Generation of Mosaic Mammary Organoids by Differential Trypsinization

Summary

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

Abstract

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

Introduction

The mammary gland (MG) is a tree-like, tubular epithelial structure embedded within an adipocyte rich stroma. The bilayered ductal epithelium comprises an outer, basal layer of contractile, myoepithelial cells (MyoECs) and an inner layer of luminal, secretory epithelial cells (LECs), encircling a central lumen¹. During lactation when the outer MyoECs contract to squeeze milk from the inner alveolar LECs, the MG undergoes numerous changes that are under the control of growth factors (e.g., EGF and FGF) and hormones (e.g. progesterone, insulin, and prolactin). These changes cause the differentiation of specialized structures, alveoli, which synthesize and secrete milk during lactation¹. The mammary epithelia can be experimentally manipulated using techniques in which either epithelial tissue fragments, cells, or even a single basal cell are transplanted into host mammary fat pads, precleared of endogenous mammary parenchyma, and allowed to grow out to reconstitute an entire, functional epithelial tree^2,3,4,5. Transplantation is a powerful technique, but it is time-consuming and impossible if a mutation results in early embryonic lethality (prior to E14) that prevents the rescue of transplantable mammary anlage. Furthermore, investigators frequently wish to research the roles of the two different compartments, which are derived from lineage-restricted progenitor cells. While Cre-lox technology allows differential genetic manipulation of MyoECs and LECs, this is also a time-consuming and expensive undertaking. Thus, since the 1950s, investigators have used in vitro mammary organoids as a relatively easy and efficient way to address questions concerning mammary tissue structure and function^6,7.

In early protocols describing the isolation and culture of primary mammary epithelial cells, investigators found that a basement membrane matrix (BME), composed of a plasma clot and chicken embryo extract, was required for MG fragments grown on a dish⁶. In the following decades, extracellular matrices (ECMs, collagen, and jellylike protein matrix secreted by Engelbreth-Holm-Swarm murine sarcoma cells) were developed to facilitate 3D culture and better mimic the in vivo environment^7,8,9,10. Culturing cells in 3D matrices revealed by multiple criteria (morphology, gene expression, and hormone responsiveness) that such a microenvironment better models in vivo physiological processes^9,10,11,12. Research using primary murine cells identified key growth factors and morphogens necessary for the extended maintenance and differentiation of organoids¹³. These studies have set the stage for the protocol presented here, and for the culture of human breast cells as 3D organoids, which is now a modern clinical tool, allowing for drug discovery and drug testing on patient samples¹⁴. Overall, organoid culturing highlights the self-organization capacities of primary cells and their contributions to morphogenesis and differentiation.

Presented here is a protocol to culture murine epithelia that can be differentiated into milk-producing acini. A differential trypsinization technique is used to isolate the MyoECs and LECs that comprise the two distinct MG cell compartments. These separated cell fractions can then be genetically manipulated to overexpress or knockdown gene function. Because lineage-intrinsic, self-organization is an innate property of mammary epithelial cells^15,16,17, recombining these cell fractions allows researchers to generate bilayered, mosaic organoids. We begin by enzymatically digesting the adipose tissue, and then incubating the mammary fragments on a tissue culture dish for 24 h (Figure 1). The tissue fragments settle on polystyrene dishes as bilayered fragments with their in vivo organization: outer myoepithelial layer surrounding inner luminal layers. This cellular organization allows for the isolation of the outer MyoECs by trypsin-EDTA (0.05%) treatment for 3-6 min followed by a second round of trypsin-EDTA (0.05%) treatment that detaches the remaining inner LECs (Figure 2). Thus, these cell types with different trypsin sensitivity are isolated and can subsequently be mixed and plated in ECM (Figure 3). The cells undergo self-organization to form bilayered spheres, comprising an outer layer of MyoECs surrounding inner LECs. Lumen formation occurs as the cells grow in a medium containing a cocktail of growth factors (see recipes for Growth Medium)¹³. After 5 days, organoids can be differentiated into milk-producing acini by switching to Alveologenesis Medium (see recipes and Figure 3F) and incubated for another 5 days. Alternatively, organoids will continue to expand and branch in Growth Medium for at least 10 days. Organoids can be analyzed using immunofluorescence (Figure 3D-F) or released from the ECM using a recovery solution (see Table of Materials) and analyzed via other methods (e.g., immunoblot, RT-qPCR).

Protocol

All methods described here have been approved by the Institutional Animal Care and Use Committee (IACUC) of the University of California, Santa Cruz.

1. Day 1: Mammary gland digestion

1. Prepare to harvest the MGs from mature female mice 10-14 weeks of age.
   1. Perform the harvesting on an open bench under aseptic conditions.
   2. Sterilize all surgical supplies, cork boards, and pins by autoclaving and soaking in 70% alcohol for 20 min prior to surgery.
   3. Anesthetize animals with sodium pentobarbital (2X anesthetic dose of 0.06 mg/g body weight) delivered via intraperitoneal injection with a 0.5 mL insulin syringe.
   4. Monitor the level of anesthesia by pinching the animal's toes to check for a reflex response and commence the protocol only after the animal is fully anesthetized.
   5. Place the animal on its back, pin its appendages to the corkboard, and wipe down its abdomen and chest with ethanol.
2. To harvest the #2, 3, 4, and 5 MGs from one mouse (i.e., 8 MGs, Figure 1A), identify the midline between the two hind legs and make a small incision (1 cm) on the abdominal skin with sharp scissors, then extend the cut up to the neck¹⁸.
3. Follow by making small cuts laterally towards the legs and arms to allow for the release of the skin using a cotton swab. Pull the skin away and stretch it tight before pinning it down on one side (Figure 1B, step 1)¹⁸. Remove the MGs by cutting under them, and remove the lymph nodes from the #4 glands (Figure 1B, steps 2, 3)¹⁸. Repeat the procedure on the other side of the body.
4. Collect the MG tissue in 50 mL of 4 °C Dulbecco's Modified Eagle's Media (DMEM)/Nutrient Mixture F12 (F12) supplemented with 5% fetal bovine serum (FBS) and 1X Antibiotic-Antimycotic (Anti-Anti)¹⁸.
5. Chop the glands in a 35 mm dish or on a ceramic plate using a razor blade or tissue chopper. Rotate the plate every five manual chops or every round on the tissue chopper until the tissue pieces can fit through a 1 mL micropipette tip with ease (~0.1 mm/fragment, Figure 1C).
6. Digest the MGs in Digestion Medium (see Table 1) for 14 h in a 6 well low adhesion dish at 37 °C, 5% CO₂.

2. Day 2: Isolation of mammary epithelial tissue fragments

1. After 14 h of digestion, gently mix by pipetting the digested tissue 10X using a 1 mL micropipette to break down any remaining stroma or adipose tissue, ensuring that neither bubbles nor excess mechanical force are generated.
   NOTE: If there is incomplete digestion after 14 h, this could be due to the accumulation of sheared DNA. In this case, add 1 µL of 1 mg/mL deoxyribonuclease I (DNase I) per 2 mL of Digestion Medium. Incubate for another 30 min at 37 °C, 5% CO₂.
2. Collect tissue in a 15 mL tube and rinse the well used for digestion with 2-3 mL of tissue culture grade 1X Dulbecco's Phosphate Buffered Saline (DPBS) free of Ca²⁺ and Mg²⁺. Centrifuge at 600 x g for 10 min.
3. Evacuate the supernatant containing the lipid layer and medium, and then resuspend the pellet in 5 mL of DPBS and switch to a new 15 mL tube. Centrifuge at 600 x g for 10 min.
4. During centrifugation place a 70 µm nylon cell strainer in a 50 mL tube and prewet the strainer using 10 mL of 37 °C DMEM/F12.
5. Resuspend tissue fragments from protocol step 2.4 using 5 mL of DPBS and pass the suspension through a prewet 70 µm nylon cell strainer to remove stromal cells and single cells (Figure 1D).
6. Collect the tissue fragments on the cell strainer. Rinse 4X with 10 mL of 37 °C DMEM/F12 (Figure 1D).
   CAUTION: Incomplete rinsing will result in cultures contaminated with non-epithelial cells.
7. Release the tissue fragments by holding the strainer tab with gloved fingers, inverting the strainer over a 60 mm tissue culture dish and passing 1 mL aliquots of Maintenance Medium (see Table 1) through the bottom of the strainer 4X (Figure 1E).
8. Check the strainer for tissue fragment remnants, which will be visible by the naked eye, and rinse the strainer 1X more with 1 mL of Maintenance Medium if any fragments are still adhering to the strainer. The rinsed tissue fragments should now be free of stromal cells.
9. Quickly examine the 60 mm dish containing the MG fragments from protocol step 2.9 under an inverted microscope (4X or 10X objective, Figure 1F). A typical preparation of eight MGs yields ~500 fragments. Look for single cells or fat droplets and whether there are contaminating cells.
   NOTE: If there are contaminating cells, repeat the filtration step by collecting the medium and fragments from the 60 mm dish using a 5 mL pipette and filtering the fragment again through a fresh 70 µm strainer, repeating protocol steps 2.6, 2.8-2.10.
10. Incubate 24 h at 37 °C, 5% CO₂, allowing the tissue fragment to adhere and generate bilayered fragments (Figure 2A).
    NOTE:If the fragments have not settled by 24 h, continue to incubate until adhered. If the fragments do not adhere well, the separation of the cell compartments will not work. If researchers are concerned about adhesion, the tissue culture plates can be treated to promote fragment attachment (e.g., poly-L-lysine).

3. Day 3: Differential trypsinization of myoepithelial and luminal epithelial cells

1. To separate MyoECs from LECs, empty the media from the dish, rinse 1x with 1 mL of DPBS and add 1 mL of fresh trypsin-EDTA (0.05%), and carefully monitor the digestion under an inverted microscope (10X or 20X objective, Figure 2B,C,F). The detachment of the outer MyoEC layer will require 3-6 min, depending on trypsin-EDTA (0.05%) strength.
   NOTE: Please see Figure 2 for representative images showing this process. Under brightfield illumination, the MyoECs appear rounded and have a brighter appearance in comparison to the LECs, which remain adhered in the center and appear darker.
2. Collect the MyoEC fraction in a 15 mL tube containing 2 mL 10% FBS/DPBS. Without disturbing the LECs, gently rinse the 60 mm dish with 2 mL of DPBS and then dispose of the DPBS (Figure 2H-I).
   NOTE: The usual recovery for MyoECs is within a range of (3.5 x 10⁶-1.5 x 10⁶) depending on the size of the MGs.
3. To remove the LEC fraction, add 1 mL of trypsin-EDTA (0.05%) to the dish again and incubate 7-15 min, monitoring carefully to prevent overdigestion. Quench the trypsin-EDTA (0.05%) on the dish with 2 mL of 10% FBS/DPBS. Collect the LEC fraction in a new 15 mL tube.
   NOTE: The usual recovery for LECs is within a range (2 x 10⁶-4.2 x 10⁶) depending on the size of the MGs. Routinely, the purity of both fractions as assayed by immunohistochemistry is ~90%¹⁹ (Figure 2E).
4. Centrifuge each fraction for 5 min at 300 x g to remove the trypsin-EDTA (0.05%). Resuspend the pellet in 250 µL of Maintenance Medium and count each cell population using a hemocytometer or automated cell counter. Place the cells on ice while counting.
   NOTE: If genetic manipulation of the cell fractions is desired, primary cells can be grown on low adhesion dishes and infected with lentivirus²⁰.

4. Day 3: Combining and embedding cell fractions in an extracellular matrix

NOTE: Once the MyoEC and LEC fractions have been collected and counted, they can be combined. The typical MyoEC/LEC ratio is 1:3 (Figure 3A)¹⁹. Different studies can be performed. For example, to perform mosaic studies, fractions can be generated from wild type (WT) and mutant (Mut) mice and combined (MyoEC/LEC: WT/WT; WT/Mut; Mut/WT; Mut/Mut)²¹, or fractions can be combined using different ratios of MyoECs/LECs¹⁹.

1. Based on cell counts, calculate the number of wells (8 well chamber, see Table of Materials) that need to be prepared for 12,000 cells/well (e.g. 3,000 MyoECs:9,000 LECs).
2. Establish the base layer for 3D culture by adding 90 µL of 50% ECM (50% ECM/50% DMEM/F12, without phenol red - see the Table of Materials) to each well. Ensure there are no bubbles and the wells are coated evenly. To solidify the base layer, incubate the slides at 37 °C, 5% CO₂ for 30 min.
   NOTE: The ECM needs to stay ice-cold until this step, otherwise it will polymerize prematurely and lead to uneven base coating and polymerization. Using a base ECM enhances organoid growth in a single plane, which aids image capture. This also obtains faster organoid growth and uses less ECM²².
3. During polymerization, prepare the cell mixes. Pellet the MyoEC and LEC fractions at 300 x g for 5 min and resuspend each cell fraction in 10% ECM/90% Growth Medium so each well has 100 µL (see Table 1 for how to make Growth Medium).
   NOTE: For ease of preparation, replicate wells using the same cell mixes. These can be combined and prepared in one tube (e.g., four wells of the same cell mix can be prepared in 400 µL of 10% ECM/90% Growth Medium).
4. Add 100 µL of each cell mix in 10% ECM/90% Growth Medium to each well and allow organoids to settle for 20 min at 37 °C, 5% CO₂.
5. Once the cells have settled, gently add 100 µL of Growth Medium by gently pipetting down the chamber wall of each well. Incubate the slides at 37 °C, 5% CO₂ (see Figure 3A for the total composition of each well).
   NOTE: The Rho Kinase inhibitor, R-spondin, and Nrg1 are factors that have been identified as important for the long-term culture of organoids grown from both primary murine mammary cells and human breast cancer cells^13,14. In addition, the stem cell factors B27 and N2 extend the time that organoids can be cultured.
6. Image cells every 24 h to track their growth and gently renew the Growth Medium every 2-3 days using 100 µL/well (Figure 3B-E).
   NOTE: Use extreme care when renewing the medium. Tilt the chamber slides to collect the medium at one corner of the wells. Remove ≤100 µL of the medium and replenish with care to leave the ECM layer undisturbed.
7. If researchers are interested in investigating lactation/alveologenesis, switch to Alveologenesis Medium (see Table 1) on day 5 and continue to renew the medium every 2-3 days until day 10 (Figure 3F) or beyond by passaging using recovery solution (see the Table of Materials)¹³.
   NOTE: At this point, organoids can be isolated from the ECM by incubating at 4 °C in 400 µL of 4 °C recovery solution (see Table of Materials for protocol and reagent info).

5. Day 5 or 10: Fixing and immunostaining organoids

1. Remove the medium carefully by gently pipetting off the media (a bulb pipette works best). Rinse each well using 200 µL of 1x Dulbecco's Phosphate Buffered Saline (DPBS, see recipes).
2. Fix the organoids using cold (4 °C) 4% (w/v) paraformaldehyde (PFA, see recipes) for 10 min at room temperature.
   CAUTION: PFA is hazardous. Wear personal protective equipment (lab coat, gloves, and safety glasses). This step should be performed inside a fume hood.
   NOTE: The ECM is dissolved by the PFA treatment. Incomplete ECM removal can lead to background staining when the organoids are analyzed by immunofluorescence.
3. Remove the 4% PFA and add 200 µL of 0.2% (w/v) glycine/DPBS (see Table 1) to each well. Incubate the slides at room temperature for 30 min or 4 °C overnight on a rocking surface set to a slow setting.
   NOTE: The organoids can be stored for 1-3 days in DPBS at 4 °C prior to the next step.
4. Permeabilize the organoids using DPBS + 0.25% Triton X-100 (PBST, see Table 1) for 10 min at room temperature.
5. Block the organoids using 5% donkey serum (DS) (or other serum matching the species of the secondary antibody) in DPBS for 1 h on a rocking surface.
   NOTE: This step can be performed overnight at 4 °C on a rocking surface.
6. Prepare primary antibodies in 1% DS/DPBS. Use 125-200 µL for each well. Perform immunostaining by incubating the organoids in primary antibody overnight at 4 °C on a rocking surface.

6. Day 11: Complete immunofluorescence

1. Wash each well 2X with 200 µL PBST for 5 min. Add secondary antibody in 1% DS/DPBS using 125-200 µL for each well. Incubate at room temperature on a rocking surface for 45 min.
2. Wash each well 2X using 200 µL PBST per well.
3. Stain the nuclei using Hoechst DNA dye in DPBS (1:2,000 in DPBS) for 5 min at room temperature.
4. Remove all liquid left on the well by gently suctioning with a vacuum.
5. Carefully remove the chambers and gasket, place one drop (~30 µL) of mounting media (see Table of Materials) on each well and coverslip, taking care to remove bubbles. Allow the slide to dry in a dark space for 1-2 days. Seal with clear nail polish. Image the organoids on a confocal microscope (Figure 3E-F).

Results

The protocol presented here describes a method for investigating specific lineage contributions of mammary epithelial cells by making use of mosaic organoids. To obtain primary murine cells for organoids, the mammary gland epithelium must first be isolated from the surrounding adipocyte rich stroma (Figure 1). This process is described briefly here and is also described in a previously published study¹⁸. To obtain enough cells, it is r...

Discussion

Here, a method is presented detailing how researchers can generate 3D organoid cultures using primary MG cells. The difference between this and other protocols is that we detail a method to separate the two, distinct MG cell compartments: the outer basal MyoECs and inner LECs. Our method employs a two-step trypsin-EDTA (0.05%) treatment that we call differential trypsinization¹⁹. This procedure allows researchers to isolate MyoECs and LECs without using sophisticated flow cytometry and thus can be...

Materials

Name	Company	Catalog Number	Comments
15 ml High-Clarity Polypropylene Conical Tube (BD Falcon)	Fisher Scientific	352096
24 well ultra-low attachment plate (Corning)	Fisher Scientific	CLS3473-24EA
35 mm TC-treated Easy-Grip Style Cell Culture Dish (BD Falcon)	Fisher Scientific	353001
50 ml High-Clarity polypropylene conical tube (BD Falcon)	Fisher Scientific	352098
60 mm TC-treated Easy-Grip Style Cell Culture Dish (BD Falcon)	Fisher Scientific	353004
70 µM nylon cell strainer (Corning)	Fisher Scientific	08-771-2
Antibiotic-Antimycotic (100X)	Thermo Fisher Scientific	15240062	Pen/Strep also works
B27 supplement without vitamin A (50x)	Thermo Fisher Scientific	12587010
B6 ACTb-EGFP mice	The Jackson Laboratory	003291
BD Insulin syringe 0.5 mL	Thermo Fisher Scientific	14-826-79
Class 2 Dispase (Roche)	Millipore Sigma	4942078001
Class 3 Collagenase	Worthington Biochemical	LS004206
Corning Cell Recovery solution	Fisher Scientific	354253	Follow the guidelines for use – Extraction of Three-Dimensional Structures from Corning Matrigel Matrix
Corning Costar Ultra-Low Attachment 6-well	Fisher Scientific	CLS3471
Dexamethasone	Millipore Sigma	D4902-25MG
DMEM/F12, no phenol red	Thermo Fisher Scientific	11039-021
DNase (Deoxyribonuclease I)	Worthington Biochemical	LS002007
Donkey anti-Goat 647	Thermo Fisher Scientific	A21447	Use at 1:500, Lot: 1608641, stock 2 mg/mL, RRID:AB_2535864
Donkey anti-Mouse 647	Jackson ImmunoResearch	715-606-150	Use at 1:1000, Lot: 140554, stock 1.4 mg/mL
Dulbecco's Modified Eagle Medium: Nutrient Mixture F-12 (DMEM/F12)	Thermo Fisher Scientific	11330-057
Dulbecco's phosphate-buffered saline (DPBS)	Thermo Fisher Scientific	14190-250	Without Mg2+/Ca2+
EGF	Fisher Scientific	AF-100-15-100ug
Fetal Bovine Serum	VWR	97068–085	100% US Origin, premium grade, Lot: 059B18
Fluoromount-G (Southern Biotech)	Fisher Scientific	0100-01	Referred to as mounting media in text
Gentamicin	Thermo Fisher Scientific	15710064
Glycine	Fisher Scientific	BP381-5
Goat anti-WAP	Santa Cruz Biotech	SC-14832	Use at 1:250, Lot: J1011, stock 200 µg/mL, RRID:AB_677601
Hoechst 33342	AnaSpec	AS-83218	Use 1:2000, stock is 20mM
Insulin	Millipore Sigma	I6634-100mg
KCl	Fisher Scientific	P217-500
KH2PO4	Fisher Scientific	P285-500
KRT14–CreERtam	The Jackson Laboratory	5107
Matrigel Growth Factor Reduced (GFR); Phenol Red-Free; 10 mL	Fisher Scientific	CB-40230C	Lot: 8204010, stock concentration 8.9 mg/mL
MillexGV Filter Unit 0.22 µm	Millipore Sigma	SLGV033RS
Millicell EZ SLIDE 8-well glass, sterile	Millipore Sigma	PEZGS0816	These chamber slides are great for gasket removal but other brands can work well (e.g. Lab Tek II).
Mouse anti-SMA	Millipore Sigma	A2547	Use at 1:500, Lot: 128M4881V, stock 5.2 mg/mL, RRID:AB_476701
N-2 Supplement (100x)	Thermo Fisher Scientific	17502048
NaCl	Fisher Scientific	S671-3
NaH2PO4	Fisher Scientific	S468-500
Nrg1	R&D	5898-NR-050
Ovine Pituitary Prolactin	National Hormone and Peptide Program		Purchased from Dr. Parlow at Harbor-UCLA Research and Education Institute
Paraformaldahyde	Millipore Sigma	PX0055-3
Pentobarbital	Millipore Sigma	P3761
R26R-EYFP	The Jackson Laboratory	6148
Rho inhibitor Y-27632	Tocris	1254
R-spondin	Peprotech	120-38
Sodium Hydroxide	Fisher Scientific	S318-500
Sterile Filtered Donkey Serum	Equitech-Bio Inc.	SD30-0500
Sterile Filtered Donkey Serum	Equitech-Bio Inc.	SD30-0500
Triton X-100	Millipore Sigma	x100-500ML	Laboratory grade
Trypsin EDTA 0.05%	Thermo Fisher Scientific	25300-062