Bioinformatic Analysis Reveals the Association of Human N-Terminal Acetyltransferase Complexes with Distinct Transcriptional and Post-Transcriptional Processes.

N-terminal acetyltransferases (NAT) are the protein complexes that deposit the abundant N-terminal acetylation (Nt-Ac) on eukaryotic proteins, with seven human complexes currently identified. Despite the increasing recognition of their biological and clinical importance, NAT regulation remains elusive. In this study, we performed a bioinformatic investigation to identify transcriptional and post-transcriptional processes that could be involved in the regulation of human NAT complexes. First, co-expression analysis of independent transcriptomic datasets revealed divergent pathway associations for human NAT, which are potentially connected to their distinct cellular functions. One interesting connection uncovered was the coordinated regulation of the NatA and proteasomal genes in cancer and immune cells, confirmed by analysis of multiple datasets and in isolated primary T cells. Another distinctive association was of NAA40 (NatD) with DNA replication, in cancer and non-cancer settings. The link between NAA40 transcription and DNA replication is potentially mediated through E2F1, which we have experimentally shown to bind the promoter of this NAT. Second, the coupled examination of transcriptomic and proteomic datasets revealed a much greater intra-complex concordance of NAT subunits at the protein compared to the transcript level, indicating the predominance of post-transcriptional processes for achieving their coordination. In agreement with this concept, we also found that the effects of somatic copy number alterations affecting NAT genes are attenuated post-transcriptionally. In conclusion, this study provides novel insights into the regulation of human NAT complexes.

Glutamine addiction in virus-infected mammalian cells: A target of the innate immune system?

Control of core cell metabolism is a key aspect of the evolutionary conflict between viruses and the host's defence mechanisms. From their side, the invading viruses press the accelerator on their host cell's glycolysis, fatty acid, and glutaminolytic metabolic processes among others. It is also well established that activation of innate immune system responses modulates facets of metabolism such as that of polyamine, cholesterol, tryptophan and many more. But what about glutamine, a proteogenic amino acid that is a crucial nutrient for multiple cellular biosynthetic processes? Although mammalian cells can normally synthesize glutamine de novo, it has been noted that infections with genetically and phylogenetically diverse viruses are followed by the acquisition of a dependency on supplies of exogenous glutamine i.e. "glutamine addiction". Here we present our novel hypothesis that glutamine metabolism is also a target of the innate immune system, possibly through the action of interferons, as part of the evolutionary conserved antiviral metabolic reprogramming.

Mitochondrial MTHFD isozymes display distinct expression, regulation, and association with cancer.

Mitochondrial folate metabolism is central to the generation of nucleotides, fuelling methylation reactions, and redox homeostasis. Uniquely among the reactions of the mitochondrial folate pathway, the key step of the oxidation of 5,10-methylene-tetrahydrofolate (CH2-THF) can be catalysed by two isozymes, MTHFD2 and MTHFD2L. The MTHFD2 enzyme has recently received considerable attention as an oncogenic enzyme upregulated in several tumour types, which is additionally required by cancer cells in vitro and in vivo. However, much less is currently known about MTHFD2L and its expression in cancer. In this study, we examine and compare the expression and regulation of the two mitochondrial MTHFD isozymes in normal human and cancer cells. We found that normal and cancer cells express both enzymes, although MTHFD2 has a much higher baseline expression. Unlike MTHFD2, the MTHFD2L isozyme does not show an association with proliferation and growth factor stimulation. In addition, we did not find evidence of a compensatory increase of MTHFD2L following suppression of its isozyme. This study supports that MTHFD2L is unlikely to have an important function in increased proliferation or cancer. Furthermore, therapeutic strategies aiming to block the mitochondrial folate pathway in cancer should focus on MTHFD2, with MTHFD2L being unlikely to be involved in the development of chemoresistance to targeting of its mitochondrial isozyme.

Systematic integration of molecular profiles identifies miR-22 as a regulator of lipid and folate metabolism in breast cancer cells.

Dysregulated microRNA (miRNA) mediate malignant phenotypes, including metabolic reprogramming. By performing an integrative analysis of miRNA and metabolome data for the NCI-60 cell line panel, we identified an miRNA cluster strongly associated with both c-Myc expression and global metabolic variation. Within this cluster the cancer-associated and cardioprotective miR-22 was shown to repress fatty acid synthesis and elongation in tumour cells by targeting ATP citrate lyase and fatty acid elongase 6, as well as impairing mitochondrial one-carbon metabolism by suppression of methylene tetrahydrofolate dehydrogenase/cyclohydrolase. Across several data sets, expression of these target genes were associated with poorer outcomes in breast cancer patients. Importantly, a beneficial effect of miR-22 on clinical outcomes in breast cancer was shown to depend on the expression levels of the identified target genes, demonstrating the relevance of miRNA/mRNA interactions to disease progression in vivo. Our systematic analysis establishes miR-22 as a novel regulator of tumour cell metabolism, a function that could contribute to the role of this miRNA in cellular differentiation and cancer development. Moreover, we provide a paradigmatic example of effect modification in outcome analysis as a consequence of miRNA-directed gene targeting, a phenomenon that could be exploited to improve patient prognosis and treatment.

The cooked meat-derived mammary carcinogen 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) elicits estrogenic-like microRNA responses in breast cancer cells.

The cooking of meat results in the generation of heterocyclic amines (HCA), the most abundant of which is 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP). Data from epidemiological, mechanistic, and animal studies indicate that PhIP could be causally linked to breast cancer incidence. Besides the established DNA damaging and mutagenic activities of PhIP, the chemical is reported to have oestrogenic activity that could contribute to its tissue specific carcinogenicity. In this study we investigated the effect of treatment with PhIP and 17-ß-estradiol (E2) on global microRNA (miRNA) expression of the oestrogen responsive MCF-7 human breast adenocarcinoma cell line. PhIP and E2 caused widespread and largely over-lapping effects on miRNA expression, with many of the commonly affected miRNA reported to be regulated by oestrogen and have been implicated in the initiation and progression of breast cancer. The regulatory activity of the miRNAs we show here to be responsive to PhIP treatment, are also predicted to mediate cellular phenotypes that are associated with PhIP exposure. Consequently, this study offers further support to the ability of PhIP to induce widespread effects via activation of oestrogen receptor alpha (ERα). Moreover, this study indicates that deregulation of miRNA by PhIP could potentially be an important non-DNA-damaging carcinogenic mechanism in breast cancer.

Using microRNA profiles to predict and evaluate hepatic carcinogenic potential.

Novel chemical entities have to be assessed for potential adverse effects in exposed human populations, including increased cancer incidence. The liver is an organ of particular interest for such evaluations, due to its central metabolic and detoxifying functions that render it a frequent target of exogenous carcinogens. In recent years a number of studies have investigated the use of microRNA (miRNA) biomarkers to facilitate the identification, characterization, and mechanistic understanding of chemical hepatocarcinogens. In this review we discuss the main findings of these studies, the potential biological significance of observed miRNA perturbations, and avenues of future research.