Group of Biomedical Research in Digestive Tract Tumors, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron, 119-129, 08035, Barcelona, Spain.
Group of Molecular Oncology, IRBLleida, 25198, Lleida, Spain.
Clin Epigenetics. 2021 Apr 23;13(1):88. doi: 10.1186/s13148-021-01070-0.
Cancer initiation and progression are driven by genetic and epigenetic changes. Although genome/exome sequencing has significantly contributed to the characterization of the genetic driver alterations, further investigation is required to systematically identify cancer driver genes regulated by promoter hypermethylation.
Using genome-wide analysis of promoter methylation in 45 colorectal cancer cell lines, we found that higher overall methylation levels were associated with microsatellite instability (MSI), faster proliferation and absence of APC mutations. Because epigenetically silenced genes could represent important oncogenic drivers, we used mRNA expression profiling of colorectal cancer cell lines and primary tumors to identify a subset of 382 (3.9%) genes for which promoter methylation was negatively associated with gene expression. Remarkably, a significant enrichment in zinc finger proteins was observed, including the transcriptional repressor ZBTB18. Re-introduction of ZBTB18 in colon cancer cells significantly reduced proliferation in vitro and in a subcutaneous xenograft mouse model. Moreover, immunohistochemical analysis revealed that ZBTB18 is frequently lost or reduced in colorectal tumors, and reduced ZBTB18 expression was found to be associated with lymph node metastasis and shorter survival of patients with locally advanced colorectal cancer.
We identified a set of 382 genes putatively silenced by promoter methylation in colorectal cancer that could significantly contribute to the oncogenic process. Moreover, as a proof of concept, we demonstrate that the epigenetically silenced gene ZBTB18 has tumor suppressor activity and is a novel prognostic marker for patients with locally advanced colorectal cancer.
癌症的发生和发展是由遗传和表观遗传变化驱动的。尽管基因组/外显子测序极大地促进了对遗传驱动改变的特征描述，但仍需要进一步研究来系统地识别受启动子超甲基化调控的癌症驱动基因。
我们通过对 45 个结直肠癌细胞系的启动子甲基化进行全基因组分析，发现总体甲基化水平较高与微卫星不稳定（MSI）、较快的增殖和 APC 突变缺失有关。由于表观遗传沉默的基因可能代表重要的致癌驱动基因，我们使用结直肠癌细胞系和原发肿瘤的 mRNA 表达谱分析来鉴定出 382 个（3.9%）基因，这些基因的启动子甲基化与基因表达呈负相关。值得注意的是，观察到锌指蛋白的显著富集，包括转录抑制因子 ZBTB18。在结肠癌细胞中重新引入 ZBTB18 显著降低了体外和皮下异种移植小鼠模型中的增殖。此外，免疫组织化学分析显示 ZBTB18 在结直肠肿瘤中经常丢失或减少，并且发现 ZBTB18 表达减少与局部晚期结直肠癌的淋巴结转移和患者生存时间缩短相关。
我们确定了一组在结直肠癌中可能通过启动子甲基化沉默的 382 个潜在基因，这些基因可能对致癌过程有重要贡献。此外，作为概念验证，我们证明了表观遗传沉默基因 ZBTB18 具有肿瘤抑制活性，并且是局部晚期结直肠癌患者的新的预后标志物。
