This work was supported by NIH grants R01 CA107469, R01 CA125577, and U01CA154224 to C.G. Kleer, the University of Michigan's Cancer Center Support.

1. Preparation of Materials and Culture Media
<ol>
	<li>Thaw growth factor reduced (GFR) Matrigel at 4 &#176;C O/N.</li>
	<li>Warm up complete media for required cell line at 37 &#176;C. MCF10A- ATCC specified media; HME- Ham's F-12 medium supplemented with 5% fetal bovine serum, 1 &#181;g/ml hydrocortisone, 5 &#181;g/ml insulin, 10 ng/ml epidermal growth factor, and 100 ng/ml cholera toxin; SUM149- Ham's F-12 media supplemented with 5% FBS, 2 &#181;g/ml hydrocortisone and 5 &#181;g/ml insulin; and MDA-MB-231-10% FBS-DMEM</li>
	<li>Precool an 8-well chamber slide on ice.</li>
	<li>Prepare tissue culture hood and supplies.</li>
</ol>
2. Three Dimensional Culture in 8-well Chamber Slide 
<ol>
	<li>Coat each well of the 8-well slide with 40 &#181;l of GFR Matrigel. Add the Matrigel in the center of the slide and then spread using a P200 pipette tip. Try to spread as evenly as possible, avoiding bubbles and overspreading which can lead to meniscus formation.</li>
	<li>Incubate the slides at 37 &#176;C under 5% CO2. While the Matrigel is solidifying, trypsinize the cells, collect and spin at 150 x g in tissue culture centrifuge for 4 min.</li>
	<li>Count the cells and dilute to 12,500 cells/ml in complete media of the respective cell line. Add GFR Matrigel to 2% and add 400 &#181;l to each well of a Matrigel precoated chamber slide.</li>
	<li>Incubate the slides in the CO2 incubator. Give fresh complete media changes every 4th day until 15 days.</li>
	<li>Treatment with pharmacologic inhibitors: For inhibitor studies add small molecule inhibitors to the complete media at the time of plating followed by fresh media changes supplemented with the inhibitors every three days while growing the cells on GFR Matrigel.</li>
	<li>Treatment with purified protein: 
	<ol>
		<li>Plate the cells following steps 2.1-2.3. Allow the cultures to grow for 4 days followed by serum starvation for 16 hr.</li>
		<li>At day 5, treat the cells with appropriate concentration of purified protein in 0.1% FBS supplemented media to the serum starved cells. Give fresh media change with purified protein after 2 days.</li>
		<li>At day 10 replace the conditioned media with complete HME media. Allow the cultures to grow for another 5 days.</li>
	</ol>
	</li>
	<li>Immunofluorescence staining of acinar structures grown on Matrigel: 
	<ol>
		<li>Prepare 2% paraformaldehyde, 0.5% Triton X-100 and 100 mM glycine in 1x PBS, pH 7.4. Prepare immunofluorescence buffer (IF buffer) that comprises of 1x PBS containing 0.1% bovine serum albumin, 0.2% triton X-100, 0.05% Tween-20.</li>
		<li>Use a P200 pipette tip to carefully aspirate the conditioned media.</li>
		<li>Fix the acinar structures with 2% freshly prepared paraformaldehyde at room temperature (RT) for 20 min.</li>
		<li>Permeabilize the cells with 0.5% Triton X-100 for 10 min at 4 &#176;C.</li>
		<li>Wash the cultures three times with 100 mM glycine, 10-15 min for each wash.</li>
		<li>Block the cells with 10% goat serum in IF buffer, called primary block, for 1 hr at RT.</li>
		<li>Incubate the cultures with a 20 &#181;g/ml goat anti mouse F(ab&#180;)2 fragment in primary block buffer for 30 min. This step is important to block the immunoreactive mouse IgG species in the Matrigel.</li>
		<li>Incubate with primary antibody in the second blocking solution (Primary block+20 &#181;g/ml goat anti mouse F(ab&#180;)2 fragment) O/N at 4 &#176;C.</li>
		<li>Wash three times with IF buffer for 10-15 min each with gentle rocking.</li>
		<li>Incubate with fluorescent conjugated secondary antibodies in IF buffer for 45 min.</li>
		<li>Wash 3x for 10 min each with IF buffer with gentle rocking.</li>
		<li>Mount the slides with anti-fade reagent containing DAPI to visualize the nuclei.</li>
		<li>Allow the slides to dry O/N at RT.</li>
		<li>Image acquisition: Acquire confocal images at the colony midsection of cells grown on top of Matrigel. For more information acquire a series of optical sections throughout the entire length of the acinar structure by Z stacking.</li>
	</ol>
	</li>
</ol>
3. Three Dimensional Culture in 2-well Chamber Slides for Immunoblotting
<ol>
	<li>Precool a 2-well chamber slide on ice. Follow steps 2.1-2.4 scaling up the reagents for the 2-well chamber slide e.g. coat with 160 &#181;l of Matrigel and add 1.6 ml of cell/Matrigel mix to each well of the 2-well slide.</li>
	<li>Harvest the acinar structures from the Matrigel using the commercially available 3D culture cell harvesting kit following manufacturer's instructions.</li>
	<li>Dilute the cell wash and cell harvesting buffers to 1x and precool to 4 &#176;C. Washing and dislodging of Matrigel should be carried out on ice.</li>
	<li>Wash the acinar structures 3x using the cell wash buffer.</li>
	<li>Collect the acini into 15 ml centrifuge tubes using cell harvesting buffer followed by 30 min incubation on a rocker at 4 &#176;C. Mix suspension well with a 1 ml pipette. This will break the Matrigel in small pieces and release most of the cells in the cell harvesting buffer.</li>
	<li>Pellet the cells at 200 x g in a culture centrifuge. Remove the floating layer of hydrogel from the pelleted cells with a P200 pipette tip.</li>
	<li>Resuspend the lysates in SDS sample buffer provided with the kit. RIPA lysis buffer can also be used.</li>
</ol>
4. Quantification of Malignant vs. Benign Breast Phenotype
<ol>
	<li>Grow cells in triplicates for each treatment set following steps 2.1-2.4.</li>
	<li>Take phase contrast images of acinar structures from each well at 5X or 10X resolution using a phase contrast microscope attached to a slide shifter and a computer. Take the images by moving the slide from one frame to another and thus covering the entire well of the chambered slide.</li>
	<li>Count the total number of acinar structures, the number of single round flat acini and the number of multiacinar structures or haphazardly growing structures lacking organization and with branching processes emanating from it.</li>
	<li>Calculate the percentage of single round flat acinar structures vs. malignant structures and plot as column graph. Calculate the significance by Student&#39;s t-test.</li>
</ol>

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	<li>Arendt, L. M., Rudnick, J. A., Keller, P. J., Kuperwasser, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Stroma+in+breast+development+and+disease.">Stroma in breast development and disease.</a> Semin. Cell Dev. Biol. 21, 11-18 (2009).</li><li>Debnath, J., Muthuswamy, S. K., Brugge, J. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Morphogenesis+and+oncogenesis+of+MCF-10A+mammary+epithelial+acini+grown+in+three-dimensional+basement+membrane+cultures.">Morphogenesis and oncogenesis of MCF-10A mammary epithelial acini grown in three-dimensional basement membrane cultures.</a> Methods. 30, 256-268 (2003).</li><li>Lee, G. Y., Kenny, P. A., Lee, E. H., Bissell, M. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Three-dimensional+culture+models+of+normal+and+malignant+breast+epithelial+cells.">Three-dimensional culture models of normal and malignant breast epithelial cells.</a> Nat. Methods. 4, 359-365 (2007).</li><li>Li, Q., Chow, A. B., Mattingly, R. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Three-dimensional+overlay+culture+models+of+human+breast+cancer+reveal+a+critical+sensitivity+to+mitogen-activated+protein+kinase+kinase+inhibitors.">Three-dimensional overlay culture models of human breast cancer reveal a critical sensitivity to mitogen-activated protein kinase kinase inhibitors.</a> J. Pharmacol. Exp. Ther. 332, 821-828 (2010).</li><li>Rosen, P. P., Rosen, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Rosen's breast pathology. , (2008).</li><li>Weaver, V. M., Fischer, A. H., Peterson, O. W., Bissell, M. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+importance+of+the+microenvironment+in+breast+cancer+progression:+recapitulation+of+mammary+tumorigenesis+using+a+unique+human+mammary+epithelial+cell+model+and+a+three-dimensional+culture+assay.">The importance of the microenvironment in breast cancer progression: recapitulation of mammary tumorigenesis using a unique human mammary epithelial cell model and a three-dimensional culture assay.</a> Biochem. Cell Biol. 74, 833-851 (1996).</li><li>Kenny, P. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+morphologies+of+breast+cancer+cell+lines+in+three-dimensional+assays+correlate+with+their+profiles+of+gene+expression.">The morphologies of breast cancer cell lines in three-dimensional assays correlate with their profiles of gene expression.</a> Mol. Oncol. 1, 84-96 (2007).</li><li>Pal, A., Huang, W., Li, X., Toy, K. A., Nikolovska-Coleska, Z., Kleer, C. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=CCN6+modulates+BMP+signaling+via+the+Smad-independent+TAK1/p38+pathway,+acting+to+suppress+metastasis+of+breast+cancer.">CCN6 modulates BMP signaling via the Smad-independent TAK1/p38 pathway, acting to suppress metastasis of breast cancer.</a> Cancer Res. 15, 4818-4828 (2012).</li><li>Pal, A., Huang, W., Toy, K. A., Kleer, C. 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The authors declare no competing financial interests.

We have described here the three dimensional culture of breast epithelial cells on a reconstituted basement membrane and the usefulness of this system to differentiate between malignant vs. benign breast phenotype. This system can also be used to culture different cell types from other glandular tissues and has been reported to have been successfully used to culture prostate epithelial, bronchial epithelial, and thyroid epithelial cells, to name a few12-14. The importance of 3D culture lies in the fact that it...

Three dimensional culture (3D) of breast epithelial cells on reconstituted basement membrane is an important model system to study the complex phenotype and associated signaling of normal breast and breast cancer2,3. The functional unit of breast is the terminal duct lobular unit (TDLU) which consists of a small duct which branches into acini. The acini are highly organized structures, composed of two cell layers, epithelial and myoepithelial cells, which are surrounded by a basement membrane5. The most distinguishing features of normal acini are cellular polarization, attachment to the underlying basement membrane and specialized cell-cell contacts. This intricate organization is disrupted in invasive carcinomas. The widely used 2D cultures, where cells are grown as monolayers, do not allow for the formation of acini. Thus, the monolayer culture is lacking in providing a system to capture the intricate relationship between epithelial cells in normal breast and their deregulation in breast cancer. Functional monotypic epithelial cultures of breast cells have been developed in several laboratories2,3. 3D culture involves the growth of breast cells on Matrigel, which is a solubilized extract derived from Engelbreth-Holm-Swarm mouse sarcoma cells and is available commercially. Other 3D substrata like collagen I are also used. The breast cells can be cultured in 3D by 3D embedded assay, where cells are cultured embedded in Matrigel2. Alternatively, cells can be cultured by 3D on top assay, also called 3D overlay assay, which is cost effective as it requires lesser volume of Matrigel, and facilitates time lapse monitoring of colony formation by phase contrast imaging and is ideal for in situ imaging2-3. The 3D on top assay has been used to define the correlation between the acinar phenotype and gene expression profile7.
3D culture can be effectively used to distinguish normal and benign cells from invasive carcinoma. Normal and benign breast cells form growth arrested polarized structures with a well-defined lumen in the center on Matrigel whereas invasive carcinoma cells grow prolifically and haphazardly with no clearing of the lumen. E6/E7 immortalized human mammary epithelial cells and MCF10A cell line, which is a spontaneously immortalized cell line isolated from a 36 year old patient with fibrocystic changes, have been successfully used to recapture the benign breast phenotype in 3D3,8 and have served as a model system to study the oncogenic and tumor suppressor function of several molecules8,9. These benign cells can be engineered to manipulate gene(s) of interest by the introduction of lentivirus/retrovirus. If the gene(s) of interest is a tumor suppressor, shRNA mediated knockdown will lead to a malignant transformation whereas if the gene of interest is an oncogene overexpression in benign cells should show a malignant phenotype. In both cases the acinar structures formed in 3D can capture the malignant transformation.
Benign single cells plated in 3D start to proliferate and form round spherical structures. By day 5-8 this spherical aggregate of cells will differentiate into a surrounding polarized layer of cells that is in contact with the Matrigel, and an inner mass of less polarized cells, which lack contact with the Matrigel. In the next 10-15 days the inner cells will start to die by apoptosis forming a clear lumen. The malignant cells will grow haphazardly losing their polarity. Highly malignant cells usually form branching structures. These differences in phenotype can be captured by time lapse phase contrast imaging and by in situ immunostaining with relevant molecular markers. The most commonly used markers are alpha 6-integrin, a basal polarity marker, in combination with the proliferation marker phospho-histone 3 and the apoptotic marker cleaved caspase-3. The latter is important to determine whether there is lumen formation in the center of the acini, a feature of normal and benign breast cells. Other polarity and cell-cell contact markers include GM130, laminin, ERM, E-cadherin. Alternately the breast cancer cell lines can be engineered to manipulate the gene of interest. In this case reversion to a more growth arrested benign phenotype can be used as a read out to distinguish from the cancer phenotype.
3D culture can also be carefully used to delineate the signaling pathways involved in malignant transformation10-11. Using the above mentioned read-outs, pharmacological inhibitors, blocking antibodies or recombinant proteins can be used be pinpoint at the molecular signaling leading to malignant transformation. With continued efforts from various laboratories it is possible to extract the cells from 3D to isolate RNA and also prepare lysates for immunoblotting and immunoprecipitation. These strategies are described in a stepwise and detailed manner in the protocol.

<table border="0" cellpadding="0" cellspacing="0" width="585">
	<colgroup>
		<col />
		<col />
		<col />
		<col />
	</colgroup>
	<tbody>
		<tr height="43">
			<td height="43" style="height:43px;width:216px;">Growth Factor Reduced matrigel</td>
			<td style="width:83px;">BD biosciences</td>
			<td style="width:119px;">354230</td>
			<td style="width:167px;">Avoid repeat freeze thaw&#160;</td>
		</tr>
		<tr height="64">
			<td height="64" style="height:64px;width:216px;">Lab-Tek glass hamber slides 8-well</td>
			<td style="width:83px;">Thermo Fisher Scientific</td>
			<td style="width:119px;">177402</td>
			<td>Precool on ice&#160;</td>
		</tr>
		<tr height="64">
			<td height="64" style="height:64px;width:216px;">Lab-Tek glass chamber slides 2- well&#160;</td>
			<td style="width:83px;">Thermo Fisher Scientific</td>
			<td style="width:119px;">177380</td>
			<td>Precool on ice&#160;</td>
		</tr>
		<tr height="64">
			<td height="64" style="height:64px;width:216px;">goat anti mouse F(ab&#180;)2 fragment</td>
			<td style="width:83px;">Jackson Immunoresearch</td>
			<td style="width:119px;">115-006-006</td>
			<td></td>
		</tr>
		<tr height="64">
			<td height="64" style="height:64px;width:216px;">Normal goat serum</td>
			<td style="width:83px;">Jackson Immunoresearch</td>
			<td style="width:119px;">005-000-121</td>
			<td></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:216px;">Fluorescent conjugated Alexa antibodies</td>
			<td style="width:83px;">Molecular probes</td>
			<td style="width:119px;"></td>
			<td>Please look at molecular probes website</td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:216px;">Prolong gold antifade reagent with DAPI</td>
			<td style="width:83px;">Molecular Probes</td>
			<td style="width:119px;">P36935</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:216px;">3D Culture Cell Harvesting kit</td>
			<td style="width:83px;">Trevigen</td>
			<td style="width:119px;">3448-020-k</td>
			<td></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:216px;">Anti-Apha-6-integrin</td>
			<td style="width:83px;">Fisher Scientifics&#160;</td>
			<td style="width:119px;">MAB1378</td>
			<td>1:00 dilution for IF</td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:216px;">Anti-GM130</td>
			<td style="width:83px;">BD Biosciences</td>
			<td style="width:119px;">610822</td>
			<td>1:00 dilution for IF</td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:216px;">Anti-phospho-histone 3 (Ser10)FITC Conjugated</td>
			<td style="width:83px;">Fisher Scientifics&#160;</td>
			<td style="width:119px;">16-222</td>
			<td>1:100 dilution for IF</td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:216px;">Anti-Cleaved caspase 3 (Asp 175)</td>
			<td style="width:83px;">Cell Signaling</td>
			<td style="width:119px;">9661s</td>
			<td>1:50 dilution for IF</td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:216px;">Anti-E-cadherin</td>
			<td style="width:83px;">BD Biosciences</td>
			<td style="width:119px;">610181</td>
			<td>1:200 dilution for IF</td>
		</tr>
	</tbody>
</table>

three dimensional cultures: a tool to study normal acinar architecture vs. malignant transformation of breast cells

Invasive breast carcinomas are a group of malignant epithelial tumors characterized by the invasion of adjacent tissues and propensity to metastasize. The interplay of signals between cancer cells and their microenvironment exerts a powerful influence on breast cancer growth and biological behavior1. However, most of these signals from the extracellular matrix are lost or their relevance is understudied when cells are grown in two dimensional culture (2D) as a monolayer. In recent years, three dimensional (3D) culture on a reconstituted basement membrane has emerged as a method of choice to recapitulate the tissue architecture of benign and malignant breast cells. Cells grown in 3D retain the important cues from the extracellular matrix and provide a physiologically relevant ex&#160;vivo system2,3. Of note, there is growing evidence suggesting that cells behave differently when grown in 3D as compared to 2D4. 3D culture can be effectively used as a means to differentiate the malignant phenotype from the benign breast phenotype and for underpinning the cellular and molecular signaling involved3. One of the distinguishing characteristics of benign epithelial cells is that they are polarized so that the apical cytoplasm is towards the lumen and the basal cytoplasm rests on the basement membrane. This apico-basal polarity is lost in invasive breast carcinomas, which are characterized by cellular disorganization and formation of anastomosing and branching tubules that haphazardly infiltrates the surrounding stroma. These histopathological differences between benign gland and invasive carcinoma can be reproduced in 3D6,7. Using the appropriate read-outs like the quantitation of single round acinar structures, or differential expression of validated molecular markers for cell proliferation, polarity and apoptosis in combination with other molecular and cell biology techniques, 3D culture can provide an important tool to better understand the cellular changes during malignant transformation and for delineating the responsible signaling.

3D culture can be effectively used to differentiate malignant phenotype of human breast epithelial cells from the benign breast. Single benign cells plated on Matrigel grow as organized spherical structures that can easily be imaged as single round flat acini in one plane using phase contrast imaging. The single malignant cells plated on Matrigel grow haphazardly, show very high refractive index and are difficult to image in one plane. As shown in Figure 1, the benign HME and MCF10A cells form spherical ...

Watch this Scientific Journal Video about Three Dimensional Cultures: A Tool To Study Normal Acinar Architecture vs. Malignant Transformation Of Breast Cells at JoVE.com

Three Dimensional Cultures: A Tool To Study Normal Acinar Architecture vs. Malignant Transformation Of Breast Cells

Three dimensional culture of mammary epithelial cells on a reconstituted basement membrane is a useful method to recapitulate the in vivo architecture of the benign breast, and to differentiate the malignant phenotype from the benign breast phenotype. Importantly, this system can be applied to study invasive carcinomas in other tissues.

Invasive breast carcinomas are a group of malignant epithelial tumors characterized by the invasion of adjacent tissues and propensity to metastasize. The ...

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19.8K Views.  University of Michigan Comprehensive Cancer Center. Three dimensional culture of mammary epithelial cells on a reconstituted basement membrane is a useful method to recapitulate the in vivo architecture of the benign breast, and to differentiate the malignant phenotype from the benign breast phenotype. Importantly, this system can be applied to study invasive carcinomas in other tissues.

Video: Three Dimensional Cultures: A Tool To Study Normal Acinar Architecture vs. Malignant Transformation Of Breast Cells

Human Neuroendocrine Tumor Cell Lines as a Three-Dimensional Model for the Study of Human Neuroendocrine Tumor Therapy

Neuroendocrine tumors (NETs) are rare tumors, with an incidence of two per 100,&#x200A;000 individuals per year, and they account for 0.5% of all human malignancies.1 Other than surgery for the minority of patients who present with localized disease, there is little or no survival benefit of systemic therapy. Therefore, there is a great need to better understand the biology of NETs, and in particular define new therapeutic targets for patients with nonresectable or metastatic neuroendocrine tumors. 3D cell culture is becoming a popular method for drug screening due to its relevance in modeling the in vivo tumor tissue organization and microenvironment.2,3 The 3D multicellular spheroids could provide valuable information in a more timely and less expensive manner than directly proceeding from 2D cell culture experiments to animal (murine) models.
To facilitate the discovery of new therapeutics for NET patients, we have developed an in vitro 3D multicellular spheroids model using the human NET cell lines. The NET cells are plated in a non-adhesive agarose-coated 24-well plate and incubated under physiological conditions (5% CO2, 37 &deg;C) with a very slow agitation for 16-24 hr after plating. The cells form multicellular spheroids starting on the 3rd or 4th day. The spheroids become more spherical by the 6th day, at which point the drug treatments are initiated. The efficacy of the drug treatments on the NET spheroids is monitored based on the morphology, shape and size of the spheroids with a phase-contrast light microscope. The size of the spheroids is estimated automatically using a custom-developed MATLAB program based on an active contour algorithm. Further, we demonstrate a simple method to process the HistoGel embedding on these 3D spheroids, allowing the use of standard histological and immunohistochemical techniques. 
This is the first report on generating 3D spheroids using NET cell lines to examine the effect of therapeutic drugs. We have also performed histology on these 3D spheroids, and displayed an example of a single drug's effect on growth and proliferation of the NET spheroids. Our results support that the NET spheroids are valuable for further studies of NET biology and drug development.

We present a simple agarose overlay platform to grow 3D multicellular spheroids using neuroendocrine cancer cell lines. This method provides a very convenient way to examine the effect of therapeutic drugs on the neuroendocrine tumor cells. It could also help us establish human neuroendocrine tumor spheroids for cancer therapy.

Neuroendocrine tumors (NETs) are rare tumors, with an incidence of two per 100,&#x200A;000 individuals per year, and they account for 0.5% of all human ...

A Three-dimensional Tissue Culture Model to Study Primary Human Bone Marrow and its Malignancies

Tissue culture has been an invaluable tool to study many aspects of cell function, from normal development to disease. Conventional cell culture methods rely on the ability of cells either to attach to a solid substratum of a tissue culture dish or to grow in suspension in liquid medium. Multiple immortal cell lines have been created and grown using such approaches, however, these methods frequently fail when primary cells need to be grown ex vivo. Such failure has been attributed to the absence of the appropriate extracellular matrix components of the tissue microenvironment from the standard systems where tissue culture plastic is used as a surface for cell growth. Extracellular matrix is an integral component of the tissue microenvironment and its presence is crucial for the maintenance of physiological functions such as cell polarization, survival, and proliferation. Here we present a 3-dimensional tissue culture method where primary bone marrow cells are grown in extracellular matrix formulated to recapitulate the microenvironment of the human bone (rBM system). Embedded in the extracellular matrix, cells are supplied with nutrients through the medium supplemented with human plasma, thus providing a comprehensive system where cell survival and proliferation can be sustained for up to 30 days while maintaining the cellular composition of the primary tissue. Using the rBM system we have successfully grown primary bone marrow cells from normal donors and patients with amyloidosis, and various hematological malignancies. The rBM system allows for direct, in-matrix real time visualization of the cell behavior and evaluation of preclinical efficacy of novel therapeutics. Moreover, cells can be isolated from the rBM and subsequently used for in vivo transplantation, cell sorting, flow cytometry, and nucleic acid and protein analysis. Taken together, the rBM method provides a reliable system for the growth of primary bone marrow cells under physiological conditions.

In standard culture methods cells are taken out of their physiological environment and grown on the plastic surface of a dish. To study the behavior of primary human bone marrow cells we created a 3-D culture system where cells are grown under conditions recapitulating the native microenvironment of the tissue.

Tissue culture has been an invaluable tool to study many aspects of cell function, from normal development to disease. Conventional cell culture methods ...

Quantification of Breast Cancer Cell Invasiveness Using a Three-dimensional (3D) Model

It is now well known that the cellular and tissue microenvironment are critical regulators influencing tumor initiation and progression. Moreover, the extracellular matrix (ECM) has been demonstrated to be a critical regulator of cell behavior in culture and homeostasis in vivo. The current approach of culturing cells on two-dimensional (2D), plastic surfaces results in the disturbance and loss of complex interactions between cells and their microenvironment. Through the use of three-dimensional (3D) culture assays, the conditions for cell-microenvironment interaction are established resembling the in vivo microenvironment. This article provides a detailed methodology to grow breast cancer cells in a 3D basement membrane protein matrix, exemplifying the potential of 3D culture in the assessment of cell invasion into the surrounding environment. In addition, we discuss how these 3D assays have the potential to examine the loss of signaling molecules that regulate epithelial morphology by immunostaining procedures. These studies aid to identify important mechanistic details into the processes regulating invasion, required for the spread of breast cancer.

Quantification of Breast Cancer Cell Invasiveness Using a Three-dimensional 3D Model

This article provides detailed methodologies for the use of three-dimensional (3D) assays to quantify breast cancer cell invasion. Specifically, we discuss the procedures required to set up such assays, quantification, and data analysis, as well as methods to examine the loss of membrane integrity that occurs when cells invade.

It is now well known that the cellular and tissue microenvironment are critical regulators influencing tumor initiation and progression. Moreover, the ...

Orthotopic Injection of Breast Cancer Cells into the Mammary Fat Pad of Mice to Study Tumor Growth.

Breast cancer growth can be studied in mice using a plethora of models. Genetic manipulation of breast cancer cells may provide insights into the functions of proteins involved in oncogenic progression or help to discover new tumor suppressors. In addition, injecting cancer cells into mice with different genotypes might provide a better understanding of the importance of the stromal compartment. Many models may be useful to investigate certain aspects of disease progression but do not recapitulate the entire cancerous process. In contrast, breast cancer cells engraftment to the mammary fat pad of mice better recapitulates the location of the disease and presence of the proper stromal compartment and therefore better mimics human cancerous disease. In this article, we describe how to implant breast cancer cells into mice orthotopically and explain how to collect tissues to analyse the tumor milieu and metastasis to distant organs. Using this model, many aspects (growth, angiogenesis, and metastasis) of cancer can be investigated simply by providing a proper environment for tumor cells to grow.

Cancer is a complex disease that is influenced by the tissue surrounding the tumor as well as local pro- and anti-inflammatory mediators. Therefore, orthotropic injection models, rather than subcutaneous models may be useful to study cancer progression in a manner that better mimics human pathology.

Breast cancer growth can be studied in mice using a plethora of models. Genetic manipulation of breast cancer cells may provide insights into the ...

Using Adeno-associated Virus as a Tool to Study Retinal Barriers in Disease

M&#252;ller cells are the principal glial cells of the retina. Their end-feet form the limits of the retina at the outer and inner limiting membranes (ILM), and in conjunction with astrocytes, pericytes and endothelial cells they establish the blood-retinal barrier (BRB). BRB limits material transport between the bloodstream and the retina while the ILM acts as a basement membrane that defines histologically the border between the retina and the vitreous cavity. Labeling M&#252;ller cells is particularly relevant to study the physical state of the retinal barriers, as these cells are an integral part of the BRB and ILM. Both BRB and ILM are frequently altered in retinal disease and are responsible for disease symptoms.
There are several well-established methods to study the integrity of the BRB, such as the Evans blue assay or fluorescein angiography. However these methods do not provide information on the extent of BRB permeability to larger molecules, in nanometer range. Furthermore, they do not provide information on the state of other retinal barriers such as the ILM. To study BRB permeability alongside retinal ILM, we used an AAV based method that provides information on permeability of BRB to larger molecules while indicating the state of the ILM and extracellular matrix proteins in disease states. Two AAV variants are useful for such study: AAV5 and ShH10. AAV5&#160;has a natural tropism for photoreceptors but it cannot get across to the outer retina when administered into the vitreous when the ILM is intact (i.e., in wild-type retinas). ShH10 has a strong tropism towards glial cells and will selectively label M&#252;ller glia in both healthy and diseased retinas. ShH10 provides more efficient gene delivery in retinas where ILM is compromised. These viral tools coupled with immunohistochemistry and blood-DNA analysis shed light onto the state of retinal barriers in disease.

To investigate the blood-retinal barrier permeability and the inner limiting membrane integrity in animal models of retinal disease, we used several adeno-associated virus (AAV) variants as tools to label retinal neurons and glia. Virus mediated reporter gene expression is then used as an indicator of retinal barrier permeability.

M&#252;ller cells are the principal glial cells of the retina. Their end-feet form the limits of the retina at the outer and inner limiting membranes ...

Three-Dimensional (3D) Tumor Spheroid Invasion Assay

Invasion of surrounding normal tissues is generally considered to be a key hallmark of malignant (as opposed to benign) tumors. For some cancers in particular (e.g., brain tumors such as glioblastoma multiforme and squamous cell carcinoma of the head and neck &#8211; SCCHN) it is a cause of severe morbidity and can be life-threatening even in the absence of distant metastases. In addition, cancers which have relapsed following treatment unfortunately often present with a more aggressive phenotype. Therefore, there is an opportunity to target the process of invasion to provide novel therapies that could be complementary to standard anti-proliferative agents. Until now, this strategy has been hampered by the lack of robust, reproducible assays suitable for a detailed analysis of invasion and for drug screening. Here we provide a simple micro-plate method (based on uniform, self-assembling 3D tumor spheroids) which has great potential for such studies. We exemplify the assay platform using a human glioblastoma cell line and also an SCCHN model where the development of resistance against targeted epidermal growth factor receptor (EGFR) inhibitors is associated with enhanced matrix-invasive potential. We also provide two alternative methods of semi-automated quantification: one using an imaging cytometer and a second which simply requires standard microscopy and image capture with digital image analysis.

Three-Dimensional 3D Tumor Spheroid Invasion Assay

Invasion of surrounding normal tissues is a defining characteristic of malignant tumors. We provide here a simple, semi-automated micro-plate assay of invasion into a natural 3D biomatrix that has been exemplified with a number of models of advanced human cancers.

Invasion of surrounding normal tissues is generally considered to be a key hallmark of malignant (as opposed to benign) tumors. For some cancers in ...

In Vivo and Ex Vivo Approaches to Study Ovarian Cancer Metastatic Colonization of Milky Spot Structures in Peritoneal Adipose

High-grade serous ovarian cancer (HGSC), the cause of widespread peritoneal metastases, continues to have an extremely poor prognosis; fewer than 30% of women are alive 5 years after diagnosis. The omentum is a preferred site of HGSC metastasis formation. Despite the clinical importance of this microenvironment, the contribution of omental adipose tissue to ovarian cancer progression remains understudied. Omental adipose is unusual in that it contains structures known as milky spots, which are comprised of B, T, and NK cells, macrophages, and progenitor cells surrounding dense nests of vasculature. Milky spots play a key role in the physiologic functions of the omentum, which are required for peritoneal homeostasis. We have shown that milky spots also promote ovarian cancer metastatic colonization of peritoneal adipose, a key step in the development of peritoneal metastases. Here we describe the approaches we developed to evaluate and quantify milky spots in peritoneal adipose and study their functional contribution to ovarian cancer cell metastatic colonization of omental tissues both in vivo and ex vivo. These approaches are generalizable to additional mouse models and cell lines, thus enabling the study of ovarian cancer metastasis formation from initial localization of cells to milky spot structures to the development of widespread peritoneal metastases.

In Vivo and Ex Vivo Approaches to Study Ovarian Cancer Metastatic Colonization of Milky Spot Structures in Peritoneal Adipose

We outline a protocol that implements both in vivo and ex vivo approaches to study ovarian cancer colonization of peritoneal adipose tissues, particularly the omentum. Furthermore, we present a protocol to quantitate and analyze immune cell-structures in the omentum known as milky spots, which promote metastases of peritoneal adipose.

High-grade serous ovarian cancer (HGSC), the cause of widespread peritoneal metastases, continues to have an extremely poor prognosis; fewer than 30% of ...

Utilization of the Soft Agar Colony Formation Assay to Identify Inhibitors of Tumorigenicity in Breast Cancer Cells

Given the inherent difficulties in investigating the mechanisms of tumor progression in vivo, cell-based assays such as the soft agar colony formation assay (hereafter called soft agar assay), which measures the ability of cells to proliferate in semi-solid matrices, remain a hallmark of cancer research. A key advantage of this technique over conventional 2D monolayer or 3D spheroid cell culture assays is the close mimicry of the 3D cellular environment to that seen in vivo. Importantly, the soft agar assay also provides an ideal tool to rigorously test the effects of novel compounds or treatment conditions on cell proliferation and migration. Additionally, this assay enables the quantitative assessment of cell transformation potential within the context of genetic perturbations. We recently identified peptidylarginine deiminase 2 (PADI2) as a potential breast cancer biomarker and therapeutic target. Here we highlight the utility of the soft agar assay for preclinical anti-cancer studies by testing the effects of the PADI inhibitor, BB-Cl-amidine (BB-CLA), on the tumorigenicity of human ductal carcinoma in situ (MCF10DCIS) cells.

Here, we document the use of the soft agar colony formation assay to test the effects of a peptidylarginine deiminase (PADI) enzyme inhibitor, BB-Cl-amidine, on breast cancer tumorigenicity in vitro.

Given the inherent difficulties in investigating the mechanisms of tumor progression in vivo, cell-based assays such as the soft agar colony formation ...

Three-dimensional Alginate-bead Culture of Human Pituitary Adenoma Cells

A three-dimensional culture method is described in which primary pituitary adenoma cells are grown in alginate beads. Alginate is a polymer derived from brown sea algae. Briefly, the tumor tissue is cut into small pieces and submitted to an enzymatic digestion with collagenase and trypsin. Next, a cell suspension is obtained. The tumor cell suspension is mixed with 1.2% sodium alginate and dropped into a CaCl2 solution, and the alginate/cell suspension is gelled on contact with the CaCl2 to form spherical beads. The cells embedded in the alginate beads are supplied with nutrients provided by the culture media enriched with 20% FBS. Three-dimensional culture in alginate beads maintains the viability of adenoma cells for long periods of time, up to four months. Moreover, the cells can be liberated from the alginate by washing the beads with sodium citrate and seeded on glass coverslips for further immunocytochemical analyses. The use of a cell culture model allows for the fixation and visualization of the actin cytoskeleton with minimal disorganization. In summary, alginate beads provide a reliable culture system for the maintenance of pituitary adenoma cells.

Three-dimensional culture in alginate beads, due to its simplicity and reproducibility, was chosen to maintain the pituitary adenoma cells. The procedures included an initial enzymatic digestion and mechanical dissociation of the tumor tissue, and the subsequent cell suspension was encapsulated in alginate beads.

A three-dimensional culture method is described in which primary pituitary adenoma cells are grown in alginate beads. Alginate is a polymer derived from ...

Using Saccadometry with Deep Brain Stimulation to Study Normal and Pathological Brain Function

The oculomotor system involves a large number of brain areas including parts of the basal ganglia, and various neurodegenerative diseases including Parkinson's and Huntington's can disrupt it. People with Parkinson's disease, for example, tend to have increased saccadic latencies. Consequently, the quantitative measurement of saccadic eye movements has received considerable attention as a potential biomarker for neurodegenerative conditions. A lot more can be learned about the brain in both health and disease by observing what happens to eye movements when the function of specific brain areas is perturbed. Deep brain stimulation is a surgical intervention used for the management of a range of neurological conditions including Parkinson's disease, in which stimulating electrodes are placed in specific brain areas including several sites in the basal ganglia. Eye movement measurements can then be made with the stimulator systems both off and on and the results compared. With suitable experimental design, this approach can be used to study the pathophysiology of the disease being treated, the mechanism by which DBS exerts it beneficial effects, and even aspects of normal neurophysiology.

This paper describes the use of quantitative measurement of eye movements in conjunction with stimulation of focal areas of the deep brain in order to study physiology, pathophysiology, and the mechanisms of deep brain stimulation.

The oculomotor system involves a large number of brain areas including parts of the basal ganglia, and various neurodegenerative diseases including ...