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Summary: The mandatory usage of extracellular matrix (ECM) gels in 3D cultures limits antibody penetration and increases background, while the removal of ECM gel causes disruption of morphology and sample loss. These factors pose challenges to effective immune labeling-based staining. Here, we present a protocol for whole-mount immunofluorescence staining of gel-embedded pancreatic organoids. We describe steps for sample fixation, blocking, and antibody incubation. We detail procedures for washing antibodies and mounting. : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Summary: Pancreatic cancer is characterized by bi-directional interactions between pancreatic cancer cells and stromal cells including neural cells. The absence of neural cells in pancreatic organoids limits the investigation of cell- cell interaction and tumor innervation. This protocol describes how to generate innervated wild type (WT) and Kras+/LSLG12D Trp53fl/f lp48+/Cre (KPC) murine pancreatic organoids. To specifically investigate neurogenesis, organoids are co-cultured with iPSCs-derived neural crest cells, while co-culture with dorsal root ganglia explants is used for comparing organoids with mature neurons.For complete details on the use and execution of this protocol, please refer to Huch et al. (2013), Boj et al. (2015), and Demir et al. (2014).

Hematopoietic stem cells (HSCs) are preserved in co-cultures with UG26-1B6 stromal cells or their conditioned medium. We performed a genome-wide study of gene expression changes of UG26-1B6 stromal cells in contact with Lineage− SCA-1+ KIT+ (LSK) cells. This analysis identified connective tissue growth factor (CTGF) to be upregulated in response to LSK cells. We found that co-culture of HSCs on CTGF knockdown stroma (shCtgf) shows impaired engraftment and long-term quality. Further experiments demonstrated that CD34− CD48− CD150+ LSK (CD34− SLAM) cell numbers from shCtgf co-cultures increase in G0 and senescence and show delayed time to first cell division. To understand this observation, a CTGF signaling network model was assembled, which was experimentally validated. In co-culture experiments of CD34− SLAM cells with shCtgf stromal cells, we found that SMAD2/3-dependent signaling was activated, with increasing p27Kip1 expression and downregulating cyclin D1. Our data support the view that LSK cells modulate gene expression in the niche to maintain repopulating HSC activity.