Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.
Mol Cancer. 2010 May 27;9:125. doi: 10.1186/1476-4598-9-125.
Genome-wide DNA hypomethylation plays a role in genomic instability and carcinogenesis. LINE-1 (L1 retrotransposon) constitutes a substantial portion of the human genome, and LINE-1 methylation correlates with global DNA methylation status. LINE-1 hypomethylation in colon cancer has been strongly associated with poor prognosis. However, whether LINE-1 hypomethylators constitute a distinct cancer subtype remains uncertain. Recent evidence for concordant LINE-1 hypomethylation within synchronous colorectal cancer pairs suggests the presence of a non-stochastic mechanism influencing tumor LINE-1 methylation level. Thus, it is of particular interest to examine whether its wide variation can be attributed to clinical, pathologic or molecular features.
Utilizing a database of 869 colorectal cancers in two prospective cohort studies, we constructed multivariate linear and logistic regression models for LINE-1 methylation (quantified by Pyrosequencing). Variables included age, sex, body mass index, family history of colorectal cancer, smoking status, tumor location, stage, grade, mucinous component, signet ring cells, tumor infiltrating lymphocytes, CpG island methylator phenotype (CIMP), microsatellite instability, expression of TP53 (p53), CDKN1A (p21), CTNNB1 (beta-catenin), PTGS2 (cyclooxygenase-2), and FASN, and mutations in KRAS, BRAF, and PIK3CA.
Tumoral LINE-1 methylation ranged from 23.1 to 90.3 of 0-100 scale (mean 61.4; median 62.3; standard deviation 9.6), and distributed approximately normally except for extreme hypomethylators [LINE-1 methylation < 40; N = 22 (2.5%), which were far more than what could be expected by normal distribution]. LINE-1 extreme hypomethylators were significantly associated with younger patients (p = 0.0058). Residual plot by multivariate linear regression showed that LINE-1 extreme hypomethylators clustered as one distinct group, separate from the main tumor group. The multivariate linear regression model could explain 8.4% of the total variability of LINE-1 methylation (R-square = 0.084). Multivariate logistic regression models for binary LINE-1 hypomethylation outcomes (cutoffs of 40, 50 and 60) showed at most fair predictive ability (area under receiver operator characteristics curve < 0.63).
LINE-1 extreme hypomethylators appear to constitute a previously-unrecognized, distinct subtype of colorectal cancers, which needs to be confirmed by additional studies. Our tumor LINE-1 methylation data indicate enormous epigenomic diversity of individual colorectal cancers.
全基因组 DNA 低甲基化在基因组不稳定性和致癌作用中起作用。LINE-1(L1 反转录转座子)构成人类基因组的很大一部分,LINE-1 甲基化与全球 DNA 甲基化状态相关。结肠癌中的 LINE-1 低甲基化与预后不良强烈相关。然而,LINE-1 低甲基化是否构成一个独特的癌症亚型仍不确定。最近关于同步结直肠肿瘤对中 LINE-1 低甲基化的一致性的证据表明,存在影响肿瘤 LINE-1 甲基化水平的非随机机制。因此,特别感兴趣的是检查其广泛的变异性是否可以归因于临床、病理或分子特征。
利用两个前瞻性队列研究中 869 例结直肠癌的数据库,我们构建了 LINE-1 甲基化(通过焦磷酸测序定量)的多变量线性和逻辑回归模型。变量包括年龄、性别、体重指数、结直肠癌家族史、吸烟状况、肿瘤位置、分期、分级、粘液成分、印戒细胞、肿瘤浸润淋巴细胞、CpG 岛甲基化表型(CIMP)、微卫星不稳定性、TP53(p53)、CDKN1A(p21)、CTNNB1(β-连环蛋白)、PTGS2(环氧化酶-2)和 FASN 的表达,以及 KRAS、BRAF 和 PIK3CA 的突变。
肿瘤的 LINE-1 甲基化范围为 0-100 标度的 23.1 至 90.3(平均值 61.4;中位数 62.3;标准差 9.6),除了极端低甲基化者[LINE-1 甲基化<40;N=22(2.5%)]外,分布大致呈正态分布,这远远超过正态分布的预期。LINE-1 极端低甲基化者与年轻患者显著相关(p=0.0058)。多变量线性回归残差图显示,LINE-1 极端低甲基化者聚为一组,与主要肿瘤组分开。多变量线性回归模型可以解释 LINE-1 甲基化总变异的 8.4%(R 平方=0.084)。用于二元 LINE-1 低甲基化结果的多变量逻辑回归模型(40、50 和 60 的截断值)显示出最大的预测能力(接受者操作特征曲线下面积<0.63)。
LINE-1 极端低甲基化者似乎构成了以前未被识别的结直肠癌独特亚型,这需要通过进一步研究来证实。我们的肿瘤 LINE-1 甲基化数据表明个体结直肠癌存在巨大的表观基因组多样性。