Also @jenspuschhof.bsky.social and Cayetano Pleguezuelos for their excellent guidance & advice and Robert Barrett as the real OG of the iPSC-intestine-on-chip!

Go team!

Huge huge thanks and congrats to the entire team, especially my long-term partner in crime Renée Moerkens! So grateful for all we've been working on together.
And of course the new parters in crime Eline Smits & @scimarijn.bsky.social, and ever-awesome PI's @irisjonkers.bsky.social & Sebo Withoff.

If you’re working on gut #NAMs, #tox, or #ADME and wondering which platform to pick (or how to tune your media), we hope this gives a practical roadmap.

And if you made it this far, thanks for reading – happy to answer questions! 👇

So the take home:

With the same iPSC-derived cells, the culture system + signaling regime can shift you from fetal-like to 'adult-like' tissue and from proliferative to highly functional epithelium.

So choosing “organoid vs Transwell vs chip” is not cosmetic – it changes the biology you read out.

What does this mean for your #NAMs platform of choice?

👉For drug absorption, metabolism & DDI: you probably want the intestine-on-chip.
👉For developmental biology / early tissue states: organoids are your friend.
👉For certain barrier / ECM / EMT questions: Transwells can be very informative

When we align them with in vivo references:
- Organoids cluster closer to fetal intestine
- Intestine-on-chip clusters with pediatric/adult small intestine
- Transwells sit in between but don’t fully capture either extreme

So the chip looks most “adult gut–like” at the transcriptomic level!

What we globally find:

🔹 Organoids
Strong developmental / fetal signatures
More embryonic patterning pathways

🔹 Transwells
More ECM remodeling, cell cycle, EMT-like features

🔹 Intestine-on-chip
Highest expression of digestion, nutrient transport & drug metabolism genes

Now the head-to-head showdown 🥊

We culture the same iPSC-derived epithelium in EM - DM+D+P as:
- 3D organoids
- 2D Transwell monolayers
- @emulatebio.bsky.social intestine-on-chip under flow

Then we compare their transcriptomes + map them onto in vivo small intestine data.

What about Transwells?

The EM–DM + D + P gradient lands perfectly in between:
- Keeps renewal / cell cycle pathways active
- Already shows enhanced digestion and xenobiotic metabolism

So you can balance “crypt-like” proliferation with “villus-like” function by cleverly combining media compositions

Then we benchmark functionality using RNA-seq.

First organoids:
Compared to EM, the DM + D + P massively boosts genes for:
- Nutrient digestion
- Transporters
- Drug metabolism

These iPSC-derived cells can become strongly enterocyte-like!

Next step: How can we mimic a crypt–villus axis in-vitro?

On Transwells we installed a growth factor gradient for this:
Basolateral: EM
Apical: DM + D _or_ DM + D + P

This indeed keeps a proliferative compartment and generates differentiated cells with tight junctions and good barrier properties.

At the cell type level we see:
- EM → lots of MKI67⁺ proliferative cells
- DM / DM + D → more enterocytes + goblet cells
- DM + D + P → differentiated epithelium with detectable enteroendocrine cells

(Paneth(-like) cells behave differently depending on the platform)

We use four main media conditions:
- EM = expansion (high WNT, BMP inhibition) → stem/transit-amplifying
- DM = differentiation
- DM + D = + NOTCH inhibitor → more secretory cells
- DM + D + P = + MEK inhibitor → more enteroendocrine cells

First, we generate small intestinal epithelium from human iPSCs and then expose it to different media that tweak key pathways: WNT, BMP, NOTCH, MAPK.

This lets us push cells from a proliferative, stem-like state toward mature epithelial lineages.

Human iPSCs are a powerful source for gut #NAMs.
But the same starting cells can behave very differently depending on whether you use them as 3D organoids, 2D monolayers on Transwells or on an intestine-on-chip.

So we asked: how big is that difference, really?

www.cell.com/stem-cell-re...

I think I agree.
But cant LLMs here help kickstart the decoupling of journals and PR to maintain the quality check of the current Status Quo of PR. and once that has happened, we can move to this post publication ongoing PR sytem