Why haven't organoids solved all of drug discovery?

Thank you to Jimmy Sastra and Kitchener D. Wilson for discussions relating to this piece. All opinions are my own.

What are organoids anyway?

If someone placed a gun to the side of your temple and asked you to correctly define what exactly an "organoid" is, or else they'll shoot, you may get a little nervous. The whole concept is something, you suddenly realize, you never quite understood. It's more of a you-know-it-when-you-see-it thing, nobody in their right mind would ever ask for a clear definition, but you forgot to account for those who are not in their right mind. Desperately, you rack your brain for details. It's an aggregate of cells, right? You stammer this out, tack on 'it's three-dimensional too!', and stare at your antagonist expectantly. They consider your answer, and squeeze their hands.

If we were to interview your terrorizer later on, they would sheepishly admit that your answer is not the worst one they've heard. It really does encapsulate the many forms that organoids may take. Unfortunately, your given definition would also welcome blood clots, teratomas, and biofilms, all of which are indeed aggregates of cells arranged in three dimensions, but none of which would be considered an organoid by anybody on the planet.

You should not feel bad about this. In fact, you are in good company. The organoid field as a whole is not known to have particularly useful definitions.

One attempt at a definition comes from a 2014 Science review titled 'Organogenesis in a dish: modeling development and disease using organoid technologies', which defined an organoid as having the following traits: it is derived from either stem cells or organ progenitors, contains multiple organ-specific cell types, and recapitulates some type of organ-specific function. This feels more accurate, and swiftly removes blood clots, teratomas, and biofilms from the table.

Importantly, the organ-specific function bits of the definition help clarify something important: spheroids are not the same thing as an organoid. What is a spheroid? Here's a useful infographic:

You, at the very start, described a spheroid.

Well, that's that, right? Organoids are simply spatially complex, multicellular three-dimensional aggregates.

But we're still missing some pieces. A 2023 Stem Cell Reports paper titled 'Organoids are not organs: Sources of variation and misinformation in organoid biology' has the following complaint about the particular definition stated above:

As a generic definition of an organoid, this fails to identify the distinctions between pluripotent stem cell [PSC] and tissue stem cell-derived [TSC] organoids.

The authors go on to say why this matters, but their explanation is dense and orthogonal enough to the point that we needn't bother teasing out the details here, though we will later. What is important to understand is that PSC-derived organoids and TSC-derived organoids are doing fundamentally different things at the biological level, recapitulating different stages of tissue biology, and yet the word "organoid" is asked to contain both of them.

So: organoids are three-dimensional, multicellular, spatially organized, self-assembling structures derived from [cells] that recapitulate some aspect of [biology], though what cells and what biology will vary based on what the actual 'organoid' system is.

With regard to a definition, this is the best we can do. It is not very good, but it is good enough grounding to start discussing a very vital question.

Why haven't organoids solved all of drug discovery?

There is a reasonable reaction one may have upon learning that organoids exist: why aren't these being used all the time?

These are human, I repeat, human tissues that are lying in a dish, ones that are seemingly able to roughly organize themselves to semi-resemble complex, multicellular tissues. Why do we use mice, or any animal, at all? Hell, why do we even have clinical trials? Let's just spin up a few hundred of these things and throw drugs at them. Get the FDA on the phone! It's an emergency!

Yes, maybe the failure rate of this brave new endeavor will be high, but it's a risk we should be willing to take. It's not like we were doing so well before. After all, 99.6% of Alzheimer's drugs fail, oncology programs entering Phase I succeed less than 5% of the time, and the average cost of bringing a single drug to market now regularly exceeds $2 billion, which is a number that has roughly doubled every nine years since 1950 and is so reliable it has its own law named after it. We're terrible at this stuff. Why haven't we switched to something that is clearly better?

It's a good question! And there are a few very good answers.

How do you make an organoid? The protocol varies by organ type, but the basic process is roughly the same. You start with cells, either stem cells derived from a patient biopsy (TSC approach) or pluripotent stem cells that you will coax toward a particular cell type (the PSC approach). You embed these cells in a three-dimensional matrix, usually in a gelatinous protein mixture called Matrigel, and then add in a cocktail of growth factors and small molecules that this particular cell type demands. Then you wait.

Over the course of days to weeks, the cells proliferate, migrate, sort themselves into different populations, and begin to self-organize into something that, under the microscope, looks like it might mirror the aforementioned micro-structures you are looking for. In some very real sense, this is a very accelerated and incomplete caricature of embryogenesis.

That's the theory anyway. The problem with organoid creation starts with Matrigel—the stuff that most organoid globs are floating around in.

Matrigel is a gelatinous protein mixture secreted by Engelbreth-Holm-Swarm mouse sarcoma cells. Yes, cancer cells. And as you would expect would be the case with anything secreted by cancer cells, it is both extremely complicated and highly heterogeneous. Proteomic analysis has shown that the liquid contains 1,800 proteins, most of which we don't understand, which can vary from batch to batch.

Surely the company behind Matrigel, Corning, would try to standardize things, no? Corning's solution to the batch variability problem has been a sort of radical transparency, in which they offer the aggregate mass of proteins in a particular Matrigel—ranging from 8 to 22 mg/mL—but no information as to whether specific proteins, say laminin, are more or less prevalent. I can't find any work that studies how much this quantitatively hurts reproducibility—given that every lab is running a slightly different experiment depending on which Matrigel lot they received—but I can find a lot of papers complaining about it (here and here), so I'm going to assume it is a problem.

Why can't we just stop using it? There are alternative options on the table that are in the works: decellularized extracellular matrix, synthetic hydrogels, and gel-forming recombinant proteins. Some of these work well, sometimes, for specific tissue types, but none of them are as versatile and easy-to-use as Matrigel. Another funny reason for lack of adoption is that validating these alternatives typically requires a reference point, and that reference point is almost always Matrigel-based.

The other layer of variation is upstream: the cells that are within the Matrigel. Here, there are so many axes of variation that it would actually be easier to just explain the empirical reality observed by one paper: 'Cross-site reproducibility of human cortical (hCO) organoids reveals consistent cell type composition and architecture'.