Genomic Analyses Reveal Global Functional Alterations That Promote Tumor Growth and Novel Tumor Suppressor Genes in Natural Killer-Cell Malignancies
Authors: Kucuk Can , Iqbal Javeed , deLeeuw Ronald J. , Srivastava Gopesh , Tam Wayne , Klinkebiel David , Christman Judith K. , Shen Lijun , Dybkaer Karen , Au Wing Yan , Lam Wan L. , Chan Wing C. 
Published: October 2019

Abstract
Background: Natural Killer (NK)-cell lymphomas/leukemias (NKL) account for 1–2 % of all non-Hodgkin lymphomas. Although the incidence of NKL is relatively low, the clinical course of these lymphomas is highly aggressive. To elucidate the recurrent genomic abnormalities and the associated changes in the gene expression profile, we performed GEP and array-CGH studies on seven clinically well defined cases and eight well characterized cell lines derived from NKL patients.
Methods: Array-CGH was performed on a tiling BAC array and GEP on an Affymetrix 133 plus2 array. The two data sets were correlated to identify functional alterations associated with the genetic abnormalities. Candidate genes on del 6q21 were identified and further studied for mutations and promoter methylation.
Results: Our aCGH study identified frequent recurrent gains (> 25 %) in 1q, 2p, 7q, 13q, 17q and 20pter-qter. Regions of loss with a frequency (> 25%) included 1p, 6q, 7p, 9p, 9q, 1011q, 12q, 13q, 15q, 16p, 17p, 18p, and 18q consistent with other studies. Only 30%-50% of the genes residing in the gained or deleted regions showed corresponding increased or decreased expression. Many of the genes with increased expression were involved in cell proliferation, growth and energy metabolic processes important for the neoplastic cells. In deleted regions, genes showing decreased expression included transcription factors or repressors (e.g. SP4, PRDM1, NCOR1 and ZNF10), tumor suppressors or negative regulators of the cell cycle (e.g. CDKN2C, CDKN2A, CDKN2B, CHFR and FOXO1A). 6q21 is a frequent deleted region and we found a minimal region of involvement including only three known genes (PRDM1, ATG5 and AIM1), that had consistent low expression. Sequence analysis of these genes revealed mutations in PRDM1 and AIM1 in two out of eight cell lines resulting in truncated proteins of PRDM1 and changes in conserved amino acid sequences of AIM1. Only one cell line with a point mutation in a non-conserved region in ATG5 was detected. DNA methylation analysis showed that the promoter of PRDM1 was highly methylated in NK cell lines having low PRDM1 expression. Reversal of promoter methylation with decitabine treatment resulted in increased PRDM1 transcription consistent with down-regulation of PRDM1 expression on promoter methylation. Finally, we observed progressive up-regulation of PRDM1 expression in primary NK cells in response to IL2 treatment suggestive of a role of PRDM1 on the regulation of NK-cell activation.
Conclusion: Combination of high resolution genomic and transcriptional profiling in NK-cell malignancies has provided evidence of a general tumor promoting effect of genomic copy number alterations as well as the identification of candidate genes in a commonly deleted region in 6q. Specifically, we propose PRDM1 as a tumor suppressor gene in NK cell malignancies and loss-offunction of PRDM1 in combination with the haplo-insufficiency of ATG5 might have significant roles in the pathogenesis of NK-cell malignancies.