We then tested inflammatory and cytotoxic perturbations. IL-15 and IL-21 further increased granzyme B and IFN-γ but did not trigger epithelial killing. In contrast, enforced CD3×EpCAM engagement induced pronounced apoptosis accompanied by increased TNF and FAS ligand. [10/11]

To demonstrate biologically meaningful crosstalk, we first examined baseline co-cultures. IELs induced a strong epithelial interferon-associated response, including CXCL9, CXCL10 and CXCL11 production, without causing overt epithelial apoptosis. [9/11]

A Matrigel-bed format provides an open and experimentally tractable co-culture configuration. Unlike conventional Matrigel domes, it allows IELs to move around the organoids and establish repeated proximity to the epithelial surface, without requiring a custom device. [8/11]

A key hurdle was finding conditions that worked for both compartments. Organoids collapsed in IEL medium, while IELs did poorly in standard organoid medium. We therefore developed a shared medium that maintains epithelial growth alongside IEL viability and effector-associated features. [7/11]

And so we managed to set-up an autologous human duodenal IEL–organoid co-culture platform: Both the IELs and epithelial compartments can be expanded, cryopreserved and revived, enabling successive experiments using cells originating from the same donor. [4/11]

We’ve been cooking something for a while, but we’re very happy to share the preprint now in its current form: "An autologous human duodenal IEL–organoid co-culture platform for studying immune–epithelial interactions" Link and threat below www.biorxiv.org/content/10.6... 🧵👇

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)

Totally psyched that our paper is out in @stemcellreports.bsky.social! For human iPSC–based gut #NAMs, which platform would you trust to behave most like real intestinal tissue? We put #organoids, Transwells and @emulatebio.bsky.social intestine-chip head to head. Spoiler: the chip wins. 🧵&🔗👇

Back to back commentaries in @natureportfolio.nature.com today. Clearly NAMs are causing a stir!

FFS

Every cell is a stem cell! Even ‘terminal’ enterocytes can hit reset: Gut damage triggers a YAP/TAZ-driven fetal program → stress-proof “revival” stem cells → Lgr5⁺ CBC stem cells, rebuilding crypts from scratch and make organoids. #StemCellPlasticity #Organoids #Gut

Its honestly quite shocking. Cancer cell lines are sub-optimal systems due to genomic instability, mutations and potentially strange phenotypes. Thats known, but to see these anomalies quantified is a good moment to realize this once again. #Celllines #ImmunoSky #Jurkat

✨ Incredibly happy!! To receive the 2025 Stimulering prize from the Dutch Coeliac Disease Association! 🙌 Huge Thanks to all NCV members for your trust💚 Excited to continue our mini-gut & gut-on-a-chip research at @umcgroningen.bsky.social 💚 #coeliakie #research #minigut

Vascularized organoids! Balancing BMP signaling enables co-differentiation of mesoderm + endoderm in a single spheroid → organ-specific endothelium + vascularized gut & lung organoids! Ever increasing organoid complexity👏 #Organoids #StemCells

FDA 🤝 Organs-on-Chips The @fda.gov recently published its Roadmap to Reducing Animal Testing in Preclinical Safety Studies. This is an exciting step forward in emphasizing the adoption of New Approach Methodologies (NAMs), focusing on human-derived in vitro and in silico models.

Cheering for everyone standing up for science today! 👏👏👏

Seems obvious, but apparently, no one has really dived into it like this(?)👇 🧬 Epigenetic variation in iPSCs staged is mostly tied to genetic variation, but as cells differentiate, this dilutes out quickly: Cell type matters more than genetics. #StemCells www.nature.com/articles/s41...

“The world’s a shit show, so why not put 💩 on a chip? Scientists created an iPSC-derived intestine-on-a-chip with fecal microbiota—uncovering epithelium-specific biomarkers & microbial factors linked to melanoma outcomes. Cutting-edge #OrganOnChip tech! #ImmunoSky #MedSky”

Its stories like this that makes me incredibly excited! A gut immune–epithelial circuit regulating tolerance to food: Goblet cell protein RELMβ disrupts tolerance by depleting microbiome-derived indoles needed for protective Tregs. #microbiome #immunity #ImmunoSky www.nature.com/articles/s41...

TG2 (Transglutaminase 2) is responsible for the deamidation of gluten peptides, making them immunogenic antigens in the context of Celiac Disease - But what other functions does TG2 have?! 👇 TG2 drives epigenetic histone monoaminylation, regulating neural rhythmicity 🧠! #Celiac

Time to log off for the holidays with a timelapse: Intestinal organoid trying to resist the attack from CD8 T cells. Happy holidays! 🎄🧑‍🎄 #ImmunoSky

Arrived. Excited for a 2-day Netherlands Organ-on-Chip Consortium gathering at the @hubrechtinstitute.bsky.social #Organoids #OrganOnChip #NOCI

What do you find the most annoying piece of lab equipment and why is it the counting chamber? #PhDchat #Immunosky