Ionizing radiation represents the most effective therapy for glioblastoma (World Health Organization grade IV glioma), one of the most lethal human malignancies, but radiotherapy remains only palliative because of radioresistance. The mechanisms underlying tumour radioresistance have remained elusive. Here we show that cancer stem cells contribute to glioma radioresistance through preferential activation of the DNA damage checkpoint response and an increase in DNA repair capacity. The fraction of tumour cells expressing CD133 (Prominin-1), a marker for both neural stem cells and brain cancer stem cells, is enriched after radiation in gliomas. In both cell culture and the brains of immunocompromised mice, CD133-expressing glioma cells survive ionizing radiation in increased proportions relative to most tumour cells, which lack CD133. CD133-expressing tumour cells isolated from both human glioma xenografts and primary patient glioblastoma specimens preferentially activate the DNA damage checkpoint in response to radiation, and repair radiation-induced DNA damage more effectively than CD133-negative tumour cells. In addition, the radioresistance of CD133-positive glioma stem cells can be reversed with a specific inhibitor of the Chk1 and Chk2 checkpoint kinases. Our results suggest that CD133-positive tumour cells represent the cellular population that confers glioma radioresistance and could be the source of tumour recurrence after radiation. Targeting DNA damage checkpoint response in cancer stem cells may overcome this radioresistance and provide a therapeutic model for malignant brain cancers.

Glioma stem cells promote radioresistance by preferential activation of the DNA damage response

The comet assay (single-cell gel electrophoresis) is a simple method for measuring deoxyribonucleic acid (DNA) strand breaks in eukaryotic cells. Cells embedded in agarose on a microscope slide are lysed with detergent and high salt to form nucleoids containing supercoiled loops of DNA linked to the nuclear matrix. Electrophoresis at high pH results in structures resembling comets, observed by fluorescence microscopy; the intensity of the comet tail relative to the head reflects the number of DNA breaks. The likely basis for this is that loops containing a break lose their supercoiling and become free to extend toward the anode. The assay has applications in testing novel chemicals for genotoxicity, monitoring environmental contamination with genotoxins, human biomonitoring and molecular epidemiology, and fundamental research in DNA damage and repair. The sensitivity and specificity of the assay are greatly enhanced if the nucleoids are incubated with bacterial repair endonucleases that recognize specific kinds of damage in the DNA and convert lesions to DNA breaks, increasing the amount of DNA in the comet tail. DNA repair can be monitored by incubating cells after treatment with damaging agent and measuring the damage remaining at intervals. Alternatively, the repair activity in a cell extract can be measured by incubating it with nucleoids containing specific damage.

https://zenodo.org/record/975797/files/article.pdf

The Comet Assay for DNA Damage and Repair: Principles, Applications, and Limitations

We present a procedure for the comet assay, a gel electrophoresis-based method that can be used to measure DNA damage in individual eukaryotic cells. It is versatile, relatively simple to perform and sensitive. Although most investigations make use of its ability to measure DNA single-strand breaks, modifications to the method allow detection of DNA double-strand breaks, cross-links, base damage and apoptotic nuclei. The limit of sensitivity is approximately 50 strand breaks per diploid mammalian cell. DNA damage and its repair in single-cell suspensions prepared from yeast, protozoa, plants, invertebrates and mammals can also be studied using this assay. Originally developed to measure variation in DNA damage and repair capacity within a population of mammalian cells, applications of the comet assay now range from human and sentinel animal biomonitoring (e.g., DNA damage in earthworms crawling through toxic waste sites) to measurement of DNA damage in specific genomic sequences. This protocol can be completed in fewer than 24 h.

The comet assay: a method to measure DNA damage in individual cells.

NanoGenotoxicology: The DNA damaging potential of engineered nanomaterials

The in vivo alkaline single cell gel electrophoresis assay, hereafter the Comet assay, can be used to investigate the genotoxicity of industrial chemicals, biocides, agrochemicals and pharmaceuticals. The major advantages of this assay include the relative ease of application to any tissue of interest, the detection of multiple classes of DNA damage and the generation of data at the level of the single cell. These features give the Comet assay potential advantages over other in vivo test methods, which are limited largely to proliferating cells and/or a single tissue. The Comet assay has demonstrated its reliability in many testing circumstances and is, in general, considered to be acceptable for regulatory purposes. However, despite the considerable data published on the in vivo Comet assay and the general agreement within the international scientific community over many protocol-related issues, it was felt that a document giving detailed practical guidance on the protocol required for regulatory acceptance of the assay was required. In a recent meeting held in conjunction with the 4th International Comet Assay Workshop (Ulm, Germany, 22-25 July 2001) an expert panel reviewed existing data and recent developments of the Comet assay with a view to developing such a document. This paper is intended to act as an update to the more general guidelines which were published as a result of the International Workshop on Genotoxicity Test Procedures. The recommendations are also seen as a major step towards gaining more formal regulatory acceptance of the Comet assay.

/pdf/recommendations-for-conducting-the-in-vivo-alkaline-comet-430ynqql5f.pdf

Recommendations for conducting the in vivo alkaline Comet assay

Atthe International Workshop on Genotoxicity Test Procedures (IWGTP) held in Washington, DC, March 25-26, 1999, an expert panel met to develop guidelines for the use of the single-cell gel (SCG)/Comet assay in genetic toxicology. The expert panel reached a consensus that the optimal version of the Comet assay for identifying agents with genotoxic activity was the alkaline (pH > 13) version of the assay developed by Singh et al. [1988]. The pH > 13 version is capable of detecting DNA single-strand breaks (SSB), alkali-labile sites (ALS), DNA-DNA/DNA-protein cross-linking, and SSB associated with incomplete excision repair sites. Relative to other genotoxicity tests, the advantages of the SCG assay include its demonstrated sensitivity for detecting low levels of DNA damage, the requirement for small numbers of cells per sample, its flexibility, its low costs, its ease of application, and the short time needed to complete a study. The expert panel decided that no single version of the alkaline (pH > 13) Comet assay was clearly superior. However, critical technical steps within the assay were discussed and guidelines developed for preparing slides with agarose gels, lysing cells to liberate DNA, exposing the liberated DNA to alkali to produce single-stranded DNA and to express ALS as SSB, electrophoresing the DNA using pH > 13 alkaline conditions, alkali neutralization, DNA staining, comet visualization, and data collection. Based on the current state of knowledge, the expert panel developed guidelines for conducting in vitro or in vivo Comet assays. The goal of the expert panel was to identify minimal standards for obtaining reproducible and reliable Comet data deemed suitable for regulatory submission. The expert panel used the current Organization for Economic Co-operation and Development (OECD) guidelines for in vitro and in vivo genetic toxicological studies as guides during the development of the corresponding in vitro and in vivo SCG assay guidelines. Guideline topics considered included initial considerations, principles of the test method, description of the test method, procedure, results, data analysis and reporting. Special consideration was given by the expert panel to the potential adverse effect of DNA degradation associated with cytotoxicity on the interpretation of Comet assay results. The expert panel also discussed related SCG methodologies that might be useful in the interpretation of positive Comet data. The related methodologies discussed included: (1) the use of different pH conditions during electrophoreses to discriminate between DNA strand breaks and ALS; (2) the use of repair enzymes or antibodies to detect specific classes of DNA damage; (3) the use of a neutral diffusion assay to identify apoptotic/necrotic cells; and (4) the use of the acellular SCG assay to evaluate the ability of a test substance to interact directly with DNA. The alkaline (pH > 13) Comet assay guidelines developed by the expert panel represent a work in progress. Additional information is needed before the assay can be critically evaluated for its utility in genetic toxicology. The information needed includes comprehensive data on the different sources of variability (e.g., cell to cell, gel to gel, run to run, culture to culture, animal to animal, experiment to experiment) intrinsic to the alkaline (pH > 3) SCG assay, the generation of a large database based on in vitro and in vivo testing using these guidelines, and the results of appropriately designed multilaboratory international validation studies.

https://onlinelibrary.wiley.com/doi/epdf/10.1002/%28SICI%291098-2280%282000%2935%3A3%3C206%3A%3AAID-EM8%3E3.0.CO%3B2-J

Single cell gel/comet assay: guidelines for in vitro and in vivo genetic toxicology testing.

Two types of TK mutants are induced by genotoxic factors; normally growing (NG) TK mutants due to point mutations of targeted TK locus, and slowly growing (SG) mutants due to gross structural changes involving the growth-regulating gene outside targeted TK locus. In this study, human lymphoblstoid WTK1 cells were used to consider how bulky n- alkylated bases can induce SG mutants. For this purpose, n-alkyl methanesulfonates (AMS) having an n-alkyl group with 3-7 carbons [n-propy methanesulfonate (PMS), n-butyl methanesulfonate (BMS), n-pentyl methanesulfonate (PeMS), n- hexyl methanesulfonate (HexMS), and heptyl methanesulfonate(HepMS)] were synthesized. n-alkyl methanesulfonates having n-alkyl groups with 1-7 carbons induced NG mutants, but n-alkyl methanesulfonates having n-alkyl groups with ≥4 carbons but not with ≤3 carbons induced SG mutants. n-Alkyl methanesulfonates having n-Alkyl groups with ≥4 carbons have been shown to induce bulky adducts that cause disturbances to the helical DNA structure and are removed by nucleotide excision repair. It could be considered that n-alkyl groups with ≥4 carbons causing disturbances to the helical DNA structure induce SG mutants to result in clastogenicity rather than mutagenicity.

/pdf/how-bulky-of-base-adducts-can-be-responsible-for-2c53017e.pdf

How Bulky of Base Adducts can be Responsible for Clastogenicity rather than Mutagenicity?

The fruits of Gamazumi (Viburnum dilatatum THUNB) have been previously reported to suppress the adverse effects of oxidative stress in rats.  To reduce time and cost, we attempted to establish optimal conditions for extracting bioactive components from Gamazumi fruits using supercritical carbon dioxide.  To verify whether the conventional hexane extraction may be replaced by the supercritical carbon dioxide extraction, component analysis results and antigenotoxic potential in mice were used to compare bioactivity of the supercritical carbon dioxide and hexane extracts.   
At the same extraction pressure, the extraction rate was maximized when supercritical carbon dioxide with a low temperature was used, and extraction efficiency was improved.  GC/MS analysis revealed that vitamins E and stigmasterols were included in supercritical carbon dioxide and hexane extracts, and that no qualitative differences between supercritical carbon dioxide and hexane extracts were observed.  The antigenotoxic potential of Gamazumi extracts was studied in mice exposed to cigarette smoke inhalation.  Mice received single or 5 consecutive oral administrations of Gamazumi extracts at 0, 3, and 6 h prior to smoke inhalation.  Although single administration decreased nuclei tail length in the stomach when both administration and the intervals of smoke inhalation were short, five consecutive administrations decreased tail length in the lung and stomach regardless of the interval.  At short intervals, inhaled cigarette smoke and orally administered extracts may be simultaneously present in the gastric cavity, and direct reaction between cigarette smoke and extract is possible.  The antioxidant activity of Gamazumi extracts may result in antigenotoxic potential.  There were no differences in component analysis and antigenotoxic potential between supercritical carbon dioxide and hexane extracts of Gamazumi; thus, it is possible to replace the conventional hexane extraction with the supercritical carbon dioxide extraction.

Establishment of Optimal Conditions to Extract Bioactive Substances from Gamazumi Using Supercritical Carbon Dioxide

Along with increasing relevance of rare earth (RE) elements in industrial technology, the risk of their environmental release and occupational exposure on human health is of concern. Although many toxicological studies were reported for REs, it is not known how they affect DNA repair. In this study, the effects on DNA repair of all RE ions except radioactive promethium (Pm) were studied. Human lymphoblastoid WTK1cells were irradiated to UV followed by 2h exposure to each RE with and without DNA repair inhibitor cytosine-1β-D- arabinofuranoside (araC), and then single strand breaks (SSBs) were detected by the comet assay. UV-induced pyrimidine dimers are removed by nucleotide excision repair (NER) which consists of recognition of the DNA lesion, excision of a 24–32 nucleotide stretch containing the lesion by dual incision of the damaged DNA strand on both sides, and re-synthesis of the resulting gap by DNA polymerase, and ligation of the nick. SSBs are generated in the incision step of nucleotide excision repair (NER) and disappear in the re-synthesis step of NER. Seven REs, Yb, Lu, Dy, Er, Sc, Pr, and Ce, enhanced comet positive response without araC but not with araC, suggesting that araC is antagonistic to the 7 REs. Since araC inhibits re-synthesis of NER, these seven REs would inhibit the re-synthesis step of NER. Six REs, Tm, Sm, Tb, Gd, Eu, and Y suppressed comet positive responses with and without araC, suggesting that they decreased comet assay detectable SSBs. Therefore, these 6 REs are considered to inhibit the incision step of NER. Only La decreased tail length without araC but increased with araC, suggesting that La increased comet assay detectable SSBs and that only La would enhance the incision step of NER. Neither Nd nor Ho affected tail length with or without araC.

Y. F. Sasaki

Papers

Single cell gel/comet assay: guidelines for in vitro and in vivo genetic toxicology testing.

How Bulky of Base Adducts can be Responsible for Clastogenicity rather than Mutagenicity?

Establishment of Optimal Conditions to Extract Bioactive Substances from Gamazumi Using Supercritical Carbon Dioxide

Inhibiting and Enhancing Effects on DNA Repair of Rare Metal Elements in Cultured Human Lymphoblastoid Cells