scholarly journals Moxifloxacin Activates the SOS Response in Mycobacterium tuberculosis in a Dose- and Time-Dependent Manner

2021 ◽  
Vol 9 (2) ◽  
pp. 255
Author(s):  
Angelo Iacobino ◽  
Giovanni Piccaro ◽  
Manuela Pardini ◽  
Lanfranco Fattorini ◽  
Federico Giannoni

Previous studies on Escherichia coli demonstrated that sub-minimum inhibitory concentration (MIC) of fluoroquinolones induced the SOS response, increasing drug tolerance. We characterized the transcriptional response to moxifloxacin in Mycobacterium tuberculosis. Reference strain H37Rv was treated with moxifloxacin and gene expression studied by qRT-PCR. Five SOS regulon genes, recA, lexA, dnaE2, Rv3074 and Rv3776, were induced in a dose- and time-dependent manner. A range of moxifloxacin concentrations induced recA, with a peak observed at 2 × MIC (0.25 μg/mL) after 16 h. Another seven SOS responses and three DNA repair genes were significantly induced by moxifloxacin. Induction of recA by moxifloxacin was higher in log-phase than in early- and stationary-phase cells, and absent in dormant bacilli. Furthermore, in an H37Rv fluoroquinolone-resistant mutant carrying the D94G mutation in the gyrA gene, the SOS response was induced at drug concentrations higher than the mutant MIC value. The 2 × MIC of moxifloxacin determined no significant changes in gene expression in a panel of 32 genes, except for up-regulation of the relK toxin and of Rv3290c and Rv2517c, two persistence-related genes. Overall, our data show that activation of the SOS response by moxifloxacin, a likely link to increased mutation rate and persister formation, is time, dose, physiological state and, possibly, MIC dependent.

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 5328-5328
Author(s):  
Ruibo Zhang ◽  
Zi Ma ◽  
Shangqin Liu ◽  
Li He ◽  
Chaoping Xu ◽  
...  

Abstract Objective To understand the apoptotic effects and cereblon (CRBN) gene and protein expression induced by baicalein in MM cells. Methods Apoptotic MM cells induced baicalein,lenalidomide or combination of BAI and lenalidomide were stained by using Annexin-V and analyzed by flow cytometry. RT-PCR was used to detect CRBN gene expression in MM cells. CRBN protein expression was detected by western blot in MM cell lines. Results At the concentration of 40 μmol/L, baicalein can induce apoptosis of U266 cells in a time-dependent manner. At the different BAI treated time points (24h, 48h, 72h), the apoptotic cell percentages were 6.11%, 11.9%, 16.7%; After treated RPMI 8226 cells for 72 hours, combined application of baicalein and lenalidomide (both concentrations are 40 μmol/L) could induce more cell apoptosis than baicalein or lenalidomide alone. The apoptotic cell percentages induced by baicalein, lenalidomide or combined application of baicalein and lenalidomide were 15.9%, 4.27%, and 57.5%. CRBN gene expression detected by RT-PCR could be induced by baicalein in U266 cells in a dose-and time-dependent manner. Treated U266 cells for 24h at concentrations of 10 μmol/L, 20 μmol/L and 40 μmol/L, baicalein upregulated CRBN gene expression times were 2.246 ± 0.068, 2.399 ± 0.178 and 3.591 ± 0.061,respectively,compared to the control group. Statistically, the P values were 0.003, 0.009 and 0.001; Treated U266 cells at concentrations of 40 μmol/L at different time points (6h, 12h and 24h), baicalein upregulated CRBN gene expression times were 2.372 ± 0.079, 2.494 ± 0.189 and 3.228 ± 0.151, its P values were 0.002, 0.008 and 0.002.CRBN protein expression detected by using western blot could be induced by baicalein in both U266 and RPMI8226 cell lines. Conclusions Baicalein at suitable concentrations induced MM cells apoptosis in a time-dependent manner. Comparison with the single component used alone,combined application of baicalein and lenalidomide exhibited stronger inhibition effect on proliferation of RPMI 8226. Considering CRBN is the cellular target for lenalidomide, baicalein can up-regulate the CRBN gene and protein expression in MM cells and may enhance MM cell sensitivity to apoptotic stimuli. Therefore, baicalein up-regulated CRBN gene and protein expression and sensitized MM cells to apoptosis stimuli induced by lenalidomide. It provides us a possibility for baicalein clinical application to overcome the resistance to lenalidomide for MM patients in the future Disclosures: No relevant conflicts of interest to declare.


Endocrinology ◽  
2005 ◽  
Vol 146 (3) ◽  
pp. 1074-1096 ◽  
Author(s):  
Xiaoping Luo ◽  
Li Ding ◽  
Jingxia Xu ◽  
R. Stan Williams ◽  
Nasser Chegini

Gene microarray was used to characterize the molecular environment of leiomyoma and matched myometrium during growth and in response to GnRH analog (GnRHa) therapy as well as GnRHa direct action on primary cultures of leiomyoma and myometrial smooth muscle cells (LSMC and MSMC). Unsupervised and supervised analysis of gene expression values and statistical analysis in R programming with a false discovery rate of P ≤ 0.02 resulted in identification of 153 and 122 differentially expressed genes in leiomyoma and myometrium in untreated and GnRHa-treated cohorts, respectively. The expression of 170 and 164 genes was affected by GnRHa therapy in these tissues compared with their respective untreated group. GnRHa (0.1 μm), in a time-dependent manner (2, 6, and 12 h), targeted the expression of 281 genes (P ≤ 0.005) in LSMC and MSMC, 48 of which genes were found in common with GnRHa-treated tissues. Functional annotations assigned these genes as key regulators of processes involving transcription, translational, signal transduction, structural activities, and apoptosis. We validated the expression of IL-11, early growth response 3, TGF-β-induced factor, TGF-β-inducible early gene response, CITED2 (cAMP response element binding protein-binding protein/p300-interacting transactivator with ED-rich tail), Nur77, growth arrest-specific 1, p27, p57, and G protein-coupled receptor kinase 5, representing cytokine, common transcription factors, cell cycle regulators, and signal transduction, at tissue levels and in LSMC and MSMC in response to GnRHa time-dependent action using real-time PCR, Western blotting, and immunohistochemistry. In conclusion, using different, complementary approaches, we characterized leiomyoma and myometrium molecular fingerprints and identified several previously unrecognized genes as targets of GnRHa action, implying that local expression and activation of these genes may represent features differentiating leiomyoma and myometrial environments during growth and GnRHa-induced regression.


2006 ◽  
Vol 74 (5) ◽  
pp. 2985-2995 ◽  
Author(s):  
JoAnn M. Tufariello ◽  
Kaixia Mi ◽  
Jiayong Xu ◽  
Yukari C. Manabe ◽  
Anup K. Kesavan ◽  
...  

ABSTRACT Approximately one-third of the human population is latently infected with Mycobacterium tuberculosis, comprising a critical reservoir for disease reactivation. Despite the importance of latency in maintaining M. tuberculosis in the human population, little is known about the mycobacterial factors that regulate persistence and reactivation. Previous in vitro studies have implicated a family of five related M. tuberculosis proteins, called resuscitation promoting factors (Rpfs), in regulating mycobacterial growth. We studied the in vivo role of M. tuberculosis rpf genes in an established mouse model of M. tuberculosis persistence and reactivation. After an aerosol infection with the M. tuberculosis Erdman wild type (Erdman) or single-deletion rpf mutants to establish chronic infections in mice, reactivation was induced by administration of the nitric oxide (NO) synthase inhibitor aminoguanidine. Of the five rpf deletion mutants tested, one (ΔRv1009) exhibited a delayed reactivation phenotype, manifested by delayed postreactivation growth kinetics and prolonged median survival times among infected animals. Immunophenotypic analysis suggested differences in pulmonary B-cell responses between Erdman- and ΔRv1009-infected mice at advanced stages of reactivation. Analysis of rpf gene expression in the lungs of Erdman-infected mice revealed that relative expression of four of the five rpf-like genes was diminished at late times following reactivation, when bacterial numbers had increased substantially, suggesting that rpf gene expression may be regulated in a growth phase-dependent manner. To our knowledge, ΔRv1009 is the first M. tuberculosis mutant to have a specific defect in reactivation without accompanying growth defects in vitro or during acute infection in vivo.


2019 ◽  
Author(s):  
Nana Shanidze ◽  
Felina Lenkeit ◽  
Jörg S. Hartig ◽  
Dietmar Funck

ABSTRACTLigand-responsive synthetic riboswitches are versatile and innovative tools for external gene regulation in pro- and eukaryotes. Riboswitches are small cis-regulatory RNA elements that regulate gene expression by conformational changes in response to ligand binding. In plants, synthetic riboswitches were used to regulate gene expression in plastids, but the application of synthetic riboswitches for the regulation of nuclear-encoded genes in planta has not been reported so far. Here we characterize the properties of a theophylline-responsive synthetic aptazyme for control of nuclear-encoded transgenes in Arabidopsis (Arabidopsis thaliana). Activation of the aptazyme, inserted in the 3-UTR of the target gene, resulted in rapid self-cleavage and subsequent decay of the mRNA. This riboswitch allowed reversible, theophylline-dependent downregulation of the Green Fluorescent Protein (GFP) reporter gene in a dose- and time- dependent manner. Insertion of the riboswitch into the One Helix Protein 1 (OHP1) gene allowed complementation of ohp1 mutants and induction of the mutant phenotype by theophylline. GFP or OHP1 transcript levels were downregulated by maximally 90%, and GFP protein levels by 95%. These results establish artificial riboswitches as tools for externally controlled gene expression in synthetic biology in plants or functional crop design.One sentence summaryArtificial, ligand-responsive RNA aptazymes are an efficient tool for dose- and time-dependent external control of nuclear gene expression in plants.


2010 ◽  
Vol 192 (15) ◽  
pp. 3915-3924 ◽  
Author(s):  
Sharon E. Hoover ◽  
Weihong Xu ◽  
Wenzhong Xiao ◽  
William F. Burkholder

ABSTRACT The SOS response to DNA damage in bacteria is a well-known component of the complex transcriptional responses to genotoxic environmental stresses such as exposure to reactive oxygen species, alkylating agents, and many of the antibiotics targeting DNA replication. However, bacteria such as Bacillus subtilis also respond to conditions that perturb DNA replication via a transcriptional response mediated by the replication initiation protein DnaA. In addition to regulating the initiation of DNA replication, DnaA directly regulates the transcription of specific genes. Conditions that perturb DNA replication can trigger the accumulation of active DnaA, activating or repressing the transcription of genes in the DnaA regulon. We report here that simply growing B. subtilis in LB medium altered DnaA-dependent gene expression in a manner consistent with the accumulation of active DnaA and that this was part of a general transcriptional response to manganese limitation. The SOS response to DNA damage was not induced under these conditions. One of the genes positively regulated by DnaA in Bacillus subtilis encodes a protein that inhibits the initiation of sporulation, Sda. Sda expression was induced as cells entered stationary phase in LB medium but not in LB medium supplemented with manganese, and the induction of Sda inhibited sporulation-specific gene expression and the onset of spore morphogenesis. In the absence of Sda, manganese-limited cells initiated spore development but failed to form mature spores. These data highlight that DnaA-dependent gene expression may influence the response of bacteria to a range of environmental conditions, including conditions that are not obviously associated with genotoxic stress.


2018 ◽  
Vol 1 (2) ◽  
Author(s):  
Die Wu ◽  
Wei Cao ◽  
Beibei Luo ◽  
Dao Xiang ◽  
Peijie Chen

Objective Intestinal epithelial cells are positioned between an anaerobic lumen and a highly metabolic lamina propria, affected by reduced blood flow and tissue hypoxia. Exercise induces blood flow redistribution, leading to hypoperfusion and gastrointestinal (GI) compromise. The hypoxia-inducible factor (HIF) 1α is pivotal in the transcriptional response to oxygen flux. In this study, we hypothesized that exercise induces GI system hypoxia and accumulates HIF-1α. Methods (1) ROSA26 ODD-Luc/+ mouse model (ODD-Luc) was used to detect HIF-1α expression in the intestine (female, 8-week, n=6/group). ODD-Luc mice were randomized into 4 groups: stayed in 21% O2 as the normoxic control (C), exercise (E), injected HIF-1α inhibitor PX-478 before swimming (PS), placed in the chamber containing 9% O2 for 4 hours as the positive control (PC). (2) Exercise models were conducted by volume: Moderate Exercise (ME): mice voluntarily swam for 30 min; Heavy-intensity Exercise (HE): mice swam for 1.5 hours with 5% body weight loads attached to their tails; Long-time Exercise (LE): mice voluntarily swam for 3 hours or till fatigue. Results (1) Exercise increased HIF-1α in the abdominal area. The luciferase activities boosted after exercise, compared to the controls (ME v.s. C, P<0.05; HE v.s. C, P<0.05; LE v.s. C, P<0.05) but no differences among three exercise groups (ME v.s. HE, P>0.99; ME v.s. LE, P>0.99; HE v.s. LE, P>0.99); (2) Exercise altered HIF-1α distribution in the small intestine in a time-dependent manner. The expression of HIF-1α was significantly increased after exercise and gradually reduced to the rest level. The photons increased at the 0th hour after exercise compared to that of the normoxic control (P<0.01). The level of photons then reduced over time, while the 2nd, 4th and 6th hour post-exercise were still greater than that of the normoxic control  (2nd hour v.s. C, P<0.01; 4th hour v.s. C, P<0.01; 6th hour v.s. C, P<0.05), and returned to normal after 24 hours (24th hour v.s. C, P>0.99). Conclusions Exercise induced the distribution of HIF-1α in the small intestine. The expression of HIF-1α is shown in a time-dependent manner after exercise.


1995 ◽  
Vol 15 (2) ◽  
pp. 129-141 ◽  
Author(s):  
A Dassouli ◽  
Ch Darne ◽  
S Fabre ◽  
M Manin ◽  
G Veyssière ◽  
...  

ABSTRACT The understanding of androgen-regulated gene expression requires a cell culture system that mimics the functions of cells in vivo. In the present paper we have examined a vas deferens epithelial cell subculture system. Cultured vas deferens epithelial cells have been shown to exhibit polarized properties characteristic of functioning epithelia and to display a high level of androgen receptors. Incubation of cells with androgen caused a decrease in cellular androgen receptor mRNA that was time-dependent. Total suppression was observed after 24 h of exposure to androgen. By contrast, incubation of vas deferens epithelial cells with androgen resulted in a threefold increase in the cellular content of androgen receptor protein, as assayed by ligand binding. In response to androgens, vas deferens epithelial cells expressed mouse vas deferens protein mRNA (MVDP mRNA). Maximum expression of the MVDP gene, at both mRNA and protein levels, was observed after 24 h of androgen induction. DEAE-dextran transfection conditions were defined using the MMTV-CAT vector. Dihydrotestosterone stimulated the transcription activation of MMTV-CAT gene in vas deferens epithelial cells in a dose- and time-dependent manner. No induction was seen when fragments of the MVDP promoter region were cloned directly in front of the CAT gene and transiently transfected into vas deferens epithelial cells. It was found that cotransfection of cells with MVDP-CAT constructs and with an androgen receptor expression vector resulted in a small but consistent androgen-dependent increase in reporter gene activity. Transiently transfected vas deferens epithelial cells are a suitable model with which to study the effect of androgen on gene regulatory elements.


2004 ◽  
Vol 16 (3) ◽  
pp. 341-348 ◽  
Author(s):  
Robert J. Feezor ◽  
Heather N. Paddock ◽  
Henry V. Baker ◽  
Juan C. Varela ◽  
Joyce Barreda ◽  
...  

The global changes in gene expression in injured murine skin were characterized following a second-degree scald burn. Dorsal skin was harvested from uninjured and from burned mice at 2 h and at 3 and 14 days following immersion in 65°C water for 45 s. Gene expression was surveyed using an Affymetrix U74Av2 GeneChip, and patterns of gene expression were analyzed using hierarchical clustering and supervised analysis. Burn injury produced significant alterations in the expression of a number of genes, with the greatest changes seen 3 and 14 days after the scald burn. Using a supervised analysis with a false discovery rate of 1% or 5%, differences in the expression of 192 or 1,116 genes, respectively, discriminated among the unburned skin and the three time points after the burn injury. Gene expression was primarily a transient and time-dependent upregulation. The expression of only 24 of the 192 discriminating genes was downregulated after the burn injury. No gene exhibited a sustained increase in expression over the entire 14 days following the burn injury. Gene ontologies revealed an integrated upregulation of inflammatory and protease genes at acute time intervals, and a diminution of cytoskeletal and muscle contractile genes at 3 or 14 days after the injury. Following a second-degree scald burn, global patterns of gene expression in the burn wound change dramatically over several weeks in a time-dependent manner, and these changes can be categorized based on the biological relevance of the genes.


2021 ◽  
Author(s):  
Laura Puente-Santamaria ◽  
Lucia Sanchez-Gonzalez ◽  
Ricardo Ramos-Ruiz ◽  
Luis del Peso

Molecular gene signatures are useful tools to characterize the physiological state of cell populations according to their gene expression profiles. However, most molecular gene signatures have been developed under a very limited set of conditions and cell types, and are often restricted to a set of gene identities linked to an event or biological process, therefore making necessary to develop and test additional procedures for its application to new data. Focusing on the transcriptional response to hypoxia, we aimed to generate widely applicable classifiers capable of detecting hypoxic samples while maintaining transparency and ease of use and interpretation. Here we describe several tree-based classifiers sourced from the results of a meta-analysis of 69 differential expression datasets which included 425 individual RNA-seq experiments from 33 different human cell types exposed to different degrees of hypoxia (0.1-5%O2) for a time spanning between 2 and 48h. These decision trees include both the identities of genes key in the response to hypoxia and defined quantitative boundaries, allowing for the classification of individual samples without needing a control or normoxic reference. Despite their simplicity and ease of use, these classifiers achieve over 95% accuracy in cross validation and over 80% accuracy when applied to additional challenging datasets. Moreover, the explicit structure of the trees allowed for the identification of relevant biological features in cases where prediction was not accurate. Finally, we demonstrate that the classifiers can be applied to spatial gene expression data to identify hypoxic regions within histological sections. Although we have focused on the identification of hypoxia, this method can be applied to detect activation of other processes or cellular states.


Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 4125-4125
Author(s):  
Uri Rozovski ◽  
David M. Harris ◽  
Ping LI ◽  
Zhiming Liu ◽  
Alessandra Ferrajoli ◽  
...  

Abstract Introduction: While in CLL cells phosphorylation of STAT3 on serine 727 residues is constitutive, phosphorylation of STAT3 on tyrosine 705 residues is inducible. Cytokines, such as IL-6, or IgM antibodies that activate CLL cells' BCR, induce tyrosine phosphorylated (p) STAT3. However, whereas IL-6 induces tyrosine pSTAT3 phosphorylation within 15 minutes, IgM induces pSTAT3 within ≥ 2-4 hours. The reason for the delayed IgM-induced phosphorylation is unknown. Like STAT3, the transcription factor NF-κB is constitutively activated in CLL cells and stimulation of the BCR activates NF-κB. Whether BCR stimulation upsurges NF-κB's transcriptional activity has not been elucidated. Because IL-6 is an NF-κB-target gene and, like IL-6, IgM antibodies induce tyrosine pSTAT3, we wondered whether prolonged stimulation with IgM antibodies induces tyrosine pSTAT3 via NF-κB-mediated induction of IL-6 in CLL cells. Methods: We incubated peripheral blood CLL cells in the presence or absence of IgM antibodies or IL-6, and harvested the cells at different time points. Total RNA was extracted using TRIzol (Life technology), cDNA was synthesized with Super Script First synthesis System for RT-PCR (Invitrogen), and NF-κB-target gene expression was quantified using RT-PCR (Invitrogen Life Sciences). To measure the levels of tyrosine pSTAT3 we used flow cytometry and to assess binding of NF-κB (p65) to DNA we utilized an electromobility shift assay (EMSA) using an NF-κB-binding site labelled DNA probe. Results: The transcriptional activity of NF-κB was studied using a PCR array that profiles the expression of 83 NF-κB-target genes. To reduce the 'noise' from stochastic variability in gene expression we first identified a core of genes that are expressed in cells from all patients' samples. To that aim we ranked the Ct values in each array and considered all genes that were amplified earlier than the cycle in the 75th percentile. Using this approach we identified 35 genes (42% of genes represented in the array) that were amplified in all 6 patients' samples. Annotation analysis revealed that the key pathways common to these 35 genes included 'Positive regulation of the NF-κB cascade', 'Inflammation' and 'Negative regulation of apoptosis'. Applying stringent criteria we identified 5 genes common to all cases that were amplified prior to the cycle representing the 25th percentile. Most amplified genes detected in all samples prior to stimulation (28/35, 80%) were also detected after 4 h of IgM stimulation, confirming that NF-κB is constitutively activated in CLL cells. However, 19 addition genes (19/83, 23%of the genes in the array) were detected in all IgM-stimulated but not in unstimulated cells. Remarkably, IL-6 was detected in all cases only after IgM stimulation. Furthermore, the delta-delta Ct method identified an IgM-induced time-dependent increment in IL-6 and IL-8, suggesting that IL-6 expression is dependent on stimulation of the BCR. Indeed IL-6 neutralizing antibodies significantly reduced the levels of tyrosine pSTAT3 in CLL cells incubated for 18 h with IgM antibodies. In addition, EMSA studies using CLL cells from 4 different patients showed that stimulation of the BCR with IgM antibodies increased the binding of NF-κB to DNA in a time-dependent manner. Moreover, the JAK2 inhibitor Ruxolitinib attenuated the NF-κB-DNA binding, suggesting that long exposure to IgM antibodies induces activation of NF-κB, a process mediated in part by IL-6 that activates the JAK2/STAT3 pathway. Conclusions: The BCR of CLL cells is stimulated in the bone marrow and lymph nodes. However, whereas the immediate effects of BCR stimulation have been excessively studied, the successive effect BCR stimulation is poorly understood. We found that stimulation of the BCR induces tyrosine phosphorylation of STAT3 via NF-κB-mediated induction of IL-6, a process that requires protracted BCR stimulation. Although NF-κB is constitutively activated in CLL cells, continuous activation of the BCR further activates NF-κB. Continuous stimulation of the BCR increases the levels of IL-6 that, upon binding to its receptor, activates STAT3 that in turn activates NF-κB. Taken together, our data suggest that agents, such as Ruxolitinib, that inhibit the successive effects of BCR activation, would become effective therapeutic agents in CLL. Disclosures Rozovski: Novartis: Other: Advisory board. Wierda:Glaxo-Smith-Kline Inc.: Research Funding; Celgene Corp.: Consultancy.


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