Methylation profiles of thirty four promoter-CpG islands and concordant methylation behaviours of sixteen genes that may contribute to carcinogenesis of astrocytoma

Abstract

BackgroundAstrocytoma is a common aggressive intracranial tumor and presents a formidable challenge in the clinic. Association of altered DNA methylation patterns of the promoter CpG islands with the expression profile of cancer-related genes, has been found in many human tumors. Therefore, DNA methylation status as such may serve as an epigenetic biomarker for both diagnosis and prognosis of human tumors, including astrocytoma.MethodsWe used the methylation specific PCR in conjunction with sequencing verification to establish the methylation profile of the promoter CpG island of thirty four genes in astrocytoma tissues from fifty three patients (The WHO grading:. I: 14, II: 15, III: 12 and IV: 12 cases, respectively). In addition, compatible tissues (normal tissues distant from lesion) from three non-astrocytoma patients were included as the control.ResultsSeventeen genes (ABL, APC, APAF1, BRCA1, CSPG2, DAPK1, hMLH1, LKB1, PTEN, p14ARF, p15INK4b, p27KIP1, p57KIP2, RASSF1C, RB1, SURVIVIN, and VHL) displayed a uniformly unmethylated pattern in all the astrocytoma and non-astrocytoma tissues examined. However, the MAGEA1 gene that was inactivated and hypermethylated in non-astrocytoma tissues, was partially demethylated in 24.5% of the astrocytoma tissues (co-existence of the hypermethylated and demethylated alleles). Of the astrocytoma associated hypermethylated genes, the methylation pattern of the CDH13, cyclin a1, DBCCR1, EPO, MYOD1, and p16INK4a genes changed in no more than 5.66% (3/53) of astrocytoma tissues compared to non-astrocytoma controls, while the RASSF1A, p73, AR, MGMT, CDH1, OCT6,, MT1A, WT1, and IRF7 genes were more frequently hypermethylated in 69.8%, 47.2%, 41.5%, 35.8%, 32%, 30.2%, 30.2%, 30.2% and 26.4% of astrocytoma tissues, respectively. Demethylation mediated inducible expression of the CDH13, MAGEA1, MGMT, p73 and RASSF1A genes was established in an astrocytoma cell line (U251), demonstrating that expression of these genes is likely regulated by DNA methylation. AR gene hypermethylation was found exclusively in female patients (22/27, 81%, 0/26, 0%, P < 0.001), while the IRF7 gene hypermethylation preferentially occurred in the male counterparts (11/26, 42.3% to 3/27, 11%, P < 0.05). Applying the mathematic method "the Discovery of Association Rules", we have identified groups consisting of up to three genes that more likely display the altered methylation patterns in concert in astrocytoma.ConclusionsOf the thirty four genes examined, sixteen genes exhibited astrocytoma associated changes in the methylation profile. In addition to the possible pathological significance, the established concordant methylation profiles of the subsets consisting of two to three target genes may provide useful clues to the development of the useful prognostic as well as diagnostic assays for astrocytoma.

High Incidence of MGMT and RARβ Promoter Methylation in Primary Glioblastomas: Association with Histopathological Characteristics, Inflammatory Mediators and Clinical Outcome

“…Loss of expression of CDH13 has been found in parallel with the hypermethylated promoter CpG islands in various cancers (40). However, only one study of gliomas, in which investigation of CDH13 in low grade astrocytomas revealed no methylation patterns, had findings in accordance with our observations (18).…”

“…Furthermore, downregulation of H-cadherin due to hypermethylation in the promoter region of the CDH13 gene appears to be related to the tumorigenesis and invasiveness of these cancers. However, expression of H-cadherin and the methylation status of CDH13 in brain tissue have not been thoroughly investigated (18).…”

BRCA1 Regulates IFN-γ Signaling through a Mechanism Involving the Type I IFNs

“…IRF-7 may play a role as a tumor suppressor in its own right because it has been shown to be silenced by hypermethylation in a number of cancer cell lines and tumors (29,38,39) and to be essential for monocyte differentiation (40). It has also been proposed that IRF-7 may play a role in regulating stress response pathways and in the maintenance of genomic stability because it has been observed that IRF-7 can be activated by NH 2 -terminal phosphorylation following DNA damage (41).…”

hMLH1 and MGMT inactivation as a mechanism of tumorigenesis in monoclonal gammopathies

“…Tumour-specific methylation changes in different genes have been identified, [8][9][10][11] and the methylation profile helps us distinguish tumour types and, perhaps, their response to chemotherapeutic agents. 12 Methylation changes are often detected in premalignant or precursor lesions, (before malignant changes) and, thus, may be of use in early detection of cancer.…”