The prognostic and immunological role of MCM3 in pan-cancer and validation of prognosis in a clinical lower-grade glioma cohort.

Background: Previous studies have shown that MCM3 plays a key role in initiating DNA replication. However, the mechanism of MCM3 function in most cancers is still unknown. The aim of our study was to explore the expression, prognostic role, and immunological characteristics of MCM3 across cancers. Methods: We explored the expression pattern of MCM3 across cancers. We subsequently explored the prognostic value of MCM3 expression by using univariate Cox regression analysis. Spearman correlation analysis was performed to determine the correlations between MCM3 and immune-related characteristics, mismatching repair (MMR) signatures, RNA modulator genes, cancer stemness, programmed cell death (PCD) gene expression, tumour mutation burden (TMB), microsatellite instability (MSI), and neoantigen levels. The role of MCM3 in predicting the response to immune checkpoint blockade (ICB) therapy was further evaluated in four immunotherapy cohorts. Single-cell data from CancerSEA were analysed to assess the biological functions associated with MCM3 in 14 cancers. The clinical correlation and independent prognostic significance of MCM3 were further analysed in the TCGA and CGGA lower-grade glioma (LGG) cohorts, and a prognostic nomogram was constructed. Immunohistochemistry in a clinical cohort was utilized to validate the prognostic utility of MCM3 expression in LGG. Results: MCM3 expression was upregulated in most tumours and strongly associated with patient outcomes in many cancers. Correlation analyses demonstrated that MCM3 expression was closely linked to immune cell infiltration, immune checkpoints, MMR genes, RNA modulator genes, cancer stemness, PCD genes and the TMB in most tumours. There was an obvious difference in outcomes between patients with high MCM3 expression and those with low MCM3 expression in the 4 ICB treatment cohorts. Single-cell analysis indicated that MCM3 was mainly linked to the cell cycle, DNA damage and DNA repair. The expression of MCM3 was associated with the clinical features of LGG patients and was an independent prognostic indicator. Finally, the prognostic significance of MCM3 in LGG was validated in a clinical cohort. Conclusion: Our study suggested that MCM3 can be used as a potential prognostic marker for cancers and may be associated with tumour immunity. In addition, MCM3 is a promising predictor of immunotherapy responses.

"It changes everything": Understanding how people experience the impact of living with a lower-grade glioma.

Background: Quantitative studies show people living with a lower-grade glioma (LGG) often report low health-related quality of life. However, it is unclear how this impact is experienced; resulting supportive care needs are also poorly understood. We explored how people experience the impact of living long-term with an LGG, to help identify potential supportive care needs. Methods: We conducted semi-structured interviews with a diverse group of people with LGG (n = 28) across the United Kingdom, who had completed primary treatment (male n = 16, female n = 12, mean age 54.6 years, mean time since diagnosis 8.7 years). Interviews were transcribed and inductive thematic analysis was conducted. Results: Four themes relating to the impact experiences of people with LGG were generated: "Emotional response to the diagnosis," "Living with the 'What ifs'," "Changing relationships," and "Faltering independence." These reflect participants' experiences with symptoms (eg, fatigue, seizures) and impairments (eg, motor dysfunction, cognitive deficits), and how these, in turn, drive impacts on daily living (including on work, relationships, social activities, and transport). Participants spoke about their experiences with profound emotion throughout. Conclusions: People with LGG can experience wide-ranging everyday impacts and may have extensive supportive care needs. This study highlights how this impact is experienced and what it means to people with LGG. Best practice suggestions for conducting comprehensive needs assessments tailored to those with LGG, and the development of personalized plans to meet those needs, would be a critical step to ensure that people with LGG are best supported in living with their condition.

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.

Identification of Lower Grade Glioma Antigens Based on Ferroptosis Status for mRNA Vaccine Development.

Purpose: mRNA vaccines represent a promising and innovative strategy within the realm of cancer immunotherapy. However, their efficacy in treating lower-grade glioma (LGG) requires evaluation. Ferroptosis exhibits close associations with the initiation, evolution, and suppression of cancer. In this study, we explored the landscape of the ferroptosis-associated tumor microenvironment to facilitate the development of mRNA vaccines for LGG patients. Patients and Methods: Genomic and clinical data of the LGG patients was obtained from the Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) databases. Ferroptosis-related tumor antigens were identified based on differential expression, mutation status, correlation with antigen-presenting cells, and prognosis, relevance to immunogenic cell death (ICD). Antigen expression levels in LGG specimens and cell lines were validated using real time-polymerase chain reaction (RT-PCR). Consensus clustering was employed for patient classification. The immune landscapes of ferroptosis subtypes were further characterized, including immune responses, prognostic ability, tumor microenvironment, and tumor-related signatures. Results: Five tumor antigens, namely, HOTAIR, IDO1, KIF20A, NR5A2, and RRM2 were identified in LGG. RT-PCR demonstrated higher expression of these genes in LGG compared to the control. Twelve gene modules and four ferroptosis subtypes (FS1-FS4) of LGG were defined. FS2 and FS4, characterized as "cold" tumors due to their decreased tumor mutation burden (TMB) and immune checkpoint proteins (ICPs), were deemed appropriate candidates for the mRNA vaccine. Conclusion: HOTAIR, IDO1, KIF20A, NR5A2, and RRM2 were identified as promising candidate antigens for the development of an LGG mRNA vaccine, particularly offering potential benefits to FS2 and FS4 patients.

Cuproptosis-related gene-located DNA methylation in lower-grade glioma: Prognosis and tumor microenvironment.

Cuproptosis a novel copper-dependent cell death modality, plays a crucial part in the oncogenesis, progression and prognosis of tumors. However, the relationships among DNA-methylation located in cuproptosis-related genes (CRGs), overall survival (OS) and the tumor microenvironment remain undefined. In this study, we systematically assessed the prognostic value of CRG-located DNA-methylation for lower-grade glioma (LGG). Clinical and molecular data were sourced from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. We employed Cox hazard regression to examine the associations between CRG-located DNA-methylation and OS, leading to the development of a prognostic signature. Kaplan-Meier survival and time-dependent receiver operating characteristic (ROC) analyses were utilized to gauge the accuracy of the signature. Gene Set Enrichment Analysis (GSEA) was applied to uncover potential biological functions of differentially expressed genes between high- and low-risk groups. A three CRG-located DNA-methylation prognostic signature was established based on TCGA database and validated in GEO dataset. The 1-year, 3-year, and 5-year area under the curve (AUC) of ROC curves in the TCGA dataset were 0.884, 0.888, and 0.859 while those in the GEO dataset were 0.943, 0.761 and 0.725, respectively. Cox-regression-analyses revealed the risk signature as an independent risk factor for LGG patients. Immunogenomic profiling suggested that the signature was associated with immune infiltration level and immune checkpoints. Functional enrichment analysis indicated differential enrichment in cell differentiation in the hindbrain, ECM receptor interactions, glycolysis and reactive oxygen species pathway across different groups. We developed and verified a novel CRG-located DNA-methylation signature to predict the prognosis in LGG patients. Our findings emphasize the potential clinical implications of CRG-located DNA-methylation indicating that it may serve as a promising therapeutic target for LGG patients.

Comprehensive analyses of m1A regulator-mediated modification patterns determining prognosis in lower-grade glioma (running title: m1A in LGG).

N1-methyladenosine (m1A) modification is a crucial post-transcriptional regulatory mechanism of messenger RNA (mRNA) in living organisms. Few studies have focused on analysis of m1A regulators in lower-grade gliomas (LGG). We employed the Nonnegative Matrix Factorization (NMF) technique on The Cancer Genome Atlas (TCGA) dataset to categorize LGG patients into 2 groups. These groups exhibited substantial disparities in terms of both overall survival (OS) and levels of infiltrating immune cells. We collected the significantly differentially expressed immune-related genes between the 2 clusters, and performed LASSO regression analysis to obtain m1AScores, and established an m1A-related immune-related gene signature (m1A-RIGS). Next, we categorized all patients with LGG into high- and low-risk subgroups, predictive significance of m1AScore was confirmed by conducting univariate/multivariate Cox regression analyses. Additionally, we confirmed variations in immune-related cells and ssGSEA and among the high-/low-risk subcategories in the TCGA dataset. Finally, our study characterized the effects of MSR1 and BIRC5 on LGG cells utilizing Edu assay and flow cytometry to explore the effects of modulation of these genes on glioma. The results of this study suggested that m1A-RIGS may be an excellent prognostic indicator for patients with LGG, and could also promote development of novel immune-based treatment strategies for LGG. Additionally, BIRC5 and MSR1 may be potential therapeutic targets for LGG.

Barriers and facilitators to self-management in people living with a lower-grade glioma.

PURPOSE: Self-management can have clinical and quality-of-life benefits. However, people with lower-grade gliomas (LGG) may face chronic tumour- and/or treatment-related symptoms and impairments (e.g. cognitive deficits, seizures), which could influence their ability to self-manage. Our study aimed to identify and understand the barriers and facilitators to self-management in people with LGG. METHODS: We conducted semi-structured interviews with 28 people with LGG across the United Kingdom, who had completed primary treatment. Sixteen participants were male, mean age was 50.4 years, and mean time since diagnosis was 8.7 years. Interviews were audio-recorded and transcribed. Following inductive open coding, we deductively mapped codes to Schulman-Green et al.'s framework of factors influencing self-management, developed in chronic illness. RESULTS: Data suggested extensive support for all five framework categories ('Personal/lifestyle characteristics', 'Health status', 'Resources', 'Environmental characteristics', 'Healthcare system'), encompassing all 18 factors influencing self-management. How people with LGG experience many of these factors appears somewhat distinct from other cancers; participants described multiple, often co-occurring, challenges, primarily with knowledge and acceptance of their incurable condition, the impact of seizures and cognitive deficits, transport difficulties, and access to (in)formal support. Several factors were on a continuum, for example, sufficient knowledge was a facilitator, whereas lack thereof, was a barrier to self-management. CONCLUSIONS: People with LGG described distinctive experiences with wide-ranging factors influencing their ability to self-manage. IMPLICATIONS FOR CANCER SURVIVORS: These findings will improve awareness of the potential challenges faced by people with LGG around self-management and inform development of self-management interventions for this population.

Potential value of expression of receptor accessory protein 4 for evaluating the prognosis of lower-grade glioma patients.

BACKGROUND: REEP4 is involved in the regulation of the biological process of mitosis. Lower grade glioma (LGG), as a malignant tumor, is accompanied by abnormalities in mitosis, but there have been no reports of REEP4 so far. METHODS: We collected transcriptome data, DNA methylation data and the clinical characteristics of thousands of patients with LGG. Various big data analysis methods and molecular biology experiments were employed to reveal the impact of REEP4 on the pathological process of LGG. RESULTS: It was found that the expression of REEP4 was significantly elevated and negatively regulated by its methylation site. Therefore, both the high expression of REEP4 and low methylation state of cg16311504 showed that the patients are correlated with lower patient survival rate. In addition, high REEP4 expression participates in the regulation of various cancer-related cellular signaling pathways, such as the cell cycle, MAPK signaling pathway, NOD-like receptor signaling pathway, etc. More importantly, the level of immune cell infiltration significantly increased in the high expression group of REEP4 in the LGG tumor microenvironment and REEP4 has a high positive correlation with PD-L1 and other immune checkpoints. CONCLUSIONS: In brief, this study is the first to introduce REEP4 in malignant tumors, which can be used as an independent risk factor that participates in the malignant process of LGG. More importantly, REEP4 has the potential to become a new star in the field of anti-tumor treatment.

Is intraoperative mapping of music performance mandatory to preserve skills in professional musicians? Awake surgery for lower-grade glioma conducted from a meta-networking perspective.

OBJECTIVE: In surgery for lower-grade glioma (LGG) in professional musicians, for whom preserving music ability is essential, a critical question has emerged, namely, is it mandatory to include music performance during awake mapping, as proposed in several reports? In fact, music ability is subserved by a mosaic of interactive cognitive and emotional processes that rest on several networks. Therefore, from a meta-network perspective, the authors investigated whether an integrated multimodal monitoring of these cognitive and emotional functions during stimulation mapping could be efficient in maintaining musical skill. Indeed, it could be difficult for a patient to play a musical instrument in the surgical setting in addition to performing other tasks, such as movement and language. METHODS: An awake mapping-guided resection for LGG without intraoperative music performance was performed in 3 professional musicians. Intraoperative tests were tailored to each patient depending on the critical corticosubcortical circuits surrounding the tumor, including not only sensorimotor or language skills but also higher-order functions with a constant multitasking during the resection. RESULTS: Although music skills were not mapped during surgery, all patients resumed their professional activities, preserving the ability to play music and to perform concerts, to teach and to compose music, or to start learning a new instrument. CONCLUSIONS: A connectome-based resection without intraoperative music performance seems effective in achieving maximal glioma removal while preserving crucial networks subserving musical skills, creativity, and music learning. Neurosurgery should evolve toward a meta-networking approach to better understand higher-order functions mediating complex behavior, such as being a professional musician.

Complement and coagulation cascades are associated with prognosis and the immune microenvironment of lower-grade glioma.

Background: Abnormal coagulation is a common feature of glioma. There is a strong correlation between coagulation and the complement system, named complement and coagulation cascades (CCC). However, the role of CCC genes in lower-grade glioma (LGG) remains unclear. This study aimed to investigate the role of CCC genes in LGG. Methods: In total, 5,628 differential expressed genes were identified between 498 LGG tissues from The Cancer Genome Atlas (TCGA) and 207 normal brain tissues from Genotype-Tissue Expression Project (GTEx). Among them, 20 overlapped CCC genes were identified as differentially expressed CCC genes. Then, comprehensive bioinformatics analysis was used to investigate the role of CCC genes in LGG; 271 LGG tissues from the Chinese Glioma Genome Atlas (CGGA) were used as the validation dataset. Cell Counting Kit-8 (CCK8) proliferation assay, colony formation assay, and wound healing assay were conducted to explore the anti-glioma effect of the sensitive drugs we predicted. Results: We constructed a risk signature consisting of six CCC genes, including F2R, SERPINA1, TFPI, C1QC, C2, and C3AR1. The CCC gene-based risk signature could accurately predict the prognosis of patients with LGG. In addition, we found that the JAK-STAT, NOD-like receptor, Notch, PI3K-Akt, and Rap1 signaling pathways might be activated and had crosstalk with CCC in the high-risk group. Our findings analyses demonstrated that samples in high- and low-risk groups had different immune landscapes. Moreover, patients in the high-risk group might have greater resistance to immunotherapy. We validated the accuracy of the risk signature in predicting immunotherapy response in two public immunotherapy cohorts, GSE135222 and GSE78220. By means of oncoPredict, MG-132, BMS-536924, PLX-4720, and AZD6482 were identified as potential sensitive drugs for high-risk patients, of which MG-132 was particularly recommended for high-risk patients. We performed in vitro experiments to explore the anti-glioma effect of MG-132, and the results demonstrated MG-132 could inhibit the proliferation and migration of glioma cells. Conclusions: Our findings show that CCC genes are associated with the prognosis and immune infiltration of LGG and provide possible immunotherapeutic and novel chemotherapeutic strategies for patients with LGG based on the risk signature.

Post-craniotomy coronal suture diastases in a transformed lower grade glioma.

Cranial suture diastases are an uncommon clinical entity, with post craniotomy diastases being a previously undescribed finding in literature to our best knowledge. Herein, we report a case of a 28-year-old adult who underwent a second-stage low-grade glioma surgery 7 months after initial surgery. This study presents coronal suture diastases adjacent to the previously performed craniotomy. After literature and pathophysiology review, we found it to be unique and that the craniotomy can resemble the mechanical stress of trauma.

Integrated analysis of necroptosis related gene signature to predict clinical outcomes, immune status and drug sensitivity in lower grade Glioma.

Background: The treatment of lower grade gliomas (LGG) is currently the most challenging dilemma in the management of intracranial tumors. Necroptosis is a type of programmed cell death that is closely associated with tumor progression, However, the role of necroptosis related genes in LGG is not yet well elucidated. Methods: Online databases were used to obtain gene expression and clinical information. After gene differential expression analysis, a risk score model based on prognostic differentially expressed necroptosis-related genes (DENGs) were constructed to predict prognosis for LGG patients. The validity of the risk score model was then assessed with Kaplan-Meier survival curve. The prognostic DENGs included in the risk score model were then subjected to gene expression analysis, functional enrichment analysis, consensus clustering analysis, and single cell sequencing analysis. Finally, we investigated the correlation of the risk score and immune infiltration in LGG tumor microenvironment and drug sensitivity for LGG patients in different risk groups. Results: A survival risk score model was constructed based on seven prognostic DENGs, which demonstrated satisfactory performance in predicting the prognosis of LGG patients. According to functional enrichment analyses, these seven DENGs may play a regulatory role in LGG tumorigenesis through several immune and metabolic pathways. LGG patients could be categorized into two clusters with distinct prognosis and clinicopathologic characteristics based on the expression of seven DENGs. Single-cell sequencing analysis demonstrated that the DENG signature was differentially expressed in various types of cells in LGG and may play a vital role in oncogenesis. Additionally, drug sensitivity analysis suggested that the seven-gene signature could guide clinical medication for LGG patients. Conclusion: Our study developed a reliable necroptosis-related signature to predict the prognosis of LGG patients. This gene signature may also help estimate immune status and anti-cancer drug sensitivity in LGG patients. Our findings may pave the way to enhance our understanding of necroptosis in LGG.

'A Constant Black Cloud': The Emotional Impact of Informal Caregiving for Someone With a Lower-Grade Glioma.

Those closest to people with lower-grade gliomas (LGGs) often assume the role of informal caregiver (IC). The additional responsibilities mean ICs of people with cancer can experience adverse impacts on their own lives. We explored the emotional impact of informal caregiving for people with LGGs. This was a descriptive qualitative study within the multi-method Ways Ahead project. We conducted semi-structured interviews with individuals from the United Kingdom, who currently, or in the past 5 years, informally cared for someone with an LGG. Interviews encompassed experiences of emotional impact as a consequence of caregiving for someone with an LGG. Inductive thematic analysis was undertaken. We interviewed 19 ICs (mean age 54.6 years; 14 females, 5 males). Participants reported substantial emotional impact. Four themes and associated subthemes were generated: Emotional responses to the illness (e.g. feeling helpless), Emotional responses to the unknown (e.g. anxiety about future uncertainty), Emotional consequences of care recipient changes (e.g. challenges of changed relationship dynamics), and Emotional weight of the responsibility (e.g. feeling burnout). Emotional impact in one area often exacerbated impact in another (e.g. future uncertainty impacted feelings of helplessness). Participants detailed the factors that helped them manage the emotional impact (e.g. being resilient). ICs of people with LGGs can experience wide-ranging emotional responses to and impacts of the illness, uncertain prognosis, care recipient changes, and the toll of caregiving. Adjustment and resilience are key protective factors, though further consideration of ways to identify and fulfil the emotional support needs of ICs of people with LGGs is required.

IDH-mutant grade 4 astrocytoma: a comparison integrating the clinical, pathological, and survival features between primary and secondary patients.

OBJECTIVE: IDH-mutant grade 4 astrocytomas (AIDHmut/G4) are divided into primary de novo (pAIDHmut/G4) and secondary with a history of prior lower-grade gliomas (LGGs; sAIDHmut/G4). The mutational spectrum and DNA methylation patterns are homogeneous within de novo pAIDHmut/G4 and evolved sAIDHmut/G4, but the two groups have different diagnoses, management, and outcomes. This study sought to systematically compare the clinical, pathological, and survival characteristics between them. METHODS: Of the 871 grade 4 astrocytomas with data for IDH mutation, 698 (80.1%) were primary and 173 (19.9%) were secondary. Of the 698 primary tumors, 103 (14.8%) were pAIDHmut/G4, and of the 173 secondary tumors, 108 (62.4%) were sAIDHmut/G4. Clinical, pathological, and survival features were compared between pAIDHmut/G4 and sAIDHmut/G4. Multivariate analyses were performed to identify prognostic factors. RESULTS: Patients with sAIDHmut/G4 had significantly shorter median overall survival (OS; 11.8 vs 34.2 months, hazard ratio [HR] 2.69, 95% confidence interval [CI] 1.367-5.306, p = 0.004) and progression-free survival (PFS; 8.5 vs 24.3 months, HR 2.83, 95% CI 1.532-5.235, p = 0.001) than patients with pAIDHmut/G4. In patients with sAIDHmut/G4, resection status and chemotherapy were independent prognostic factors for OS and PFS; in patients with pAIDHmut/G4, LGG component, resection status, and O6-methylguanine DNA methyltransferase promoter methylation were independent prognostic factors. The therapeutic strategies of LGGs did not influence survival of patients with sAIDHmut/G4, but patients who had not received radiotherapy or chemotherapy when they were diagnosed with LGGs were found to benefit from radiotherapy or chemotherapy when they progressed to sAIDHmut/G4. CONCLUSIONS: The different clinical characteristics, survival, and risk factors between sAIDHmut/G4 and pAIDHmut/G4 provide a reference to guide treatment decisions in AIDHmut/G4.

CIA-II is associated with lower-grade glioma survival and cell proliferation.

BACKGROUND: The role of CIA-II has been clarified in several types of tumors; however, whether dysregulated CIA-II expression is also involved in the pathophysiology of lower-grade glioma (LGG) remains undisclosed. METHODS: A comprehensive pan-cancer analysis of the expression patterns and prognostic significance of CIA-II in miscellaneous tumors was undertaken. Subsequently, a detailed bioinformatics analysis was executed to identify putative correlations between CIA-II expression and clinical features, prognosis, biological functions, immunological characteristics, genomic alterations, and chemotherapeutics in LGG. In vitro studies were implemented to examine the potential roles of CIA-II in LGG. RESULTS: CIA-II expression was found to be abnormally elevated in a variety of tumors, including LGG. Additionally, patients with LGG with higher CIA-II expression owned worse prognosis. Importantly, the results declared that CIA-II expression was an independent prognostic indicator for LGG. Moreover, the expression of CIA-II was tightly interrelated with immune cell infiltration, gene mutations, and chemotherapeutics in LGG. In vitro studies revealed that CIA-II was increased and strongly related to the cell proliferation in LGG. CONCLUSION: CIA-II may be an independent prognostic factor and a serviceable therapeutic target in LGG.

The effect Of vascular related CeRNA genes and corresponding imaging biomarkers on survival in lower grade glioma.

BACKGROUND & AIMS: To investigate the differential expression of vascular related ceRNA regulatory genes in LGG with different mutations of IDH1 and MGMT, and to verify imaging gene markers that can be closely associated with vascular related ceRNA regulatory genes. METHOD: Five hundred fifteen patients with LGG were collected from TCGA database. CeRNA network analysis, GO analysis and Cox risk regression were used to find vascular ceRNA regulatory genes and their genetic markers related to survival. The preoperative MRI image data and postoperative tumor tissues of 14 patients with WHO grade III glioma were collected for full transcriptome analysis. The correlation between image characteristics of LGG and survival related vascular ceRNA regulatory genes was compared using nonparametric U test and Pearson correlation coefficient analysis. RESULTS: Vascular related genes ranked first in the functional enrichment analysis of differentially expressed genes in LGG. EPHA2, ETS1, YAP1 and MEIS1 could significantly affect the survival of patients in each group of LGG. The volume of enhanced region was negatively correlated with IDH1 (r = -0.622, P = 0.009) mutation and TMEM100 (r = -0.535, P = 0.024), and positively correlated with MEIS1 (r = 0.551, P = 0.021), rCBFmax value was negatively correlated with TMEM100 (r = -0.492, P = 0.037). CONCLUSIONS: Under different IDH1 mutations, lncRNA-dominated vascular-related ceRNA regulatory genes were the first differentially expressed subset of each group, and could be used as an effective risk factor affecting the survival of LGG. The image characteristics of LGG was an ideal image gene marker. It was a reliable imaging biological marker which can truly reflect the pathophysiological characteristics of glioma.

Radiogenomic landscape: Assessment of specific phagocytosis regulators in lower-grade gliomas.

Genome-wide CRISPR-Cas9 knockout screens have emerged as a powerful method for identifying key genes driving tumor growth. The aim of this study was to explore the phagocytosis regulators (PRs) specifically associated with lower-grade glioma (LGG) using the CRISPR-Cas9 screening database. Identifying these core PRs could lead to novel therapeutic targets and pave the way for a non-invasive radiogenomics approach to assess LGG patients' prognosis and treatment response. We selected 24 PRs that were overexpressed and lethal in LGG for analysis. The identified PR subtypes (PRsClusters, geneClusters, and PRs-score models) effectively predicted clinical outcomes in LGG patients. Immune response markers, such as CTLA4, were found to be significantly associated with PR-score. Nine radiogenomics models using various machine learning classifiers were constructed to uncover survival risk. The area under the curve (AUC) values for these models in the test and training datasets were 0.686 and 0.868, respectively. The CRISPR-Cas9 screen identified novel prognostic radiogenomics biomarkers that correlated well with the expression status of specific PR-related genes in LGG patients. These biomarkers successfully stratified patient survival outcomes and treatment response using The Cancer Genome Atlas (TCGA) database. This study has important implications for the development of precise clinical treatment strategies and holds promise for more accurate therapeutic approaches for LGG patients in the future.

Identification of RP11-770J1.4 as immune-related lncRNA regulating the CTXN1-cGAS-STING axis in histologically lower-grade glioma.

Human gliomas are lethal brain cancers. Emerging evidence revealed the regulatory role of long noncoding RNAs (lncRNAs) in tumors. Here, we performed a comprehensive analysis of the expression profiles of RNAs in histologically lower-grade glioma (LGG). Enrichment analysis revealed that glioma is influenced by immune-related signatures. Survival analysis further established the close correlation between network features and glioma prognosis. Subsequent experiments showed lncRNA RP11-770J1.4 regulates CTXN1 expression through hsa-miR-124-3p. Correlation analysis identified lncRNA RP11-770J1.4 was immune related, specifically involved in the cytosolic DNA sensing pathway. Downregulated lncRNA RP11-770J1.4 resulted in increased spontaneous gene expression of the cGAS-STING pathway. Single-cell RNA sequencing analysis, along with investigations in a glioblastoma stem cell model and patient sample analysis, demonstrated the predominant localization of CTXN1 within tumor cores rather than peripheral regions. Immunohistochemistry staining established a negative correlation between CTXN1 expression and infiltration of CD8+ T cells. In vivo, Ctxn1 knockdown in GL261 cells led to decreased tumor burden and improved survival while increasing infiltration of CD8+ T cells. These findings unveil novel insights into the lncRNA RP11-770J1.4-CTXN1 as a potential immune regulatory axis, highlighting its therapeutic implications for histologically LGGs.

A prognostic signature based on snoRNA predicts the overall survival of lower-grade glioma patients.

Introduction: Small nucleolar RNAs (snoRNAs) are a group of non-coding RNAs enriched in the nucleus which direct post-transcriptional modifications of rRNAs, snRNAs and other molecules. Recent studies have suggested that snoRNAs have a significant role in tumor oncogenesis and can be served as prognostic markers for predicting the overall survival of tumor patients. Methods: We screened 122 survival-related snoRNAs from public databases and eventually selected 7 snoRNAs that were most relevant to the prognosis of lower-grade glioma (LGG) patients for the establishment of the 7-snoRNA prognostic signature. Further, we combined clinical characteristics related to the prognosis of glioma patients and the 7-snoRNA prognostic signature to construct a nomogram. Results: The prognostic model displayed greater predictive power in both validation set and stratification analysis. Results of enrichment analysis revealed that these snoRNAs mainly participated in the post-transcriptional process such as RNA splicing, metabolism and modifications. In addition, 7-snoRNA prognostic signature were positively correlated with immune scores and expression levels of multiple immune checkpoint molecules, which can be used as potential biomarkers for immunotherapy prediction. From the results of bioinformatics analysis, we inferred that SNORD88C has a major role in the development of glioma, and then performed in vitro experiments to validate it. The results revealed that SNORD88C could promote the proliferation, invasion and migration of glioma cells. Discussion: We established a 7-snoRNA prognostic signature and nomogram that can be applied to evaluate the survival of LGG patients with good sensitivity and specificity. In addition, SNORD88C could promote the proliferation, migration and invasion of glioma cells and is involved in a variety of biological processes related to DNA and RNA.