Name: generation and quantitative characterization of functional and polarized biliary epithelial cysts
Uploaded: 2020-05-16T15:00:00
Description: Watch this Scientific Journal Video about Generation and Quantitative Characterization of Functional and Polarized Biliary Epithelial Cysts at JoVE.com

We thank Dr. Nicholas LaRusso (Mayo Clinic, Rochester, Minnesota, United States), who kindly provided the NRC cell line.
This work received the financial support of both the iLite RHU program (grant ANR-16-RHUS-0005) and the DHU Hepatinov.
We thank Isabelle Garcin and R&#233;seau d&#8217;Imagerie Cellulaire Paris Saclay for their support on imaging.

1. Generation of cysts
NOTE: This protocol can be performed with any type of hydrogel, if the gelation allows embedding of cells.
<ol>
	<li>Hydrogel coating 
	NOTE: Proper hydrogel coating of the chamber slide is a critical step to avoid the formation of 2D cell layers on the bottom of the well, that might interfere with subsequent cyst imaging and impair the calculation of cyst formation efficiency.
	<ol>
		<li>To ensure homogeneity of the gel solution, thaw the hydrogel at 4 &#176;C o...

<ol>
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In order to study organogenesis and maintenance of 3D cellular structures, various tissues have been modelled, using different cellular origins but also different types of extra-cellular matrices including synthetic hydrogels8,9,10,21. However, due to lack of 3D quantitative analysis that allows for comparisons between methods in terms of organoids formation or functionality7<...

In the last three decades, the field of in vitro research has advanced towards 3D culture systems. A number of protocols have emerged for culturing cells in 3D as spheroids or aggregates in the presence or absence of a scaffold/matrix, in a drop, in agitation, in microfluidic devices, or floating1. The use of 3D culture methods has proved its advantages over 2-dimensional (2D) cultures, particularly for epithelial cells, which were shown to self-organize in 3D structures, called cysts or acini. In this case, the cells form a monolayer encircling a lumen, where cells acquire their full epithelial phenotype with improved physiological specific functions2.
Numerous studies have contributed to the development of methods for forming these epithelial organoids in natural matrices. This has allowed to recapitulate in vivo cell-cell and cell-microenvironment interactions, to get the establishment and the stability of the epithelial phenotype3,4,5,6,7. Recently, and in particular with the aim of developing transplantable organoids and deciphering the requirement of the microenvironment for orchestrating the epithelial program, synthetic hydrogels have been developed to enhance the formation of epithelial acini8,9,10. Unfortunately, these studies report on qualitative data, or present calculation methods using internal references such as the ratio of cysts over non-cysts in a 2D plane8,9,10. This precludes any comparison between different studies in terms of efficiency, stability, or morphological and physiological characterization of the epithelial organoids.
Microencapsulation of epithelial cells in beads using microfluidic devices has allowed for more realistic quantitative and comparative results. Using this technology, organoids from various cell types were formed and differentiated based on the morphology among different 3D cellular structures11,12. However, this technology is not easy to work with and requires the use of clean rooms to produce the microfluidic devices. This technology has been established for a few types of hydrogels but requires technical adaptation to be applied to other hydrogels, restricting its versatility. Therefore, most studies intended to develop epithelial organoids rely on the embedding of epithelial cells in a hydrogel bulk. In these methods, the high heterogeneity of gel structuration and cell distribution inside the whole 3D culture is often neglected. Therefore, most of the analyses relate to single 2D images, which represent only very roughly the distribution of the various cellular objects in the whole 3D volume.
Diseases that affect bile ducts, such as cholangiocarcinoma, biliary atresia, primary sclerosing cholangitis, among others, are a major cause of mortality and morbidity. Except for liver transplantation, there are no effective treatments for these conditions13. Efforts to investigate bile duct formation, disease causes, and progression will allow the development of novel therapies14.
Biliary organotypic models of cysts, spheroids or tube-like structures using normal or patient-derived, differentiated, or progenitor-derived cholangiocyte cell lines have been developed15,16,17,18,19,20. Various studies have recapitulated cholangiocyte polarity, expression of cholangiocyte markers, presence of cilia, cholangiocyte secretory and reabsorptive ability, and lumen formation and obstruction; all of which represent important characteristics of cholangiocyte phenotype, morphology, and function15,17,19. Others have reported maintenance of patient-derived biliary organoids for long periods of time20. Recently, we investigated the role of biochemical and biophysical cues on biliary cysts organogenesis21. Importantly, the pathogenesis of biliary atresia was studied in biliary spheroids and tubes7,22. Furthermore, key features of primary sclerosing cholangitis such as cholangiocyte senescence, secretion of pro-inflammatory cytokines, as well as macrophage recruitment were successfully studied using biliary spheroids15,20. However, reproducible in vitro 3D quantitative models that physiologically modulate cholangiocyte phenotype, physiology, and microenvironment where these questions can be addressed are still needed. Moreover, only few publications have reported cyst formation efficiency21,23. This is an important point to establish, particularly when investigating organogenesis, disease cause, and correlation of drug responses with cholangiocyte function and polarization. In addition, with differences in scaffold/matrix used from protocol to protocol, it is difficult to compare between systems. To solve these issues, we propose a quantitative, reliable, and universal method to generate biliary cysts mimicking lumen formation, cholangiocyte polarization, and cholangiocyte secretory function. Importantly, we present a systematic analysis performed along the Z-axis across the 3D gel when evaluating over time, cyst formation efficiency, size, viability, polarization, and functionality. Furthermore, we used a natural hydrogel and normal rat cholangiocytes (NRC)s, as an example for the protocol, but other natural or synthetic hydrogels, as well as epithelial cells could be used for the formation of 3D cystic structures.

<table border="0" cellpadding="0" cellspacing="0" style="width:1005px;" width="1005">
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			<td dir="LTR" height="21" style="height:21px;width:408px;">10 &#181;l- Pipette Eppendorf Research Plus</td>
			<td dir="LTR" style="width:180px;">Thermo Fisher Scientific</td>
			<td dir="LTR" style="width:156px;">3120000020</td>
			<td style="width:261px;"></td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">100 &#181;l - Pipette Eppendorf Research Plus</td>
			<td dir="LTR" style="width:180px;">Thermo Fisher Scientific</td>
			<td dir="LTR" style="width:156px;">3120000046</td>
			<td></td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">1000 &#181;l - Pipette Eppendorf Research Plus</td>
			<td dir="LTR" style="width:180px;">Thermo Fisher Scientific</td>
			<td dir="LTR" style="width:156px;">3120000062</td>
			<td></td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">1X PBS</td>
			<td dir="LTR" style="width:180px;">Thermo Fisher Scientific</td>
			<td dir="LTR" style="width:156px;">14190-094</td>
			<td style="width:261px;"></td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">200 &#181;l - Pipette Eppendorf Research Plus</td>
			<td dir="LTR" style="width:180px;">Thermo Fisher Scientific</td>
			<td dir="LTR" style="width:156px;">3120000054</td>
			<td></td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">3,3&#8242;,5-Triiodo-L-thyronine sodium salt</td>
			<td dir="LTR" style="width:180px;">Sigma-Aldrich</td>
			<td dir="LTR" style="width:156px;">T5516</td>
			<td>NRC complete medium final concentration = 3.4 &#181;g/mL</td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">Acetic acid</td>
			<td dir="LTR" style="width:180px;">VWR</td>
			<td dir="LTR" style="width:156px;">20104-298</td>
			<td>0.02N final</td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">Aerosol barrier pipettes tips 10 &#181;l (Fisherbrand)</td>
			<td dir="LTR" style="width:180px;">Thermo Fisher Scientific</td>
			<td dir="LTR" style="width:156px;">2707439</td>
			<td style="width:261px;"></td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">Aerosol barrier pipettes tips 1000 &#181;l (Fisherbrand)</td>
			<td dir="LTR" style="width:180px;">Thermo Fisher Scientific</td>
			<td dir="LTR" style="width:156px;">2707404</td>
			<td style="width:261px;"></td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">Aerosol barrier pipettes tips 200 &#181;l (Fisherbrand)</td>
			<td dir="LTR" style="width:180px;">Thermo Fisher Scientific</td>
			<td dir="LTR" style="width:156px;">2707430</td>
			<td style="width:261px;"></td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">Antibiotic Antimicotic Solution (100X)</td>
			<td dir="LTR" style="width:180px;">Sigma-Aldrich</td>
			<td dir="LTR" style="width:156px;">A5955</td>
			<td>NRC complete medium final concentration = 1:100 dilution</td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">Bovine pituitary extract</td>
			<td dir="LTR" style="width:180px;">Thermo Fisher Scientific</td>
			<td dir="LTR" style="width:156px;">13028-014</td>
			<td>NRC complete medium final concentration = 30 &#181;g/mL</td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">Bovine serum albumin</td>
			<td dir="LTR" style="width:180px;">Sigma-Aldrich</td>
			<td dir="LTR" style="width:156px;">A2153</td>
			<td style="width:261px;">1:1000 dilution</td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">Chemically Defined Lipid Concentrate (100X)</td>
			<td dir="LTR" style="width:180px;">Thermo Fisher Scientific</td>
			<td dir="LTR" style="width:156px;">11905-031</td>
			<td>NRC complete medium final concentration = 1:100 dilution</td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">Collagen high concentration, rat tail</td>
			<td dir="LTR" style="width:180px;">Thermo Fisher Scientific</td>
			<td dir="LTR" style="width:156px;">354249</td>
			<td dir="LTR" style="width:261px;">50 &#181;g/mL final concentration</td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">Dexamethasone</td>
			<td dir="LTR" style="width:180px;">Sigma-Aldrich</td>
			<td dir="LTR" style="width:156px;">D4902</td>
			<td>NRC complete medium final concentration = 0.393 &#181;g/mL</td>
		</tr>
		<tr height="42">
			<td dir="LTR" height="42" style="height:42px;width:408px;">DMEM F12</td>
			<td dir="LTR" style="width:180px;">Thermo Fisher Scientific</td>
			<td dir="LTR" style="width:156px;">21331-020</td>
			<td style="width:261px;">NRC complete medium final concentration = 1X</td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">E-cadherin Rabbit anti-Human, Rat, Polyclonal</td>
			<td dir="LTR" style="width:180px;">Thermo Fisher Scientific</td>
			<td dir="LTR" style="width:156px;">PA5-32178</td>
			<td dir="LTR" style="width:261px;">1:400 dilution</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:22px;width:408px;">Eclipse TE300 inverted microscope</td>
			<td style="width:180px;">Nikon</td>
			<td style="width:156px;"></td>
			<td>imaging</td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">Ethanolamine</td>
			<td dir="LTR" style="width:180px;">Sigma-Aldrich</td>
			<td dir="LTR" style="width:156px;">E9508</td>
			<td>NRC complete medium final concentration = 0.32 mM</td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">Fetal calf serum</td>
			<td dir="LTR" style="width:180px;">Thermo Fisher Scientific</td>
			<td dir="LTR" style="width:156px;">10270-106</td>
			<td>NRC complete medium final concentration = 5:100 dilution</td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">Fluoroshield with DAPI (Mounting medium)</td>
			<td dir="LTR" style="width:180px;">Sigma-Aldrich</td>
			<td dir="LTR" style="width:156px;">F6057</td>
			<td style="width:261px;"></td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">Formaldehyde 16% (W/V)</td>
			<td dir="LTR" style="width:180px;">Thermo Fisher Scientific</td>
			<td dir="LTR" style="width:156px;">28906</td>
			<td>4% (W/V)</td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">Goat serum</td>
			<td dir="LTR" style="width:180px;">Thermo Fisher Scientific</td>
			<td dir="LTR" style="width:156px;">16210-064</td>
			<td style="width:261px;">1:10 dilution</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:408px;">Hamamatsu camera (Digital camera C11440 ORCA - flash 4.OLT)</td>
			<td style="width:180px;">Hamamatsu</td>
			<td style="width:156px;"></td>
			<td>imaging</td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">Hoechst 33258</td>
			<td dir="LTR" style="width:180px;">Sigma-Aldrich</td>
			<td dir="LTR" style="width:156px;">B1155</td>
			<td style="width:261px;">5 &#181;g/mL final concentration</td>
		</tr>
		<tr height="42">
			<td dir="LTR" height="42" style="height:42px;width:408px;">IgG (H+L) Highly Cross-Adsorbed Goat anti-Rabbit, Alexa Fluor Plus 647</td>
			<td dir="LTR" style="width:180px;">Thermo Fisher Scientific</td>
			<td dir="LTR" style="width:156px;">A32733</td>
			<td dir="LTR" style="width:261px;">1:500 dilution</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:408px;">ImageJ version 2.0.0-rc-69/1.52n</td>
			<td style="width:180px;"></td>
			<td style="width:156px;"></td>
			<td>Open source image processing software</td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">Insulin-Transferrin-Selenium (100X)</td>
			<td dir="LTR" style="width:180px;">Thermo Fisher Scientific</td>
			<td dir="LTR" style="width:156px;">51300-044</td>
			<td>NRC complete medium final concentration = 1:100 dilution</td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">L-Glutamine (100X)</td>
			<td dir="LTR" style="width:180px;">Thermo Fisher Scientific</td>
			<td dir="LTR" style="width:156px;">25030-024</td>
			<td>NRC complete medium final concentration = 1:100 dilution</td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">Matrigel GFR (stock concentration 9.7 mg/mL)</td>
			<td dir="LTR" style="width:180px;">Thermo Fisher Scientific</td>
			<td dir="LTR" style="width:156px;">356231</td>
			<td dir="LTR" style="width:261px;">4:10 dilution</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">NIS Elements software version 4.50.00</td>
			<td style="width:180px;">Nikon</td>
			<td style="width:156px;"></td>
			<td>image acquisition and display</td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">Non-Essential-Amino-Acids-Solution (100X)</td>
			<td dir="LTR" style="width:180px;">Thermo Fisher Scientific</td>
			<td dir="LTR" style="width:156px;">11140-035</td>
			<td>NRC complete medium final concentration = 1:100 dilution</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:408px;">Objective Plan Fluor 10X/0.30 Ph1 DL (&#8734;/1.2 WD 15.2)</td>
			<td style="width:180px;">Nikon</td>
			<td style="width:156px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">Prolong Gold Antifade Reagent</td>
			<td dir="LTR" style="width:180px;">Thermo Fisher Scientific</td>
			<td dir="LTR" style="width:156px;">P36931</td>
			<td></td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">Propidium Iodide (PI)</td>
			<td dir="LTR" style="width:180px;">Sigma-Aldrich</td>
			<td dir="LTR" style="width:156px;">P4170</td>
			<td>20 &#181;g/mL final concentration</td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">Rhodamine Phalloidin</td>
			<td dir="LTR" style="width:180px;">Thermo Fisher Scientific</td>
			<td dir="LTR" style="width:156px;">R415</td>
			<td dir="LTR" style="width:261px;">16.2 nM final concentration</td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">Sir-Actin / Verapamil kit</td>
			<td dir="LTR" style="width:180px;">Spirochrome</td>
			<td dir="LTR" style="width:156px;">SC001</td>
			<td dir="LTR" style="width:261px;">10 &#181;M final concentration</td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">Soybean trypsin inhibitor</td>
			<td dir="LTR" style="width:180px;">Thermo Fisher Scientific</td>
			<td dir="LTR" style="width:156px;">17075-029</td>
			<td>NRC complete medium final concentration = 50 &#181;g/mL</td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">Sterile cell strainer 40 &#181;m (Fisherbrand)</td>
			<td dir="LTR" style="width:180px;">Thermo Fisher Scientific</td>
			<td dir="LTR" style="width:156px;">22363547</td>
			<td></td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">Sterile pipettes 10 mL (Fisherbrand)</td>
			<td dir="LTR" style="width:180px;">Thermo Fisher Scientific</td>
			<td dir="LTR" style="width:156px;">1367811E</td>
			<td style="width:261px;"></td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">Sterile pipettes 5 mL (Fisherbrand)</td>
			<td dir="LTR" style="width:180px;">Thermo Fisher Scientific</td>
			<td dir="LTR" style="width:156px;">1367811D</td>
			<td style="width:261px;"></td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">Sterile tubes 1.5 mL (Fisherbrand)</td>
			<td dir="LTR" style="width:180px;">Thermo Fisher Scientific</td>
			<td dir="LTR" style="width:156px;">11926955</td>
			<td style="width:261px;"></td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">Sterile tubes 15 mL (Fisherbrand)</td>
			<td dir="LTR" style="width:180px;">Thermo Fisher Scientific</td>
			<td dir="LTR" style="width:156px;">7200886</td>
			<td style="width:261px;"></td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">Sterile tubes 50 mL (Fisherbrand)</td>
			<td dir="LTR" style="width:180px;">Thermo Fisher Scientific</td>
			<td dir="LTR" style="width:156px;">553913</td>
			<td style="width:261px;"></td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">Sucrose</td>
			<td dir="LTR" style="width:180px;">Sigma-Aldrich</td>
			<td dir="LTR" style="width:156px;">S0389</td>
			<td>5:100 dilution</td>
		</tr>
		<tr height="24">
			<td dir="LTR" height="24" style="height:24px;width:408px;">Tissue culture treated flask 25cm2 (Falcon)</td>
			<td dir="LTR" style="width:180px;">Thermo Fisher Scientific</td>
			<td dir="LTR" style="width:156px;">353108</td>
			<td style="width:261px;"></td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">Triton X-100</td>
			<td dir="LTR" style="width:180px;">Sigma-Aldrich</td>
			<td>T8787</td>
			<td>5:1000 dilution</td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">Trypsin-EDTA (0.05%) phenol red</td>
			<td dir="LTR" style="width:180px;">Thermo Fisher Scientific</td>
			<td dir="LTR" style="width:156px;">25300-054</td>
			<td>1X</td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">Tween-20</td>
			<td dir="LTR" style="width:180px;">Sigma-Aldrich</td>
			<td dir="LTR" style="width:156px;">P1379</td>
			<td>5:10000 dilution</td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">Vitamin (100X)</td>
			<td dir="LTR" style="width:180px;">Thermo Fisher Scientific</td>
			<td dir="LTR" style="width:156px;">11120-037</td>
			<td>NRC complete medium final concentration = 1:100 dilution</td>
		</tr>
		<tr height="21">
			<td dir="LTR" height="21" style="height:21px;width:408px;">&#956;-Slide 8 Well ibiTreat, Ibidi</td>
			<td dir="LTR" style="width:180px;">Clinisciences</td>
			<td dir="LTR" style="width:156px;">80826</td>
			<td style="width:261px;"></td>
		</tr>
	</tbody>
</table>

generation and quantitative characterization of functional and polarized biliary epithelial cysts

Cholangiocytes, the epithelial cells that line up the bile ducts in the liver, oversee bile formation and modification. In the last twenty years, in the context of liver diseases, 3-dimensional (3D) models based on cholangiocytes have emerged such as cysts, spheroids, or tube-like structures to mimic tissue topology for organogenesis, disease modeling, and drug screening studies. These structures have been mainly obtained by embedding cholangiocytes in a hydrogel. The main purpose was to study self-organization by addressing epithelial polarity, functional, and morphological properties. However, very few studies focus on cyst formation efficiency. When this is the case, the efficiency is often quantified from images of a single plane. Functional assays and structural analysis are performed without representing the potential heterogeneity of cyst distribution arising from hydrogel polymerization heterogeneities and side effects. Therefore, the quantitative analysis, when done, cannot be used for comparison from one article to another. Moreover, this methodology does not allow comparisons of 3D growth potential of different matrices and cell types. Additionally, there is no mention of the experimental troubleshooting for immunostaining cysts. In this article, we provide a reliable and universal method to show that the initial cell distribution is related to the heterogeneous vertical distribution of cyst formation. Cholangiocyte cells embedded in hydrogel are followed with Z-stacks analysis along the hydrogel depth over the time course of 10 days. With this method, a robust kinetics of cyst formation efficiency and growth is obtained. We also present methods to evaluate cyst polarity and secretory function. Finally, additional tips for optimizing immunostaining protocols are provided in order to limit cyst collapse for imaging. This approach can be applied to other 3D cell culture studies, thus opening the possibilities to compare one system to another.

Formation and characterization of cysts 
3D cell culture systems are an important tool to study organogenesis and disease modeling25. Unfortunately, most of these methods are qualitative or use internal quantification performed on a single plane by comparing the number of cysts versus non-cysts, in variable and often unspecified volumes, preventing any comparison in terms of cyst formation efficiency between the various studies7,<sup class="...

Watch this Scientific Journal Video about Generation and Quantitative Characterization of Functional and Polarized Biliary Epithelial Cysts at JoVE.com

Generation and Quantitative Characterization of Functional and Polarized Biliary Epithelial Cysts

Three-dimensional (3D) cellular systems are relevant models for investigating organogenesis. A hydrogel-based method for biliary cysts production and their characterization is proposed. This protocol unravels the barriers of 3D characterization, with a straightforward and reliable method to assess cyst formation efficiency, sizes, and to test their functionality.

Cholangiocytes, the epithelial cells that line up the bile ducts in the liver, oversee bile formation and modification. In the last twenty years, in the ...

This is the first protocol for generating biliary cysts, providing a systematic analysis that allows the evaluation of cyst formation, efficiency, and size over time. This method allows quantitative assessment of epithelial cyst formation, and makes it possible to evaluate this process as a function of the type of epithelial cells or hydrogel. Since the therapeutic options for biliary disorders are limited, this protocol opens the door for standardizing drug studies, identifying normal therapeutic targets, and understanding disease mechanisms.The simple method allows important questions about the mechanisms of new information within the bioengineering of tubular structures field to be addressed. Before beginning an experiment, thaw an appropriate hydrogel solution at four degrees Celsius and pre-cool pipette tips and an eight well chamber slide at minus 20 degrees Celsius overnight. The next morning, place the hydrogel and an eight well chamber slide on ice and add the appropriate volume of hydrogel to cold normal rat cholangiocyte complete medium to obtain 500 microliters of 40%hydrogel solution.Then use the cold pipette tips to add 50 microliters of hydrogel solution to the center of each well of the chamber slide and use a pipette tip to spread the solution over the entire surface of the well bottom as evenly as possible without bubbles. To prepare the cells for the experiment, while the hydrogel is polymerizing, wash the cells from a 70%confluent normal rat cholangiocyte culture with pre-warmed PBS and incubate the cells with five milliliters of fresh pre-warmed PBS for 20 minutes in the cell culture incubator. At the end of the incubation, replace the PBS with one milliliter of pre-warmed Trypsin-EDTA and return the flask to the cell culture incubator for five to 10 minutes.When the cells have detached, neutralize the reaction with four milliliters of pre-warmed complete normal rat cholangiocyte medium and transfer the cells to a 15 milliliter tube for centrifugation. Then re-suspend the pellet in five milliliters of pre-warmed medium and filter the cells through a 40 micron strainer into a 50 milliliter tube for counting. To generate cysts, add the appropriate volume of hydrogel to cold complete normal rat cholangiocyte medium to obtain 1, 600 microliters of an 80%hydrogel solution on ice and dilute the cells to a five times 10 to the fifth cells per milliliter of cold complete normal rat cholangiocyte medium concentration in 1, 600 microliters of medium.Immediately mix the cell and hydrogel cell solutions and add 400 microliters of cells to each well of the hydrogel coated chamber slide, taking care to avoid bubbles. To ensure the acquisition of reproducible and significant results, be sure to handle the hydrogel carefully and to thoroughly mix the initial cell hydrogen solution to obtain a homogeneous solution. When all of the cells have been seeded, place the slide in the cell culture incubator.After two days in culture, remove 250 microliters of the medium from one corner of each well, taking care not to flush out the hydrogel, and slowly replace the discarded supernatant with 250 microliters of fresh culture medium. For cyst imaging, on the appropriate day of culture, select the 10 X objective on a phase contrast microscope equipped with image acquisition software, switch on the white lamp and select the brightfield imaging option. Select play to switch on the camera and focus on a field of cysts.Set the exposure time and open the auto-capture folder window to allow automatic saving of the images. Open the capture Z-series window, reset the default position and use the Z-screw to define the top and bottom plains of the Z-stack, adjusting the Z-step depending on the objective and the level of resolution. Then click run now to launch the acquisition.After imaging, open the Z-stack in Fiji. To duplicate the stack, click image, duplicate, and duplicate stack. To create a minimum intensity projection from the duplicated stack, under the image menu, select stacks and Z project.Select minimum intensity for the projection type and click okay. To subtract the background from the projection, under the process menu, select subtract background and select 500 pixels of rolling ball radius and light background to render the cysts more contrasted than the background. To measure the approximate cyst diameter, zoom on the targeted cyst, select the straight line tool and press the T button on the keyboard.Draw a line across the diameter of each cyst on the final projection. The next region of interest created for each cyst will be added to the region of interest manager. When all of the cysts have been counted, click on the Z-stack window to select it and click show all to see the counted cysts.Move the cursor along the Z-stack to check that all of the cysts have been counted in each image, adding new cysts to the region of interest manager as necessary. When all of the cysts have been counted, select the region of interest set and click more and save to save the data. To determine the size of each cyst, with the regions of interests still selected, click measure.A window listing each cyst and its estimated size will appear. Then save the data in CSV format. As demonstrated, recording the number of cysts and their respective sizes over time allows analysis of the evolution of cyst formation and growth.The viability of the starting cell population and the 10 day old cysts can be evaluated by live/dead staining. Dead cells represent less than 3%of the cell population at day 10 and are mostly located outside of the cyst as isolated cells or as part of small aggregates, although some necrotic cell debris accumulation is observed within some large cysts. Incubation with Fluorescein diacetate and Hoechst allows assessment of the formation and secretion of Fluorescein from the basal to the apical luminal space.Notably, the secretion of Fluorescein is inhibited by pretreatment with a multi-drug resistant inhibitor, indicating that fluorescent Fluorescein accumulation within the lumen is due to secretion through the multi-drug resistant transporter and not leakage from the intercellular space. Staining for E-cadherin expression reveals that the normal rat cholangiocytes maintain their epithelial phenotype in the hydrogel for at least 10 days. When preparing the cysts for immunofluorescence evaluation, keeping the bovine serum albumin at 0.1%or less during saturation is key to maintaining cyst integrity, as higher concentrations result in cyst retraction and lumen collapse.Overnight hydrogel, thawing, pipette tip and chamber slide recording, working on ice and spreading the homogenous cell hydrogel mixture uniformly onto the cultured chamber slide are all critical for experimental success. This method can be used to generate cysts from other epithelial cells or hydrogels, allowing comparisons for better understanding of epithelial polarization. This quantitative method can be used to test the effects of drugs or genetic mutations on biliary function and organogenesis.

generation-quantitative-characterization-functional-polarized-biliary

Research

JoVE Journal

Bioengineering

Generation of Aligned Functional Myocardial Tissue Through Microcontact Printing

Advanced heart failure represents a major unmet clinical challenge, arising from the loss of viable and/or fully functional cardiac muscle cells. Despite optimum drug therapy, heart failure represents a leading cause of mortality and morbidity in the developed world. A major challenge in drug development is the identification of cellular assays that accurately recapitulate normal and diseased human myocardial physiology in vitro. Likewise, the major challenges in regenerative cardiac biology revolve around the identification and isolation of patient-specific cardiac progenitors in clinically relevant quantities. These cells have to then be assembled into functional tissue that resembles the native heart tissue architecture. Microcontact printing allows for the creation of precise micropatterned protein shapes that resemble structural organization of the heart, thus providing geometric cues to control cell adhesion spatially. Herein we describe our approach for the isolation of highly purified myocardial cells from pluripotent stem cells differentiating in vitro, the generation of cell growth surfaces micropatterned with extracellular matrix proteins, and the assembly of the stem cell-derived cardiac muscle cells into anisotropic myocardial tissue.

The generation of aligned myocardial tissue is a key requirement for adapting the recent advances in stem cell biology to clinically useful purposes. Herein we describe a microcontact printing approach for the precise control of cell shape and function. Using highly purified populations of embryonic stem cell derived cardiac progenitors, we then generate anisotropic functional myocardial tissue.

Advanced heart failure represents a major unmet clinical challenge,  arising from the loss of viable and/or fully functional cardiac muscle  cells. ...

Drug-induced Sensitization of Adenylyl Cyclase: Assay Streamlining and Miniaturization for Small Molecule and siRNA Screening Applications

Sensitization of adenylyl cyclase (AC) signaling has been implicated in a variety of neuropsychiatric and neurologic disorders including substance abuse and Parkinson&#39;s disease. Acute activation of G&#945;i/o-linked receptors inhibits AC activity, whereas persistent activation of these receptors results in heterologous sensitization of AC and increased levels of intracellular cAMP. Previous studies have demonstrated that this enhancement of AC responsiveness is observed both in vitro and in vivo following the chronic activation of several types of G&#945;i/o-linked receptors including D2 dopamine and &#956; opioid receptors. Although heterologous sensitization of AC was first reported four decades ago, the mechanism(s) that underlie this phenomenon remain largely unknown. The lack of mechanistic data presumably reflects the complexity involved with this adaptive response, suggesting that nonbiased approaches could aid in identifying the molecular pathways involved in heterologous sensitization of AC. Previous studies have implicated kinase and Gb&#947; signaling as overlapping components that regulate the heterologous sensitization of AC. To identify unique and additional overlapping targets associated with sensitization of AC, the development and validation of a scalable cAMP sensitization assay is required for greater throughput. Previous approaches to study sensitization are generally cumbersome involving continuous cell culture maintenance as well as a complex methodology for measuring cAMP accumulation that involves multiple wash steps. Thus, the development of a robust cell-based assay that can be used for high throughput screening (HTS) in a 384&#160;well format would facilitate future studies. Using two D2 dopamine receptor cellular models (i.e.&#160;CHO-D2L and HEK-AC6/D2L), we have converted our 48-well sensitization assay (&#62;20 steps 4-5 days) to a five-step, single day assay in 384-well format. This new format is amenable to small molecule screening, and we demonstrate that this assay design can also be readily used for reverse transfection of siRNA in anticipation of targeted siRNA library screening.

Persistent activation of inhibitory G protein-coupled receptors results in sensitization of adenylyl cyclase signaling. To identify the essential molecular pathways, nonbiased approaches are necessary; however, this strategy requires the development of a scalable cell-based cAMP sensitization assay. Herein, we describe a sensitization assay for small molecule and siRNA screening.

Sensitization of adenylyl cyclase (AC) signaling has been implicated in a variety of neuropsychiatric and neurologic disorders including substance abuse ...

Fabrication and Characterization of a Conformal Skin-like Electronic System for Quantitative, Cutaneous Wound Management

Recent advances in the development of electronic technologies and biomedical devices offer opportunities for non-invasive, quantitative assessment of cutaneous wound healing on the skin. Existing methods, however, still rely on visual inspections through various microscopic tools and devices that normally include high-cost, sophisticated systems and require well trained personnel for operation and data analysis. Here, we describe methods and protocols to fabricate a conformal, skin-like electronics system that enables conformal lamination to the skin surface near the wound tissues, which provides recording of high fidelity electrical signals such as skin temperature and thermal conductivity. The methods of device fabrication provide details of step-by-step preparation of the microelectronic system that is completely enclosed with elastomeric silicone materials to offer electrical isolation. The experimental study presents multifunctional, biocompatible, waterproof, reusable, and flexible/stretchable characteristics of the device for clinical applications. Protocols of clinical testing provide an overview and sequential process of cleaning, testing setup, system operation, and data acquisition with the skin-like electronics, gently mounted on hypersensitive, cutaneous wound and contralateral tissues on patients.

This article presents methods to fabricate and characterize a conformal, skin-like electronic system and protocols for the use in clinical applications, particularly on cutaneous wound management.

Recent advances in the development of electronic technologies and biomedical devices offer opportunities for non-invasive, quantitative assessment of ...

Double Emulsion Generation Using a Polydimethylsiloxane (PDMS) Co-axial Flow Focus Device

Double emulsions are useful in a number of biological and industrial applications in which it is important to have an aqueous carrier fluid. This paper presents a polydimethylsiloxane (PDMS) microfluidic device capable of generating water/oil/water double emulsions using a coaxial flow focusing geometry that can be fabricated entirely using soft lithography. Similar to emulsion devices using glass capillaries, double emulsions can be formed in channels with uniform wettability and with dimensions much smaller than the channel sizes. Three dimensional flow focusing geometry is achieved by casting a pair of PDMS slabs using two layer soft lithography, then mating the slabs together in a clamshell configuration. Complementary locking features molded into the PDMS slabs enable the accurate registration of features on each of the slab surfaces. Device testing demonstrates formation of double emulsions from 14 &#181;m to 50 &#181;m in diameter while using large channels that are robust against fouling and clogging.

Double Emulsion Generation Using a Polydimethylsiloxane PDMS Co-axial Flow Focus Device

Microfluidic double emulsions generation typically involves devices with patterned wettability or custom-fabricated glass components. Here we describe the fabrication and testing of an all polydimethylsiloxane (PDMS) double emulsion generator that does not require surface treatment or complicated fabrication processes, and is capable of producing double emulsions down to 14 &#181;m.

Double emulsions are useful in a number of biological and industrial applications in which it is important to have an aqueous carrier fluid. This paper ...

Improving 2D and 3D Skin In Vitro Models Using Macromolecular Crowding

The glycoprotein family of collagens represents the main structural proteins in the human body, and are key components of biomaterials used in modern tissue engineering. A technical bottleneck is the deposition of collagen in vitro, as it is notoriously slow, resulting in sub-optimal formation of connective tissue and subsequent tissue cohesion, particularly in skin models. Here, we describe a method which involves the addition of differentially-sized sucrose co-polymers to skin cultures to generate macromolecular crowding (MMC), which results in a dramatic enhancement of collagen deposition. Particularly, dermal fibroblasts deposited a significant amount of collagen I/IV/VII and fibronectin under MMC in comparison to controls.
The protocol also describes a method to decellularize crowded cell layers, exposing significant amounts of extracellular matrix (ECM) which were retained on the culture surface as evidenced by immunocytochemistry. Total matrix mass and distribution pattern was studied using interference reflection microscopy. Interestingly, fibroblasts, keratinocytes and co-cultures produced cell-derived matrices (CDM) of varying composition and morphology. CDM could be used as &#34;bio-scaffolds&#34; for secondary cell seeding, where the current use of coatings or scaffolds, typically from xenogenic animal sources, can be avoided, thus moving towards more clinically relevant applications.
In addition, this protocol describes the application of MMC during the submerged phase of a 3D-organotypic skin co-culture model which was sufficient to enhance ECM deposition in the dermo-epidermal junction (DEJ), in particular, collagen VII, the major component of anchoring fibrils. Electron microscopy confirmed the presence of anchoring fibrils in cultures developed with MMC, as compared to controls. This is significant as anchoring fibrils tether the dermis to the epidermis, hence, having a pre-formed mature DEJ may benefit skin graft recipients in terms of graft stability and overall wound healing. Furthermore, culture time was condensed from 5 weeks to 3 weeks to obtain a mature construct, when using MMC, reducing costs.

Improving 2D and 3D Skin In Vitro Models Using Macromolecular Crowding

We present a protocol to obtain cell-derived matrices rich in extracellular matrix proteins, using macromolecular crowders (MMC). In addition, we present a protocol which incorporates MMC in 3D organotypic skin co-culture generation, which reduces culture time while maintaining maturity of construct.

The glycoprotein family of collagens represents the main structural proteins in the human body, and are key components of biomaterials used in modern ...

Generation of ESC-derived Mouse Airway Epithelial Cells Using Decellularized Lung Scaffolds

Lung lineage differentiation requires integration of complex environmental cues that include growth factor signaling, cell-cell interactions and cell-matrix interactions. Due to this complexity, recapitulation of lung development in vitro to promote differentiation of stem cells to lung epithelial cells has been challenging. In this protocol, decellularized lung scaffolds are used to mimic the 3-dimensional environment of the lung and generate stem cell-derived airway epithelial cells. Mouse embryonic stem cell are first differentiated to the endoderm lineage using an embryoid body (EB) culture method with activin A. Endoderm cells are then seeded onto decellularized scaffolds and cultured at air-liquid interface for up to 21 days. This technique promotes differentiation of seeded cells to functional airway epithelial cells (ciliated cells, club cells, and basal cells) without additional growth factor supplementation. This culture setup is defined, serum-free, inexpensive, and reproducible. Although there is limited contamination from non-lung endoderm lineages in culture, this protocol only generates airway epithelial populations and does not give rise to alveolar epithelial cells. Airway epithelia generated with this protocol can be used to study cell-matrix interactions during lung organogenesis and for disease modeling or drug-discovery platforms of airway-related pathologies such as cystic fibrosis.

This protocol efficiently directs mouse embryonic stem cell-derived definitive endoderm to mature airway epithelial cells. This differentiation technique uses 3-dimensional decellularized lung scaffolds to direct lung lineage specification, in a defined, serum-free culture setting.

Lung lineage differentiation requires integration of complex environmental cues that include growth factor signaling, cell-cell interactions and ...

Detection of Endotoxin in Nano-formulations Using Limulus Amoebocyte Lysate (LAL) Assays

When present in pharmaceutical products, a Gram-negative bacterial cell wall component endotoxin (often also called lipopolysaccharide) can cause inflammation, fever, hypo- or hypertension, and, in extreme cases, can lead to tissue and organ damage that may become fatal. The amounts of endotoxin in pharmaceutical products, therefore, are strictly regulated. Among the methods available for endotoxin detection and quantification, the Limulus Amoebocyte Lysate (LAL) assay is commonly used worldwide. While any pharmaceutical product can interfere with the LAL assay, nano-formulations represent a particular challenge due to their complexity. The purpose of this paper is to provide a practical guide to researchers inexperienced in estimating endotoxins in engineered nanomaterials and nanoparticle-formulated drugs. Herein, practical recommendations for performing three LAL formats including turbidity, chromogenic and gel-clot assays are discussed. These assays can be used to determine endotoxin contamination in nanotechnology-based drug products, vaccines, and adjuvants.

Detection of Endotoxin in Nano-formulations Using Limulus Amoebocyte Lysate LAL Assays

Detection of endotoxins in engineered nanomaterials represents one of the grand challenges in the field of nanomedicine. Here, we present a case study that describes the framework composed of three different LAL formats to estimate potential endotoxin contamination in nanoparticles.

When present in pharmaceutical products, a Gram-negative bacterial cell wall component endotoxin (often also called lipopolysaccharide) can cause ...

Scalable Generation of Mature Cerebellar Organoids from Human Pluripotent Stem Cells and Characterization by Immunostaining

The cerebellum plays a critical role in the maintenance of balance and motor coordination, and a functional defect in different cerebellar neurons can trigger cerebellar dysfunction. Most of the current knowledge about disease-related neuronal phenotypes is based on postmortem tissues, which makes understanding of disease progression and development difficult. Animal models and immortalized cell lines have also been used as models for neurodegenerative disorders. However, they do not fully recapitulate human disease. Human induced pluripotent stem cells (iPSCs) have great potential for disease modeling and provide a valuable source for regenerative approaches. In recent years, the generation of cerebral organoids from patient-derived iPSCs improved the prospects for neurodegenerative disease modeling. However, protocols that produce large numbers of organoids and a high yield of mature neurons in 3D culture systems are lacking. The protocol presented is a new approach for reproducible and scalable generation of human iPSC-derived organoids under chemically-defined conditions using scalable single-use bioreactors, in which organoids acquire cerebellar identity. The generated organoids are characterized by the expression of specific markers at both mRNA and protein level. The analysis of specific groups of proteins allows the detection of different cerebellar cell populations, whose localization is important for the evaluation of organoid structure. Organoid cryosectioning and further immunostaining of organoid slices are used to evaluate the presence of specific cerebellar cell populations and their spatial organization.

This protocol describes a dynamic culture system to produce controlled size aggregates of human pluripotent stem cells and further stimulate differentiation in cerebellar organoids under chemically-defined and feeder-free conditions using a single-use bioreactor.

The cerebellum plays a critical role in the maintenance of balance and motor coordination, and a functional defect in different cerebellar neurons can ...

Generation of Dynamical Environmental Conditions using a High-Throughput Microfluidic Device

Mimicking in vivo environmental conditions is crucial for in vitro studies on complex life machinery. However, current techniques targeting live cells and organs are either highly expensive, like robotics, or lack nanoliter volume and millisecond time accuracy in liquid manipulation. We herein present the design and fabrication of a microfluidic system, which consists of 1,500 culture units, an array of enhanced peristaltic pumps and an on-site mixing modulus. To demonstrate the capacities of the microfluidic device, neural stem cell (NSC) spheres are maintained in the proposed system. We observed that when the NSC sphere is exposed to CXCL in day 1 and EGF in day 2, the round-shaped conformation is well maintained. Variation in the input order of 6 drugs causes morphological changes to the NSC sphere and the expression level representative marker for NSC stemness (i.e., Hes5 and Dcx). These results indicate that dynamic and complex environmental conditions have great effects on NSC differentiation and self-renewal, and the proposed microfluidic device is a suitable platform for high throughput studies on the complex life machinery.

We present a microfluidic system for high throughput studies on complex life machinery, which consists of 1500 culture units, an array of enhanced peristaltic pumps and an on-site mixing modulus. The microfluidic chip allows for the analysis of the highly complex and dynamic micro-environmental conditions in vivo.

Mimicking in vivo environmental conditions is crucial for in vitro studies on complex life machinery. However, current techniques targeting live cells and ...

Reliably Engineering and Controlling Stable Optogenetic Gene Circuits in Mammalian Cells

Reliable gene expression control in mammalian cells requires tools with high fold change, low noise, and determined input-to-output transfer functions, regardless of the method used. Toward this goal, optogenetic gene expression systems have gained much attention over the past decade for spatiotemporal control of protein levels in mammalian cells. However, most existing circuits controlling light-induced gene expression vary in architecture, are expressed from plasmids, and utilize variable optogenetic equipment, creating a need to explore characterization and standardization of optogenetic components in stable cell lines. Here, the study provides an experimental pipeline of reliable gene circuit construction, integration, and characterization for controlling light-inducible gene expression in mammalian cells, using a negative feedback optogenetic circuit as a case example. The protocols also illustrate how standardizing optogenetic equipment and light regimes can reliably reveal gene circuit features such as gene expression noise and protein expression magnitude. Lastly, this paper may be of use for laboratories unfamiliar with optogenetics who wish to adopt such technology. The pipeline described here should apply for other optogenetic circuits in mammalian cells, allowing for more reliable, detailed characterization and control of gene expression at the transcriptional, proteomic, and ultimately phenotypic level in mammalian cells.

Reliably controlling light-responsive mammalian cells requires the standardization of optogenetic methods. Toward this goal, this study outlines a pipeline of gene circuit construction, cell engineering, optogenetic equipment operation, and verification assays to standardize the study of light-induced gene expression using a negative-feedback optogenetic gene circuit as a case study.

Reliable gene expression control in mammalian cells requires tools with high fold change, low noise, and determined input-to-output transfer functions, ...