Promoter-specific inhibition of transcription by daunorubicin in Saccharomyces cerevisiae

Anthracyclines Suppress Both NADPH Oxidase- Dependent and -Independent NETosis in Human Neutrophils

Neutrophil extracellular traps (NETs) are cytotoxic DNA-protein complexes that play positive and negative roles in combating infection, inflammation, organ damage, autoimmunity, sepsis and cancer. However, NETosis regulatory effects of most of the clinically used drugs are not clearly established. Several recent studies highlight the relevance of NETs in promoting both cancer cell death and metastasis. Here, we screened the NETosis regulatory ability of 126 compounds belonging to 39 classes of drugs commonly used for treating cancer, blood cell disorders and other diseases. Our studies show that anthracyclines (e.g., epirubicin, daunorubicin, doxorubicin, and idarubicin) consistently suppress both NADPH oxidase-dependent and -independent types of NETosis in human neutrophils, ex vivo. The intercalating property of anthracycline may be enough to alter the transcription initiation and lead NETosis inhibition. Notably, the inhibitory doses of anthracyclines neither suppress the production of reactive oxygen species that are necessary for antimicrobial functions nor induce apoptotic cell death in neutrophils. Therefore, anthracyclines are a major class of drug that suppresses NETosis. The dexrazoxane, a cardioprotective agent, used for limiting the side effects of anthracyclines, neither affect NETosis nor alter the ability of anthracyclines to suppress NETosis. Hence, at correct doses, anthracyclines together with dexrazoxane could be considered as a therapeutic candidate drug for suppressing unwanted NETosis in NET-related diseases.

A specific transcriptional response of yeast cells to camptothecin dependent on the Swi4 and Mbp1 factors

Topoisomerase I (Top1) is the specific target of the anticancer drug camptothecin (CPT) that interferes with enzyme activity promoting Top1-mediated DNA breaks and inhibition of DNA and RNA synthesis. To define the specific transcriptional response to CPT, we have determined the CPT-altered transcription profiles in yeast by using a relatively low concentration of the drug. CPT could alter global expression profiles only if a catalytically active Top1p was expressed in the cell, demonstrating that drug interference with Top1 was the sole trigger of the response. A total of 95 genes showed a statistically-significant alterations. Gene Ontology term analyses suggested that the cell response was mainly to the inhibition of nucleic acid synthesis and cell cycle progression. Promoter sequence analyses of the 22 up-regulated genes and expression studies in gene-deleted strains showed that the transcription factors, Swi4p and Mbp1p, mediate at least partially the transcriptional response to CPT. The MBP1 gene deletion abrogates a transient cell growth delay caused by CPT whereas the SWI4 gene deletion increases yeast resistance to CPT. Thus, the findings show that yeast cells have a highly selective and sensitive transcriptional response to CPT depending on SWI4 and MBP1 genes suggesting a complex regulation of cell cycle progression by the two factors in the presence of CPT.

Genomewide expression profiling of cryptolepine-induced toxicity in Saccharomyces cerevisiae

We have used the budding yeast Saccharomyces cerevisiae to identify genes that may confer sensitivity in vivo to the antimalarial and cytotoxic agent cryptolepine. Five S. cerevisiae strains, with different genetic backgrounds in cell permeability and DNA damage repair mechanisms, were exposed to several concentrations of cryptolepine. Cryptolepine showed a relatively mild toxicity for wild-type strains, which was augmented by either increasing cell permeability (Deltaerg6 or ISE2 strains) or disrupting DNA damage repair (Deltarad52 strains). These results are compatible with the ability of cryptolepine to intercalate into DNA and thus promote DNA lesions. The effects of low concentrations of cryptolepine (20% and 40% inhibitory concentrations [IC(20) and IC(40)]) were analyzed by comparing the gene expression profiles of treated and untreated Deltaerg6 yeast cells. Significant changes in expression levels were observed for 349 genes (117 upregulated and 232 downregulated). General stress-related genes constituted the only recognizable functional cluster whose expression was increased upon cryptolepine treatment, making up about 20% of upregulated genes. In contrast, analysis of the characteristics of downregulated genes revealed a specific effect of cryptolepine on genes related to iron transport or acid phosphatases, as well as a significant proportion of genes related to cell wall components. The effects of cryptolepine on the transcription of iron transport-related genes were consistent with a loss of function of the iron sensor Aft1p, indicating a possible disruption of iron metabolism in S. cerevisiae. Since the interference of cryptolepine with iron metabolism is considered one of its putative antimalarial targets, this finding supports the utility of S. cerevisiae in drug-developing schemes.

Selective inhibition of yeast regulons by daunorubicin: a transcriptome-wide analysis

Background

The antitumor drug daunorubicin exerts some of its cytotoxic effects by binding to DNA and inhibiting the transcription of different genes. We analysed this effect in vivo at the transcriptome level using the budding yeast Saccharomyces cerevisiae as a model and sublethal (IC₄₀) concentrations of the drug to minimise general toxic effects.

Results

Daunorubicin affected a minor proportion (14%) of the yeast transcriptome, increasing the expression of 195 genes and reducing expression of 280 genes. Daunorubicin down-regulated genes included essentially all genes involved in the glycolytic pathway, the tricarboxylic acid cycle and alcohol metabolism, whereas transcription of ribosomal protein genes was not affected or even slightly increased. This pattern is consistent with a specific inhibition of glucose usage in treated cells, with only minor effects on proliferation or other basic cell functions. Analysis of promoters of down-regulated genes showed that they belong to a limited number of transcriptional regulatory units (regulons). Consistently, data mining showed that daunorubicin-induced changes in expression patterns were similar to those observed in yeast strains deleted for some transcription factors functionally related to the glycolysis and/or the cAMP regulatory pathway, which appeared to be particularly sensitive to daunorubicin.

Conclusion

The effects of daunorubicin treatment on the yeast transcriptome are consistent with a model in which this drug impairs binding of different transcription factors by competing for their DNA binding sequences, therefore limiting their effectiveness and affecting the corresponding regulatory networks. This proposed mechanism might have broad therapeutic implications against cancer cells growing under hypoxic conditions.

Sp1 transcription factor as a target for anthracyclines: effects on gene transcription

The analysis of how anthracyclines interfere with DNA-protein complexes, and the evaluation of their effects on gene transcription, can promote the development of new more specific anti-tumour agents. Daunorubicin and the bisintercalating anthracycline WP631 (which binds more tightly to DNA) have been compared for their ability to inhibit Sp1-DNA interactions and gene transcription. WP631 is more efficient at inhibiting transcription initiation from promoters containing an Sp1-binding site, and it is a potent inhibitor of Sp1-activated transcription both in vitro and in human cell lines. The analysis of gene expression profiles using arrays, which include several genes containing Sp1-putative binding sites, suggests that changes in the transcriptome induce cell cycle arrest and drive a time-dependent response of cells to death stimuli through distinct pathways, which rely on the anthracycline used and its concentration.

Effect of axial coordination on the electronic structure and biological activity of dirhodium(II,II) complexes

The reactivities toward biomolecules of a series of three dirhodium(II,II) complexes that possess an increasing number of accessible axial coordination sites are compared. In cis-[Rh2(OAc)2(np)2]2+ (1; np=1,8-naphthyridine) both axial sites are available for coordination, whereas for cis-[Rh2(OAc)2(np)(pynp)]2+ (2; pynp=2-(2-pyridyl)1,8-naphthyridine) and cis-[Rh2(OAc)2(pynp)2]2+ (3) the bridging pynp ligand blocks one and two of the axial coordination sites in the complexes, respectively. The electronic absorption spectra of the complexes are consistent with strong metal-to-ligand charge transfer transitions at low energy and ligand-centered peaks localized on the np and/or pynp ligands in the UV and near-UV regions. Time-dependent density functional theory calculations were used to aid in the assignments. The three complexes exhibit metal-centered oxidations and reductions, localized on the aromatic ligands. The ability of the complexes to stabilize duplex DNA and to inhibit transcription in vitro is greatly affected by the availability of an open axial coordination site. The present work shows that open axial coordination sites on the dirhodium complexes are necessary for biological activity.

Yeast strains designed for screening of reversal agents and genetic suppressors of multidrug resistance

Multidrug resistance in yeast results from over-expression of drug efflux transporter genes due to gain-of-function mutations in transcription factors. To suppress multidrug resistance at the level of gene expression, we have developed a yeast-based screening system for the detection of compounds down-regulating the major multidrug ABC transporter Pdr5p expressed under the control of Pdr3p transcription factor. Here, we report the construction and properties of the improved set of yeast strains designed along with such screening also for a global analysis of genetic suppressors of multidrug resistance. The basic components of this system, the P(GAL1)-PDR3 and P(PDR5)-pma1(D378N) fusion genes, were individually or simultaneously integrated into corresponding chromosomes of a hypersensitive S. cerevisiae strain deleted in the PDR1 and PDR3 genes. This resulted in increased mitotic stability of a set of new test strains compared with the original prototrophic strain ZK11-1 developed previously. In addition, some of the strains designed are auxotrophic for leucine, uracil and histidine allowing them to be used in genetic screens for positive selection of multicopy or loss-of-function genetic suppressors of multidrug resistance.

Effect of equatorial ligands of dirhodium(II,II) complexes on the efficiency and mechanism of transcription inhibition in vitro

The nature of the equatorial ligands spanning the dirhodium core was shown to affect the ability and mechanism of various lantern-type complexes to inhibit transcription in vitro. The inhibition of transcription by Rh(2)(mu-O(2)CCF(3))(4), Rh(2)(mu-HNCOCF(3))(4), and [Rh(2)(mu-O(2)CCH(3))(2)(CH(3)CN)(6)](2+) appears to proceed predominantly via binding of the complexes to T7-RNA polymerase (T7-RNAP) and is dependent on the concentration of enzyme and Mg(2+) ions in solution. The concentrations of the aforementioned complexes required to inhibit 50% of the transcription, C(inh)(50), are similar to that measured for activated cisplatin, whereas a significantly higher concentration of Rh(2)(mu-HNCOCH(3))(4) is required to effect similar inhibition; the inhibition induced by Rh(2)(mu-HNCOCH(3))(4) does not involve binding to T7-RNAP. The spectral changes observed for each complex upon addition of enzyme are consistent with Rh(2)(mu-O(2)CCF(3))(4), Rh(2)(mu-HNCOCF(3))(4), and [Rh(2)(mu-O(2)CCH(3))(2)(CH(3)CN)(6)](2+) binding to the enzyme and may involve partial displacement of the equatorial (eq) groups by the Lewis basic sites of T7-RNAP. In contrast, addition of enzyme to solutions of Rh(2)(mu-HNCOCH(3))(4) does not result in significant spectral changes, a finding consistent with lack of enzyme dependence in the transcription inhibition. These differences in reactivity and transcription inhibition mechanism among complexes with different bridging ligands are explained by variations of the Lewis acidity of the axial (ax) sites in the series of complexes Rh(2)(mu-O(2)CCF(3))(4), Rh(2)(mu-HNCOCF(3))(4), and Rh(2)(mu-HNCOCH(3))(4). The Lewis acidity of the ax sites is expected to affect the initial interaction of the complexes with the biomolecules, followed by their rearrangement to eq positions if the bridging ligands are labile.

Daunorubicin-induced variations in gene transcription: commitment to proliferation arrest, senescence and apoptosis

We used a human cDNA macroarray containing various oncogenes and tumour suppressor genes to assess gene expression profiles in early-passage Jurkat T lymphocytes treated with clinically relevant concentrations of the antitumour antibiotic daunorubicin. Several oncogenes and tumour suppressor genes were either up- or down-regulated depending on the daunorubicin concentration used. The expression levels of some of these genes were confirmed by semi-quantitative reverse transcriptase-PCR. We also compared the changes in cell-cycle distribution and the apoptotic morphological characteristics of the cells treated with daunorubicin, using flow cytometry and fluorescence microscopy. Exposure to 182 nM daunorubicin (its IC(75) in Jurkat T cells: where IC(75) is the drug concentration that inhibits growth by 75%) resulted in cell-cycle arrest in G(1) and almost immediate apoptosis. In contrast, decreasing the drug concentration to 91 nM (close to the IC(50)) caused G(2) arrest and cell senescence-like growth arrest, whereas features of apoptosis and necrosis appeared only after longer incubation times. Gene expression profiles, cell-cycle distribution, the presence of DNA damage and the time-dependent response of Jurkat T cells to cell death were correlated clearly. The general behaviour of the genes suggests that cell-cycle arrest and cell death follow distinct pathways depending on drug concentration.