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Background  Astrocytoma 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.    Methods  We 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.    Results  Seventeen genes ( ABL, APC, APAF1, BRCA1, CSPG2, DAPK1, hMLH1, LKB1, PTEN, p14 ARF , p15 INK4b , p27 KIP1 , p57 KIP2 , 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  p16   INK4a   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.    Conclusions  Of 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.

bmc cancer

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