Hypermethylation of tumour suppressor genes in ocular adnexal lymphoma

Purpose Promoter hypermethylation occurs in various tumours, including ocular adnexal lymphomas (OAL), and is a mechanism by which tumour suppressor genes can be inactivated during tumourigenesis. This study aimed to investigate the levels of hypermethylation and specific genes that are hypermethylated in different subtypes of OAL using methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) and pryrosequencing. Methods DNA was extracted from formalin-fixed, paraffin-embedded tissues from 33 extra-marginal zone B-cell lymphomas (EMZL) and 37 non-EMZL. Using two MS-MLPA assays (MRC-Holland) the methylation status and copy number of 36 genes was detected. MS-MLPA results were validated using pyrosequencing. Results MLPA and pyrosequencing results were comparable with 75-100% concordancy. Ten common genes were hypermethylated in the EMZL and non-EMZL, diffuse large B-cell lymphomas (DLBCL) and mantle cell lymphomas (CDH13, DAPK1, ESR1, GATA5, IGSF4, PAX6, RARβ, THBS1, TIMP3, and WT1). In non-EMZLs, a greater number of genes showed hypermethylation when diagnosed in the orbit and patients had a poorer prognosis. Deletion of the 9p21 region was seen in 7/13 DLBCLs including the p14ARF, p15 and p16 genes. Conclusion Hypermethylation is a feature of OALs suggesting a role for epigenetic deregulation in OAL development. In non-EMZLs greater epigenetic deregulation may be indicative of poorer patient prognosis. We hypothesise that EMZL, DLBCL and mantle cell lymphomas share a similar epigenetic aetiology and that genes in the 9p21 region may be important to DLBCL development. Correlation of hypermethylation and copy number data with clinical presentation and follow-up could reveal biomarkers of diagnostic and prognostic value in OALs.