We are grateful for the guidance of Pavel Lobachevsky, PhD in establishing this protocol. We&#39;d also like to acknowledge Washington University&#39;s School of Medicine in St. Louis&#39;s Department of Obstetrics and Gynecology and Division of Gynecologic Oncology, Washington University&#39;s Dean&#39;s Scholar Program, Gynecologic Oncology Group Foundation, and the Reproductive Scientist Development Program for their support of this project.

Tumor tissue and ascites were obtained after obtaining patient consent as part of a gynecologic oncology biorepository that was approved by the Washington University in St. Louis Institutional Review Board (IRB). Patients were included if they had advanced stage high-grade serous ovarian cancer (HGSOC). All procedures were performed at room temperature on the bench unless otherwise specified. All reagents were prepared at room temperature (unless otherwise indicated) and stored at 4 &#176;C.
1. Organoid generation
<ol>
	<li>Generate the organoids following the previously published report20.</li>
</ol>
2. Plating and irradiation of organoids
<ol>
	<li>Using organoids in culture, dislodge the tabs of the organoids from the culture dish through manual manipulation of a pipette tip. Collect the organoids in a 15 mL conical tube.</li>
	<li>Centrifuge the conical tube at 1,650 x g for 5 min at 4 &#176;C. Using a pipette, aspirate off the supernatant carefully.</li>
	<li>Add 1,000 &#181;L of an animal origin-free, recombinant enzyme to the pellet (see Table of Materials). Mix the solution and incubate for 15 min at 37 &#176;C.</li>
	<li>Centrifuge the solution at 1,650 x g for 5 min at 4 &#176;C. Using a pipette, carefully aspirate off the supernatant.</li>
	<li>After centrifugation and aspiration, resuspend the pellet in 1,000 &#181;L of phosphate-buffered saline.</li>
	<li>Transfer 10 &#181;L of the solution to a 1.5 mL microcentrifuge tube and mix with 10 &#181;L of trypan blue.</li>
	<li>Take 10 &#181;L of the trypan blue cell solution into a cell counting chamber slide and insert it into the cell counting machine (see Table of Materials).</li>
	<li>Plate 40,000 cells per 20 &#181;L of basement membrane extract (BME) into an 8-well glass chamber slide (see Table of Materials). This maintains the organoids for 3-5 days to allow the cells to form organoids and grow to a suitable size.</li>
	<li>To induce double-strand DNA breaks, radiate the plated organoids with 10 Gray (Gy) of &#611;-irradiation (see Table of Materials for irradiator details). 
	NOTE: This could take up to 5-10 min.</li>
	<li>Incubate the organoids in their culture media in a humidified incubator at 37 &#176;C and 5% CO2 for 4 h.</li>
</ol>
3. Immunofluorescence staining
NOTE: Volumes refer to the amount per well of the 8-well chamber slide (~300 &#181;L).
<ol>
	<li>After irradiation and incubation of the organoids, aspirate the media with a pipette, carefully so as not to disrupt the 3D matrix. Wash with 300 &#181;L of PBS.</li>
	<li>Fix the organoids in 300 &#181;L of 2% paraformaldehyde (PFA) for 10 min. 
	NOTES: Do not leave for too long, as the BME will depolymerize and could be aspirated off.</li>
	<li>Wash the organoids with 300 &#181;L of staining buffer (see Table of Materials). Place on a shaker for 5 min.</li>
	<li>For permeabilization, gently add 300 &#181;L of permeabilization buffer (see Table of Materials) and incubate for 20 min. Wash with 300 &#181;L of staining buffer. Place on a shaker for 5 min.</li>
	<li>Add 300 &#181;L of staining buffer to block the permeabilization step. Place on a shaker for 30 min. Aspirate off the staining buffer using a pipette.</li>
	<li>Add 300 &#181;L of primary antibodies (rabbit anti-RAD51, mouse anti-Geminin, rabbit anti-RPA, mouse anti-&#611;H2AX, rabbit anti-Geminin, mouse anti-53BP1; see Table of Materials) diluted in staining buffer. Incubate at 4 &#176;C for 16 h. 
	NOTE: Avoid co-staining with the same host animal. Leave the lid off to avoid the antibodies mixing into neighboring wells.</li>
	<li>Remove the primary antibody solution. Perform three washes with 300 &#181;L of staining buffer for 5 min each on the shaker.</li>
	<li>Add 300 &#181;L of secondary antibody (goat anti-mouse Alexa fluor 488 and goat anti-rabbit Alexa fluor 647; see Table of Materials) solution diluted in staining buffer and incubate for 1 h in the dark. 
	NOTE: All subsequent steps must be performed in the dark.</li>
	<li>Aspirate the secondary antibody solution. Add 300 &#181;L of diluted DAPI. Place on a shaker for 5 min.</li>
	<li>Perform three washes with 300 &#181;L of staining buffer for 5 min each on the shaker. Remove the staining buffer and detach the chambers using the removal kit included with the chamber slides (see Table of Materials). 
	NOTE: Ensure not to push too far forward so as to disrupt the 3D matrix.</li>
	<li>Using a p200 pipette tip with the tip cut off, add mounting medium (see Table of Materials) to cover each well with an organoid tab (e.g., 20-30 &#181;L for each organoid tab).</li>
	<li>Place a coverslip over the specimen, avoiding bubbles.</li>
	<li>Take clear nail polish and paint it onto the sides of the cover glass to seal the slide. Let it harden for 1 h and place it at -20 &#176;C. 
	&#8203;NOTE: After imaging, the slide can be stored for at least 6 months with minimal loss of fluorescence.</li>
</ol>
4. Imaging
<ol>
	<li>Acquire images using a confocal microscope (see Table of Materials) at 63x objective with immersion oil. 
	NOTE: If imaging nuclear proteins, 63x is advantageous, but 40x is also acceptable.</li>
	<li>Use DAPI to locate the organoids through the eyepiece. Select the appropriate filters for microscopy based on the fluorophores used. Set the parameters for capturing the z-stack images. 
	NOTE: The fluorophores used in the study were DAPI, 488, and 647. The 405, 488, and 638 lasers were turned on to visualize the staining. 
	NOTE: The recommended z-stack depends on the resolving power of the objective.</li>
	<li>Adjust the live image: set focus, laser intensity, etc. 
	NOTE: The higher the laser intensity, the more likely the sample will photo-bleach. Therefore, select an optimum laser intensity.</li>
	<li>Acquire the z-stack. 
	NOTE: This could take up to 5-10 min.</li>
	<li>From the images collected in the z-stack, screenshot at least three images per stack. 
	NOTE: Ensure to obtain screenshots throughout the stack so as to not duplicate the nuclei when quantifying.</li>
	<li>Save each file as a TIFF and proceed to analysis (step 5).</li>
</ol>
5. Analysis
NOTE: Use JCountPro for all image analysis following the previously published report21. To obtain this software, reference the associated publication.
<ol>
	<li>Under the object analysis panel (top of the program) in the file selection tab (bottom of the program), select the TIFF files.</li>
	<li>Click Add to move the selected files to the selected files group. Select Display.</li>
	<li>Under the segmentation tab, select blue as the color of the nuclei. Select Auto segmentation to optimize the threshold of the nuclei. 
	NOTE: If the auto segmentation does not accurately identify the objects, then the user can adjust the fine tune and raw tune to the image or see the user manual to further optimize the segmentation.</li>
	<li>Under the objects panel, select Auto split large objects and optimize the size of the nuclei. 
	NOTE: The nuclei typically have an unconditional size of 5,000 pixels, while the conditional size is 1,500 pixels. See the user manual to further optimize the size of the objects.</li>
	<li>Select Identify objects to test the parameters. 
	NOTE: If these parameters are not accurate, the size and tuning can be adjusted along with other settings. See the user manual for instructions regarding further optimization.</li>
	<li>After adjusting the parameters to the image, select Identify Objects in All Images to identify the nuclei in all the images selected.</li>
	<li>Select the Foci Analysis&#160;panel (top of the program).</li>
	<li>Under the select files tab (bottom of the program), select the TIFF files that were used for object analysis and select the Arrow Buttons (&#62;&#62;) to move the images to the image files group.</li>
	<li>In the directory group underneath the image files that were moved, double click the Manual Edit folder and select to move the ioc files into the object collection files group. 
	NOTE: All TIFFs selected must have matched ioc files.</li>
	<li>Press Select to move the files into the selected files group. Select the Foci counting tab at the bottom of the program.</li>
	<li>Optimize the parameters following the steps below.
	<ol>
		<li>Top hat settings index: 12.</li>
		<li>Focus channel: Select the color of the foci (green: &#611;-H2AX; red: RAD51).</li>
		<li>H dome settings: dome height %: 30; threshold %: 28 and 28.</li>
		<li>Shape/size setting: Min focus size, pixels: 5. Select Apply Shape/Size. Max focus size (conditional): 32. Min roundness, x100: 96. Max focus, pixels: 60.</li>
		<li>Noise filter: size 1. 
		NOTE: If determining if a nucleus is positive for geminin staining, under the second channel select green, and under analysis select intensity.</li>
	</ol>
	</li>
	<li>To test the parameters set, select the below buttons in order: Top Hat &#62; H-Dome &#62; Foci Count. 
	NOTE: If these parameters do not work, the size and tuning can be adjusted along with other settings. See user manual to learn more about how the image can be further optimized.</li>
	<li>Once the parameters are optimized for the selected images, select Auto count to count the foci in each image per nuclei. If the second channel is desired, the program will determine the intensity which can be used.</li>
</ol>

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The authors have nothing to disclose.

The DNA damage response plays an integral role in both the development of ovarian cancer and chemotherapy resistance. Therefore, a thorough understanding of DNA repair mechanisms is imperative. Here, a methodology is presented to study DNA damage repair proteins in 3D, intact organoids. A reproducible, reliable protocol is developed utilizing hallmark antibodies to evaluate DNA damage, homologous recombination, non-homologous end joining, and replication stress. Importantly, these methods are validated using genetically ...

Ovarian cancer is the leading cause of death due to gynecologic malignancy. The majority of patients are treated with DNA-damaging drugs such as carboplatin, and those with homologous recombination repair (HRR)-deficient tumors can be given poly (ADP-ribose) polymerase (PARP) inhibitors1,2. However, most patients develop resistance to these therapies and die within 5 years of diagnosis. Dysregulation of the DNA damage response (DDR) has been associated with the development of ovarian cancer and both chemotherapy and PARP inhibitor resistance3. Thus, study of the DDR is imperative in understanding the pathophysiology of ovarian cancer, potential biomarkers, and novel targeted therapies.
Current methods to evaluate the DDR utilize immunofluorescence (IF), as this allows for the accurate identification and localization of DNA damage proteins and nucleotide analogs. Once there is a double-stranded break (DSB) in the DNA, the histone protein H2AX is rapidly phosphorylated, forming a focus where DNA damage repair proteins congregate4. This phosphorylation can be easily identified utilizing IF; in fact, the &#611;-H2AX assay has commonly been employed to confirm the induction of a DSB5,6,7,8,9. Increased DNA damage has been associated with platinum sensitivity and efficacy of DNA damaging agents10,11,12, and &#611;-H2AX has been proposed as a biomarker associated with chemotherapy response in other cancer treatments13. Upon a DSB, a cell proficient in HRR performs a series of events that leads to BRCA1 and BRCA2 recruiting RAD51 to replace replication protein A (RPA) and bind to the DNA. HRR repair uses a DNA template to faithfully repair the DSB. However, when tumors are deficient in HRR, they rely on alternative repair pathways such as non-homologous end joining (NHEJ). NHEJ is known to be error-prone and creates a high mutational burden on the cell, which uses 53BP1 as a positive regulator14. These DNA damage proteins can all be accurately identified as foci using IF. In addition to staining for proteins, IF can be used to study fork protection and single-stranded DNA gap formation. The ability to have stable forks has been correlated with platinum response, and recently, gap assays have shown the potential to predict the response to PARP inhibitors6,15,16,17. Therefore, staining for the nucleotide analogs after introduction into the genome is another way to study the DDR.
To date, evaluation of the DDR in ovarian cancer has been largely limited to homogenous 2D cell lines that do not recapitulate the clonal heterogeneity, microenvironment, or architecture of in vivo tumors18,19. Recent research suggests organoids are superior to 2D cell lines in studying complex biologic processes such as DDR mechanisms6. The present methodology evaluates RAD51, &#611;-H2AX, 53BP1, RPA, and geminin in PDOs. These methods assess the intact organoid and allow for the study of DDR mechanisms in a setting more similar to the in vivo tumor microenvironment. Together with confocal microscopy and automated foci counting, this methodology can aid in understanding the DDR pathway in ovarian cancer and personalizing treatment plans for patients.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>1x phosphate buffered saline with calcium and magnesium (PBS++)</td>
			<td>Sigma</td>
			<td>14-040-133</td>
			<td></td>
		</tr>
		<tr>
			<td>1x phosphate buffered saline without calcium and magnesium (PBS)</td>
			<td>Fisher Scientific&#160;</td>
			<td>ICN1860454</td>
			<td></td>
		</tr>
		<tr>
			<td>Ant-53BP1 Antibody&#160;</td>
			<td>BD Biosciences</td>
			<td>612522</td>
			<td>diluted to 1:500 in staining buffer</td>
		</tr>
		<tr>
			<td>Ant-Geminin Antibody&#160;</td>
			<td>Abcam</td>
			<td>ab104306</td>
			<td>diluted to 1:200 in staining buffer</td>
		</tr>
		<tr>
			<td>Anti-Geminin Antibody&#160;</td>
			<td>ProteinTech</td>
			<td>10802-1-AP</td>
			<td>diluted to 1:400 in staining buffer</td>
		</tr>
		<tr>
			<td>Anti-RAD51 Antibody&#160;</td>
			<td>Abcam</td>
			<td>ab133534</td>
			<td>diluted to 1:1000 in staining buffer</td>
		</tr>
		<tr>
			<td>Anti-yH2AX Antibody&#160;</td>
			<td>Millipore-Sigma</td>
			<td>05-636</td>
			<td>diluted to 1:500 in staining buffer</td>
		</tr>
		<tr>
			<td>Ant-phospho-RPA32 (S4/S8) Antibody</td>
			<td>Bethyl Laboratories&#160;</td>
			<td>A300-245A-M</td>
			<td>diluted to 1:200 in staining buffer</td>
		</tr>
		<tr>
			<td>Bovine Serum Albumin (BSA)</td>
			<td>Fisher Scientific&#160;</td>
			<td>BP1605 100</td>
			<td></td>
		</tr>
		<tr>
			<td>Centrifuge; Sorvall St 16R Centrifuge</td>
			<td>Thermo Scientific&#160;</td>
			<td>75004240</td>
			<td></td>
		</tr>
		<tr>
			<td>Confocal Microscope, Leica SP5 confocal system DMI4000</td>
			<td>Leica&#160;</td>
			<td>389584</td>
			<td></td>
		</tr>
		<tr>
			<td>Conical Tubes, 15 mL</td>
			<td>Corning&#160;</td>
			<td>14-959-53A</td>
			<td></td>
		</tr>
		<tr>
			<td>Countess 3 FL Automated Cell Counter (Cell Counting Machine)&#160;</td>
			<td>Thermo Scientific&#160;</td>
			<td>AMQAF2000</td>
			<td></td>
		</tr>
		<tr>
			<td>Countess Cell Counting Chamber Slides</td>
			<td>Thermo Scientific&#160;</td>
			<td>C10228</td>
			<td></td>
		</tr>
		<tr>
			<td>Cover Slip</td>
			<td>LA Colors</td>
			<td></td>
			<td>Any clear nail polish will suffice</td>
		</tr>
		<tr>
			<td>Cultrex&#160;RGF Basement Membrane Extract, Type 2</td>
			<td>&#160;R&#38;D Systems&#160;</td>
			<td>3533-010-02</td>
			<td>Could probably use Matrigel or other BME Matrix&#160;</td>
		</tr>
		<tr>
			<td>DAPI&#160;</td>
			<td>Thermo Scientific&#160;</td>
			<td>&#160;R37606</td>
			<td>NucBlue Fixed Cell ReadyProbes Reagent, Diluted in 1x PBS&#160;</td>
		</tr>
		<tr>
			<td>Glycine&#160;</td>
			<td>Fisher Scientific&#160;</td>
			<td>NC0756056</td>
			<td></td>
		</tr>
		<tr>
			<td>JCountPro</td>
			<td>JCountPro</td>
			<td></td>
			<td>For access to the software, Email: jcountpro@gmail.com&#160;</td>
		</tr>
		<tr>
			<td>Microcentrifuge Tubes&#160;</td>
			<td>Fisher Scientific&#160;</td>
			<td>07-000-243</td>
			<td></td>
		</tr>
		<tr>
			<td>Nail Polish&#160;</td>
			<td>StatLab</td>
			<td>SL102450</td>
			<td></td>
		</tr>
		<tr>
			<td>Parafomraldehyde (PFA), 2%&#160;</td>
			<td>Electron Microscopy Sciences&#160;</td>
			<td>157-4</td>
			<td>Dilute to 4% PFA in PBS++ to obtain 2% PFA</td>
		</tr>
		<tr>
			<td>Permeabilization Buffer</td>
			<td>Made in Lab</td>
			<td></td>
			<td>0.2% X-100 Triton in PBS++&#160;</td>
		</tr>
		<tr>
			<td>Pipette</td>
			<td>Rainin</td>
			<td>17014382</td>
			<td></td>
		</tr>
		<tr>
			<td>Pipette Tips&#160;</td>
			<td>Rainin&#160;</td>
			<td>17014967</td>
			<td></td>
		</tr>
		<tr>
			<td>ProLong Gold Antifade Mountant</td>
			<td>Thermo Scientific&#160;</td>
			<td>&#160;P36930</td>
			<td></td>
		</tr>
		<tr>
			<td>Staining Buffer&#160;</td>
			<td>Made in Lab</td>
			<td></td>
			<td>0.5% BSA, 0.15% Glycine, 0.1% X-100 Triton in PBS++&#160;</td>
		</tr>
		<tr>
			<td>Thermo Scientific Nunc Lab-Tek II Chamber Slide System&#160;</td>
			<td>Thermo Scientific&#160;</td>
			<td>12-565-8</td>
			<td></td>
		</tr>
		<tr>
			<td>Triton X-100</td>
			<td>Sigma-Alderich&#160;</td>
			<td>11332481001</td>
			<td></td>
		</tr>
		<tr>
			<td>Trypan Blue Solution, 0.4%</td>
			<td>Thermo Scientific&#160;</td>
			<td>15250061</td>
			<td></td>
		</tr>
		<tr>
			<td>TrypLE Express</td>
			<td>Invitrogen</td>
			<td>12604013</td>
			<td>animal origin-free, recombinant enzyme</td>
		</tr>
		<tr>
			<td>X-RAD 320 Biological Irradiator&#160;</td>
			<td>Precision X-Ray Irradiation&#160;</td>
			<td>X-RAD320</td>
			<td></td>
		</tr>
	</tbody>
</table>

visualizing dna damage repair proteins in patient-derived ovarian cancer organoids via immunofluorescence assays

Immunofluorescence is one of the most widely used techniques to visualize target antigens with high sensitivity and specificity, allowing for the accurate identification and localization of proteins, glycans, and small molecules. While this technique is well-established in two-dimensional (2D) cell culture, less is known about its use in three-dimensional (3D) cell models. Ovarian cancer organoids are 3D tumor models that recapitulate tumor cell clonal heterogeneity, the tumor microenvironment, and cell-cell and cell-matrix interactions. Thus, they are superior to cell lines for the evaluation of drug sensitivity and functional biomarkers. Therefore, the ability to utilize immunofluorescence on primary ovarian cancer organoids is extremely beneficial in understanding the biology of this cancer. The current study describes the technique of immunofluorescence to detect DNA damage repair proteins in high-grade serous patient-derived ovarian cancer organoids (PDOs). After exposing the PDOs to ionizing radiation, immunofluorescence is performed on intact organoids to evaluate nuclear proteins as foci. Images are collected using z-stack imaging on confocal microscopy and analyzed using automated foci counting software. The described methods allow for the analysis of temporal and special recruitment of DNA damage repair proteins and colocalization of these proteins with cell-cycle markers.

The presented protocol can successfully stain, visualize, and quantify nuclear DNA damage repair proteins in organoids. This technique was used to stain and evaluate PDOs both before and after irradiation. PDOs were exposed to 10 Gy of radiation and evaluated for the following biomarkers: &#611;-H2AX (Figure 1), a marker of DNA damage; RAD51 (Figure 2), a marker for HRR; 53BP1, a marker of NHEJ; RPA, a marker of replication stress (Figure 3<...

Watch this Scientific Journal Video about Visualizing DNA Damage Repair Proteins in Patient-Derived Ovarian Cancer Organoids via Immunofluorescence Assays at JoVE.com

Visualizing DNA Damage Repair Proteins in Patient-Derived Ovarian Cancer Organoids via Immunofluorescence Assays

The present protocol describes methods for evaluating DNA damage repair proteins in patient-derived ovarian cancer organoids. Included here are comprehensive plating and staining methods, as well as detailed, objective quantification procedures.

Visualizing DNA Damage Repair Proteins in Patient-Derived Ovarian Cancer Organoids via Immunofluorescence Assays

Immunofluorescence is one of the most widely used techniques to visualize target antigens with high sensitivity and specificity, allowing for the accurate ...

visualizing-dna-damage-repair-proteins-patient-derived-ovarian-cancer

Research

JoVE Journal

Cancer Research

1.5K Views.  Washington University in St. Louis. The present protocol describes methods for evaluating DNA damage repair proteins in patient-derived ovarian cancer organoids. Included here are comprehensive plating and staining methods, as well as detailed, objective quantification procedures. 

Video: Visualizing DNA Damage Repair Proteins in Patient-Derived Ovarian Cancer Organoids via Immunofluorescence Assays

Evaluating In Vitro DNA Damage Using Comet Assay

DNA damage is a common phenomenon for each cell during its lifespan, and is defined as an alteration of the chemical structure of genomic DNA. Cancer therapies, such as radio- and chemotherapy, introduce enormous amount of additional DNA damage, leading to cell cycle arrest and apoptosis to limit cancer progression. Quantitative assessment of DNA damage during experimental cancer therapy is a key step to justify the effectiveness of a genotoxic agent. In this study, we focus on a single cell electrophoresis assay, also known as the comet assay, which can quantify single and double-strand DNA breaks in vitro. The comet assay is a DNA damage quantification method that is efficient and easy to perform, and has low time/budget demands and high reproducibility. Here, we highlight the utility of the comet assay for a preclinical study by evaluating the genotoxic effect of olaparib/temozolomide combination therapy to U251 glioma cells.

Evaluating In Vitro DNA Damage Using Comet Assay

The comet assay is an efficient method to detect DNA damage including single and double-stranded DNA breaks. We describe alkaline and neutral comet assays to measure DNA damage in cancer cells to evaluate the therapeutic effect of chemotherapy.

DNA damage is a common phenomenon for each cell during its lifespan, and is defined as an alteration of the chemical structure of genomic DNA. Cancer ...

Characterizing DNA Repair Processes at Transient and Long-lasting Double-strand DNA Breaks by Immunofluorescence Microscopy

The repair of double-stranded breaks (DSBs) in DNA is a highly coordinated process, necessitating the formation and resolution of multi-protein repair complexes. This process is regulated by a myriad of proteins that promote the association and disassociation of proteins to these lesions. Thanks in large part to the ability to perform functional screens of a vast library of proteins, there is a greater appreciation of the genes necessary for the double-strand DNA break repair. Often knockout or chemical inhibitor screens identify proteins involved in repair processes by using increased toxicity as a marker for a protein that is required for DSB repair. Although useful for identifying novel cellular proteins involved in maintaining genome fidelity, functional analysis requires the determination of whether the protein of interest promotes localization, formation, or resolution of repair complexes. 
The accumulation of repair proteins can be readily detected as distinct nuclear foci by immunofluorescence microscopy. Thus, association and disassociation of these proteins at sites of DNA damage can be accessed by observing these nuclear foci at representative intervals after the induction of double-strand DNA breaks. This approach can also identify mis-localized repair factor proteins, if repair defects do not simultaneously occur with incomplete delays in repair. In this scenario, long-lasting double-strand DNA breaks can be engineered by expressing a rare cutting endonuclease (e.g., I-SceI) in cells where the recognition site for the said enzyme has been integrated into the cellular genome. The resulting lesion is particularly hard to resolve as faithful repair will reintroduce the enzyme's recognition site, prompting another round of cleavage. As a result, differences in the kinetics of repair are eliminated. If repair complexes are not formed, localization has been impeded. This protocol describes the methodology necessary to identify changes in repair kinetics as well as repair protein localization.

Repair of double-strand DNA breaks is a dynamic process, requiring not only formation of repair complexes at the breaks, but also their resolution after the lesion is addressed. Here, we use immunofluorescence microscopy for transient and long-lasting double-stranded breaks as a tool to dissect this genome maintenance mechanism.

The repair of double-stranded breaks (DSBs) in DNA is a highly coordinated process, necessitating the formation and resolution of multi-protein repair ...

Testing Targeted Therapies in Cancer using Structural DNA Alteration Analysis and Patient-Derived Xenografts

We present here an integrative approach for testing efficacy of targeted therapies that combines the next generation sequencing technolo-gies, therapeutic target analyses and drug response monitoring using patient derived xenografts (PDX). This strategy was validated using ovarian tumors as an example. The mate-pair next generation sequencing (MPseq) protocol was used to identify structural alterations and followed by analysis of potentially targetable alterations. Human tumors grown in immunocompromised mice were treated with drugs selected based on the genomic analyses. Results demonstrated a good correlation between the predicted and the observed responses in the PDX model. The presented approach can be used to test the efficacy of combination treatments and aid personalized treatment for patients with recurrent cancer, specifically in cases when standard therapy fails and there is a need to use drugs off label.

Here we present a protocol to test the efficacy of targeted therapies selected based on the genomic makeup of a tumor. The protocol describes identification and validation of structural DNA rearrangements, engraftment of patients&#8217; tumors into mice and testing responses to corresponding drugs.

We present here an integrative approach for testing efficacy of targeted therapies that combines the next generation sequencing technolo-gies, therapeutic ...

Immunofluorescence Imaging of DNA Damage and Repair Foci in Human Colon Cancer Cells

The purpose of the manuscript is to provide a step-by-step protocol for performing immunofluorescence microscopy to study the radiation-induced DNA damage response induced by neutron-gamma mixed-beam used in boron neutron capture therapy (BNCT). Specifically, the proposed methodology is applied for the detection of repair proteins activation which can be visualized as foci using antibodies specific to DNA double-strand breaks (DNA-DSBs). DNA repair foci were assessed by immunofluorescence in colon cancer cells (HCT-116) after irradiation with the neutron-mixed beam. DNA-DSBs are the most genotoxic lesions and are repaired in mammalian cells by two major pathways: non-homologous end-joining pathway (NHEJ) and homologous recombination repair (HRR). The frequencies of foci, immunochemically stained, for commonly used markers in radiobiology like &#947;-H2AX, 53BP1 are associated with DNA-DSB number and are considered as efficient and sensitive markers for monitoring the induction and repair of DNA-DSBs. It was established that &#947;-H2AX foci attract repair proteins, leading to a higher concentration of repair factors near a DSB. To monitor DNA damage at the cellular level, immunofluorescence analysis for the presence of DNA-PKcs representative repair protein foci from the NHEJ pathway and Rad52 from the HRR pathway was planned. We have developed and introduced a reliable immunofluorescence staining protocol for the detection of radiation-induced DNA damage response with antibodies specific for repair factors from NHEJ and HRR pathways and observed radiation-induced foci (RIF). The proposed methodology can be used for investigating repair protein that is highly activated in the case of neutron-mixed beam radiation, thereby indicating the dominance of the repair pathway.

Radiation-induced DNA damage response activated by neutron mixed-beam used in boron neutron capture therapy (BNCT) has not been fully established. This protocol provides a step-by-step procedure to detect radiation-induced foci (RIF) of repair proteins by immunofluorescence staining in human colon cancer cell lines after irradiation with the neutron-mixed beam.

The purpose of the manuscript is to provide a step-by-step protocol for performing immunofluorescence microscopy to study the radiation-induced DNA damage ...

High-Throughput In Vitro Assay using Patient-Derived Tumor Organoids

Patient-derived tumor organoids (PDOs) are expected to be a preclinical cancer model with better reproducibility of disease than traditional cell culture models. PDOs have been successfully generated from a variety of human tumors to recapitulate the architecture and function of tumor tissue accurately and efficiently. However, PDOs are unsuitable for an in vitro high-throughput assay system (HTS) or cell analysis using 96-well or 384-well plates when evaluating anticancer drugs because they are heterogeneous in size and form large clusters in culture. These cultures and assays use extracellular matrices, such as Matrigel, to create tumor tissue scaffolds. Therefore, PDOs have a low throughput and high cost, and it has been difficult to develop a suitable assay system. To address this issue, a simpler and more accurate HTS was established using PDOs to evaluate the potency of anticancer drugs and immunotherapy. An in vitro HTS was created that uses PDOs established from solid tumors cultured in 384-well plates. An HTS was also developed for assessment of antibody-dependent cellular cytotoxicity activity to represent the immune response using PDOs cultured in 96-well plates.

High-Throughput In Vitro Assay using Patient-Derived Tumor Organoids

A highly accurate in vitro high-throughput assay system was developed to evaluate anticancer drugs using patient-derived tumor organoids (PDOs), similar to cancer tissues but are unsuitable for in vitro high-throughput assay systems with 96-well and 384-well plates.

Patient-derived tumor organoids (PDOs) are expected to be a preclinical cancer model with better reproducibility of disease than traditional cell culture ...

Profiling Sensitivity to Targeted Therapies in EGFR-Mutant NSCLC Patient-Derived Organoids

Novel 3D cancer organoid cultures derived from clinical patient specimens represent an important model system to evaluate intratumor heterogeneity and treatment response to targeted inhibitors in cancer. Pioneering work in gastrointestinal and pancreatic cancers has highlighted the promise of patient-derived organoids (PDOs) as a patient-proximate culture system, with an increasing number of models emerging. Similarly, work in other cancer types has focused on establishing organoid models and optimizing culture protocols. Notably, 3D cancer organoid models maintain the genetic complexity of original tumor specimens and thus translate tumor-derived sequencing data into treatment with genetically informed targeted therapies in an experimental setting. Further, PDOs might foster the evaluation of rational combination treatments to overcome resistance-associated adaptation of tumors in the future. The latter focuses on intense research efforts in non-small-cell lung cancer (NSCLC), as resistance development ultimately limits the treatment success of targeted inhibitors. An early assessment of therapeutically targetable mechanisms using NSCLC PDOs could help inform rational combination treatments. This manuscript describes a standardized protocol for the cell culture plate-based assessment of drug sensitivities to targeted inhibitors in NSCLC-derived 3D PDOs, with potential adaptability to combinational treatments and other treatment modalities.

This protocol describes a standardized evaluation of drug sensitivities to targeted signaling inhibitors in NSCLC patient-derived organoid models.

Novel 3D cancer organoid cultures derived from clinical patient specimens represent an important model system to evaluate intratumor heterogeneity and ...

Generation and Culturing of High-Grade Serous Ovarian Cancer Patient-Derived Organoids

Organoids are 3D dynamic tumor models that can be grown successfully from patient-derived ovarian tumor tissue, ascites, or pleural fluid and aid in the discovery of novel therapeutics and predictive biomarkers for ovarian cancer. These models recapitulate clonal heterogeneity, the tumor microenvironment, and cell-cell and cell-matrix interactions. Additionally, they have been shown to match the primary tumor morphologically, cytologically, immunohistochemically, and genetically. Thus, organoids facilitate research on tumor cells and the tumor microenvironment and are superior to cell lines. The present protocol describes distinct methods to generate patient-derived ovarian cancer organoids from patient tumors, ascites, and pleural fluid samples with a higher than 97% success rate. The patient samples are separated into cellular suspensions by both mechanical and enzymatic digestion. The cells are then plated utilizing a basement membrane extract (BME) and are supported with optimized growth media containing supplements specific to the culturing of high-grade serous ovarian cancer (HGSOC). After forming initial organoids, the PDOs can sustain long-term culture, including passaging for expansion for subsequent experiments.

Patient-derived organoids (PDO) are a three-dimensional (3D) culture that can mimic the tumor environment in vitro. In high-grade serous ovarian cancer, PDOs represent a model to study novel biomarkers and therapeutics.

Organoids are 3D dynamic tumor models that can be grown successfully from patient-derived ovarian tumor tissue, ascites, or pleural fluid and aid in the ...

Quantifying Replication Stress in Ovarian Cancer Cells Using Single-Stranded DNA Immunofluorescence

Replication stress is a hallmark of several ovarian cancers. Replication stress can emerge from multiple sources, including double-strand breaks, transcription-replication conflicts, or amplified oncogenes, inevitably resulting in the generation of single-stranded DNA (ssDNA). Quantifying ssDNA, therefore, presents an opportunity to assess the level of replication stress in different cell types and under various DNA-damaging conditions or treatments. Emerging evidence also suggests that ssDNA can be a predictor of responses to chemotherapeutic drugs that target DNA repair. Here, we describe a detailed immunofluorescence-based methodology to quantify ssDNA. This methodology involves labeling the genome with a thymidine analog, followed by the antibody-based detection of the analog at the chromatin under non-denaturing conditions. Stretches of ssDNA can be visualized as foci under a fluorescence microscope. The number and intensity of the foci directly co-relate with the level of ssDNA present in the nucleus. We also describe an automated pipeline to quantify the ssDNA signal. The method is rapid and reproducible. Furthermore, the simplicity of this methodology makes it amenable to high-throughput applications such as drug and genetic screens.

Here, we describe an immunofluorescence-based method to quantify the levels of single-stranded DNA in cells. This efficient and reproducible method can be utilized to examine replication stress, a common feature in several ovarian cancers. Additionally, this assay is compatible with an automated analysis pipeline, which further increases its efficiency.

Replication stress is a hallmark of several ovarian cancers. Replication stress can emerge from multiple sources, including double-strand breaks, ...

Establishment and Culture of Patient-Derived Breast Organoids

Breast cancer is a complex disease that has been classified into several different histological and molecular subtypes. Patient-derived breast tumor organoids developed in our laboratory consist of a mix of multiple tumor-derived cell populations, and thus represent a better approximation of tumor cell diversity and milieu than the established 2D cancer cell lines. Organoids serve as an ideal in vitro model, allowing for cell-extracellular matrix interactions, known to play an important role in cell-cell interactions and cancer progression. Patient-derived organoids also have advantages over mouse models as they are of human origin. Furthermore, they have been shown to recapitulate the genomic, transcriptomic as well as metabolic heterogeneity of patient tumors; thus, they are capable of representing tumor complexity as well as patient diversity. As a result, they are poised to provide more accurate insights into target discovery and validation and drug sensitivity assays. In this protocol, we provide a detailed demonstration of how patient-derived breast organoids are established from resected breast tumors (cancer organoids) or reductive mammoplasty-derived breast tissue (normal organoids). This is followed by a comprehensive account of 3D organoid culture, expansion, passaging, freezing, as well as thawing of patient-derived breast organoid cultures.

A detailed protocol is provided here for establishing human breast organoids from patient-derived breast tumor resections or normal breast tissue. The protocol provides comprehensive step-by-step instructions for culturing, freezing, and thawing human patient-derived breast organoids.

Breast cancer is a complex disease that has been classified into several different histological and molecular subtypes. Patient-derived breast tumor ...

Ovarian Cancer Patient-Derived Organoid Models for Pre-Clinical Drug Testing

Ovarian cancer is a fatal gynecologic cancer and the fifth leading cause of cancer death among women in the United States. Developing new drug treatments is crucial to advancing healthcare and improving patient outcomes. Organoids are in-vitro three-dimensional multicellular miniature organs. Patient-derived organoid (PDO) models of ovarian cancer may be optimal for drug screening because they more accurately recapitulate tissues of interest than two-dimensional cell culture models and are inexpensive compared to patient-derived xenografts. In addition, ovarian cancer PDOs mimic the variable tumor microenvironment and genetic background typically observed in ovarian cancer. Here, a method is described that can be used to test conventional and novel drugs on PDOs derived from ovarian cancer tissue and ascites. A luminescence-based adenosine triphosphate (ATP) assay is used to measure viability, growth rate, and drug sensitivity. Drug screens in PDOs can be completed in 7-10 days, depending on the rate of organoid formation and drug treatments.

We present a protocol that can be used to conduct therapeutic drug testing with patient-derived ovarian cancer organoids.

Ovarian cancer is a fatal gynecologic cancer and the fifth leading cause of cancer death among women in the United States. Developing new drug treatments ...