Molecular subtyping reveals immune alterations in <scp><i>IDH</i></scp> wild‐type lower‐grade diffuse glioma

Wu, Fan; Li, Guanzhang; Liu, Han-Jie; Zhao, Zheng; Chai, Rui‐Chao; Liu, Yuqing; Jiang, Haiyan; Zhai, You; Feng, Yuemei; Li, Renpeng; Zhang, Wei

doi:10.1002/path.5468

Cited by 48 publications

(44 citation statements)

References 54 publications

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“…Previous studies [ 10 , [22] , [23] , [24] ] pointed out that tumor-infiltrating immune cells have emerged as a key regulator of tumor growth and progression in LGG. Tumor-infiltrating immune cells are part of the complex microenvironment and are associated with the biological behavior and patient survival in LGG [ [25] , [26] , [27] , [28] , [29] ].…”

Section: Discussionmentioning

confidence: 99%

“…In addition, we performed a comprehensive meta-analysis to assess the overall prognostic significance of ARL9 using data from four public databases. Moreover, as substantial attention has been focused on the crucial role of the immune microenvironment in the progression of LGG [ [10] , [11] , [12] , [13] ], we also mined Tumor Immune Estimation Resource (TIMER) database to evaluate the potential correlation between ARL9 and immune infiltration levels in LGG. Finally, we examined the biological processes of ARL9 in which ARL9 is involved through gene enrichment analysis, to study the functional mechanism of ARL9 in LGG.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2020

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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.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

et al. 2020

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“…A lot of studies have found that tumour-in ltrating immune cells play an important role in the progression and development of cancer [24][25][26][27]. Few studies have pointed out the relationship between EMILIN2 and immune in ltration.…”

Section: Discussion/conclusionmentioning

confidence: 99%

EMILIN2 Correlated With Its Methylation and Immune Infiltration Could Be an Independent Prognostic Biomarker in LGG

Wang¹,

Zhang²,

Tan³

et al. 2021

Preprint

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Low-grade gliomas (LGGs) are slow-growing brain cancer in central nervous system neoplasms. EMILIN2 is an extracellular matrix (ECM) protein which could influence the progress of some tumour which is unclear in LGG. In our study, the methylation, expression, prognosis and immune value of EMILIN2 were analysed in LGG through bioinformatics analysis. we first analysed the LGG data from TCGA and discovered that the EMILIN2 expression, negatively correlated to the EMILIN2 methylation could predict a poor prognosis and associated with different clinical parameters. Moreover, univariate and multivariate Cox regression were performed in CGGA showed that the EMILIN2 could be an independent prognostic biomarker in LGG. Finally, EMILIN2 expression showed a correlation with gene makers in some immune cells which identified the significance of EMILIN2 in immune infiltration. In conclusion, EMILIN2 could act as an independent prognostic biomarker which might be associated with the malignancy and development of gliomas and play a crucial role in glioma in immune infiltration.

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“…Using R package ‘ConsensusClusterPlus’, consensus clustering was performed for class discovery based on the comparison of alternative splicing profile 21‐23 . Measured by median absolute deviation (MAD > 0.16), the most variable AS events were retained for subsequent clustering.…”

Section: Methodsmentioning

confidence: 99%

Characterization and prognostic significance of alternative splicing events in lower‐grade diffuse gliomas

Zhao

Liu

et al. 2020

J Cellular Molecular Medi

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Alternative splicing (AS) is assumed to play important roles in the progression and prognosis of cancer. Currently, the comprehensive analysis and clinical relevance of AS in lower‐grade diffuse gliomas have not been systematically addressed. Here, we gathered alternative splicing data of lower‐grade diffuse gliomas from SpliceSeq. Based on the Percent Spliced In (PSI) values of 515 lower‐grade diffuse glioma patients from the Cancer Genome Atlas (TCGA), we performed subtype‐differential AS analysis and consensus clustering to determine robust clusters of patients. A total of 48 050 AS events in 10 787 genes in lower‐grade diffuse gliomas were profiled. Subtype‐differential splicing analysis and functional annotation revealed that spliced genes were significantly enriched in numerous cancer‐related biological phenotypes and signalling pathways. Consensus clustering using AS events identified three robust clusters of patients with distinguished pathological and prognostic features. Moreover, each cluster was also associated with distinct genomic alterations. Finally, we developed and validated an AS‐related signature with Cox proportional hazards model. The signature, significantly associated with clinical and molecular features, could serve as an independent prognostic factor for lower‐grade diffuse gliomas. Thus, our results indicated that AS events could discriminate molecular subtypes and have prognostic impact in lower‐grade diffuse gliomas.

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Molecular subtyping reveals immune alterations in IDH wild‐type lower‐grade diffuse glioma

Cited by 48 publications

References 54 publications

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

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

EMILIN2 Correlated With Its Methylation and Immune Infiltration Could Be an Independent Prognostic Biomarker in LGG

Characterization and prognostic significance of alternative splicing events in lower‐grade diffuse gliomas

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