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...

Human colorectal cancer (CRC) is a major cause of cancer mortality and frequently harbors activating mutations in the KRAS gene. To understand the role of oncogenic KRAS in CRC, we engineered a mouse model of metastatic CRC that harbors an inducible oncogenic Kras allele (Kras mut ) and conditional null alleles of Apc and Trp53 (iKAP). The iKAP model recapitulates tumor progression from adenoma through metastases. Whole-exome sequencing revealed that the Kras mut allele was heterogenous in primary tumors yet homogenous in metastases, a pattern consistent with activated Kras mut signaling being a driver of progression to metastasis. System-level and functional analyses revealed the TGF-β pathway as a key mediator of Kras mut -driven invasiveness. Genetic extinction of Kras mut resulted in specific elimination of the Kras mut subpopulation in primary and metastatic tumors, leading to apoptotic elimination of advanced invasive and metastatic disease. This faithful CRC model provides genetic evidence that Kras mut drives CRC invasion and maintenance of metastases.