Epithelial zonation along the mouse and human small intestine defines five discrete metabolic domains – Nature Cell Biology

  • San Roman, A. K. & Shivdasani, R. A. Boundaries, junctions and transitions in the gastrointestinal tract. Exp. Cell. Res. 317, 2711–2718 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Brown, H. & Esterhazy, D. Intestinal immune compartmentalization: implications of tissue specific determinants in health and disease. Mucosal Immunol. 14, 1259–1270 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Esterhazy, D. et al. Compartmentalized gut lymph node drainage dictates adaptive immune responses. Nature 569, 126–130 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Altmann, G. G. & Leblond, C. P. Factors influencing villus size in the small intestine of adult rats as revealed by transposition of intestinal segments. Am. J. Anat. 127, 15–36 (1970).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Bates, M. D. et al. Novel genes and functional relationships in the adult mouse gastrointestinal tract identified by microarray analysis. Gastroenterology 122, 1467–1482 (2002).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Haber, A. L. et al. A single-cell survey of the small intestinal epithelium. Nature 551, 333–339 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Elmentaite, R. et al. Cells of the human intestinal tract mapped across space and time. Nature 597, 250–255 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Burclaff, J. et al. A proximal-to-distal survey of healthy adult human small intestine and colon epithelium by single-cell transcriptomics. Cell Mol. Gastroenterol. Hepatol. 13, 1554–1589 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wang, Y. et al. Single-cell transcriptome analysis reveals differential nutrient absorption functions in human intestine. J. Exp. Med. 217, jem.20191130 (2020).

    Article 

    Google Scholar
     

  • Hickey, J. W. et al. Organization of the human intestine at single-cell resolution. Nature 619, 572–584 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fawkner-Corbett, D. et al. Spatiotemporal analysis of human intestinal development at single-cell resolution. Cell 184, 810–826 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zwick, R. K., Ohlstein, B. & Klein, O. D. Intestinal renewal across the animal kingdom: comparing stem cell activity in mouse and Drosophila. Am. J. Physiol. Gastrointest. Liver Physiol. 316, G313–G322 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Buchon, N. et al. Morphological and molecular characterization of adult midgut compartmentalization in Drosophila. Cell Rep. 3, 1725–1738 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Marianes, A. & Spradling, A. C. Physiological and stem cell compartmentalization within the Drosophila midgut. eLife 2, e00886 (2013).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Driver, I. & Ohlstein, B. Specification of regional intestinal stem cell identity during Drosophila metamorphosis. Development 141, 1848–1856 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hudry, B. et al. Sex differences in intestinal carbohydrate metabolism promote food intake and sperm maturation. Cell 178, 901–918 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Middendorp, S. et al. Adult stem cells in the small intestine are intrinsically programmed with their location-specific function. Stem Cells 32, 1083–1091 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kayisoglu, O. et al. Location-specific cell identity rather than exposure to GI microbiota defines many innate immune signalling cascades in the gut epithelium. Gut 70, 687–697 (2021).

    Article 
    PubMed 

    Google Scholar
     

  • Kraiczy, J. et al. DNA methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development. Gut 68, 49–61 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • McGinnis, C. S. et al. MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices. Nat. Methods 16, 619–626 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Moor, A. E. et al. Spatial reconstruction of single enterocytes uncovers broad zonation along the intestinal villus axis. Cell 175, 1156–1167 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Tibshirani, R., Walther, G. & Hastie, T. Estimating the number of clusters in a data set via the gap statistic. J. R. Stat. Soc. Ser. B Stat. Methodol. 63, 411–423 (2001).

    Article 

    Google Scholar
     

  • Peng, M., Li, Y., Wamsley, B., Wei, Y. & Roeder, K. Integration and transfer learning of single-cell transcriptomes via cFIT. Proc. Natl Acad. Sci. USA 118, e2024383118 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sullivan, Z. A. et al. γδ T cells regulate the intestinal response to nutrient sensing. Science 371, eaba8310 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Enriquez, J. R. et al. A dietary change to a high-fat diet initiates a rapid adaptation of the intestine. Cell Rep. 41, 111641 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Goda, T. Regulation of the expression of carbohydrate digestion/absorption-related genes. Br. J. Nutr. 84, S245–S248 (2000).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Clara, R. et al. Metabolic adaptation of the small intestine to short- and medium-term high-fat diet exposure. J. Cell. Physiol. 232, 167–175 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ko, C.-W., Qu, J., Black, D. D. & Tso, P. Regulation of intestinal lipid metabolism: current concepts and relevance to disease. Nat. Rev. Gastroenterol. Hepatol. 17, 169–183 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Gebert, N. et al. Region-specific proteome changes of the intestinal epithelium during aging and dietary restriction. Cell Rep. 31, 107565 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Biton, M. et al. T helper cell cytokines modulate intestinal stem cell renewal and differentiation. Cell 175, 1307–1320 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Maimets, M. et al. Mesenchymal-epithelial crosstalk shapes intestinal regionalisation via Wnt and Shh signalling. Nat. Commun. 13, 715 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Spence, J. R., Lauf, R. & Shroyer, N. F. Vertebrate intestinal endoderm development. Dev. Dyn. 240, 501–520 (2011).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Thompson, C. A., DeLaForest, A. & Battle, M. A. Patterning the gastrointestinal epithelium to confer regional-specific functions. Dev. Biol. 435, 97–108 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Thompson, C. A. et al. GATA4 is sufficient to establish jejunal versus ileal identity in the small intestine. Cell Mol. Gastroenterol. 3, 422–446 (2017).


    Google Scholar
     

  • Chen, C., Fang, R. X., Davis, C., Maravelias, C. & Sibley, E. Pdx1 inactivation restricted to the intestinal epithelium in mice alters duodenal gene expression in enterocytes and enteroendocrine cells. Am. J. Physiol. Gastrintest. Liver Physiol. 297, G1126–G1137 (2009).

    Article 
    CAS 

    Google Scholar
     

  • Battle, M. A. et al. GATA4 is essential for jejunal function in mice. Gastroenterology 135, 1676–1686 (2008).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Bosse, T. et al. Gata4 is essential for the maintenance of jejunal-ileal identities in the adult mouse small intestine. Mol. Cell. Biol. 26, 9060–9070 (2006).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Keenan, A. B. et al. ChEA3: transcription factor enrichment analysis by orthogonal omics integration. Nucleic Acids Res. 47, W212–W224 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Aibar, S. et al. SCENIC: single-cell regulatory network inference and clustering. Nat. Methods 14, 1083–1086 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zorn, A. M. & Wells, J. M. Vertebrate endoderm development and organ formation. Annu. Rev. Cell Dev. Biol. 25, 221–251 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Verzi, M. P., Shin, H., Ho, L. L., Liu, X. S. & Shivdasani, R. A. Essential and redundant functions of caudal family proteins in activating adult intestinal genes. Mol. Cell. Biol. 31, 2026–2039 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hryniuk, A., Grainger, S., Savory, J. G. A. & Lohnes, D. Cdx function is required for maintenance of intestinal identity in the adult. Dev. Biol. 363, 426–437 (2012).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Bonhomme, C. et al. Cdx1, a dispensable homeobox gene for gut development with limited effect in intestinal cancer. Oncogene 27, 4497–4502 (2008).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Doktorova, M. et al. Intestinal PPARdelta protects against diet-induced obesity, insulin resistance and dyslipidemia. Sci. Rep. 7, 846 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Beyaz, S. et al. High-fat diet enhances stemness and tumorigenicity of intestinal progenitors. Nature 531, 53–58 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Mana, M. D. et al. High-fat diet-activated fatty acid oxidation mediates intestinal stemness and tumorigenicity. Cell Rep. 35, 109212 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Seiler, K. M. et al. Single-cell analysis reveals regional reprogramming during adaptation to massive small bowel resection in mice. Cell Mol. Gastroenterol. Hepatol. 8, 407–426 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nusse, Y. M. et al. Parasitic helminths induce fetal-like reversion in the intestinal stem cell niche. Nature 559, 109–113 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Schneider, C. et al. A metabolite-triggered tuft cell-ILC2 circuit drives small intestinal remodeling. Cell 174, 271–284 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cheng, C. W. et al. Ketone body signaling mediates intestinal stem cell homeostasis and adaptation to diet. Cell 178, 1115–1131 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Stine, R. R. et al. PRDM16 maintains homeostasis of the intestinal epithelium by controlling region-specific metabolism. Cell Stem Cell 25, 830–845 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Obniski, R., Sieber, M. & Spradling, A. C. Dietary lipids modulate notch signaling and influence adult intestinal development and metabolism in Drosophila. Dev. Cell 47, 98–111 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gajendran, M., Loganathan, P., Catinella, A. P. & Hashash, J. G. A comprehensive review and update on Crohn’s disease. Dis. Mon. 64, 20–57 (2018).

    Article 
    PubMed 

    Google Scholar
     

  • Pan, S. Y. & Morrison, H. Epidemiology of cancer of the small intestine. World J. Gastrointest. Oncol. 3, 33–42 (2011).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Schottenfeld, D., Beebe-Dimmer, J. L. & Vigneau, F. D. The epidemiology and pathogenesis of neoplasia in the small intestine. Ann. Epidemiol. 19, 58–69 (2009).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Brown, E. M., Clardy, J. & Xavier, R. J. Gut microbiome lipid metabolism and its impact on host physiology. Cell Host Microbe 31, 173–186 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Tian, H. et al. A reserve stem cell population in small intestine renders Lgr5-positive cells dispensable. Nature 478, 255–259 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Huch, M. et al. In vitro expansion of single Lgr5+ liver stem cells induced by Wnt-driven regeneration. Nature 494, 247–250 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Platt, R. J. et al. CRISPR-Cas9 knockin mice for genome editing and cancer modeling. Cell 159, 440–455 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Madisen, L. et al. A robust and high-throughput Cre reporting and characterization system for the whole mouse brain. Nat. Neurosci. 13, 133–140 (2010).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Smillie, C. S. et al. Intra- and inter-cellular rewiring of the human colon during ulcerative colitis. Cell 178, 714–730 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Melsted, P. et al. Modular, efficient and constant-memory single-cell RNA-seq preprocessing. Nat. Biotechnol. 39, 813–818 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Lun, A. T. L. et al. EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data. Genome Biol. 20, 63 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhu, Q., Conrad, D. N. & Gartner, Z. J. deMULTIplex2: Robust Sample Demultiplexing for scRNA-seq (Cold Spring Harbor Laboratory, 2023).

  • Alquicira-Hernandez, J., Sathe, A., Ji, H. P., Nguyen, Q. & Powell, J. E. scPred: accurate supervised method for cell-type classification from single-cell RNA-seq data. Genome Biol. 20, 264 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Stuart, T. et al. Comprehensive integration of single-cell data. Cell 177, 1888–1902 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573–3587 (2021).

  • Hafemeister, C. & Satija, R. Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression. Genome Biol. 20, 296 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cunningham, F. et al. Ensembl 2022. Nucleic Acids Res. 50, D988–D995 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kolde, R. Pheatmap: pretty heatmaps. R package version 1.2 (CRAN.R Project, 2012); https://cran.r-project.org/package=pheatmap

  • Lin, J. H. Divergence measures based on the Shannon entropy. IEEE Trans. Inf. Theory 37, 145–151 (1991).

    Article 

    Google Scholar
     

  • Drost, H.-G. Philentropy: information theory and distance quantification with R.J. Open Source Softw 3, 765 (2018).

    Article 

    Google Scholar
     

  • Kotliar, D. et al. Identifying gene expression programs of cell-type identity and cellular activity with single-cell RNA-Seq. eLife 8, e43803 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wu, T. Z. et al. clusterProfiler 4.0: a universal enrichment tool for interpreting omics data. Innovation 2, 100141 (2021).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • van de Sande, B. et al. A scalable SCENIC workflow for single-cell gene regulatory network analysis. Nat. Protoc. 15, 2247–2276 (2020).

    Article 
    PubMed 

    Google Scholar
     

  • Street, K. et al. Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics. BMC Genomics 19, 477 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Bankhead, P. et al. QuPath: Open source software for digital pathology image analysis. Sci. Rep. 7, 16878 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Castillo-Azofeifa, D. et al. Atoh1+ secretory progenitors possess renewal capacity independent of Lgr5+ cells during colonic regeneration. EMBO J. 38, e99984 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • McKinley, K. L. Employing CRISPR/Cas9 genome engineering to dissect the molecular requirements for mitosis. Methods Cell. Biol. 144, 75–105 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Gilbert, L. A. et al. Genome-scale CRISPR-mediated control of gene repression and activation. Cell 159, 647–661 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Adamson, B. et al. A multiplexed single-cell CRISPR screening platform enables systematic dissection of the unfolded protein response. Cell 167, 1867–1882 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sanjana, N. E., Shalem, O. & Zhang, F. Improved vectors and genome-wide libraries for CRISPR screening. Nat. Methods 11, 783–784 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Koo, B. K. et al. Controlled gene expression in primary Lgr5 organoid cultures. Nat. Methods 9, 81–83 (2012).

    Article 
    CAS 

    Google Scholar
     

  • Bray, N. L., Pimentel, H., Melsted, P. & Pachter, L. Near-optimal probabilistic RNA-seq quantification. Nat. Biotechnol. 34, 525–527 (2016).

  • Risso, D., Ngai, J., Speed, T. P. & Dudoit, S. Normalization of RNA-seq data using factor analysis of control genes or samples. Nat. Biotechnol. 32, 896–902 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar