Biology subjects

Verzi, M.

Publications and source records attributed to Verzi, M..

9 recordsLinked to original sources

bioRxiv2025

Pharmacologic activation of HNF4α/γ restores epithelial barrier function in Crohn's disease.

Background & Aims: Ileal barrier dysfunction in Crohn,s disease (CD) can occur in macroscopically non-inflamed mucosa, persist despite clinical and endoscopic remission, and predict adverse outcomes. The epithelial mechanisms underlying this defect remain unclear. We investigated whether coordinated reduction of hepatocyte nuclear factor 4, (HNF4) and HNF4{gamma} defines an epithelial-intrinsic, barrier-defective state in ileal CD. Methods: Barrier-associated transcriptional programs were compared in small-intestinal and colonic epithelium from wild-type mice and mice with intestinal epithelial deletion of Hnf4, Hnf4{gamma}, or both paralogs. Paracellular permeability was assessed in wild-type and Hnf4/{gamma} double-knockout (Hnf4{gamma}DKO) small-intestinal organoids. HNF4, HNF4{gamma}, and the direct HNF4 transcriptional target claudin-15 (CLDN15) were evaluated in human ileal CD tissue, patient-derived organoids (PDOs) generated from macroscopically non-inflamed ileal mucosa, and ileal tissue and organoids from Tnf{delta}ARE/+ mice. The effects of HNF4 agonists N-trans-caffeoyltyramine (NCT) and N-trans-feruloyltyramine (NFT) were assessed in CD PDOs and Tnf{delta}ARE/+ organoids. Results: Combined, but not individual, loss of HNF4-paralog broadly disrupted small-intestinal transcriptional programs governing tight junction (TJ) organization, epithelial polarity, junctional-cytoskeletal coupling, and TJ repair, with limited effects in the colon. Hnf4{gamma}DKO organoids exhibited size-selective paracellular permeability in the absence of inflammatory and stromal cells, demonstrating that combined Hnf4{gamma} loss is sufficient to produce an epithelial-intrinsic barrier defect. HNF4, HNF4{gamma}, and CLDN15 were coordinately reduced in human ileal CD epithelium and this HNF4-low phenotype was retained in PDOs from macroscopically non-inflamed ileal mucosa. Chronic TNF-driven ileitis reproduced this HNF4-low state, which was retained ex vivo in organoids. HNF4 agonists restored HNF4, HNF4{gamma}, and CLDN15 expression and improved transepithelial electrical resistance (TEER) in CD PDOs. They also increased HNF4 and CLDN15 expression in Tnf{delta}ARE/+ organoids. Conclusions: Coordinated HNF4/{gamma} suppression defines an epithelial-intrinsic, barrier-defective state in ileal CD that is present in PDOs derived from macroscopically non-inflamed ileal mucosa and retained ex vivo without continued exposure to the inflammatory tissue environment. Its pharmacologic reversibility identifies incomplete restoration of the HNF4-dependent epithelial program as a potential mechanism of persistent ileal barrier dysfunction and supports further evaluation of HNF4-directed barrier-restorative strategies.

pathology↗

bioRxiv2025

A Spatial and Temporal Transcriptomic Atlas of Mouse Intestinal Regeneration

Background & AimsThe intestinal epithelium exhibits a remarkable capacity for regeneration following injury. However, the spatial and temporal dynamics of the injury-repair cycle remain incompletely understood. MethodsWe employ spatial transcriptomics to create an atlas of the damage and repair response to ionizing radiation in the mouse intestine. We map molecular events driving epithelial recovery over a six-day period and 23 biological samples, spanning the early apoptotic response to tissue remodeling and repair. ResultsThe datasets capture mRNA of 19,042 genes in [~]26 million bins at 2{micro}m resolution. Analysis revealed transcriptional patterns and niche signals that would remain undetected in bulk or single-cell approaches, including a non-random activation of interferon-target genes. Temporal shifts in cytokine and growth factor gene expression, particularly in the crypt and lower villus regions, corroborate published studies and reveal new predictions of the mechanisms governing intestinal healing. Global transcriptional upregulation was observed in the regenerating epithelium, suggesting hypertranscription is a hallmark of intestinal repair. Furthermore, we observe altered cellular differentiation trajectories and villus patterning at the early stages of regeneration. ConclusionsTogether, our work provides a detailed spatiotemporal map of intestinal regeneration at subcellular resolution and nearly whole-genome scale. These data lay the groundwork for future discoveries and therapeutic strategies to enhance epithelial repair in inflammatory bowel diseases and other gastrointestinal pathologies or in response to side-effects of cancer therapies.

molecular biology↗

bioRxiv2025

APC loss promotes intestinal transformation through induction of bistable stem cell states

Colorectal cancer (CRC) is a leading cause of cancer deaths, predominantly initiated by genetic inactivation of the APC tumor suppressor. Current dogma holds that APC inactivation promotes tumorigenesis via hyperactivation of the WNT pathway transcriptional effector, {beta}-CATENIN. Although {beta}-CATENIN activation is required for tumor initiation, activating mutations in {beta}-CATENIN are infrequent. Here, we ask what underlies the selective pressure for APC inactivation by comparing the oncogenic effects of APC loss to {beta}-CATENIN hyperactivation. We find that APC loss activates a {beta}-CATENIN-independent fetal intestinal transcriptional program driven by dysregulation of GSK-3 activity upon the LIM-domain protein AJUBA, a positive regulator of YAP. This results in AJUBA stabilization and downstream transcriptional activation of the YAP-driven fetal intestinal gene expression program. We find that {beta}-CATENIN- and YAP-driven transcriptional states are mutually exclusive, existing in an interchangeable bistable balance among APC-null cells. This results in more robust tumor initiation and metastatic progression downstream of APC loss relative to {beta}-CATENIN activation. Taken together, our findings explain the preferential selection for APC inactivation in CRC development and illuminate how {beta}-CATENIN- and YAP-driven gene expression programs coexist to promote tumorigenesis.

cancer biology↗

bioRxiv2023

KAT2 paralogs prevent dsRNA accumulation and interferon signaling to maintain intestinal stem cells

Histone acetyltransferases KAT2A and KAT2B are paralogs highly expressed in the intestinal epithelium, but their functions are not well understood. In this study, double knockout of murine Kat2 genes in the intestinal epithelium was lethal, resulting in robust activation of interferon signaling and interferon-associated phenotypes including the loss of intestinal stem cells. Use of pharmacological agents and sterile organoid cultures indicated a cell-intrinsic double-stranded RNA trigger for interferon signaling. Acetyl-proteomics and dsRIP-seq were employed to interrogate the mechanism behind this response, which identified mitochondria-encoded double-stranded RNA as the source of intrinsic interferon signaling. Kat2a and Kat2b therefore play an essential role in regulating mitochondrial functions as well as maintaining intestinal health. Highlights of the workO_LIKat2a and Kat2b double knockout in the murine intestinal epithelium triggers activation of the interferon signaling pathway C_LIO_LIKat2a/Kat2b knockout leads to intestinal stem cell loss and other mucosal phenotypes consistent with interferon activation C_LIO_LIHistone PTM mass spec profiling reveals the first in vivo study showing H3K9ac-specific loss with Kat2a and Kat2b double knockout, yet without correlation to interferon signaling pathway genes C_LIO_LIComprehensive proteomic analysis identifies non-histone acetyl-lysine targets of KAT2 in the mouse intestine in vivo, including mitochondrial proteins C_LIO_LIMitochondrial function is compromised upon Kat2 loss C_LIO_LIdsRIP-seq identifies double-stranded RNA from the mitochondria as a trigger for the intrinsic immune response upon Kat2 double knockout C_LI

molecular biology↗

bioRxiv2022

A MTA2-SATB2 chromatin complex restrains colonic plasticity toward small intestine by retaining HNF4A at colonic chromatin

Plasticity between cell lineages is a fundamental but poorly understood property of regenerative tissues. In the gut tube, small intestine absorbs nutrients whereas colon absorbs electrolytes. In a striking display of inherent plasticity, adult colonic mucosa lacking the chromatin factor SATB2 is converted to small intestine. Using proteomics and CRISPR-Cas9 screen, we identified MTA2 as a crucial component of the molecular machinery that, together with SATB2, restrain colonic plasticity. MTA2 loss in adult mouse colon activated lipid absorptive genes and functional lipid uptake. Mechanistically, MTA2 co-binds with HNF4A, an activating pan-intestine transcription factor (TF), on colonic chromatin. MTA2 loss leads to HNF4A release from colonic and gain on small intestinal chromatin. SATB2 similarly restrains colonic plasticity through a HNF4A-dependent mechanism. Our study provides a generalizable model of lineage plasticity in which broadly-expressed TFs are retained on tissue-specific enhancers to maintain cell identity and prevent activation of alternative lineages; their release unleashes plasticity.

developmental biology↗

bioRxiv2022

Maf Family Transcription Factors are Required for Nutrient Uptake in the Neonatal Gut

There are fundamental differences in the way that neonatal and adult intestines absorb nutrients. In adults, macromolecules are efficiently broken down into simpler molecular components in the lumen of the small intestine, then absorbed. In contrast, neonates are thought to rely more on bulk intake of nutrients and subsequent degradation in the lysosome. Here, we identify the Maf family transcription factors, MafB and cMaf, as markers of terminally-differentiated intestinal enterocytes throughout life. The expression of these factors is regulated by HNF4/{gamma}, master regulators of the enterocyte cell fate. Loss of Maf factors results in a neonatal-specific failure to thrive and loss of bulk uptake of nutrients. RNA-Seq and CUT&RUN analyses defined an endo-lysosomal program as being downstream of these transcription factors. We demonstrate major transcriptional changes in metabolic pathways, including fatty acid oxidation and increases in peroxisome number in response to loss of Mafs. Finally, we show that deletion of Blimp1, which represses adult enterocyte genes in the neonatal gut, shows highly overlapping changes in gene expression and similar defects in nutrient uptake. This work defines transcriptional regulators that are necessary for bulk uptake in neonatal enterocytes.

physiology↗

bioRxiv2022

β-catenin obstructs γδ T cell immunosurveillance in colon cancer through loss of BTNL expression

WNT/{beta}-catenin signaling endows cancer cells with proliferative capacity and immune-evasive functions that impair anti-cancer immunosurveillance by conventional, cytoxtoic T cells. However, the impact of dysregulated WNT signalling on unconventional, tissue-resident T cells, specifically in colon cancer is unknown. Here, we show that cancer cells in Apc-mutant mouse models escape immunosurveillance from gut-resident intraepithelial lymphocytes (IELs) expressing {gamma}{delta} T cell receptors ({gamma}{delta}TCRs). Analysis of late-stage tumors from mice and humans revealed that {gamma}{delta}IELs are largely absent from the tumor microenvironment, and that butyrophilin-like (BTNL) molecules, which can critically regulate {gamma}{delta}IEL through direct {gamma}{delta}TCR-interactions, are also downregulated. We could attribute this to {beta}-catenin stabilization, which rapidly decreased expression of the transcription factors, HNF4A and HNF4G, that we found to bind promoter regions of Btnl genes, thereby driving their expression in normal gut epithelial cells. Indeed, inhibition of {beta}-catenin signaling restored Btnl1 gene expression and {gamma}{delta} T cell infiltration into tumors. These observations highlight an immune-evasion mechanism specific to WNT-driven colon cancer cells that disrupts {gamma}{delta}IEL immunosurveillance and furthers cancer progression.

cancer biology↗

bioRxiv2022

MFGE8 links absorption of dietary fatty acids with catabolism of enterocyte lipid stores through HNF4 γ- dependent transcription of CES enzymes

Enterocytes modulate the extent of postprandial lipemia, a potent risk factor for developing atherosclerotic disease, by storing dietary fats in cytoplasmic lipid droplets (cLDs). We have previously demonstrated that the integrin ligand MFGE8 links absorption of dietary fats with activation of triglyceride (TG) hydrolases that catabolize cLDs for chylomicron production. The hydrolase(s) responsible for mobilization of TG from diet-derived cLDs is unknown though recent evidence indicates that this process is independent of the canonical pathway of TG hydrolysis mediated by ATGL. Here we identify CES1D as the key hydrolase downstream of the MFGE8-v{beta}5 integrin pathway that regulates catabolism of diet-drive cLDs. Mfge8 KO enterocytes have reduced CES1D transcript and protein levels and reduced protein levels of the transcription factor HNF4{gamma}. Mice KO for Ces1d or Hnf4{gamma} have decreased enterocyte TG hydrolase activity coupled with retention of TG in cLDs. Mechanistically, MFGE8-dependent fatty acid uptake through CD36 leads to stabilization of HNF4{gamma} protein levels; HNF4{gamma} then increases Ces1d transcription. Our work identifies a regulatory network by which MFGE8 and v{beta}5 regulate the severity of postprandial lipemia by linking dietary fat absorption with protein stabilization of a transcription factor that increases expression of enterocyte TG hydrolases that catabolize diet-derived cLDs.

physiology↗

bioRxiv2018

The Lineage-Specific Transcription Factor CDX2 Navigates Dynamic Chromatin to Control Distinct Stages of Intestine Development

Lineage-restricted transcription factors, such as the intestine-specifying factor CDX2, often have dual requirements across developmental time. Embryonic-loss of CDX2 triggers homeotic transformation of intestinal fate, while adult-onset Cdx2-loss compromises critical physiological functions but preserves intestinal identity. It is unclear how such diverse requirements are executed across the developmental continuum. Using primary and engineered human tissues, mouse genetics, and a multi-omics approach, we demonstrate that divergent CDX2 loss-of-function phenotypes in embryonic versus adult intestines correspond to divergent CDX2 chromatin-binding profiles in embryonic versus adult stages. CDX2 binds and activates distinct target genes in developing versus adult mouse and human intestinal cells. We find that temporal shifts in chromatin accessibility correspond to these context-specific CDX2 activities. Thus, CDX2 is not sufficient to activate a mature intestinal program, but rather, CDX2 responds to its environment, targeting stage-specific genes to contribute to either intestinal patterning or maturity. This study provides insights into the mechanisms through which lineage-specific regulatory factors achieve divergent functions over developmental time.

developmental biology↗