Intestinal organoids as tools for enriching and studying specific and rare cell types: advances and future directions

Abstract

Adult tissue-derived organoids allow for the expansion and maintenance of primary epithelial cells in a near-native state. These 3-dimensional and self-organizing organotypic cultures derived from adult tissues have been increasingly used in fundamental and translational research. A key feature of this organoid system is that it recapitulates the stem cell lineage and thus, the differentiated cell type heterogeneity of the in vivo tissue of origin. Importantly, we and others have shown that organoids can be manipulated to expand different cell lineages, allowing for the study of rare cell types that would otherwise be very difficult to analyze. Here, focusing specifically on organoids of the small intestine, we discuss recent advances and future directions of this new avenue of organoid research. We highlight methods used to enrich for specific cell types including stem cells, enterocytes, Paneth cells, goblet cells, micro-fold (M)-cells, tuft cells, and enteroendocrine cells (EECs) in intestinal organoids, and focus on what each of these methods has taught us about the differentiation of adult intestinal stem cells (ISCs) to specific cell fates. Furthermore, we highlight how these new cell type-enriched intestinal organoids can be used to answer a diversity of questions relevant to human biology and disease.

Assessing donor-to-donor variability in human intestinal organoid cultures

“…Importantly, only markers of enterocytes, goblet, Paneth, and enteroendocrine cells could be detected (Figures 1, 2, and 5); rarer cell types such as tuft and microfold (M) cell markers were not detected (data not shown). This is consistent with previous work showing that differentiation toward rare cell type linages requires the addition of specific cytokines (Boonekamp et al, 2020).…”

Single‐cell analyses reveal SARS‐CoV‐2 interference with intrinsic immune response in the human gut

“…First, intestinal organoids are grown and maintained in a high Wnt media which keeps them constantly proliferating which is very different from the normal environment found within the body (Sato et al, 2011). Second, to induce differentiation, media conditions are changed and these conditions must be slightly adapted to promote differentiation toward specific cell types (Boonekamp et al, 2020;Ding et al, 2020). Most importantly, organoids are lacking the environmental features of the body (e.g., microbiota, immune cells, hypoxia) which is likely ◀ Figure 6.…”

Characterization of an in vitro 3D intestinal organoid model by using massive RNAseq-based transcriptome profiling

“…VPA and EPZ6438 was revealed to be indispensable for epigenome reprogramming and regeneration in Hyper-organoids by functioning through epigenetically regulating YAP signaling. Furthermore, Boonekamp et al 34 had recapitulated that intestinal organoids could be manipulated for enriching different cell types by applying different compounds to the ENR medium to direct development signaling (e.g. Notch, EGF, BMP and Wnt).…”