Long non‐coding <scp>RNA</scp>s in brain tumours: Focus on recent epigenetic findings in glioma

Pop, Sevinci; Enciu, Ana‐Maria; Necula, Laura; Tănase, Cristiana

doi:10.1111/jcmm.13781

Cited by 31 publications

(24 citation statements)

References 102 publications

(240 reference statements)

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“…The expression of these genes also highly correlates with risk score and expression of 7 well-established immune checkpoints. Most of the candidate immune checkpoint genes have been previously associated with glioma [37][38][39]. Kiang et al [40] reported that CRNDE is elevated in glioma and might be modulated by EGFR signaling to promote gliomagenesis.…”

Section: Discussionmentioning

confidence: 99%

A 1p/19q Codeletion-Associated Immune Signature for Predicting Lower Grade Glioma Prognosis

Liu

et al. 2020

Cell Mol Neurobiol

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Background: Lower grade gliomas (LGGs) with codeletion of chromosomal arms 1p and 19q (1p/19 codeletion) has a favorable outcome. However, its overall survival (OS) varies. Here, we established an immune signature associated with 1p/19q codeletion for accurate prediction of prognosis of LGGs. Methods: We extracted RNA sequencing and corresponding clinical data of LGGs from the Chinese Glioma Genome Atlas (CGGA) and The Cancer Genome Atlas (TCGA). The CGGA and TCGA databases were dichotomized into training group and testing group. The immune-related differentially expressed genes (DEGs) associated with 1p/19q codeletion were screened using Cox proportional hazards regression analyses. A prognostic signature was established using dataset from CGGA and tested in TCGA datasets. Subsequently, we explored the correlation between the prognostic signature and immune response. Results: Thirteen immune genes associated with 1p/19q codeletion were identi ed and used to construct a prognostic signature. The 1-, 3-, 5-year survival rates of the low-risk group were approximately 97%, 89%, and 79%, while those of the high-risk group were 81%, 50% and 34%, respectively in the training group. The nomogram which comprised of age, world health organization (WHO) grade, primary or recurrent types, 1p/19q codeletion status and risk score provided accurate prediction for the survival rate of glioma. DEGs that were highly expressed in the high-risk group clustered with many immune-related pathways. Immune checkpoints including T cell immunoglobulin domain and mucin domain 3 (TIM3), programmed cell death 1 (PD1), PD1 interacting with programmed death ligand 1 (PDL1), cytotoxic T lymphocyte antigen 4 (CTLA4), T cell immunoreceptor with Ig and ITIM domains (TIGIT), long non-coding RNA MIR 155 host gene (MIR155HG), and CD48 were correlated with the risk score. VAV3 and TNFRFSF11B were found to be candidate immune checkpoints. Conclusion: The 1p/19q codeletion-associated immune signature provides accurate prediction of OS. VAV3 and TNFRFSF11B are novel immune checkpoints.

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Section: Discussionmentioning

confidence: 99%

A 1p/19q Codeletion-Associated Immune Signature for Predicting Lower Grade Glioma Prognosis

Liu

et al. 2020

Cell Mol Neurobiol

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“…Long non-coding RNAs (lncRNAs) are a class of transcripts that are greater than 200 nts in length and lack of coding potential [11,13]. Nowadays, more and more lncRNAs have been suggested to be dysregulated in glioma tissues and involved in regulating glioma cell proliferation, differentiation, apoptosis, cell cycle, and autophagy [21–23,27].…”

Section: Introductionmentioning

confidence: 99%

Low LINC00599 expression is a poor prognostic factor in glioma

Zhou

et al. 2019

Bioscience Reports

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LINC00599 has been suggested to be involved in physiological and pathological processes including carcinogenesis. However, the clinical and prognostic significance of LINC00599 in glioma patients and the effect of LINC00599 on glioma cell migration and invasion remain unknown. In our results, we first observe the expression of LINC00599 in 31 types of human cancers including tumor tissues and corresponding normal tissues at The Cancer Genome Atlas (TCGA) database, and found that LINC00599 expression levels were only reduced in lower grade glioma (LGG) tissues and glioblastoma multiforme (GBM) tissues compared with normal brain tissues. Moreover, we confirmed levels of LINC00599 expression were decreased in glioma tissues and cell lines compared with matched adjacent normal tissues and normal human astrocytes (NHAs), respectively. Meanwhile, we found that glioma tissues with WHO III-IV grade exhibited lower levels of LINC00599 expression than glioma tissues with I-II grade. The survival analysis at TCGA data showed low LINC00599 expression was associated with poor disease-free survival and overall survival in glioma patients. In vitro study suggested up-regulation of LINC00599 depressed glioma cell migration and invasion through regulating epithelial–mesenchymal transition (EMT) process. In conclusion, LINC00599 acts as a tumor-suppressing long non-coding RNA (lncRNA) in glioma.

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“…Long non-coding RNAs are increasingly recognized as important players in cancer research [19], particularly as biomarkers and/or therapeutic targets [32][33][34][35][36], including in brain tumors [20,[37][38][39][40]. However, there is a lack of knowledge of lncRNAs' involvement in MBs.…”

Section: Discussionmentioning

confidence: 99%

In silico analysis of long non-coding RNAs in medulloblastoma and its subgroups

Joshi

Perera

2019

Preprint

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AbstractMedulloblastoma is the most common malignant pediatric brain tumor with high fatality rate. Recent large-scale studies utilizing genome-wide technologies have sub-grouped medulloblastomas into four major subgroups: wingless (WNT), sonic hedgehog (SHH), group 3, and group 4. However, there has yet to be a global analysis of long non-coding RNAs, a crucial part of the regulatory transcriptome, in medulloblastoma. Here, we performed bioinformatic analysis of RNA-seq data from 175 medulloblastoma patients. Differential lncRNA expression sub-grouped medulloblastomas into the four main molecular subgroups. Some of these lncRNAs were subgroup-specific, with a random forest-based machine-learning algorithm identifying an 11-lncRNA diagnostic signature. We also validated the diagnostic signature in patient derived xenograft (PDX) models. We further identified a 17-lncRNA prognostic model using LASSO based penalized Cox’ PH model (Score HR= 13.6301, 95% CI= 8.857-20.98, logrank p-value=< 2e-16). Our analysis represents the first global lncRNA analysis in medulloblastoma. Our results identify putative candidate lncRNAs that could be evaluated for their functional role in medulloblastoma genesis and progression or as diagnostic and prognostic biomarkers.

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Long non‐coding RNAs in brain tumours: Focus on recent epigenetic findings in glioma

Cited by 31 publications

References 102 publications

A 1p/19q Codeletion-Associated Immune Signature for Predicting Lower Grade Glioma Prognosis

A 1p/19q Codeletion-Associated Immune Signature for Predicting Lower Grade Glioma Prognosis

Low LINC00599 expression is a poor prognostic factor in glioma

In silico analysis of long non-coding RNAs in medulloblastoma and its subgroups

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