染色质可及性分析鉴定 GSTM1 为人类胶质母细胞瘤患者的预后标志物。
Chromatin accessibility analysis identifies GSTM1 as a prognostic marker in human glioblastoma patients.
机构信息
Department of Neurosurgery, Chang Gung Memorial Hospital at Linkou, Taoyuan, 333, Taiwan.
Department of Medicine, Chang Gung University, Taoyuan, 333, Taiwan.
出版信息
Clin Epigenetics. 2021 Nov 3;13(1):201. doi: 10.1186/s13148-021-01181-8.
BACKGROUND
Glioblastoma (GBM) is a malignant human brain tumor that has an extremely poor prognosis. Classic mutations such as IDH (isocitrate dehydrogenase) mutations, EGFR (epidermal growth factor receptor) alternations, and MGMT (O6-methylguanine-methyltransferase) promoter hypermethylation have been used to stratify patients and provide prognostic significance. Epigenetic perturbations have been demonstrated in glioblastoma tumorigenesis. Despite the genetic markers used in the management of glioblastoma patients, new biomarkers that could predict patient survival independent of known biomarkers remain to be identified.
METHODS
ATAC-seq (assay for transposase accessible chromatin followed by sequencing) and RNA-seq have been used to profile chromatin accessible regions using glioblastoma patient samples with short-survival versus long-survival. Cell viability, cell cycle, and Western blot analysis were used to characterize the cellular phenotypes and identify signaling pathways.
RESULTS
Analysis of chromatin accessibility by ATAC-seq coupled with RNA-seq methods identified the GSTM1 (glutathione S-transferase mu-1) gene, which featured higher chromatin accessibility in GBM tumors with short survival. GSTM1 was confirmed to be a significant prognostic marker to predict survival using a different GBM patient cohort. Knockdown of GSTM1 decreased cell viability, caused cell cycle arrest, and decreased the phosphorylation levels of the NF-kB (nuclear factor kappa B) p65 subunit and STAT3 (signal transducer and activator of transcription 3) (pSer727).
CONCLUSIONS
This report demonstrates the use of ATAC-seq coupled with RNA-seq to identify GSTM1 as a prognostic marker of GBM patient survival. Activation of phosphorylation levels of NF-kB p65 and STAT3 (pSer727) by GSTM1 is shown. Analysis of chromatin accessibility in patient samples could generate an independent biomarker that can be used to predict patient survival.
背景
胶质母细胞瘤（GBM）是一种恶性人类脑肿瘤，预后极差。经典的突变，如 IDH（异柠檬酸脱氢酶）突变、EGFR（表皮生长因子受体）改变和 MGMT（O6-甲基鸟嘌呤甲基转移酶）启动子超甲基化，已被用于对患者进行分层并提供预后意义。在胶质母细胞瘤的发生过程中已经证明了表观遗传扰动。尽管在胶质母细胞瘤患者的管理中使用了遗传标志物，但仍需要鉴定新的生物标志物，这些标志物可以独立于已知的标志物预测患者的生存。
方法
使用 ATAC-seq（转座酶可及染色质测序）和 RNA-seq profiling 短存活与长存活的胶质母细胞瘤患者样本中的染色质可及区域。细胞活力、细胞周期和 Western blot 分析用于表征细胞表型并鉴定信号通路。
结果
通过 ATAC-seq 与 RNA-seq 方法分析染色质可及性，鉴定出 GSTM1（谷胱甘肽 S-转移酶 mu-1）基因，该基因在短存活的 GBM 肿瘤中具有更高的染色质可及性。使用不同的 GBM 患者队列证实 GSTM1 是预测生存的重要预后标志物。GSTM1 的敲低降低了细胞活力，导致细胞周期停滞，并降低了 NF-kB（核因子 kappa B）p65 亚基和 STAT3（信号转导和转录激活因子 3）（pSer727）的磷酸化水平。
结论
本报告证明了使用 ATAC-seq 与 RNA-seq 相结合来鉴定 GSTM1 作为 GBM 患者生存的预后标志物。显示了 GSTM1 对 NF-kB p65 和 STAT3（pSer727）磷酸化水平的激活。对患者样本中染色质可及性的分析可以生成独立的生物标志物，可用于预测患者的生存。
Zotero 插件