Lymphomas are a complex group of cancers arising from mature lymphoid cells. Despite advances in the treatment and management of this disease, it remains a health challenge as response to treatment and survival outcomes differ in various lymphoma subtypes. The exact causes driving lymphomagenesis remain unknown, and although several risk factors have been identified, the complexity of this disorder indicates that different molecular mechanisms drive the disease. One primary event evident in this disease is the presence of epigenetic alterations. Epigenetic alterations could arise due to changes in the pattern of deoxyribonucleic acid (DNA) methylation or histone modifications. Enhancer of zeste homolog 2 (EZH2) modifies histone and mediates gene silencing by selectively catalyzing lysine 27 trimethylation on histone H3 (H3K27me3). Consequently, genes responsible for tumor suppression and differentiation are repressed, cells undergo uncontrolled proliferation, and this leads to tumor formation. EZH2 has been mentioned to be a driver oncogene that plays an important role in tumor initiation and progression, especially when overexpressed or when gain-of function mutations occur in this gene. These hotspot gain-of-function mutations (Tyr646, Ala682 and Ala692) that result in increased EZH2 activity, are associated with increased H3K27me3 in several cancer types including lymphomas. Therefore, EZH2 inhibition could be an alternative strategy for lymphoma therapy. We treated aggressive B-cell lymphoma cell lines with 3-Deazaneplanocin A (DZNep), an epigenetic drug that inhibits EZH2 indirectly and promotes apoptosis in various tumor entities including lymphomas. We aimed to investigate the apoptotic efficacy of DZNep in these lymphoma cell lines, to understand the mechanisms of resistance to DZNep and to determine predictive biomarkers that could be of importance for EZH2 inhibition with DZNep. Using a combination of molecular and cell biological techniques such as flow cytometry, Western blot, Sanger sequencing, fluorescence in situ hybridization (FISH) and real-time reverse transcriptase polymerase chain reaction (RT-PCR), we showed that DZNep possesses a strong apoptotic and anti-proliferative effect on B-cell lymphoma cell lines. This effect was independent of the lymphoma type, the presence of EZH2 gain-of-function mutations or the presence of known prognostic lymphoma biomarkers such as translocations of MYC, BCL2 and BCL6. To investigate the molecular mechanism behind resistance to DZNep, we generated a DZNep-resistant clone from a B-cell lymphoma cell line that was initially sensitive to DZNep. This clone was used as a model to elucidate this mechanism. Upon molecular characterization, comparison of this clone with the parent cell line of origin revealed differences in the karyotype, copy number alterations, proliferation rate and response to DZNep. Clonality studies of the rearranged immunoglobulin genes however, demonstrated that the resistant clone and the parent cell line were clonally identical. Whole exome sequencing performed on this clone in relation to its corresponding control revealed among others, a genomic amplification of the AHCY gene - a direct target of DZNep. Methods such as copy number variation assays, FISH, gene expression assays and immunohistochemistry were used to validate this massive AHCY gain at the DNA, chromosomal, transcriptional and translational levels respectively. Functional validation of AHCY showed that in a DZNep-sensitive osteosarcoma cell line, AHCY overexpression was associated with resistance to DZNep. Unfortunately, reproduction of AHCY function in lymphoma cell lines was not successful due to technical reasons. Further evaluation of the whole exome sequencing data from DZNep-resistant cell lines demonstrated in one of the cell lines, a mutation in the AHCY gene. This mutation was predicted from online databases to have a likely damaging effect on the protein. This study thus presents alterations in the AHCY gene as a potential mechanism of resistance to DZNep. It also reveals that molecular mechanisms of acquired resistance are quite distinct from those of intrinsic resistance to DZNep, which themselves, may further differ from one DZNep-resistant lymphoma entity to the next. AHCY could therefore, be a promising biomarker to evaluate prior to the initiation of therapy with DZNep.
