º£½ÇÆÆ½â°æ

Q&A: The Hidden Variable in Your Intestinal Organoids

In the on-demand webinar, “The Hidden Variable in Your Intestinal Organoids: Enhancing Differentiation for a More Predictive Modelâ€, Dr. Martin Stahl explores how cellular composition affects organoid performance in drug response and toxicity assays. He also introduces IntestiCultâ„¢ Plus Organoid Growth Medium, a next-generation organoid medium that supports simultaneous expansion and differentiation of intestinal organoids.

Below are answers to the audience questions following the live webinar. The answers have been edited for brevity and clarity.

Meet the Speaker

Headshot of Dr. Martin Stahl

Martin Stahl, PhD

Dr. Martin Stahl is a Senior Scientist with the Intestinal Team at º£½ÇÆÆ½â°æ Technologies. Martin received a PhD in Microbiology at the University of Ottawa and conducted his postdoctoral research at the University of British Columbia and the BC Children’s Hospital Research Institute, where he studied infection and immunity in the gut.

For labs currently making their own media, what are the key advantages of switching to a system like IntestiCultâ„¢?

There are a few major advantages. First, IntestiCult™ Plus is a brand new, proprietary formulation that improves on existing literature. Second, it's consistent. There’s no conditioned medium involved, which eliminates a major source of variability, and it’s quality controlled, so there’s no lot-to-lot variation to worry about. That kind of reliability makes a big difference when you're trying to get reproducible data.

What are some challenges in achieving and maintaining physiological proportions of differentiated cell types over time in culture?

When using IntestiCultâ„¢ Plus as recommended, achieving a balanced cell population is straightforward and occurs naturally. Media components can be adjusted to shift the balance between stem and differentiated cells. For example, increasing Wnt levels favors stem cells, while its removal promotes differentiation.

You showed enrichment for M cells and tuft cells. Have you tried enriching other cell populations?

Yes, we have. For example, goblet cells can be enriched using a gamma-secretase inhibitor like DAPT. Just be cautious with dosing, since overdoing it can affect viability. We’ve also successfully enriched enteroendocrine cells using a combination of MEK and gamma-secretase.

Have you tried this media on embryonic stem cell (ESC)-derived colon organoids? Does it help mature these organoids?

We have, and it does work. That said, ESC-derived systems using protocols like those from our STEMdiff™ kits or those from labs like Jim Wells’ or Michael Helmrath’s often run into issues like fibroblast overgrowth. Fibroblasts love this media too. So while IntestiCult™ Plus can support those organoids, you might get better results with the STEMdiff™ Intestinal Organoid Kit, which is designed specifically for ESC-derived systems.

Is IntestiCultâ„¢ Plus compatible with non-human species, like mouse or even alpaca?

We’ve confirmed compatibility with human, mouse, and rat organoids. It actually works really well with mouse-derived cells, though we also offer a mouse-specific formulation. As for other species—we haven’t tested every model, but given how the core components are designed, we suspect it will support a wide range of mammalian cells. We’d love to hear from researchers working with less common species.

How long do tuft or M cells need to be induced/enriched with specific factors such as TNF-alpha or IL-13 when cultured in IntestiCultâ„¢ Plus?

M cells differentiate quite fast when using RANKL (Receptor Activator of Nuclear Factor κB Ligand) or TNF-alpha, sometimes almost too fast. You can quickly get a large population, and if you're not careful, they can overtake the culture and reduce viability. Tuft cells are slower to develop, but you can enrich them over several days to a couple of weeks without seeing the same viability issues we’ve seen with M cells.

Does this cell population come from one cell type, or do you seed bulk cells and IntestiCultâ„¢ Plus supports the growth for all of the cells?

Either approach works. We often prefer to seed crypts or intestinal fragments, which naturally contain LGR5+ stem cells. But IntestiCult™ Plus also supports single-cell seeding and passaging. Regardless of the starting material, whether that’s single LGR5+ stem cells or intestinal crypts or fragments, you’ll end up with all the relevant intestinal cell types when cultured with IntestiCult™ Plus.

If you’re generating colorectal cancer organoids from a subcutaneous PDX tumor, what would be the ideal medium to culture those organoids?

In general, IntestiCult™ Plus works well with tumor-derived organoids, including those from subcutaneous PDX models. Depending on the tumor’s genetic makeup, you might see differences in how well they grow, but overall, we’ve had good success.

What was your method of counting cells (viability) over the days in the drug testing assay?

We usually use Promega’s CellTiter-Glo® 3D to measure ATP levels, which correlates with cell viability. We’ve also used live/dead staining and the LDH-Glo® assay, which detects cell death. Each method gives you slightly different information, so sometimes we use a combination to get a fuller picture of what's going on in the culture.

Is there colon-specific differentiation media?

If you’re working with primary, patient-derived organoids, IntestiCult™ Plus supports both small intestine and colon cultures. For human pluripotent stem cell (hPSC)-derived systems, we do offer a publicly available protocol that adapts the STEMdiff™ Intestinal Organoid Kit for colonic differentiation.

In your drug toxicity studies, you seem to use 3D organoids rather than monolayers, likely because monolayer formation takes more time. Is there a risk that drugs aren’t interacting with the correct side of the cells? Have you compared the two formats for consistency?

Great question. Most of our toxicity testing is done using 3D organoids, where compounds are applied to the basolateral side. For many drugs, that works well. But depending on the drug’s mechanism of action, the apical side may be more relevant. In those cases, a monolayer format can be more appropriate.

That said, monolayers grow more slowly and tend to have lower proliferation, which can influence how drugs behave, especially those targeting dividing cells. So it adds another variable to consider.

We do use monolayers frequently for barrier function assays, like transepithelial electrical resistance (TEER) or FITC-dextran permeability. In those cases, the apical side is exposed and we can track both permeability and viability. So while we don't typically use monolayers for routine toxicity testing, they are definitely a valid and informative model when used for the right application.

How did RANKL help your system? Could it be used across other tissues?

We use RANKL because it's a well-established way to induce M cell differentiation. That’s the main context we’ve tested. We can’t speak to its effects in other tissues.

Does organoid size or density impact drug testing results?

Yes, it can have a significant impact. Larger organoids tend to contain a higher population of differentiated cells, while smaller ones tend to be more proliferative. This difference can influence how the organoids respond to drugs, especially if the compound targets a specific cell type or relies on proliferation status.

To get consistent results across experiments, it’s important to standardize both organoid size and density. To support this, º£½ÇÆÆ½â°æ Technologies has developed Organoid Culture Plates, designed to help with this standardization. These tools can be especially valuable when you’re conducting drug testing and need reproducible, reliable outcomes.

In the functional assays and characterization of organoids, did you compare first-generation differentiation medium vs. IntestiCultâ„¢ Plus? If so, how different are they?

In many ways, it’s quite different. First-generation differentiation media (e.g. IntestiCult™ Organoid Differentiation Medium) tends to eliminate the stem cell population, which limits proliferation and restricts some assay types. IntestiCult™ Plus keeps that balance—you retain stem cells while also achieving differentiation. This makes it more versatile and relevant for a broader range of experiments, especially those involving toxicity or rare cell types.

Can IntestiCultâ„¢ Plus be used to grow hPSC-derived intestinal organoid monolayers?

We do not recommend IntestiCult™ Plus for organoid-monolayer establishment or for hPSC-derived organoids at this time. We recommend following our protocol on “How to Generate Monolayers from hPSC-Derived Organoids Using IntestiCult™†which uses IntestiCult™ Organoid Differentiation Medium with hPSC-derived intestinal organoids previously expanded with the STEMdiff™ Intestinal Organoid Kit.

A 3D rendering of an intestinal organoid coloured red with a dark background.

On-Demand Human Intestinal Organoid Course

Learn the basics of culturing human intestinal organoids and applying them to your research. Our knowledgeable instructors will guide you through the foundations of intestinal organoid culture, including culturing human intestinal organoids, assessing their morphology, understanding their applications, and more.

Register Now >

Have you tried IntestiCultâ„¢ Plus on normal gastric organoids? Or on tissue sources from other gastrointestinal cancers such as pancreatic cancer?

IntestiCult™ Plus does not currently support gastric organoids or cancerous tissue from other GI regions such as pancreas. Gastric organoids need something a bit different than what is currently in IntestiCult™ Plus. We’re actively exploring these areas for future development, so stay tuned.

What is the best way to quantify total cell number with intestinal organoids?

We recommend dissociating a representative sample to single cells using 0.05% Trypsin-EDTA or a similar reagent, then counting using a hemocytometer or automated counter. Organoids can take longer to break apart than 2D cultures, so give it some time.

I’m currently using IntestiCultâ„¢ Organoid Growth Medium (Mouse) to generate colon organoids. When transitioning them to a monolayer format, º£½ÇÆÆ½â°æ recommends using IntestiCultâ„¢ Organoid Differentiation Medium (Human). Would IntestiCultâ„¢ Plus be intended for this application?

If you’re growing mouse colonic organoids for a monolayer, you typically use the first-generation human expansion medium (i.e. IntestiCult™ Organoid Growth Medium Human) to expand the organoids, followed by the same expansion medium plus 10 µM Y-27632 for the monolayer itself. The human IntestiCult™ Organoid Differentiation Medium is ideal for human organoid-monolayers, but not for mouse cultures. For mouse monolayer applications, we recommend sticking with the first-generation human expansion medium. It contains serum, which helps mouse cells adhere, a known challenge when working with this model. IntestiCult™ Plus isn’t optimal for this step due to its serum-free formulation.

Does º£½ÇÆÆ½â°æ offer media for organoid types other than intestinal, such as lung organoids?

Yes, º£½ÇÆÆ½â°æ Technologies offers a wide range of organoid media products for various organ types including, lung, hepatic, pancreatic, kidney, neural, and reproductive. Explore our organoids products here.

Where can I find the protocol for generating M cells, specifically the recommended concentrations of TNF-alpha and RANKL?

Please see the following publication as one of several published methods: Wood MB, Rios D, Williams IR. TNF-α augments RANKL-dependent intestinal M cell differentiation in enteroid cultures. Am J Physiol Cell Physiol. 2016 Sep 1;311(3):C498-507. .

IntestiCultâ„¢ Plus supports the generation of more physiologically relevant organoids, but how physiologically accurate is the medium itself in terms of insulin, glucose, and fatty acid concentrations?

In vitro systems don’t allow for constant replenishment like in vivo, so we use slightly elevated concentrations of factors like insulin and glucose. We’ve been careful not to overshoot, and the formulation aims to maintain a practical balance between physiological realism and in vitro viability.

Do you have experience culturing organoids on a microphysiological system (MPS) platform? If so, have you observed any changes in organoid attachment to the wells?

Not extensively. Although, we recommend using the first-generation expansion and differentiation media for these platforms as it supports better cell adhesion in those systems. We currently have collaborations with both MIMETAS and Emulate that leverage our first-generation media to support their MPS platforms.

What is your preferred method for evaluating drug toxicity?

We recommend following our published protocol, “Toxicity Testing for Drug Development Using Human Intestinal Organoids and IntestiCult™†for evaluating drug toxicity, which uses Promega CellTitler-Glo® for cytotoxicity following the treatment phase.

Have you characterized transporters other than P-gp in the intestinal organoids?

Yes, while P-gp has been the transporter we have evaluated in the most depth, we have also done some work with BCRP, MRP2, OAT, and SLC family transporters as well.

Explore These Resources

Brochure
Redefine Intestinal Organoid Culture: IntestiCultâ„¢ Plus Organoid Growth Medium
Scientific Poster
A New Organoid Culture Platform for Forskolin-Induced Swelling Assays and Drug Screening Applications