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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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><tbody><tr><td>Growth Factor Reduced Matrigel</td><td>BD Biosciences</td><td>354230</td><td>Avoid repeat freeze thaw&amp;nbsp;</td></tr><tr><td>Lab-Tek glass hamber slides 8-well</td><td>Thermo Fisher Scientific</td><td>177402</td><td>Precool on ice&amp;nbsp;</td></tr><tr><td>Lab-Tek glass chamber slides 2-well&amp;nbsp;</td><td>Thermo Fisher Scientific</td><td>177380</td><td>Precool on ice&amp;nbsp;</td></tr><tr><td>Goat anti mouse F(ab&amp;acute;)&lt;sub&gt;2 &lt;/sub&gt;fragment</td><td>Jackson Immunoresearch</td><td>115-006-006</td><td></td></tr><tr><td>Normal goat serum</td><td>Jackson Immunoresearch</td><td>005-000-121</td><td></td></tr><tr><td>Fluorescent conjugated Alexa antibodies</td><td>Molecular Probes</td><td></td><td>Please look at molecular probes website</td></tr><tr><td>Prolong gold antifade reagent with DAPI</td><td>Molecular Probes</td><td>P36935</td><td></td></tr><tr><td>3D Culture Cell Harvesting kit</td><td>Trevigen</td><td>3448-020-k</td><td></td></tr><tr><td>Anti-Apha-6-integrin</td><td>Fisher Scientific</td><td>MAB1378</td><td>1:100 dilution for IF</td></tr><tr><td>Anti-GM130</td><td>BD Biosciences</td><td>610822</td><td>1:100 dilution for IF</td></tr><tr><td>Anti-phospho-histone 3 (Ser10)FITC Conjugated</td><td>Fisher Scientific</td><td>16-222</td><td>1:100 dilution for IF</td></tr><tr><td>Anti-Cleaved caspase 3 (Asp 175)</td><td>Cell Signaling</td><td>9661s</td><td>1:50 dilution for IF</td></tr><tr><td>Anti-E-cadherin</td><td>BD Biosciences</td><td>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 ...

three-dimensional-cultures-tool-to-study-normal-acinar-architecture

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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

Analyzing the Communication Between Monocytes and Primary Breast Cancer Cells in an Extracellular Matrix Extract (ECME)-based Three-dimensional System

Embedded in the extracellular matrix (ECM), normal and neoplastic epithelial cells intimately communicate with hematopoietic and non-hematopoietic cells, thus greatly influencing normal tissue homeostasis and disease outcome. In breast cancer, tumor-associated macrophages (TAMs) play a critical role in disease progression, metastasis, and recurrence; therefore, understanding the mechanisms of monocyte chemoattraction to the tumor microenvironment and their interactions with tumor cells is important to control the disease. Here, we provide a detailed description of a three-dimensional (3D) co-culture system of human breast cancer (BrC) cells and human monocytes. BrC cells produced high basal levels of regulated on-activation, normal T-cell expressed and secreted (RANTES), monocyte chemoattractant protein-1 (MCP-1), and granulocyte-macrophage colony-stimulating factor (G-CSF), while in co-culture with monocytes, pro-inflammatory cytokines Interleukin (IL)-1 beta (IL-1&#946;) and IL-8 were enriched together with matrix metalloproteinases (MMP)-1, MMP-2, and MMP-10. This tumor stroma microenvironment promoted resistance to anoikis in MCF-10A 3D acini-like structures, chemoattraction of monocytes, and invasion of aggressive BrC cells. The protocols presented here provide an affordable alternative to study intra-tumor communication and are an example of the great potential that in vitro 3D cell systems provide to interrogate specific features of tumor biology related to tumor aggression.

Analyzing the Communication Between Monocytes and Primary Breast Cancer Cells in an Extracellular Matrix Extract ECME-based Three-dimensional System

Here, we describe a three-dimensional culture method to analyze the morphology of primary breast cancer cells, as well as to study their direct/indirect interactions with monocytes and the outcomes such as collagen degradation, immune cell recruitment, cell invasion, and promotion of cancer-related inflammation.

Embedded in the extracellular matrix (ECM), normal and neoplastic epithelial cells intimately communicate with hematopoietic and non-hematopoietic cells, ...

Cancer Research

Spheroid Assay to Measure TGF-&#946;-induced Invasion

TGF-&beta; has opposing roles in breast cancer progression by acting as a tumor suppressor in the initial phase, but stimulating invasion and metastasis at later stage1,2. Moreover, TGF-&beta; is frequently overexpressed in breast cancer and its expression correlates with poor prognosis and metastasis 3,4. The mechanisms by which TGF-&beta; induces invasion are not well understood.
TGF-&beta; elicits its cellular responses via TGF-&beta; type II (T&beta;RII) and type I (T&beta;RI) receptors. Upon TGF-&beta;-induced heteromeric complex formation, T&beta;RII phosphorylates the T&beta;RI. The activated T&beta;RI initiates its intracellular canonical signaling pathway by phosphorylating receptor Smads (R-Smads), i.e. Smad2 and Smad3. These activated R-Smads form heteromeric complexes with Smad4, which accumulate in the nucleus and regulate the transcription of target genes5. In addition to the previously described Smad pathway, receptor activation results in activation of several other non-Smad signaling pathways, for example Mitogen Activated Protein Kinase (MAPK) pathways6.
To study the role of TGF-&beta; in different stages of breast cancer, we made use of the MCF10A cell system. This system consists of spontaneously immortalized MCF10A1 (M1) breast epithelial cells7, the H-RAS transformed M1-derivative MCF10AneoT (M2), which produces premalignant lesions in mice8, and the M2-derivative MCF10CA1a (M4), which was established from M2 xenografts and forms high grade carcinomas with the ability to metastasize to the lung9. This MCF10A series offers the possibility to study the responses of cells with different grades of malignancy that are not biased by a different genetic background.
For the analysis of TGF-&beta;-induced invasion, we generated homotypic MCF10A spheroid cell cultures embedded in a 3D collagen matrix in vitro (Fig 1). Such models closely resemble human tumors in vivo by establishing a gradient of oxygen and nutrients, resulting in active and invasive cells on the outside and quiescent or even necrotic cells in the inside of the spheroid10. Spheroid based assays have also been shown to better recapitulate drug resistance than monolayer cultures11. This MCF10 3D model system allowed us to investigate the impact of TGF-&beta; signaling on the invasive properties of breast cells in different stages of malignancy.

An assay to quantitatively measure Transforming Growth Factor (TGF)-&#x03B2;-induced invasion in 3-dimensional collagen gels is described. This assay takes advantage of the MCF10A series of cell lines, which represent different stages of breast cancer development. This method can be adopted to be used with other cell lines and might be used to investigate other potential activators or inhibitors of invasion.

TGF-&beta; has opposing roles in breast cancer progression by acting as a tumor suppressor in the initial phase, but stimulating invasion and metastasis ...

Mimicking and Manipulating Pancreatic Acinar-to-Ductal Metaplasia in 3-dimensional Cell Culture

The differentiation of acinar cells to ductal cells during pancreatitis and in the early development of pancreatic cancer is a key process that requires further study. To understand the mechanisms regulating acinar-to-ductal metaplasia (ADM), ex vivo 3D culture and differentiation of primary acinar cells to ductal cells offers many advantages over other systems. With the technique herein, modulation of protein expression is simple and quick, requiring only one day to isolate, stimulate or virally infect, and begin culturing primary acinar cells to investigate the ADM process. In contrast to using basement membrane matrix, the seeding of acinar cell clusters in collagen I extracellular matrix, allows acinar cells to retain their acinar identity before manipulation. This is vital when testing the contribution of various components to the induction of ADM. Not only are the effects of cytokines or other ectopically administered factors testable through this technique, but the contribution of common mutations, increased protein expression, or knockdown of protein expression is testable via viral infection of primary acinar cells, using adenoviral or lentiviral vectors. Moreover, cells can be re-isolated from collagen or basement membrane matrix at the endpoint and analyzed for protein expression.

Primary acinar cell isolation, protein expression or activity modulation, culture, and down-stream applications are abundantly useful in the ex vivo study of acinar-to-ductal metaplasia (ADM), an early event in the development of pancreatic cancer.

The differentiation of acinar cells to ductal cells during pancreatitis and in the early development of pancreatic cancer is a key process that requires ...

In Vitro Evaluation of Oncogenic Transformation in Human Mammary Epithelial Cells

Tumorigenesis is a multi-step process in which cells acquire capabilities&#160;that allow their growth, survival, and dissemination under hostile conditions. Different tests seek to identify and quantify these hallmarks of cancerous cells; however, they often focus on a single aspect of cellular transformation and, in fact, multiple tests are required for their proper characterization. The purpose of this work is to provide researchers with a set of tools to assess cellular transformation in vitro from a broad perspective, thereby making it possible to draw sound conclusions.
A sustained proliferative signaling activation is the major feature of tumoral tissues and can be easily monitored under in vitro conditions by calculating the number of population doublings achieved over time. Besides, the growth of cells in 3D cultures allows their interaction with surrounding cells, resembling what occurs in vivo. This enables the evaluation of cellular aggregation and, together with immunofluorescent labeling of distinctive cellular markers, to obtain information on another relevant feature of tumoral transformation: the loss of proper organization. Another remarkable characteristic of transformed cells is their capacity to grow without attachment to other cells and to the extracellular matrix, which can be evaluated with the anchorage assay.
Detailed experimental procedures to evaluate cell growth rate, to perform immunofluorescent labeling of cell lineage markers in 3D cultures, and to test anchorage-independent cell growth in soft agar are provided. These methodologies are optimized for Breast Primary Epithelial Cells (BPEC) due to its relevance in breast cancer; however, procedures can be applied to other cell types after some adjustments.

This protocol provides experimental in vitro tools to evaluate the transformation of human mammary cells. Detailed steps to follow-up cell proliferation rate, anchorage-independent growth capacity, and distribution of cell lineages in 3D cultures with basement membrane matrix are described.

Tumorigenesis is a multi-step process in which cells acquire capabilities&#160;that allow their growth, survival, and dissemination under hostile ...

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 ...

Phospholipid Mediator Induced Transformation in Three-Dimensional Cultures

Several models have been developed to study cancer, such as rodent models and established cell lines. Valuable insights into carcinogenesis have been provided by studies using these models. Cell lines have provided an understanding of the deregulation of molecular signaling associated with breast tumorigenesis, while rodent models are widely used to study cellular and molecular characteristics of breast cancer in vivo. The establishment of 3D cultures of breast epithelial and cancerous cells aids in bridging the gap between in vivo and in vitro models by mimicking the in vivo conditions in vitro. This model can be used to understand the deregulation of complex molecular signaling events and the cellular characteristics during breast carcinogenesis. Here, a 3D culture system is modified to study a phospholipid mediator-induced (Platelet Activating Factor, PAF) transformation. Immunomodulators and other secreted molecules play a major role in tumor initiation and progression in the breast. In the present study, 3D acinar cultures of breast epithelial cells are exposed to PAF exhibited transformation characteristics such as loss of polarity and altered cellular characteristics. This 3D culture system will assist in shedding light on genetic and/or epigenetic perturbations induced by various small molecule entities in the tumor microenvironment. Additionally, this system will also provide a platform for the identification of novel as well as known genes that may be involved in the process of transformation.

The present protocol describes the setting up of 3D 'on top' cultures of a non-transformed breast epithelial cell line, MCF10A, that has been modified to study Platelet Activating Factor (PAF) induced transformation. Immuno-fluorescence has been used to assess the transformation and is discussed in detail.

Several models have been developed to study cancer, such as rodent models and established cell lines. Valuable insights into carcinogenesis have been ...

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 ...

Preparation and Analysis of In Vitro Three Dimensional Breast Carcinoma Surrogates

Three dimensional (3D) culture is a more physiologically relevant method to model cell behavior in vitro than two dimensional culture. Carcinomas, including breast carcinomas, are complex 3D tissues composed of cancer epithelial cells and stromal components, including fibroblasts and extracellular matrix (ECM). Yet most in vitro models of breast carcinoma consist only of cancer epithelial cells, omitting the stroma and, therefore, the 3D architecture of a tumor in vivo. Appropriate 3D modeling of carcinoma is important for accurate understanding of tumor biology, behavior, and response to therapy. However, the duration of culture and volume of 3D models is limited by the availability of oxygen and nutrients within the culture. Herein, we demonstrate a method in which breast carcinoma epithelial cells and stromal fibroblasts are incorporated into ECM to generate a 3D breast cancer surrogate that includes stroma and can be cultured as a solid 3D structure or by using a perfusion bioreactor system to deliver oxygen and nutrients. Following setup and an initial growth period, surrogates can be used for preclinical drug testing. Alternatively, the cellular and matrix components of the surrogate can be modified to address a variety of biological questions. After culture, surrogates are fixed and processed to paraffin, in a manner similar to the handling of clinical breast carcinoma specimens, for evaluation of parameters of interest. The evaluation of one such parameter, the density of cells present, is explained, where ImageJ and CellProfiler image analysis software systems are applied to photomicrographs of histologic sections of surrogates to quantify the number of nucleated cells per area. This can be used as an indicator of the change in cell number over time or the change in cell number resulting from varying growth conditions and treatments.

Preparation and Analysis of In Vitro Three Dimensional Breast Carcinoma Surrogates

We demonstrate a method to generate 3D breast cancer surrogates, which can be cultured using a perfusion bioreactor system to deliver oxygen and nutrients. Following growth, surrogates are fixed and processed to paraffin for evaluation of parameters of interest. The evaluation of one such parameter, cell density, is explained.

Three dimensional (3D) culture is a more physiologically relevant method to model cell behavior in vitro than two dimensional culture. Carcinomas, ...

Bioengineering

Generation of Mosaic Mammary Organoids by Differential Trypsinization

Organoids offer self-organizing, three-dimensional tissue structures that recapitulate physiological processes in the convenience of a dish. The murine mammary gland is composed of two distinct epithelial cell compartments, serving different functions: the outer, contractile myoepithelial compartment and the inner, secretory luminal compartment. Here, we describe a method by which the cells comprising these compartments are isolated and then combined to investigate their individual lineage contributions to mammary gland morphogenesis and differentiation. The method is simple and efficient and does not require sophisticated separation technologies such as fluorescence activated cell sorting. Instead, we harvest and enzymatically digest the tissue, seed the epithelium on adherent tissue culture dishes, and then use differential trypsinization to separate myoepithelial from luminal cells with ~90% purity. The cells are then plated in an extracellular matrix where they organize into bilayered, three-dimensional (3D) organoids that can be differentiated to produce milk after 10 days in culture. To test the effects of genetic mutations, cells can be harvested from wild type or genetically engineered mouse models, or they can be genetically manipulated prior to 3D culture. This technique can be used to generate mosaic organoids that allow investigation of gene function specifically in the luminal or myoepithelial compartment.

The mammary gland is a bilayered structure, comprising outer myoepithelial and inner luminal epithelial cells. Presented is a protocol to prepare organoids using differential trypsinization. This efficient method allows researchers to separately manipulate these two cell types to explore questions concerning their roles in mammary gland form and function.

Organoids offer self-organizing, three-dimensional tissue structures that recapitulate physiological processes in the convenience of a dish. The murine ...

Developmental Biology

Isolation of Mammary Epithelial Cells from Three-dimensional Mixed-cell Spheroid Co-culture

While enormous efforts have gone into identifying signaling pathways and molecules involved in normal and malignant cell behaviors1-2, much of this work has been done using classical two-dimensional cell culture models, which allow for easy cell manipulation. It has become clear that intracellular signaling pathways are affected by extracellular forces, including dimensionality and cell surface tension3-4. Multiple approaches have been taken to develop three-dimensional models that more accurately represent biologic tissue architecture3. While these models incorporate multi-dimensionality and architectural stresses, study of the consequent effects on cells is less facile than in two-dimensional tissue culture due to the limitations of the models and the difficulty in extracting cells for subsequent analysis.
The important role of the microenvironment around tumors in tumorigenesis and tumor behavior is becoming increasingly recognized4. Tumor stroma is composed of multiple cell types and extracellular molecules. During tumor development there are bidirectional signals between tumor cells and stromal cells5. Although some factors participating in tumor-stroma co-evolution have been identified, there is still a need to develop simple techniques to systematically identify and study the full array of these signals6. Fibroblasts are the most abundant cell type in normal or tumor-associated stromal tissues, and contribute to deposition and maintenance of basement membrane and paracrine growth factors7.
Many groups have used three dimensional culture systems to study the role of fibroblasts on various cellular functions, including tumor response to therapies, recruitment of immune cells, signaling molecules, proliferation, apoptosis, angiogenesis, and invasion8-15. We have optimized a simple method for assessing the effects of mammary fibroblasts on mammary epithelial cells using a commercially available extracellular matrix model to create three-dimensional cultures of mixed cell populations (co-cultures)16-22. With continued co-culture the cells form spheroids with the fibroblasts clustering in the interior and the epithelial cells largely on the exterior of the spheroids and forming multi-cellular projections into the matrix. Manipulation of the fibroblasts that leads to altered epithelial cell invasiveness can be readily quantified by changes in numbers and length of epithelial projections23. Furthermore, we have devised a method for isolating epithelial cells out of three-dimensional co-culture that facilitates analysis of the effects of fibroblast exposure on epithelial behavior. We have found that the effects of co-culture persist for weeks after epithelial cell isolation, permitting ample time to perform multiple assays. This method is adaptable to cells of varying malignant potential and requires no specialized equipment. This technique allows for rapid evaluation of in vitro cell models under multiple conditions, and the corresponding results can be compared to in vivo animal tissue models as well as human tissue samples.

A simple method is described for analyzing effects of tissue fibroblasts on associated epithelial cells. The combination of this method and three-dimensional tissue culture can facilitate analysis of cells after isolation from 3D. The technique is applicable to cells of varying malignant potential, allowing systematic study of effects of tumor-associated stroma on tumor cells.

While enormous efforts have gone into identifying signaling pathways and molecules involved in normal and malignant cell behaviors1-2, much of this work ...

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

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Analyzing the Communication Between Monocytes and Primary Breast Cancer Cells in an Extracellular Matrix Extract (ECME)-based Three-dimensional System

Spheroid Assay to Measure TGF-β-induced Invasion

Mimicking and Manipulating Pancreatic Acinar-to-Ductal Metaplasia in 3-dimensional Cell Culture

In Vitro Evaluation of Oncogenic Transformation in Human Mammary Epithelial Cells

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

Phospholipid Mediator Induced Transformation in Three-Dimensional Cultures

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

Preparation and Analysis of In Vitro Three Dimensional Breast Carcinoma Surrogates

Generation of Mosaic Mammary Organoids by Differential Trypsinization

Isolation of Mammary Epithelial Cells from Three-dimensional Mixed-cell Spheroid Co-culture