Sox4 Promotes Atoh1-Independent Intestinal Secretory Differentiation Toward Tuft and Enteroendocrine Fates

Gracz AD, Samsa LA, Fordham MJ, Trotier DC, Zwarycz B, Lo YH, Bao K, Starmer J, Raab JR, Shroyer NF, Reinhardt RL, Magness ST

Gastroenterology. 2018 Nov;155(5):1508-1523. Epub 2018 Jul 25 PMID: 30055169



BACKGROUND & AIMS: The intestinal epithelium is maintained by intestinal stem cells (ISCs), which produce postmitotic absorptive and secretory epithelial cells. Initial fate specification toward enteroendocrine, goblet, and Paneth cell lineages requires the transcription factor Atoh1, which regulates differentiation of the secretory cell lineage. However, less is known about the origin of tuft cells, which participate in type II immune responses to parasite infections and appear to differentiate independently of Atoh1. We investigated the role of Sox4 in ISC differentiation. METHODS: We performed experiments in mice with intestinal epithelial-specific disruption of Sox4 (Sox4fl/fl:vilCre; SOX4 conditional knockout [cKO]) and mice without disruption of Sox4 (control mice). Crypt- and single-cell-derived organoids were used in assays to measure proliferation and ISC potency. Lineage allocation and gene expression changes were studied by immunofluorescence, real-time quantitative polymerase chain reaction, and RNA-seq analyses. Intestinal organoids were incubated with the type 2 cytokine interleukin 13 and gene expression was analyzed. Mice were infected with the helminth Nippostrongylus brasiliensis and intestinal tissues were collected 7 days later for analysis. Intestinal tissues collected from mice that express green fluorescent protein regulated by the Atoh1 promoter (Atoh1GFP mice) and single-cell RNA-seq analysis were used to identify cells that coexpress Sox4 and Atoh1. We generated SOX4-inducible intestinal organoids derived from Atoh1fl/fl:vilCreER (ATOH1 inducible knockout) mice and assessed differentiation. RESULTS: Sox4cKO mice had impaired ISC function and secretory differentiation, resulting in decreased numbers of tuft and enteroendocrine cells. In control mice, numbers of SOX4+ cells increased significantly after helminth infection, coincident with tuft cell hyperplasia. Sox4 was activated by interleukin 13 in control organoids; SOX4cKO mice had impaired tuft cell hyperplasia and parasite clearance after infection with helminths. In single-cell RNA-seq analysis, Sox4+/Atoh1- cells were enriched for ISC, progenitor, and tuft cell genes; 12.5% of Sox4-expressing cells coexpressed Atoh1 and were enriched for enteroendocrine genes. In organoids, overexpression of Sox4 was sufficient to induce differentiation of tuft and enteroendocrine cells-even in the absence of Atoh1. CONCLUSIONS: We found Sox4 promoted tuft and enteroendocrine cell lineage allocation independently of Atoh1. These results challenge the longstanding model in which Atoh1 is the sole regulator of secretory differentiation in the intestine and are relevant for understanding epithelial responses to parasitic infection.

Organoid Cultures for Assessing Intestinal Epithelial Differentiation and Function in Response to Type-2 Inflammation

Zwarycz B, Gracz AD, Magness ST

Methods Mol Biol. 2018;1799:397-417. PMID: 29956167



During helminth infection of the gastrointestinal tract, a complex Type-2 inflammatory response involving immunological and mucosal components is mounted to clear the infection and reestablish a physiologically normal state. This response is characterized by the secretion of key interleukins, which impact epithelial lineage allocation and drive tuft and goblet cell hyperplasia to lead to eventual clearance of parasitic organisms. While there have been advances toward understanding Type-2 inflammatory responses in the intestine, detailed cellular and molecular mechanisms of epithelial responses to general inflammation and specific inflammatory cytokines remain to be explored. Intestinal organoids represent a physiologically relevant in vitro model to study how Type-2 inflammation impacts stem cell maintenance and differentiation and offer a new approach for investigators to test compounds that modulate mechanisms involved in worm clearance. The methods described in this chapter include: (1) intestinal crypt and single cell isolation; (2) organoid culture and cytokine treatment, as well as methods for downstream organoid analyses; (3) gene expression analysis by qRT-PCR; (4) protein analysis by western blot, immunohistochemistry, and florescence-activated cell sorting; and (5) organoid self-renewal by serial passaging.

SOX9 Maintains Reserve Stem Cells and Preserves Radio-resistance in Mouse Small Intestine.


Roche KC, Gracz AD, Liu XF, Newton V, Akiyama H, Magness ST

Gastroenterology. 2015 Nov;149(6):1553-1563. Epub 2015 Jul 11. PMID: 26170137



BACKGROUND & AIMS: Reserve intestinal stem cells (rISCs) mediate epithelial regeneration following tissue damage. Unlike active intestinal stem cells (aISCs), rISCs slowly cycle under homeostatic conditions, allowing for their identification with label retention assays. In response to certain epithelial injuries, rISCs convert to an actively dividing state and demonstrate multipotency and self-renewal, which are defining properties of stem cells. Little is known about the genetic mechanisms that regulate the production and maintenance of rISCs. High expression levels of the transcription factor Sox9 (Sox9high) have been associated with rISCs. We investigated the role of SOX9 in maintaining rISCs. METHODS: We performed single-cell analyses to characterize the expression of active and reserve ISC markers in Lgr5high cells (aISC) and Sox9high cells (rISC) isolated from reporter mice by fluorescence-activated cell sorting. We used label-retention assays to determine the proliferative capacity of Sox9high cells. Lineage-tracing experiments were performed in Sox9-CreERT2 mice to measure the stem cell capacities and radio-resistance of Sox9-expressing cells. Conditional knockout (SOX9cKO) and inducible-conditional (SOX9iKO) knockout mice were used to determine whether SOX9 was required to maintain label-retaining cells (LRCs) and rISC function. RESULTS: Lgr5high and a subset of crypt-based Sox9high cells co-express markers of aISC and rISC (Lgr5, Bmi1, Lrig1, and Hopx). LRCs express high levels of Sox9 and are lost in SOX9-knockout mice. SOX9 is required for epithelial regeneration following high-dose irradiation. Crypts from SOX9-knockout mice have increased sensitivity to radiation, compared with control mice, which could not be attributed to impaired cell cycle arrest or DNA repair. CONCLUSIONS: Sox9 limits proliferation in LRCs and imparts radiation resistance to rISCs in mice.

Distinct SOX9 Levels Differentially Mark Stem/Progenitor Populations and Enteroendocrine Cells of the Small Intestine Epithelium

Formeister EJ., Sionas AL, Lorance DK, Barkley CL, Lee GH, Magness ST

Am J Physiol Gastrointest Liver Physiol. 2009, May; 296(5):G1108-18. Epub 2009 Feb 19 PMID: 19228882



SOX transcription factors have the capacity to modulate stem/progenitor cell proliferation and differentiation in a dose-dependent manner. SOX9 is expressed in the small intestine epithelial stem cell zone. Therefore, we hypothesized that differential levels of SOX9 may exist, influencing proliferation and/or differentiation of the small intestine epithelium. Sox9 expression levels in the small intestine were investigated using a Sox9 enhanced green fluorescent protein (Sox9(EGFP)) transgenic mouse. Sox9(EGFP) levels correlate with endogenous SOX9 levels, which are expressed at two steady-state levels, termed Sox9(EGFPLO) and Sox9(EGFPHI). Crypt-based columnar cells are Sox9(EGFPLO) and demonstrate enriched expression of the stem cell marker, Lgr5. Sox9(EGFPHI) cells express chromogranin A and substance P but do not express Ki67 and neurogenin3, indicating that Sox9(EGFPHI) cells are postmitotic enteroendocrine cells. Overexpression of SOX9 in a crypt cell line stopped proliferation and induced morphological changes. These data support a bimodal role for SOX9 in the intestinal epithelium, where low SOX9 expression supports proliferative capacity, and high SOX9 expression suppresses proliferation.