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1.
RNA ; 26(1): 58-68, 2020 01.
Article in English | MEDLINE | ID: mdl-31658992

ABSTRACT

In response to foreign RNA, cellular antiviral mechanisms stimulate high expression of interferon-induced proteins with tetratricopeptide repeats (IFITs). Two members of the IFIT protein family, IFIT1 and IFIT5, are capable of binding the very terminal 5' end of mRNA. In eukaryotes, these mRNA termini contain a cap structure (m7GpppN, cap 0) that is often subjected to further modifications. Here, we performed a thorough examination of IFIT1 and IFIT5 binding to a wide spectrum of differently capped as well as fully uncapped mRNAs. The kinetic analysis of IFIT1 and IFIT5 interactions with mRNA ligands indicates that the cap structure modifications considerably influence the stability of IFIT1/RNA complexes. The most stable complexes were formed between IFIT1 and GpppG/A- and m7GpppG/A-RNAs. Unexpectedly, we found that NAD+- and NADH-capped RNAs associate with IFIT5 with kinetic parameters comparable to pppG-RNA. Finally, we measured interactions of IFIT1 with mRNAs bearing modified synthetic cap analogs that start to become the important tools in biotechnological and medicinal research. We found that incorporation of modified cap analogs to the RNA protects the latter, to a certain degree, from the translational inhibition caused by IFIT1 protein.


Subject(s)
Adaptor Proteins, Signal Transducing/metabolism , Neoplasm Proteins/metabolism , RNA Caps/genetics , RNA, Messenger/genetics , RNA-Binding Proteins/metabolism , Adaptor Proteins, Signal Transducing/genetics , Humans , Kinetics , NAD/genetics , Neoplasm Proteins/genetics , Protein Binding , RNA Cap Analogs , RNA-Binding Proteins/genetics
2.
Biochem Biophys Res Commun ; 533(3): 391-396, 2020 12 10.
Article in English | MEDLINE | ID: mdl-32962861

ABSTRACT

The interferon-induced proteins with tetratricopeptide repeats (IFITs) are a family of RNA-binding proteins that are very highly expressed during antiviral response of immune system. IFIT proteins recognize and tightly bind foreign RNA particles. These are primarily viral RNAs ended with triphosphate at the 5' or lacking methylation of the first cap-proximal nucleotide but also in vitro transcribed RNA synthesized in the laboratory. Recognition of RNA by IFIT proteins leads to the formation of stable RNA/IFIT complexes and translational shut off of non-self transcripts. Here, we present a fluorescent-based assay to study the interaction between RNA molecules and IFIT family proteins. We have particularly focused on two representatives of this family: IFIT1 and IFIT5. We found a probe that competitively with RNA binds the positively charged tunnel in these IFIT proteins. The use of this probe for IFIT titration allowed us to evaluate the differences in binding affinities of mRNAs with different variants of 5' ends.


Subject(s)
Adaptor Proteins, Signal Transducing/chemistry , Anilino Naphthalenesulfonates/chemistry , Biological Assay , Fluorescent Dyes/chemistry , Neoplasm Proteins/chemistry , RNA Cap-Binding Proteins/chemistry , RNA Caps/chemistry , RNA-Binding Proteins/chemistry , Adaptor Proteins, Signal Transducing/genetics , Adaptor Proteins, Signal Transducing/metabolism , Binding Sites , Binding, Competitive , Humans , Hydrogen Bonding , Kinetics , Molecular Docking Simulation , Neoplasm Proteins/genetics , Neoplasm Proteins/metabolism , Protein Binding , Protein Conformation , RNA Cap Analogs/chemistry , RNA Cap Analogs/metabolism , RNA Cap-Binding Proteins/genetics , RNA Cap-Binding Proteins/metabolism , RNA Caps/genetics , RNA Caps/metabolism , RNA-Binding Proteins/genetics , RNA-Binding Proteins/metabolism , Spectrometry, Fluorescence , Static Electricity , Thermodynamics
3.
Cytometry A ; 97(6): 557-562, 2020 06.
Article in English | MEDLINE | ID: mdl-32511890

ABSTRACT

Briefly depicted are the publications in CYTOMETRY that received the highest frequency of citations. Among them are seminal papers describing application of metachromatic fluorochrome acridine orange to differentially stain DNA versus RNA or to analyze susceptibility of DNA in situ to denaturation; both features being markers of different sections of the cell cycle including identification of noncycling quiescent cells. The papers reviewing detection of cyclins D1, E, A or B1, each in relation to cell cycle phase, were also among the highly cited ones. The highest citation rates received publications describing development of the TUNEL methodology to detect apoptotic DNA fragmentation, and more recently expression of ϒH2AX to reveal DNA damage. © 2020 International Society for Advancement of Cytometry.


Subject(s)
Acridine Orange , DNA , Cell Cycle , Flow Cytometry , Fluorescent Dyes
4.
Biophys J ; 116(4): 648-658, 2019 02 19.
Article in English | MEDLINE | ID: mdl-30691677

ABSTRACT

The overexpression of multidrug efflux pumps is an important mechanism of clinical resistance in Gram-negative bacteria. Recently, four small molecules were discovered that inhibit efflux in Escherichia coli and interact with the AcrAB-TolC efflux pump component AcrA. However, the binding site(s) for these molecules was not determined. Here, we combine ensemble docking and molecular dynamics simulations with tryptophan fluorescence spectroscopy, site-directed mutagenesis, and antibiotic susceptibility assays to probe binding sites and effects of binding of these molecules. We conclude that clorobiocin and SLU-258 likely bind at a site located between the lipoyl and ß-barrel domains of AcrA.


Subject(s)
Anti-Bacterial Agents/pharmacology , Carrier Proteins/metabolism , Escherichia coli Proteins/antagonists & inhibitors , Escherichia coli Proteins/metabolism , Lipoproteins/antagonists & inhibitors , Lipoproteins/metabolism , Membrane Transport Proteins/metabolism , Anti-Bacterial Agents/metabolism , Binding Sites , Escherichia coli Proteins/chemistry , Escherichia coli Proteins/genetics , Lipoproteins/chemistry , Lipoproteins/genetics , Membrane Transport Proteins/chemistry , Membrane Transport Proteins/genetics , Molecular Docking Simulation , Molecular Dynamics Simulation , Mutation , Novobiocin/analogs & derivatives , Novobiocin/metabolism , Novobiocin/pharmacology , Protein Domains
5.
Cytometry A ; 95(6): 683-690, 2019 06.
Article in English | MEDLINE | ID: mdl-30422397

ABSTRACT

Described is the new cytometric approach do detect either stimulation or a collapse of lysosomal proton pump (lysosomes rupture) combined with activation of transglutaminase 2 (TG2) during induction of apoptosis. Apoptosis of human lymphoblastoid TK6 cells was induced by combination of 2-deoxyglucose with the isoquinoline alkaloid berberine, by DNA topoisomerase I inhibitor camptothecin, its analog topotecan, topoisomerase II inhibitors etoposide or mitoxantrone, as well as by the cytotoxic anticancer ribonuclease ranpirnase (onconase). Activity of the proton pump of lysosomes was assessed by measuring entrapment and accumulation of the basic fluorochrome acridine orange (AO) resulting in its metachromatic red luminescence (F>640 ) within these organelles. Activation of TG2 was detected in the same cell subpopulation by the evidence of crosslinking of cytoplasmic proteins revealed by the increased intensity of the side light scatter (SSC) as well as following cell lysis by detergent, by its red fluorescence after staining by sulforhodamine 101. Because at low AO concentration nuclear DNA of the lysed cells was stoichiometrically stained green (F530 ) its quantity provided information on effects of the drug treatments on cell cycle in relation to activation of TG2. The data reveal that activation of lysosomal proton pump was evident in subpopulations of cells treated with 2-deoxyglucose plus berberine, topotecan, etoposide and mitoxantrone but not with ranpirnase. The collapse of lysosomal proton pump possibly reporting rupture of these organelles was observed in definite cell subpopulations after treatment with each of the studied drugs. Because regardless of the inducer of apoptosis TG2 activation invariably was correlated with lysosomes rupture it is likely that it was triggered by calcium ions or protons released from the ruptured lysosomes. This new methodological approach offers the means to investigate mechanisms and factors affecting autophagic lysosomes proton pump activity vis-à-vis TG2 activation that are common in several pathological states. © 2019 International Society for Advancement of Cytometry.


Subject(s)
Antineoplastic Agents/pharmacology , Apoptosis/drug effects , GTP-Binding Proteins/metabolism , Image Cytometry/methods , Lysosomes/enzymology , Proton Pumps/drug effects , Transglutaminases/metabolism , Acridine Orange/metabolism , Autophagosomes/drug effects , Autophagosomes/enzymology , Cell Cycle/drug effects , Fluorescence , HL-60 Cells , Humans , Lysosomes/drug effects , Lysosomes/metabolism , Protein Glutamine gamma Glutamyltransferase 2 , Proton Pumps/metabolism
6.
J Biol Chem ; 292(40): 16746-16759, 2017 10 06.
Article in English | MEDLINE | ID: mdl-28842482

ABSTRACT

Gene 33 (Mig6, ERRFI1) is an adaptor protein with multiple cellular functions. We recently linked Gene 33 to the DNA damage response (DDR) induced by hexavalent chromium (Cr(VI)), but the molecular mechanism remains unknown. Here we show that ectopic expression of Gene 33 triggers DDR in an ATM serine/threonine kinase (ATM)-dependent fashion and through pathways dependent or not dependent on ABL proto-oncogene 1 non-receptor tyrosine kinase (c-Abl). We observed the clear presence of Gene 33 in the nucleus and chromatin fractions of the cell. We also found that the nuclear localization of Gene 33 is regulated by its 14-3-3-binding domain and that the chromatin localization of Gene 33 is partially dependent on its ErbB-binding domain. Our data further indicated that Gene 33 may regulate the targeting of c-Abl to chromatin. Moreover, we observed a clear association of Gene 33 with histone H2AX and that ectopic expression of Gene 33 promotes the interaction between ATM and histone H2AX without triggering DNA damage. In summary, our results reveal nuclear functions of Gene 33 that regulate DDR. The nuclear localization of Gene 33 also provides a spatial explanation of the previously reported regulation of apoptosis by Gene 33 via the c-Abl/p73 pathway. On the basis of these findings and our previous studies, we propose that Gene 33 is a proximal regulator of DDR that promotes DNA repair.


Subject(s)
Adaptor Proteins, Signal Transducing/biosynthesis , Ataxia Telangiectasia Mutated Proteins/metabolism , DNA Damage/physiology , Gene Expression Regulation/physiology , Histones/metabolism , Tumor Suppressor Proteins/biosynthesis , A549 Cells , Adaptor Proteins, Signal Transducing/genetics , Ataxia Telangiectasia Mutated Proteins/genetics , ErbB Receptors/genetics , ErbB Receptors/metabolism , Histones/genetics , Humans , Protein Domains , Proto-Oncogene Mas , Proto-Oncogene Proteins c-abl/genetics , Proto-Oncogene Proteins c-abl/metabolism , Tumor Protein p73/genetics , Tumor Protein p73/metabolism , Tumor Suppressor Proteins/genetics
7.
Cytometry A ; 93(8): 771-784, 2018 08.
Article in English | MEDLINE | ID: mdl-30144297

ABSTRACT

The nuclear-targeting chemical probe, for the detection and quantification of DNA within cells, has been a mainstay of cytometry-from the colorimetric Feulgen stain to smart fluorescent agents with tuned functionality. The level of nuclear structure and function at which the probe aims to readout, or indeed at which a DNA-targeted drug acts, is shadowed by a wide range of detection modalities and analytical methods. These methods are invariably limited in terms of the resolution attainable versus the volume occupied by targeted chromatin structures. The scalar challenge arises from the need to understand the extent and different levels of compaction of genomic DNA and how such structures can be re-modeled, reported, or even perturbed by both probes and drugs. Nuclear cytometry can report on the complex levels of chromatin order, disorder, disassembly, and even active disruption by probes and drugs. Nuclear probes can report defining features of clinical and therapeutic interest as in NETosis and other cell death processes. New cytometric approaches continue to bridge the scalar challenges of analyzing chromatin organization. Advances in super-resolution microscopy address the resolution and depth of analysis issues in cellular systems. Typical of recent insights into chromatin organization enabled by exploiting a DNA interacting probe is ChromEM tomography (ChromEMT). ChromEMT uses the unique properties of the anthraquinone-based cytometric dye DRAQ5™ to reveal that local and global 3D chromatin structures effect differences in compaction. The focus of this review is nuclear and chromatin cytometry, with linked reference to DNA targeting probes and drugs as exemplified by the anthracenediones.


Subject(s)
Cell Nucleus/genetics , Chromatin/genetics , Flow Cytometry/methods , Nucleosomes/genetics , DNA/genetics , Histones/genetics , Humans , Microscopy, Fluorescence
8.
Apoptosis ; 22(2): 229-238, 2017 Feb.
Article in English | MEDLINE | ID: mdl-27796611

ABSTRACT

Utilizing a variety of flow cytometric methods evidence was obtained indicating that a combination of the glucose analog 2-deoxy-D-glucose (2-dG) and the plant alkaloid berberine (BRB) produces synergistic effect in the induction of apoptosis in human lymphoblastoid TK6 cells. The synergistic effect is seen at concentrations of the drugs at which each of them alone shows no cytotoxicity at all. The data suggest that the combination of these drugs, which are known in terms of their overall toxicity, side effects and pharmacokinetics may be considered for further studies as chemopreventive and cancer treatment modalities. Of interest are results indicating that rapamycin, which similarly to BRB, suppresses mTOR signaling, when combined with 2-dG shows no synergistic properties. Metformin, on other hand, requires much higher concentration to show the synergy with 2-dG. Also of interest are the findings pertaining to the methodology of the present study. Specifically, dynamic assessment of cellular viability was performed by using the DRAQ7 cell exclusion fluorochrome present in cultures from 0 to 72 h. Concurrent measurement of lysosomal proton pump using acridine orange as the probe shows activation of lysosomes in the cells treated with 2-dG or BRB alone as well as with the drugs combined. Apoptosis was assessed by measuring DNA fragmentation, cell cycle, activation of caspase-3 and tissue transglutaminase (Tgase). A novel cytometric method was developed based on analysis of lysosomal (acidic vesicles) proton pump in live cells followed by cell lysis with detergent and fluorochrome labeling of proteins and DNA to analyze Tgase activation concurrently with cell cycle, in same population of cells. The data show that the cell subpopulation undergoing apoptosis has increased side (right-angle) light scatter likely due to the presence of the crosslinked (solid state) proteins, the consequence Tgase activation.


Subject(s)
Apoptosis/drug effects , Berberine/pharmacology , Deoxyglucose/pharmacology , Transglutaminases/genetics , Apoptosis/genetics , Autophagy/drug effects , Autophagy/genetics , Cell Line , Cell Survival/drug effects , Drug Synergism , Flow Cytometry , Humans , Lysosomes/drug effects , Lysosomes/genetics , Metformin/pharmacology , Proton Pumps/genetics
9.
Nucleic Acids Res ; 42(16): 10245-64, 2014.
Article in English | MEDLINE | ID: mdl-25150148

ABSTRACT

Modified mRNA cap analogs aid in the study of mRNA-related processes and may enable creation of novel therapeutic interventions. We report the synthesis and properties of 11 dinucleotide cap analogs bearing a single boranophosphate modification at either the α-, ß- or γ-position of the 5',5'-triphosphate chain. The compounds can potentially serve either as inhibitors of translation in cancer cells or reagents for increasing expression of therapeutic proteins in vivo from exogenous mRNAs. The BH3-analogs were tested as substrates and binding partners for two major cytoplasmic cap-binding proteins, DcpS, a decapping pyrophosphatase, and eIF4E, a translation initiation factor. The susceptibility to DcpS was different between BH3-analogs and the corresponding analogs containing S instead of BH3 (S-analogs). Depending on its placement, the boranophosphate group weakened the interaction with DcpS but stabilized the interaction with eIF4E. The first of the properties makes the BH3-analogs more stable and the second, more potent as inhibitors of protein biosynthesis. Protein expression in dendritic cells was 2.2- and 1.7-fold higher for mRNAs capped with m2 (7,2'-O)GppBH3pG D1 and m2 (7,2'-O)GppBH3pG D2, respectively, than for in vitro transcribed mRNA capped with m2 (7,3'-O)GpppG. Higher expression of cancer antigens would make mRNAs containing m2 (7,2'-O)GppBH3pG D1 and m2 (7,2'-O)GppBH3pG D2 favorable for anticancer immunization.


Subject(s)
Boranes/chemistry , Phosphates/chemistry , Protein Synthesis Inhibitors/chemistry , RNA Cap Analogs/chemistry , Animals , Caenorhabditis elegans Proteins/metabolism , Dendritic Cells/metabolism , Endoribonucleases/metabolism , Eukaryotic Initiation Factor-4E/metabolism , Humans , Neoplasms/drug therapy , Protein Biosynthesis/drug effects , Protein Synthesis Inhibitors/pharmacology , Pyrophosphatases/metabolism , RNA Cap Analogs/chemical synthesis , RNA Cap Analogs/metabolism , RNA Cap Analogs/pharmacology , Stereoisomerism
10.
Int J Mol Sci ; 17(5)2016 May 19.
Article in English | MEDLINE | ID: mdl-27213347

ABSTRACT

The DNA damage response (DDR) is a molecular mechanism that cells have evolved to sense DNA damage (DD) to promote DNA repair, or to lead to apoptosis, or cellular senescence if the damage is too extensive. Recent evidence indicates that microRNAs (miRs) play a critical role in the regulation of DDR. Dietary bioactive compounds through miRs may affect activity of numerous genes. Among the most studied bioactive compounds modulating expression of miRs are epi-gallocatechin-3-gallate, curcumin, resveratrol and n3-polyunsaturated fatty acids. To compare the impact of these dietary compounds on DD/DDR network modulation, we performed a literature search and an in silico analysis by the DIANA-mirPathv3 software. The in silico analysis allowed us to identify pathways shared by different miRs involved in DD/DDR vis-à-vis the specific compounds. The results demonstrate that certain miRs (e.g., -146, -21) play a central role in the interplay among DD/DDR and the bioactive compounds. Furthermore, some specific pathways, such as "fatty acids biosynthesis/metabolism", "extracellular matrix-receptor interaction" and "signaling regulating the pluripotency of stem cells", appear to be targeted by most miRs affected by the studied compounds. Since DD/DDR and these pathways are strongly related to aging and carcinogenesis, the present in silico results of our study suggest that monitoring the induction of specific miRs may provide the means to assess the antiaging and chemopreventive properties of particular dietary compounds.


Subject(s)
Aging/metabolism , DNA Damage , Diet , MicroRNAs/metabolism , Neoplasms , RNA, Neoplasm/metabolism , Computer Simulation , Female , Humans , Male , Neoplasms/metabolism , Neoplasms/prevention & control
11.
Biochem Biophys Res Commun ; 464(1): 89-93, 2015 Aug 14.
Article in English | MEDLINE | ID: mdl-26049109

ABSTRACT

Scavenger decapping enzymes (DcpS) are involved in eukaryotic mRNA degradation process. They catalyze the cleavage of residual cap structure m(7)GpppN and/or short capped oligonucleotides resulting from exosom-mediated the 3' to 5' digestion. For the specific cap recognition and efficient degradation by DcpS, the positive charge at N7 position of guanine moiety is required. Here we examine the role the N7 substitution within the cap structure on the interactions with DcpS (human, Caenorhabditis elegans and Ascaris suum) comparing the hydrolysis rates of dinucleotide cap analogs (m(7)GpppG, et(7)GpppG, but(7)GpppG, bn(7)GpppG) and the binding affinities of hydrolysis products (m(7)GMP, et(7)GMP, but(7)GMP, bn(7)GMP). Our results show the conformational flexibility of the region within DcpS cap-binding pocket involved in the interaction with N7 substituted guanine, which enables accommodation of substrates with differently sized N7 substituents.


Subject(s)
Caenorhabditis elegans Proteins/chemistry , Endoribonucleases/chemistry , Pyrophosphatases/chemistry , RNA Cap Analogs/chemistry , RNA Stability/genetics , Recombinant Fusion Proteins/chemistry , Animals , Ascaris suum/genetics , Ascaris suum/metabolism , Caenorhabditis elegans/genetics , Caenorhabditis elegans/metabolism , Caenorhabditis elegans Proteins/genetics , Caenorhabditis elegans Proteins/metabolism , Endoribonucleases/genetics , Endoribonucleases/metabolism , Enzyme Assays , Escherichia coli/genetics , Escherichia coli/metabolism , Gene Expression , Humans , Isoenzymes/chemistry , Isoenzymes/genetics , Isoenzymes/metabolism , Kinetics , Nucleic Acid Conformation , Pyrophosphatases/genetics , Pyrophosphatases/metabolism , RNA Cap Analogs/metabolism , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/metabolism , Static Electricity
12.
Cytometry A ; 85(9): 785-97, 2014 Sep.
Article in English | MEDLINE | ID: mdl-24894899

ABSTRACT

Mathematical modeling allows relating molecular events to single-cell characteristics assessed by multiparameter cytometry. In the present study we labeled newly synthesized DNA in A549 human lung carcinoma cells with 15-120 min pulses of EdU. All DNA was stained with DAPI and cellular fluorescence was measured by laser scanning cytometry. The frequency of cells in the ascending (left) side of the "horseshoe"-shaped EdU/DAPI bivariate distributions reports the rate of DNA replication at the time of entrance to S phase while their frequency in the descending (right) side is a marker of DNA replication rate at the time of transition from S to G2 phase. To understand the connection between molecular-scale events and scatterplot asymmetry, we developed a multiscale stochastic model, which simulates DNA replication and cell cycle progression of individual cells and produces in silico EdU/DAPI scatterplots. For each S-phase cell the time points at which replication origins are fired are modeled by a non-homogeneous Poisson Process (NHPP). Shifted gamma distributions are assumed for durations of cell cycle phases (G1, S and G2 M), Depending on the rate of DNA synthesis being an increasing or decreasing function, simulated EdU/DAPI bivariate graphs show predominance of cells in left (early-S) or right (late-S) side of the horseshoe distribution. Assuming NHPP rate estimated from independent experiments, simulated EdU/DAPI graphs are nearly indistinguishable from those experimentally observed. This finding proves consistency between the S-phase DNA-replication rate based on molecular-scale analyses, and cell population kinetics ascertained from EdU/DAPI scatterplots and demonstrates that DNA replication rate at entrance to S is relatively slow compared with its rather abrupt termination during S to G2 transition. Our approach opens a possibility of similar modeling to study the effect of anticancer drugs on DNA replication/cell cycle progression and also to quantify other kinetic events that can be measured during S-phase.


Subject(s)
Cell Division/genetics , DNA Replication/genetics , DNA/biosynthesis , Flow Cytometry/methods , Laser Scanning Cytometry/methods , Algorithms , Cell Line, Tumor , Computer Simulation , DNA/genetics , Deoxyuridine/analogs & derivatives , Deoxyuridine/metabolism , G2 Phase/genetics , Humans , Lung Neoplasms/genetics , Microscopy, Confocal , Models, Theoretical , S Phase/genetics
13.
Cytometry A ; 85(5): 386-99, 2014 May.
Article in English | MEDLINE | ID: mdl-24677687

ABSTRACT

This review presents the evidence in support of the IGF-1/mTOR/S6K1 signaling as the primary factor contributing to aging and cellular senescence. Reviewed are also specific interactions between mTOR/S6K1 and ROS-DNA damage signaling pathways. Outlined are critical sites along these pathways, including autophagy, as targets for potential antiaging (gero-suppressive) and/or chemopreventive agents. Presented are applications of flow- and laser scanning- cytometry utilizing phospho-specific Abs, to monitor activation along these pathways in response to the reported antiaging drugs rapamycin, metformin, berberine, resveratrol, vitamin D3, 2-deoxyglucose, and acetylsalicylic acid. Specifically, effectiveness of these agents to attenuate the level of constitutive mTOR signaling was tested by cytometry and confirmed by Western blotting through measuring phosphorylation of the mTOR-downstream targets including ribosomal protein S6. The ratiometric analysis of phosphorylated to total protein along the mTOR pathway offers a useful parameter reporting the effects of gero-suppressive agents. In parallel, their ability to suppress the level of constitutive DNA damage signaling induced by endogenous ROS was measured. While the primary target of each of these agents may be different the data obtained on several human cancer cell lines, WI-38 fibroblasts and normal lymphocytes suggest common downstream mechanism in which the decline in mTOR/S6K1 signaling and translation rate is coupled with a reduction of oxidative phosphorylation and ROS that leads to decreased oxidative DNA damage. The combined assessment of constitutive γH2AX expression, mitochondrial activity (ROS, ΔΨm), and mTOR signaling provides an adequate gamut of cell responses to test effectiveness of gero-suppressive agents. Described is also an in vitro model of induction of cellular senescence by persistent replication stress, its quantitative analysis by laser scanning cytometry, and application to detect the property of the studied agents to attenuate the induction of senescence. Discussed is cytometric analysis of cell size and heterogeneity of size as a potential biomarker used to asses gero-suppressive agents and longevity.


Subject(s)
Aging/drug effects , Insulin-Like Growth Factor I/genetics , Signal Transduction/genetics , TOR Serine-Threonine Kinases/genetics , Autophagy/genetics , Cellular Senescence/drug effects , Cellular Senescence/genetics , DNA Damage/genetics , Humans , Laser Scanning Cytometry , Mitochondria/metabolism , Nuclear Proteins/genetics , Phosphorylation , RNA-Binding Proteins/genetics , Reactive Oxygen Species/metabolism
14.
Cytometry A ; 83(6): 533-9, 2013 Jun.
Article in English | MEDLINE | ID: mdl-23404939

ABSTRACT

A new low-molecular-weight fluorescent probe, Col-F, that exhibits affinity to collagen and elastin, was used successfully in imaging of extracellular matrix in freshly excised animal tissues. Col-F readily penetrates between live cells into tissues and binds to fibers of collagen and elastin by a noncovalent mechanism. Fibers of collagen and elastin have been stained in a variety of tissues, including tendon, skeletal muscle, connective tissue, and arteries. Cells migrating in a Col-F-stained collagenous biomaterial were also imaged. No phototoxic effects were detected when live keratocytes were imaged in the in vitro culture in the presence of Col-F. In conclusion, Col-F provides a simple and convenient tool for fluorescence three-dimensional imaging of intricate collagenous and elastic structures in live and fixed animal tissues, as well as in collagen-containing biomaterials.


Subject(s)
Collagen/ultrastructure , Elastin/ultrastructure , Extracellular Matrix/ultrastructure , Fluoresceins/chemical synthesis , Fluorescent Dyes/chemical synthesis , Imaging, Three-Dimensional/methods , Physostigmine/analogs & derivatives , Animals , Arteries/chemistry , Arteries/ultrastructure , Biological Transport , Collagen/chemistry , Connective Tissue/chemistry , Connective Tissue/ultrastructure , Elastin/chemistry , Extracellular Matrix/chemistry , Fluoresceins/metabolism , Fluorescent Dyes/metabolism , HeLa Cells , Humans , Mice , Microscopy, Fluorescence , Muscle, Skeletal/chemistry , Muscle, Skeletal/ultrastructure , Physostigmine/chemical synthesis , Physostigmine/metabolism , Tendons/chemistry , Tendons/ultrastructure
15.
Cytometry A ; 83(11): 979-88, 2013 Nov.
Article in English | MEDLINE | ID: mdl-24115313

ABSTRACT

The "click chemistry" approach utilizing 5-ethynyl-2'-deoxyuridine (EdU) as a DNA precursor was recently introduced to assess DNA replication and adapted to flow- and imaging-cytometry. In the present study, we observed that EdU, once incorporated into DNA, induces DNA damage signaling (DDS) such as phosphorylation of ATM on Ser1981, of histone H2AX on Ser139, of p53 on Ser15, and of Chk2 on Thr68. It also perturbs progression of cells through the cell cycle and subsequently induces apoptosis. These effects were observed in non-small cell lung adenocarcinoma A549 as well as in B-cell human lymphoblastoid TK6 and WTK1 cells, differing in the status of p53 (wt versus mutated). After 1 h EdU pulse-labeling, the most affected was cells progression through the S phase subsequent to that at which they had incorporated EdU. This indicates that DNA replication using the template containing incorporated EdU is protracted and triggers DDS. Furthermore, progression of cells having DNA pulse-labeled with EdU led to accumulation of cells in G2 , likely by activating G2 checkpoint. Consistent with the latter was activation of p53 and Chk2. Although a correlation was observed in A549 cells between the degree of EdU incorporation and the extent of γH2AX induction, such correlation was weak in TK6 and WTK1 cells. The degree of perturbation of the cell cycle kinetics by the incorporated EdU was different in the wt p53 TK6 cells as compared to their sister WTK1 cell line having mutated p53. The data are thus consistent with the role of p53 in modulating activation of cell cycle checkpoints in response to impaired DNA replication. The confocal microscopy analysis of the 3D images of cells exposed to EdU for 1 h pulse and then grown for 24 or 48 h revealed an increased number of colocalized γH2AX and p53BP1 foci considered to be markers of DNA double-strand breaks and enlarged nuclei.


Subject(s)
Click Chemistry/methods , DNA Damage/genetics , DNA/genetics , Deoxyuridine/analogs & derivatives , Apoptosis/drug effects , Cell Cycle/drug effects , Cell Line, Tumor , DNA/drug effects , DNA/isolation & purification , DNA Damage/drug effects , Deoxyuridine/chemistry , Histones/genetics , Histones/isolation & purification , Humans , Laser Scanning Cytometry/methods , Signal Transduction , Tumor Suppressor Protein p53/genetics , Tumor Suppressor Protein p53/isolation & purification
16.
Cytometry A ; 83(10): 925-32, 2013 Oct.
Article in English | MEDLINE | ID: mdl-23900967

ABSTRACT

Sites of DNA replication (EdU incorporation) and DNA damage signaling (γH2AX) induced by camptothecin (Cpt) or hydrogen peroxide (H2O2) form characteristic patterns of foci in cell nuclei. The overlap between these patterns is a function of the number of DNA double strand breaks (DSBs) formed in replication sites. The goal of this study was to optimize a method of quantitative assessment of a degree of correlation between these two patterns. Such a correlation can be used to estimate a probability of inducing damage in sections of replicating DNA. The damage and replication foci are imaged in 3D with confocal microscopy and their respective positions within nuclei are determined with adaptive image segmentation. Using correlation functions spatial proximity of the resultant point patterns is quantified over the range of distances in cells in early-, mid- and late S-phase. As the numbers (and nuclear densities) of γH2AX and replication foci differ significantly in the subsequent substages of S phase, the detected association values were corrected for the expected random overlap between both classes of foci. Thus, the probability of their nonrandom association was estimated. Moreover, self association (clustering) of DNA replication sites in different stages of S-phase of the cell cycle was detected and accounted for. While the analysis revealed a strong correlation between the γH2AX foci and the sites of DNA replication in cells treated with Cpt, only a low correlation was apparent in cells exposed to H2O2. © 2013 International Society for Advancement of Cytometry.


Subject(s)
DNA Damage/physiology , DNA Replication/physiology , Image Processing, Computer-Assisted/methods , Imaging, Three-Dimensional/methods , Oxidative Stress/physiology , Camptothecin/toxicity , Cells, Cultured , DNA Replication/drug effects , Histones/metabolism , Humans , Microscopy, Confocal , Topoisomerase I Inhibitors/pharmacology
17.
Cytometry A ; 83(2): 227-34, 2013 Feb.
Article in English | MEDLINE | ID: mdl-23165976

ABSTRACT

The exclusion of charged fluorescent dyes by intact cells has become a well-established assay for determining viability of cells. In search for a noninvasive fluorescent probe capable of long-term monitoring of cell death in real-time, we evaluated a new anthracycline derivative DRAQ7. The novel probe does not penetrate the plasma membrane of living cells but when the membrane integrity is compromised, it enters and binds readily to nuclear DNA to report cell death. It proved to be nontoxic to a panel of cancer cell lines grown continuously for up to 72 h and did not induce any detectable DNA damage signaling when analyzed using laser scanning microscopy and flow cytometry. The DRAQ7 provided a sensitive, real-time readout of cell death induced by a variety of stressors such as hypoxia, starvation, and drug-induced cytotoxicity. The overall responses to anticancer agents and resulting pharmacological dose-response profiles were not affected by the growth of tumor cells in the presence DRAQ7. Moreover, we for the first time introduced a near real-time microflow cytometric assay based on combination of DRAQ7 and mitochondrial inner membrane potential (ΔΨ(m) ) sensitive probe TMRM. We provide evidence that this low-dosage, real-time labeling procedure provides multiparameter and kinetic fingerprint of anticancer drug action.


Subject(s)
Anthracyclines/chemistry , Apoptosis , Fluorescent Dyes/chemistry , Anthracyclines/pharmacology , Benzamides/pharmacology , Biphenyl Compounds/pharmacology , Cell Line, Tumor , Cell Survival/drug effects , DNA Damage , Dactinomycin/pharmacology , Etoposide/pharmacology , Flow Cytometry , Fluorescent Dyes/pharmacology , Histones/metabolism , Humans , Inhibitory Concentration 50 , Membrane Potential, Mitochondrial/drug effects , Nitrophenols/pharmacology , Piperazines/pharmacology , Rhodamines/chemistry , Staurosporine/pharmacology , Sulfonamides/pharmacology , Sulfones/pharmacology
19.
Postepy Hig Med Dosw (Online) ; 67: 1166-72, 2013 Dec 02.
Article in English | MEDLINE | ID: mdl-24379257

ABSTRACT

Ranpirnase (onconase; ONC) is an endoribonuclease obtained from the frog Rana pipiens. This enzyme exhibits anticancer properties mediated by degradation of cellular RNA and induction of apoptosis. In this study we assessed cytotoxicity of ONC in combination with currently used anticancer drugs on a human diffuse large B-cell lymphoma (DLBCL)-derived cell line (Toledo). Cytotoxic activity was measured by the exclusion of propidium iodide assay while apoptosis was assessed using the annexin-V binding method. Additionally, flow cytometry was used to assess the decline of mitochondrial potential and to determine activation of caspases 3, 8 and 9. It was observed that in vitro treatment with ONC in combination with rituximab, mafosfamide, vincristine, doxorubicin, and dexamethasone (drugs corresponding with elements of R-CHOP regimen) resulted in increased cytotoxicity. As a result ONC showed marked cytotoxicity against Toledo cells. Importantly, in combination of ONC with drugs imitating the R-CHOP regimen, this effect was significantly intensified. The main mechanism responsible for this event was induction of apoptosis along a mitochondrial dependent pathway. In conclusion, these data indicate that further preclinical and eventually clinical studies assessing activity of ONC+R-CHOP treatment are warranted.


Subject(s)
Antibodies, Antineutrophil Cytoplasmic/therapeutic use , Antineoplastic Combined Chemotherapy Protocols/administration & dosage , Lymphoma, Large B-Cell, Diffuse/drug therapy , Ribonucleases/administration & dosage , Antibodies, Monoclonal, Murine-Derived/administration & dosage , Apoptosis/drug effects , Cell Line , Cyclophosphamide/administration & dosage , Doxorubicin/administration & dosage , Humans , Prednisone/administration & dosage , Rituximab , Treatment Outcome , Vincristine/administration & dosage
20.
Cancers (Basel) ; 15(8)2023 Apr 07.
Article in English | MEDLINE | ID: mdl-37190127

ABSTRACT

Thyroid cancer (TC) is the most common endocrine malignancy, with an approximately three-fold higher incidence in women. TCGA data indicate that androgen receptor (AR) RNA is significantly downregulated in PTC. In this study, AR-expressing 8505C (anaplastic TC) (84E7) and K1 (papillary TC) cells experienced an 80% decrease in proliferation over 6 days of exposure to physiological levels of 5α-dihydrotestosterone (DHT). In 84E7, continuous AR activation resulted in G1 growth arrest, accompanied by a flattened, vacuolized cell morphology, with enlargement of the cell and the nuclear area, which is indicative of senescence; this was substantiated by an increase in senescence-associated ß-galactosidase activity, total RNA and protein content, and reactive oxygen species. Additionally, the expression of tumor suppressor proteins p16, p21, and p27 was significantly increased. A non-inflammatory senescence-associated secretory profile was induced, significantly decreasing inflammatory cytokines and chemokines such as IL-6, IL-8, TNF, RANTES, and MCP-1; this is consistent with the lower incidence of thyroid inflammation and cancer in men. Migration increased six-fold, which is consistent with the clinical observation of increased lymph node metastasis in men. Proteolytic invasion potential was not significantly altered, which is consistent with unchanged MMP/TIMP expression. Our studies provide evidence that the induction of senescence is a novel function of AR activation in thyroid cancer cells, and may underlie the protective role of AR activation in the decreased incidence of TC in men.

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