We thank the Flow Cytometry Facility team at the German Cancer Research Center (DKFZ) for their support.

1. Preparation
<ol>
	<li>Prepare &#8805;1 x 105 cells/sample in any type of culture vessel as starting material.
	<ol>
		<li>For example, conduct a time-course experiment after exposure of U87 glioblastoma cells to ionizing radiation: Irradiate sub-confluent U87 cells in T25 flasks in triplicates for each time point. Choose early time-points (15 min up to 8 h after irradiation) to follow the kinetics of DSB repair (&#947;H2AX level) and late time points (24 h up to 96 h) to assess residual D...

<ol>
	<li>Jensen, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Treatment+of+non-small+cell+lung+cancer+with+intensity-modulated+radiation+therapy+in+combination+with+cetuximab:+the+NEAR+protocol+(NCT00115518).">Treatment of non-small cell lung cancer with intensity-modulated radiation therapy in combination with cetuximab: the NEAR protocol (NCT00115518).</a> BMC Cancer. 6, 122 (2006).</li><li>Oertel, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Human+Glioblastoma+and+Carcinoma+Xenograft+Tumors+Treated+by+Combined+Radiation+and+Imatinib+(Gleevec).">Human Glioblastoma and Carcinoma Xenograft Tumors Treated by Combined Radiation and Imatinib (Gleevec).</a> Strahlentherapie und Onkologie. 182 (7), 400-407 (2006).</li><li>Timke, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Combination+of+Vascular+Endothelial+Growth+Factor+Receptor/Platelet-Derived+Growth+Factor+Receptor+Inhibition+Markedly+Improves+Radiation+Tumor+Therapy.">Combination of Vascular Endothelial Growth Factor Receptor/Platelet-Derived Growth Factor Receptor Inhibition Markedly Improves Radiation Tumor Therapy.</a> Clinical Cancer Research. 14 (7), 2210-2219 (2008).</li><li>Zhang, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Trimodal+glioblastoma+treatment+consisting+of+concurrent+radiotherapy,+temozolomide,+and+the+novel+TGF-&#946;+receptor+I+kinase+inhibitor+LY2109761.">Trimodal glioblastoma treatment consisting of concurrent radiotherapy, temozolomide, and the novel TGF-&#946; receptor I kinase inhibitor LY2109761.</a> Neoplasia. 13 (6), 537-549 (2011).</li><li>Blattmann, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Suberoylanilide+hydroxamic+acid+affects+expression+in+osteosarcoma,+atypical+teratoid+rhabdoid+tumor+and+normal+tissue+cell+lines+after+irradiation.">Suberoylanilide hydroxamic acid affects expression in osteosarcoma, atypical teratoid rhabdoid tumor and normal tissue cell lines after irradiation.</a> Strahlentherapie und Onkologie. 188 (2), 168-176 (2012).</li><li>Hoeijmakers, J. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DNA+Damage,+Aging,+and+Cancer.">DNA Damage, Aging, and Cancer.</a> New England Journal of Medicine. 361 (15), 1475-1485 (2015).</li><li>Rodgers, K., McVey, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Error-Prone+Repair+of+DNA+Double-Strand+Breaks.">Error-Prone Repair of DNA Double-Strand Breaks.</a> Journal of Cellular Physiology. 231 (1), 15-24 (2016).</li><li>Ciccia, A., Elledge, S. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+DNA+Damage+Response:+Making+It+Safe+to+Play+with+Knives.">The DNA Damage Response: Making It Safe to Play with Knives.</a> Molecular Cell. 40 (2), 179-204 (2010).</li><li>Rothkamm, K., Kr&#252;ger, I., Thompson, L. H., L&#246;brich, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Pathways+of+DNA+double-strand+break+repair+during+the+mammalian+cell+cycle.">Pathways of DNA double-strand break repair during the mammalian cell cycle.</a> Molecular and Cellular Biology. 23 (16), 5706-5715 (2003).</li><li>Escribano-D&#237;az, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+Cell+Cycle-Dependent+Regulatory+Circuit+Composed+of+53BP1-RIF1+and+BRCA1-CtIP+Controls+DNA+Repair+Pathway+Choice.">A Cell Cycle-Dependent Regulatory Circuit Composed of 53BP1-RIF1 and BRCA1-CtIP Controls DNA Repair Pathway Choice.</a> Molecular Cell. 49 (5), 872-883 (2013).</li><li>Bakr, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Functional+crosstalk+between+DNA+damage+response+proteins+53BP1+and+BRCA1+regulates+double+strand+break+repair+choice.">Functional crosstalk between DNA damage response proteins 53BP1 and BRCA1 regulates double strand break repair choice.</a> Radiotherapy and Oncology. 119 (2), 276-281 (2015).</li><li>Mladenov, E., Magin, S., Soni, A., Iliakis, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DNA+double-strand-break+repair+in+higher+eukaryotes+and+its+role+in+genomic+instability+and+cancer:+Cell+cycle+and+proliferation-dependent+regulation.">DNA double-strand-break repair in higher eukaryotes and its role in genomic instability and cancer: Cell cycle and proliferation-dependent regulation.</a> Seminars in Cancer Biology. 37-38, 51-64 (2016).</li><li>Lopez Perez, R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DNA+damage+response+of+clinical+carbon+ion+versus+photon+radiation+in+human+glioblastoma+cells.">DNA damage response of clinical carbon ion versus photon radiation in human glioblastoma cells.</a> Radiotherapy and Oncology. 133, 77-86 (2019).</li><li>Oertel, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Combination+of+suberoylanilide+hydroxamic+acid+with+heavy+ion+therapy+shows+promising+effects+in+infantile+sarcoma+cell+lines.">Combination of suberoylanilide hydroxamic acid with heavy ion therapy shows promising effects in infantile sarcoma cell lines.</a> Radiation oncology. 6 (1), 119 (2011).</li><li>Blattmann, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Suberoylanilide+hydroxamic+acid+affects+&#947;H2AX+expression+in+osteosarcoma,+atypical+teratoid+rhabdoid+tumor+and+normal+tissue+cell+lines+after+irradiation.">Suberoylanilide hydroxamic acid affects &#947;H2AX expression in osteosarcoma, atypical teratoid rhabdoid tumor and normal tissue cell lines after irradiation.</a> Strahlentherapie und Onkologie. 188 (2), 168-176 (2012).</li><li>Thiemann, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+vivo+efficacy+of+the+histone+deacetylase+inhibitor+suberoylanilide+hydroxamic+acid+in+combination+with+radiotherapy+in+a+malignant+rhabdoid+tumor+mouse+model.">In vivo efficacy of the histone deacetylase inhibitor suberoylanilide hydroxamic acid in combination with radiotherapy in a malignant rhabdoid tumor mouse model.</a> Radiation Oncology. 7 (1), 52 (2012).</li><li>Nicolay, N. H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mesenchymal+stem+cells+retain+their+defining+stem+cell+characteristics+after+exposure+to+ionizing+radiation.">Mesenchymal stem cells retain their defining stem cell characteristics after exposure to ionizing radiation.</a> International Journal of Radiation Oncology Biology Physics. 87 (5), 1171-1178 (2013).</li><li>Nicolay, N. H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mesenchymal+stem+cells+are+resistant+to+carbon+ion+radiotherapy.">Mesenchymal stem cells are resistant to carbon ion radiotherapy.</a> Oncotarget. 6 (4), 2076-2087 (2015).</li><li>Nicolay, N. H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mesenchymal+stem+cells+exhibit+resistance+to+topoisomerase+inhibition.">Mesenchymal stem cells exhibit resistance to topoisomerase inhibition.</a> Cancer letters. 374 (1), 75-84 (2016).</li><li>Nicolay, N. H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mesenchymal+stem+cells+maintain+their+defining+stem+cell+characteristics+after+treatment+with+cisplatin.">Mesenchymal stem cells maintain their defining stem cell characteristics after treatment with cisplatin.</a> Scientific Reports. 6, 20035 (2016).</li><li>Nicolay, N. H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mesenchymal+stem+cells+are+sensitive+to+bleomycin+treatment.">Mesenchymal stem cells are sensitive to bleomycin treatment.</a> Scientific Reports. 6, 26645 (2016).</li><li>R&#252;hle, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cisplatin+radiosensitizes+radioresistant+human+mesenchymal+stem+cells.">Cisplatin radiosensitizes radioresistant human mesenchymal stem cells.</a> Oncotarget. 8 (50), 87809-87820 (2017).</li><li>M&#252;nz, F., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Human+mesenchymal+stem+cells+lose+their+functional+properties+after+paclitaxel+treatment.">Human mesenchymal stem cells lose their functional properties after paclitaxel treatment.</a> Scientific Reports. 8 (1), 312 (2018).</li><li>R&#252;hle, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Radiation+Resistance+of+Human+Multipotent+Mesenchymal+Stromal+Cells+Is+Independent+of+Their+Tissue+of+Origin.">The Radiation Resistance of Human Multipotent Mesenchymal Stromal Cells Is Independent of Their Tissue of Origin.</a> International Journal of Radiation Oncology Biology Physics. 100 (5), 1259-1269 (2018).</li><li>Dean, P. N., Jett, J. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mathematical+analysis+of+DNA+distributions+derived+from+flow+microfluorometry.">Mathematical analysis of DNA distributions derived from flow microfluorometry.</a> Journal of Cell Biology. 60 (2), 523-527 (1974).</li><li>Fox, M. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+model+for+the+computer+analysis+of+synchronous+DNA+distributions+obtained+by+flow+cytometry.">A model for the computer analysis of synchronous DNA distributions obtained by flow cytometry.</a> Cytometry. 1 (1), 71-77 (1980).</li><li>Costes, S. V., Boissi&#232;re, A., Ravani, S., Romano, R., Parvin, B., Barcellos-Hoff, M. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Imaging+features+that+discriminate+between+foci+induced+by+high-+and+low-LET+radiation+in+human+fibroblasts.">Imaging features that discriminate between foci induced by high- and low-LET radiation in human fibroblasts.</a> Radiation Research. 165 (5), 505-515 (2006).</li><li>Meyer, B., Voss, K. -. O., Tobias, F., Jakob, B., Durante, M., Taucher-Scholz, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Clustered+DNA+damage+induces+pan-nuclear+H2AX+phosphorylation+mediated+by+ATM+and+DNA-PK.">Clustered DNA damage induces pan-nuclear H2AX phosphorylation mediated by ATM and DNA-PK.</a> Nucleic Acids Research. 41 (12), 6109-6118 (2013).</li><li>Lopez Perez, R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Superresolution+light+microscopy+shows+nanostructure+of+carbon+ion+radiation-induced+DNA+double-strand+break+repair+foci.">Superresolution light microscopy shows nanostructure of carbon ion radiation-induced DNA double-strand break repair foci.</a> FASEB. 30 (8), 2767-2776 (2016).</li><li>Schipler, A., Iliakis, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DNA+double-strand-break+complexity+levels+and+their+possible+contributions+to+the+probability+for+error-prone+processing+and+repair+pathway+choice.">DNA double-strand-break complexity levels and their possible contributions to the probability for error-prone processing and repair pathway choice.</a> Nucleic Acids Research. 41 (16), 7589-7605 (2013).</li><li>Stenerlow, B., Hoglund, E., Carlsson, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DNA+fragmentation+by+charged+particle+tracks.">DNA fragmentation by charged particle tracks.</a> Advances in Space Research. 30 (4), 859-863 (2002).</li><li>Friedland, W., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comprehensive+track-structure+based+evaluation+of+DNA+damage+by+light+ions+from+radiotherapy-relevant+energies+down+to+stopping.">Comprehensive track-structure based evaluation of DNA damage by light ions from radiotherapy-relevant energies down to stopping.</a> Scientific Reports. 7, 45161 (2017).</li><li>Pang, D., Chasovskikh, S., Rodgers, J. E., Dritschilo, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Short+DNA+Fragments+Are+a+Hallmark+of+Heavy+Charged-Particle+Irradiation+and+May+Underlie+Their+Greater+Therapeutic+Efficacy.">Short DNA Fragments Are a Hallmark of Heavy Charged-Particle Irradiation and May Underlie Their Greater Therapeutic Efficacy.</a> Frontiers in Oncology. 6, 130 (2016).</li><li>B&#246;cker, W., Iliakis, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Computational+Methods+for+analysis+of+foci:+validation+for+radiation-induced+gamma-H2AX+foci+in+human+cells.">Computational Methods for analysis of foci: validation for radiation-induced gamma-H2AX foci in human cells.</a> Radiation Research. 165 (1), 113-124 (2006).</li><li>L&#246;brich, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=&#947;H2AX+foci+analysis+for+monitoring+DNA+double-strand+break+repair:+Strengths,+limitations+and+optimization.">&#947;H2AX foci analysis for monitoring DNA double-strand break repair: Strengths, limitations and optimization.</a> Cell Cycle. 9 (4), 662-669 (2010).</li></ol>

The authors have nothing to disclose.

The featured method is easy to use and offers a fast, accurate and reproducible measurement of the DNA damage response including double-strand break (DSB) induction and repair, cell cycle effects and apoptotic cell death. The combination of these endpoints provides a more complete picture of their interrelations than individual assays. The method can be widely applied as a comprehensive genotoxicity assay in the fields of radiation biology, therapy and protection, and more generally in oncology (e.g., for environmental r...

The goal of oncology is to kill or to inactivate cancer cells without harming normal cells. Many therapies either directly or indirectly induce genotoxic stress in cancer cells, but also to some extend in normal cells. Chemotherapy or targeted drugs are often combined with radiotherapy to enhance the radiosensitivity of the irradiated tumor1,2,3,4,5, which allows for a reduction of the radiation dose to minimize normal tissue damage.
Ionizing radiation and other genotoxic agents induce different kinds of DNA damage, including base modifications, strand crosslinks and single- or double-strand breaks. DNA double-strand breaks (DSBs) are the most serious DNA lesions and their induction is key to the cell killing effect of ionizing radiation and various cytostatic drugs in radiochemotherapy. DSBs do not only harm the integrity of the genome, but also promote the formation of mutations6,7. Therefore, different DSB repair pathways, and mechanisms to eliminate irreparably damaged cells like apoptosis have developed during evolution. The entire DNA damage response (DDR) is regulated by a complex network of signaling pathways that reach from DNA damage recognition and cell cycle arrest to allow for DNA repair, to programmed cell death or inactivation in case of repair failure8.
The presented flow cytometric method has been developed to investigate the DDR after genotoxic stress in one comprehensive assay that covers DSB induction and repair, as well as consequences of repair failure. It combines the measurement of the widely applied DSB marker &#947;H2AX with analysis of the cell cycle and induction of apoptosis, using classical subG1 analysis and more specific evaluation of caspase-3 activation.
The combination of these endpoints in one assay not only reduces time, labor and cost expenses, but also enables cell cycle-specific measurement of DSB induction and repair, as well as caspase-3 activation. Such analyses would not be possible with independently conducted assays, but they are highly relevant for a comprehensive understanding of the DNA damage response after genotoxic stress. Many anti-cancer drugs, such as cytostatic compounds, are directed against dividing cells and their efficiency is strongly dependent on the cell cycle stage. The availability of different DSB repair processes is also dependent on the cell cycle stage and pathway choice which is critical for the repair accuracy, and in turn determines the fate of the cell9,10,11,12. In addition, cell cycle-specific measurement of DSB levels is more accurate than pooled analysis, because DSB levels are not only dependent on the dose of a genotoxic compound or radiation, but also on the DNA content of the cell.
The method has been used to compare the efficacy of different radiotherapies to overcome resistance mechanisms in glioblastoma13 and to dissect the interplay between ionizing radiation and targeted drugs in osteosarcoma14,15 and atypical teratoid rhabdoid cancers16. Additionally, the described method has been widely used to analyze side effects of radio- and chemotherapy on mesenchymal stem cells17,18,19,20,21,22,23,24, which are essential for the repair of treatment-induced normal tissue damage and have a potential application in regenerative medicine.

<table border="0" cellpadding="0" cellspacing="0" style="width:1064px;" width="1063">
	<colgroup>
		<col />
		<col />
		<col />
		<col />
	</colgroup>
	<tbody>
		<tr height="40">
			<td height="40" style="height:40px;width:405px;">1000 &#181;L filter tips</td>
			<td style="width:151px;">Nerbe plus</td>
			<td style="width:169px;">07-693-8300</td>
			<td style="width:339px;"></td>
		</tr>
		<tr height="96">
			<td height="96" style="height:97px;">100-1000 &#181;L pipette</td>
			<td>Eppendorf</td>
			<td>3123000063</td>
			<td style="width:339px;"></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">12 x 75 mm Tubes with Cell Strainer Cap, 35 &#181;m mesh pore size</td>
			<td>BD Falcon</td>
			<td>352235</td>
			<td style="width:339px;"></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">15 mL tubes</td>
			<td>BD Falcon</td>
			<td>352096</td>
			<td style="width:339px;"></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">200 &#181;L filter tips</td>
			<td>Nerbe plus</td>
			<td>07-662-8300</td>
			<td style="width:339px;"></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">20-200 &#181;L pipette</td>
			<td>Eppendorf</td>
			<td>3123000055</td>
			<td style="width:339px;"></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">4&#8217;,6-Diamidin-2-phenylindol (DAPI)</td>
			<td>Sigma-Aldrich</td>
			<td>D9542</td>
			<td style="width:339px;">Dissolve in water at 200 &#181;g/ml and store aliquots at -20 &#176;C</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:405px;">Alexa Fluor 488 anti-H2A.X Phospho (Ser139) Antibody, RRID: AB_2248011</td>
			<td>BioLegend</td>
			<td>613406</td>
			<td style="width:339px;">Dilute 1:20</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:405px;">Alexa Fluor 647 Rabbit Anti-Active Caspase-3 Antibody, AB_1727414</td>
			<td>BD Pharmingen</td>
			<td>560626</td>
			<td style="width:339px;">Dilute 1:20</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">BD FACSClean solution</td>
			<td>BD Biosciences</td>
			<td>340345</td>
			<td style="width:339px;">For cytometer cleaning routine after measurement</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">BD FACSRinse solution</td>
			<td>BD Biosciences</td>
			<td>340346</td>
			<td style="width:339px;">For cytometer cleaning routine after measurement</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Dulbecco&#8217;s Phosphate Buffered Saline (PBS)</td>
			<td>Biochrom</td>
			<td>L 182</td>
			<td style="width:339px;">Dissolve in water to 1x concentration</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Dulbecco&#39;s Modified Eagle&#39;s Medium with stable glutamin</td>
			<td>Biochrom</td>
			<td>FG 0415</td>
			<td style="width:339px;">Routine cell culture material for the example cell line used in the protocol</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Ethanol absolute</td>
			<td>VWR</td>
			<td>20821.330</td>
			<td style="width:339px;"></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Excel software</td>
			<td>Microsoft</td>
			<td></td>
			<td style="width:339px;"></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">FBS Superior (fetal bovine serum)</td>
			<td>Biochrom</td>
			<td>S 0615</td>
			<td style="width:339px;">Routine cell culture material for the example cell line used in the protocol</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">FlowJo v10 software</td>
			<td>LLC</td>
			<td>online order</td>
			<td style="width:339px;"></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Fluoromount-G</td>
			<td>SouthernBiotech</td>
			<td>0100-01</td>
			<td style="width:339px;">Embedding medium for optional preparation of microscopic slides from stained samples</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">folded cellulose filters, grade 3hw</td>
			<td>NeoLab</td>
			<td>11416</td>
			<td style="width:339px;"></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">LSRII or LSRFortessa cytometer</td>
			<td>BD Biosciences</td>
			<td></td>
			<td style="width:339px;"></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">MG132</td>
			<td>Calbiochem</td>
			<td>474787</td>
			<td style="width:339px;">optional drug for apoptosis positive control</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Multifuge 3SR+</td>
			<td>Heraeus</td>
			<td></td>
			<td style="width:339px;"></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Paraformaldehyde</td>
			<td>AppliChem</td>
			<td>A3813</td>
			<td style="width:339px;">Prepare 4.5% solution fresh. Dilute in PBS by heating to 80 &#176;C with slow stirring under the fume hood. Cover the flask with aluminium foil to prevent heat loss. Let the solution cool to room temperature and adjust the final volume. Pass the solution through a cellulose filter.</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:405px;">Phospho-Histone H3 (Ser10) (D2C8) XP Rabbit mAb (Alexa Fluor&#174; 555 Conjugate) RRID: AB_10694639</td>
			<td>Cell Signaling Technology</td>
			<td>#3475</td>
			<td style="width:339px;">Dilute 3:200</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">PIPETBOY acu 2</td>
			<td>Integra Biosciences</td>
			<td>155 016</td>
			<td style="width:339px;"></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Serological pipettes, 10 mL</td>
			<td>Corning</td>
			<td>4488</td>
			<td style="width:339px;"></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Serological pipettes, 25 mL</td>
			<td>Corning</td>
			<td>4489</td>
			<td style="width:339px;"></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Serological pipettes, 5 mL</td>
			<td>Corning</td>
			<td>4487</td>
			<td style="width:339px;"></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">SuperKillerTRAIL (modified TNF-related apoptosis-inducing ligand)</td>
			<td>Biomol</td>
			<td>AG-40T-0002-C020</td>
			<td style="width:339px;">optional drug for apoptosis positive control</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">T25 cell culture flasks</td>
			<td>Greiner bio-one</td>
			<td>690160</td>
			<td style="width:339px;">Routine cell culture material for the example cell line used in the protocol</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Trypsin/EDTA</td>
			<td>PAN Biotech</td>
			<td>P10-025500</td>
			<td style="width:339px;">Routine cell culture material for the example cell line used in the protocol</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">U87 MG glioblastoma cells</td>
			<td>ATCC</td>
			<td>ATCC-HTB-14</td>
			<td style="width:339px;">Example cell line used in the protocol</td>
		</tr>
	</tbody>
</table>

cell cycle-specific measurement of &#947;h2ax and apoptosis after genotoxic stress by flow cytometry

The presented method or slightly modified versions have been devised to study specific treatment responses and side effects of various anti-cancer treatments as used in clinical oncology. It enables a quantitative and longitudinal analysis of the DNA damage response after genotoxic stress, as induced by radiotherapy and a multitude of anti-cancer drugs. The method covers all stages of the DNA damage response, providing endpoints for induction and repair of DNA double-strand breaks (DSBs), cell cycle arrest and cell death by apoptosis in case of repair failure. Combining these measurements provides information about cell cycle-dependent treatment effects and thus allows an in-depth study of the interplay between cellular proliferation and coping mechanisms against DNA damage. As the effect of many cancer therapeutics including chemotherapeutic agents and ionizing radiation is limited to or strongly varies according to specific cell cycle phases, correlative analyses rely on a robust and feasible method to assess the treatment effects on the DNA in a cell cycle-specific manner. This is not possible with single-endpoint assays and an important advantage of the presented method. The method is not restricted to any particular cell line and has been thoroughly tested in a multitude of tumor and normal tissue cell lines. It can be widely applied as a comprehensive genotoxicity assay in many fields of oncology besides radio-oncology, including environmental risk factor assessment, drug screening and evaluation of genetic instability in tumor cells.

Human U87 or LN229 glioblastoma cells were irradiated with 4 Gy of photon or carbon ion radiation. Cell cycle-specific &#947;H2AX levels and apoptosis were measured at different time points up to 48 h after irradiation using the flow cytometric method presented here (Figure 3). In both cell lines, carbon ions induced higher &#947;H2AX peak levels that declined slower and remained significantly elevated at 24 to 48 h compared to photon radiation at the same physical dose (<strong class="xfig"...

Watch this Scientific Journal Video about Cell Cycle-specific Measurement of Î³H2AX and Apoptosis After Genotoxic Stress by Flow Cytometry at JoVE.com

Cell Cycle-specific Measurement of &amp;#947;H2AX and Apoptosis After Genotoxic Stress by Flow Cytometry

The presented method combines the quantitative analysis of DNA double-strand breaks (DSBs), cell cycle distribution and apoptosis to enable cell cycle-specific evaluation of DSB induction and repair as well as the consequences of repair failure.

Cell Cycle-specific Measurement of &#947;H2AX and Apoptosis After Genotoxic Stress by Flow Cytometry

The presented method or slightly modified versions have been devised to study specific treatment responses and side effects of various anti-cancer ...

The method provides information about cell cycle dependent treatment effects and allows and in depth study of the interplay between cellular proliferation and coping mechanisms against DNA damage. This method combines important endpoints from the DNA damage response including double-strand frag recognition and repair, cell cycle effects, and eventual cell death by apoptosis into one comprehensive assay. We have used this technique mainly to investigate specific treatment responses and side effects of radiochemotherapeutic treatments in clinical oncology.The assay is very useful for correlative studies in the fields of radiobiology and radiotherapy, but it can also be applied to various other areas of oncology. After collecting the cells from the culture according to standard cell collection procedures, resuspend the pellet in one milliliter of PBS. And transfer the cells into two milliliters of fixation solution in a hood.After a 10 minute incubation at room temperature, collect the cells by centrifugation and decant the supernatant. It is important to fix the cells as a single cell suspension, and to keep the fixation time constant for all of the samples. Give adherent cells enough time to detach to obtain nicely rounded cells for analysis.Then loosen the pellet by tapping and resuspend the cells in three milliliters of 70%ethanol. To wash the cells before staining, sediment the cells by centrifugation, and loosen the pellet by tapping. Then resuspend the cells with two consecutive washes with three milliliters of washing solution and one wash with one milliliter of washing solution.Discarding the supernatant between each wash. After the last wash, carefully aspirate the supernatant without disturbing the pellet and resuspend the lucent pellet in 100 microliters of the antibody cocktail of interest. After one hour at room temperature, collect the cells by centrifugation and carefully aspirate the supernatant without disturbing the pellet.Then, resuspend the loosened pellet in 100 to 250 microliters of DNA staining solution and dispense the cells through the cell strainer cap of a sample tube with a 35 micrometer mesh pore size. To analyze the cells by flow cytometry, open the parameters tab in the cytometer window and select the parameters as indicated in the table. Next, open the worksheet window and create plots as indicated.Load a control sample onto the cytometer and press the run button. Select the first tube in the browser window and click the tube name. Adjust the detector voltages for forward and side scatter and DAPI in the parameters tab of the inspector window.Press the standby button to continue with the worksheet setup in the software. Use the polygon gate tool to define the cells'population in the forward scatter area versus the side scatter area plot and use the rectangle gate tool to define the single cells'population in the DAPI with versus DAPI area plot. Press control G to show the population hierarchy and click on the default gate names to rename them.Subsequently, right click on all of the histograms to select show populations and single cells from the context menu. Acquire control and treated samples to optimize the detector voltages for the antibody-coupled fluorophores to cover the full dynamic range of signal. To measure the samples, press the run button on the cytometer and use the acquisition dashboard in the software to measure the samples.Then select file, export, and experiments to select directory export in the dialog box to save the data as dot FCS files. To evaluate the data, drag and drop the dot FCS files into the sample browser of the flow cytometric analysis software. And use the polygon tool to define the cells'population in the forward versus side scatter area plot and to exclude debris from the analysis.In the DAPI with versus DAPI area plot, use the rectangle tool to define the single cells'population and to exclude any cell doublets or clumps from the analysis. In the DAPI area histogram, use the bisector tool to distinguish single cells with a normal DNA content from apoptotic cells with degraded DNA. Select tool biology and cell cycle to open the cell cycle modeling tool and select Dean-Jett Fox to estimate the frequency of cells in the G one S and G two M phases.Create G one S and G two and M phase gates in the DAPI with versus DAPI area plot of the cell cycle population to enable a cell cycle specific gamma H two A X measurement. Use the bisector tool to distinguish phosphohistone H three positive and negative cells in the Alexa 555 area histogram of the cell cycle population and to distinguish CAS base three positive and negative cells in the Alexa 647 area histogram of the single cells'population. Press control T to open the table editor and configure the table as indicated.Then select To File to set the format and destination in the output section of the menu ribbon and export the data into a spread sheet. Carbon ions induce higher gamma H two AX peak levels in glioblastoma cells that decline more slowly and remain significantly elevated in 24 to 48 hours compared to photon radiation at the same physical dose. For both carbon ions and photon radiation, the gamma H two AX levels were highest in G one phase cells likely because DNA double strand break repair is limited to the pathway of nonhomologous end joining at this stage in the cell cycle.In line with the higher double strand break induction rate and slower repair kinetics, carbon ions induce a stronger and longer lasting cell cycle arrest in G two phase and a higher rate of apoptosis than do photons. Depending on the strength of the treatment effect, the resolution of the different cell cycle phases can be challenging. In some cell lines, the DAPI concentration has a big impact on the quality of the cell cycle profile and needs to be adjusted.Slides can be prepared from the remaining samples after flow cytometry to evaluate the number, size, and shape of gamma H two AX foci and to distinguish between focal and parnuclear gamma H two AX staining. Using our method, we could show that mesenchymal stem cells are relatively resistant against ionizing radiations and topoisomerase inhibition but sensitive to gliomyacin. As PFA fumes are toxic, always use a fume hood when preparing the fixation solution and during the fixation step.Also remember to wear gloves when handling DAPI.

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Cancer Research

13.2K Views.  German Cancer Research Center. The method provides information about cell cycle dependent treatment effects and allows and in depth study of the interplay between cellular proliferation and coping mechanisms against DNA damage. This method combines important endpoints from the DNA damage response including double-strand frag recognition and repair, cell cycle effects, and eventual cell death by apoptosis into one comprehensive assay. We have used this technique mainly to investigate specific treatment responses and side ef...