Lack of B and T cell reactivity towards IDH1R132H in blood and tumor tissue from LGG patients

The potential applications of peptide-loading complex in cancer treatment

Immunotherapy for cancer has made significant strides in the last several years. The prognosis for cancer patients has significantly improved as a result, particularly in hematological diseases. However, it was discovered that translating these achievements to solid tumors proved challenging. The peptide-loading complex (PLC), a temporary multisubunit membrane assembly in the endoplasmic reticulum (ER), is crucial for initiating a hierarchical immune response. Chaperones calreticulin and tapasin make up the PLC, unique to class I glycoproteins, thiooxido-reductase ERp57, and a transporter associated with antigen processing. The loading and editing of major histocompatibility complex class I (MHC-I) molecules with peptide translocation into the ER are synchronized by the PLC. One of the immune escape strategies revealed for tumors so far is changes in the expression of MHC molecules. This is because MHC antigens are crucial in presenting antigens to T-lymphocytes and controlling NK cell activity. Furthermore, decreased MHC-I expression has been linked to malignancies resistant to T-cell-based cancer immunotherapies (adoptive transfer of antitumor CD8 T-cells or checkpoint inhibition). The PLC is essential for T-cell priming, differentiation, and tumor growth control because it can bind to a wide range of MHC-I allomorphs. In this review, we have looked into PLC's function and effects in all forms of cancer to improve cancer therapy techniques.

Analysis of glutathione Stransferase mu class 5 gene methylation as a prognostic indicator in low-grade gliomas

BACKGROUND

Low-grade gliomas (LGG) are a variety of brain tumors that show different clinical outcomes. The methylation of the GSTM5 gene has been noted in the development of LGG, however, its prognostic importance remains uncertain.

OBJECTIVE

The objective of this study was to examine the correlation between GSTM5 DNA methylation and clinical outcomes in individuals diagnosed with LGG.

METHODS

Analysis of GSTM5 methylation levels in LGG samples was conducted using data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. The overall survival based on GSTM5 methylation status was evaluated using Kaplan-Meier curves. The DNA methylation heatmap for particular CpG sites in the GSTM5 gene was visualized using the "pheatmap" R package.

RESULTS

The study analyzed that LGG tumors had higher levels of GSTM5 methylation than normal tissues. There was an inverse relationship discovered between GSTM5 expression and methylation. LGG patients with hypermethylation of GSTM5 promoter experienced a positive outcome. Age, grade, and GSTM5 methylation were determined as independent prognostic factors in LGG through both univariate and multivariate Cox regression analyses.

CONCLUSION

Methylation of GSTM5 DNA, specifically at certain CpG sites, is linked to a positive outlook in patients with LGG. Utilizing the "pheatmap" R package to visualize GSTM5 methylation patterns offers important information for identifying prognostic markers and therapeutic targets in low-grade gliomas.

Arachidonate lipoxygenases 5 is a novel prognostic biomarker and correlates with high tumor immune infiltration in low-grade glioma

Objective: To investigate the prognostic value of arachidonate lipoxygenases 5 (ALOX5) expression and methylation, and explore the immune functions of arachidonate lipoxygenases 5 expression in low-grade glioma (LGG). Materials and Methods: Using efficient bioinformatics approaches, the differential expression of arachidonate lipoxygenases 5 and the association of its expression with clinicopathological characteristics were evaluated. Then, we analyzed the prognostic significance of arachidonate lipoxygenases 5 expression and its methylation level followed by immune cell infiltration analysis. The functional enrichment analysis was conducted to determine the possible regulatory pathways of arachidonate lipoxygenases 5 in low-grade glioma. Finally, the drug sensitivity analysis was performed to explore the correlation between arachidonate lipoxygenases 5 expression and chemotherapeutic drugs. Results: arachidonate lipoxygenases 5 mRNA expression was increased in low-grade glioma and its expression had a notable relation with age and subtype (p < 0.05). The elevated mRNA level of arachidonate lipoxygenases 5 could independently predict the disease-specific survival (DSS), overall survival (OS), and progression-free interval (PFI) (p < 0.05). Besides, arachidonate lipoxygenases 5 expression was negatively correlated with its methylation level and the arachidonate lipoxygenases 5 hypomethylation led to a worse prognosis (p < 0.05). The arachidonate lipoxygenases 5 expression also showed a positive connection with immune cells, while low-grade glioma patients with higher immune cell infiltration had poor survival probability (p < 0.05). Further, arachidonate lipoxygenases 5 might be involved in immune- and inflammation-related pathways. Importantly, arachidonate lipoxygenases 5 expression was negatively related to drug sensitivity. Conclusion: arachidonate lipoxygenases 5 might be a promising biomarker, and it probably occupies a vital role in immune cell infiltration in low-grade glioma.

NCAPG as a Novel Prognostic Biomarker in Glioma

BACKGROUND

Non-SMC condensin I complex subunit G (NCAPG) is expressed in various human cancers, including gliomas. However, its biological function in glioma remains unclear. The present study was designed to determine the biological functions of NCAPG in glioma and to evaluate the association of NCAPG expression with glioma progression.

METHODS

Clinical data on patients with glioma were obtained from The Cancer Genome Atlas (TCGA), the Chinese Glioma Genome Atlas (CGGA), the Gene Expression Omnibus (GEO), and the Rembrandt and Gravendeel databases. The correlations among NCAPG expression, pathological characteristics, and clinical outcome were evaluated. In addition, the correlations of NCAPG expression with immune cell infiltration and glioma progression were analyzed.

RESULTS

NCAPG expression was higher in gliomas than in adjacent normal tissues. Higher expression of NCAPG in gliomas correlated with poorer prognosis, unfavorable histological features, absence of mutations in the isocitrate dehydrogenase gene (IDH), absence of chromosome 1p and 19q deletions, and responses to chemoradiotherapy. Univariate and multivariate Cox analysis demonstrated, in addition to patient age, tumor grade, absence of IDH mutations, and absence of chromosome 1p and 19q deletions, NCAPG expression was independently prognostic of overall survival, disease-free survival, and progression-free survival in patients with glioma. In addition, high expression of NCAPG correlated with tumor infiltration of B cells, CD4+ T cells, CD8+ T cells, neutrophils, macrophages, and dendritic cells. Gene set enrichment analysis (GSEA) indicated that high NCAPG expression was associated with cell proliferation and immune response-related signaling pathways. NCAPG knockdown in glioma cell lines significantly reduced cell survival, proliferation, and migration.

CONCLUSION

NCAPG expression correlates with glioma progression and immune cell infiltration, suggesting that NCAPG expression may be a useful prognostic biomarker for glioma.

CCNB2 is a novel prognostic factor and a potential therapeutic target in Low-grade glioma (LGG)

Background: Cyclin B2 (CCNB2) is an important component of the cyclin pathway and plays a key role in the occurrence and development of cancer. However, the correlation between prognosis of low-grade glioma (LGG), CCNB2, and tumor infiltrating lymphocytes is not clear. Methods: The expression of CCNB2 in LGG was queried in Gene Expression Profiling Interactive Analysis 2 (GEPIA2) and TIMER databases. The relationships between CCNB2 and the clinicopathological features of LGG were analyzed using the Chinese Glioma Genome Atlas (CGGA) database. The relationship between CCNB2 expression and overall survival (OS) was evaluated by GEPIA2. The correlation between CCNB2 and LGG immune infiltration was analyzed by the TIMER database. Finally, quantitative real-time polymerase chain reaction (qRT-PCR) was performed to detect CCNB2 expression. Results: The expression of CCNB2 differed across different tumor tissues, but was higher in LGG than in normal tissues. LGG patients with high expression of CCNB2 have poorer prognosis. The expression of CCNB2 was correlated with age, WHO grade, IDH mutational status, 1p/19q codeletion status, and other clinicopathological features. The expression of CCNB2 in LGG was positively correlated with the infiltration level of B cells, dendritic cells, and macrophages. qRT-PCR results revealed that the expression of CCNB2 in LGG tissues was higher than normal tissues and higher expression of CCNB2 was associated with worse prognosis. Conclusion: CCNB2 may be used as a potential biomarker to determine the prognosis of LGG and is also related to immune infiltration.

Methylation and Expression of the Exercise-Related TLR1 Gene Is Associated With Low Grade Glioma Prognosis and Outcome

Background: Exercise improves function, reduces disability, maintains independence, and improves quality of life for low-grade glioma (LGG) patients. Exercise can also improve the effectiveness of cancer treatment. The goal of this research was to find potential exercise related genes that may be used to predict exercise levels and may be used as a biomarker for cancer outcomes.

Methods: The GSE111551 database was thoroughly examined in this research, and the resulting conclusion of exercise-related genes was reached. The protein interaction network (PPI) was used to examine the differentially expressed genes (DEGs). Then the exercise-related gene TLR1 was chosen. The expression, methylation degree, prognosis, and immune relevance of TLR1 were investigated using bioinformatics. In addition, we verified the role of TLR1 in Glioma cell lines.

Results: LGG patients with reduced TLR1 expression and hypermethylation had a better overall survival (OS) and progression free survival (PFS), using the TCGA database. Low TLR1 expression and hypermethylation of TLR1 were found to be independent biomarkers for OS using Cox regression. Furthermore, the CGGA database was used to confirm the prognostic function of TLR1 in this cancer. Finally, most methylation sites of TLR1 were strongly correlated with immune infiltration and immune checkpoint. Then, reducing TLR1 expression substantially slowed the cell cycle and decreased LGG cell proliferation, emigration, and infiltration in vitro.

Conclusions: Exercise-related gene TLR1 has the potential to be a useful prognostic biomarker, and it is thought to be involved in immune cell infiltration and immunotherapy in LGG.

Emerging targets for anticancer vaccination: IDH

The development of anticancer vaccines as a pillar of cancer immunotherapy has been hampered by the scarcity of suitable tumor-specific antigens. While response to immune checkpoint inhibitors is driven by T cells recognizing mutated antigens, the vast majority of these neoantigens are patient-specific, mandating personalized approaches. In addition, neoantigens are often subclonal present in only a fraction of tumor cells resulting in immune evasion of neoantigen-negative tumor cells. Isocitrate dehydrogenase (IDH)1 mutations, most frequently encoding for the neomorphic protein IDH1R132H, are frequent driver mutations found in the majority of diffuse World Health Organization grade 2 and 3 gliomas. In addition, IDH1R132H generates a shared clonal neoepitope that is recognized by mutation-specific T-helper cells. A recent phase 1 trial (NOA-16, NCT02454634) demonstrated safety and immunogenicity of IDH1-vac, a long IDH1R132H peptide vaccine in patients with newly diagnosed astrocytoma and provided evidence of biological efficacy based on imaging parameters. In addition, vaccine-induced IDH1R132H-reactive tumor-infiltrating T cells were identified. Here we discuss clinical and scientific implications and future developments of IDH-directed immunotherapies.

Identification of Critical m6A RNA Methylation Regulators with Prognostic Value in Lower-Grade Glioma

Increasing evidences have revealed that N⁶-methyladenosine (m⁶A) RNA methylation regulators participate in the tumorigenesis and development of multiple tumors. So far, there has been little comprehension about the effects of m⁶A RNA methylation regulators on lower-grade gliomas (LGG). Here, we systematically investigated the expression profiles and prognostic significance of 36 m⁶A RNA methylation regulators in LGG patients from the TCGA and CGGA databases. Most of the m⁶A RNA methylation regulators are differentially expressed in LGG tissues as compared with normal brain tissues and glioblastoma (GBM) tissues. The consensus clustering for these m⁶A RNA methylation regulators identified three clusters. Patients in cluster 3 exhibited worse prognosis. In addition, we constructed an m⁶A-related prognostic signature, which exhibited excellent performance in prognostic stratification of LGG patients according to the results of the Kaplan-Meier curves, ROC curves, and univariate and multivariate Cox regression analyses. In addition, a significant correlation was observed between the m⁶A-related prognostic signature and the immune landscape of the LGG microenvironment. The high-risk group exhibited higher immune scores, stromal scores, and ESTIMATE scores but lower tumor purity and lower abundance of activated NK cells. Moreover, the expression level of immune checkpoints was positively correlated with the risk score. To conclude, the current research systematically demonstrated the prognostic roles of m⁶A RNA methylation regulators in LGG.

Illuminating the cross-talk between tumor metabolism and immunity in IDH-mutated cancers

Mutations in the genes encoding isocitrate dehydrogenase 1 (IDH1) and 2 (IDH2) are key drivers of diverse cancers, including gliomas and hematological malignancies. IDH mutations cause neomorphic enzymatic activity that results in the production of the oncometabolite 2-hydroxyglutarate (2-HG). In addition to 2-HG's well-known effects on tumor cells themselves, it has become increasingly clear that 2-HG directly influences the tumor microenvironment (TME). In particular, the non-cell-autonomous impact of 2-HG on the immune system likely plays a major role in shaping disease development and response to therapy. It is therefore critical to understand how IDH mutations affect the metabolism, epigenetics, and functions of tumor-infiltrating immune cells. Such knowledge may point towards new therapeutic approaches to treat IDH-mutant cancers.

Current biomarker-associated procedures of cancer modeling-a reference in the context of IDH1 mutant glioma

Isocitrate dehydrogenases (IDH1/2) are central molecular markers for glioblastoma. Providing in vitro or in vivo models with mutated IDH1/2 can help prepare facilities to understand the biology of these mutated genes as glioma markers, as well as help, improve therapeutic strategies. In this review, we first summarize the biology principles of IDH and its mutations and outline the core primary findings in the clinical context of neuro-oncology. Given the extensive research interest and exciting developments in current stem cell biology and genome editing, the central part of the manuscript is dedicated to introducing various routes of disease modeling strategies of IDH mutation (IDHMut) glioma and comparing the scientific-technological findings from the field using different engineering methods. Lastly, by giving our perspective on the benefits and limitations of patient-derived and donor-derived disease modeling respectively, we aim to propose leading research questions to be answered in the context of IDH1 and glioma.

Needle in a Haystack: The Naïve Repertoire as a Source of T Cell Receptors for Adoptive Therapy with Engineered T Cells

T cell engineering with antigen-specific T cell receptors (TCRs) has allowed the generation of increasingly specific, reliable, and versatile T cell products with near-physiological features. However, a broad applicability of TCR-based therapies in cancer is still limited by the restricted number of TCRs, often also of suboptimal potency, available for clinical use. In addition, targeting of tumor neoantigens with TCR-engineered T cell therapy moves the field towards a highly personalized treatment, as tumor neoantigens derive from somatic mutations and are extremely patient-specific. Therefore, relevant TCRs have to be de novo identified for each patient and within a narrow time window. The naïve repertoire of healthy donors would represent a reliable source due to its huge diverse TCR repertoire, which theoretically entails T cells for any antigen specificity, including tumor neoantigens. As a challenge, antigen-specific naïve T cells are of extremely low frequency and mostly of low functionality, making the identification of highly functional TCRs finding a "needle in a haystack." In this review, we present the technological advancements achieved in high-throughput mapping of patient-specific neoantigens and corresponding cognate TCRs and how these platforms can be used to interrogate the naïve repertoire for a fast and efficient identification of rare but therapeutically valuable TCRs for personalized adoptive T cell therapy.

Prognostic significance of ARL9 and its methylation in low-grade glioma

This study aimed to determine the value of ARL9 expression or methylation as a biomarker for LGG survival. We investigated the expression, methylation, prognosis and immune significance of ARL9 through bioinformatics analysis. ARL9 is negatively regulated by ARL9 methylation, leading to its low expression in LGG tissues. Both low ARL9 expression and hypermethylation predicted favorable OS and PFS in LGG patients, according to the TCGA database. Cox regression demonstrated that low ARL9 expression and ARL9 hypermethylation were independent biomarkers for OS. Moreover, three other glioma databases were utilized to verify the prognostic role of ARL9 in LGG, and the similar results were reached. A meta-analysis revealed that low ARL9 expression was closely relevant to better OS. Finally, ARL9 expression exhibited a close correlation with some immune cells, especially CD8+ T cells. ARL9 could constitute a promising prognostic biomarker, and probably plays an important role in immune cell infiltration in LGG.

•

This is the first study to report the clinical and prognostic significance of ARL9, a methylation-driven gene，in LGG.

•

Meta-analysis could be used for bioinformatics analysis to assess the overall effect of the gene from different datasets.

•

ARL9 probably plays a role in the infiltration of immune cells, and acts as a promising prognostic marker in LGG patients.

SYT16 is a prognostic biomarker and correlated with immune infiltrates in glioma: A study based on TCGA data

BACKGROUND

Glioma is the most lethal primary brain tumor. Lower-grade glioma (LGG) is the crucial pathological type of Glioma. Immune-infiltration of the tumor microenvironment positively associated with overall survival in LGG. SYT16 is a gene has not been reported in cancer. We assess the role of SYT16 in LGG, via the publicly available TCGA database.

METHODS

Gene Expression Profiling Interactive Analysis (GEPIA) was used to analyze the expression of SYT16 in LGG. We evaluated the influence of SYT16 on survival of LGG patients by survival module. Then, datasets of LGG were downloaded from TCGA. The correlations between the clinical information and SYT16 expression were analyzed using logistic regression. Univariable survival and Multivariate Cox analysis was used to compare several clinical characteristics with survival. we also explore the correlation between SYT16 and cancer immune infiltrates using CIBERSORT and correlation module of GEPIA. Gene set enrichment analysis (GSEA) was performed using the TCGA dataset. In addition, we use TIMER to explore the collection of SYT16 Expression and Immune Infiltration Level in LGG and to explore cumulative survival in LGG.

RESULTS

The univariate analysis using logistic regression, indicated that increased SYT16 expression significantly correlated with the tumor grade. Moreover, multivariate analysis revealed that the up-regulated SYT16 expression is an independent prognostic factor for good prognosis. Specifically, SYT16 expression level has significant negative correlations with infiltrating levels of B cell, CD4+ T cells, Macrophages, Neutrophils and DCs in LGG. In addition, GSEA identified ingle organism behavior, gated channel activity, cognition, transporter complex and ligand gated channel activity  in Gene Ontology (GO) were differentially enriched in the high SYT16 expression phenotype pathway. Neuroactive ligand receptor interaction, calcium signaling pathway, long term potentiation, type II diabetes mellitus and long term depression were identified as differentially enriched  pathway in Kyoto Encyclopedia of Genes and Genomes (KEGG).

CONCLUSION

SYT16 is a Prognostic Biomarker and Correlated with Immune Infiltrates in LGG.