Determinants of long-term survival in patients with IDH-mutant gliomas.

BACKGROUND: Survival times of patients with IDH-mutant gliomas are variable and can extend to decades. Many studies provide progression-free rather than overall survival times and prognostic factors remain ill-defined. Here we explored characteristics of short- and long-term survivors within a cohort of patients with extended follow-up. METHODS: This single-center, case-control study included 86 patients diagnosed between 1998 and 2023 who either died within 6 years after diagnosis or survived at least 15 years. Patient characteristics and prognostic factors were stratified by short- (< 6 years) versus long-term (≥ 15 years) survival. RESULTS: Forty-seven patients (55%) diagnosed with astrocytoma and 39 patients (45%) with oligodendroglioma were included retrospectively. Median follow-up of the survivors was 16.6 years (range 15-28.9). Thirty-four deaths (40%) had been reported at database closure. Long-term survival was associated with CNS WHO grade 2 (p < 0.01), smaller tumor volumes (p = 0.01), lack of contrast enhancement (p < 0.01), wait-and-scan strategies (p < 0.01) and female sex (p = 0.04). In multivariate analyses for oligodendroglioma, larger T2 tumor volumes were associated with shorter survival (HR 1.02; 95% CI 1.01-1.05; p = 0.04). In patients with astrocytoma, lack of contrast enhancement (HR 0.38; 95% CI 0.15-0.94; p = 0.04) and wait-and-scan strategies (HR 5.75; 95% CI 1.66-26.61; p = 0.01) were associated with longer survival. CONCLUSION: Large T2 tumor volume and contrast enhancement may be important risk factors for shorter survival, while age might be of lesser importance. Wait-and-scan strategies may yield excellent long-term survival in some patients with astrocytoma.

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.

A Novel Mitochondrial-Related Gene Signature for the Prediction of Prognosis and Therapeutic Efficacy in Lower-Grade Glioma.

Lower-grade glioma (LGG) is a common primary brain tumor with a highly heterogeneous clinical presentation, and its prognosis cannot be accurately predicted by current histopathology. It has been found that mitochondria play an important role in hypoxia, angiogenesis, and energy metabolism in glioma, and mitochondrial function may have an important impact on LGG prognosis. The goal of this study was to develop a novel prognostic model based on Mitochondrial-related genes (MRGs). We first analyzed the somatic alterations profiles of MRGs in patients with LGG and found that somatic alterations were common in LGG and correlated with prognosis. Using RNA-seq data from TCGA and CGGA, 12 prognosis-related MRGs were identified to construct a mitochondrial activation score (MiAS) model by combining univariate regression and LASSO regression analysis. The model and nomogram were evaluated using the area under the ROC curve with AUC = 0.910. The model was closely correlated with the clinical characteristics of LGG patients and performed well in predicting the prognosis of LGG patients with significantly shorter overall survival (OS) time in the high-MiAS group. GSVA and GSEA results showed that oxidative stress, pro-cancer, and immune-related pathways were significantly enriched in the high-MiAS group. CIBERSORT results showed that MiAS was significantly associated with immune cell infiltration in LGG. Macrophage M1 and follicular helper T cells had increased infiltration in the high-MiAS group. TIDE predicted a better immunotherapy outcome in patients in the low-MiAS group. Finally, using data from the CTRPv2 and GDSC2 datasets to assess chemotherapy response in LGG, it was predicted that the chemotherapeutic agents AZD6482, MG-132, and PLX-4720 might be potential agents for patients in the high-MiAS group of LGG. In addition, we performed in vitro experiments and found that knockdown of OCIAD2 expression reduced the abilities of glioma cells to proliferate, migrate, and invade. In contrast, overexpression of OCIAD2 enhanced these abilities of glioma cells. This study found that MRGs were correlated with LGG patient prognosis, which is expected to provide new treatment strategies for LGG patients with different MiAS.

'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.

An N6-methyladenosine regulation- and mRNAsi-related prognostic index reveals the distinct immune microenvironment and immunotherapy responses in lower-grade glioma.

BACKGROUND: N6-methyladenosine (m6A) modification is involved in tumorigenesis and progression as well as closely correlated with stem cell differentiation and pluripotency. Moreover, tumor progression includes the acquisition of stemness characteristics and accumulating loss of differentiation phenotype. Therefore, we integrated m6A modification and stemness indicator mRNAsi to classify patients and predict prognosis for LGG. METHODS: We performed consensus clustering, weighted gene co-expression network analysis, and least absolute shrinkage and selection operator Cox regression analysis to identify an m6A regulation- and mRNAsi-related prognostic index (MRMRPI). Based on this prognostic index, we also explored the differences in immune microenvironments between high- and low-risk populations. Next, immunotherapy responses were also predicted. Moreover, single-cell RNA sequencing data was further used to verify the expression of these genes in MRMRPI. At last, the tumor-promoting and tumor-associated macrophage polarization roles of TIMP1 in LGG were validated by in vitro experiments. RESULTS: Ten genes (DGCR10, CYP2E1, CSMD3, HOXB3, CABP4, AVIL, PTCRA, TIMP1, CLEC18A, and SAMD9) were identified to construct the MRMRPI, which was able to successfully classify patients into high- and low-risk group. Significant differences in prognosis, immune microenvironment, and immunotherapy responses were found between distinct groups. A nomogram integrating the MRMRPI and other prognostic factors were also developed to accurately predict prognosis. Moreover, in vitro experiments illustrated that inhibition of TIMP1 could inhibit the proliferation, migration, and invasion of LGG cells and also inhibit the polarization of tumor-associated macrophages. CONCLUSION: These findings provide novel insights into understanding the interactions of m6A methylation regulation and tumor stemness on LGG development and contribute to guiding more precise immunotherapy strategies.

Quality of life after surgery for lower grade gliomas.

BACKGROUND: Few large studies have investigated quality of life (QOL) for adults diagnosed with lower grade glioma (LGG). METHODS: QOL was assessed for 320 adults with LGG (World Health Organization grade 2/3) enrolled in the International Low Grade Glioma Registry by using the Medical Outcomes Study 36-Item Short Form health survey. Data on symptoms were also collected. QOL outcomes were examined by treatment group and also compared to those from a population-based case-control study of meningioma (the Meningioma Consortium), in which 1722 meningioma cases diagnosed among residents of Connecticut, Massachusetts, California, Texas, and North Carolina from May 1, 2006 through March 14, 2013 were enrolled and frequency matched to 1622 controls by age, sex, and geography. RESULTS: The LGG sample average age is 45 years at the time of interview and 53.1% male. Almost 55% of patients had received radiation and chemotherapy (primarily temozolomide); 32.4% had received neither treatment. Two-thirds of participants with LGG report difficulty with speaking, memory, or thinking, and over one of three reports personality change or difficulty driving. After controlling for age and other comorbidities, individuals with LGG report levels of physical, emotional, and mental health functioning below those reported in a meningioma as well as a general healthy population. CONCLUSIONS: Despite being relatively young, persons with LGG report significantly reduced QOL compared to persons with nonmalignant brain tumors and to a control population, which highlights the need to better acknowledge and manage these symptoms for this group of patients diagnosed in the prime of life.

Molecular subtypes based on PANoptosis-related genes and tumor microenvironment infiltration characteristics in lower-grade glioma.

The growth of cancer, the effectiveness of treatment, and prognosis are all closely related to PANoptosis (include pyroptosis, apoptosis, and necroptosis). It remains unclear whether PANoptosis genes (PANGs) may contribute to lower-grade glioma (LGG) tumor microenvironment (TME). In this study, we collected 1203 LGG samples from three public databases and reported that PANoptosis involves TME interaction and prognosis. Firstly, we provided a comprehensive review of the pan-cancer landscape of PANGs in terms of expression characteristics, prognostic value, mutational profile, and pathway regulation. Then, we identified two distinct PANclusters, each with its own molecular, clinical, and immunological profile. We then developed a scoring system for LGG patients called PANscore. As well as investigating immune characteristics, tumor mutational characteristics, and drug sensitivity, we examined the differences between groups with high PANscores and those with low PANscores. Based on this PANscore and clinicopathological variables, an instant nomogram for predicting clinical survival in LGG patients was developed. Our thorough examination of PANGs in LGG revealed their probable function in TME, as well as their clinicopathological characteristics and prognosis. These discoveries could deepen our comprehension of PANGs in LGG and provide doctors fresh perspectives on how to forecast prognosis and create more efficient, individualized treatment plans.

Cuproptosis-related classification and personalized treatment in lower-grade gliomas to prompt precise oncology.

BACKGROUND: Cuproptosis is implicated in regulating tricarboxylic acid cycle and associated with tumor therapeutic sensitivity, patient outcomes and tumorigenesis. However, the classification and prognostic effect of cuproptosis-associated genes (CAGs), the relationship between cuproptosis and tumor microenvironment (TME) and the treatment of lower-grade glioma (LrGG) remain enigmatic. METHODS: The genetic and transcriptional alterations, prognostic value and classification related to cuproptosis were systematically analyzed. Subtypes of cuproptosis and cuproptosis score (Cuscore) were constructed and further confirmed by two external cohorts. The relationships between cuproptosis and TME, prognosis, and treatment response were also evaluated. RESULTS: Four clusters were identified based on cuproptosis-associated genes. The associations between cuproptosis-associated clusters and clinical features, prognosis, immune cell infiltration, and chemotherapy sensitivity were observed. The Cuscore is an independent prognostic indicator in LrGG patients. The nomogram is constructed according to Cuscore and clinical characteristics, and has good predictive ability and calibration. Patients with high Cuscore had a worse prognosis and advanced performance. A higher Cuscore also indicated a higher stromal score, abundant immune infiltration, and increased tumor mutation burden. A high Cuscore was remarkably related to immune checkpoint inhibitors, immunotherapy response and immune phenotype. CONCLUSIONS: This study demonstrates the clinical effect of CAGs, and suggests that cuproptosis could be a potential therapeutic target in LrGG.

The central role of the left inferior longitudinal fasciculus in the face-name retrieval network.

Unsuccessful retrieval of proper names (PNs) is commonly observed in patients suffering from neurological conditions such as stroke or epilepsy. While a large body of works has suggested that PN retrieval relies on a cortical network centered on the left anterior temporal lobe (ATL), much less is known about the white matter connections underpinning this process. Sparse studies provided evidence for a possible role of the uncinate fasciculus, but the inferior longitudinal fasciculus (ILF) might also contribute, since it mainly projects into the ATL, interconnects it with the posterior lexical interface and is engaged in common name (CN) retrieval. To ascertain this hypothesis, we assessed 58 patients having undergone a neurosurgery for a left low-grade glioma by means of a famous face naming (FFN) task. The behavioural data were processed following a multilevel lesion approach, including location-based analyses, voxel-based lesion-symptom mapping (VLSM) and disconnection-symptom mapping. Different statistical models were generated to control for sociodemographic data, familiarity, biographical knowledge and control cognitive performances (i.e., semantic and episodic memory and CN retrieval). Overall, VLSM analyses indicated that damage to the mid-to-anterior part of the ventro-basal temporal cortex was especially associated with PN retrieval deficits. As expected, tract-oriented analyses showed that the left ILF was the most strongly associated pathway. Our results provide evidence for the pivotal role of the ILF in the PN retrieval network. This novel finding paves the way for a better understanding of the pathophysiological bases underlying PN retrieval difficulties in the various neurological conditions marked by white matter abnormalities.

An artificial neural network model based on DNA damage response genes to predict outcomes of lower-grade glioma patients.

Although the prognosis of lower-grade glioma (LGG) patients is better than others, outcomes are highly heterogeneous. Isocitrate dehydrogenase (IDH) mutation and 1p/19q codeletion status can identify patient subsets with different prognosis. However, in the era of precision medicine, there is still a lack of biomarkers that can accurately predict the individual prognosis of each patient. In this study, we found that most DNA damage response (DDR) genes were aberrantly expressed in LGG patients and were associated with their prognosis. Consequently, we developed an artificial neural network (ANN) model based on DDR genes to predict outcomes of LGG glioma patients. Then, we validated the predictive ability in an independent external dataset and found that the concordance indexes and area under time-dependent receiver operating characteristic curves of the predict index (PI) calculated based on the model were superior to those of the mutation markers. Subgroup analyses demonstrated that the model could accurately identify patients with the same mutation status but different prognosis. Moreover, the model can also identify patients with favorable prognostic mutation status but poor prognosis or vice versa. Finally, we also found that the PI was associated with the mutation status and with the altered immune microenvironment. These results demonstrated that the ANN model can accurately predict outcomes of LGG patients and will contribute to individualized therapies. In addition, a web-based application program for the model was developed.

Integrated machine learning survival framework develops a prognostic model based on inter-crosstalk definition of mitochondrial function and cell death patterns in a large multicenter cohort for lower-grade glioma.

BACKGROUND: Lower-grade glioma (LGG) is a highly heterogeneous disease that presents challenges in accurately predicting patient prognosis. Mitochondria play a central role in the energy metabolism of eukaryotic cells and can influence cell death mechanisms, which are critical in tumorigenesis and progression. However, the prognostic significance of the interplay between mitochondrial function and cell death in LGG requires further investigation. METHODS: We employed a robust computational framework to investigate the relationship between mitochondrial function and 18 cell death patterns in a cohort of 1467 LGG patients from six multicenter cohorts worldwide. A total of 10 commonly used machine learning algorithms were collected and subsequently combined into 101 unique combinations. Ultimately, we devised the mitochondria-associated programmed cell death index (mtPCDI) using machine learning models that exhibited optimal performance. RESULTS: The mtPCDI, generated by combining 18 highly influential genes, demonstrated strong predictive performance for prognosis in LGG patients. Biologically, mtPCDI exhibited a significant correlation with immune and metabolic signatures. The high mtPCDI group exhibited enriched metabolic pathways and a heightened immune activity profile. Of particular importance, our mtPCDI maintains its status as the most potent prognostic indicator even following adjustment for potential confounding factors, surpassing established clinical models in predictive strength. CONCLUSION: Our utilization of a robust machine learning framework highlights the significant potential of mtPCDI in providing personalized risk assessment and tailored recommendations for metabolic and immunotherapy interventions for individuals diagnosed with LGG. Of particular significance, the signature features highly influential genes that present further prospects for future investigations into the role of PCD within mitochondrial function.

A threshold for mitotic activity and post-surgical residual volume defines distinct prognostic groups for astrocytoma IDH-mutant.

AIMS: The distinction between CNS WHO grade 2 and grade 3 is instrumental in choosing between observational follow-up and adjuvant treatment for resected astrocytomas IDH-mutant. However, the criteria of CNS WHO grade 2 vs 3 have not been updated since the pre-IDH era. METHODS: Maximal mitotic activity in consecutive high-power fields corresponding to 3 mm2 was examined for 118 lower-grade astrocytomas IDH-mutant. The prognostic value for time-to-treatment (TTT) and overall survival (OS) of mitotic activity and other putative prognostic factors (including age, performance status, pre-surgical tumour volume, multilobar involvement, post-surgical residual tumour volume and midline involvement) was assessed for tumours with ATRX loss and the absence of CDKN2A homozygous deletion or CDK4 amplification, contrast enhancement, histological necrosis and microvascular proliferation. RESULTS: Seventy-one per cent of the samples had <6 mitoses per 3 mm2 . Mitotic activity, residual volume and multilobar involvement were independent prognostic factors of TTT. The threshold of ≥6 mitoses per 3 mm2 identified patients with a shorter TTT (median 18.5 months). A residual volume ≥1 cm3 also identified patients with a shorter TTT (median 24.5 months). The group defined by <6 mitoses per 3 mm2 and a residual volume <1 cm3 had the longest TTT (median 73 months) and OS (100% survival at 7 years). These findings were confirmed in a validation cohort of 52 tumours. CONCLUSIONS: Mitotic activity and post-surgical residual volume can be combined to evaluate the prognosis for patients with resected astrocytomas IDH-mutant. Patients with <6 mitoses per 3 mm2 and a residual volume <1 cm3 were the best candidates for observational follow-up.

T2-FLAIR mismatch sign correlates with 11C-methionine uptake in lower-grade diffuse gliomas.

PURPOSE: The T2-FLAIR mismatch sign is recognized as an imaging finding highly suggestive of IDH-mutant astrocytomas. This study was designed to determine whether the T2-FLAIR mismatch sign correlates with uptake of 11C-methionine in lower-grade gliomas. METHODS: We included 78 histopathologically verified lower-grade gliomas (grade 2: 31 cases, grade 3: 47 cases) in this study. 78 patients underwent 11C-methionine positron emission tomography (MET-PET) scans and magnetic resonance (MR) imaging scans prior to histological diagnosis. The tumor-to-normal ratio (T/N) of 11C-methionine uptake was calculated by dividing the maximum standardized uptake value (SUV) for the tumor by the mean SUV of the normal brain. MR imaging scans were evaluated for the presence of the T2-FLAIR mismatch sign by three independent reviewers. We compared molecular status, the T2-FLAIR mismatch sign and 11C-methionine uptake among patients with different lower-grade glioma molecular types. RESULTS: The 78 lower-grade gliomas were assigned to one of three molecular groups: Group A (IDH-mutant and 1p/19q non-codeleted, n = 22), Group O (IDH-mutant and 1p/19q codeleted, n = 20), and Group W (IDH wildtype, n = 36). T2-FLAIR mismatch was found in 16 cases (20.5%) that were comprised of 8 (36.4%), 0 (0%), 8 (22.2%) cases in the molecular group A, O and W, respectively. The median T/N ratio of MET-PET in tumors with T2-FLAIR mismatch was 1.50, which was significantly lower than that of tumors without T2-FLAIR mismatch (1.83, p < 0.001, Mann-Whitney U test). In the Groups A and W (excluding Group O), the median T/N ratio on MET-PET in groups A and W (but not group O) with T2-FLAIR mismatch was 1.50, which was significantly lower than that of tumors without T2-FLAIR mismatch (1.81, p = 0.002, Mann-Whitney U test). CONCLUSION: The T2-FLAIR mismatch sign correlated with lower 11C-methionine uptake in lower grade gliomas.

Isocitrate-dehydrogenase-mutant lower grade glioma in elderly patients: treatment and outcome in a molecularly characterized contemporary cohort.

PURPOSE: Lower-grade glioma (LGG) is rare among patients above the age of 60 ("elderly"). Previous studies reported poor outcome, likely due to the inclusion of isocitrate dehydrogenase (IDH) wildtype astrocytomas and advocated defensive surgical and adjuvant treatment. This study set out to question this paradigm analyzing a contemporary cohort of patients with IDH mutant astrocytoma and oligodendroglioma WHO grade 2 and 3. METHODS: Elderly patients treated in our department for a supratentorial, hemispheric LGG between 2009 and 2019 were retrospectively analyzed for patient-, tumor- and treatment-related factors and progression-free survival (PFS) and compared to patients aged under 60. Inclusion required the availability of subtype-defining molecular data and pre- and post-operative tumor volumes. RESULTS: 207 patients were included, among those 21 elderlies (10%). PFS was comparable between elderly and younger patients (46 vs. 54 months; p = 0.634). Oligodendroglioma was more common in the elderly (76% vs. 46%; p = 0.011). Most patients underwent tumor resection (elderly: 81% vs. younger: 91%; p = 0.246) yielding comparable residual tumor volumes (elderly: 7.8 cm3; younger: 4.1 cm3; p = 0.137). Adjuvant treatment was administered in 76% of elderly and 61% of younger patients (p = 0.163). Uni- and multi-variate survival analyses identified a tumor crossing the midline, surgical strategy, and pre- and post-operative tumor volumes as prognostic factors. CONCLUSION: Elderly patients constitute a small fraction of molecularly characterized LGGs. In contrast to previous reports, favorable surgical and survival outcomes were achieved in our series comparable to those of younger patients. Thus, intensified treatment including maximal safe resection should be advocated in elderly patients whenever feasible.

DKK3 expression is associated with immunosuppression and poor prognosis in glioblastoma, in contrast to lower-grade gliomas.

PURPOSE: We previously reported that expression of dickkopf-3 (DKK3), which is involved in the Wnt/ß-catenin pathway, is significantly associated with prognosis in patients with glioblastoma multiforme (GBM). The aim of this study was to compare the association of DKK3 with other Wnt/ß-catenin pathway-related genes and immune responses between lower grade glioma (LGG) and GBM. METHODS: We obtained the clinicopathological data of 515 patients with LGG (World Health Organization [WHO] grade II and III glioma) and 525 patients with GBM from the Cancer Genome Atlas (TCGA) database. We performed Pearson's correlation analysis to investigate the relationships between Wnt/ß-catenin-related gene expression in LGG and GBM. Linear regression analysis was performed to identify the association between DKK3 expression and immune cell fractions in all grade II to IV gliomas. RESULTS: A total of 1,040 patients with WHO grade II to IV gliomas were included in the study. As the grade of glioma increased, DKK3 showed a tendency to be more strongly positively correlated with the expression of other Wnt/ß-catenin pathway-related genes. DKK3 was not associated with immunosuppression in LGG but was associated with downregulation of immune responses in GBM. We hypothesized that the role of DKK3 in the Wnt/ß-catenin pathway might be different between LGG and GBM. CONCLUSION: According to our findings, DKK3 expression had a weak effect on LGG but a significant effect on immunosuppression and poor prognosis in GBM. Therefore, DKK3 expression seems to play different roles, through the Wnt/ß-catenin pathway, between LGG and GBM.

Integrated Bioinformatic Analysis of the Correlation of HOXA10 Expression with Survival and Immune Cell Infiltration in Lower Grade Glioma.

Homeobox A10 (HOXA10) encodes a transcription factor that regulates developmental processes. Whether HOXA10 mRNA levels in lower grade glioma (LGG) correlate with survival and immune cell infiltration has not been evaluated. The differential expression of HOXA10 in different tumors and their corresponding normal tissues was evaluated by exploring public datasets. The correlations between HOXA10 and survival, tumor immune cell infiltration, diverse gene mutation characteristics, and tumor mutation burden in LGG were also investigated using several independent datasets. Pathway enrichment analysis was conducted to identify HOXA10-associated signaling pathways. We found that HOXA10 expression levels did not significantly differ between LGG tumors and normal tissues. Upon assessing the association between HOXA10 expression and immune cell infiltration in LGG, as expected, HOXA10 gene mRNA levels were positively associated with B-cell and dendritic cell infiltration levels in public online datasets. Different HOXA10 expression groups showed diverse gene mutation characteristics and TMB, and low HOXA10 expression was closely related to improved LGG patient survival. Pathway enrichment analysis of HOXA10-associated genes indicated that the cell cycle signaling pathway may participate in affecting the outcomes of LGG patients. Our findings showed that HOXA10 expression was associated with LGG prognosis and tumor immunity.

DLL3 expression and methylation are associated with lower-grade glioma immune microenvironment and prognosis.

Notch signalling pathway, particularly its ligand delta-ligand 3 (DLL3), is important in glioma, however, little is known about DLL3 regulation and prognostic effects. Immunohistochemistry on a cohort of 163 gliomas revealed DLL3 upregulation in IDH1 mutant gliomas, where it was associated with a favourable prognosis (HR[95% CI]: 0.28[0.09-0.87]; p = 0.021). We investigated the epigenetic regulation of DLL3, and identified individual CpG sites correlating with DLL3 mRNA expression, which were significant prognostic markers in LGG. In silico analysis revealed that infiltrating immune cells significantly correlated with DLL3 expression, methylation and somatic copy number alterations. The prognostic effects of DLL3 expression was significantly affected by infiltration of immune cells. RNA Sequencing of 83 LGGs and GO Term analysis of differentially expressed genes showed that low DLL3 expression was related to ciliogenesis, which was confirmed by TCGA LGG analysis. Thus, DLL3 may play an important role in the immune microenvironment and prognosis of LGGs.

Study of MDM2 as Prognostic Biomarker in Brain-LGG Cancer and Bioactive Phytochemicals Inhibit the p53-MDM2 Pathway: A Computational Drug Development Approach.

An evaluation of the expression and predictive significance of the MDM2 gene in brain lower-grade glioma (LGG) cancer was carried out using onco-informatics pipelines. Several transcriptome servers were used to measure the differential expression of the targeted MDM2 gene and search mutations and copy number variations. GENT2, Gene Expression Profiling Interactive Analysis, Onco-Lnc, and PrognoScan were used to figure out the survival rate of LGG cancer patients. The protein-protein interaction networks between MDM2 gene and its co-expressed genes were constructed by Gene-MANIA tool. Identified bioactive phytochemicals were evaluated through molecular docking using Schrödinger Suite Software, with the MDM2 (PDB ID: 1RV1) target. Protein-ligand interactions were observed with key residues of the macromolecular target. A molecular dynamics simulation of the novel bioactive compounds with the targeted protein was performed. Phytochemicals targeting MDM2 protein, such as Taxifolin and (-)-Epicatechin, have been shown with more highly stable results as compared to the control drug, and hence, concluded that phytochemicals with bioactive potential might be alternative therapeutic options for the management of LGG patients. Our once informatics-based designed pipeline has indicated that the MDM2 gene may have been a predictive biomarker for LGG cancer and selected phytochemicals possessed outstanding interaction results within the macromolecular target's active site after utilizing in silico approaches. In vitro and in vivo experiments are recommended to confirm these outcomes.

Genome-wide methylomic analyses identify prognostic epigenetic signature in lower grade glioma.

Glioma is the most malignant and aggressive type of brain tumour with high heterogeneity and mortality. Although some clinicopathological factors have been identified as prognostic biomarkers, the individual variants and risk stratification in patients with lower grade glioma (LGG) have not been fully elucidated. The primary aim of this study was to identify an efficient DNA methylation combination biomarker for risk stratification and prognosis in LGG. We conducted a retrospective cohort study by analysing whole genome DNA methylation data of 646 patients with LGG from the TCGA and GEO database. Cox proportional hazard analysis was carried out to screen and construct biomarker model that predicted overall survival (OS). The Kaplan-Meier survival curves and time-dependent ROC were constructed to prove the efficiency of the signature. Then, another independent cohort was used to further validate the finding. A two-CpG site DNA methylation signature was identified by multivariate Cox proportional hazard analysis. Further analysis indicated that the signature was an independent survival predictor from other clinical factors and exhibited higher predictive accuracy compared with known biomarkers. This signature was significantly correlated with immune-checkpoint blockade, immunotherapy-related signatures and ferroptosis regulator genes. The expression pattern and functional analysis showed that these two genes corresponding with two methylation sites contained in the model were correlated with immune infiltration level, and involved in MAPK and Rap1 signalling pathway. The signature may contribute to improve the risk stratification of patients and provide a more accurate assessment for precision medicine in the clinic.

An integrative multi-omics analysis based on liquid-liquid phase separation delineates distinct subtypes of lower-grade glioma and identifies a prognostic signature.

BACKGROUND: Emerging evidences have indicated that the aberrant liquid-liquid phase separation (LLPS) leads to the dysfunction of biomolecular condensates, thereby contributing to the tumorigenesis and progression. Nevertheless, it remains unclear whether or how the LLPS of specific molecules affects the prognosis and tumor immune microenvironment (TIME) of patients with lower-grade glioma (LGG). METHODS: We integrated the transcriptome information of 3585 LLPS-related genes to comprehensively evaluate the LLPS patterns of 423 patients with LGG in The Cancer Genome Atlas (TCGA) cohort. Then, we systematically demonstrated the differences among four LLPS subtypes based on multi-omics analyses. In addition, we constructed the LLPS-related prognostic risk score (LPRS) for individualized integrative assessment. RESULTS: Based on the expression profiles of 85 scaffolds, 355 regulators, and 3145 clients in LGG, we identified four LLPS subtypes, namely LS1, LS2, LS3 and LS4. We confirmed that there were significant differences in prognosis, clinicopathological features, cancer hallmarks, genomic alterations, TIME patterns and immunotherapeutic responses among four LLPS subtypes. In addition, a prognostic signature called LPRS was constructed for individualized integrative assessment. LPRS exhibited a robust predictive capacity for prognosis of LGG patients in multiple cohorts. Moreover, LPRS was found to be correlated with clinicopathological features, cancer hallmarks, genomic alterations and TIME patterns of LGG patients. The predictive power of LPRS in response to immune checkpoint inhibitor (ICI) therapy was also prominent. CONCLUSIONS: This study provided a novel classification of LGG patients based on LLPS. The constructed LPRS might facilitate individualized prognosis prediction and better immunotherapy options for LGG patients.