Michael Paul Verzi

STCS reconstructs cell-level gene expression from spatial transcriptomics data, improving accuracy across platforms and tissues.

This study identifies coordinated suppression of HNF4α and HNF4γ as an epithelial-intrinsic barrier defect in ileal Crohn's disease, reversible with HNF4 agonists.

This study creates a spatiotemporal transcriptomic atlas of mouse intestinal regeneration following ionizing radiation, revealing transcriptional patterns and mechanisms of epithelial repair.

This study shows that microbiota enhance CD39 expression in γδ IELs via TCR and IL-15 signaling, leading to regulatory IEL expansion and reduced inflammation.

This study identifies that APC loss in colorectal cancer drives a β-CATENIN-independent fetal intestinal transcriptional program through YAP activation, leading to bistable stem cell states and enhanced tumorigenesis.

The paper shows Pdgfra+ fibroblasts reprogram during WNT-driven oncogenesis to promote a regenerative state in the epithelium, facilitating tumor formation.

This study investigates the role of intestinal ESRRA in diet-induced obesity using mouse genetics and genomics, finding that ESRRA's effect is independent of intestinal function.

This study shows that Smad4 loss in the mouse intestinal epithelium reduces pathological fibrosis and improves mucosal repair after DSS-induced injury.

The paper identifies MTA2 and SATB2 as a chromatin complex that maintains colonic identity by retaining HNF4A on colonic chromatin, preventing plasticity toward small intestine.

The paper identifies dynamic RNA Polymerase II recruitment as the main driver of transcriptomic changes during intestinal differentiation, with HNF4 playing a key role in this process.

This study shows that KAT2A and KAT2B prevent dsRNA accumulation and interferon signaling, which is critical for maintaining intestinal stem cells in mice.

The paper identifies EPIREGULIN as a niche factor that enables spatial organization in human intestinal organoids, mimicking the native intestine's structure and gene expression.

This study identifies major sources of transcriptomic variation in human intestinal organoids, showing that culture methods like substrate and format have large effects compared to experimental manipulations.

The paper identifies HNF4 factors as critical for fetal intestinal maturation, showing their role in chromatin accessibility and gene regulation during the embryonic-to-fetal transition.

This study shows CDX2 has different chromatin-binding profiles in embryonic and adult intestines, leading to distinct gene activation patterns and developmental outcomes.