Non-homologous DNA end joining in normal and cancer cells and its dependence on break structures

DNA double-strand breaks (DSBs) are a serious threat to the cell, for if not or miss-repaired, they can lead to chromosomal aberration, mutation and cancer. DSBs in human cells are repaired via non-homologous DNA end joining (NHEJ) and homologous recombination repair pathways. In the former process, the structure of DNA termini plays an important role, as does the genetic constitution of the cells, through being different in normal and pathological cells. In order to investigate the dependence of NHEJ on DSB structure in normal and cancer cells, we used linearized plasmids with various, complementary or non-complementary, single-stranded or blunt DNA termini, as well as whole-cell extract isolated from normal human lymphocytes, chronic myeloid leukemia K562 cells and lung cancer A549 cells. We observed a pronounced variability in the efficacy of NHEJ reaction depending on the type of ends. Plasmids with complementary and blunt termini were more efficiently repaired than the substrate with 3' protruding single-strand ends. The hierarchy of the effectiveness of NHEJ was on average, from the most effective to the least, A549/ normal lymphocytes/ K562. Our results suggest that the genetic constitution of the cells together with the substrate terminal structure may contribute to the efficacy of the NHEJ reaction. This should be taken into account on considering its applicability in cancer chemo- or radiotherapy by pharmacologically modulating NHEJ cellular responses.     

Rapid assessment of two major repair activities against DNA double-strand breaks in vertebrate cells

A linearized plasmid DNA, in which tandem repeats of 400bp flank the breakpoints, was transfected into vertebrate cells, and breakpoint junctions of plasmid DNA circularized in the cells were analyzed to assess the repair activities against DNA double-strand break (DSB) by non-homologous end joining and homology-directed repair (i.e., homologous recombinational repair and single-strand annealing). The circularization by non-homologous end joining repair of the breakpoints depended on the expression of DNA-PKcs, while that by homology-directed repair through the repeats depended on the length of the repeats, indicating that these two DSB repair activities can be rapidly assessed by this assay. Predominance in circularization by either non-homologous end joining or homology-directed repair differed among cells examined, and circularization was exclusively undertaken by homology-directed repair in DT40 cells known to show a high homologous recombination rate against gene-targeting vectors. Thus, this assay will be helpful in studies on mechanisms and inter-cellular variations of DSB repair.     

Flow sorting of tumor cells for morphometric analysis,particularly of rare cells

Using flow cytometric DNA measurement and sorting combined with morphometric light microscopy, different groups of cells were studied in a human melanoma pleural effusion, a human melanoma lymph node metastasis and a mouse tumor, as well as in normal reference tissues. Beside cells of the predominant tumor cell population, three types of rare tumor cells were studied after enrichment by sorting: a) giant cells from the >8c region, comprising about 5% of the tumor cells, b) binucleated and multinucleated cells with unequal nuclear sizes within the same cell, found at frequencies of about 1.5%, and c) <2c cells which were derived from the so-called “debris”-region of the DNA histogram, found at frequencies of about 1 to 6%. All these rare cells were found only in the malignant tumors and not in the benign reference tissues. Morphometry showed that the increase in the cellular DNA content in the different fractions of tumor cells was combined with an increase in the cellular and nuclear sizes. However, the n/c-ratio was constant in the whole range of tumor cell fractions, including the fractions from the the <2c and the >8c regions. The n/c-ratio of the <2c cells and giant cells differed from that of corresponding normal cells underlining their origin from the predominant tumor cell population. The possible linkage between the occurrence of the three rare cell types and genetic instability of tumors related to faulty nucleus and cell division is discussed.     

Flow cytometric cell cycle analysis of cultured brown bear fibroblast cells

The aim of this study was to assess by flow cytometry the cell cycle of brown bear fibroblast cells cultured under different growth conditions. Skin biopsies were taken in Cantabria (Spain) from a live, anaesthetized brown bear. DNA analysis was performed by flow cytometry following cell DNA staining with propidium iodide. Serum starvation increased (P<0.01) the percentage of G0/G1 phase cells (92.7+/-0.86) as compared to cycling cells (39.7+/-0.86) or cells cultured to confluency (87.3+/-0.86). DMSO included for 48h in the culture significantly increased (P<0.01) the percentage of G0/G1 phase of the cell cycle at all concentrations used and decreased percentages of S phase in a dose-dependent fashion. Roscovitine increased the G0/G1 phase of the cell cycle (P<0.01) at 15microM concentration. Interestingly, the G2/M stage significantly increased at 30 and 50microM compared to the control and 15microM (P<0.02). The cell cycle of brown bear adult fibroblast cells can be successfully synchronized under a variety of culture conditions.     

Cell sorting in cancer research—Diminishing degree of cell heterogeneity

Increasing evidence of intratumor heterogeneity and its augmentation due to selective pressure of microenvironment and recent achievements in cancer therapeutics lead to the need to investigate and track the tumor subclonal structure. Cell sorting of heterogeneous subpopulations of tumor and tumor-associated cells has been a long established strategy in cancer research. Advancement in lasers, computer technology and optics has led to a new generation of flow cytometers and cell sorters capable of high-speed processing of single cell suspensions. Over the last several years cell sorting was used in combination with molecular biological methods, imaging and proteomics to characterize primary and metastatic cancer cell populations, minimal residual disease and single tumor cells. It was the principal method for identification and characterization of cancer stem cells. Analysis of single cancer cells may improve early detection of tumors, monitoring of circulating tumor cells, evaluation of intratumor heterogeneity and chemotherapeutic treatments. The aim of this review is to provide an overview of major cell sorting applications and approaches with new prospective developments such as microfluidics and microchip technologies.     

Differences in repair profiles of interstitial telomeric sites between normal and DNA double-strand break repair deficient Chinese hamster cells

Interstitial Telomeric Repeat Sequence (ITRS) blocks are recognized as hot spots for spontaneous and ionizing radiation-induced chromosome breakage and recombination. Background and ionizing radiation-induced DNA breaks in large blocks of ITRS from Chinese hamster cell lines were analyzed using the DNA Breakage Detection-Fluorescence In Situ Hybridization (DBD-FISH) procedure. Our results indicate an extremely alkali-sensitivity of ITRS. Furthermore, it appears that ITRS blocks exhibit a particular chromatin structure, being enriched in short unpaired DNA segments. These segments could be liable to severe topological stress in highly compacted areas of the genome resulting in their spontaneous fragility and thus explaining their alkali-sensitivity. The induction and repair kinetics of DNA single-strand breaks (ssb) and DNA double-strand breaks (dsb) induced by ionizing radiation were assessed by DBD-FISH on neutral comets using Chinese hamster cells deficient in either DNA-PKcs or Rad51C. Our results indicate that the initial rejoining rate of dsb within ITRS is slower than that in the whole genome, in wild-type cells, demonstrating an intragenomic heterogeneity in dsb repair. Interestingly, in the absence of DNA-PKcs activity, the rejoining rate of dsb within ITRS is not modified, unlike in the whole genome. This was also found in the case of Rad51C mutant cells. Our results suggest the possibility that different DNA sequences or chromatin organizations may be targeted by specific dsb repair pathways. Furthermore, it appears that additional unknown dsb repair pathways may be operational in mammalian cells.     

Role for Artemis nuclease in the repair of radiation-induced DNA double strand breaks by alternative end joining

Exposure of cells to ionizing radiation or radiomimetic drugs generates DNA double-strand breaks that are processed either by homologous recombination repair (HRR), or by canonical, DNA-PKcs-dependent non-homologous end-joining (C-NHEJ). Chemical or genetic inactivation of factors involved in C-NHEJ or HRR, but also their local failure in repair proficient cells, promotes an alternative, error-prone end-joining pathway that serves as backup (A-EJ). There is evidence for the involvement of Artemis endonuclease, a protein deficient in a human radiosensitivity syndrome associated with severe immunodeficiency (RS-SCID), in the processing of subsets of DSBs by HRR or C-NHEJ. It is thought that within HRR or C-NHEJ Artemis processes DNA termini at complex DSBs. Whether Artemis has a role in A-EJ remains unknown. Here, we analyze using pulsed-field gel electrophoresis (PFGE) and specialized reporter assays, DSB repair in wild-type pre-B NALM-6 lymphocytes, as well as in their Artemis^−/−, DNA ligase 4^−/− (LIG4^−/−), and LIG4^−/−/Artemis^−/− double mutant counterparts, under conditions allowing evaluation of A-EJ. Our results substantiate the suggested roles of Artemis in C-NHEJ and HRR, but also demonstrate a role for the protein in A-EJ that is confirmed in Artemis deficient normal human fibroblasts. We conclude that Artemis is a nuclease participating in DSB repair by all major repair pathways.     

Timing the changes of cyclin E cell content in G1 in exponentially growing cells

We present a method for measuring the content of immunocytochemically detected proteins in individual cells progressing through G(1) phase and its application in the analysis of cyclin E levels. The sequence of G(1) events is tracked under unaltered cycling conditions, in a cell line in the phase of balanced growth in vitro, to avoid the pitfalls of synchronization. Cells were pulse-labeled with BrdUrd and analyzed sequentially by multiparameter flow cytometry, focusing on the subpopulation of labeled cells progressively entering G(1). We use the time-from-birth ("age") of individual cells to track their position inside G(1). Using the average content of cyclin E in the whole population of G(1) cells as the internal reference for each sample, we analyzed the time course of the frequency histograms of cyclin E content within BrdUrd-labeled G(1) cells by exploiting the properties of the age distributions of asynchronous populations. This way we could calculate the average cyclin E content of cells in each age cohort. Cyclin E values were low until age 3 h, after which they rose gradually, reaching six times the value of newborn cells at the end of G(1).     

Cell cycle-dependent disruption of microtubules by methyl jasmonate in tobacco BY-2 cells

Summary Methyl jasmonate, a growth-regulating substance that is ubiquitous in the plant kingdom, was found to disrupt cortical microtubules in tobacco cultured cells. It exerted a microtubule-disrupting effect only in cells at the S phase of the cell cycle. Neither microtubules in preprophase bands, spindles and phragmoplasts nor cortical microtubules at stages of the cell cycle other than the S phase were disrupted by methyl jasmonate. Jasmonic acid was as effective as methyl jasmonate in disrupting cortical microtubules.Abbreviations BUdR 5-bromo-2-deoxyuridine - 2,4-D 2,4-dichlorophenoxyacetic acid - DMSO dimethyl sulfoxide - EGTA ethylene glycol bis(2-aminoethyl ether)-tetraacetic acid - FITC fluorescein isothiocyanate - FUdR 5-fluoro-2-deoxyuridine - JA jasmonic acid - JA-Me methyl jasmonate - PBS phosphate-buffered saline - PMSF phenylmethylsulfonyl fluoride     

A mathematical model for analysis of the cell cycle in cell lines derived from human tumors

The growth of human cancers is characterised by long and variable cell cycle times that are controlled by stochastic events prior to DNA replication and cell division. Treatment with radiotherapy or chemotherapy induces a complex chain of events involving reversible cell cycle arrest and cell death. In this paper we have developed a mathematical model that has the potential to describe the growth of human tumour cells and their responses to therapy. We have used the model to predict the response of cells to mitotic arrest, and have compared the results to experimental data using a human melanoma cell line exposed to the anticancer drug paclitaxel. Cells were analysed for DNA content at multiple time points by flow cytometry. An excellent correspondence was obtained between predicted and experimental data. We discuss possible extensions to the model to describe the behaviour of cell populations in vivo.     

Ki67与核酸荧光共染在细胞周期研究中的应用

病原微生物与宿主细胞的相互作用是感染过程中的一个重要环节,也是研究肿瘤生物学的一项重要内容。动态研究细胞周期变化对了解病原体作用于细胞具有重要意义。本研究用Ki67/4′,6-二脒基-2-苯基吲哚(4′,6-diamidino-2-phenylindole,DAPI)和Ki67/碘化丙啶(propidium iodide,PI)共染技术分析了小鼠脾细胞的细胞周期变化,并介绍其具体应用。     

利用405nm激光激发Hoechst33342染色细胞DNA的流式细胞技术

目的:探讨流式细胞仪上405 nm激光激发Hoechst33342染色细胞DNA的效果及影响检测结果的因素。方法:SW480和A549两种细胞经Hoechst33342染色后,流式细胞仪405 nm激光激发检测DNA含量,利用软件计算出处于G0/G1期、S期和G2/M期细胞的百分比,以PI染色法结果作为对照。结果:SW480和A549细胞经Hoechst33342染色后各期的细胞百分比与PI染色法基本一致,无明显差异(P0.05)。结论:405 nm激光激发Hoechst33342染色细胞DNA结果可靠,可作为紫外检测的替代方法。     

Mechanism and regulation of DNA end resection in eukaryotes

The repair of DNA double-strand breaks (DSBs) by homologous recombination (HR) is initiated by nucleolytic degradation of the 5′-terminated strands in a process termed end resection. End resection generates 3′-single-stranded DNA tails, substrates for Rad51 to catalyze homologous pairing and DNA strand exchange, and for activation of the DNA damage checkpoint. The commonly accepted view is that end resection occurs by a two-step mechanism. In the first step, Sae2/CtIP activates the Mre11–Rad50–Xrs2/Nbs1 (MRX/N) complex to endonucleolytically cleave the 5′-terminated DNA strands close to break ends, and in the second step Exo1 and/or Dna2 nucleases extend the resected tracts to produce long 3′-ssDNA-tailed intermediates. Initiation of resection commits a cell to repair a DSB by HR because long ssDNA overhangs are poor substrates for non-homologous end joining (NHEJ). Thus, the initiation of end resection has emerged as a critical control point for repair pathway choice. Here, I review recent studies on the mechanism of end resection and how this process is regulated to ensure the most appropriate repair outcome.     

Combined analysis of DNA methylation and cell cycle in cancer cells

DNA methylation is a chemical modification of DNA involved in the regulation of gene expression by controlling the access to the DNA sequence. It is the most stable epigenetic mark and is widely studied for its role in major biological processes. Aberrant DNA methylation is observed in various pathologies, such as cancer. Therefore, there is a great interest in analyzing subtle changes in DNA methylation induced by biological processes or upon drug treatments. Here, we developed an improved methodology based on flow cytometry to measure variations of DNA methylation level in melanoma and leukemia cells. The accuracy of DNA methylation quantification was validated with LC-ESI mass spectrometry analysis. The new protocol was used to detect small variations of cytosine methylation occurring in individual cells during their cell cycle and those induced by the demethylating agent 5-aza-2''-deoxycytidine (5AzadC). Kinetic experiments confirmed that inheritance of DNA methylation occurs efficiently in S phase and revealed a short delay between DNA replication and completion of cytosine methylation. In addition, this study suggests that the uncoupling of 5AzadC effects on DNA demethylation and cell proliferation might be related to the duration of the DNA replication phase.     

Modelling cell death in human tumour cell lines exposed to the anticancer drug paclitaxel

Most anti-cancer drugs in use today exert their effects by inducing a programmed cell death mechanism. This process, termed apoptosis, is accompanied by degradation of the DNA and produces cells with a range of DNA contents. We have previously developed a phase transition mathematical model to describe the mammalian cell division cycle in terms of cell cycle phases and the transition rates between these phases. We now extend this model here to incorporate a transition to a programmed cell death phase whereby cellular DNA is progressively degraded with time. We have utilised the technique of flow cytometry to analyse the behaviour of a melanoma cell line (NZM13) that was exposed to paclitaxel, a drug used frequently in the treatment of cancer. The flow cytometry profiles included a complex mixture of living cells whose DNA content was increasing with time and dying cells whose DNA content was decreasing with time. Application of the mathematical model enabled estimation of the rate constant for entry of mitotic cells into apoptosis (0.035 per hour) and the duration of the period of DNA degradation (51 hours). These results provide a dynamic model of the action of an anticancer drug that can be extended to improve the clinical outcome in individual cancer patients.Revised version: 9 October 2003     

Flow cytometry analysis of early DNA content changes in human and monkey cells following infection with simian virus 40

Simian virus 40 (SV₄₀) is capable of inducing cellular DNA synthesis in permissive and nonpermissive cells. Utilizing flow cytometry, we analyzed the DNA content changes in two diploid human cell strains and two monkey cell lines. The osteogenesis imperfects (OI) human skin fibroblasts were induced into DNA synthesis, and within one to two cell generations, a polyploid cell population was produced. With WI-38 phase II cells, a similar pattern of increased cycling of cells into DNA synthesis was observed; however, the majority (～60%) of the cells were blocked in the G₂ + M phase of the cell cycle. At later time intervals, an increase in the G₁ population was demonstrated. The two monkey cell lines responded to SV₄₀ virus with an accumulation of cells in the G₂ + M phase of the cell cycle. Thus, two diploid human cell strains exhibited different cell cycle kinetics early after infection with SV₄₀ virus. The one strain (WI-38) behaved similarly to the two monkey cell lines studied. The other strain (OI) responded similarly to nonpermissive (transformin) cells infected with SV₄₀ virus.     

DNA end resection is needed for the repair of complex lesions in G1-phase human cells

Repair of DNA double strand breaks (DSBs) is influenced by the chemical complexity of the lesion. Clustered lesions (complex DSBs) are generally considered more difficult to repair and responsible for early and late cellular effects after exposure to genotoxic agents. Resection is commonly used by the cells as part of the homologous recombination (HR) pathway in S- and G2-phase. In contrast, DNA resection in G1-phase may lead to an error-prone microhomology-mediated end joining. We induced DNA lesions with a wide range of complexity by irradiation of mammalian cells with X-rays or accelerated ions of different velocity and mass. We found replication protein A (RPA) foci indicating DSB resection both in S/G2- and G1-cells, and the fraction of resection-positive cells correlates with the severity of lesion complexity throughout the cell cycle. Besides RPA, Ataxia telangiectasia and Rad3-related (ATR) was recruited to complex DSBs both in S/G2- and G1-cells. Resection of complex DSBs is driven by meiotic recombination 11 homolog A (MRE11), CTBP-interacting protein (CtIP), and exonuclease 1 (EXO1) but seems not controlled by the Ku heterodimer or by phosphorylation of H2AX. Reduced resection capacity by CtIP depletion increased cell killing and the fraction of unrepaired DSBs after exposure to densely ionizing heavy ions, but not to X-rays. We conclude that in mammalian cells resection is essential for repair of complex DSBs in all phases of the cell-cycle and targeting this process sensitizes mammalian cells to cytotoxic agents inducing clustered breaks, such as in heavy-ion cancer therapy.     

Analysis of the cell cycle in an arbuscular mycorrhizal fungus by flow cytometry and bromodeoxyuridine labelling

Summary The cell cycle of an arbuscular mycorrhizal fungus,Glomus versiforme, was determined by flow cytometric analysis of nuclei isolated from spores and mycorrhizal roots of leek, and by immunogold staining after bromodeoxyuridine (BrdU) uptake by DNA. The aims of our work were to establish: (i) whether there are changes in ploidy during fungal growth and morphogenesis, (ii) when and where the cell cycle is activated. Our results demonstrate that nuclei isolated from quiescent spores ofG. versiforme are arrested in the GO/G1 phase (99.2%), whereas fungal nuclei from mycorrhizal roots are in the synthetic (S) (10.1%) and G2/M phase (3.9%). Nuclei undergoing DNA synthesis were detected in situ after BrdU uptake. Labelled nuclei were observed in intercellular hyphae and in large arbuscular trunks. This paper demonstrates that colonization of an arbuscular mycorrhizal fungus is linked to activation of its cell cycle.Abbreviations AM fungi arbuscular mycorrhizal fungi - BrdU 5-bromo-2-deoxyuridine - PI propidium iodide - DAPI 4,6-diamidino-2-phenylindole