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一种基于14个染色质调节因子相关基因的新型风险评分模型,用于预测低级别胶质瘤患者的总生存期。

A novel risk score model based on fourteen chromatin regulators-based genes for predicting overall survival of patients with lower-grade gliomas.

作者信息

Zhang Yongfeng, Yu Beibei, Tian Yunze, Ren Pengyu, Lyu Boqiang, Fu Longhui, Chen Huangtao, Li Jianzhong, Gong Shouping

机构信息

Department of Neurourgery, The Second Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China.

Department of Thoracic Surgery, The Second Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China.

出版信息

Front Genet. 2022 Sep 26;13:957059. doi: 10.3389/fgene.2022.957059. eCollection 2022.

Abstract

Low grade gliomas(LGGs) present vexatious management issues for neurosurgeons. Chromatin regulators (CRs) are emerging as a focus of tumor research due to their pivotal role in tumorigenesis and progression. Hence, the goal of the current work was to unveil the function and value of CRs in patients with LGGs. RNA-Sequencing and corresponding clinical data were extracted from The Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA) database. A single-cell RNA-seq dataset was sourced from the Gene Expression Omnibus (GEO) database. Altogether 870 CRs were retrieved from the published articles in top academic journals. The least absolute shrinkage and selection operator (LASSO) algorithm and Cox regression analysis were applied to construct the prognostic risk model. Patients were then assigned into high- and low-risk groups based on the median risk score. The Kaplan-Meier (K-M) survival curve and receiver operating characteristic curve (ROC) were performed to assess the prognostic value. Sequentially, functional enrichment, tumor immune microenvironment, tumor mutation burden, drug prediction, single cell analysis and so on were analyzed to further explore the value of CR-based signature. Finally, the expression of signature genes were validated by immunohistochemistry (IHC) and quantitative real-time PCR (qRT-PCR). We successfully constructed and validated a 14 CRs-based model for predicting the prognosis of patients with LGGs. Moreover, we also found 14 CRs-based model was an independent prognostic factor. Functional analysis revealed that the differentially expressed genes were mainly enriched in tumor and immune related pathways. Subsequently, our research uncovered that LGGs patients with higher risk scores exhibited a higher TMB and were less likely to be responsive to immunotherapy. Meanwhile, the results of drug analysis offered several potential drug candidates. Furthermore, tSNE plots highlighting the magnitude of expression of the genes of interest in the cells from the scRNA-seq assay. Ultimately, transcription expression of six representative signature genes at the mRNA level was consistent with their protein expression changes. Our findings provided a reliable biomarker for predicting the prognosis, which is expected to offer new insight into LGGs management and would hopefully become a promising target for future research.

摘要

低级别胶质瘤(LGGs)给神经外科医生带来了棘手的管理问题。染色质调节因子(CRs)因其在肿瘤发生和进展中的关键作用,正成为肿瘤研究的一个焦点。因此,当前工作的目标是揭示CRs在LGGs患者中的功能和价值。从癌症基因组图谱(TCGA)和中国胶质瘤基因组图谱(CGGA)数据库中提取RNA测序数据及相应的临床数据。单细胞RNA测序数据集来自基因表达综合数据库(GEO)。总共从顶级学术期刊上发表的文章中检索到870个CRs。应用最小绝对收缩和选择算子(LASSO)算法及Cox回归分析来构建预后风险模型。然后根据中位风险评分将患者分为高风险组和低风险组。绘制Kaplan-Meier(K-M)生存曲线和受试者工作特征曲线(ROC)以评估预后价值。随后,进行功能富集、肿瘤免疫微环境、肿瘤突变负荷、药物预测、单细胞分析等,以进一步探索基于CRs的特征的价值。最后,通过免疫组织化学(IHC)和定量实时PCR(qRT-PCR)验证特征基因的表达。我们成功构建并验证了一个基于14个CRs的模型,用于预测LGGs患者的预后。此外,我们还发现基于14个CRs的模型是一个独立的预后因素。功能分析表明,差异表达基因主要富集在肿瘤和免疫相关途径中。随后,我们的研究发现,风险评分较高的LGGs患者表现出较高的肿瘤突变负荷,且对免疫治疗反应的可能性较小。同时,药物分析结果提供了几种潜在的候选药物。此外,tSNE图突出显示了来自scRNA-seq分析的细胞中感兴趣基因的表达程度。最终,六个代表性特征基因在mRNA水平的转录表达与其蛋白质表达变化一致。我们的研究结果提供了一个可靠的预后预测生物标志物,有望为LGGs的管理提供新的见解,并有望成为未来研究的一个有前景的靶点。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8908/9554745/574e070a49b0/fgene-13-957059-g001.jpg

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