We describe step-by-step instructions to: 1) efficiently engineer intestinal organoids using magnetic nanoparticles for lenti- or retroviral transduction, and, 2) generate frozen sections from engineered organoids. This approach provides a powerful tool to efficiently alter gene expression in organoids for investigation of downstream effects.
Intestinal organoid cultures provide a unique opportunity to investigate intestinal stem cell and crypt biology in vitro, although efficient approaches to manipulate gene expression in organoids have made limited progress in this arena. While CRISPR/Cas9 technology allows for precise genome editing of cells for organoid generation, this strategy requires extensive selection and screening by sequence analysis, which is both time-consuming and costly. Here, we provide a detailed protocol for efficient viral transduction of intestinal organoids. This approach is rapid and highly efficient, thus decreasing the time and expense inherent in CRISPR/Cas9 technology. We also present a protocol to generate frozen sections from intact organoid cultures for further analysis with immunohistochemical or immunofluorescent staining, which can be used to confirm gene expression or silencing. After successful transduction of viral vectors for gene expression or silencing is achieved, intestinal stem cell and crypt function can be rapidly assessed. Although most organoid studies employ in vitro assays, organoids can also be delivered to mice for in vivo functional analyses. Moreover, our approaches are advantageous for predicting therapeutic responses to drugs because currently available therapies generally function by modulating gene expression or protein function rather than altering the genome.
The ability to culture mouse or human crypts cells as three dimensional (3D) organoids from the small intestines or colon over prolonged time periods provided a major breakthrough because these cultures display defining features of intestinal epithelium in vivo1,2,3. Organoids derived from primary crypts are capable of self-renewal and self-organization, exhibiting cellular functions similar to their tissues of origin. Indeed, organoids recapitulate not only the structural organization of crypts in vivo, but also many molecular features, thus providing useful tools to study normal biology and disease states. To illustrate, organoid studies have revealed novel molecular pathways involved in tissue regeneration1,2,3,4,5 as well as drugs that could enhance function in pathologic settings6,7.
The study of intestinal stem cells is of particular interest because the intestinal lining is among the most highly regenerative mammalian tissues, renewing itself every 3-5 days to protect the organism from bacteria, toxins, and other pathogens within the intestinal lumens. Intestinal stem cells (ISCs) are responsible for this remarkable regenerative capability and thus provide a unique paradigm for studying adult stem cell function1,2. Lineage-tracing experiments in mice demonstrated that isolated Lgr5-positive stem cells can be cultured to generate 3D organoids or 'mini-guts' in vitro where they closely mirror their in vivo counterparts. Organoid cultures can also be derived from intestinal crypt cell isolates comprised of progenitors, ISCs, and Paneth cells, the latter of which constitute the epithelial niche cells in vivo. In fact, organoid culture from primary intestinal crypt cells has evolved into a relatively routine technique that is easy to implement in most laboratories using widely available reagents. This model is also amenable to quantitative analysis of gene expression by RNA-sequencing (RNA-Seq) and proteins by mass spectrometry, immunohistochemistry, or immunofluorescent staining2,4,8. In addition, functional genetics can be studied using gain-of-function (gene overexpression or expression of an activating mutant gene) or loss-of-function (gene silencing or expression of a loss-of-function mutant) approaches2.
Importantly, low efficiency and high toxicity of standard plasmid DNA or viral transduction protocols with polybrene remain a major hurdle in the field. Although CRISPR/Cas9 technology allows for precise genome editing, this approach requires time-consuming selection followed by sequence validation9. Here, we present a viral transduction protocol for primary intestinal organoids that optimizes delivery of viral particles by conjugation to magnetic nanoparticles and application of a magnetic field. Key modifications to prior protocols4,5,10,11,12,13 and recommendations to enhance efficiency are provided. We also describe an approach to generate frozen sections from intact organoids cultured in 3D matrigel (henceforth referred to as basement membrane matrix or matrix) for further analysis with immunohistochemistry or immunofluorescent staining.
This protocol was approved by the Johns Hopkins Medical Institutions Animal Care and Use Committee (IACUC). This protocol is modified from a previously published methods10,11,12,13.
1. Preparation of Reagents
2. Lentivirus or Retrovirus Particle Production
3. Isolating Crypts
4. Organoid Fragment Preparation
5. Genetic Engineering of Organoids or Crypt Cells by Viral Transduction
NOTE: See Figure 2.
6. Seeding of Infected Organoid Fragments
7. Selection (If Applicable)
8. Confirmation of Successful Transduction and Gene Expression or Silencing
9. Organoid Cryosection in Basement Membrane Matrix
NOTE: See Figure 3.
Here, we describe a rapid and highly efficient transduction technique which harnesses magnetic nanoparticles exposed to a magnetic field to deliver lentivirus to cells of interest. With readily available tools, we have applied this approach not only to transduce freshly isolated crypt cells (Figure 1A), but also for organoids (Figure 2) and other cells that are refractory to more routine transduction approaches. Lentiviral particles can be easily conjugated to magnetic nanoparticles and the resulting virus-nanoparticle complexes are delivered efficiently by applying a magnetic field using a magnetic plate. To optimize this approach, we first tested lentiviral vectors linked to GFP such that GFP could be used to identify transduced cells with fluorescence microscopy. The GFP can be visualized at each stage in organoid development, including early on when crypt cells organize into cyst-like structures (Figure 4A), or at later time points when organoids form buds (Figure 4B). Successfully transduced intestinal organoids can then undergo functional analysis for alterations in development by staining cell membranes and nuclei to enumerate total cell number in addition to lineage markers, such as lysozyme to identify Paneth cells (Figure 4C).
The genetically engineered organoids can be used for further analysis by generating frozen sections as outlined here (Figure 3). After embedding organoids, frozen blocks can be stored and later sectioned for future studies. This approach is also efficient (estimated to be ~95% based on percentage of GFP(+) organoids to total organoids). This approach can be performed with standard laboratory reagents, thus providing tissues that are amenable to diverse investigations, including cell number, cell fate, and the presence and levels of specific proteins2. For example, we used frozen sections and immunofluorescent staining to identify individual cells and ascertain cell type (Figure 4C).
Figure 1: Isolated crypts and villi with cartoons showing typical morphology. (A) Isolated crypts form round or oval structures. (B) Villi are identified as finger-like structures. Scale bar = 50 µm. Please click here to view a larger version of this figure.
Figure 2: Schematic of viral transduction of organoids using magnetic nanoparticles and exposure to a magnetic field. The most critical steps of the transduction protocol are shown. (A) Incubate virus and magnetic nanoparticle solution for 15 min at RT in a 1.5 mL tube. (B) Add the magnetic nanoparticles/virus mixture to the cells to be transduced. (C) Place the cell culture plate on the magnetic plate and incubate for 2 h in a standard tissue culture incubator. Longer incubation times can also be used (~6 h); the representative well is shown here on the magnetic plate. (D) A cell being transduced with the virus and magnetic nanoparticle is shown. (E) Transfer the infected organoid cell clusters and transduction media from each well into a 1.5 mL tube and centrifuge at 500 x g for 5 min. Discard the supernatant with gentle suction and cool the tube containing the pellet on ice for 5 min. (F) Add 120 µL of basement membrane matrix and resuspend the pellet by pipetting slowly up and down. (G) Seed drops of 30 µL containing matrix-cell mixture into each well in a new 48-well plate. Please click here to view a larger version of this figure.
Figure 3: Schematic of frozen sectioning of organoids in 3D matrix. The most critical steps of the frozen sectioning protocol are shown. (A) A single well within a 24-well cell culture plate is depicted. (B) Add just enough embedding compound to cover the matrix layer (~300 µL/well) and incubate at RT for 5 min. (C) Place samples at -80 C in a freezer for 10 min or until the embedding compound turns solid and white. Next, place the dish at RT to allow for slight melting along the edges of the sample. (D) Use a scalpel to separate the block from the walls of the well. (E) Remove the matrix-embedding compound block using forceps and place in an appropriate shallow container or mold for freezing tissues. Fill the mold completely with embedding compound (OCT). (F) Freeze block at -80 C in a freezer for 30 min. (G) The block is ready for sectioning or storage in -80 C freezer for further use. Please click here to view a larger version of this figure.
Figure 4: Representative images of transduced intestinal organoids. (A) Representative image of small intestinal organoids under light microscope showing (left) fluorescence microscopy, and, (Right) standard microscopy of transgene expression (EGFP) at day 3 after transduction. Scale bar = 50 µm. (B) Example of overexpression of gene encoding GFP in organoid after transduction using magnetic nanoparticles. Organoid cells were transduced with lentivirus expressing GFP (FUGW; Top) or lentivirus overexpressing Hmga1 (FUGW-Hmga1; Bottom) as shown at day 12 after transduction. Scale bar = 50 µm. (C) Immunofluorescence imaging of formalin fixed frozen section of organoids. Organoid sections (4 µm) were stained with anti-lysozyme (red), anti-EpCAM (green) and DAPI (blue). EpCAM demarcates cell borders, DAPI indicated individual nuclei, and lysozyme stains Paneth cells. Scale bar = 50 µm. Please click here to view a larger version of this figure.
Organoid culture medium (ENR) | 100 mL |
DMEM/F12+ | 96 mL |
L-alanyl-L-glutamine dipeptide supplement (e.g. Glutamax) | 1 mL |
NEAA | 1 mL |
Pen/Strep | 1 mL |
HEPES | 1 mL |
EGF (100 µg/ mL) | 5 µL |
Noggin (100 µg/ mL) | 10 µL |
R-spondin (100 µg/ mL) | 10 µL |
or R-spondin condition medium (CM) | 20 mL |
Human recombinant insulin (10 mg/ mL) | 5 µL |
Transduction medium | 5 mL |
ENR medium | 2.4 mL |
Wnt condition medium (CM) | 2.5 mL |
Nicotinamide (1M) | 100 µL |
Y27632 (10 µM) | 10 µL |
Crypts dissociation buffer | 100 mL |
PBS (without Ca2+, Mg2+) | 99 mL |
Pen/Strep | 1 mL |
0.5 M EDTA | 100 µL |
0.1 M DTT (dithiothreitol) | 100 µL |
293T medium | 100 mL |
DMEM | 90 mL |
FBS | 10 mL |
Virus Collection Medium | 100 mL |
DMEM | 99 mL |
FBS | 1 mL |
Organoid digestion buffer | 1 mL |
DMEM/F12+ | 1 mL |
Dispase I (10 mg/ mL) | 6 µL |
Dnase I (10 mg/ mL) | 2.5 µL |
Table 1: Media used in the protocol.
Plates | 10 cm | 15 cm |
Lentivirus transducing vector | 6 µg | 9 µg |
CMVΔR8.91 | 8 µg | 12 µg |
MD.G | 2 µg | 3 µg |
Total vectors | ≤16 µg | ≤24 µg |
Table 2: Quantity of plasmid DNA for transfection.
Plate | Magnetic beads (µL) | Volume of virus (µL) | Final TransductionVolume (µL) |
48-well | 6 | 50 | 250 |
24-well | 12 | 100 | 500 |
Table 3: Volume of magnetic bead solution and vector.
Primary culture of adult intestinal epithelium as organoids provides a powerful tool to study molecular mechanisms involved in stem cell function, intestinal epithelial homeostasis, and pathology1,2,3,4. Although CRISPR/Cas9 technology can be used to genetically engineer organoids9, it is limited by the need for extensive screening and selection based on sequence analysis for the desired genetic changes. The goal of this protocol is to provide clear and concise instructions with video-based tutorials for magnetic nanoparticle delivery of lenti- or retrovirus to intestinal organoids, followed by frozen sectioning for further analysis.
This protocol is a rapid and efficient method to genetically engineer intestinal organoids and analyze the consequences of gene overexpression or silencing from frozen sections. Critical steps are outlined in Figure 2, Figure 3. This strategy allows for investigation of the biologic significance of genetic alterations (overexpression or silencing) in intestinal stem cells and their progeny cultured under 3D conditions2,13. We have also used this magnetic nanoparticle-based delivery of viral vectors to enhance cell transduction and transgene expression in vitro in different primary cells2,13.
With this approach, viral particles are coated with magnetic nanoparticles and delivered to cells by exposure to a magnetic field. Compared to current transduction methods, such as polybrene with or without spinoculation10,15, magnetic nanoparticle-viral complexes are less toxic to cells because uptake of the genetic material is mediated by endocytosis and pinocytosis, two naturally-occurring biological processes that do not induce significant damage to cell membranes. Thus, both cell viability and transduction efficiency are enhanced. Transduction efficiency may be increased further using small crypt fragments or single cells (see step 4.8) instead of larger crypts or entire organoids as reported previously2,10,13,16. Magnetically guided nanoparticle delivery results in rapid accumulation, penetration, and uptake of viral vectors into target cells2,13. The magnetic nanoparticles are made of iron oxide, which is fully biodegradable and coated with specific proprietary cationic molecules. Nanoparticle association with viral vectors is achieved by salt-induced colloidal aggregation and electrostatic interactions. The nanoparticles are then concentrated onto cells by an external magnetic field generated by the magnetic plate placed under the culture dish. While transduction efficiency approaches 95%, not all cells are transduced, which is a limitation to this technique. In addition, endogenously expressed genes of interest are not altered as with CRISPR/Cas9 approaches.
Following gene overexpression or silencing, the organoids can be used for a myriad of studies, depending upon the scientific objectives, including analysis of gene expression, proteomic alterations within cells or secreted by cells, metabolic alterations, and morphologic changes. As with living tissues, frozen sections can be obtained for immunohistochemical and immunofluorescence studies of specific proteins such as transcription factors, cytoplasmic molecules, or cell surface markers. Our article includes an effective approach to obtain frozen sections from organoids without disturbing their position and organization in 3D culture. This is advantageous because prior techniques require the removal of the organoid from basement membrane matrix before freezing16. Processing organoids by removal from matrix could disrupt the structural organization of the organoid rather than reflect the in vitro growth and development.
This protocol to genetically engineer intestinal organoids can also be adapted to study other cell-based models and organoid systems. For example, pancreatic, colonic, hepatic, cardiac, and cerebral organoid systems could be transduced with this approach. Even cells growing under more standard culture techniques are amenable to nanoparticle technology. Furthermore, this approach can be applied to study the molecular mechanisms of diseases, not only in the context of stem cell-derived organoid systems, but also in tumor organoids.
In summary, the key modifications described in these protocols for intestinal organoid studies will hopefully empower scientists to elucidate the role of important factors and downstream pathways involved in the biology of intestinal stem cells and their progeny. These approaches should provide the means to learn more about molecular mechanisms underlying self-renewal, cell fate determination, tissue homeostasis, and intestinal epithelial regeneration, under both physiologic and pathologic conditions.
The authors have nothing to disclose.
This work was supported by grants from the National Institute of Health (R01DK102943, R03CA182679, R03CA191621), the Maryland Stem Cell Research Fund (2015-MSCRFE-1759, 2017-MSCRFD-3934), the American Lung Association, the Allegheny Health Network – Johns Hopkins Research Fund and the Hopkins Digestive Diseases Basic Research Core Center.
DMEM | Thermo Fisher Scientific | 11965092 | Base medium for 293T cells |
DMEM/F12+ | Thermo Fisher Scientific | 12634010 | Base medium for organoid culture medium and organoid digestion buffer |
OPTI-MEM | Thermo Fisher Scientific | 11058021 | Virus plasmids transfection medium |
Fetal Bovine Serum | Corning | 35-011-CV | Component of virus collection medium and 293T medium |
Pen/Strep | Thermo Fisher Scientific | 15140122 | Component of organoid culture medium and crypt dissociation buffer |
PBS (without Ca2+, Mg2+) | Thermo Fisher Scientific | 10010049 | A wash buffer and component of crypt dissociation buffer |
Mem-NEAA | Thermo Fisher Scientific | 11140050 | Component of organoid culture medium |
GlutamaxII | Thermo Fisher Scientific | 35050061 | Component of organoid culture medium |
HEPES | Thermo Fisher Scientific | 15630080 | Component of organoid culture medium |
EGF | Millipore Sigma | E9644 | Component of organoid culture medium |
Noggin | Peprotech | 250-38 B | Component of organoid culture medium |
R-spondin | R&D | 7150-RS-025/CF | Component of organoid culture medium |
Human recombinant insulin | Millipore Sigma | I9278-5ml | Component of organoid culture medium |
Nicotinamide | Millipore Sigma | N3376-100G | Component of Transduction medium |
Wnt3A | R&D | 5036-WN-010 | Component of Transduction medium |
Y27632 | Millipore Sigma | Y0503-1MG | Component of Transduction medium |
0.5M EDTA | Thermo Fisher Scientific | 15575020 | Component of Crypts dissociation buffer |
DTT (dithiothreitol) | Thermo Fisher Scientific | R0861 | Component of Crypts dissociation buffer |
Dispase I | Millipore Sigma | D4818-2MG | Component of organoid digestion buffer |
DNase I | Millipore Sigma | 11284932001 | Component of organoid digestion buffer |
matrigel(Growth factor reduced) | Corning | 356231 | Used as a matrix to embed organoids |
Opti-MEM | Thermo Fisher Scientific | 31985070 | Medium for transfection in viral production |
ViralMag R/L | Oz Biosiences | RL40200 | Magnetic particles of viral transduction |
Magnetic plate | Oz Biosiences | MF10000 | Magnetic plate to facilitate viral transduction |
Lipofectamine 2000 | Thermo Fisher Scientific | 11668019 | Transfection agent in viral production |
Poly-D-Lysine | Millipore Sigma | A-003-E | Coating for plates before seeding 293T cells |
4% Formaldehyde Solution | Boster | AR1068 | Solution to fix organoids |
O.C.T embedding compound | Thermo Fisher Scientific | 4583S | For embedding of the the organoids |
5 mL Falcon polystyrene tubes | Corning | 352054 | |
50 mL Falcon Tubes | Sarstedt | 62.547.100 | |
Orbitron rotator II Rocker Shaker | Boekel Scientific | 260250 | |
Olympus Inverted microscop CK30 | Olympus | CK30 | for scanning and counting crypts |
Zeiss Axiovert 200 inverted fluorescence | Nikon | Axiovert 200 | for viewing fluorescence in the crypts |
Amicon Ultra-15 Centrifugal Filter unit with Ultracel-100 membrane | Milipore Sigma | UFC910024 | For concentrating viruses |
pluriStrainer 20 µm (Cell Strainer) | pluriSelect | SKU 43-50020 | For preparing organoid fragments |
Falcon Cell Strainer | Fisher Scientific | 352340 | For preparing cyrpts of similar size after crypt isolation |
Greiner CELLSTAR multiwell culture plates 48 wells (TC treated with lid) | Millipore Sigma | M8937-100EA | ForD2:D37+D16:D37g organoid fragments |
Animal strain: C57BL/6J | Jackson Lab | #000664 | For organoid culture |