Using Human Intestinal Organoids to Understand the Small Intestine Epithelium at the Single Cell Transcriptional Level

Summary

The protocol combines human intestinal organoid technology with single cell transcriptomic analysis to provide significant insight into previously unexplored intestinal biology.

Abstract

Single cell transcriptomics has revolutionized our understanding of the cell biology of the human body. State-of-the-art human small intestinal organoid cultures provide ex vivo model systems that bridge the gap between animal models and clinical studies. The application of single cell transcriptomics to human intestinal organoid (HIO) models is revealing previously unrecognized cell biology, biochemistry, and physiology of the GI tract. The advanced single cell transcriptomics platforms use microfluidic partitioning and barcoding to generate cDNA libraries. These barcoded cDNAs can be easily sequenced by next generation sequencing platforms and used by various visualization tools to generate maps. Here, we describe methods to culture and differentiate human small intestinal HIOs in different formats and procedures for isolating viable cells from these formats that are suitable for use in single-cell transcriptional profiling platforms. These protocols and procedures facilitate the use of small intestinal HIOs to obtain an increased understanding of the cellular response of human intestinal epithelium at the transcriptional level in the context of a variety of different environments.

Introduction

The small intestinal epithelium has two distinct zones: the crypt that houses the intestinal stem cell (ISC) and the villus, which is comprised of differentiated cells of the secretory and absorptive lineages. Adding to this complexity is the regional specificity of the epithelium that provides unique functional properties between the regions of the small intestine. Pioneering work established culture conditions in which both the human small intestinal crypt and villus zones can be generated ex vivo from surgical tissues or tissue biopsies¹. These cultures are bridging the gap between animal studies and clinical trials and are revealing previously unrecognized cell biology, biochemistry, and physiology of the gastrointestinal tract. The HIOs are propagated as 3D spherical structures using a media with growth factors that promote stem cell viability and extracellular support matrices. These conditions result in a crypt-like HIO model that consists mostly of progenitors and stem cells. Removal of the growth factors promotes ISC differentiation (villus-like model) and production of mature intestinal epithelial cells (goblet, enteroendocrine, tuft, enterocyte) in appropriate ratios along with cell proliferation and differentiation, polarization, barrier integrity, regional specific features, and appropriate physiological responses². HIO cultures are genetically stable and can be propagated indefinitely in their crypt-like state. Easy access to the apical surface of these cultures is provided by culture conditions that allow growth in a monolayer format³. HIOs also allow considerations of host individual variability such as genetics, age, sex, ethnicity, and disease status to be included in biological analyses. Analytic and functional assessment tools are identical to those used in approaches centered on transformed cell lines and include a variety of molecular techniques such as flow cytometry, microscopy, transcriptomics, proteomics, and metabolomics.

Single cell transcriptomics is revolutionizing our understanding of the biology and physiology of the small intestine by providing insight into the individual contributions of each cell type to a biological process. Pioneering work using this technology has provided a landscape of the cell types present in the native human intestine^4,5,6. Single cell transcriptional profiling platforms allow exploration of the transcriptional landscape of individual cells, allowing cell heterogeneity to come to the forefront of scientific exploration. In some single cell transcriptional profiling platforms, microfluidic partitioning and barcoding are used to generate cDNA libraries from cellular polyadenylated mRNAs obtained from up to 10,000 cells per sample. On this platform, droplets containing single cells, barcoded oligonucleotides, reverse transcription reagents, and oil form a reaction vesicle that results in all cDNAs from a single cell having the same barcode. The barcoded cDNAs can then be efficiently sequenced using next generation sequencing. Data generated can be handled through software and visualization tools, which convert the barcoded sequences into visualization maps and single cell transcriptional profiles. Cell populations can be identified using publicly available databases of human small intestinal epithelium^4,5,6. Although many studies have utilized this platform to interrogate murine intestinal organoids at the single cell level, the analysis of single cell transcriptional responses of HIOs has lagged behind^{7,8,9,10,11,12}.

Here, we provide a step-by-step guide to isolating viable cells from small intestinal HIOs for processing on single cell transcriptional profiling platforms (Figure 1). We provide culturing and differentiation guidelines along with media components that have been optimized for epithelial differentiation. We outline cell recovery methods for three different culture formats: three dimensional (3D) and monolayer cultures either on plastic or on membrane cell culture inserts. We provide sample clustering data obtained using open-source software to derive differentially expressed genes in each cluster.

Protocol

The organoid lines used here were obtained from the Texas Medical Center Digestive Disease Center GEMS Core. Briefly, to initially establish organoid lines, donor tissue samples were washed and enzymatically digested to release the intestinal crypts. Crypts were embedded in a basement membrane and cultured in a medium. The Institutional Review Board at Baylor College of Medicine approved the study protocol to obtain tissue samples from which organoid lines were established, and informed consent was obtained from all donors to establish organoid lines from the donated tissue.

1. Passaging of 3D HIOs to expand for differentiation

1. Remove and discard medium from wells of organoids grown in 24-well plates (around the solid basement membrane) with a P1000 pipet. Add 300 µL of 0.05% Trypsin-EDTA to the well and mechanically break up organoids by pipetting with a P1000 pipet up and down 5x.
2. Incubate plate at 37 °C for 4 min. Add 500 µL of complete media without growth factors (CMGF- medium) with 10% FBS to each well (Table 1). Use a P1000 pipet and pipet CMGF medium and HIO mixture, 10x back and forth in the well. Transfer the entire volume into a 15 mL tube. Combine passage from multiple wells into the same 15 mL tube. Do not combine more than 10 wells per tube.
3. Spin down cells at 4 °C using a swing rotor centrifuge at 100 x g for 5 min. Remove all the medium, keeping the pellet at the bottom of the tube. Keep the tube on ice.
4. Calculate the amount of basement membrane needed for the number of HIO plated, and resuspend the HIO pellet in 30 µL/well of basement membrane using cold P200 pipet tips. Pipette the HIO basement membrane mixture as a droplet into the center of a 24-well plate using cold P200 pipet tips.
5. Transfer the plate to a 37 °C incubator. Let the basement membrane solidify for 5-10 min, then add 500 µL of room temperature complete medium containing WNT, R-spondin, noggin, EGF, and ROCK inhibitor (WRNE+Y; Table 1) to each well and culture in a 37 °C incubator. Refresh culture with WRNE+Y every other day for 7 days.
   NOTE: A healthy HIO will be cystic in shape with a shiny budding epithelium (Figure 2). Cells in the middle of the cyst cannot be visualized. An unhealthy HIO will look dull and have a thick epithelium with a solid middle. The most important characteristic is the shiny appearance.

2. HIO differentiation: 3D format

1. Use one well of 3D HIOs for 3 wells of 3D differentiated HIOs 1 week after culturing.
2. Remove media from wells. Disperse basement membrane and HIOs using a P1000 pipet and add cold 500 µL of CMGF- per well and pipet up and down at least 5x. Spin down HIOs at 4 °C using a swing rotor centrifuge at 100 x g for 5 min. Remove all the medium keeping the pellet at the bottom of the tube.
3. Add 30 µL of basement membrane per well of HIOs being plated. Pipette the 30 µL droplet of basement membrane with HIOs into a well of a 24-well plate. Incubate at 37 °C for 10 min. Add 500 µL of WRNE+Y/Diff (50/50) media.
4. Switch the medium to differentiation medium after 24 h for 3 additional days, refreshing the medium every other day. Prepare 3 wells per sample to pool to reduce technical variability.

3. HIO differentiation: Monolayer format

1. Coat the membrane cell culture inserts or wells of a 96-well plate with 100 µL/well of human placental collagen IV (1mg/ml in 100mM acetic acid) diluted in cold H₂O (1:30). Incubate at 37 °C for a minimum of 1.5 h or maximum overnight. For membrane cell culture insert, add sterile H₂O in the plate space to humidify the plate; for 96-well plate, add sterile H₂O in the unused wells.
2. Collect 3D HIOs cultured in WRNE for 7 days by removing the media and recovering the basement membrane and cells by adding 500 µL/well of cold 0.5 mM EDTA (0.5 M EDTA diluted 1:1000 in sterile PBS). Use a P1000 pipet to pipet organoids and solution up and down 5x and transfer to a 15 mL microcentrifuge tube. Do not pool more than 10 wells of organoids per tube. Centrifuge for 5 min at 300 x g in a swinging bucket rotor at 4 °C.
   NOTE: To prepare 3 wells on a 96-well plate, use 1 well of 3D HIOs. To prepare 1 membrane cell culture insert, use 1 well of 3D HIOs (seeding density of single cells is approximately 1-2 x 10⁵ cells/well for 96-well plate, 2.5-3 x 10⁵ cells/well for membrane cell culture insert).
3. Remove 500 µL of media, leaving the pellet at the bottom of the tube. Dissociate the HIOs by adding 500 µL of 0.05% Trypsin/0.5 mM EDTA and incubating for 4-5 min at 37 °C. Vigorously pipette up and down for ~50x using a P1000. Avoid making bubbles by pipetting against the side of the tube.
4. Inactivate the trypsin by adding 1 mL of CMGF- containing 10% FBS. Filter out large clumps of undigested cells by wetting a 40 µm cell strainer with 1 mL of CMGF- containing 10% FBS and adding the cells to the top of the cell strainer. Use gravity to allow the cells to pass through the strainer and discard the cell strainer containing cell clumps.
5. Collect the cells by centrifugation for 5 min at 400 x g in a swinging bucket rotor at room temperature.
6. Remove the liquid from the collagen-coated membrane cell culture insert or from the 96-well plate. Resuspend the HIO pellet in 100 µL/well of WRNE containing 10 µM Y-27632, then pipette into the upper compartment of the membrane cell culture insert or into the 96-well plate. For membrane cell culture insert, add 600 µL of WRNE containing 10 µM Y-27632 into the lower compartment of the well.
7. Remove the medium after 24 h from both the upper and lower part of the membrane cell culture insert or from the 96-well plate and replace with differentiation medium for 5 days. Prepare 3 wells per sample to pool to reduce technical variability.

4. Preparation of single cell suspensions from differentiated 3D HIOs for single cell transcriptomics

1. Place enzymatic cell digestion reagent at 37 °C in a CO₂ incubator to thaw and warm 30 min prior to initiation of 3D HIO digestion. Check the HIOs using a bright field microscope at 10x to ensure cell health.
2. Remove the media from the wells and add 500 µL of cold cell recovery solution to the wells. Pipette up and down a few times to liberate the cells from the basement membrane using a P1000 pipette and standard pipette tips. Transfer the cell suspension to a 1.5 mL microcentrifuge tube.
   NOTE: The use of replicate wells ensures adequate cell numbers and reduces well-to-well variation. Do not combine wells before step 4.7 below.
3. Incubate the tubes of cells on ice for 10 min, pipetting up and down every 5 min. Collect the cells by centrifugation for 3 min at 400 x g at 4 °C.
4. Remove the liquid from the tube, taking care not to disturb the cell pellet. Resuspend the cells in 500 µL of pre-warmed enzymatic cell digestion reagent. Pipette up and down with a P1000 at least 10x.
5. Incubate the HIOs for 30 min at 37 °C in a CO₂ incubator. Every 10 min, pipette the entire volume 10x using a P1000 pipette to help dissociate the cells. Avoid introducing air bubbles into the cell suspension.
6. Pellet the cells for 3 min at 400 x g at 4 °C. Remove the supernatant, resuspend the cells in 1 mL of differentiation media, and store on ice.
   NOTE: From this point on, the HIOs must always be kept on ice.
7. Pipette the cells up and down 50x rapidly using a P1000 to ensure HIOs are dissociated into single cells. Take care not to introduce air bubbles at this step, as it will cause cell loss.
8. Filter the entire volume through a 70 µm tip strainer using a P1000 pipette tip. Use a 1.5 mL microcentrifuge tube to collect the eluate.
   NOTE: The filter tip will not become clogged if digestion time is sufficient. Use multiple filter tips if the filter becomes clogged; do not force the volume through the filter.
9. Repeat step 4.8 with a 40 µm tip strainer. Store samples on ice.
10. Count viable single cells on a cell counting chamber using trypan blue exclusion by adding 5 µL of 0.4% trypan blue to 5 µL of cell suspension. Dilute the sample as needed to 1000 cells/µL. If the cell density is less than 1000 cells/µL, pellet cells for 2 min at 400 x g at 4 °C, remove the original media, and resuspend in cell culture media. This protocol typically yields 5 x 10⁵-1 x 10⁶ cells.
    NOTE: Preparation of a high-quality suspension (90% viable and 90% single cells) is essential for high quality single-cell data. However, experience indicates viability as low as 75% can be accepted in cases where treatment, such as infection or small molecule application, impact viability.
11. Prepare DNA libraries for single cell transcriptional profiling platforms according to the manufacturer's protocols. Process the data according to best practice protocols for scRNAseq data analysis^13,14.

5. Preparation of single cell suspensions from HIOs differentiated on membrane cell culture insert

1. Place enzymatic cell digestion reagent at 37 °C in a CO₂ incubator to thaw and warm 30 min prior to initiation of HIO membrane cell culture insert digestion. Divide the pre-warmed enzymatic cell digestion reagent into 200 µL aliquots in 1.5 mL microcentrifuge tubes, 1 tube per membrane cell culture insert. Keep the tubes in the 37 °C incubator until ready for use.
2. Prepare PBS-EDTA by adding 5 µL of 0.5 M EDTA to 5 mL of PBS. Aliquot 500 µL of PBS-EDTA into a 24-well plate, 1 well per membrane cell culture insert.
3. Wash the cells with PBS-EDTA: transfer the membrane cell culture inserts from wells containing growth media to the wells containing PBS-EDTA. Remove the cell culture media from the apical side and replace it with 100 µL of PBS-EDTA. Take care not to disturb the cell layer.
4. Immediately discard the PBS-EDTA added to the apical side of the membrane cell culture inserts. Remove the membrane cell culture insert from the well, blot it by gently touching the edge to a paper towel, and then invert it on the benchtop. Use a sharp scalpel blade to remove the membrane from the insert by cutting around the inner circumference of the membrane. Work quickly to prevent drying.
5. Use forceps to transfer the membrane to the pre-warmed 1.5 mL microcentrifuge tube filled with enzymatic cell digestion reagent and ensure the membrane is completely submerged. Repeat for all additional membrane cell culture inserts.
   NOTE: Increasing the volume of the enzymatic cell digestion reagent to 500 µL may aid in dissociating dense monolayers.
6. Dissociate the cells by incubating tubes with membranes at 37 °C in a CO₂ incubator. Mix by gently pipetting the entire volume 5x with a 200 µL pipette every 10 min for a total of 30 min. Avoid bubbles and suction of the membrane to preserve viability.
7. Transfer a small aliquot of cells (1-2 µL) to a glass slide every 10 min to assess dissociation by qualitatively assessing the percent of single cells. It may take up to 50 min with additional pipetting to achieve 80%-90% single cells, depending on the HIO type. Gently scrape the membrane with a pipette tip during mixing steps to encourage dissociation, particularly for hard to dissociate cells, however scraping may impact viability.
8. Combine 3 replicate wells per condition in a single 1.5 mL microcentrifuge tube (600 µL total). Add 400 µL of cell culture media (diff) + 10 µM ROCKi (1 mL total volume). Mix gently by pipetting.
   NOTE: The use of replicate wells ensures adequate cell numbers and reduces well-to-well variation. Wells should be pooled at this step.
9. Filter the entire volume through a 70 µm tip strainer using a 1 mL pipette tip. Collect the flow through in a fresh 1.5 mL microcentrifuge tube.
   NOTE: The filter tip will not become clogged if digestion time is sufficient. Use multiple filter tips if the filter becomes clogged; do not force the volume through.
10. Repeat step 5.9 with a 40 µm tip strainer. Store samples on ice.
11. Count viable single cells on a cell counting chamber using trypan blue exclusion by adding 5 µL of 0.4% trypan blue to 5 µL of cell suspension. Dilute sample as needed to 1000 cells/ µL. If the cell density is less than 1000 cells/ µL, spin 2 min at 400 x g at 4 °C to pellet the cells, remove the original media, and resuspend in WRNE+Y at the desired cell density. This protocol typically yields 4 x 10⁵ - 6 x 10⁵ cells.
    NOTE: Preparation of high-quality suspension (90% viable and 90% single cells) is essential for high quality single-cell data. However, experience indicates viability as low as 75% can be accepted in cases where treatment, such as infection or small molecule application, impact viability.
12. Prepare DNA libraries for the single cell transcriptional profiling platforms according to the manufacturer's protocols. Process the data according to best practice protocols for scRNAseq data analysis^13,14.

6. Preparation of single cell suspensions from HIOs differentiated as 96-well monolayers

1. Place enzymatic cell digestion reagent at 37 °C in a CO₂ incubator to thaw and warm 30 min prior to initiation of monolayer HIO digestion.
2. Prepare PBS-EDTA by adding 5 µL of 0.5 M EDTA to 5 mL of PBS. Discard the cell culture media from the 96-well plate and replace it with 100 µL of PBS-EDTA. Take care not to disturb the cell layer.
3. Dissociate the cells: Discard the PBS-EDTA and add 100 µL of warm enzymatic cell digestion reagent to each well. Place the plate in the 37 °C in a 5% CO₂ incubator and mix by gently pipetting the entire volume 5x with a 200 µL pipette tip every 10 min for 20-30 min. Avoid bubbles to preserve viability.
   NOTE: Increasing the volume of enzymatic cell digestion reagent to 500 µL may aid in dissociating dense monolayers.
4. Transfer a small aliquot of cells (1-2 µL) to a glass slide every 10 min to assess dissociation. It may take up to 50 min to achieve 80%-90% single cells, depending on the HIO type. Gently scrape the plate with a pipette tip during mixing steps to encourage dissociation, particularly for hard to dissociate cells; however, scraping may impact viability.
5. Combine 3 replicate wells per condition in a single 1.5 mL microcentrifuge tube (300 µL total). Add 700 µL of cell culture media (diff) + 10 uM ROCKi (1 mL total volume). Mix gently by pipetting.
   NOTE: The use of replicate grown wells ensures adequate cell numbers and reduces well-to-well variation.
6. Filter the entire volume through a 70 µm tip strainer using a 1 mL pipette tip. Collect the flow through in a fresh 1.5 mL microcentrifuge tube.
   NOTE: The filter tip will not become clogged if enzymatic cell digestion reagent digestion time is sufficient. Use multiple filter tips if the filter becomes clogged; do not force the volume through.
7. Repeat step 6.6 with a 40 µm tip strainer. Store samples on ice.
8. Count viable single cells on a cell counting chamber using trypan blue exclusion by adding 5 µL of 0.4% trypan blue to 5 µL of cell suspension. Dilute as needed to 1000 cells/µL. If the cell density is less than 1000 cells/µL, spin 2 min at 400 x g 4 °C to pellet the cells, remove the original media, and resuspend in cell culture media + ROCKi at the desired cell density. This protocol typically yields 2 x 10⁵ - 6 x 10⁵ cells.
   NOTE: Preparation of high-quality suspension (90% viable and 90% single cells) is essential for high quality single-cell data. However, experience indicates viability as low as 75% can be accepted in cases where treatment, such as infection or small molecule application, impact viability.
9. Prepare DNA libraries according to the single cell transcriptional profiling platform manufacturer's protocols. Process the data according to best practice protocols for scRNAseq data analysis^13,14.

Results

Single-cell suspensions were pooled from 2-3 wells of membrane cell culture insert, monolayer, and 3D HIOs to ensure sufficient cell yield and reduce well-to-well variation. Single cell libraries were prepared using reagents specific to the single cell transcriptional profiling platform. and sequenced with paired end reads on a next generation sequencing platform, 30,000 reads/cell. Reads were mapped, counted, and analyzed using analytical tools for single cell genomics. Low-quality cells with more than 20% mitochondrial...

Discussion

Using single cell genomics platforms, complex biological systems, such as tissue derived HIO cultures that model the intestinal epithelium, can be broken down to yield individual cellular contributions to overall biological response^4,5,6. Cellular heterogeneity and rare cell populations can also be identified and interrogated. Cellular input needs to be optimized to maximize output using single cell transcriptomic-based platform...

Materials

Name	Company	Catalog Number	Comments
[Leu15]-Gastrin I	Sigma-Aldrich	G9145	10 nM
0.05% Trypsin-EDTA	Invitrogen	25300054
0.4% Trypan blue	Millipore-Sigma	T8154
0.5 M EDTA	Corning	46-034-CI
1x PBS Ca- Mg-	Corning	21-040-CM
24 mm Transwell	Costar	3412
24 well Nunclon delta surface tissue culture dish	Thermo Scientific	142475
40 µm cell strainer	Falcon	352340
40 µm Flowmi tip strainer	SP Bel-Art Labware	H13680-0040
70 µm Flowmi tip strainer	SP Bel-Art Labware	H13680-0070
96 well plate	Corning	3595
A-83-01	Tocris	2939	500 nM
Accutase	StemCell Technologies	7920
Advanced DMEM/F12	Invitrogen	12634-028
B27 supplement	Invitrogen	17504-044	1X
Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1	10x Genomics	PN-1000128
Collagen IV	Sigma-Aldrich	C5533-5MG	33 µg/mL
Corning Cell Recovery Solution	VWR	354253
DPBS (Mg2-, Ca2-)	Invitrogen	14190-136	1X
GlutaMAX-I	Invitrogen	35050-061	2 mM
HEPES 1M	Invitrogen	15630-080	10 mM
L-WRN conditioned media	ATCC	CRL-3276
Matrigel, GFR, phenol free	Corning	356231
mouse recombinant EGF	Invitrogen	PMG8043	50 ng/mL
N2 supplement	Invitrogen	17502-048	1X
N-Acetylcysteine	Sigma-Aldrich	A9165-5G	500 µM
Nicotinamide	Sigma-Aldrich	N0636	10 mM
SB202190	Sigma-Aldrich	S7067	10 µM
Transwell	Corning	3413
Y27632	Stem Cell Technologies	72308	10 µM