2Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Building 10-Hatfield CRC, Room 2-5952, Bethesda, MD 20892-1210 USA.
1Department of Urology, University of California, Mail code 1695, 550 16th Street, 6th Floor, San Francisco, CA 94143 USA.
Clin Epigenetics. 2018 Feb 12;10:19. doi: 10.1186/s13148-018-0451-x. eCollection 2018.
Elucidation of epigenetic alterations in bladder cancer will lead to further understanding of the biology of the disease and hopefully improved therapies. Our aim was to perform an integrative epigenetic analysis of invasive urothelial carcinoma of the bladder to identify the epigenetic abnormalities involved in the development and progression of this cancer.
Pre-processed methylation data and RNA-seq data were downloaded from The Cancer Genome Atlas (TCGA) and processed using the R package TCGA-Assembler. An R package MethylMix was used to perform an analysis incorporating both methylation and gene expression data on all samples, as well as a subset analysis comparing patients surviving less than 2 years and patients surviving more than 2 years. Genes associated with poor prognosis were individually queried. Pathway analysis was performed on statistically significant genes identified by MethylMix criteria using ConsensusPathDB. Validation was performed using flow cytometry on bladder cancer cell lines.
A total of 408 patients met all inclusion criteria. There were a total of 240 genes differentially methylated by MethylMix criteria. Review of individual genes specific to poor-prognosis patients revealed the majority to be candidate tumor suppressors in other cancer types. Pathway analysis showed increase in methylation of genes involved in antioxidant pathways including glutathione and NRF2. Genes involved in estrogen metabolism were also hypermethylated while genes involved in the EGFR pathway were found to be hypomethylated. EGFR expression was confirmed to be elevated in six bladder cancer cell lines.
In patients with invasive urothelial carcinoma, we found differential methylation in patients with better and worse prognosis after cystectomy. Differentially methylated genes are involved in many relevant oncologic pathways, including EGFR and antioxidant pathways, that may be a target for therapy or chemoprevention.
阐明膀胱癌的表观遗传改变将有助于进一步了解疾病的生物学特性，并有望改善治疗方法。我们的目的是对浸润性膀胱癌进行综合表观遗传学分析，以确定涉及这种癌症发生和进展的表观遗传异常。
从癌症基因组图谱（TCGA）下载预处理的甲基化数据和 RNA-seq 数据，并使用 R 包 TCGA-Assembler 进行处理。使用 R 包 MethylMix 对所有样本进行分析，同时对生存时间少于 2 年和生存时间超过 2 年的患者进行亚组分析，将甲基化和基因表达数据结合起来进行分析。对与预后不良相关的基因进行单独查询。使用 ConsensusPathDB 对 MethylMix 标准确定的具有统计学意义的基因进行通路分析。使用流式细胞术在膀胱癌细胞系中进行验证。
共有 408 名患者符合所有纳入标准。MethylMix 标准有 240 个基因发生差异甲基化。对预后不良患者特定的个别基因进行审查发现，大多数是其他癌症类型的候选肿瘤抑制基因。通路分析显示，抗氧化途径（包括谷胱甘肽和 NRF2）中参与甲基化的基因增加。雌激素代谢相关基因也呈高甲基化，而 EGFR 途径相关基因呈低甲基化。证实 EGFR 表达在六种膀胱癌细胞系中升高。
在接受膀胱切除术的浸润性膀胱癌患者中，我们发现预后较好和较差的患者存在差异甲基化。差异甲基化基因涉及许多相关的肿瘤学途径，包括 EGFR 和抗氧化途径，这些途径可能是治疗或化学预防的靶点。
