The Hamilton laboratory is organized around interconnected research themes aimed at understanding how intestinal epithelial cells function in human health and disease.
|
Theme 1: RNA binding proteins and epithelial cell fate
How do RNA binding proteins regulate intestinal epithelial cell fate
and function?
Gene expression is regulated at multiple levels. Our lab investigates how post-transcriptional mechanisms — those controlling RNA stability, translation, and modification — direct epithelial cells to respond and adapt to their environment. A central focus is the RNA binding protein IMP1 (IGF2BP1) and its role as a reader of N6-methyladenosine (m⁶A)-modified mRNAs in intestinal epithelial cells. Our work established a molecular connection between IMP1 and the autophagy pathway, finding that IMP1 suppresses translation of the autophagy transcript MAP1LC3B. Current studies explore how IMP1 and m⁶A RNA modification regulate epithelial responses to hypoxia during inflammation — a clinically relevant stress in IBD — and how this axis contributes to disease in both IBD and celiac disease. These studies use colonoid and enteroid systems, including patient-derived organoids, to bridge mechanistic discovery with human disease relevance.
Theme 2: RNA quality control and intestinal epithelial homeostasis
How does RNA quality control maintain intestinal epithelial integrity?
Cells rely on RNA quality control mechanisms to degrade aberrant or excess transcripts and prevent proteotoxic stress. We are currently evaluating critical roles for SKIV2L — an RNA helicase and core component of the cytoplasmic RNA exosome complex — in maintaining intestinal epithelial homeostasis. We preliminarily find that intestinal epithelial-specific deletion of SKIV2L in mice leads to spontaneous enterocolitis, driven in part by activation of the integrated stress response (ISR) through the PERK/eIF2α branch. Loss-of-function variants in SKIV2L cause Trichohepatoenteric syndrome (THES), a rare and severe congenital diarrheal disorder that can present as VEO-IBD. This work connects RNA quality control to ER stress and mucosal inflammation, generating new insight into how SKIV2L variants may drive disease, identifying potential therapeutic targets in this pathway, and providing a key model for preclinical gene therapy testing.
Theme 3: Autophagy and intestinal epithelial regeneration
How does the autophagy pathway contribute to epithelial regeneration?
Autophagy itself is a critical regulator of intestinal epithelial regeneration. Genome-wide association studies have identified autophagy gene risk alleles in IBD patients, and autophagy-deficient mice show increased susceptibility to inflammatory injury and impaired barrier recovery after radiation. Our studies revealed that secretory cells with high autophagy activity can act as facultative stem cells — re-entering the stem cell pool to regenerate the epithelium after injury. We find that blocking autophagy impairs this plasticity, and that high-autophagy cells are protected from radiation-induced DNA damage. Together, these findings support a dual role for intestinal epithelial autophagy: promoting non-stem cell plasticity and protecting cells from genotoxic stress. Current work is exploring the intersection of autophagy and YAP signaling in this regenerative response.
Theme 4: Patient-derived organoids as models of IBD, celiac disease, and VEO-IBD
Do intestinal epithelial stem cells behave differently in patients with chronic inflammatory gastrointestinal disease?
Our laboratory uses patient-derived 3D enteroids and colonoids to directly compare epithelial stem cell biology in health versus disease — including IBD, celiac disease, and very early-onset IBD (VEO-IBD). This platform allows us to ask how disease-associated genetic variants, immune signals, and environmental exposures alter epithelial behavior in a human, patient-specific context. Active projects include: defining the cytokine signals that induce disease-driven ISP (inflammatory secretory progenitor) cell states in colonoids; benchmarking celiac enteroids as a platform for studying gluten-driven epithelial responses; and using single-patient organoid models to understand monogenic variants causing VEO-IBD. These efforts are supported by and conducted through the CHOP Gastrointestinal Epithelium Modeling (GEM) Program, a core facility co-directed by Dr. Hamilton and Dr. Amanda Muir. Interested in using patient-derived organoids in your research? Contact us to learn more about the GEM Program.
|
|
|
|