# Proinflammatory cytokines modify Ca2+ signaling and induce an apoptotic lipidome in murine small intestinal organoids

**Authors:** Svenja Mareike Pauer, Alina Schindler, Parviz Ghezellou, Bernhard Spengler, Martin Diener, Jasmin Ballout

PMC · DOI: 10.3389/fphys.2026.1738447 · Frontiers in Physiology · 2026-02-06

## TL;DR

Proinflammatory cytokines cause fluid secretion and cell death in intestinal organoids by altering calcium signaling and lipid composition.

## Contribution

The study reveals how cytokines affect calcium signaling and lipid profiles in intestinal organoids over time.

## Key findings

- Cytokine mix increases organoid lumen size via Cl− secretion.
- Cytokines enhance Ca2+ signaling and upregulate IP3R1 and STIM2 gene expression.
- Lipidomic analysis shows increased ceramides and apoptotic cells in organoids.

## Abstract

Inflammatory bowel diseases (IBD) are associated with elevated levels of proinflammatory cytokines exerting a detrimental effect on the intestinal epithelium. Since contradictory studies regarding time-dependent actions on epithelial secretion exist, intestinal organoids were treated with a mix of proinflammatory cytokines.

Long-term (1–5 days) effects of a cytokine mix consisting of tumor necrosis factor α, interleukin-1β and interferon-γ on murine small intestinal epithelial organoids were investigated using live cell imaging, immunofluorescent staining, qPCR, scanning microprobe matrix-assisted laser desorption/ionization mass spectrometry imaging (AP-SMALDI MSI), and liquid-chromatography tandem mass spectrometry (UHPLC MS/MS).

Treatment with the cytokine mix resulted in an enlarged organoid lumen. Stimulation of Cl– secretion seems to underly this swelling since it was inhibited by bumetanide, a blocker of Na+-K+-2Cl– cotransporters. Ca2+ imaging experiments revealed that the cytokine mix time-dependently enhanced the response to carbachol, a Ca2+-dependent secretagogue, which would favor Ca2+-dependent Cl− secretion. This was concomitant with an upregulated gene expression of inositol-1,4,5-trisphosphate receptor type 1 (IP3R1) and stromal interaction molecule 2 (STIM2), which is involved in store-operated Ca2+ entry. The cytokines induced apoptosis in organoids confirmed by an increase in caspase 3-immunopositive cells. Lipidomic analysis using UHPLC MS/MS revealed an upregulation of ceramides, sphingomyelins and ether-linked lipids within the epithelial cells. AP-SMALDI MSI showed an accumulation of ceramide-positive (apoptotic) cells within the organoid lumen.

Proinflammatory cytokines induce fluid secretion and transiently upregulate Ca2+ signaling concomitant with the induction of an apoptotic lipidome in small intestinal organoids.

## Linked entities

- **Genes:** ITPR1 (inositol 1,4,5-trisphosphate receptor type 1) [NCBI Gene 3708], STIM2 (stromal interaction molecule 2) [NCBI Gene 57620]
- **Chemicals:** bumetanide (PubChem CID 2471), carbachol (PubChem CID 5831)

## Full-text entities

- **Genes:** Ifng (interferon gamma) [NCBI Gene 15978] {aka IFN-g, If2f, Ifg}, Orai2 (ORAI calcium release-activated calcium modulator 2) [NCBI Gene 269717] {aka A730041O15Rik, Tmem142b}, Plcb3 (phospholipase C, beta 3) [NCBI Gene 18797] {aka mKIAA4098}, Slc12a2 (solute carrier family 12, member 2) [NCBI Gene 20496] {aka 9330166H04Rik, BSC2, Nkcc1, mBSC2, mNKCC1, sy-ns}, Cldn2 (claudin 2) [NCBI Gene 12738], Tjp1 (tight junction protein 1) [NCBI Gene 21872] {aka ZO1}, Pcx (pyruvate carboxylase) [NCBI Gene 18563] {aka Pc, Pcb}, Il1b (interleukin 1 beta) [NCBI Gene 16176] {aka IL-1beta, Il-1b}, TNF (tumor necrosis factor) [NCBI Gene 7124] {aka DIF, IMD127, TNF-alpha, TNFA, TNFSF2, TNLG1F}, Gusb (glucuronidase, beta) [NCBI Gene 110006] {aka Gur, Gus, Gus-r, Gus-s, Gus-t, Gus-u}, Cldn3 (claudin 3) [NCBI Gene 12739] {aka Cpetr2, mRVP1}, Casp3 (caspase 3) [NCBI Gene 12367] {aka A830040C14Rik, AC-3, CASP-3, CC3, CPP-32, CPP32}, Nfkb1 (nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105) [NCBI Gene 18033] {aka NF-KB1, NF-kappaB, NF-kappaB1, p105, p50, p50/p105}, Mapk14 (mitogen-activated protein kinase 14) [NCBI Gene 26416] {aka CSBP2, Crk1, Csbp1, Mxi2, PRKM14, PRKM15}, Stim2 (stromal interaction molecule 2) [NCBI Gene 116873], Ocln (occludin) [NCBI Gene 18260] {aka Ocl}, Ryr3 (ryanodine receptor 3) [NCBI Gene 20192] {aka C230090H21, RYR-3}, IL1B (interleukin 1 beta) [NCBI Gene 3553] {aka IL-1, IL1-BETA, IL1F2, IL1beta}, Cftr (cystic fibrosis transmembrane conductance regulator) [NCBI Gene 12638] {aka Abcc7}, Tnfrsf1b (tumor necrosis factor receptor superfamily, member 1b) [NCBI Gene 21938] {aka CD120b, TNF-R-II, TNF-R2, TNF-R75, TNF-alphaR2, TNFBR}, Ano1 (anoctamin 1, calcium activated chloride channel) [NCBI Gene 101772] {aka Tmem16a}, Itpr1 (inositol 1,4,5-trisphosphate receptor 1) [NCBI Gene 16438] {aka D6Pas2, Gm10429, IP3R 1, IP3R1, InsP3R, Ip3r}, Atp2a1 (ATPase, Ca++ transporting, cardiac muscle, fast twitch 1) [NCBI Gene 11937] {aka SERCA1}, Gapdh (glyceraldehyde-3-phosphate dehydrogenase) [NCBI Gene 14433] {aka Gapd}, Atp2a3 (ATPase, Ca++ transporting, ubiquitous) [NCBI Gene 53313] {aka SERCA3b, Serca3}, Cldn4 (claudin 4) [NCBI Gene 12740] {aka Cep-r, Cpetr, Cpetr1}, Ryr1 (ryanodine receptor 1, skeletal muscle) [NCBI Gene 20190] {aka RYR-1, Ryr, skrr}, IFNG (interferon gamma) [NCBI Gene 3458] {aka IFG, IFI, IMD69}, CXCL10 (C-X-C motif chemokine ligand 10) [NCBI Gene 3627] {aka C7, IFI10, INP10, IP-10, SCYB10, crg-2}, Orai1 (ORAI calcium release-activated calcium modulator 1) [NCBI Gene 109305] {aka D730049H07Rik, Tmem142a, orai-1}, Tnf (tumor necrosis factor) [NCBI Gene 21926] {aka DIF, TNF-a, TNF-alpha, TNFSF2, TNFalpha, Tnfa}, Mapk1 (mitogen-activated protein kinase 1) [NCBI Gene 26413] {aka 9030612K14Rik, ERK, Erk2, MAPK2, PRKM2, Prkm1}
- **Diseases:** diarrhea (MESH:D003967), colonic tumor (MESH:D003110), chronic inflammation (MESH:D007249), swelling (MESH:D004487), abdominal pain (MESH:D015746), organoid swelling (MESH:D054000), IBD (MESH:D015212), proinflammatory cytokines (MESH:D000080424), ulcerative colitis (MESH:D003093), arthritis (MESH:D001168), anemia (MESH:D000740), weight loss (MESH:D015431), colitis (MESH:D003092), Crohn's disease (MESH:D003424)
- **Chemicals:** PGE2 (MESH:D015232), acetylcholine (MESH:D000109), luminal (MESH:D010634), Lanthanum (MESH:D007811), H2O (MESH:D014867), phospholipids (MESH:D010743), IP3 (MESH:D015544), 4-hydroxy-3-methoxycinnamaldehyde (MESH:C075384), Cer (MESH:D002518), B (MESH:D001895), NaOH (MESH:D012972), ethanol (MESH:D000431), HCl (MESH:D006851), Fura-2 (MESH:D016257), propan-2-ol (MESH:D019840), CaCl2 (MESH:D002122), phosphate (MESH:D010710), Ammonium formate (MESH:C030544), thapsigargin (MESH:D019284), NaCl (MESH:D012965), methanol (MESH:D000432), 9-AA (MESH:D000585), Carbachol (MESH:D002217), MgCl2 (MESH:D015636), Triton-X-100 (MESH:D017830), ACN (MESH:C032159), nitrogen (MESH:D009584), PIP2 (MESH:D019269), CPA (MESH:C000543), EDTA (MESH:D004492), prostaglandins (MESH:D011453), 2-methoxy-2-methylpropane (MESH:C043243), PFA (MESH:C003043), lipid (MESH:D008055), CO2 (MESH:D002245), DSS (MESH:D016264), AM (MESH:D000576), CA (MESH:D002118), sphingosine (MESH:D013110), ice (MESH:D007053), DAPI (MESH:C007293), DMSO (MESH:D004121), glucose (MESH:D005947), H (MESH:D006859), diacylglycerol (MESH:D004075), PBS (MESH:D007854), Bumetanide (MESH:D002034), KCl (MESH:D011189), LaCl3 (MESH:C028521), HEPES (MESH:D006531), Na (MESH:D012964), 2,5-Dihydroxybenzoic acid (MESH:C010925), phosphatidylethanolamine (MESH:C483858), sphingomyelin (MESH:D013109), eicosanoids (MESH:D015777), Alexa488 (-), acetone (MESH:D000096), PC (MESH:D010713), phosphatidylserine (MESH:D010718), Cl (MESH:D002713)
- **Species:** Mus musculus (house mouse, species) [taxon 10090], Homo sapiens (human, species) [taxon 9606]
- **Mutations:** C-25  C, C) for 30
- **Cell lines:** S2 — Drosophila melanogaster (Fruit fly), Spontaneously immortalized cell line (CVCL_Z232), HT-29 — Homo sapiens (Human), Colon adenocarcinoma, Cancer cell line (CVCL_0320), Caco-2 — Homo sapiens (Human), Colon adenocarcinoma, Cancer cell line (CVCL_0025), HT29 cl.19A — Homo sapiens (Human), Colon adenocarcinoma, Cancer cell line (CVCL_0323)

## Full text

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## Figures

8 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12920202/full.md

## References

66 references — full list in the complete paper: https://tomesphere.com/paper/PMC12920202/full.md

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Source: https://tomesphere.com/paper/PMC12920202