Abstract
Regulation of gene expression is one of several roles proposed for the stress-induced nucleotide diadenosine tetraphosphate (Ap4A). We have examined this directly by a comparative RNA-Seq analysis of KBM-7 chronic myelogenous leukemia cells and KBM-7 cells in which the NUDT2 Ap4A hydrolase gene had been disrupted (NuKO cells), causing a 175-fold increase in intracellular Ap4A. 6,288 differentially expressed genes were identified with P < 0.05. Of these, 980 were up-regulated and 705 down-regulated in NuKO cells with a fold-change ≥ 2. Ingenuity® Pathway Analysis (IPA®) was used to assign these genes to known canonical pathways and functional networks. Pathways associated with interferon responses, pattern recognition receptors and inflammation scored highly in the down-regulated set of genes while functions associated with MHC class II antigens were prominent among the up-regulated genes, which otherwise showed little organization into major functional gene sets. Tryptophan catabolism was also strongly down-regulated as were numerous genes known to be involved in tumor promotion in other systems, with roles in the epithelial-mesenchymal transition, proliferation, invasion and metastasis. Conversely, some pro-apoptotic genes were up-regulated. Major upstream factors predicted by IPA® for gene down-regulation included NFκB, STAT1/2, IRF3/4 and SP1 but no major factors controlling gene up-regulation were identified. Potential mechanisms for gene regulation mediated by Ap4A and/or NUDT2 disruption include binding of Ap4A to the HINT1 co-repressor, autocrine activation of purinoceptors by Ap4A, chromatin remodeling, effects of NUDT2 loss on transcript stability, and inhibition of ATP-dependent regulatory factors such as protein kinases by Ap4A. Existing evidence favors the last of these as the most probable mechanism. Regardless, our results suggest that the NUDT2 protein could be a novel cancer chemotherapeutic target, with its inhibition potentially exerting strong anti-tumor effects via multiple pathways involving metastasis, invasion, immunosuppression and apoptosis.
Highlights
Nudix hydrolases regulate the levels of a wide variety of canonical and modified nucleotides and some non-nucleotide phosphorylated substrates as well as participating in essential processes such as mRNA decapping [1, 2]
The parent KBM-7 line used in this study contains the BCR-ABL1 gene fusion and potentially inactivating mutations in TP53 and NOTCH1, but lacks the other common genetic aberrations found in myeloid malignancies [38]
Two competing schools of thought have arisen, one suggesting that Ap4A is a physiologically important regulator whose level is finely tuned by the NUDT2 Ap4A hydrolase, and the other that it is an unavoidable, non-functional by-product of several enzyme activities and that NUDT2 exists to eliminate it, lest it cause molecular mayhem by interfering with essential, adenine nucleotide-dependent metabolic and regulatory pathways [4]
Summary
Nudix hydrolases regulate the levels of a wide variety of canonical and modified nucleotides and some non-nucleotide phosphorylated substrates as well as participating in essential processes such as mRNA decapping [1, 2]. One of the best studied is mammalian NUDT2. This enzyme has been isolated from many sources [3, 4] and its principal substrate is believed to be diadenosine 50,5000-P1,P4-tetraphosphate (Ap4A). Synthesis usually involves transfer of AMP from an acyl-AMP or enzyme-AMP reaction intermediate to an ATP acceptor. It can be degraded by a number of enzymes in addition to NUDT2, including FHIT [8], aprataxin [9] and non-specific phosphodiesterases [3]. NUDT2 is believed to be principally responsible for maintaining the low level of intracellular Ap4A [10,11,12]
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