Michael A Schumacher

Assistant Professor of Research Pediatrics

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My lab studies fundamental immune and epithelial drivers of tissue remodeling & regeneration in the gut with a focus on discovering new ways to treat inflammatory disease like ulcerative colitis & Crohn’s disease.

Using large-scale transcriptomic datasets paired with organoid experiments and in vivo analysis, our studies address how immune signals in the intestinal tract interact with stem and crypt base secretory cells (e.g., deep crypt secretory cells) to promote intestinal health and the response to disease.


  • NIDDK: NIH K01, 2022-2025
  • CHLA TSRI: Ellison RCDA, 2022-2024
  • Crohn’s and Colitis Foundation: CDA, 2018-2021
  • Crohn’s and Colitis Foundation: RFA, 2015-2018
  • Albert J Ryan Foundation: Ryan Fellowship, 2012-2014


  • Microbiota-derived butyrate restricts tuft cell differentiation via histone deacetylase 3 to modulate intestinal type 2 immunityImmunity. 2024 Feb 13; 57(2):319-332. e6. . View in PubMed
  • The emerging roles of deep crypt secretory cells in colonic physiology Am J Physiol Gastrointest Liver Physiol. 2023 12 01; 325(6):G493-G500. . View in PubMed
  • Deletion of Endogenous Neuregulin-4 Limits Adaptive Immunity During Interleukin-10 Receptor-Neutralizing Colitis Inflamm Bowel Dis. 2023 11 02; 29(11):1778-1792. . View in PubMed
  • Deep Crypt Secretory Cell Differentiation in the Colonic Epithelium Is Regulated by Sprouty2 and Interleukin 13 Cell Mol Gastroenterol Hepatol. 2023; 15(4):971-984. . View in PubMed
  • Sonic Hedgehog acts as a macrophage chemoattractant during regeneration of the gastric epithelium NPJ Regen Med. 2022 Jan 12; 7(1):3. . View in PubMed
  • Sprouty2 limits intestinal tuft and goblet cell numbers through GSK3ß-mediated restriction of epithelial IL-33 Nat Commun. 2021 02 05; 12(1):836. . View in PubMed
  • NRG4-ErbB4 signaling represses proinflammatory macrophage activity Am J Physiol Gastrointest Liver Physiol. 2021 06 01; 320(6):G990-G1001. . View in PubMed
  • Growth Factors in the Intestinal Tract in Physiology of the Gastrointestinal Tract 2018; 71-101. . View in PubMed
  • The ErbB3 receptor tyrosine kinase negatively regulates Paneth cells by PI3K-dependent suppression of Atoh1 Cell Death Differ. 2017 05; 24(5):855-865. . View in PubMed
  • ErbB4 signaling stimulates pro-inflammatory macrophage apoptosis and limits colonic inflammation Cell Death Dis. 2017 02 23; 8(2):e2622. . View in PubMed
  • Co-culture of Gastric Organoids and Immortalized Stomach Mesenchymal Cells Methods Mol Biol. 2016; 1422:23-31. . View in PubMed
  • Characterization of stem/progenitor cell cycle using murine circumvallate papilla taste bud organoid Sci Rep. 2015 Nov 24; 5:17185. . View in PubMed
  • Helicobacter pylori targets cancer-associated apical-junctional constituents in gastroids and gastric epithelial cells Gut. 2015 May; 64(5):720-30. . View in PubMed
  • The use of murine-derived fundic organoids in studies of gastric physiology J Physiol. 2015 Apr 15; 593(8):1809-27. . View in PubMed
  • CD44 plays a functional role in Helicobacter pylori-induced epithelial cell proliferation PLoS Pathog. 2015 Feb; 11(2):e1004663. . View in PubMed
  • Helicobacter. 2015 Feb; 20(1):19-28. . View in PubMed
  • Modelling human development and disease in pluripotent stem-cell-derived gastric organoids Nature. 2014 Dec 18; 516(7531):400-4. . View in PubMed
  • Motility and chemotaxis mediate the preferential colonization of gastric injury sites by Helicobacter pylori PLoS Pathog. 2014 Jul; 10(7):e1004275. . View in PubMed
  • Gastritis promotes an activated bone marrow-derived mesenchymal stem cell with a phenotype reminiscent of a cancer-promoting cell Dig Dis Sci. 2014 Mar; 59(3):569-82. . View in PubMed
  • Crosstalks between cytokines and Sonic Hedgehog in Helicobacter pylori infection: a mathematical model PLoS One. 2014; 9(11):e111338. . View in PubMed
  • Establishment of Gastrointestinal Epithelial Organoids Curr Protoc Mouse Biol. 2013 Dec 19; 3(4):217-40. . View in PubMed
  • Sonic Hedgehog contributes to gastric mucosal restitution after injury Lab Invest. 2013 Jan; 93(1):96-111. . View in PubMed
  • Gastric Sonic Hedgehog acts as a macrophage chemoattractant during the immune response to Helicobacter pyloriGastroenterology. 2012 May; 142(5):1150-1159. e6. . View in PubMed
  • Chronic maternal infusion of full-length adiponectin in pregnant mice down-regulates placental amino acid transporter activity and expression and decreases fetal growth J Physiol. 2012 Mar 15; 590(6):1495-509. . View in PubMed
  • Techniques for following labeled cells in vivo: use of X/Y FISH, techniques to optimize fluorescent detection, and beta-galactosidase detection Methods Mol Biol. 2012; 921:227-38. . View in PubMed
  • Hedgehog signaling regulates E-cadherin expression for the maintenance of the actin cytoskeleton and tight junctions Am J Physiol Gastrointest Liver Physiol. 2010 Dec; 299(6):G1252-65. . View in PubMed
  • Loss of parietal cell expression of Sonic hedgehog induces hypergastrinemia and hyperproliferation of surface mucous cellsGastroenterology. 2010 Feb; 138(2):550-61561. e1-8. . View in PubMed