High-resolution mapping of DNA hypermethylation and hypomethylation in lung cancer

Abstract

Changes in DNA methylation patterns are an important characteristic of human cancer. Tumors have reduced levels of genomic DNA methylation and contain hypermethylated CpG islands, but the full extent and sequence context of DNA hypomethylation and hypermethylation is unknown. Here, we used methylated CpG island recovery assay-assisted high-resolution genomic tiling and CpG island arrays to analyze methylation patterns in lung squamous cell carcinomas and matched normal lung tissue. Normal tissues from different individuals showed overall very similar DNA methylation patterns. Each tumor contained several hundred hypermethylated CpG islands. We identified and confirmed 11 CpG islands that were methylated in 80 -100% of the SCC tumors, and many hold promise as effective biomarkers for early detection of lung cancer. In addition, we find that extensive DNA hypomethylation in tumors occurs specifically at repetitive sequences, including short and long interspersed nuclear elements and LTR elements, segmental duplications, and subtelomeric regions, but single-copy sequences rarely become demethylated. The results are consistent with a specific defect in methylation of repetitive DNA sequences in human cancer.DNA methylation ͉ tiling arrays ͉ CpG islands C hanges in DNA methylation patterns are frequent events in human tumors (1). DNA hypomethylation in cancer tissue was first observed more than two decades ago (2-6) and may be mechanistically linked to tumorigenesis (7). In the 1990s, researchers reported hypermethylation of CpG islands of several known and putative tumor suppressor genes and other genes involved in important genome defense pathways, such as DNA repair (1,(8)(9)(10)(11)(12). Today, there are many reports that have documented methylation of CpG islands associated with a large number of different genes, including almost every type of human cancer. In lung cancer, several CpG islands known to be methylated include those associated with CDKN2A, RASSF1A, RARbeta, MGMT, GSTP1, CDH13, APC, DAPK, TIMP3,. The methylation frequency (i.e., the percentage of tumors analyzed that carry methylated alleles) ranges from Ͻ10% to Ϸ80%, but these numbers differ widely depending on the tumor histology, the study population, and/or the methodology used to assess methylation. Detection of methylated CpG islands in easily accessible biological materials such as serum or sputum has the potential to be useful for the early diagnosis of lung cancer and other malignancies (18)(19)(20).Repetitive DNA elements, such as short and long interspersed nuclear elements (SINEs and LINEs, respectively) and simple repeat sequences, are often found hypomethylated in tumors (21-26). Although it seems clear that methylation-induced silencing of tumor suppressor genes can be an important event in tumorigenesis, the magnitude, exact sequence specificity, and biological significance of tumor-associated DNA hypomethylation is much less understood (21, 26). In particular, the extent and sequence context of single-copy gene and general genome hy...

DNA hypermethylation in lung cancer is targeted at differentiation-associated genes

“…We obtained previously published CpG island methylation data for five human NSCLCs (GSE9622) (Rauch et al, 2008). In this study, a methylated-CpG island recovery assay was combined with CpG island-tiling arrays to characterize genome-wide methylation levels at high resolution.…”

“…We compared the distribution of log2 (tumor/normal) values for each primary tumor sample and verified that all were approximately normal with a slight bias toward methylation. To identify the hypermethylated gene sets for each primary tumor sample, we used the method used by Rauch et al (2008). A CpG island was considered hypermethylated if it contained at least two adjacent probes (allowing a one-probe gap) exhibiting a fold change of X2 in the tumor sample vs the matched normal tissue.…”

“…In lung cancer, the hypermethylation of CpG islands in promoter regions appears to be a common occurrence, as demonstrated by the analysis of genes from primary tumors, cell lines, patient sputum and serum (Rauch et al, 2008;Pfeifer and Rauch, 2009). Methylation 'signatures' with promising diagnostic and prognostic ability have emerged as potential biomarkers for lung cancer progression (Tsou et al, 2002;Belinsky, 2004;Safar et al, 2005).…”

Chromatin maps, histone modifications and leukemia

“…8,9 Recent years have witnessed genome-wide methylation maps, with different levels of resolution on the basis of the corresponding technology employed (reviewed in 10 ). Genome-wide DNA methylation studies have been published for solid tumors such as lung cancer, 11,12 and for leukemias. AML cell lines 13 and primary samples have been studied, and in one study relapse was associated with increased methylation of CpG islands.…”

Profils de méthylation de l’ADN dans les cellules normales et cancéreuses

“…De telles régions hypométhylées ont aussi été récemment observées dans les cellules de cancer du sein [14]. En plus de ces régions, les éléments répétés du génome sont également fréquemment hypométhylés dans les cellules cancéreuses [15]. Les conséquences de ces hypométhylations à grande échelle sont encore mal connues, mais il est probable qu'elles affectent la stabilité du génome et favorisent les recombinaisons.…”