Distinct hypermethylation patterns occur at altered chromosome loci in human lung and colon cancer.

Abstract

Regional increases in DNA methylation occur in normally unmethylated cytosine-rich areas in neoplastic cells. These changes could potentially alter chromatin structure to inactivate gene transcription or generate DNA instability. We now show that, in human lung and colon cancer DNA, hypermethylation of such a region consistently occurs on chromosome 17p in an area that is frequently reduced to homozygosity in both tumor types. Over the progression stages of colon neoplasia, this methylation change increases in extent and precedes the allelic losses on 17p that are characteristic of colon carcinomas. We also show on chromosome 3p that regional hypermethylation may nonrandomly accompany chromosome changes in human neoplasia. Increased methylation is consistent in small-cell lung carcinoma DNA at two 3p loci that are constantly reduced to homozygosity in this tumor, but it is not seen in colon cancer DNA, in which these loci are infrequently structurally altered.Alterations in DNA cytosine methylation are one of the most consistent, but poorly understood, molecular changes in human cancers (reviewed in refs. 1 and 2). These abnormalities appear early in progression of tumors and reflect an imbalance in the DNA methylation process that includes widespread hypomethylation (3), regional areas of hypermethylation (4), and an increased cellular capacity to methylate DNA (5, 6). The regional hypermethylation may be particularly important. Our laboratory (4) and others (7,8) have found this change in clusters of CpG dinucleotides near regulatory areas of genes. A normally unmethylated status of these "CpG islands" appears to be essential for active gene transcription (reviewed in ref. 9). Conversely, cytosine methylation within CpG islands can either stabilize or cause alterations in chromatin structure that render chromosome regions transcriptionally inactive (for review, ref. 10) or subject to DNA instability (11).We now explore whether chromosomal regions that are distinctively altered in human cancers are nonrandomly associated with hypermethylation and how the timing of this abnormality relates to changes in chromosome structure during tumor progression. A CpG-island-rich area on chromosome 17p, consistently reduced to homozygosity in both lung and colon cancers, is extensively hypermethylated in both tumor types. During progression stages for colon neoplasia, this abnormal methylation occurs early, increases in extent, and precedes allelic losses of the involved region. We also find that regions of chromosome 3p that are consistently reduced to homozygosity in lung, but not colon, cancers are hypermethylated only in lung cancer. We suggest that DNA hypermethylation nonrandomly marks chromosome regions altered during the development of specific tumors.

Concordant methylation of the ER and N33 genes in glioblastoma multiforme

“…In a previous study of HIC1 methylation status in neural tumors, we found hypermethylation of all NotI sites in and around the region of the gene in virtually all low-and mid-grade astrocytomas but only in 50% of high grade gliomas (Makos et al, 1993a). In the present study, a range of methylation was seen in the majority of tumors ( Figure 1c) and these patterns must be put into perspective with the methylation status of HIC1 in normal brain.…”

“…HIC1 is now known to exhibit partial methylation in normal cells in a tissue speci®c way ranging from no methylation in sites such as blood and bone marrow cells (Issa et al, 1997b), ®broblasts, skin and colon (Wales et al, 1995), to methylation of only 2 ± 3 of the most 5' NotI sites in kidney (Makos et al, 1993b) and bronchial epithelium (Vertino et al, 1993), to a most interesting pattern of 50% completely methylated and 50% unmethylated alleles in breast (Issa JPJ, unpublished observations) and prostate epithelium (Morton et al, 1996). Our present data suggest that cells of the central nervous system are also characterized by partial methylation at the HIC1 locus.…”

“…Neuroblastomas, as well as a fraction of GBM, appear to have less methylation than normal brain (Makos et al, 1993a) and this may be due to loss of the methylated allele in the tumor, true demethylation, or cancer initiation in a totally unmethylated cell. The functional signi®cance of HIC1 methylation in GBM will have to await careful expression studies in normal and neoplastic brain tissues.…”

“…Molecular alterations described in GBM involve overexpression of oncogenes (Furnari et al, 1995) (EGFR, VEGF, Ras, PDGF, PDGFR), mutational inactivation of TSG (Steck et al, 1997;Li et al, 1997;Furnari et al, 1995) (P53, P16, RB, PTEN/ MMAC1) and hypermethylation of the HIC1, P16 and P15 genes (Makos et al, 1993a;Herman et al, 1995Herman et al, , 1996Costello et al, 1996;Fueyo et al, 1996). The factors that lead to promoter methylation in GBM and the interactions between di erent methylation events remain poorly de®ned.…”

Methylation of the HIC-1 candidate tumor suppressor gene in human breast cancer

“…Whereas VHL and MTS-1/p16 were both initially established as tumor suppressor genes by linkage to hereditary cancers and by ®ndings of tumor speci®c somatic mutations, the HIC-1 candidate tumor suppressor gene was identi®ed by cloning of a 17p13.3 chromosomal region which contained a dense CpG island that is hypermethylated in tumor cell DNA (Makos-Wales et al, 1995). The HIC-1 gene has been found to be extensively methylated in primary glioblastomas, colon and renal cell carcinomas (Makos et al, 1992(Makos et al, , 1993a and in cell lines derived from cancers of the brain, breast, colon and lung (Makos-Wales et al, 1995). In established cell lines, this methylation has been found to be associated with transcriptional inactivation of the gene (Makos-Wales et al, 1995).…”