Name: tumorsphere derivation and treatment from primary tumor cells isolated from mouse rhabdomyosarcomas
Uploaded: 2019-09-13T13:30:00
Description: Watch this Scientific Journal Video about Tumorsphere Derivation and Treatment from Primary Tumor Cells Isolated from Mouse Rhabdomyosarcomas at JoVE.com

This work was supported by the Ellison Medical Foundation grant AG-NS-0843-11, and the NIH Pilot Grant within the NCI Cancer Center Support Grant P30CA030199 to A.S.

The housing, treatment, and sacrifice of mice were performed following the approved IACUC protocol of the Sanford Burnham Prebys Medical Discovery Institute.
1. Reagent preparation
<ol>
	<li>Prepare 100 mL of cell isolation media: F10 medium supplemented with 10% horse serum (HS).</li>
	<li>Prepare 50 mL of collagenase type II solution: dissolve 1 g of collagenase type II powder in 50 mL of cell isolation media (note the units of the enzyme per 1 mL of media, since the number of units change...

<ol>
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D., 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+Transcriptional+Coactivator+TAZ+Is+a+Potent+Mediator+of+Alveolar+Rhabdomyosarcoma+Tumorigenesis.">The Transcriptional Coactivator TAZ Is a Potent Mediator of Alveolar Rhabdomyosarcoma Tumorigenesis.</a> Clinical Cancer Research. 24 (11), 2616-2630 (2018).</li><li>Boscolo Sesillo, F., Fox, D., Sacco, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Muscle+Stem+Cells+Give+Rise+to+Rhabdomyosarcomas+in+a+Severe+Mouse+Model+of+Duchenne+Muscular+Dystrophy.">Muscle Stem Cells Give Rise to Rhabdomyosarcomas in a Severe Mouse Model of Duchenne Muscular Dystrophy.</a> Cell Reports. 26 (3), 689-701 (2019).</li><li>Chamberlain, J. S., Metzger, J., Reyes, M., Townsend, D., Faulkner, J. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dystrophin-deficient+mdx+mice+display+a+reduced+life+span+and+are+susceptible+to+spontaneous+rhabdomyosarcoma.">Dystrophin-deficient mdx mice display a reduced life span and are susceptible to spontaneous rhabdomyosarcoma.</a> The FASEB Journal. 21 (9), 2195-2204 (2007).</li><li>Kessel, 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=High-Throughput+3D+Tumor+Spheroid+Screening+Method+for+Cancer+Drug+Discovery+Using+Celigo+Image+Cytometry.">High-Throughput 3D Tumor Spheroid Screening Method for Cancer Drug Discovery Using Celigo Image Cytometry.</a> SLAS Technology. 22 (4), 454-465 (2017).</li><li>Johnson, S., Chen, H., Lo, P. 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Multiple methods have been employed for isolation and characterization of TPCs from tumor heterogeneous cell populations: tumor clonogenic assays, FACS isolation, and tumorsphere formation assay. The tumor clonogenic assay was first described in 1971, used for stem cell studies, and only subsequently applied to cancer biology29,30. This method is based on the cancer stem cells intrinsic property to expand without constraints in soft gels cultures<sup class='xref'...

Cancer is a heterogeneous disease; furthermore, the same type of tumor can present different genetic mutations in different patients, and within a patient a tumor is composed by multiple populations of cells1. Heterogeneity presents a challenge in the identification of cells responsible for initiating and propagating cancer, but their characterization is essential for the development of efficient treatments. The notion of tumor propagating cells (TPC), a rare population of cells that contribute to tumor development, has been previously extensively reviewed2. Despite the fact that TPCs have been characterized in multiple types of cancer, the identification of markers for their reliable isolation remains a challenge for several tumor types3,4,5,6,7,8,9. Thus, a method that does not rely on molecular markers but rather on TPC functional properties (high self-renewal and the ability to grow in low-attachment conditions), known as the tumorsphere formation assay, can be widely applied for the identification of TPCs from most tumors. Importantly, this assay can also be employed for expansion of TPCs and thus directly applied to cancer drug screening and studies on cancer resistance1,10.
Rhabdomyosarcoma (RMS) is a rare form of soft tissue sarcoma most common in young children11. Althoug RMS can be histologically identified through assessment of expression of myogenic markers, the RMS cell of origin has not been univocally characterized due to the multiple tumor subtypes and high heterogeneity of the tumor developmental stimuli. Indeed, recent studies have generated significant scientific discussion about whether RMS is of myogenic or non-myogenic origins, suggesting that RMS may derive from different cells types depending on the context12,13,14,15,16,17. Numerous studies on RMS cell lines have been performed employing the tumorsphere formation assay for the identification of pathways involved in tumor development and characterization of markers associated with highly self-renewal populations18,19,20,21.
However, despite the tumorsphere formation assay&#39;s potential for identifying RMS cells of origin, a reliable method that can be employed on primary RMS cells has not yet been described. In this context, a recent study from our group employed an optimized tumorsphere formation assay for the identification of the RMS cells of origin in a Duchenne muscular dystrophy (DMD) mouse model22. Multiple pre-tumorigenic cell types, isolated from muscle tissues, are tested for their ability to grow in low-attachment conditions, allowing the identification of muscle stem cells as cells of origin for RMS in dystrophic contexts. Described here is a reproducible and reliable protocol for the tumorsphere formation assay (Figure 1), which has been successfully employed for the identification of extremely rare cell populations that are responsible for mouse RMS development.

<table>
	<tbody>
		<tr>
			<td>Accutase cell dissociation reagent</td>
			<td>Gibco</td>
			<td>A1110501</td>
			<td>Detach adherent cells and dissociate tumorspheres</td>
		</tr>
		<tr>
			<td>Celigo</td>
			<td>Nexcelom</td>
			<td>Celigo</td>
			<td>Microwell plate based image cytometer for adherent and suspension cells</td>
		</tr>
		<tr>
			<td>Collagenase, Type II</td>
			<td>Life Technologies</td>
			<td>17101015</td>
			<td>Tissue digestion enzyme</td>
		</tr>
		<tr>
			<td>Dispase II, protease</td>
			<td>Life Technologies</td>
			<td>17105041</td>
			<td>Tissue digestion enzyme</td>
		</tr>
		<tr>
			<td>DMEM high glucose media</td>
			<td>Gibco</td>
			<td>11965092</td>
			<td>Component of tumor cells media</td>
		</tr>
		<tr>
			<td>DMEM/F12 Media</td>
			<td>Gibco</td>
			<td>11320033</td>
			<td>Component of tumosphere media</td>
		</tr>
		<tr>
			<td>EDTA</td>
			<td>ThermoFisher</td>
			<td>S312500</td>
			<td>Component of FACS buffer</td>
		</tr>
		<tr>
			<td>EGF recombinant mouse protein</td>
			<td>Gibco</td>
			<td>PMG8041</td>
			<td>Component of tumosphere media</td>
		</tr>
		<tr>
			<td>FACSAria II Flow Cytometry</td>
			<td>BD Biosciences</td>
			<td>650033</td>
			<td>Fluorescent activated cell sorter</td>
		</tr>
		<tr>
			<td>Fetal Bovine Serum</td>
			<td>Omega Scientific</td>
			<td>FB-11</td>
			<td>Component of tumor cells media</td>
		</tr>
		<tr>
			<td>Fluriso (Isofluornae) anesthetic agent</td>
			<td>MWI Vet Supply</td>
			<td>502017</td>
			<td>Anesthetic reagent for animals</td>
		</tr>
		<tr>
			<td>FxCycle Violet Stain</td>
			<td>Life Technologies</td>
			<td>F10347</td>
			<td>Discriminate live and dead cells</td>
		</tr>
		<tr>
			<td>Goat Serum</td>
			<td>Life Technologies</td>
			<td>16210072</td>
			<td>Component of FACS buffer</td>
		</tr>
		<tr>
			<td>Ham&#39;s F10 Media</td>
			<td>Life Technologies</td>
			<td>11550043</td>
			<td>Component of FACS buffer</td>
		</tr>
		<tr>
			<td>Horse Serum</td>
			<td>Life Technologies</td>
			<td>16050114</td>
			<td>Component of cell isolation media</td>
		</tr>
		<tr>
			<td>Lipofectamine 3000 transfection reagent</td>
			<td>ThermoFisher</td>
			<td>L3000015</td>
			<td>Transfection Reagent</td>
		</tr>
		<tr>
			<td>Matrigel membrane matrix</td>
			<td>Corning</td>
			<td>CB40234</td>
			<td>Provides support to trasplanted cells</td>
		</tr>
		<tr>
			<td>N-2 Supplemtns (100X)</td>
			<td>Gibco</td>
			<td>17502048</td>
			<td>Component of tumosphere media</td>
		</tr>
		<tr>
			<td>Neomycin-Polymyxin B Sulfates-Bacitracin Zinc Ophthalmic Ointment</td>
			<td>MWI Vet Supply</td>
			<td>701008</td>
			<td>Eyes ointment</td>
		</tr>
		<tr>
			<td>PBS</td>
			<td>Gibco</td>
			<td>10010023</td>
			<td>Component of FACS buffer and used for washing cells</td>
		</tr>
		<tr>
			<td>pEGFP-C1</td>
			<td>Addgene</td>
			<td>6084-1</td>
			<td>GFP plasmid</td>
		</tr>
		<tr>
			<td>Penicillin - Streptomyocin</td>
			<td>Life Technologies</td>
			<td>15140163</td>
			<td>Component of tumosphere and tumor cells media</td>
		</tr>
		<tr>
			<td>Recombinant Human &#946;FGF-basic</td>
			<td>Peprotech</td>
			<td>10018B</td>
			<td>Component of tumosphere media</td>
		</tr>
		<tr>
			<td>Recombinant mouse Flt-3 Ligand Protein</td>
			<td>R&#38;D Systems</td>
			<td>427-FL-005</td>
			<td>Recombinant protein</td>
		</tr>
		<tr>
			<td>Trypan blue</td>
			<td>ThermoFisher</td>
			<td>15250061</td>
			<td>Discriminate live and dead cells</td>
		</tr>
	</tbody>
</table>

tumorsphere derivation and treatment from primary tumor cells isolated from mouse rhabdomyosarcomas

Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children. Although significant efforts have enabled the identification of common mutations associated with RMS and allowed discrimination of different RMS subtypes, major challenges still exist for the development of novel treatments to further improve prognosis. Although identified by the expression of myogenic markers, there is still significant controversy over whether RMS has myogenic or non-myogenic origins, as the cell of origin is still poorly understood. In the present study, a reliable method is provided for the tumorsphere assay for mouse RMS. The assay is based on functional properties of tumor cells and allows the identification of rare populations in the tumor with tumorigenic functions. Also described are procedures for testing recombinant proteins, integrating transfection protocols with the tumorsphere assay, and evaluating candidate genes involved in tumor development and growth. Described further is a procedure for allograft transplantation of tumorspheres into recipient mice to validate tumorigenic function in vivo. Overall, the described method allows reliable identification and testing of rare RMS tumorigenic populations that can be applied to RMS arising in different contexts. Finally, the protocol can be utilized as a platform for drug screening and future development of therapeutics.

Tumorspheres detection 
Cell isolation was optimized to obtain the maximum heterogeneity of cell populations present in the tumor tissue. First, since isolated tissues presented morphologically dissimilar areas, to enhance the chances of isolating uniform rare cell populations, sampling was performed from multiple areas of the tumor (Figure 1A, first panel on the left). Second, mechanical dissociation of the harvested samples was perform...

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Tumorsphere Derivation and Treatment from Primary Tumor Cells Isolated from Mouse Rhabdomyosarcomas

This protocol describes a reproducible method for isolation of mouse rhabdomyosarcoma primary cells, tumorsphere formation and treatment, and allograft transplantation starting from tumorspheres cultures.

Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children. Although significant efforts have enabled the identification of common ...

Rhabdomyosarcoma is a rare form of soft-tissue sarcomas characterized histologically by tissue morphology and the expression of myogenic markers. However, given the existence of different subtypes of these tumors and the heterogeneity of the stimuli that contributes to its formation, the identification of the cell of origin has been very challenging. Here we describe reproducible and reliable methods for the identification of the cell of origin of rhabdomyosarcomas starting from freshly harvest tumor tissues from mice and this assay is the tumorsphere formation assay.The main advantages of tumorsphere formation assay is that it relies on cellular properties that are known to be present in tumor-originating cells and it can also be used for expansion and enrichment of the specific cell population. Furthermore, its spheroid structure mimic the tumor environment, thus they can be used as drug-screening studies. This method has the potential to be applied to others type of tumors because it does not require prior knowledge of molecular markers but it may require optimization of culture conditions.Tumorsphere may take some time to form, especially if trying to identify a rare cell population within your tumor. Thus, it's not suggested to look at your subculture plate every day, since it might negatively affect the results of your experiments. Start by warming up a 10-centimeter plate with five milliliters of isolation media in an incubator at 37 degrees Celsius.Weigh 500 to 1, 000 milligrams of the tumor tissue and place it in the plate. Bring the plate with the tumor tissue to a sterile culture hood and mince it with a razor blade. For optimal digestion, make sure that the sizes of the minced pieces are uniform.Transfer the minced tissue and cell isolation media to a 15-milliliter centrifuge tube. Wash the plate with another four milliliters of media and add that to the tube. Add 700 units per milliliter of collagenase solution to the tube and incubate it in a shaking water bath at 37 degrees Celsius for 1 1/2 hours.After the incubation, spin down the tissue at 300 times g for five minutes at room temperature. Aspirate the supernatant without disrupting the pellet, then resuspend the pellet in 10 milliliters of second digestion solution and incubate in the shaking water bath for 30 more minutes. After the second digestion, pipette the cell suspension up and down and pass it through a 70-micrometer nylon filter on a 50-milliliter centrifuge tube.Then wash the filter with 10 milliliters of cell isolation media and spin down the tissue at 300 times g for five minutes. Aspirate the supernatant and resuspend the pellet in 20 milliliters of tumor cell media. Transfer the suspension to a 15-centimeter culture plate and place the cells in a 37 degrees Celsius incubator overnight.On the next day, change the media to remove debris and dead cells that may negatively influence cell survival. At this point, assess cell confluency and allow the cells to grow in the incubator until it reaches 90%Monitor the cells every day and change the media every two days. For tumorsphere derivation, use cells at Passage P1 or P2 to avoid cell selection through multiple passages.Wash the cell dish with PBS and then cover them with detachment solution. Place them in the incubator for five to 10 minutes and then confirm detachment by looking at the plate under a brightfield microscope. Once the cells have detached, add tumor cell media to the plate and transfer the cell suspension to a centrifuge tube.Spin the cells down at 300 times g for five minutes, remove supernatant, and resuspend the cells in tumorsphere media. After resuspending the cells, count them using Trypan blue and calculate cell concentration. Plate the proper number of cells in a 96-well low-attachment plate and place the cells in the incubator until the end of the experiment, taking care not to disturb the plate unless replenishing media.After completion of the experiment, identify tumorspheres manually under a brightfield microscope or using Celigo software. The number and size of the tumorspheres can be evaluated as a result of this assay. To prepare tumorspheres for allograft transplantation, pull together all tumorspheres obtained from a specific cell type or treatment.Centrifuge the tumorspheres and carefully remove the supernatant with a one-millimeter pipette followed by a 200-microliter pipette, then wash them with 10 milliliters of sterile PBS. Spin the tumorspheres down again and aspirate the PBS. Add 500 microliters to one milliliter of cell detachment solution on top of the tumorsphere pellet and incubate the cells in a shaking water bath at 37 degrees Celsius.Check progression of digestion every 10 minutes. The entire process make take up to 30 minutes. If digestion of tumorsphere in the shaking water bath is not enough to obtain a single-cell solution, mechanical disruption through pipetting up and down is suggested.Note that after spinning the tumorspheres do not form a stable pellet, so aspirating the supernatant should be done carefully with a one-milliliter pipette and 200-microliter pipettes. Once a single-cell solution is obtained, add a volume of tumor cell media and spin it down at 300 times g for five minutes at 4 degrees Celsius. After this centrifugation, all subsequent steps must be performed on ice.Resuspend the cells in cold tumor cell media and count live cells using Trypan blue exclusion. Determine the proper number of cells for the allograft and dilute it in 50 microliters of cold tumor cell media. Place a pipette tip in cold tumor cell media to cool it and then use it to take 50 microliters of cold ECM solution and add it to the tube with cells, making sure not to remove the ECM tube from ice during this process.Maintain the cells on ice until transplantation and place a capped, 0.5-milliliter insulin syringe with a 29-gauge needle on ice. After confirming that the mouse has been properly anesthetized, shave the right side of the animal, aspirate the cell solution into the cooled syringe, and inject the cells subcutaneously into the shaved area. If the injection is performed correctly, a visible bump will form under the skin.This protocol can be used to reliably form tumorspheres for identification of rare cell populations that are responsible for soft-tissue sarcoma development. A fundamental part of this assay is discrimination between tumorspheres and cell clusters, which exhibit clear morphological differences. To determine the optimal concentration at which a protein of interest triggers an effect on tumor cells, it is necessary to assess the level of expression of the protein's downstream targets.Three of the tested genes showed a dose-dependent response to recombinant protein treatment and one did not. In order to establish an efficient protocol, the effects of transfection on inherent tumor cells were analyzed;two different amounts of reagent were tested and efficiency was assessed with a GFP-reporter plasmid. Lower amounts of reagent resulted in higher transfection efficiency.A two-step protocol had to be implemented to perform transfection on cells in suspension. Transfection was performed on adherent cells and 24 hours later they were detached and plated in suspension;after seven days, controlled tumorspheres were expressing GFP. After tumorspheres are obtained, treated, and transplanted it is possible to compare the effect of this different treatment in tumor growth in vivo.These methods will allow scientists to answer the still-standing questions of the cell of origin of rhabdomyosarcomas while at the same time setting the basis for drug screening.

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Genetics

From a Natural Product to Its Biosynthetic Gene Cluster: A Demonstration Using Polyketomycin from Streptomyces diastatochromogenes T&#252;6028

Streptomyces strains are known for their capability to produce a lot of different compounds with various bioactivities. Cultivation under different conditions often leads to the production of new compounds. Therefore, production cultures of the strains are extracted with ethyl acetate and the crude extracts are analyzed by HPLC. Furthermore, the extracts are tested for their bioactivity by different assays. For structure elucidation the compound of interest is purified by a combination of different chromatography methods.
Genome sequencing coupled with genome mining allows the identification of a natural product biosynthetic gene cluster using different computer programs. To confirm that the correct gene cluster has been identified, gene inactivation experiments have to be performed. The resulting mutants are analyzed for the production of the particular natural product. Once the correct gene cluster has been inactivated, the strain should fail to produce the compound.
The workflow is shown for the antibacterial compound polyketomycin produced by Streptomyces diastatochromogenes T&#252;6028. Around ten years ago, when genome sequencing was still very expensive, the cloning and identification of a gene cluster was a very time-consuming process. Fast genome sequencing combined with genome mining accelerates the trial of cluster identification and opens up new ways to explore biosynthesis and to generate novel natural products by genetic methods. The protocol described in this paper can be assigned to any other compound derived from a Streptomyces strain or another microorganism.

Here we present a detailed protocol of (A) the identification of a natural product with antibiotic activity, (B) the purification of the compound, (C) the first model of its biosynthesis, (D) genome sequencing/-mining and the (E) verification of the biosynthetic gene cluster.

Streptomyces strains are known for their capability to produce a lot of different compounds with various bioactivities. Cultivation under different ...

Chromatin Spread Preparations for the Analysis of Mouse Oocyte Progression from Prophase to Metaphase II

Chromatin spread techniques have been widely used to assess the dynamic localization of various proteins during gametogenesis, particularly for spermatogenesis. These techniques allow for visualization of protein and DNA localization patterns during meiotic events such as homologous chromosome pairing, synapsis and DNA repair. While a few protocols have been described in the literature, general chromatin spread techniques using mammalian prophase oocytes are limited and difficult due to the timing of meiosis initiation in fetal ovaries. In comparison, prophase spermatocytes can be collected from juvenile male mice with higher yields without the need for microdissection. However, it is difficult to obtain a pure synchronized population of cells at specific stages due to the heterogeneity of meiotic and post-meiotic germ cell populations in the juvenile and adult testis. For later stages of meiosis, it is advantageous to assess oocytes undergoing meiosis I (MI) or meiosis II (MII), because groups of mature oocytes can be collected from adult female mice and stimulated to resume meiosis in culture. Here, methods for meiotic chromatin spread preparations using oocytes dissected from fetal, neonatal and adult ovaries are described with accompanying video demonstrations. Chromosome missegregation events in mammalian oocytes are frequent, particularly during MI. These techniques can be used to assess and characterize the effects of different mutations or environmental exposures during various stages of oogenesis. As there are distinct differences between oogenesis and spermatogenesis, the techniques described within are invaluable to increase our understanding of mammalian oogenesis and the sexually dimorphic features of chromosome and protein dynamics during meiosis.

Oogenesis in mammals is known to be error-prone, particularly due to chromosome missegregation. This manuscript describes chromatin spread preparation methods for mouse prophase, metaphase I and II-staged oocytes. These fundamental techniques allow for the study of chromatin-bound proteins and chromosome morphology throughout mammalian oogenesis.

Chromatin spread techniques have been widely used to assess the dynamic localization of various proteins during gametogenesis, particularly for ...

Isolating, Sequencing and Analyzing Extracellular MicroRNAs from Human Mesenchymal Stem Cells

Extracellular and circulating RNAs (exRNA) are produced by many cell types of the body and exist in numerous bodily fluids such as saliva, plasma, serum, milk and urine. One subset of these RNAs are the posttranscriptional regulators &#8211; microRNAs (miRNAs). To delineate the miRNAs produced by specific cell types, in vitro culture systems can be used to harvest and profile exRNAs derived from one subset of cells. The secreted factors of mesenchymal stem cells are implicated in alleviating numerous diseases and is used as the in vitro model system here. This paper describes the process of collection, purification of small RNA and library generation to sequence extracellular miRNAs. ExRNAs from culture media differ from cellular RNA by being low RNA input samples, which calls for optimized procedures. This protocol provides a comprehensive guide to small exRNA sequencing from culture media, showing quality control checkpoints at each step during exRNA purification and sequencing.

This protocol demonstrates how to purify extracellular microRNAs from cell culture media for small RNA library construction and next generation sequencing. Various quality control checkpoints are described to allow readers to understand what to expect when working with low input samples like exRNAs.

Extracellular and circulating RNAs (exRNA) are produced by many cell types of the body and exist in numerous bodily fluids such as saliva, plasma, serum, ...

Generation of Cancer Cell Clones to Visualize Telomeric Repeat-containing RNA TERRA Expressed from a Single Telomere in Living Cells

Telomeres are transcribed, giving rise to telomeric repeat-containing long noncoding RNAs (TERRA), which have been proposed to play important roles in telomere biology, including heterochromatin formation and telomere length homeostasis. Recent findings revealed that TERRA molecules also interact with internal chromosomal regions to regulate gene expression in mouse embryonic stem (ES) cells. In line with this evidence, RNA fluorescence in situ hybridization (RNA-FISH) analyses have shown that only a subset of TERRA transcripts localize at chromosome ends. A better understanding of the dynamics of TERRA molecules will help define their function and mechanisms of action. Here, we describe a method to label and visualize single-telomere TERRA transcripts in cancer cells using the MS2-GFP system. To this aim, we present a protocol to generate stable clones, using the AGS human stomach cancer cell line, containing MS2 sequences integrated at a single subtelomere. Transcription of TERRA from the MS2-tagged telomere results in the expression of MS2-tagged TERRA molecules that are visualized by live-cell fluorescence microscopy upon co-expression of a MS2 RNA-binding protein fused to GFP (MS2-GFP). This approach enables researchers to study the dynamics of single-telomere TERRA molecules in cancer cells, and it can be applied to other cell lines.

Here, we present a protocol to generate cancer cell clones containing a MS2 sequence tag at a single subtelomere. This approach, relying on the MS2-GFP system, enables visualization of the endogenous transcripts of telomeric repeat-containing RNA (TERRA) expressed from a single telomere in living cells.

Telomeres are transcribed, giving rise to telomeric repeat-containing long noncoding RNAs (TERRA), which have been proposed to play important roles in ...

ATAC-seq Assay with Low Mitochondrial DNA Contamination from Primary Human CD4+ T Lymphocytes

ATAC-seq has become a widely used methodology in the study of epigenetics due to its rapid and simple approach to mapping genome-wide accessible chromatin. In this paper we present an improved ATAC-seq protocol that reduces contaminating mitochondrial DNA reads. While previous ATAC-seq protocols have struggled with an average of 50% contaminating mitochondrial DNA reads, the optimized&#160;lysis buffer introduced in this protocol reduces mitochondrial DNA contamination to an average of 3%. This improved ATAC-seq protocol allows for a near 50% reduction in the sequencing cost. We demonstrate how these high-quality ATAC-seq libraries can be prepared from activated CD4+ lymphocytes, providing step-by-step instructions from CD4+ lymphocyte isolation from whole blood through data analysis. This improved ATAC-seq protocol has been validated in a wide range of cell types and will be of immediate use to researchers studying chromatin accessibility.

Here, we present a protocol to perform an assay for transposase-accessible chromatin sequencing (ATAC-seq) on activated CD4+ human lymphocytes. The protocol has been modified to minimize contaminating mitochondrial DNA reads from 50% to 3% through the introduction of a new lysis buffer.

ATAC-seq has become a widely used methodology in the study of epigenetics due to its rapid and simple approach to mapping genome-wide accessible ...

An In Vitro Protocol for Evaluating MicroRNA Levels, Functions, and Associated Target Genes in Tumor Cells

MicroRNAs (miRNAs) are small regulatory RNAs which are recognized to modulate numerous intracellular signaling pathways in several diseases including cancers. These small regulatory RNAs mainly interact with the 3&#8217; untranslated regions (3&#8217; UTR) of their target messenger RNAs (mRNAs) ultimately resulting in the inhibition of decoding processes of mRNAs and the augmentation of target mRNA degradations. Based on the expression levels and intracellular functions, miRNAs are able to serve as regulatory factors of oncogenic and tumor-suppressive mRNAs. Identification of bona fide target genes of a miRNA among hundreds or even thousands of computationally predicted targets is a crucial step to discern the roles and basic molecular mechanisms of a miRNA of interest. Various miRNA target prediction programs are available to search possible miRNA-mRNA interactions. However, the most challenging question is how to validate direct target genes of a miRNA of interest. This protocol describes a reproducible strategy of key methods on how to identify miRNA targets related to the function of a miRNA. This protocol presents a practical guide on step-by-step procedures to uncover miRNA levels, functions, and related target mRNAs using the probe-based real-time polymerase chain reaction (PCR), sulforhodamine B (SRB) assay following a miRNA mimic transfection, dose-response curve generation, and luciferase assay along with the cloning of 3&#8217; UTR of a gene, which is necessary for proper understanding of the roles of individual miRNAs.

This protocol uses a probe-based real-time polymerase chain reaction (PCR), a sulforhodamine B (SRB) assay, 3&#8217; untranslated regions (3&#8217; UTR) cloning, and a luciferase assay to verify the target genes of a miRNA of interest and to understand the functions of miRNAs.

MicroRNAs (miRNAs) are small regulatory RNAs which are recognized to modulate numerous intracellular signaling pathways in several diseases including ...

Generation of Tumor Organoids from Genetically Engineered Mouse Models of Prostate Cancer

Methods based on homologous recombination to modify genes have significantly furthered biological research. Genetically engineered mouse models (GEMMs) are a rigorous method for studying mammalian development and disease. Our laboratory has developed several GEMMs of prostate cancer (PCa) that lack expression of one or multiple tumor suppressor genes using the site-specific Cre-loxP recombinase system and a prostate-specific promoter. In this article, we describe our method for necropsy of these PCa GEMMs, primarily focusing on dissection of mouse prostate tumors. New methods developed over the last decade have facilitated the culture of epithelial-derived cells to model organ systems in vitro in three dimensions. We also detail a 3D cell culture method to generate tumor organoids from mouse PCa GEMMs. Pre-clinical cancer research has been dominated by 2D cell culture and cell line-derived or patient-derived xenograft models. These methods lack tumor microenvironment, a limitation of using these techniques in pre-clinical studies. GEMMs are more physiologically-relevant for understanding tumorigenesis and cancer progression. Tumor organoid culture is an in vitro model system that recapitulates tumor architecture and cell lineage characteristics. In addition, 3D cell culture methods allow for growth of normal cells for comparison to tumor cell cultures, rarely possible using 2D cell culture techniques. In combination, use of GEMMs and 3D cell culture in pre-clinical studies has the potential to improve our understanding of cancer biology.&#160;

We show a method for necropsy and dissection of mouse prostate cancer models, focusing on prostate tumor dissection. A step-by-step protocol for generation of mouse prostate tumor organoids is also presented.

Methods based on homologous recombination to modify genes have significantly furthered biological research. Genetically engineered mouse models (GEMMs) ...

The Use of Mouse Mammary Tumor Cells in an In Vitro Invasion Assay as a Measure of Oncogenic Cell Behavior

The in vitro invasion assay uses a protein-rich matrix in a Boyden chamber to measure the ability of cultured cells to pass through the matrix and a porous membrane in a process analogous to the initial steps of cancer cell metastasis. The tested cells can be altered for the gene expression or treated with inhibitors to test for changes in the invasion potential. This experiment tests the aggressive phenotype of the mouse mammary tumor cells to discover and characterize the potential oncogenes that promote cell invasion. This technique, however, can be versatile and adapted to many different applications. The experiment itself can be done in one day and the results are acquired by light microscopy in less than a day. The results include counts of the number of invading cells for comparison and analysis. The in vitro invasion assay is a rapid, inexpensive, and clear-cut method for determining cell behavior in a culture that can be used as an initial assessment before more involved in vivo assays.

The in vitro cell invasion assay is used to measure the potential of cancer metastasis by quantifying the cellular potential for invasion and migration using cell culture inserts containing protein matrix. Cells are challenged to migrate through the protein matrix and a porous membrane, towards a chemoattractant, and then quantified by light microscopy.

The in vitro invasion assay uses a protein-rich matrix in a Boyden chamber to measure the ability of cultured cells to pass through the matrix and a ...

A FACS-based Protocol to Isolate RNA from the Secondary Cells of Drosophila Male Accessory Glands

To understand the function of an organ, it is often useful to understand the role of its constituent cell populations. Unfortunately, the rarity of individual cell populations often makes it difficult to obtain enough material for molecular studies. For example, the accessory gland of the Drosophila male reproductive system contains two distinct secretory cell types. The main cells make up 96% of the secretory cells of the gland, while the secondary cells (SC) make up the remaining 4% of cells (about 80 cells per male). Although both cell types produce important components of the seminal fluid, only a few genes are known to be specific to the SCs. The rarity of SCs has, thus far, hindered transcriptomic analysis study of this important cell type. Here, a method is presented that allows for the purification of SCs for RNA extraction and sequencing. The protocol consists in first dissecting glands from flies expressing a SC-specific GFP reporter and then subjecting these glands to protease digestion and mechanical dissociation to obtain individual cells. Following these steps, individual, living, GFP-marked cells are sorted using a fluorescent activated cell sorter (FACS) for RNA purification. This procedure yields SC-specific RNAs from ~40 males per condition for downstream RT-qPCR and/or RNA sequencing in the course of one day. The rapidity and simplicity of the procedure allows for the transcriptomes of many different flies, from different genotypes or environmental conditions, to be determined in a short period of time.

A FACS-based Protocol to Isolate RNA from the Secondary Cells of Drosophila Male Accessory Glands

Here, we present a protocol to dissociate and sort a specific cell population from the Drosophila male accessory glands (secondary cells) for RNA sequencing and RT-qPCR. Cell isolation is accomplished through FACS purification of GFP-expressing secondary cells after a multistep-dissociation process requiring dissection, proteases digestion and mechanical dispersion.

To understand the function of an organ, it is often useful to understand the role of its constituent cell populations. Unfortunately, the rarity of ...

Preparation of Meiotic Chromosome Spreads from Zebrafish Spermatocytes

Meiosis is the key cellular process required to create haploid gametes for sexual reproduction. Model organisms have been instrumental in understanding the chromosome events that take place during meiotic prophase, including the pairing, synapsis, and recombination events that ensure proper chromosome segregation. While the mouse has been an important model for understanding the molecular mechanisms underlying these processes, not all meiotic events in this system are analogous to human meiosis. We recently demonstrated the exciting potential of the zebrafish as a model of human spermatogenesis. Here we describe, in detail, our methods to visualize meiotic chromosomes and associated proteins in chromosome spread preparations. These preparations have the advantage of allowing high resolution analysis of chromosome structures. First, we describe the procedure for dissecting testes from adult zebrafish, followed by cell dissociation, lysis, and spreading of the chromosomes. Next, we describe the procedure for detecting the localization of meiotic chromosome proteins, by immunofluorescence detection, and nucleic acid sequences, by fluorescence in situ hybridization (FISH). These techniques comprise a useful set of tools for the cytological analysis of meiotic chromatin architecture in the zebrafish system. Researchers in the zebrafish community should be able to quickly master these techniques and incorporate them into their standard analyses of reproductive function.

Nuclear surface spreads are an indispensable tool for studying chromosome events during meiosis. Here we demonstrate a method to prepare and visualize meiotic chromosomes during prophase I from zebrafish spermatocytes.

Meiosis is the key cellular process required to create haploid gametes for sexual reproduction. Model organisms have been instrumental in understanding ...