This study was supported by grants RO1 CA 135561, R01 CA151494, R01 CA174432 and P3013330 from the National Institutes of Health.
We would like to thank Michele Houston, Elena Dhima and Dr. Anna Velcich for their valuable comments in developing the crypt isolation protocol.
We also thank the Diabetes Training and Research Center of the Albert Einstein College of Medicine supported by NIH P60DK20541, and Dr. Michael Brownlee and Dr. Xue-Liang Du, who direct and operate the Seahorse facility, respectively.

This study was performed in accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. The protocol was approved by the Committee on the Ethics of Animal Experiments of the Albert Einstein College of Medicine.
1. Crypt Isolation and Culture
<ol>
	<li>Isolation of Crypts from the Small Intestine:
	<ol>
		<li>Isolate intestinal crypts from any mice model of interest. Euthanize the mice with CO2 followed by cervical dislocation.</li>
		<li>Open up the abdomen longitudinally and fill the small intestine (SI) with ice cold phosphate buffered saline, PBS (-Ca2+; -Mg2+) with 2x antibiotic&#8211;antimycotic (anti&#8211;anti). Rapidly isolate small intestine.</li>
		<li>Thoroughly dissect free of mesenteric fat using a scalpel. Be careful not to perforate the tissue &#8211; at all times keep the tissue moist with ice cold PBS. Open up intestine longitudinally and wash thoroughly with ice cold PBS.</li>
		<li>Cut small intestine into two sections and flatten out using a wet cotton tip, gently scrape off the villi using a pre-cooled slide. Wash vigorously in ice-cold PBS several times.</li>
		<li>Incubate 3 min in 20 ml 1x PBS per 3 mM ethylenediaminetetraacetic acid (EDTA)/0.5 mM dithiothreitol (DTT) for non-enzymatic dissociation of the tissue.</li>
		<li>Cut tissue into small pieces (2-4 mm) using a razor blade on a pre-cooled slide. Transfer the pieces into a 50 ml tube containing 20 ml ice cold PBS.</li>
		<li>Pipette up and down gently 10x using a 10 ml sterile disposable pipette. Let tissue fragments sediment by gravity. Remove the supernatant with a pipette. Repeat three additional times; make sure supernatant is clear.</li>
		<li>Add 20 ml of PBS per 2 mM EDTA. Swirl and incubate at 4 &#176;C for 30 min with gentle rocking.</li>
		<li>Let tissue sediment and discard supernatant. Add 15 ml ice cold PBS and pipette up and down 5x with a 10 ml pipette. Let the tissue fragments sediment and collect the supernatant as Fraction 1 (F1). Repeat collecting F2-F5, each fraction maintained separately.</li>
		<li>Add 15 ml ice cold PBS and this time shake vigorously by hand for 15 sec. Collect F6 and repeat for F7, F8. If tissue pieces start to float, tap to help them settle.</li>
		<li>Inspect an aliquot of each fraction under the microscope. Pool those fractions containing crypts.</li>
		<li>Pass the pooled fractions through a 70 &#181;m nylon cell strainer, collecting crypts in a 50 ml tube.</li>
		<li>Centrifuge at 100 x g for 5 min at 4 &#176;C, discard the supernatant and resuspend pellet in 10 ml ice cold PBS with 2x anti&#8211;anti and transfer crypts to a 15 ml tube. Repeat the wash one more time.</li>
		<li>Wash the crypts once with 10 ml ice-cold ADF, Advanced DMEM/F-12 (Dulbecco&#34;s Modified Eagle Medium/Ham&#34;s F-12) &#8211; 2x anti&#8211;anti.</li>
		<li>Wash the crypts once with 10 ml ADF &#8211; 1x anti&#8211;anti.</li>
		<li>Count the crypts using a hemocytometer. Adjust the crypt solution volume and transfer to a 1.5 ml tube so that the final crypt concentration when resuspended will be 100-500 crypts per 50 &#181;l of gelatinous protein mixture (Matrigel). Centrifuge at 100 x g for 5 min at 4 &#176;C and resuspend crypts in the gelatinous protein mixture.</li>
		<li>Plate 50 &#181;l of crypt &#8211; gelatinous protein mixture suspension per well in a 24-well plate (growth area: 2 cm2), carefully placing the suspension drop in the center of each well. Maintain the plate in a CO2, 37 &#176;C incubator for ~30 min until the suspension solidifies.</li>
		<li>Add 500 &#181;l ice cold complete culture media (Advanced DMEM/F12 with 1x anti &#8211; anti, 10 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES), 1x GlutaMAX, 1x B27 Supplement, 1x N2 Supplement, 1 mM N-Acetyl-L-Cysteine (NAC), 50 ng/ml Epidermal growth factor (EGF), 100 ng/ml Noggin, 500 ng/ml R-Spondin).
		<ol>
			<li>Reconstitute growth factors in 0.1% Bovine Serum Albumin (BSA) in PBS.</li>
		</ol>
		</li>
	</ol>
	</li>
	<li>Crypt Organoid Culture and Passage:
	<ol>
		<li>Passage crypt organoids 14-21 days post seeding (or as needed) as follows:
		<ol>
			<li>Change media every Friday and Monday. On Wednesdays, replace half the media with fresh media.</li>
		</ol>
		</li>
		<li>Remove the culture medium. Wash the sample twice with 500 &#181;l PBS at 5 min intervals.</li>
		<li>Remove PBS and gently break up the gelatinous protein mixture using a sterile P1000 micro pipette tip.</li>
		<li>Add 1 ml complete culture media to a single well and resuspend the organoids in 1 ml media.</li>
		<li>Gently disrupt the organoids using a P1000 by pipetting up and down 20-30x (check under the microscope for proper organoid dissociation with a good crypt yield until a consistent technique is developed).</li>
		<li>Transfer the crypts to a 1.5 ml microcentrifuge tube; centrifuge at 100 x g at 4 &#176;C, 5 min.</li>
		<li>Wash the pellet twice with 1 ml complete culture media.</li>
		<li>Split at a ratio of 1:3 or 1:6 as needed, resuspending crypts in 50 &#181;l Matrigel per well. Proceed as described above (section 1.1.16-18).</li>
	</ol>
	</li>
	<li>Crypt Organoid Freezing:
	<ol>
		<li>Remove the culture medium. Wash the sample in 500 &#181;l PBS.</li>
		<li>Disperse the gelatinous protein mixture using a P1000 pipette tip.</li>
		<li>Add 1 ml media to a single well and resuspend the organoids in 1 ml media.</li>
		<li>Gently break up the organoids using a P1000 by pipetting up and down 20-30x.</li>
		<li>Transfer the organoids to a 1.5 ml tube. Centrifuge at 100 x g at 4 &#176;C, 5 min.</li>
		<li>Wash the pellet twice with 1 ml complete culture media.</li>
		<li>Resuspend crypts in 500 &#181;l freezing media.</li>
		<li>Transfer crypts to a cryotube, place the tube in a freezing container and store in a -80 &#176;C freezer overnight.</li>
		<li>Transfer crypts to liquid N2 tank.
		<ol>
			<li>Recover frozen crypt organoids by rapidly thawing in a 37 &#176;C water bath. Wash with 500 &#181;l complete culture media once, centrifuge at 100 x g, 5 min and resuspend in gelatinous protein mixture, and culture as described above. For better recovery, add ROCK inhibitor (Y-27632) to the freezing media.</li>
		</ol>
		</li>
	</ol>
	</li>
</ol>
2. Crypt Organoid Metabolism Assay
<ol>
	<li>24-well Plate Preparation:
	<ol>
		<li>Isolate and count crypts according to the protocol (see section 1.1 for crypt isolation and section 1.2 for crypt passage).</li>
		<li>Resuspend crypts in gelatinous protein mixture (100-200 crypts per 20 &#181;l).</li>
		<li>Plate crypt-gelatinous protein mixture suspension in a 24-well assay plate (make sure there are at least triplicates for each sample) and allow the suspension to solidify at 37 &#176;C in a CO2 incubator; then add 500 &#181;l complete culture media.</li>
		<li>Culture crypts (as described in section 1.1) and observe under microscope until crypts grow into fully developed organoids.</li>
	</ol>
	</li>
	<li>Extracellular Flux Assay:
	<ol>
		<li>Hydrate cartridge overnight in a non-CO2 (0% CO2), 37 &#176;C incubator.</li>
		<li>Remove the culture medium and wash organoids twice with 500 &#181;l DMEM (without: glucose, L-glutamine, sodium pyruvate and sodium bicarbonate; and with: phenol red). Wait 5 min.</li>
		<li>Add 675 &#181;l per well assay medium (DMEM with 2 mM L-glutamine and 5 mM D-glucose) to each well.</li>
		<li>Check crypt organoids microscopic morphology to ensure that organoids and the gelatinous protein mixture are intact after the washes. Incubate 1 hr in a non-CO2, 37 &#176;C incubator.</li>
		<li>Prepare 10 &#181;M injectable compounds (oligomycin, carbonyl cyanide-p-trifluoro-methoxy-phenyl-hydrazone (FCCP), rotenone) in assay medium.</li>
		<li>Set-up the cartridge by loading 75 &#181;l of 10 &#181;M injectable compounds into the ports of the cartridge sequentially: Port A - oligomycin; Port B - FCCP; and Port C - rotenone (The final concentrations during the assay will be 1 &#181;M).</li>
		<li>Incubate cartridge 30 min &#8211; 1 hr at 37 &#176;C in a non-CO2 incubator.</li>
		<li>Simultaneously, turn on the XF Analyzer and create the assay protocol template.</li>
		<li>Place cartridge and utility plate into XF Analyzer and run &#8220;calibrate&#8221; cartridge.</li>
		<li>Check crypt organoids microscopically to make sure they are attached to the gelatinous protein mixture.</li>
		<li>Load cell culture plate into instrument and run assay protocol.</li>
	</ol>
	</li>
</ol>

<ol>
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We tested the oxygen consumption rate (OCR) and the extracellular acidification rate (ECAR) of crypts isolated from 8-month old mice and grown into organoids ex vivo. After measurement of the basal rate, crypt metabolism was evaluated by adding oligomycin, carbonyl cyanide-p-trifluoromethoxyphenylhydrazone (FCCP) and rotenone, sequentially.
Basal OCR and basal ECAR were recorded from 0 - 29 min (Figure 2A and 2B). At the 29th min, oligomyci...

Colorectal cancer (CRC) is the third leading cause of cancer related deaths in the United States. Sporadic colon cancer &#8211; i.e. that arising later in life (&#62;50 years of age) and with no clear predisposing genetic factors &#8211; accounts for ~80% of all cases, with incidence strongly influenced by long term dietary patterns1,2. These tumors exhibit a metabolic shift towards dependence on oxidative glycolysis, known as the Warburg effect, which may in part make higher concentrations of cellular building blocks and energy available (through glutaminolysis) to permit and perhaps drive high rates of tumor cell proliferation3-5. Studies of colon cancer as well as other gastrointestinal cancers including small intestine cancers provide important insight into the cause of tumor formation. Investigating the metabolic differences between normal, pro-tumorigenic and tumorigenic states of gastrointestinal organ systems may assist determination of relative risk for tumor development as well as early detection of neoplasia. Moreover, understanding bioenergetic metabolism involving mitochondrial respiration and glycolysis will provide fundamental insight into how cell physiology, aging and disease state perturbs intestinal homeostasis. Utilization of the bioenergetics assay technology for extracellular flux analysis can assess the rates of mitochondrial respiration and glycolysis simultaneously in cells growing in culture in real time6,7.
Until recently, in vitro studies of small intestine were limited to cell lines derived from either benign or malignant tumors8,9 and did not represent the physiology of normal intestinal epithelia and the influence of the microenvironment in which they reside. In 2009, Sato et al.10 introduced an ex vivo culture system to grow three-dimensional (3D) mouse intestinal epithelial organoids, or epithelial &#8220;mini-guts&#8221;, suitable for experimental, diagnostic and therapeutic investigations10,11. Moreover, crypts isolated from calorically restricted mice maintain their altered growth properties as organoids in such cultures12. Compared to transformed cell lines, crypt organoid cultures can be used to generate physiologically relevant data presenting a far better model to understand the in vivo state.
We adapted bioenergetics analysis technology to assay energy metabolism of intestinal crypt organoids. Mouse intestinal crypt organoids were cultured ex vivo to develop the crypt organoid energy metabolism studies presented. The oxygen consumption rate (OCR) and the extracellular acidification rate (ECAR) of crypt organoids were measured in the absence and presence of two different metabolic inhibitors (oligomycin, rotenone) and an ion carrier (carbonyl cyanide-p-trifluoromethoxyphenylhydrazone). The crypt organoid metabolic response to these chemical compounds were successfully reflected through changing ECAR and OCR values.
Cellular bioenergetic studies will elucidate the reciprocal interactions between metabolic state and disease risk and phenotype in cancer, obesity, diabetes, metabolic disorders and mitochondrial diseases and help advance screening methods with direct implications for translational medicine. Here, we describe a detailed protocol to isolate small intestinal crypts and to culture crypt organoids. Moreover, we introduce a novel method to use crypt organoid cultures for metabolic assays.

<table border="0" cellpadding="0" cellspacing="0" width="1633">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:815px;">BD Matrigel Basement Membrane Matrix, GFR, Phenol Red-free, LDEV-free</td>
			<td style="width:229px;">BD Biosciences</td>
			<td style="width:135px;">356231</td>
			<td style="width:456px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:815px;">PBS (phosphate buffered saline), no magnesium, no calcium, pH 7.2</td>
			<td style="width:229px;">Life Technologies</td>
			<td style="width:135px;">20012-027</td>
			<td style="width:456px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:815px;">Advanced DMEM/F-12 (1X)</td>
			<td style="width:229px;">Life Technologies</td>
			<td style="width:135px;">12634-028</td>
			<td style="width:456px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:815px;">Dulbecco&#8242;s Modified Eagle&#8242;s Medium without glucose, L-glutamine, Phenol Red, sodium pyruvate and sodium bicarbonate</td>
			<td style="width:229px;">Sigma-Aldrich</td>
			<td style="width:135px;">D5030</td>
			<td style="width:456px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:815px;">Phenol Red sodium salt&#160;</td>
			<td style="width:229px;">Sigma-Aldrich</td>
			<td style="width:135px;">P4758</td>
			<td style="width:456px;">Final Concentration 15 mg / L in DMEM (D5030) - step 2.2.2</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:815px;">Antibiotic-Antimycotic, 100X, 100ml</td>
			<td style="width:229px;">Life Technologies</td>
			<td style="width:135px;">15240-062&#160;</td>
			<td style="width:456px;">Final Concentration 1 X or 2 X</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:815px;">Penicilin-Streptomycin, liquid</td>
			<td style="width:229px;">Life Technologies</td>
			<td style="width:135px;">15140-122</td>
			<td style="width:456px;">Final Concentration 1 X</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:815px;">Gibco&#174; GlutaMAX&#8482; supplement</td>
			<td style="width:229px;">Life Technologies</td>
			<td style="width:135px;">35050061</td>
			<td style="width:456px;">Final Concentration 1 X</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:815px;">Gibco&#174; HEPES (N-2-hydroxyethylpiperazine-N-2-ethane sulfonic acid), 1 M</td>
			<td style="width:229px;">Life Technologies</td>
			<td style="width:135px;">15630-080</td>
			<td style="width:456px;">Final Concentration 10 mM</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:815px;">N-Acetyl-L-Cysteine, 25g</td>
			<td style="width:229px;">Sigma-Aldrich</td>
			<td style="width:135px;">A9165-25G</td>
			<td style="width:456px;">Final Concentration 1 mM</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:815px;">100X N-2 supplement, liquid</td>
			<td style="width:229px;">Invitrogen</td>
			<td style="width:135px;">17502-048</td>
			<td style="width:456px;">Final Concentration 1 X</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:815px;">50X B-27&#174; supplement minus Vitamin A, liquid</td>
			<td style="width:229px;">Invitrogen</td>
			<td style="width:135px;">12587-010</td>
			<td style="width:456px;">Final Concentration 1 X</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:815px;">Recombinant Mouse R-Spondin 1, CF, 50ug</td>
			<td style="width:229px;">R&#38;D Systems</td>
			<td style="width:135px;">3474-RS-050&#160;</td>
			<td style="width:456px;">Final Concentration 500 ng / mL</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:815px;">Recombinant Murine EGF, 100ug&#160;</td>
			<td style="width:229px;">Peprotech</td>
			<td style="width:135px;">315-09&#160;</td>
			<td style="width:456px;">Final Concentration 50 ng / mL</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:815px;">Recombinant Murine Noggin, 20ug&#160;</td>
			<td style="width:229px;">Peprotech</td>
			<td style="width:135px;">250-38</td>
			<td style="width:456px;">Final Concentration 100 ng / mL</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:815px;">Gibco&#174; L-glutamine, 200 mM</td>
			<td style="width:229px;">Life Technologies</td>
			<td style="width:135px;">25030-081</td>
			<td style="width:456px;">Final Concentration 2 mM</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:815px;">Gibco&#174; Glucose powder</td>
			<td style="width:229px;">Life Technologies</td>
			<td style="width:135px;">15023-021</td>
			<td style="width:456px;">Final Concentration 5 mM</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:815px;">Ambion&#174; 0.5 M EDTA (Ethylenediaminetetraacetic acid), pH 8.0</td>
			<td style="width:229px;">Life Technologies</td>
			<td style="width:135px;">AM9260G</td>
			<td style="width:456px;">Final Concentration 3 mM for step 1.1.5; 2 mM for step 1.1.8&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:815px;">DTT (Dithiothreitol), 1M</td>
			<td style="width:229px;">Life Technologies</td>
			<td style="width:135px;">P2325</td>
			<td style="width:456px;">Final Concentration 3 mM</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:815px;">Albumin from bovine serum (BSA)</td>
			<td style="width:229px;">Sigma-Aldrich</td>
			<td style="width:135px;">A2058</td>
			<td style="width:456px;">0.1 % in PBS</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:815px;">Fetal Bovine Serum (FBS)</td>
			<td style="width:229px;">Life Technologies</td>
			<td style="width:135px;">16000-044</td>
			<td style="width:456px;">1 % in PBS</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:815px;">Recovery&#8482; Cell Culture Freezing Medium</td>
			<td style="width:229px;">Life Technologies</td>
			<td style="width:135px;">12648-010</td>
			<td style="width:456px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:815px;">ROCK inhibitor (Y-27632)&#160;</td>
			<td style="width:229px;">Sigma-Aldrich</td>
			<td style="width:135px;">Y0503</td>
			<td style="width:456px;">Final Concentration 10 &#181;M</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:815px;">Oligomycin</td>
			<td style="width:229px;">Sigma-Aldrich</td>
			<td style="width:135px;">O4876</td>
			<td style="width:456px;">Final Concentration 1 &#181;M&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:815px;">Carbonyl cyanide-p-trifluoro-methoxy-phenyl-hydrazone (FCCP)</td>
			<td style="width:229px;">Sigma-Aldrich</td>
			<td style="width:135px;">C2920</td>
			<td style="width:456px;">Final Concentration 1 &#181;M&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:815px;">Rotenone</td>
			<td style="width:229px;">Sigma-Aldrich</td>
			<td style="width:135px;">R8875</td>
			<td style="width:456px;">Final Concentration 1 &#181;M&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:815px;">Sodium hydroxide</td>
			<td style="width:229px;">Sigma-Aldrich</td>
			<td style="width:135px;">221465</td>
			<td style="width:456px;">Final Concentration 0.1 N in PBS</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:815px;">XF24 Extracellular Flux Analyzer (XF Analyzer)</td>
			<td style="width:229px;">Seahorse Bioscience</td>
			<td style="width:135px;"></td>
			<td style="width:456px;"></td>
		</tr>
	</tbody>
</table>

real time analysis of metabolic profile in ex vivo mouse intestinal crypt organoid cultures

The small intestinal mucosa exhibits a repetitive architecture organized into two fundamental structures: villi, projecting into the intestinal lumen and composed of mature enterocytes, goblet cells and enteroendocrine cells; and crypts, residing proximal to the submucosa and the muscularis, harboring adult stem and progenitor cells and mature Paneth cells, as well as stromal and immune cells of the crypt microenvironment. Until the last few years, in vitro studies of small intestine was limited to cell lines derived from either benign or malignant tumors, and did not represent the physiology of normal intestinal epithelia and the influence of the microenvironment in which they reside. Here, we demonstrate a method adapted from Sato et al. (2009) for culturing primary mouse intestinal crypt organoids derived from C57BL/6 mice. In addition, we present the use of crypt organoid cultures to assay the crypt metabolic profile in real time by measurement of basal oxygen consumption, glycolytic rate, ATP production and respiratory capacity. Organoids maintain properties defined by their source and retain aspects of their metabolic adaptation reflected by oxygen consumption and extracellular acidification rates. Real time metabolic studies in this crypt organoid culture system are a powerful tool to study crypt organoid energy metabolism, and how it can be modulated by nutritional and pharmacological factors.

Crypt organoids were established from 8 month old C57BL/6 mice fed purified rodent diet American Institute of Nutrition 76A (AIN76A). Intestinal crypt organoids can be grown in culture for extended periods from a single crypt (Figure 1A, single red arrow). Organoids grow out crypt-like structures in 18-20 days in culture (Figure 1B, red arrows). Crypts were passaged every 3 weeks and organoids efficiently recovered following each passage.
Seahorse bioenergetic...

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Real Time Analysis of Metabolic Profile in Ex Vivo Mouse Intestinal Crypt Organoid Cultures

Small intestinal crypt organoids cultured ex vivo provide a tissue culture system that recapitulates growth of crypts dependent on stem cells and their niche. We established a method to assay the metabolic profile in real time in primary mouse crypt organoids. We found organoids maintain physiological properties defined by their source.

Real Time Analysis of Metabolic Profile in Ex Vivo Mouse Intestinal Crypt Organoid Cultures

The small intestinal mucosa exhibits a repetitive architecture organized into two fundamental structures: villi, projecting into the intestinal lumen and ...

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Research

JoVE Journal

Biology

16.2K Views.  Albert Einstein College of Medicine.  Малые кишечные склеп органоиды культивировали экс естественных обеспечить систему культуры тканей, что повторяет рост склепов, зависящих от стволовых клеток и их нишу. Мы создали метод для анализа метаболического профиля в режиме реального времени в п?...

Video: Real Time Analysis of Metabolic Profile in Ex Vivo Mouse Intestinal Crypt Organoid Cultures

Eukaryotic Polyribosome Profile Analysis

Protein synthesis is a complex cellular process that is regulated at many levels. For example, global translation can be inhibited at the initiation phase or the elongation phase by a variety of cellular stresses such as amino acid starvation or growth factor withdrawal. Alternatively, translation of individual mRNAs can be regulated by mRNA localization or the presence of cognate microRNAs. Studies of protein synthesis frequently utilize polyribosome analysis to shed light on the mechanisms of translation regulation or defects in protein synthesis. In this assay, mRNA/ribosome complexes are isolated from eukaryotic cells.  A sucrose density gradient separates mRNAs bound to multiple ribosomes known as polyribosomes from mRNAs bound to a single ribosome or monosome. Fractionation of the gradients allows isolation and quantification of the different ribosomal populations and their associated mRNAs or proteins. Differences in the ratio of polyribosomes to monosomes under defined conditions can be indicative of defects in either translation initiation or elongation/termination. Examination of the mRNAs present in the polyribosome fractions can reveal whether the cohort of individual mRNAs being translated changes with experimental conditions. In addition, ribosome assembly can be monitored by analysis of the small and large ribosomal subunit peaks which are also separated by the gradient. In this video, we present a method for the preparation of crude ribosomal extracts from yeast cells, separation of the extract by sucrose gradient and interpretation of the results.  This procedure is readily adaptable to mammalian cells.

This article describes a protocol for the extraction of translating ribosomes from eukaryotic cells. Once extracted, ribosomes are separated into monosomes and polyribosomes by sucrose gradient fractionation to allow different ribosomal populations to be analyzed. As such, this method is the gold standard for examining the regulation of translation.

Protein synthesis is a complex cellular process that is regulated at many levels. For example, global translation can be inhibited at the initiation phase ...

In vivo Imaging and Therapeutic Treatments in an Orthotopic Mouse Model of Ovarian Cancer

Human cancer and response to therapy is better represented in orthotopic animal models. This paper describes the development of an orthotopic mouse model of ovarian cancer, treatment of cancer via oral delivery of drugs, and monitoring of tumor cell behavior in response to drug treatment in real time using in vivo imaging system. In this orthotopic model, ovarian tumor cells expressing luciferase are applied topically by injecting them directly into the mouse bursa where each ovary is enclosed. Upon injection of D-luciferin, a substrate of firefly luciferase, luciferase-expressing cells generate bioluminescence signals. This signal is detected by the in vivo imaging system and allows for a non-invasive means of monitoring tumor growth, distribution, and regression in individual animals. Drug administration via oral gavage allows for a maximum dosing volume of 10 mL/kg body weight to be delivered directly to the stomach and closely resembles delivery of drugs in clinical treatments. Therefore, techniques described here, development of an orthotopic mouse model of ovarian cancer, oral delivery of drugs, and in vivo imaging, are useful for better understanding of human ovarian cancer and treatment and will improve targeting this disease.

In vivo Imaging and Therapeutic Treatments in an Orthotopic Mouse Model of Ovarian Cancer

Orthotopic animal models of ovarian cancer replicate better human disease and therefore enhance our understanding of cancer progression and tumor response to therapy. A mouse model receives an intrabursal injection of luciferase-expressing ovarian tumor cells. Treatment is administered via oral gavage. Tumor growth is monitored by in vivo imaging system.

Human cancer and response to therapy is better represented in orthotopic animal models.  This paper describes the development of an orthotopic mouse model ...

Metabolic Profile Analysis of Zebrafish Embryos

A growing goal in the field of metabolism is to determine the impact of genetics on different aspects of mitochondrial function. Understanding these relationships will help to understand the underlying etiology for a range of diseases linked with mitochondrial dysfunction, such as diabetes and obesity. Recent advances in instrumentation, has enabled the monitoring of distinct parameters of mitochondrial function in cell lines or tissue explants. Here we present a method for a rapid and sensitive analysis of mitochondrial function parameters in vivo during zebrafish embryonic development using the Seahorse bioscience XF 24 extracellular flux analyser. This protocol utilizes the Islet Capture microplates where a single embryo is placed in each well, allowing measurement of bioenergetics, including: (i) basal respiration; (ii) basal mitochondrial respiration (iii) mitochondrial respiration due to ATP turnover; (iv) mitochondrial uncoupled respiration or proton leak and (iv) maximum respiration. Using this approach embryonic zebrafish respiration parameters can be compared between wild type and genetically altered embryos (mutant, gene over-expression or gene knockdown) or those manipulated pharmacologically. It is anticipated that dissemination of this protocol will provide researchers with new tools to analyse the genetic basis of metabolic disorders in vivo in this relevant vertebrate animal model.

Zebrafish represent a powerful vertebrate model that has been under-utilised for metabolic studies. Here we describe a rapid way to measure the in vivo metabolic profile of developing zebrafish that allows the comparison of different mitochondrial function parameters between genetically or pharmacologically manipulated embryos, thereby increasing the applicability of this organism.

A growing goal in the field of metabolism is to determine the impact of genetics on different aspects of mitochondrial function. Understanding these ...

Metabolic Labeling and Membrane Fractionation for Comparative Proteomic Analysis of Arabidopsis thaliana Suspension Cell Cultures

Plasma membrane microdomains are features based on the physical properties of the lipid and sterol environment and have particular roles in signaling processes. Extracting sterol-enriched membrane microdomains from plant cells for proteomic analysis is a difficult task mainly due to multiple preparation steps and sources for contaminations from other cellular compartments. The plasma membrane constitutes only about 5-20% of all the membranes in a plant cell, and therefore isolation of highly purified plasma membrane fraction is challenging. A frequently used method involves aqueous two-phase partitioning in polyethylene glycol and dextran, which yields plasma membrane vesicles with a purity of 95% 1. Sterol-rich membrane microdomains within the plasma membrane are insoluble upon treatment with cold nonionic detergents at alkaline pH. This detergent-resistant membrane fraction can be separated from the bulk plasma membrane by ultracentrifugation in a sucrose gradient 2. Subsequently, proteins can be extracted from the low density band of the sucrose gradient by methanol/chloroform precipitation. Extracted protein will then be trypsin digested, desalted and finally analyzed by LC-MS/MS. Our extraction protocol for sterol-rich microdomains is optimized for the preparation of clean detergent-resistant membrane fractions from Arabidopsis thaliana cell cultures.
We use full metabolic labeling of Arabidopsis thaliana suspension cell cultures with K15NO3 as the only nitrogen source for quantitative comparative proteomic studies following biological treatment of interest 3. By mixing equal ratios of labeled and unlabeled cell cultures for joint protein extraction the influence of preparation steps on final quantitative result is kept at a minimum. Also loss of material during extraction will affect both control and treatment samples in the same way, and therefore the ratio of light and heave peptide will remain constant. In the proposed method either labeled or unlabeled cell culture undergoes a biological treatment, while the other serves as control 4.

Metabolic Labeling and Membrane Fractionation for Comparative Proteomic Analysis of Arabidopsis thaliana Suspension Cell Cultures

Here we describe a robust method for the fractionation of plant plasma membranes into detergent resistant and detergent soluble membranes based on a mixture of unlabeled and in vivo fully 15N labeled Arabidopsis thaliana cell cultures. The procedure is applied for comparative proteomic studies to understand signaling processes.

Plasma membrane microdomains are features based on the physical properties of the lipid and sterol environment and have particular roles in signaling ...

A Video Protocol of Retroviral Infection in Primary Intestinal Organoid Culture

Lgr5-positive stem cells can be supplemented with the essential growth factors Egf, Noggin, and R-Spondin, which allows us to culture ever-expanding primary 3D epithelial structures in vitro. Both the architecture and physiological properties of these &#39;mini-guts&#39;, also called organoids, closely resemble their in vivo counterparts. This makes them an attractive model system for the small intestinal epithelium. Using retroviral transduction, functional genetics can now be performed by conditional gene overexpression or knockdown. This video demonstrates the procedure of organoid culture, the generation of retroviruses, and the retroviral transduction of organoids to assist phenotypic analysis of the small intestinal epithelium in vitro. This novel organotypic model system in combination with retroviral mediated gene expression provides a valuable tool for rapid analysis of gene function in vitro without the need of costly and time-consuming generation for transgenic animals.

This protocol explains primary Lgr5-positve organoid culture and the subsequent performance of retroviral transduction. This enables Cre-inducible overexpression or knockdown of the delivered transgene and allows functional studies to be carried out in the novel in vitro organotypic model system.

Lgr5-positive stem cells can be supplemented with the essential growth factors Egf, Noggin, and R-Spondin, which allows us to culture ever-expanding ...

Measuring the Stiffness of Ex Vivo Mouse Aortas Using Atomic Force Microscopy

Arterial stiffening is a significant risk factor and biomarker for cardiovascular disease and a hallmark of aging. Atomic force microscopy (AFM) is a versatile analytical tool for characterizing viscoelastic mechanical properties for a variety of materials ranging from hard (plastic, glass, metal, etc.) surfaces to cells on any substrate. It has been widely used to measure the stiffness of cells, but less frequently used to measure the stiffness of aortas. In this paper, we will describe the procedures for using AFM in contact mode to measure the ex vivo elastic modulus of unloaded mouse arteries. We describe our procedure for isolation of mouse aortas, and then provide detailed information for the AFM analysis. This includes step-by-step instructions for alignment of the laser beam, calibration of the spring constant and deflection sensitivity of the AFM probe, and acquisition of force curves. We also provide a detailed protocol for data analysis of the force curves.

Measuring the Stiffness of Ex Vivo Mouse Aortas Using Atomic Force Microscopy

We present detailed protocols for isolation of aortas from mouse and measurement of their elastic modulus using atomic force microscopy.

Arterial stiffening is a significant risk factor and biomarker for cardiovascular disease and a hallmark of aging. Atomic force microscopy (AFM) is a ...

Mixed Primary Cultures of Murine Small Intestine Intended for the Study of Gut Hormone Secretion and Live Cell Imaging of Enteroendocrine Cells

The gut is the largest endocrine organ of the body, with hormone-secreting enteroendocrine cells located along the length of the gastrointestinal epithelium. Despite their physiological importance, enteroendocrine cells represent only a small fraction of the epithelial cell population and in the past, their characterization has presented a considerable challenge resulting in a reliance on cell line models. Here, we provide a detailed protocol for the isolation and culture of mixed murine small intestinal cells. These primary cultures have been used to identify the signaling pathways underlying the stimulation and inhibition of gut peptide secretion in response to a number of nutrients and neuropeptides as well as pharmacological agents. Furthermore, in combination with the use of transgenic fluorescent reporter mice, we have demonstrated that these primary cultures become a powerful tool for the examination of fluorescently-tagged enteroendocrine cells at the intracellular level, using methods such as patch clamping and single-cell calcium and cAMP-FRET imaging.

This protocol describes the isolation and culture of mixed murine small intestinal cells. These primary intestinal cultures enable the investigation of signaling pathways underlying gut peptide secretion using a number of techniques.

The gut is the largest endocrine organ of the body, with hormone-secreting enteroendocrine cells located along the length of the gastrointestinal ...

Real-time In Vivo Recording of Arabidopsis Calcium Signals During Insect Feeding Using a Fluorescent Biosensor

Calcium ions are predicted to be key signaling entities during biotic interactions, with calcium signaling forming an established part of the plant defense response to microbial elicitors and to wounding caused by chewing insects, eliciting systemic calcium signals in plants. However, the role of calcium in vivo during biotic stress is still unclear. This protocol describes the use of a genetically-encoded calcium sensor to detect calcium signals in plants during feeding by a hemipteran pest. Hemipterans such as aphids pierce a small number of cells with specialized, elongated sucking mouthparts, making them the ideal tool to study calcium dynamics when a plant is faced with a biotic stress, which is distinct from a wounding response. In addition, fluorescent biosensors are revolutionizing the measurement of signaling molecules in vivo in both animals and plants. Expressing a GFP-based calcium biosensor, GCaMP3, in the model plant Arabidopsis thaliana allows for the real-time imaging of plant calcium dynamics during insect feeding, with a high spatial and temporal resolution. A repeatable and robust assay has been developed using the fluorescence microscopy of detached GCaMP3 leaves, allowing for the continuous measurement of cytosolic calcium dynamics before, during, and after insect feeding. This reveals a highly-localized rapid calcium elevation around the aphid feeding site that occurs within a few minutes. The protocol can be adapted to other biotic stresses, such as additional insect species, while the use of Arabidopsis thaliana allows for the rapid generation of mutants to facilitate the molecular analysis of the phenomenon.

Real-time In Vivo Recording of Arabidopsis Calcium Signals During Insect Feeding Using a Fluorescent Biosensor

This protocol outlines a simple method for analyzing calcium signals in plants generated by feeding hemipteran insects, such as aphids. Arabidopsis thaliana transformed with the GFP calcium biosensor GCaMP3 allow for the real-time in vivo imaging of calcium dynamics with a high temporal and spatial resolution.

Calcium ions are predicted to be key signaling entities during biotic interactions, with calcium signaling forming an established part of the plant ...

An Ex Vivo Choroid Sprouting Assay of Ocular Microvascular Angiogenesis

Pathological choroidal angiogenesis, a salient feature of age-related macular degeneration, leads to vision impairment and blindness. Endothelial cell (EC) proliferation assays using human retinal microvascular endothelial cells (HRMECs) or isolated primary retinal ECs are widely used in vitro models to study retinal angiogenesis. However, isolating pure murine retinal endothelial cells is technically challenging and retinal ECs may have different proliferation responses than choroidal endothelial cells and different cell/cell interactions. A highly reproducible ex vivo choroidal sprouting assay as a model of choroidal microvascular proliferation was developed. This model includes the interaction between choroid vasculature (EC, macrophages, pericytes) and retinal pigment epithelium (RPE). Mouse RPE/choroid/scleral explants are isolated and incubated in growth-factor-reduced basal membrane extract (BME) (day 0). Medium is changed every other day and choroid sprouting is quantified at day 6. The images of individual choroid explant are taken with an inverted phase microscope and the sprouting area is quantified using a semi-automated macro plug-in to the ImageJ software developed in this lab. This reproducible ex vivo choroidal sprouting assay can be used to assess compounds for potential treatment and for microvascular disease research to assess pathways involved in choroidal micro vessel proliferation using wild type and genetically modified mouse tissue.

This protocol presents choroid sprouting assay, an ex vivo model of microvascular proliferation. This assay can be used to assess pathways involved in proliferating choroidal micro vessels and assess drug treatments using wild type and genetically modified mouse tissue.

Pathological choroidal angiogenesis, a salient feature of age-related macular degeneration, leads to vision impairment and blindness. Endothelial cell ...

Organoid-Derived Epithelial Monolayer: A Clinically Relevant In Vitro Model for Intestinal Barrier Function

In the past, intestinal epithelial model systems were limited to transformed cell lines and primary tissue. These model systems have inherent limitations as the former do not faithfully represent original tissue physiology, and the availability of the latter is limited. Hence, their application hampers fundamental and drug development research. Adult stem-cell-based organoids (henceforth referred to as organoids) are miniatures of normal or diseased epithelial tissue from which they are derived. They can be established very efficiently from different gastrointestinal (GI) tract regions, have long-term expandability, and simulate tissue- and patient-specific responses to treatments in vitro. Here, the establishment of intestinal organoid-derived epithelial monolayers has been demonstrated along with methods to measure epithelial barrier integrity, permeability and transport,&#160;antimicrobial protein secretion, as well as histology. Moreover, intestinal organoid-derived monolayers can be enriched with proliferating stem and transit-amplifying cells as well as with key differentiated epithelial cells. Therefore, they represent a model system that can be tailored to study the effects of compounds on target cells and their mode of action. Although organoid cultures are technically more demanding than cell lines, once established, they can reduce failures in the later stages of drug development as they truly represent in vivo epithelium complexity and interpatient heterogeneity.

Here, we describe the preparation of human organoid-derived intestinal epithelial monolayers for studying intestinal barrier function, permeability, and transport. As organoids represent original epithelial tissue response to external stimuli, these models combine the advantages of expandability of cell lines and the relevance and complexity of primary tissue.

In the past, intestinal epithelial model systems were limited to transformed cell lines and primary tissue. These model systems have inherent limitations ...