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Single-cell RNA-seq reveals distinct maturation stages of the Paneth cell lineage

ABSTRACT: Paneth cells (PCs) are long-lived secretory cells that reside at the bottoms of small intestinal crypts. Besides serving as niche cells for the neighboring Lgr5-positive stem cells, PCs secrete granules containing a broad spectrum of antimicrobial proteins, including lysozymes and defensins1. Here, we have used single-cell RNA sequencing to explore PC differentiation. We found a maturation gradient from early secretory progenitors to mature PCs, capturing the full maturation path of PCs. Moreover, differential expression of a subset of defensin genes in lysozyme-high PCs, e.g. Defa20, reveals at least two distinct stages of maturation. We traced Lgr5+ stem cells from Lgr5-CreERT2 C57Bl6/J mice bred to a Rosa26LSL-YFP reporter mice and sorted YFP+ cells 5 days, 3 weeks and 8 weeks after tamoxifen injection.

ORGANISM(S): Mus musculus

SUBMITTER: Kay Wiebrands

PROVIDER: E-GEOD-76408 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Single-cell RNA-seq reveals distinct maturation stages of the Paneth cell lineage

Project description:Paneth cells (PCs) are long-lived secretory cells that reside at the bottoms of small intestinal crypts. Besides serving as niche cells for the neighboring Lgr5-positive stem cells, PCs secrete granules containing a broad spectrum of antimicrobial proteins, including lysozymes and defensins1. Here, we have used single-cell RNA sequencing to explore PC differentiation. We found a maturation gradient from early secretory progenitors to mature PCs, capturing the full maturation path of PCs. Moreover, differential expression of a subset of defensin genes in lysozyme-high PCs, e.g. Defa20, reveals at least two distinct stages of maturation.

2016-06-23 | GSE76408 | GEO

single cell RNA-seq on FACS purfied murine paneth cells

Project description:The small intestinal crypts harbour secretory Paneth cells (PCs) which express bactericidal peptides that are crucial for maintaining intestinal homeostasis. Considering the diverse environmental conditions throughout the course of the small intestine, multiple subtypes of PCs are expected to exist. We applied single cell RNA-sequencing of PCs combined with deep bulk RNA-sequencing on PC populations of different small intestinal locations and discovered several expression-based PC clusters. Some of these are discrete and resemble tuft cell-like PCs, goblet cell (GC)-like PCs, PCs expressing stem cell markers, and atypical PCs. Other clusters are less discrete but appear to be derived from different locations along the intestinal tract and have environment-dictated functions such as food digestion and antimicrobial peptide production

2024-09-18 | GSE273983 | GEO

Paneth cells constitute the niche for Lgr5 stem cells in intestinal crypts

Project description:Homeostasis of self-renewing small intestinal crypts results from neutral competition between Lgr5 stem cells, small cycling cells located at crypt bottoms1, 2. Lgr5 stem cells are interspersed between terminally differentiated Paneth cells, that are known to produce bactericidal products such as lysozyme and cryptdins/defensins3. Single Lgr5-expressing stem cells can be cultured to form long-lived, self-organizing crypt-villus organoids in the absence of non-epithelial niche cells4. Here, we note a close physical association of Lgr5 stem cells with Paneth cells in vivo and in vitro. CD24+ Paneth cells express EGF, TGF?, Wnt3 and the Notch-ligand Dll4, all essential signals for stem cell maintenance in culture. Co-culturing of sorted stem cells with Paneth cells dramatically improves organoid formation. This Paneth cell requirement can be substituted by a pulse of exogenous Wnt. Genetic removal of Paneth cells in vivo results in the concomitant loss of Lgr5 stem cells. In colon crypts, CD24+ cells residing between Lgr5 stem cells may represent the Paneth cell equivalents. We conclude that Lgr5 stem cells compete for essential niche signals provided by a specialized daughter cell, the Paneth cell. We used intestinal cell fractions from Lgr5-EGFP-ires-CreERT2 mice, expressing GFP under the control of the Lgr5 promoter. RNA was isolated from two FACS sorted cell populations: stem cells were sorted based on high level of GFP expression (GFPhi) and Paneth cells were sorted based on high level of CD24 expression (CD24hi) and high side-scatter (SSChi). Differentially labelled cRNA from GFPhi and CD24hi/SSChi cells from two different sorts (each combining ten individual mice) were hybridized on 4X44K Agilent Whole Mouse Genome dual colour Microarrays (G4122F) in two dye swap experiments, resulting in four individual arrays.

2010-11-29 | E-GEOD-25109 | biostudies-arrayexpress

Paneth cells constitute the niche for Lgr5 stem cells in intestinal crypts

2010-11-29 | GSE25109 | GEO

RNA-seq on FACS sorted paneth cells from the murine duodenum, jejunum and ileum

Project description:The small intestinal crypts harbour secretory Paneth cells (PCs), which express bactericidal peptides that are crucial for maintaining intestinal homeostasis. Considering the diverse environmental conditions throughout the course of the small intestine, multiple subtypes of PCs are expected to exist. We applied single cells RNA-sequencing of PCs combined with deep bulk RNA-sequencing on PC populations of different locations (duodenum, jejunum, ileum) and discovered several expression-based clusters. Some of these are discrete and resemble tuft cell-like PCs, goblet cell-like PCs, PCs expressing stem cell markers, and senescent PCs. Other clusters are less discrete, but based on bulk RNA-seq appear to be derived from different locations along the small intestinal tract. Furthermore, a comprehensive spatial analysis was conducted using the Resolve bioscience technique, identifying different PCs clusters along the small intestine, but not along the crypts themselves.

2024-03-07 | GSE255507 | GEO

Chemically Induced Paneth Cells Provide Superior In Vivo Mimic to Organoid-derived Analog

Project description:Paneth cells (PCs) are post-mitotic secretory cells of the small intestine that produce antimicrobials, growth factors, and cytokines. Multiple diseases have been linked to alterations in PC function. Past studies of PCs have relied on in vivo models, and limited in vitro models, including organoids. While useful, whether the in vitro models recapitulate in vivo biology is an important, yet unanswered question. Here, we present a bona fide in vitro PC-enriched population derived via chemically-induced (CI) differentiation of primary murine adult stem cells. We define the identity of PCs in our system and compare to PCs of established organoid systems and those found in vivo. Importantly, we demonstrate stimulant-induced and microbe-responsive antimicrobial function of our CI-PCs – hallmark functions of PCs in vivo. Thus, we define and produce the most physiologically-relevant in vitro PC population to date, providing a superior tool to study cellular development, host-microbe interactions, and inflammatory disease.

2018-04-02 | GSE100274 | GEO

CU44_WGS of YFP+ sorted tumor cells from murine PKCY and A3A_PKCY pancreatic tumors

Project description:We aimed to decipher human APOBEC3A driven genomic differences in pancreatic tumors in vivo using a genetically engineered mouse model for pancreatic cancer. Murine pancreatic tumor formation was driven by p53fl/+;KrasLSL-G12D/+;Pdx1-Cre;Rosa26LSL-YFP (PKCY) and p53fl/+;KrasLSL-G12D/+;Pdx1-Cre; Rosa26LSL-YFP; A3A+/- (A3A PKCY).

2021-09-06 | E-MTAB-9843 | biostudies-arrayexpress

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2021-09-06 | E-MTAB-9966 | biostudies-arrayexpress

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Project description:We aimed to decipher human APOBEC3A driven mutational differences in pancreatic tumor in vivo using a genetically engineered mouse model of pancreatic cancer. Murine pancreatic tumor formation was driven by p53fl/+;KrasLSL-G12D/+;Pdx1-Cre;Rosa26LSL-YFP (PKCY) and p53fl/+;KrasLSL-G12D/+;Pdx1-Cre; Rosa26LSL-YFP; A3A+/- (A3A PKCY).

2021-09-06 | E-MTAB-9972 | biostudies-arrayexpress

Characterisation of epithelial and mesenchymal cells in murine pancreatic tumours

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2022-04-08 | GSE157134 | GEO

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