DEVELOPMENT OF A PERSONALIZED HUMAN PANETH CELL MODEL USING INTESTINAL ORGANOIDS
Authors: Patel Shachi , Wagner Monica Silveira , Bay Olivia , Zgarbova Eliska , Valencia Christian Wong , Michelsen Kathrin , Targan Stephan , Barrett Robert 
Published: January 2024

Abstract

INTRODUCTION
Paneth cells are a specialized intestinal epithelial cell subtype whose major function is to produce antimicrobial peptides (AMPs). Alterations in Paneth cell function are associated with Crohn’s disease (CD) but the confounding influences of environmental factors and/or genetic variations makes it difficult to identify the cause of this. Human intestinal organoid (HIO) technology now allows for the generation of intestinal epithelium from any individual but there are relatively few protocols that allow for the enrichment of Paneth cells within organoids. Our goal was to specifically enrich the Paneth cell population in HIOs derived from induced pluripotent stem cells (iPSCs).

METHODS
iPSCs from a control individual and 2 CD patients were directed to HIOs and then dissociated to generate purified populations of epithelial only-HIOs (eHIOs). eHIOs were passaged weekly in proliferation medium (EGF, Noggin and CHIR99021) and the γ-secretase inhibitor, DAPT, was added to direct towards a Paneth cell fate. Flow cytometry, qPCR and immunocytochemistry were used to determine Paneth cell numbers, and gene and protein expression of various AMPs respectively.

RESULTS
iPSC-derived eHIOs from the control individual, which were used to develop this enrichment protocol, could be maintained for at least 4 months in proliferation medium. Flow cytometry analysis of the Paneth marker lysozyme revealed that the population of Paneth cells in eHIOs significantly increased from ~1% in proliferation media to ~28% upon treatment with DAPT. qPCR analysis demonstrated that DAPT treatment significantly increased the expression of the Paneth cell associated genes DEFA5, DEFA6, ITLN2, REG3A and PLA2G2A. Immunocytochemistry revealed that DAPT treated eHIOs were enriched for cells possessing granulated lysozyme, and also for additional AMPs such as DEFA5, ITLN2 and REG3A. The presence of the bacterial sensors TLR2, TLR5 and NOD2 were also detected in our Paneth cells. Finally, to confirm the applicability to CD patients, we applied our protocol and found the population of Paneth cells in CD eHIOs significantly increased from ~1% in proliferation media to ~10% upon treatment with DAPT, had significantly increased expression of the Paneth cell related genes and were also were enriched for cells with granulated AMPs.

CONCLUSION
We have successfully developed a methodology to enrich Paneth cells in iPSC-derived HIOs from both healthy and CD patients. Given that iPSCs can be generated from donor cells stored in well characterized biorepositories or obtained from a small blood draw from any CD patient, this modeling system now opens up a new avenue of research by allowing an examination of how environmental factors (microbes/cytokines) and/or genetic variations influence human Paneth cell function in a personalized manner.

Fluorescent image showing the presence of granulated DEFA5 (green) in E-cadherin+ (red) human iPSC-derived intestinal organoids treated with DAPT (X60).

qPCR analysis of Paneth cell related genes in proliferation media compared to DAPT treatment. *P &lt; .05, **P &lt; .01, ***P &lt; .001, and ****P &lt; .0001 as compared to gene expression in proliferation media.