Genomic analyses reveal global functional alterations that promote tumor growth and novel tumor suppressor genes in natural killer-cell malignancies

Abstract

Natural killer (NK)-cell malignancies are among the most aggressive lymphoid neoplasms with very poor prognosis. We performed array comparative genomic hybridization analysis on a number of NK cell lines and primary tumors to gain better understanding of the pathogenesis and tumor biology of these malignancies. We also obtained transcriptional profiles of genes residing in these regions and compared them with normal and activated NK cells. Only 30-50% of the genes residing in the gained or deleted regions showed corresponding increased or decreased expression. However, many of the upregulated genes in regions of gain are functionally important for the proliferation and growth of the neoplastic population. Genes downregulated in regions of loss included many transcription factors or repressors, tumor suppressors or negative regulators of the cell cycle. The minimal common region of deletion in 6q21 included three known genes (PRDM1, ATG5 and AIM1) showing generally low expression. Mutations resulting in truncated PRDM1 and changes in conserved amino-acid sequences of AIM1 were detected. Highly methylated CpG islands 5 0 of PRDM1 and AIM1 correlated with low expression of the transcripts. Reversal of methylation by Decitabine induced expression of PRDM1 and cell death. In conclusion, we have shown a general tumorpromoting effect of genetic alterations and have identified PRDM1 as the most likely target gene in del6q21. ATG5, an essential gene for autophagy and AIM1, a gene implicated in melanoma, may also participate in the functional abnormalities.

Natural killer cell lymphoma shares strikingly similar molecular features with a group of non-hepatosplenic γδ T-cell lymphoma and is highly sensitive to a novel aurora kinase A inhibitor in vitro

“…18 The geneset-enrichment-analysis findings of chromosome 6q gene enrichment in gd-PTCL (NHS) compared with NKCL is likely related to the frequent deletion of 6q in the NK-cell counterpart. 31 This deletion is not observed in the gd T-cell lines, 41 and may be similarly true for gd-PTCLs (NHS) as well. Gene signatures associated with IL12 signaling, shown to be critical for gd T-cell proliferation by resisting apoptosis, 42 were up-regulated in gd-PTCL (NHS) compared with NKCL.…”

“…The expression of the protein was seen in all NK-lymphoma cell lines (Figure 4b and c). AURKA is located at a frequently (450%) amplified locus (20q13) in lymphomas derived from NKCL 31 and is involved in multiple pathways, promoting the proliferative function of MYC 32 and WNT signaling, 33 while inhibiting TP53. 34 Moreover, AURKA is upregulated by hypoxia 35 that is frequently observed in ENKTL.…”

Activating mutations of STAT5B and STAT3 in lymphomas derived from γδ-T or NK cells

“…Two NK cell lines (SNK6, NKYS) and the gd-T cell lines (SNT8, SNT13, and SNT15) were obtained from Dr Norio Shimizu (Tokyo Medical and Dental University). Culture conditions of NK and gd-T cell lines were as described previously 30,31 . The DHL16 cell line, purchased from ATCC (American Type Culture Condition), was cultured in RPMI-1640 (GibcoInvitrogen) including 10% FBS; penicillin G (100 units ml À 1 ) and streptomycin (100 mg ml À 1 ) at 37°C in 5% CO 2 .…”

“…The sensitivity of mutation detection was evaluated by applying Sanger sequencing on the G to A mutation detected in the intron4/exon5 splice junction of PRDM1 detected previously ( Supplementary Fig. 4A) 30 . Uniform linear amplification of genomic DNA from each NK sample was tested with PCR, which generatedB3 kb amplicons using KAI3 cell line or NKTCL cases ( Supplementary Fig.…”

“…Q-RT-PCR primers used in this study are as follows: BCL-XL forward: Western blot. Western blot was performed as described previously with the following modifications 30 . RIPA buffer supplemented with a protease inhibitor cocktail (Sigma-Aldrich, St Louis, MO) and phosphatase inhibitor cocktails 2 and 3 (Sigma-Aldrich) was used to prepare the whole-cell lysate.…”