune Single-cell Hub website. Gene set enrichment analysis was employed to investigate TAP1-associated functional mechanisms and processes. Immune cell infiltration was explored using Tumor Immune Estimation Resource 2.0. Pan-cancer correlations between TAP1 expression and immunotherapy biomarkers were explored using the Spearman's correlation test. Associations with immunotherapy responses were also investigated using clinicopathological and prognostic information from cohorts of patients with cancer receiving immune checkpoint inhibitors. RESULTS: TAP1 expression was elevated in most cancer types and exhibited distinct prognostic value. Immune cells expressed more TAP1 than malignant cells within most tumors. TAP1 expression was significantly correlated with immune-related pathways, T-lymphocyte infiltration, and immunotherapeutic biomarkers. Clinical cohort validation revealed a significant correlation with immune therapeutic effects and verified the prognostic role of TAP1 in immunotherapy. Western blot assay indicated that TAP1 is upregulated in glioblastoma compared with adjacent normal brain tissues. CONCLUSION: TAP1 is a robust tumor prognostic biomarker and a novel predictor of clinical prognosis and immunotherapeutic responses in various cancer types.

Identification of a robust scoring system based on metabolic genes followed by in-depth validation of ATP1A3 in glioma.

AIMS: In the past few decades, the prognosis of glioma patients has not significantly improved. Therefore, to provide more precise medical services for glioma patients, it is urgent to identify more clinically meaningful subtypes, establish more robust clinical prediction models, and find more effective therapeutic targets. MATERIALS AND METHODS: Four distinct metabolic-associated subtypes were identified by the NMF algorithm based on metabolic genes (MEGs). A robust scoring system was constructed based on the differentially expressed genes (DEGs) screened from the four metabolic-associated subtypes with the LASSO regression algorithm and multivariate Cox regression analysis. Further analysis of scoring systems was done by different R packages. In addition, the ATP1A3 gene was screened and bioinformatics analysis of it was conducted on several public websites. GSEA software was utilized to search hallmark signaling pathways closely related to ATP1A3. Cytological experiments were used to investigate the role of ATP1A3 in the malignant progression of glioblastoma (GBM) cells. KEY FINDINGS: Four metabolic-associated subtypes with significantly different clinicopathological characteristics were identified, and a robust scoring system with outstanding clinical application value was established. In addition, a tumor suppressor gene ATP1A3 was found, which is expected to be a potential therapeutic target for glioma. SIGNIFICANCE: This study is of great significance in the diagnosis, prognosis, and prediction of the response to immune checkpoint blockers (ICBs) for glioma patients. More importantly, this study found a potential therapeutic target for glioma.

Ferroptosis in tumor immunity and therapy.

Ferroptosis is a type of regulated cell death (RCD), and it plays an important role in the occurrence of diseases, especially the development of tumors. Ferroptosis of tumor cells affects the antitumor immunity and the immune response to treatment to varying degrees. Ferroptosis also plays a key role in immune cells. This review outlines the mechanism of the immune-related effects of ferroptosis pathways in tumor progression and treatment, and it discusses potential methods for improving antitumor immunity and enhancing the efficacy of current cancer treatments by targeting ferroptosis.

Intrinsic immune evasion patterns predict temozolomide sensitivity and immunotherapy response in lower-grade gliomas.

BACKGROUND: Although intrinsic immune-evasion is important in cancer proliferation, metastasis and response to treatment, it is unclear whether intrinsic immune-evasion patterns of gliomas can aid in predicting clinical prognosis and determining treatment. METHODS: A total of 182 immune-evasion genes intrinsic to cancer were subjected to consensus clustering to identify immune-evasion patterns in 1421 patients with lower-grade glioma (LGG). The levels of each cancer hallmark were determined by the Gene Set Variant Analysis (GSVA) method, and immune cell infiltrations were quantified using two algorithms, the single-sample Gene Set Enrichment Analysis (ssGSEA) and the Cell-type Identification By Estimating Relative Subsets Of RNA Transcripts (CIBERSORT) methods. IEVscore was determined by a method that combined univariate Cox regression analysis, least absolute shrinkage and selection operator (LASSO) regression and principal component analysis (PCA). RESULTS: Transcriptional and genomic analysis showed that most immune evasion genes (IEVGs) were upregulated in LGGs, with aberrant expression driven by alterations in copy number variants (CNV). Based on the mRNA expression profiles of cancer-intrinsic IEVGs could be divided into three LGG subgroups with distinct prognosis, clinicopathological features and immune infiltrations. A combined scoring scheme designed to assess the immune-evasion levels of LGGs divided these 1421 patients into two subgroups that differed in IEVscores. LGG patients with low-IEVscore had a better prognosis, would be more likely to benefit from immune check-point inhibitors and would be more susceptible to temozolomide (TMZ) chemotherapy. CONCLUSION: Intrinsic immune evasion in the tumor microenvironment (TME) has a crucial effect on glioma formation. Quantitatively assessing the IEV scores of individual LGG patients could enhance knowledge about the intra-glioma microenvironment and lead to the development of individualized therapeutic strategies for patients with LGG.

Immune Characteristics and Prognosis Analysis of the Proteasome 20S Subunit Beta 9 in Lower-Grade Gliomas.

Glioma is a common intracranial malignancy in adults and has a high mortality due to its poor prognosis and high recurrence rate. Dysregulation of protein degradation is one of the main promoting factors in glioma development. As an indispensable unit of the proteasome, Proteasome 20S Subunit Beta 9 (PSMB9) is one of the major enzymes in ubiquitin-dependent protein degradation in cells. In addition, proteasomes also participate in a series of cellular processing, like immune regulation, nerve signal transduction, material transport through channels, cell adhesion, and various signaling pathways. However, the relationship between the PSMB9 expression and the occurrence of lower-grade glioma (LGG) is still unknown. First, we collected the RNA-seq and clinical information about LGG clinical samples from The Cancer Genome Atlas (TCGA) cohort, Chinese Glioma Genome Atlas (CGGA; including CGGAseq1 and CGGAseq2) cohort, and Gene Expression Omnibus (GEO; GSE16011, GSE61374, and Rembrandt) cohort. Then, these data were used for differential analysis, survival analysis, enrichment analysis, clinical model construction, etc. In addition, we combine immune-related data for immune-related analysis, including immune infiltration and immunotherapy. Through the above research, we have provided a new biomarker for LGG prognosis prediction and more comprehensively explained the role of PSMB9 in the development of LGG. This study determined that PSMB9 can be used as an immunotherapy target through the analysis of immune data, providing new ideas for the clinical treatment of LGG.

HSPA6 is Correlated With the Malignant Progression and Immune Microenvironment of Gliomas.

Gliomas are primary intracranial space lesions with a high mortality rate. Current treatments for glioma are very limited. Recently, immunotargeted therapy of the glioma microenvironment has been developed. Members of the 70 kDa heat shock protein (HSP70) family are involved in the development of many tumors and immunity. HSPA6 protein belongs to the HSP70 family; However, the biological function of this protein in gliomas has yet to be evaluated. In the present study, a range of analyses, involving protein networks, survival, clinical correlation, and function, revealed that the expression of HSPA6 was negatively correlated with clinical prognosis and closely associated with immunity, invasion, and angiogenesis. Quantitative protein analysis confirmed that HSPA6 was expressed at high levels in patients with glioblastoma. Vitro experiments further verified that HSPA6 enhanced the malignant progression of glioma cells by promoting proliferation, invasion and anti-apoptosis. We also found that HSPA6 was closely correlated with genomic variations and tumor microenvironment. Collectively, we demonstrated that HSPA6 may represent a new therapeutic target to improve the prognosis of patients with gliomas.

CLCF1 Is a Novel Potential Immune-Related Target With Predictive Value for Prognosis and Immunotherapy Response in Glioma.

Background: Cardiotrophin-like cytokine factor 1 (CLCF1) has been described as an oncogene and a potential therapeutic target in a variety of cancers, but its role in glioma remains unknown. Methods: Based on The Cancer Genome Atlas (TCGA), we conducted a bioinformatics analysis to investigate the clinical significance and biological functions of CLCF1 in glioma at the transcriptional level and predicted the response to immunotherapy of glioma patients with different CLCF1 expression levels. All the results were further verified in Chinese Glioma Genome Altas(CGGA) Data processing and figure generating were performed with R language. Results: Elevated CLCF1 expression was common in cancers and usually predicted poor prognosis, which was also consistent with gliomas. In Univariate Cox Regression analysis and Kaplan-Meier survival analysis, tumor patients with higher CLCF1 expression tended to experience a worse prognosis. In the multivariate Cox proportional hazard model, the expression of CLCF1 was an independent prognostic factor in gliomas. The biological function analysis of CLCF1 in glioma showed that CLCF1 was closely associated with immune signatures, including immune-related pathways, immune cell infiltration, and immune checkpoints. Moreover, glioma patients with low CLCF1 expression showed a greater tendency to respond to anti-PD1/PD-L1 immunotherapy, indicating CLCF1 also had potential clinical significance in guiding immunotherapy. And CLCF1 as a member of the IL6 family had a better predictive value for prognosis and immunotherapy response in glioma than that of IL6 and other IL6 family members. Conclusion: CLCF1 expression is an independent prognosticator and a promising therapeutic target correlated with immunotherapy in glioma.

Comprehensive analysis of the prognostic and role in immune cell infiltration of MSR1 expression in lower-grade gliomas.

BACKGROUND: The therapeutic effects of conventional treatment on gliomas are not promising. The tumor microenvironment (TME) has a close association with the invasiveness of multiple types of tumors, including low-grade gliomas (LGG). This study aims to validate the prognostic and immune-related role of macrophage scavenger receptor 1 (MSR1) in LGG patients. METHODS: Data in this study were obtained from public databases. The differential expression of MSR1 was analyzed in LGG patients with different clinicopathological characteristics. Kaplan-Meier survival analysis, a time-dependent receiver operating characteristic (ROC) curve, and Cox regression analysis were used to assess the prognostic value of MSR1. Differentially expressed genes (DEGs) were screened between the high and low expression groups of MSR1. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to annotate the function of these DEGs. Hallmark gene sets were identified based on MSR1 by Gene Set Enrichment Analysis (GSEA). Difference analysis and correlation analysis were used to study the relationship between MSR1 and TME-related scores, tumor-infiltrating immune cells (TIICs), immune-related gene sets, and immune checkpoints (ICPs). The single-cell sequencing data were processed to identify the cell types expressing MSR1. The quantification of TIICs in TME was calculated by single-sample gene set enrichment analysis (ssGSEA). The differential expression of MSR1 in LGG and control brain tissues was verified by experiments. RESULTS: There were significant differences in the expression level of MSR1 in different types of tissues and cells. MSR1 has a high prognostic value in LGG patients and can be used as an independent prognostic factor. MSR1 is closely related to TME and may play an important role in the immunotherapy of LGG patients. CONCLUSIONS: The result of our study demonstrated that MSR1 is an independent prognostic biomarker in LGG patients and may play an important role in the TME of LGGs.

CBX3 promotes glioma U87 cell proliferation and predicts an unfavorable prognosis.

BACKGROUND: Chromobox protein homolog 3 (CBX3) is one of the heterochromatin protein 1 (HP1) family members. Among multiple cancers, it is usually overexpressed. However, the mechanism and function of CBX3 in glioma remain incompletely illustrated. METHODS: The expression level of CBX3 as well as its correlation with glioma are detected through TCGA and Oncomine database. The expressions of CBX3 mRNA and protein in glioma tissues and normal brain tissues have been identified by qRT-PCR and Western blot. The prognostic role of CBX3 has been assessed in a retrospective cohort study. Additionally, the correlation between CBX3 expression and the clinicopathological characteristics of glioma patients were also discussed. To better understand the role of CBX3 in glioma, a lentiviral vector expressing CBX3-shRNA and cyclin dependent kinase inhibitor 1A (CDKN1A) siRNA were established and transfected into the glioma U87 cells. Besides, the CBX3 and CDKN1A expression levels in glioma U87 cells after transfected with CBX3-shRNA were gauged by qRT-PCR and Western blot. CCK-8, colony formation and EdU assays have been applied to evaluate the influence of CBX3 on U87 cells proliferation, and flow cytometry has been applied to manage the changes in cell cycle and cell apoptosis after transfection with CBX3-shRNA. Xenograft tumors have been examined in vivo for the carcinogenic effects and prognostic value of CBX3 in glioma tissues. RESULTS: In the present study, CBX3 was demonstrated to be highly expressed in human glioma tissues, and high CBX3 expression predicted the dismal recurrence-free survival (RFS) and poor overall survival (OS) for glioma patients. High CBX3 expression was dependent on the tumor size, Karnofsky performance scale (KPS) score, WHO grade, recurrence and survival status. Moreover, CBX3 expression knockdown could remarkably suppress the proliferation and colony formation ability of U87 cells, which was achieved through blocking cell arrest at G0/G1 phase and inducing apoptosis. Additionally, our findings also suggested that, compared with shRNA-Ctrl transfection, the mRNA and protein expression levels of CDKN1A have been dramatically up-regulated in vitro after transfection with shRNA-CBX3. Consistent with the results of in vitro assays, the outcomes of xenograft assay and immunohistochemistry (IHC) also indicated that, the tumor growth and Ki-67 expression level were restrained in response to CBX3 inhibition, while the CDKN1A expression level in vivo was up-regulated. Down-regulation of CDKN1A expression partially restored the ability of cell proliferation in the U87 cells, which was inhibited by shRNA-CBX3 CONCLUSIONS: In conclusion, results of the current research suggest that a high CBX3 expression level predicts the poor prognosis for glioma patients. CBX3 can stimulate the growth of glioma U87 cells through targeting CDKN1A and CBX3 may become a novel target in the clinical treatment for glioma.

CDCA7L promotes glioma proliferation by targeting CCND1 and predicts an unfavorable prognosis.

Cell division cycle associated 7 like (CDCA7L) belongs to the JPO protein family, recently identified as a target gene of c­Myc and is frequently dysregulated in multiple cancers. However, to the best of our knowledge, no studies to date have been carried out to investigate the functions of CDCA7L in glioma. Thus, in this study, the expression level of CDCA7L and its association with the prognosis in glioma were detected through the TCGA database. The mRNA expression levels of CDCA7L in glioblastoma (GBM) tissues and normal brain tissues were detected by RT­qPCR and western blot analysis. To explore the role of CDCA7L in glioma, CDCA7L siRNA was constructed and transfected into U87 glioma cells. The expression levels of CDCA7L and cyclin D1 (CCND1) in glioma U87 cells following transfection with CDCA7L siRNA were measured by RT­qPCR and western blot analysis. CCK­8, colony formation, EdU and Transwell assays were used to measure the effects of CDCA7L on U87 cell proliferation, and flow cytometry was used to monitor the changes in the cell cycle following transfection with CDCA7L siRNA. Xenograft tumors were examined in vivo for the carcinogenic effects, as well as the mechanisms and prognostic value of CDCA7L in glioma tissues. The results revealed that CDCA7L was highly expressed in human GBM tissues, and a high expression of CDCA7L was associated with a poor prognosis of glioma patients through the TCGA database. We demonstrated that CDCA7L was highly expressed in human GBM tissues and 3 glioma cell lines. The downregulation CDCA7L expression significantly inhibited the proliferation and colony formation ability of U87 cells by blocking cell cycle progression in the G0/G1 phase. In addition, we found that the mRNA and protein levels of CCND1 were markedly decreased following transfection with CDCA7L siRNA compared with NC siRNA in vitro. The downregulation CDCA7L expression reduced the number of invading cells. Consistent with the results of the in vitro assays, the xenograft assay, immunohistochemistry (IHC) assay and western blot analysis demonstrated that, in response to CDCA7L inhibition, tumor growth was inhibited, Ki­67 and CCND1 expression levels were decreased in vivo. On the whole, the results of the current study indicate that CDCA7L is highly expressed in human glioma tissues and that a high CDCA7L expression predicts a poor prognosis of glioma patients. CDCA7L promotes glioma U87 cell growth through CCND1.

Increased intracranial pressure in Guillain-Barré syndrome: A case report.

RATIONALE: Guillain-Barré syndrome (GBS) is an inflammatory autoimmune demyelinating polyneuropathy that affects most of the peripheral nervous system. Papilledema and raised intracranial pressure (ICP) are seen in some patients, and are thought to be associated with elevated cerebrospinal fluid (CSF) protein-though CSF protein levels are normal in some patients, thus the specific mechanisms remain unclear. Interleukin (IL)-17 levels are elevated in the CSF and plasma in GBS patients, and elevated IL-17 in the CSF of patients with idiopathic intracranial hypertension has been reported. Intravenous immunoglobulin (IVIG) exerts therapeutic effects by downregulating IL-17 in GBS patients. PATIENT CONCERNS: Herein we describe a case of a 14-year-old girl who initially presented with relapsing limb weakness. DIAGNOSES: Magnetic resonance imaging revealed an enlarged ventricle, electromyography, and nerve conduction studies were suggestive of polyradiculopathy, and lumbar puncture revealed elevated ICP with normal cells and elevated protein values. INTERVENTIONS: She was treated with IVIG 0.4 g/kg per day for 5 days. OUTCOMES: At a 6-month follow-up there had been no recurrence. LESSONS SUBSECTIONS: In GBS patients who have a relapsing course and develop papilledema with possible immunological disturbance, an accurate early diagnosis in conjunction with the prompt initiation of immunotherapy may improve clinical symptoms and the prognosis.

Meta-analysis of the prognostic value of long non-coding RNA AFAP1-AS1 for cancer patients in China.

LncRNA actin filament-associated protein 1 antisense RNA 1 (AFAP1-AS1) is often dysregulated in cancer. We performed this meta-analysis to clarify the usefulness of AFAP1-AS1 as a prognostic marker in malignant tumors. The PubMed, Medline, OVID, Cochrane Library, and Web of Science databases were searched from inception to Augest 7, 2017. Sixteen studies with a total of 1,386 patients were included in the study. The pooled hazard ratio (HR) suggested high AFAP1-AS1 expression correlated with poor overall survival (OS) (HR = 1.98, 95% confidence interval (CI): 1.71-2.28), disease-free survival (DFS) (HR = 1.54, 95% CI: 1.22-1.95), and progression-free survival (PFS) (HR = 2.17, 95% CI:1.64-2.88) in cancer patients, without obvious heterogeneity. High AFAP1-AS1 expression also correlated with larger tumor size (odds ratio (OR) = 2.04, 95% CI: 1.54-2.72), advanced tumor stage (OR=2.35, 95% CI: 1.70-3.26), poor histological grade (OR =1.39, 95% CI: 1.02-1.90), lymph node metastasis (OR = 2.71, 95% CI: 1.98-3.72) and distant metastasis (OR = 2.96, 95% CI: 2.03-4.32). Thus high AFAP1-AS1 expression is predictive of poor OS, DFS, PFS, lymph node metastasis, distant metastasis, histological grade, larger tumor size and tumor stage, which suggests high AFAP1-AS1 expression may serve as a novel biomarker of poor prognosis in cancer.