Name: silencing of brca2 to identify novel brca2-regulated biological functions in cultured human cells
Uploaded: 2015-08-12T14:00:00.000+00:00
Duration: 9 min 24 s
Description: Watch this Scientific Journal Video about Silencing of BRCA2 to Identify Novel BRCA2-regulated Biological Functions in Cultured Human Cells at JoVE.com

This work was supported by FIRB-Merit grants RBNE08YFN3_005 and RBNE08HWLZ_012, and the Italian Ministry of Economy and Finance to the CNR for the Project &#8220;FaReBio di Qualit&#224;&#8221;.

1. Prepare siRNA solutions
<ol>
	<li>Resuspend 5 nmol of scrambled (Ctrl) and 5 nmol of BRCA2 siRNA dried pellets in 100 &#181;l of RNase-free water (final siRNA concentration: 50 &#181;M). This is the siRNA stock and must be stored at -20 &#176;C in 10 &#181;l aliquots.</li>
	<li>Take an aliquot of 10 &#181;l from the siRNA stock and add 40 &#181;l of RNase-free water to obtain the 10 &#181;M siRNA working solution. This dilution must be stored at -20 &#176;C until use. 
	NOTE: The siRNA working solution should not undergo freezing/thawing more than 3 times.</li>
</ol>
2. Seeding of Human Epithelial Cell Lines
<ol>
	<li>Remove the growth medium from human epithelial cell lines growing as cell monolayers in tissue culture plates in a humidified incubator at 37 &#176;C, 5% CO2.</li>
	<li>Wash the cells in the plate once with RT PBS (10 ml of PBS for a 100 mm plate).</li>
	<li>To detach the cells from the plate, add 2 ml of 0.25% trypsin/0.53 mM EDTA solution and incubate 3-5 min depending on the cell type.</li>
	<li>Before collecting the detached cells, neutralize trypsin by adding 2 ml of complete growth medium containing 10% fetal bovine serum.</li>
	<li>Transfer the cells to a 15 ml tube.</li>
	<li>Centrifuge the cells at 320-330 x g for 3 min at 4 &#176;C in a swinging bucket rotor.</li>
	<li>Resuspend the cell pellets in 5 ml of antibiotics-free medium.</li>
	<li>Count the cells under the microscope in a Burker chamber or by using an automated counting system according to the manufacturer&#8217;s instructions.</li>
	<li>Seed the cells in 6-well plates to be about 80% confluent after 24 hr (0.5-1 x106 cells in 2 ml of medium for each well). Optimal cell number to be seeded may vary depending on the specific cell lines and the growth rate. 
	NOTE: Do not add antibiotics in the medium at this point because antibiotics will negatively interfere with the efficiency of transfection. It is very important that the cells are at low culture passages (&#60; 10) to achieve high efficiency of BRCA2 siRNA transfection.</li>
</ol>
3. Transfect cells with siRNA
<ol>
	<li>Twenty-four hours after plating the cells, proceed with the first round of transfection.
	<ol>
		<li>Dilute 6 &#181;l of lipid-based 10 siRNA specific transfection reagent in 130 &#181;l of reduced serum medium.</li>
		<li>Dilute 3 &#181;l of 10 &#181;M siRNA (30 pmol) in 130 &#181;l of reduced serum medium.</li>
		<li>Combine the diluted siRNA with the diluted transfection reagent and incubate for 5-10 min at RT.</li>
		<li>During the incubation, remove the medium from the cells and add 2 ml of fresh medium pre-warmed at 37 &#176;C (without antibiotics).</li>
		<li>Add 250 &#181;l of the siRNA-transfection reagent complexes to the cells (this amount is for a single well of a 6-well plate).</li>
		<li>Incubate the cells in a humidified incubator at 37 &#176;C with 5% CO2.</li>
	</ol>
	</li>
	<li>After 24 hr, proceed with the second round of transfection by repeating steps 3.1.1-3.1.5 with the following modification for step 3.1.2: dilute 5 &#181;l of 10 &#181;M siRNA (50 pmol) in 130 &#181;l of reduced serum medium.
	<ol>
		<li>Incubate the cells for 1-2 days at 37 &#176;C before analysis. 
		NOTE: Two rounds of transfections and use of a high siRNA/transfection reagent ratio in the second round are essential to get high efficiency of BRCA2 silencing.</li>
	</ol>
	</li>
</ol>
4. Lyse cells for immunoblotting analysis
<ol>
	<li>&#160;Prepare fresh lysis buffer with PBS (pH 7.4) containing 1% of the nonionic, non-denaturing detergent octylphenoxypolyethoxyethanol, 5 mM sodium pyrophosphate, 1 mM sodium orthovanadate, 10 mM sodium fluoride, 2 mM phenylmethylsulfonyl fluoride, 10 &#181;g/ml leupeptin, 10 &#181;g/ml aprotinin. Keep it on ice.</li>
	<li>Remove the medium from the cells and wash them once with cold PBS (2 ml/well) in the plate. To prevent any PBS carryover, completely remove it from the plate.</li>
	<li>Add 200 &#181;l of lysis buffer to each well. 
	NOTE: If the cells have to be used also for other assays, trypsinize the cells as described in step 2.1-2.6 and resuspend the cells in appropriate buffer/medium according to the application to be used.</li>
	<li>Gently rotate the plate to uniformly distribute the lysis buffer and incubate for 15 min at 4 &#176;C on a rotator.</li>
	<li>Collect the cell lysate in a microcentrifuge tube on ice using a cell scraper.</li>
	<li>Centrifuge at 17,900 x g for 25 min at 4 &#176;C and collect the supernatant in a new tube.</li>
	<li>Measure the protein concentration using a commercially available protein assay according to the manufacturer&#39;s instructions.</li>
</ol>
5. BRCA2 immunoblotting analysis
<ol>
	<li>Prepare the running buffer by diluting 50 ml of 20x Tris-Acetate SDS running buffer (50 mM Tricine, 50 mM Tris Base, 0.1% SDS, pH 8.24) with 950 ml of distilled water.</li>
	<li>Prepare the sample as follows: add 15 &#181;g of total cell lysate, 5 &#181;l of 4x sample buffer containing lithium dodecyl sulfate at pH 8.4, 2 &#181;l of 10x sample reducing agent (0.5 M DTT), and lysis buffer to a final volume of 20 &#181;l. 
	NOTE: This protocol allows detection of BRCA2 in normal cell lines also when using a lower amount of total proteins (down to 5 &#181;g).</li>
	<li>Denature samples at 55 &#176;C for 10 min. 
	NOTE: It is crucial to use 55 &#176;C. Since BRCA2 protein is thermosensitive 11, higher denaturing temperatures result in consistent loss of intact full-length (390 kDa) BRCA2 protein.</li>
	<li>Set up the electrophoretic chamber according to the manufacturer&#39;s instructions.</li>
	<li>Load the samples and 10 &#181;l of high-molecular weight pre-stained protein standard on a precasted gel (Tris-Acetate 3-8%) and run at 120 V for about 2 hr 12. Stop the electrophoretic run before the 55 kDa blue marker leaves the precasted gel.</li>
	<li>Prepare the transfer buffer with 50 ml of 20x transfer buffer, 100 ml of 100% methanol and 850 ml water.</li>
	<li>Activate PVDF membrane (0.45 &#181;m pore size) by soaking in 100% methanol for 5 min, rinse with distilled water and equilibrate in transfer buffer at least for 5 min. Soak the sponges of the transfer apparatus in Transfer buffer at 4 &#176;C until use.</li>
	<li>When the electrophoretic run is over, assemble the sandwich in the transfer stack in the following order (bottom-up): three sponges saturated in transfer buffer, one 3MM grade paper sheet saturated in transfer buffer, the gel, activated PVDF membrane, one 3MM grade paper sheet saturated in transfer buffer, three sponges saturated in transfer buffer 13,14. Place the stack into the apparatus and transfer proteins at 350 mA for 4 hr at 4 &#176;C or at 180 mA overnight at 4 &#176;C. 
	NOTE: Being BRCA2 a very large protein, it is crucial to extend the transfer time from 1 hr (as suggested by the manufacturer and most transfer protocols) to 4 hr or overnight to ensure complete transfer of high-molecular weight proteins. In addition, due to the long transfer time, it is essential to perform the blotting in a cold room at 4 &#176;C to minimize overheating and facilitate sandwich disassembling. Semi-dry transfer systems are not good for transferring large proteins.</li>
	<li>After transfer, wash the membrane with TBS, block it for 1 hr at RT in TBS-Tween 0.25% (TBS-T) containing 5% nonfat dry milk and probe overnight at 4 &#176;C with 30 &#956;l anti-BRCA2 rabbit polyclonal antibody (200 &#956;g/ml), diluted in 9 ml TBS-T + 5% nonfat dry milk [1:300 (v/v) dilution].</li>
	<li>Wash the membrane three times (10 min each) with TBS-T, then incubate the filter for 1 hr with 1 &#956;l of horseradish peroxidase-conjugated anti-rabbit secondary antibody diluted in 10 ml of TBS-T + 5% nonfat dry milk. Thereafter, wash the membrane three times (10 min each) with TBS-T.</li>
	<li>Perform immunodetection by ECL to reveal BRCA2 protein using enhanced chemiluminescence (ECL) Western Blotting Detection Reagent, following the manufacturer&#39;s instructions. Visualize immunochemiluminescent bands on high resolution ECL films.</li>
	<li>Perform immunodetection with an antibody for a housekeeping gene, like &#946;-tubulin (55 kDa), on the same filter as loading control by using a monoclonal antibody to &#946;-tubulin diluted at 1:1,000 (10 &#181;l of anti-tubulin antibody in 10 ml TBS-T+5% non-fat dry milk) for 1 hr at RT. Wash and incubate secondary antibody as described for BRCA2 (5.10-5.11), except for the use of horseradish peroxidase-conjugated anti-mouse instead of anti-rabbit secondary antibody.</li>
	<li>Acquire a digital image of the films impressed with immunochemiluminescent bands and analyze the band intensity by dedicated image analysis software (e.g., ImageJ).</li>
</ol>

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The authors have nothing to disclose.

Because germline mutations of the BRCA2 gene lead to increased risk of several cancer types, including female and male breast cancer, ovarian cancer, prostate cancer, pancreatic cancer, and melanoma 3,4, a number of studies have been undertaken to understand the biological function of the BRCA2 protein. Most of these studies are genetic-based mainly due to technical difficulties in analyzing a giant protein like BRCA2. The method described here for silencing and analyzing BRCA2 protein expression prov...

The BRCA2 (BReast CAncer susceptibility gene-2) gene encodes for a tumor suppressor protein that plays a crucial role in repairing DNA double-strand breaks by regulating the function of the recombinase enzyme Rad51 1. BRCA2 has also been implicated in the modulation of transcription and in cell cycle control 2. Germline mutations in the BRCA2 gene induce an autosomal dominant susceptibility to breast and ovarian cancer in women and prostate cancer in men, as well as predisposition to other cancer types 3,4. However, despite the increased risk in developing cancer, BRCA2 mutations that suppress or reduce BRCA2 function may render cancer cells more vulnerable to chemotherapeutic agents that cause DNA damage 5-7. Sporadic cancers exhibit a low rate of BRCA2 mutations (&#60; 3%) though reduced levels of BRCA2 protein have been detected in some cancer types, suggesting that BRCA2 protein may be lost during tumorigenesis in sporadic cancers through non-mutational-dependent mechanisms 7,8. Thus, it is important to fully understand BRCA2 functions in the context of cancer biology as well as in other biological settings.
A powerful tool used to identify novel functions of a gene in mammalian cells is to silence its expression. As an example, silencing BRCA2 expression in a variety of normal epithelial cells has recently led to the identification of a novel function of BRCA2 as regulator of anoikis resistance, an important step during acquisition of cancer cell invasive and metastatic ability 9. Gene silencing can be achieved by introducing in the cells either small interfering (si) RNA or short hairpin (sh) RNA molecules targeting the specific gene. The high potency of siRNA and its ease of use make it the preferential tool for silencing experiments aimed at gaining new insights into critical biological processes and to identify novel therapeutic targets. However, efficient knockdown of gene expression may not be easily achievable for all genes and may be highly variable depending on the cell type. Because a decrease in intracellular protein levels is the most relevant phenotype under investigation, it is crucial to quantify gene silencing by immunoblotting analysis of the gene product. With this respect, the BRCA2 protein presents a further challenge: being a large protein (approximately 390 kDa), technical difficulties do exist for conventional biochemical analysis, including immunoblotting.
We report here a protocol optimized for efficient silencing of BRCA2 in human epithelial cell lines and for rapid and successful detection of BRCA2 protein knockdown by immunoblotting analysis.

<table><tbody><tr><td>BRCA2 siRNA</td><td>Dharmacon</td><td>L-003462-00</td><td>SMARTpool: ON-TARGETplus BRCA2 siRNA</td></tr><tr><td>Ctrl siRNA</td><td>Dharmacon</td><td>&amp;nbsp;D-001810-10-05</td><td>ON-TARGETplus Non-targeting Pool</td></tr><tr><td>Lipofectamine RNAiMAX Reagent&amp;nbsp;</td><td>Life Technologies</td><td>&lt;a href=&quot;http://www.lifetechnologies.com/order/catalog/product/13778075&quot;&gt;13778075&lt;/a&gt;</td><td>Transfection Reagent</td></tr><tr><td>OPTI-MEM I Reduced Serum Medium</td><td>Life Technologies</td><td>31985-070</td><td>Medium for transfection procedure</td></tr><tr><td>NuPAGE Tris-Acetate 3-8% 1,5 mm Gel precast</td><td>Life Technologies</td><td>EA0378</td><td>Gel for protein electrophoresis</td></tr><tr><td>NuPAGE LDS Sample buffer&amp;nbsp;</td><td>Life Technologies</td><td>NP0007</td><td>Reagent for protein electrophoresis</td></tr><tr><td>NuPAGE Sample Reducing agent (10x)</td><td>Life Technologies</td><td>NP0004</td><td>Reagent for protein electrophoresis</td></tr><tr><td>NuPAGE Antioxidant</td><td>Life Technologies</td><td>NP0005</td><td>Reagent for protein electrophoresis</td></tr><tr><td>HiMark Pre-stained protein standard</td><td>Life Technologies</td><td>LC5699</td><td>Prestained marker for gel electrophoresis</td></tr><tr><td>XCell SureLoc Mini-Cell&amp;nbsp; System</td><td>Life Technologies</td><td>EI0002</td><td>Equipment for protein electrophoresis/transfer</td></tr><tr><td>NuPAGE Tris-Acetate SDS Running Buffer</td><td>Life Technologies</td><td>LA0041</td><td>Reagent for Western blotting</td></tr><tr><td>PVDF membrane</td><td>Millipore</td><td>IPVH00010</td><td>Reagent for Western blotting</td></tr><tr><td>NuPAGE Transfer Buffer</td><td>Life Technologies</td><td>NP0006-1</td><td>Reagent for Western blotting</td></tr><tr><td>BRCA2 H-300 rabbit polyclonal antibody</td><td>Santa Cruz Biotechnology</td><td>sc-8326</td><td>1:300 dilution</td></tr><tr><td>Beta-tubulin monoclonal antibody</td><td>Sigma Aldrich</td><td>T4026-100UL</td><td>1:1,000 dilution</td></tr><tr><td>Skim Milk powder</td><td>Sigma Aldrich</td><td>70166</td><td>Reagent for Western blotting</td></tr><tr><td>Tween-20</td><td>Sigma Aldrich</td><td>P1379</td><td>Reagent for Western blotting</td></tr><tr><td>SuperSignal West Pico/Femto Chemiluminescent Substrate</td><td>Pierce Thermo Scientific</td><td>34080/34096</td><td>Chemiluminescence system</td></tr><tr><td>PNT1A cells</td><td>SIGMA Aldrich (for ECACC)</td><td>95012614</td><td>PNT1A human, normal prostate epithelium immortalized with SV40</td></tr><tr><td>Nthy cells</td><td>SIGMA Aldrich (for ECACC)</td><td>90011609</td><td>Nthy-ori 3-1 Cell Line human, thyroid follicular epithelial cells</td></tr><tr><td>Cell Proliferation Kit I (MTT)</td><td>Roche</td><td>11465007001</td><td>Kit for cell proliferation assays</td></tr></tbody></table>

silencing of brca2 to identify novel brca2-regulated biological functions in cultured human cells

Silencing of the tumor suppressor protein BRCA2 and its detection by conventional biochemical analyses represent a great technical challenge owing to the large size of the human BRCA2 protein (approximately 390 kDa). We report modifications of standard siRNA transfection and immunoblotting protocols to silence human BRCA2 and detect endogenous BRCA2 protein, respectively, in human epithelial cell lines. Key steps include a high siRNA to transfection reagent ratio and two subsequent rounds of siRNA transfection within the same experiment. Using these and other modifications to the standard protocol we consistently achieve more than 70% silencing of the human BRCA2 gene as judged by immunoblotting analysis with anti-BRCA2 antibodies. In addition, denaturation of the cell lysates at 55 &#176;C instead of the conventional 70-100 &#176;C and other technical optimizations of the immunoblotting procedure allow detection of intact BRCA2 protein even when very low amounts of starting material are available or when BRCA2 protein expression levels are very low. Efficient silencing of BRCA2 in human cells offers a valuable strategy to disrupt BRCA2 function in cells with intact BRCA2, including tumor cells, to examine new molecular pathways and cellular functions that may be affected by pathogenic BRCA2 mutations in tumors. Adaptation of this protocol for efficient silencing and analysis of other &#39;large&#39; proteins like BRCA2 should be readily achievable.

Before proceeding with a biological/biochemical assay to examine the effect of BRCA2 silencing on cell functions, the first step is to confirm the specificity of the silencing by using a scrambled siRNA (non-targeting siRNA) side by side with BRCA2 siRNA (Figure 1A). It is important to perform a second round of siRNA transfection with a high siRNA/transfection ratio to get a high efficiency of BRCA2 silencing. Indeed, performing only one round of siRNA transfection or using a lower siRN...

Watch this Scientific Journal Video about Silencing of BRCA2 to Identify Novel BRCA2-regulated Biological Functions in Cultured Human Cells at JoVE.com

Silencing of BRCA2 to Identify Novel BRCA2-regulated Biological Functions in Cultured Human Cells

Gene silencing by siRNA represents a convenient experimental strategy to analyze BRCA2-dependent biological functions with immediate implications to better understand cancer biology. A method to efficiently silence BRCA2, along with the experimental procedure to detect and quantify changes in BRCA2 protein expression by immunoblotting in human cell lines, is presented.

Silencing of BRCA2 to Identify Novel BRCA2-regulated Biological Functions in Cultured Human Cells

Silencing of the tumor suppressor protein BRCA2 and its detection by conventional biochemical analyses represent a great technical challenge owing to the ...

silencing-brca2-to-identify-novel-brca2-regulated-biological

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9.0K Views.  National Research Council. Gene silencing by siRNA represents a convenient experimental strategy to analyze BRCA2-dependent biological functions with immediate implications to better understand cancer biology. A method to efficiently silence BRCA2, along with the experimental procedure to detect and quantify changes in BRCA2 protein expression by immunoblotting in human cell lines, is presented. 

Video: Silencing of BRCA2 to Identify Novel BRCA2-regulated Biological Functions in Cultured Human Cells

Utilizing Functional Genomics Screening to Identify Potentially Novel Drug Targets in Cancer Cell Spheroid Cultures

The identification of functional driver events in cancer is central to furthering our understanding of cancer biology and indispensable for the discovery of the next generation of novel drug targets. It is becoming apparent that more complex models of cancer are required to fully appreciate the contributing factors that drive tumorigenesis in vivo and increase the efficacy of novel therapies that make the transition from pre-clinical models to clinical trials.
Here we present a methodology for generating uniform and reproducible tumor spheroids that can be subjected to siRNA functional screening. These spheroids display many characteristics that are found in solid tumors that are not present in traditional two-dimension culture. We show that several commonly used breast cancer cell lines are amenable to this protocol. Furthermore, we provide proof-of-principle data utilizing the breast cancer cell line BT474, confirming their dependency on amplification of the epidermal growth factor receptor HER2 and mutation of phosphatidylinositol-4,5-biphosphate 3-kinase (PIK3CA) when grown as tumor spheroids. Finally, we are able to further investigate and confirm the spatial impact of these dependencies using immunohistochemistry.

Identifying novel drug targets that transition from pre-clinical testing to human trials is a scientific priority. To that end, here we describe a functional genomics approach for examining the impact of gene depletion on cancer cell line spheroids, which more appropriately model human cancers in vivo.

The identification of functional driver events in cancer is central to furthering our understanding of cancer biology and indispensable for the discovery ...

Cancer Research

Time-lapse Imaging of Primary Preneoplastic Mammary Epithelial Cells Derived from Genetically Engineered Mouse Models of Breast Cancer

Time-lapse imaging can be used to compare behavior of cultured primary preneoplastic mammary epithelial cells derived from different genetically engineered mouse models of breast cancer. For example, time between cell divisions (cell lifetimes), apoptotic cell numbers, evolution of morphological changes, and mechanism of colony formation can be quantified and compared in cells carrying specific genetic lesions. Primary mammary epithelial cell cultures are generated from mammary glands without palpable tumor. Glands are carefully resected with clear separation from adjacent muscle, lymph nodes are removed, and single-cell suspensions of enriched mammary epithelial cells are generated by mincing mammary tissue followed by enzymatic dissociation and filtration. Single-cell suspensions are plated and placed directly under a microscope within an incubator chamber for live-cell imaging. Sixteen 650 &mu;m x 700 &mu;m fields in a 4x4 configuration from each well of a 6-well plate are imaged every 15 min for 5 days. Time-lapse images are examined directly to measure cellular behaviors that can include mechanism and frequency of cell colony formation within the first 24 hr of plating the cells (aggregation versus cell proliferation), incidence of apoptosis, and phasing of morphological changes. Single-cell tracking is used to generate cell fate maps for measurement of individual cell lifetimes and investigation of cell division patterns. Quantitative data are statistically analyzed to assess for significant differences in behavior correlated with specific genetic lesions.

Time-lapse imaging is used to assess behavior of primary preneoplastic mammary epithelial cells derived from genetically engineered mouse models of breast cancer risk to determine if there are correlations between specific behavioral parameters and distinct genetic lesions.

Time-lapse  imaging can be used to compare behavior of cultured primary preneoplastic  mammary epithelial cells derived from different genetically ...

Medicine

Functional Assessment of BRCA1 variants using CRISPR-Mediated Base Editors

Recent studies have investigated the risks associated with BRCA1 gene mutations using various functional assessment methods such as fluorescent reporter assays, embryonic stem cell viability assays, and therapeutic drug-based sensitivity assays. Although they have clarified a lot of BRCA1 variants, these assays involving the use of exogenously expressed BRCA1 variants are associated with overexpression issues and cannot be applied to post-transcriptional regulation. To resolve these limitations, we previously reported a method for functional analysis of BRCA1 variants via CRISPR-mediated cytosine base editor that induce targeted nucleotide substitution in living cells. Using this method, we identified variants whose functions remain ambiguous, including c.-97C&#62;T, c.154C&#62;T, c.3847C&#62;T, c.5056C&#62;T, and c.4986+5G&#62;A, and confirmed that CRISPR-mediated base editors are useful tools for reclassifying the variants of uncertain significance in BRCA1. Here, we describe a protocol for functional analysis of BRCA1 variants using CRISPR-based cytosine base editor. This protocol provides guidelines for the selection of target sites, functional analysis and evaluation of BRCA1 variants.

Functional Assessment of BRCA1 variants using CRISPR-Mediated Base Editors

People with BRCA1 mutations have a higher risk of developing cancer, which warrants accurate evaluation of the function of BRCA1 variants. Herein, we described a protocol for functional assessment of BRCA1 variants using CRISPR-mediated cytosine base editors that enable targeted C:G to T:A conversion in living cells.

Recent studies have investigated the risks associated with BRCA1 gene mutations using various functional assessment methods such as fluorescent reporter ...

Isolation and Functional Assessment of Human Breast Cancer Stem Cells from Cell and Tissue Samples

Breast cancer stem cells (BCSCs) are cancer cells with inherited or acquired stem cell-like characteristics. Despite their low frequency, they are major contributors to breast cancer initiation, relapse, metastasis and therapy resistance. It is imperative to understand the biology of breast cancer stem cells in order to identify novel therapeutic targets to treat breast cancer. Breast cancer stem cells are isolated and characterized based on expression of unique cell surface markers such as CD44, CD24 and enzymatic activity of aldehyde dehydrogenase (ALDH). These ALDHhighCD44+CD24- cells constitute the BCSC population and can be isolated by fluorescence-activated cell sorting (FACS) for downstream functional studies. Depending on the scientific question, different in vitro and in vivo methods can be used to assess the functional characteristics of BCSCs. Here, we provide a detailed experimental protocol for isolation of human BCSCs from both heterogenous populations of breast cancer cells as well as primary tumor tissue obtained from breast cancer patients. In addition, we highlight downstream in vitro and in vivo functional assays including colony forming assays, mammosphere assays, 3D culture models and tumor xenograft assays that can be used to assess BCSC function.

This experimental protocol describes the isolation of BCSCs from breast cancer cell and tissue samples as well as the in vitro and in vivo assays that can be used to assess BCSC phenotype and function.

Breast cancer stem cells (BCSCs) are cancer cells with inherited or acquired stem cell-like characteristics. Despite their low frequency, they are major ...

Profiling of Estrogen-regulated MicroRNAs in Breast Cancer Cells

Estrogen plays vital roles in mammary gland development and breast cancer progression. It mediates its function by binding to and activating the estrogen receptors (ERs), ER&#945;, and ER&#946;. ER&#945; is frequently upregulated in breast cancer and drives the proliferation of breast cancer cells. The ERs function as transcription factors and regulate gene expression. Whereas ER&#945;&#39;s regulation of protein-coding genes is well established, its regulation of noncoding microRNA (miRNA) is less explored. miRNAs play a major role in the post-transcriptional regulation of genes, inhibiting their translation or degrading their mRNA. miRNAs can function as oncogenes or tumor suppressors&#160;and are also promising biomarkers. Among the miRNA assays available, microarray and quantitative real-time polymerase chain reaction (qPCR) have been extensively used to detect and quantify miRNA levels. To identify miRNAs regulated by estrogen signaling in breast cancer, their expression in ER&#945;-positive breast cancer cell lines were compared before and after estrogen-activation using both the &#181;Paraflo-microfluidic microarrays and Dual Labeled Probes-low density arrays. Results were validated using specific qPCR assays, applying both Cyanine dye-based and Dual Labeled Probes-based chemistry. Furthermore, a time-point assay was used to identify regulations over time. Advantages of the miRNA assay approach used in this study is that it enables a fast screening of mature miRNA regulations in numerous samples, even with limited sample amounts. The layout, including the specific conditions for cell culture and estrogen treatment, biological and technical replicates, and large-scale screening followed by in-depth confirmations using separate techniques, ensures a robust detection of miRNA regulations,&#160;and eliminates false positives and other artifacts. However, mutated or unknown miRNAs, or regulations at the primary and precursor transcript level, will not be detected. The method presented here represents a thorough investigation of estrogen-mediated miRNA regulation.

Molecular signaling through both estrogen and microRNAs are critical in breast cancer development and growth. Estrogen activates the estrogen receptors, which are transcription factors. Many transcription factors can regulate the expression of microRNAs, and estrogen-regulated microRNAs can be profiled using different large-scale techniques.

Estrogen plays vital roles in mammary gland development and breast cancer progression. It mediates its function by binding to and activating the estrogen ...

Evaluation of Stem Cell Properties in Human Ovarian Carcinoma Cells Using Multi and Single Cell-based Spheres Assays

Years of research indicates that ovarian cancers harbor a heterogeneous mixture of cells including a subpopulation of so-called &#8220;cancer stem cells&#8221; (CSCs) responsible for tumor initiation, maintenance and relapse following conventional chemotherapies. Identification of ovarian CSCs is therefore an important goal. A commonly used method to assess CSC potential in vitro is the spheres assay in which cells are plated under non-adherent culture conditions in serum-free medium supplemented with growth factors and sphere formation is scored after a few days. Here, we review currently available protocols for human ovarian cancer spheres assays and perform a side-by-side analysis between commonly used multi cell-based assays and a more accurate system based on single cell plating. Our results indicate that both multi cell-based as well as single cell-based spheres assays can be used to investigate sphere formation in vitro. The more laborious and expensive single cell-based assays are more suitable for functional assessment of individual cells and lead to overall more accurate results while multi cell-based assays can be strongly influenced by the density of plated cells and require titration experiments upfront. Methylcellulose supplementation to multi cell-based assays can be effectively used to reduce mechanical artifacts.

In vitro spheres assays are commonly used to identify cancer stem cells. Here we compare single with multi cell-based spheres assays. The more laborious single cell-based assays or methylcellulose supplementation give more accurate results while multi cell-based assays performed in liquid medium can be highly influenced by cell density.

Years of research indicates that ovarian cancers harbor a heterogeneous mixture of cells including a subpopulation of so-called &#8220;cancer stem ...

Evaluating the Effectiveness of Cancer Drug Sensitization In Vitro and In Vivo

Due to the high level of heterogeneity and mutations inherent in human cancers, single agent therapies, or combination regimens which target the same pathway, are likely to fail. Emphasis must be placed upon the inhibition of pathways that are responsible for intrinsic and/or adaptive resistance to therapy. An active field of investigation is the development and testing of DNA repair inhibitors that promote the action of, and prevent resistance to, commonly used chemotherapy and radiotherapy. We used a novel protocol to evaluate the effectiveness of BRCA2 inhibition as a means to sensitize tumor cells to the DNA damaging drug cisplatin. Tumor cell metabolism (acidification and respiration) was monitored in real-time for a period of 72 hr to delineate treatment effectiveness on a minute by minute basis. In combination, we performed an assessment of metastatic frequency using a chicken embryo chorioallantoic membrane (CAM) model of extravasation and invasion. This protocol addresses some of the weaknesses of commonly used in vitro and in vivo methods to evaluate novel cancer therapy regimens. It can be used in addition to common methods such as cell proliferation assays, cell death assays, and in vivo murine xenograft studies, to more closely discriminate amongst candidate targets and agents, and select only the most promising candidates for further development.

Evaluating the Effectiveness of Cancer Drug Sensitization In Vitro and In Vivo

Here, real-time monitoring of tumor cell metabolism, combined with an in vivo chicken embryo chorio-allantoic membrane (CAM) model of metastasis, are used to evaluate novel anti-cancer targets/agents for their ability to sensitize tumor cells to DNA damaging chemotherapeutics.

Due to the high level of heterogeneity and mutations inherent in human cancers, single agent therapies, or combination regimens which target the same ...

Identifying the Effects of BRCA1 Mutations on Homologous Recombination using Cells that Express Endogenous Wild-type BRCA1

The functional analysis of missense mutations can be complicated by the presence in the cell of the endogenous protein. Structure-function analyses of the BRCA1 have been complicated by the lack of a robust assay for the full length BRCA1 protein and the difficulties inherent in working with cell lines that express hypomorphic BRCA1 protein1,2,3,4,5. We developed a system whereby the endogenous BRCA1 protein in a cell was acutely depleted by RNAi targeting the 3'-UTR of the BRCA1 mRNA and replaced by co-transfecting a plasmid expressing a BRCA1 variant. One advantage of this procedure is that the acute silencing of BRCA1 and simultaneous replacement allow the cells to grow without secondary mutations or adaptations that might arise over time to compensate for the loss of BRCA1 function. This depletion and add-back procedure was done in a HeLa-derived cell line that was readily assayed for homologous recombination activity. The homologous recombination assay is based on a previously published method whereby a recombination substrate is integrated into the genome (Figure 1)6,7,8,9. This recombination substrate has the rare-cutting I-SceI restriction enzyme site inside an inactive GFP allele, and downstream is a second inactive GFP allele. Transfection of the plasmid that expresses I-SceI results in a double-stranded break, which may be repaired by homologous recombination, and if homologous recombination does repair the break it creates an active GFP allele that is readily scored by flow cytometry for GFP protein expression. Depletion of endogenous BRCA1 resulted in an 8-10-fold reduction in homologous recombination activity, and add-back of wild-type plasmid fully restored homologous recombination function. When specific point mutants of full length BRCA1 were expressed from co-transfected plasmids, the effect of the specific missense mutant could be scored. As an example, the expression of the BRCA1(M18T) protein, a variant of unknown clinical significance10, was expressed in these cells, it failed to restore BRCA1-dependent homologous recombination. By contrast, expression of another variant, also of unknown significance, BRCA1(I21V) fully restored BRCA1-dependent homologous recombination function. This strategy of testing the function of BRCA1 missense mutations has been applied to another biological system assaying for centrosome function (Kais et al, unpublished observations). Overall, this approach is suitable for the analysis of missense mutants in any gene that must be analyzed recessively.

We provide a method for testing BRCA1 variants in a tissue culture based assay for homologous recombination repair of DNA damage by depleting endogenous BRCA1 protein from a cell using RNAi and replacing it with a BRCA1 point mutant that contains a coding change.

The functional analysis of missense mutations can be complicated by the presence in the cell of the endogenous protein. Structure-function analyses of the ...

Investigating the Extent of DNA Breaks Occurring During DNA Replication 

Detection of DNA Breaks in Dividing Human Cells by Neutral Comet Assay

DNA replication is constantly challenged by a wide variety of endogenous and exogenous stressors that can damage DNA. Such lesions encountered during genome duplication can stall replisomes and convert replication forks into double-strand breaks. If left unrepaired, these toxic DNA breaks can trigger chromosomal rearrangements, leading to heightened genome instability and an increased likelihood of cellular transformation. Additionally, cancer cells exhibit persistent replication stress, making the targeting of replication fork vulnerabilities in tumor cells an attractive strategy for chemotherapy. A highly versatile and powerful technique to study DNA breaks during replication is the comet assay. This gel electrophoresis technique reliably detects the induction and repair of DNA breaks at the single-cell level. Herein, a protocol is outlined that allows investigators to measure the extent of DNA damage in mitotically dividing human cells using fork-stalling agents across multiple cell types. Coupling this with automated comet scoring facilitates rapid analysis and enhances the reliability in studying induction of DNA breaks.

Author Spotlight: Unveiling the Role of SNF2L in Replication Fork Stability and Genome Duplication

This protocol is designed to investigate the extent of DNA damage occurring during DNA replication. Under neutral conditions, the induction of DNA breaks can be readily assessed within a short time frame. Additionally, the protocol is adaptable to other cell types and various replication stress reagents.

DNA replication is constantly challenged by a wide variety of endogenous and exogenous stressors that can damage DNA. Such lesions encountered during ...

Bioengineering

gDNA Enrichment by a Transposase-based Technology for NGS Analysis of the Whole Sequence of BRCA1, BRCA2, and 9 Genes Involved in DNA Damage Repair

The widespread use of Next Generation Sequencing has opened up new avenues for cancer research and diagnosis. NGS will bring huge amounts of new data on cancer, and especially cancer genetics. Current knowledge and future discoveries will make it necessary to study a huge number of genes that could be involved in a genetic predisposition to cancer. In this regard, we developed a Nextera design to study 11 complete genes involved in DNA damage repair. This protocol was developed to safely study 11 genes (ATM, BARD1, BRCA1, BRCA2, BRIP1, CHEK2, PALB2, RAD50, RAD51C, RAD80, and TP53) from promoter to 3&#39;-UTR in 24 patients simultaneously. This protocol, based on transposase technology and gDNA enrichment, gives a great advantage in terms of time for the genetic diagnosis thanks to sample multiplexing. This protocol can be safely used with blood gDNA.

gDNA Enrichment by a Transposase-based Technology for NGS Analysis of the Whole Sequence of BRCA1, BRCA2, and 9 Genes Involved in DNA Damage Repair

gDNA enrichment for NGS sequencing is an easy and powerful tool for the study of constitutional mutations. In this article, we present the procedure to analyse simply the complete sequence of 11 genes involved in DNA damage repair.

The widespread use of Next Generation Sequencing has opened up new avenues for cancer research and diagnosis. NGS will bring huge amounts of new data on ...

Silencing of BRCA2 to Identify Novel BRCA2-regulated Biological Functions in Cultured Human Cells

Summary

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Chapters in this video

Utilizing Functional Genomics Screening to Identify Potentially Novel Drug Targets in Cancer Cell Spheroid Cultures

Time-lapse Imaging of Primary Preneoplastic Mammary Epithelial Cells Derived from Genetically Engineered Mouse Models of Breast Cancer

Functional Assessment of BRCA1 variants using CRISPR-Mediated Base Editors

Isolation and Functional Assessment of Human Breast Cancer Stem Cells from Cell and Tissue Samples

Profiling of Estrogen-regulated MicroRNAs in Breast Cancer Cells

Evaluation of Stem Cell Properties in Human Ovarian Carcinoma Cells Using Multi and Single Cell-based Spheres Assays

Evaluating the Effectiveness of Cancer Drug Sensitization In Vitro and In Vivo

Identifying the Effects of BRCA1 Mutations on Homologous Recombination using Cells that Express Endogenous Wild-type BRCA1

Detection of DNA Breaks in Dividing Human Cells by Neutral Comet Assay

gDNA Enrichment by a Transposase-based Technology for NGS Analysis of the Whole Sequence of BRCA1, BRCA2, and 9 Genes Involved in DNA Damage Repair