Biology subjects

Reyes, E.

Publications and source records attributed to Reyes, E..

4 recordsLinked to original sources

bioRxiv2023

Epithelial zonation along the mouse and human small intestine defines five discrete metabolic domains

A key aspect of nutrient absorption is the exquisite division of labor across the length of the small intestine, with individual classes of micronutrients taken up at different positions. For millennia, the small intestine was thought to comprise three segments with indefinite borders: the duodenum, jejunum, and ileum. By examining fine-scale longitudinal segmentation of the mouse and human small intestines, we identified transcriptional signatures and upstream regulatory factors that define five domains of nutrient absorption, distinct from the three traditional sections. Spatially restricted expression programs were most prominent in nutrient-absorbing enterocytes but initially arose in intestinal stem cells residing in three regional populations. While a core signature was maintained across mice and humans with different diets and environments, domain properties were influenced by dietary changes. We established the functions of Ppar- and Cdx1 in patterning lipid metabolism in distal domains and generated a predictive model of additional transcription factors that direct domain identity. Molecular domain identity can be detected with machine learning, representing the first systematic method to computationally identify specific intestinal regions in mice. These findings provide a foundational framework for the identity and control of longitudinal zonation of absorption along the proximal:distal small intestinal axis.

genomics↗

bioRxiv2021

Intracellular pH dynamics regulates intestinal stem cell fate

Intracellular pH (pHi) dynamics is increasingly recognized to regulate myriad cell behaviors, including proliferation, migration, differentiation, and transformation. Here we report a new finding that pHi dynamics also regulates adult stem cell lineage specification. In mouse small intestinal organoids, we identify a pHi gradient along the crypt axis, lower at the crypt base and higher toward the villus, and find that dissipating this gradient by inhibiting Na+-H+ exchanger 1 (NHE1) activity genetically or pharmacologically abolishes crypt budding. Using single-cell RNA sequencing and lineage tracing we demonstrate that pHi dynamics acts downstream of ATOH1, with increased pHi promoting differentiation toward the secretory lineage, while reduced pHi biases differentiation into the absorptive lineage. Consistent with these results, disrupting the pHi gradient blocks new Paneth cell differentiation. Paneth cells provide an essential WNT signal to ISCs in organoids, and we find that the loss of crypt budding with inhibiting NHE1 activity is rescued with exogenous WNTs. Our findings indicate that pHi dynamics is tightly regulated in the ISC lineage and that an increase in pHi is required for the specification of secretory lineage, including Paneth cell differentiation that contributes to crypt maintenance. These observations reveal a previously unreported role for pHi dynamics in cell fate decisions within an adult stem cell lineage.

cell biology↗

bioRxiv2021

Th17 immunity in the colon is controlled by two novel subsets of colon-specific mononuclear phagocytes

Intestinal immunity is coordinated by specialized mononuclear phagocyte populations, constituted by a diversity of cell subsets. Although the cell subsets constituting the mononuclear phagocyte network are thought to be similar in both small and large intestine, these organs have distinct anatomy, microbial composition, and immunological demands. Whether these distinctions demand organ-specific mononuclear phagocyte populations with dedicated organ-specific roles in immunity are unknown. Here we implement a new strategy to subset murine intestinal mononuclear phagocytes and identify two novel subsets which are colon-specific: a macrophage subset and a Th17-inducing dendritic cell (DC) subset. Colon-specific DCs and macrophages co-expressed CD24 and CD14, and surprisingly, both were dependent on the transcription factor IRF4. Novel IRF4-dependent CD14+CD24+ macrophages were markedly distinct from conventional macrophages and failed to express classical markers including CX3CR1, CD64 and CD88, and surprisingly expressed little IL-10, which was otherwise robustly expressed by all other intestinal macrophages. We further found that colon-specific CD14+CD24+ mononuclear phagocytes were essential for Th17 immunity in the colon, and provide definitive evidence that colon and small intestine have distinct antigen presenting cell requirements for Th17 immunity. Our findings reveal unappreciated organ-specific diversity of intestine-resident mononuclear phagocytes and organ-specific requirements for Th17 immunity.

immunology↗

bioRxiv2019

Lactoferrin Reverses Methotrexate Driven Epithelial Barrier Defect by Inhibiting TGF-β Mediated Epithelial to Mesenchymal Transition

BACKGROUND AND AIMSMethotrexate is an important tool in the arsenal of oncologists, gastroenterologists, and rheumatologists. At low doses it induces intestinal barrier dysfunction that may induce side effects such as gastrointestinal discomfort and liver injury. Previous studies suggest that lactoferrin can improve barrier function in a variety of contexts. This study set out to determine the mechanism of methotrexate induced barrier dysfunction and assess the effect of lactoferrin and other components of human breast milk on this dysfunction. METHODSUsing a murine enteroid model and Caco2 spheroids, we measured flux of basolateral-administered fluorescent dextran into the lumen. Barrier dysfunction was induced using methotrexate (220 nM) or lipopolysaccharide (20 nM). Human lactoferrin was added at 0.8 mg/ml (10 {micro}M). RNAseq was performed on exposed samples. RESULTSLactoferrin blocks methotrexate-induced barrier dysfunction in murine enteroids. Similar results were observed when barrier dysfunction was induced in Caco2 spheroids with methotrexate and LPS, but not ML7. RNAseq revealed activation of TGF-{beta} response genes and epithelial-mesenchymal transition (EMT) by methotrexate, which normalized in the presence of lactoferrin. TGF-{beta} receptor inhibition (RepSox) blocked methotrexate induced barrier dysfunction in Caco2 spheroids. 20 nM TGF-{beta} induced barrier dysfunction in Caco2 spheroids which was also inhibited by lactoferrin. CONCLUSIONSMethotrexate induces barrier dysfunction by activation of an EMT program promoted by TGF-{beta} signaling and inhibited by lactoferrin. Lactoferrin is also protective of barrier function in an LPS-induced model. The likely mechanism of this effect is blockade of EMT programs induced by TGF-{beta}.

cell biology↗