Abstract #LB-170: Genetic and epigenetic alterations in NK-cell malignancies

Genetic and epigenetic changes contribute to the deregulation of gene expression and development of human cancer. To identify tumor suppressor genes silenced by hypermethylation in NK-cell lymphoma/leukemia, we performed genome-wide mRNA expression analysis on 2 NK lymphoma (SNK-6, NK-YS) and 3 NK leukemia (KHYG-1, NK-92, YT) cell lines treated with 5-Aza-2-deoxycytidine (Aza-dC; DNA methyl transferase inhibitor) alone or in combination Trichostatin A (TSA; histone deacetylase inhibitor). Reactivation of gene expression upon drug treatment was assessed by using Affymetrix-Human Genome U133 Plus 2.0 Array. Only the genes with >2 fold increase in expression upon treatment were considered as upregulated. After Aza-dC treatment, several previously reported hypermethylated genes in NK-cell lymphoma were found to be upregulated in at least 1 of the 5 NK cell lines: DAPK1 (80%), DLC1 (20%), PSMD9 (20%), PTPN6 (SHP-1, 20%). Two hundred and eighty-eight and 295 genes were reactivated in the 2 NK lymphoma cell lines and the 3 NK leukemia cell lines, respectively. Ninety-two genes were upregulated in all of the 5 NK cell lines. Significantly, only about 5% of these genes were located within the frequently deleted region identified in NK-cell lymphoma by previous studies. The genes which were located in frequently deleted regions and were reactivated in all of the 5 NK cell lines included SFN (1p36.11), C1orf93 (1p36.32), DMRTB1 (1p32.3), SORT1 (1p21.3-p13.1), GPR109B (12q24.31), and ATP7B (13q14.4). Reactivation of genes involved in cytokine/cytokine receptor interaction (IL2RA, IL6, IL6R, IL10, IL13, IL22, IL23A, IL26, CCL17, CCL19, OSMR, IFNGR2, CXCL9, CXCL10, TNFRSF9), growth differentiation (GDF15, MAL), interferon regulation (IRF7, IFI27), G protein signaling (GPRC5B), MAP kinase signaling (HSPB1), and genes belong to G antigen family (GAGE2, GAGE4, GAGE5, GAGE6, GAGE7, and GAGE12I) and melanoma antigen family which encodes antigens recognized by cytolytic T lymphocytes (MAGEA4, MAGEA5, MAGEA6, MAGEA12 and PRAME) were observed in both types of NK lymphoma and leukemia cell lines. However, some distinct pathways were observed uniquely in NK-cell lymphoma or NK-cell leukemia cell types. Reactivation of genes involved in apoptosis (DAPK1, BIK, BAG3, and TP53I3) were observed in NK lymphoma cell lines only while activation of genes belonging to killer cell Ig-like receptors (KIR2DS3, KIR3DL1, KIR3DL2, KIR3DS1) were observed in NK leukemia cell lines only. Addition of histone deacetylase inhibitor TSA in combination with Aza-dC in the 2 NK lymphoma cell lines resulted in more enhanced upregulation of 273 genes which were reactivated by Aza-dC alone. In conclusion, genome-wide mRNA profiling provides comprehensive information on the genes silenced by methylation and histone chromatin modification in NK-cell lymphoma/leukemia.

Citation Information: In: Proc Am Assoc Cancer Res; 2009 Apr 18-22; Denver, CO. Philadelphia (PA): AACR; 2009. Abstract nr LB-170.