We thank the IISER Pune Microscopy Facility for access to equipment and infrastructure and support for the experiments. This study was supported by a grant from the Department of Biotechnology (DBT), Govt. of India (BT/PR8699/MED/30/1018/2013), Science and Engineering Research Board (SERB), Govt. of India (EMR/2016/001974) and partly by IISER, Pune Core funding. A. K. was funded by CSIR-SRF fellowship, L.A. was funded through DST-INSPIRE fellowship, V.C was funded by DBT (BT/PR8699/MED/30/1018/2013).

1. Seeding MCF10A cells in lrECM
<ol>
	<li>Maintain MCF10A cells (adherent breast epithelial cells) in the growth medium. Passage the cells every 4 days. 
	NOTE: Composition of growth medium: high glucose DMEM without sodium pyruvate containing horse serum (5%), insulin (10 &#181;g/mL), hydrocortisone (0.5 &#181;g/mL), epidermal growth factor, EGF (20 ng/mL), of cholera toxin (100 ng/mL), and penicillin-streptomycin (100 units/mL) (see Table of Materials).</li>
	<li>Thaw lrECM (see Table of Materials) on ice 20 min before the start of the experiment. The day of seeding the cells is generally considered Day 0.</li>
	<li>For trypsinizing the cells, aspirate the medium, and wash with 2 mL of PBS. Add 900 &#181;L of 0.05% Trypsin-EDTA and incubate at 37 &#176;C for ~15 min or till the cells are completely trypsinized.</li>
	<li>Prepare a bed of lrECM in eight wells of a chambered cover glass slide (see Table of Materials).
	<ol>
		<li>When the cells are trypsinizing, coat each well with 60 &#181;L of lrECM and place it in a 37 &#176;C CO2 incubator for a maximum of 15 min.</li>
	</ol>
	</li>
	<li>Prepare the cell suspension following the steps below.
	<ol>
		<li>Following the complete dislodging of cells, add 5 mL of re-suspension medium to quench trypsin activity and spin the cells at 112 x g for 10 min at 25 &#176;C. 
		NOTE: Composition of re-suspension medium: high glucose DMEM without sodium pyruvate, supplemented with horse serum (20%) and penicillin-streptomycin (100 units/mL).</li>
		<li>Aspirate the spent medium and re-suspend the cells in 2 mL of assay medium. Mix the suspension well to ensure the formation of a single cell suspension. 
		NOTE: Composition of assay medium: high glucose DMEM without sodium pyruvate, supplemented with horse serum (2%), hydrocortisone (0.5 &#181;g/mL), cholera toxin (100 ng/mL), insulin (10 &#181;g/mL), and penicillin-streptomycin (100 units/mL).</li>
		<li>Count the cells using a hemocytometer and calculate the volume of cell suspension needed to seed 6 x 103 cells in each well. 
		NOTE: It is generally preferred to include one extra well in the calculation to account for any pipetting errors.</li>
		<li>According to the number of wells required, dilute the cell suspension in overlay medium. 
		NOTE: Overlay medium composition for a single well is as follows: 400 &#181;L of assay medium, 8 &#181;L of lrECM (2% final), and 0.02 &#181;L of 100 &#181;g/mL of EGF (5 ng/mL final).</li>
	</ol>
	</li>
	<li>Perform seeding of the cells.
	<ol>
		<li>Add 400 &#181;L of the diluted cell suspension to the prepared lrECM beds (step 1.4), carefully ensuring not to disturb the lrECM bed. Incubate at 37 &#176;C in a humidified 5% CO2 incubator.</li>
	</ol>
	</li>
</ol>
2. PAF treatment
<ol>
	<li>Add PAF 3 h following the seeding of cells. Prepare a 100 &#181;M stock of PAF in PBS and add the required volume of 0.2 &#181;L in each well (which corresponds to 200 nM).</li>
	<li>Add the same concentration of PAF during every media change.</li>
</ol>
3. Re-feeding with fresh media
<ol>
	<li>Replenish the cells with fresh medium every 4 days (i.e., Day 4, Day 8, Day 12, and Day 16).</li>
</ol>
4. Immunofluorescence study to detect phenotypic changes induced by prolonged PAF exposure
<ol>
	<li>After 20 days of culturing, carefully pipette out the medium from each well and wash the wells with 400 &#181;L of pre-warmed PBS.</li>
	<li>Fix the acinar structures by adding 400 &#181;L of 4% paraformaldehyde (freshly prepared by diluting 16% paraformaldehyde in 1x PBS) and incubating for 20 min at room temperature.</li>
	<li>Rinse the wells once with ice-cold PBS and permeabilize with PBS containing 0.5% Triton X-100 for 10 min at 4 &#176;C.</li>
	<li>After 10 min, immediately but carefully pipette out the Triton-X 100 solution and rinse with 400 &#181;L of PBS-glycine (freshly prepared by adding a pinch of glycine in 1x PBS). This is repeated thrice for 15 min each.</li>
	<li>Add 400 &#181;L of the primary blocking solution comprising 10% goat serum (see Table of Materials) in immunofluorescence (IF) buffer and incubate at room temperature for 60 min. 
	NOTE: Composition of IF buffer: 0.05% sodium azide, 0.1% BSA, 0.2% Triton-X 100, and 0.05% Tween (20 in 1 PBS).</li>
	<li>Remove the primary blocking solution, add 200 &#181;L of 2% secondary blocking antibody (F(ab&#39;)2 fragment of antibody raised in goat against mouse antigen, see Table of Materials) prepared in primary blocking solution, and leave it for 45-60 min at room temperature.</li>
	<li>Prepare the primary antibody (see Table of Materials) in 2% secondary blocking antibody solution in a 1:100 dilution. After removing the secondary blocking solution, add the freshly prepared antibody and incubate overnight at 4 &#176;C.</li>
	<li>The previous step may elicit liquefaction of the basement membrane. Before proceeding with the experiment, wait until the slide reaches room temperature. Carefully pipette the primary antibody solution and wash it thrice with 400 &#181;L of IF buffer.</li>
	<li>During the last wash with IF buffer, prepare a 1:200 dilution of the fluorophore-conjugated secondary antibody (see Table of Materials) in the primary blocking solution. Incubate the slides in the secondary antibody solution for 40-60 min at room temperature.</li>
	<li>Rinse the slides with 400 &#181;L of IF buffer for 20 min, followed by two washes with PBS for 10 min each.</li>
	<li>Counter-stain the nuclei with PBS containing 0.5 ng/mL of nuclear stain (see Table of Materials) for 5-6 min at room temperature. Wash the slides thrice with 400 &#181;L of PBS to remove excess stain.</li>
	<li>Carefully pipette out the entire PBS and ensure removal of the residual solution. Add one drop of mounting reagent (see Table of Materials) into each well and allow it to stand at room temperature overnight.</li>
	<li>Store the slides at room temperature and image the slides as soon as possible.</li>
	<li>Image under 40x or 63x magnification on a confocal microscope (see Table of Materials), taking optical Z-sections of 0.6 mm step size (NA = 1.4).</li>
	<li>Open the acquired images with an image processing software (see Table of Materials). Demonstrate the morphological differences using 3D projections. 
	NOTE: The centermost optical Z-section can be best used to show differences in the localization of polarity markers. These can be quantified manually to represent the percentage of spheroids showing that specific staining pattern.</li>
	<li>To illustrate differences in the expression of proteins, perform a semi-quantitative analysis measuring the mean grey value or calculating corrected total cell fluorescence (CTCF)23. Represent the data as violin or dot plots.</li>
</ol>

The authors declare no potential conflicts of interest.

Established cell line-based models are widely used to study the process of carcinogenesis. Monolayer cultures of cells continue to provide insights into the various molecular signaling pathways that mediate characteristic changes in cancer cells32. Studies on the role of well-known oncogenes such as Ras, Myc, and mutated p53 were first reported using monolayer cultures as the model system33,34,35,</s...

A myriad of models are available to study the progression of cancer, each of them being unique and representing a subtype of this complex disease. Each model provides unique and valuable insights into cancer biology and has improved the means to mimic the actual disease condition. Established cell lines grown as a monolayer have provided valuable insights into vital processes in vitro, such as proliferation, invasiveness, migration, and apoptosis1. Though two-dimensional (2D) cell culture has been the traditional tool to investigate the response of mammalian cells to several environmental perturbations, extrapolation of these findings to predict tissue-level responses does not seem sufficiently convincing. The major limitation of the 2D cultures is that the microenvironment created differs largely from that of the breast tissue itself2. 2D culture lacks the interaction of the cells with the extracellular matrix, which is vital for the growth of any tissue. Also, tensile forces experienced by the cell in monolayer cultures hinder the polarity of these cells, thus altering cell signaling and behavior3,4,5. Three-dimensional (3D) culture systems have opened up a new avenue in the field of cancer research with their ability to mimic the in vivo conditions in vitro. Many crucial microenvironmental cues that are lost in 2D cell culture could be re-established using 3D cultures of laminin-rich extracellular matrix (lrECM)6.
Various studies have identified the importance of the tumor microenvironment in carcinogenesis7,8. Inflammation-associated factors are a major part of the microenvironment. Platelet Activating Factor (PAF) is a phospholipid mediator secreted by various immune cells that mediates multiple immune responses9,10. High levels of PAF are secreted by different breast cancer cell lines and are associated with enhanced proliferation11. Studies from our lab have shown that the prolonged presence of PAF in acinar cultures leads to the transformation of breast epithelial cells12. PAF activates the PAF receptor (PAFR), activating the PI3K/Akt signaling axis13. PAFR is also reported to be associated with EMT, invasion, and metastasis14.
The present protocol demonstrates a model system to study PAF-induced transformation, using 3D cultures of breast epithelial cells, as has been previously described by Chakravarty et al.12. The breast epithelial cells grown on the extracellular matrix (3D cultures) tend to form polarized growth-arrested spheroids. These are called acini and closely resemble the acini of breast tissue, the smallest functional unit of the mammary gland, in vivo15. These spheroids (Figure 1A,B) consist of a monolayer of closely packed polarized epithelial cells surrounding a hollow lumen and attached to the basement membrane (Figure 1C). This process of morphogenesis has been well described in literature16. When seeded on lrECM, the cells undergo division and differentiation to form a cluster of cells, which then polarize from Day 4 onwards. By Day 8, the acini consist of a group of polarized cells that are in direct contact with the extracellular matrix and a cluster of unpolarized cells enclosed within the outer polarized cells, with no contact to the matrix. These unpolarized cells are known to undergo apoptosis by Day 12 of culture, forming a hollow lumen. By Day 16, growth-arrested structures are formed16.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/64146/64146fig01.jpg" /> 
Figure 1: Nuclei of cells in acini stained with a nuclear stain. (A) 3D construction of the acini. (B)&#160;Phase Contrast image of MCF10A acini grown on Matrigel for 20 days. (C) The centermost section shows the presence of a hollow lumen. Scale bar = 20 &#181;m. <a href="https://www.jove.com/files/ftp_upload/64146/64146fig01large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
Unlike 2D cultures, acinar cultures aid in distinguishing normal and transformed cells through apparent morphology changes. Non-transformed breast epithelial cells form acini with a hollow lumen, mimicking the normal human breast acini. These spheroids, upon transformation, show a disrupted morphology characterized by a major loss of polarity (one of the hallmarks of cancer), absence of a lumen, or disruption of the hollow lumen (due to evasion of apoptosis) that may be induced due to deregulation of various genes17,18,19,20. These transformations can be studied using commonly used techniques such as immunofluorescence. Thus, the 3D cell culture model can function as a simple method to investigate the process of breast acinar morphogenesis and breast carcinogenesis. Establishing a 3D culture system to understand the effect of a phospholipid mediator, PAF, will assist in high throughput preclinical drug screening.
This work has adapted the 3D &#39;on top&#39; culture protocol16,21 for studying transformation induced by PAF22. The phenotypic changes induced by exposure of the acini to the phospholipid mediator were studied using immunofluorescence. Various polarity and epithelial to mesenchymal transition (EMT) markers12,16 were used in the study. Table 1 mentions their normal localization and their expected phenotype upon transformation.
<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Antibodies</td>
			<td>Marks</td>
			<td>Normal localization</td>
			<td>Transformed phenotype</td>
		</tr>
		<tr>
			<td>&#945;6-Integrin</td>
			<td>Basolateral</td>
			<td>Basal with weak lateral stain</td>
			<td>Strong lateral / Apical stain</td>
		</tr>
		<tr>
			<td>&#946;-Catenin</td>
			<td>Cell-cell junction</td>
			<td>Basolateral</td>
			<td>Abnormal / nuclear or cytoplasmic localization</td>
		</tr>
		<tr>
			<td>Vimentin</td>
			<td>EMT</td>
			<td>Absent / weak presence</td>
			<td>Up-regulation</td>
		</tr>
	</tbody>
</table>
Table 1: Markers used in the study. Different markers used with their localization in the presence and absence of PAF treatment.
This method can be best utilized to study/screen plausible drugs and target genes for various breast cancer subtypes. This can provide a drug response data closer to the in vivo scenario, aiding in faster and more reliable drug development. Also, this system can be used to study the molecular signaling associated with drug response and drug resistance.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>0.05% Trypsin EDTA</td>
			<td>Invitrogen</td>
			<td>25300062</td>
			<td></td>
		</tr>
		<tr>
			<td>16% paraformaldehyde</td>
			<td>Alfa Aesar</td>
			<td>AA433689M</td>
			<td></td>
		</tr>
		<tr>
			<td>Anti Mouse Alexa Flour 488</td>
			<td>Invitrogen</td>
			<td>A11029</td>
			<td></td>
		</tr>
		<tr>
			<td>Anti Rabbit Alexa Flour 488</td>
			<td>Invitrogen</td>
			<td>A-11008</td>
			<td></td>
		</tr>
		<tr>
			<td>BSA</td>
			<td>Sigma</td>
			<td>A7030</td>
			<td></td>
		</tr>
		<tr>
			<td>Chamber Coverglass</td>
			<td>Nunc</td>
			<td>155409</td>
			<td></td>
		</tr>
		<tr>
			<td>Cholera Toxin</td>
			<td>Sigma</td>
			<td>C8052-1MG</td>
			<td>1 mg/mL in dH2O</td>
		</tr>
		<tr>
			<td>Confocal Microscope</td>
			<td>Leica</td>
			<td>Leica SP8</td>
			<td></td>
		</tr>
		<tr>
			<td>DMEM</td>
			<td>Gibco</td>
			<td>11965126</td>
			<td></td>
		</tr>
		<tr>
			<td>EDTA</td>
			<td>Sigma</td>
			<td>E6758</td>
			<td></td>
		</tr>
		<tr>
			<td>EGF</td>
			<td>Sigma</td>
			<td>E9644-0.2MG</td>
			<td>100 mg/mL in dH2O</td>
		</tr>
		<tr>
			<td>F(ab&#8217;)2 fragment of antibody raised in goat against mouse antigen</td>
			<td>Jackson Immunoresearch</td>
			<td>115-006-006</td>
			<td></td>
		</tr>
		<tr>
			<td>GM130 antibody</td>
			<td>Abcam</td>
			<td>ab52649</td>
			<td></td>
		</tr>
		<tr>
			<td>Goat Serum</td>
			<td>Abcam</td>
			<td>ab7481</td>
			<td></td>
		</tr>
		<tr>
			<td>Hoechst</td>
			<td>Invitrogen</td>
			<td>33258</td>
			<td></td>
		</tr>
		<tr>
			<td>Horse Serum</td>
			<td>Gibco</td>
			<td>16050122</td>
			<td></td>
		</tr>
		<tr>
			<td>Hydrocortisone</td>
			<td>Sigma</td>
			<td>H0888</td>
			<td>1 mg/mL in ethanol</td>
		</tr>
		<tr>
			<td>Image Processing Software</td>
			<td>ImageJ</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Insulin</td>
			<td>Sigma</td>
			<td>I1882</td>
			<td>10 mg/mL stock dH2O</td>
		</tr>
		<tr>
			<td>lrECM (Matrigel)</td>
			<td>Corning</td>
			<td>356231</td>
			<td></td>
		</tr>
		<tr>
			<td>Mounting reagent (Slow fade Gold Anti-fade)</td>
			<td>Invitrogen</td>
			<td>S36937</td>
			<td></td>
		</tr>
		<tr>
			<td>Nuclear Stain&#160; (Hoechst)</td>
			<td>Invitrogen</td>
			<td>33258</td>
			<td></td>
		</tr>
		<tr>
			<td>PAF</td>
			<td>Cayman Chemicals</td>
			<td>91575-58-5</td>
			<td>Methylcarbamyl PAF C-16, procured as a 10 mg/mL in ethanol</td>
		</tr>
		<tr>
			<td>Penicillin-Streptomycin</td>
			<td>Lonza</td>
			<td>17-602E</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium Azide</td>
			<td>Sigma</td>
			<td>S2002</td>
			<td></td>
		</tr>
		<tr>
			<td>Tris Base</td>
			<td>Sigma</td>
			<td>B9754</td>
			<td></td>
		</tr>
		<tr>
			<td>Triton X-100</td>
			<td>Sigma</td>
			<td>T8787</td>
			<td></td>
		</tr>
		<tr>
			<td>Tween 20</td>
			<td>Sigma</td>
			<td>P9416</td>
			<td></td>
		</tr>
		<tr>
			<td>Vimentin antibody</td>
			<td>Abcam</td>
			<td>ab92547</td>
			<td></td>
		</tr>
		<tr>
			<td>&#945;6-integrin antibody</td>
			<td>Millipore</td>
			<td>MAB1378</td>
			<td></td>
		</tr>
	</tbody>
</table>

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.

MCF10A cells, upon exposure to PAF treatment, form acinar structures with very distinct phenotypes. &#945;6-integrin was found to be mislocalized with more apical staining. A few acini also showed discontinuous staining (Figure 2A). Both these phenotypes indicate the loss of basal polarity, as evidenced from literature24,25. Earlier reports indicate the controversial role of &#945;6-integrin in cancer metastasis. &#945;6-integrin is ...

Watch this Scientific Journal Video about Phospholipid Mediator Induced Transformation in Three-Dimensional Cultures at JoVE.com

Phospholipid Mediator Induced Transformation in Three-Dimensional Cultures

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 ...

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Cancer Research

2.3K Views.  Indian Institute of Science Education and Research. 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.

Video: Phospholipid Mediator Induced Transformation in Three-Dimensional Cultures

Moving Upwards: A Simple and Flexible In Vitro Three-dimensional Invasion Assay Protocol

Although 3D invasion assays have been developed, the challenge remains to study cells without affecting the integrity of their microenvironment. Traditional 3D assays such as the Boyden Chamber require that cells are displaced from the original culture location and moved to a new environment. Not only does this disrupt the cellular processes that are intrinsic to the microenvironment, but it often results in a loss of cells. These problems are especially challenging when dealing with cells that are either rare, or extremely sensitive to their microenvironment. Here, we describe the development of a 3D invasion assay that avoids both concerns. In this assay, cells are plated within a small well and an ECM matrix containing a chemoattractant is laid atop the cells. This requires no cell displacement, and allows the cells to invade upwards into the matrix. In this assay, cell invasion as well as cell morphology can be assessed within the collagen gel. Using this assay, we characterize the invasive capacity of rare and sensitive cells; the hybrid cells resulting from fusion between breast cancer cells MCF7 and mesenchymal/multipotent stem/stroma cells (MSCs).

Moving Upwards: A Simple and Flexible In Vitro Three-dimensional Invasion Assay Protocol

This protocol describes an inverted vertical invasion assay that could be used to quantify the migration and invasion capabilities of cells in a three-dimensional setting while preserving the cell microenvironment. This assay is suitable for rare and/or sensitive cells.

Although 3D invasion assays have been developed, the challenge remains to study cells without affecting the integrity of their microenvironment. ...

Generation of High-Throughput Three-Dimensional Tumor Spheroids for Drug Screening

Cancer cells have routinely been cultured in two dimensions (2D) on a plastic surface. This technique, however, lacks the true environment a tumor mass is exposed to in vivo. Solid tumors grow not as a sheet attached to plastic, but instead as a collection of clonal cells in a three-dimensional (3D) space interacting with their neighbors, and with distinct spatial properties such as the disruption of normal cellular polarity. These interactions cause 3D-cultured cells to acquire morphological and cellular characteristics which are more relevant to in vivo tumors. Additionally, a tumor mass is in direct contact with other cell types such as stromal and immune cells, as well as the extracellular matrix from all other cell types. The matrix deposited is comprised of macromolecules such as collagen and fibronectin.
In an attempt to increase the translation of research findings in oncology from bench to bedside, many groups have started to investigate the use of 3D model systems in their drug development strategies. These systems are thought to be more physiologically relevant because they attempt to recapitulate the complex and heterogeneous environment of a tumor. These systems, however, can be quite complex, and, although amenable to growth in 96-well formats, and some now even in 384, they offer few choices for large-scale growth and screening. This observed gap has led to the development of the methods described here in detail to culture tumor spheroids in a high-throughput capacity in 1536-well plates. These methods represent a compromise to the highly complex matrix-based systems, which are difficult to screen, and conventional 2D assays. A variety of cancer cell lines harboring different genetic mutations are successfully screened, examining compound efficacy by using a curated library of compounds targeting the Mitogen-Activated Protein Kinase or MAPK pathway. The spheroid culture responses are then compared to the response of cells grown in 2D, and differential activities are reported. These methods provide a unique protocol for testing compound activity in a high-throughput 3D setting.

Across a wide variety of disease indications, more physiologically relevant models are being developed and implemented into drug discovery programs. The new model system described here demonstrates how three-dimensional tumor spheroids can be cultured and screened in a high-throughput 1536-well plate-based system to search for new oncology drugs.

Cancer cells have routinely been cultured in two dimensions (2D) on a plastic surface. This technique, however, lacks the true environment a tumor mass is ...

A Three-dimensional Thymic Culture System to Generate Murine Induced Pluripotent Stem Cell-derived Tumor Antigen-specific Thymic Emigrants

The inheritance of pre-rearranged T cell receptors (TCRs) and their epigenetic rejuvenation make induced pluripotent stem cell (iPSC)-derived T cells a promising source for adoptive T cell therapy (ACT). However, classical in vitro methods for producing regenerated T cells from iPSC result in either innate-like or terminally differentiated T cells, which are phenotypically and functionally distinct from na&#239;ve T cells. Recently, a novel three-dimensional (3D) thymic culture system was developed to generate a homogenous subset of CD8&#945;&#946;+ antigen-specific T cells with a na&#239;ve T cell-like functional phenotype, including the capacity for proliferation, memory formation, and tumor suppression in vivo. This protocol avoids aberrant developmental fates, allowing for the generation of clinically relevant iPSC-derived T cells, designated as iPSC-derived thymic emigrants (iTE), while also providing a potent tool to elucidate the subsequent functions necessary for T cell maturation after thymic selection.

This article describes a novel method to generate tumor antigen-specific induced pluripotent stem cell-derived thymic emigrants (iTE) by a three-dimensional (3D) thymic culture system. iTE are a homogenous subset of T cells closely related to na&#239;ve T cells with the capacity for proliferation, memory formation, and tumor suppression.

The inheritance of pre-rearranged T cell receptors (TCRs) and their epigenetic rejuvenation make induced pluripotent stem cell (iPSC)-derived T cells a ...

Three-Dimensional Bone Extracellular Matrix Model for Osteosarcoma

Osteosarcoma (OS) is the most common and a highly aggressive primary bone tumor. It is characterized with anatomic and histologic variations along with diagnostic or prognostic difficulties. OS comprises genotypically and phenotypically heterogeneous cancer cells. Bone microenvironment elements are proved to account for tumor heterogeneity and disease progression. Bone extracellular matrix (BEM) retains the microstructural matrices and biochemical components of native extracellular matrix. This tissue-specific niche provides a favorable and long-term scaffold for OS cell seeding and proliferation. This article provides a protocol for the preparation of BEM model and its further experimental application. OS cells can grow and differentiate into multiple phenotypes consistent with the histopathological complexity of OS clinical specimens. The model also allows visualization of diverse morphologies and their association with genetic alterations and underlying regulatory mechanisms. As homologous to human OS, this BEM-OS model can be developed and applied to the pathology and clinical research of OS.

The bone extracellular matrix (BEM) model for osteosarcoma (OS) is well established and shown here. It can be used as a suitable scaffold for mimicking primary tumor growth in vitro and providing an ideal model for studying the histologic and cytogenic heterogeneity of OS.

Osteosarcoma (OS) is the most common and a highly aggressive primary bone tumor. It is characterized with anatomic and histologic variations along with ...

Fully Human Tumor-based Matrix in Three-dimensional Spheroid Invasion Assay

Two-dimensional cell culture-based assays are commonly used in in vitro cancer research. However, they lack several basic elements that form the tumor microenvironment. To obtain more reliable in vitro results, several three-dimensional (3D) cell culture assays have been introduced. These assays allow cancer cells to interact with the extracellular matrix. This interaction affects cell behavior, such as proliferation and invasion, as well as cell morphology. Additionally, this interaction could induce or suppress the expression of several pro- and anti-tumorigenic molecules. Spheroid invasion assay was developed to provide a suitable 3D in vitro method to study cancer cell invasion. Currently, animal-derived matrices, such as mouse sarcoma-derived matrix (MSDM) and rat tail type I collagen, are mainly used in the spheroid invasion assays. Taking into consideration the differences between the human tumor microenvironment and animal-derived matrices, a human myoma-derived matrix (HMDM) was developed from benign uterus leiomyoma tissue. It has been shown that HMDM induces migration and invasion of carcinoma cells better than MSDM. This protocol provided a simple, reproducible, and reliable 3D human tumor-based spheroid invasion assay using the HMDM/fibrin matrix. It also includes detailed instructions on imaging and analysis. The spheroids grow in a U-shaped ultra-low attachment plate within the HMDM/fibrin matrix and invade through it. The invasion is daily imaged, measured, and analyzed using ilastik and Fiji ImageJ software. The assay platform was demonstrated using human laryngeal primary and metastatic squamous cell carcinoma cell lines. However, the protocol is suitable also for other solid cancer cell lines.

Tumor microenvironment is an essential part of cancer growth and invasion. To mimic carcinoma progression, a biologically relevant human matrix is needed. This protocol introduces an improvement for the in vitro three-dimensional spheroid invasion assay by applying a human leiomyoma-based matrix. The protocol also introduces a computer-based cell invasion analysis.

Two-dimensional cell culture-based assays are commonly used in in vitro cancer research. However, they lack several basic elements that form the tumor ...

Evaluating Cell Death Using Cell-Free Supernatant of Probiotics in Three-Dimensional Spheroid Cultures of Colorectal Cancer Cells

This manuscript describes a protocol to evaluate cancer cell deaths in three dimensional (3D) spheroids of multicellular types of cancer cells using supernatants from Lactobacillus fermentum cell culture, considered as probiotics cultures. The use of 3D cultures to test Lactobacillus cell-free supernatant (LCFS) are a better option than testing in 2D monolayers, especially as L. fermentum can produce anti-cancer effects within the gut. L. fermentum supernatant was identified to possess increased anti-proliferative effects against several colorectal cancer (CRC) cells in 3D culture conditions. Interestingly, these effects were strongly related to the culture model, demonstrating the notable ability of L. fermentum to induce cancer cell death. Stable spheroids were generated from diverse CRCs (colorectal cancer cells) using the protocol presented below. This protocol of generating 3D spheroid is time saving and cost effective. This system was developed to easily investigate the anti-cancer effects of LCFS in multiple types of CRC spheroids. As expected, CRC spheroids treated with LCFS strongly induced cell death during the experiment and expressed specific apoptosis molecular markers as analyzed by qRT-PCR, western blotting, and FACS analysis. Therefore, this method is valuable for exploring cell viability and evaluating the efficacy of anti-cancer drugs.

Here methods are presented to understand anti-cancer effects of Lactobacillus cell-free supernatant (LCFS). Colorectal cancer cell lines show cell deaths when treated with LCFS in 3D cultures. The process of generating spheroids can be optimized depending on the scaffold and the analysis methods presented are useful for evaluating the involved signaling pathways.

This manuscript describes a protocol to evaluate cancer cell deaths in three dimensional (3D) spheroids of multicellular types of cancer cells using ...

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 Model of Spheroids to Study Colon Cancer Stem Cells

Colorectal cancers are characterized by heterogeneity and a hierarchical organization comprising a population of cancer stem cells (CSCs) responsible for tumor development, maintenance, and resistance to drugs. A better understanding of CSC properties for their specific targeting is, therefore, a pre-requisite for effective therapy. However, there is a paucity of suitable preclinical models for in-depth investigations. Although in vitro two-dimensional (2D) cancer cell lines provide valuable insights into tumor biology, they do not replicate the phenotypic and genetic tumor heterogeneity. In contrast, three-dimensional (3D) models address and reproduce near-physiological cancer complexity and cell heterogeneity. The aim of this work was to design a robust and reproducible 3D culture system to study CSC biology. The present methodology describes the development and optimization of conditions to generate 3D spheroids, which are homogenous in size, from Caco2 colon adenocarcinoma cells, a model that can be used for long-term culture. Importantly, within the spheroids, the cells which were organized around lumen-like structures, were characterized by differential cell proliferation patterns and by the presence of CSCs expressing a panel of markers. These results provide the first proof-of-concept for the appropriateness of this 3D approach to study cell heterogeneity and CSC biology, including the response to chemotherapy.

This protocol presents a novel, robust, and reproducible culture system to generate and grow three-dimensional spheroids from Caco2 colon adenocarcinoma cells. The results provide the first proof-of-concept for the appropriateness of this approach to study cancer stem cell biology, including the response to chemotherapy.

Colorectal cancers are characterized by heterogeneity and a hierarchical organization comprising a population of cancer stem cells (CSCs) responsible for ...

Three-Dimensional In Vitro Biomimetic Model of Neuroblastoma Using Collagen-Based Scaffolds

Neuroblastoma is the most common extracranial solid tumor in children, accounting for 15% of overall pediatric cancer deaths. The native tumor tissue is a complex three-dimensional (3D) microenvironment involving layers of cancerous and non-cancerous cells surrounded by an extracellular matrix (ECM). The ECM provides physical and biological support and contributes to disease progression, patient prognosis, and therapeutic response.
This paper describes a protocol for assembling a 3D scaffold-based system to mimic the neuroblastoma microenvironment using neuroblastoma cell lines and collagen-based scaffolds. The scaffolds are supplemented with either nanohydroxyapatite (nHA) or glycosaminoglycans (GAGs), naturally found at high concentrations in the bone and bone marrow, the most common metastatic sites of neuroblastoma. The 3D porous structure of these scaffolds allows neuroblastoma cell attachment, proliferation and migration, and the formation of cell clusters. In this 3D matrix, the cell response to therapeutics is more reflective of the in vivo situation.
The scaffold-based culture system can maintain higher cell densities than conventional two-dimensional (2D) cell culture. Therefore, optimization protocols for initial seeding cell numbers are dependent on the desired experimental timeframes. The model is monitored by assessing cell growth via DNA quantification, cell viability via metabolic assays, and cell distribution within the scaffolds via histological staining.
This model&#39;s applications include the assessment of gene and protein expression profiles as well as cytotoxicity testing using conventional drugs and miRNAs. The 3D culture system allows for the precise manipulation of cell and ECM components, creating an environment more physiologically similar to native tumor tissue. Therefore, this 3D in vitro model will advance the understanding of the disease pathogenesis and improve the correlation between results obtained in vitro, in vivo in&#160;animal models, and human subjects.

Three-Dimensional In Vitro Biomimetic Model of Neuroblastoma Using Collagen-Based Scaffolds

This paper lists the steps required to seed neuroblastoma cell lines on previously described three-dimensional collagen-based scaffolds, maintain cell growth for a predetermined timeframe, and retrieve scaffolds for several cell growth and cell behavior analyses and downstream applications, adaptable to satisfy a range of experimental aims.

Neuroblastoma is the most common extracranial solid tumor in children, accounting for 15% of overall pediatric cancer deaths. The native tumor tissue is a ...

A Three-Dimensional Spheroid Model to Investigate the Tumor-Stromal Interaction in Hepatocellular Carcinoma

The aggressiveness and lack of well-tolerated and widely effective treatments for advanced hepatocellular carcinoma (HCC), the predominant form of liver cancer, rationalize its rank as the second most common cause of cancer-related death. Preclinical models need to be adapted to recapitulate the human conditions to select the best therapeutic candidates for clinical development and aid the delivery of personalized medicine. Three-dimensional (3D) cellular spheroid models show promise as an emerging in vitro alternative to two-dimensional (2D) monolayer cultures. Here, we describe a 3D tumor spheroid&#160;model which exploits the ability of individual cells to aggregate when maintained in hanging droplets, and is more representative of an in vivo environment than standard monolayers. Furthermore, 3D spheroids can be produced by combining homotypic or heterotypic cells, more reflective of the cellular heterogeneity in vivo, potentially enabling the study of environmental interactions that can influence progression and treatment responses. The current research optimized the cell density to form 3D homotypic and heterotypic tumor spheroids by immobilizing cell suspensions on the lids of standard 10 cm3 Petri dishes. Longitudinal analysis was performed to generate growth curves for homotypic versus heterotypic tumor/fibroblasts spheroids. Finally, the proliferative impact of fibroblasts (COS7 cells) and liver myofibroblasts (LX2) on homotypic tumor (Hep3B) spheroids was investigated. A seeding density of 3,000 cells (in 20 &#181;L media) successfully yielded Huh7/COS7 heterotypic spheroids, which displayed a steady increase in size up to culture day 8, followed by growth retardation. This finding was corroborated using Hep3B homotypic spheroids cultured in LX2 (human hepatic stellate cell line) conditioned medium (CM). LX2 CM triggered the proliferation of Hep3B spheroids compared to control tumor spheroids. In conclusion, this protocol has shown that 3D tumor spheroids can be used as a simple, economical, and prescreen in vitro tool to study tumor-stromal interactions more comprehensively.

Comprehensive in vitro models that faithfully recapitulate the relevant human disease are lacking. The current study presents three-dimensional (3D) tumor spheroid creation and culture, a reliable in vitro tool to study the tumor-stromal interaction in human hepatocellular carcinoma.

The aggressiveness and lack of well-tolerated and widely effective treatments for advanced hepatocellular carcinoma (HCC), the predominant form of liver ...