Biology subjects

Butto, L.

Publications and source records attributed to Butto, L..

3 recordsLinked to original sources

bioRxiv2025

Deciphering the zebrafish hepatic duct heterogeneity and cell plasticity using lineage tracing and single-cell transcriptomics

Despite the livers recognized regenerative potential, the role of the hepatic ductal cells (a.k.a. biliary epithelial cells), its heterogeneity, and functionality remain incompletely understood in this process. This study provides a comprehensive examination of the molecular and cellular mechanisms underpinning liver ductal development and liver regeneration in zebrafish, with a spotlight on the functional roles of her family genes in these processes. Using state-of-the-art knock-in zebrafish models and single-cell transcriptomics we reveal the differential expression patterns of the different her genes, of which her2, her6, and her9, were identified as specific molecular signatures for distinguishing different ductal cell types with unique morphology and spatial distribution. Particularly, her9 serves as a pan-ductal marker and shows responsiveness to the synergistic effect of Notch and BMP signaling. By analyzing multiple single-cell RNA-seq datasets, we identify numerous ductal markers which are functional proteins for ductal integrity, and most notably CRISPR mutagenesis demonstrates that her9 is essential for hepatocyte recovery. Using multiple transgenic and knock-in zebrafish lines and genetic fate mapping, we provide a detailed characterization of the ductal remodeling process under development and extreme loss of intra-hepatic duct, highlighting the remarkable ductal cell plasticity. Single-cell transcriptomics of lineage-traced her9-expressing liver ducts in static and regenerative states uncover distinct cell clusters with unique molecular signatures and morphology, reflecting the livers regenerative dynamics and highlight relevant key biological processes that could be leveraged to expedite liver regeneration.

developmental biology↗

bioRxiv2024

TAK1 operates at the primary cilium in non-canonical TGFB/BMP signaling to control heart development

Transforming Growth Factor-Beta-Activated Kinase 1 (TAK1/MAP3K7), along with its upstream regulators TAK1-Binding Protein 2 (TAB2) and the catalytic alpha-subunit of Protein Kinase A (PKA-C/PRKACA), has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease (CHD) and rare variants in PKA-C and TAK1 cause cardioacrofacial dysplasia (CAFD), and Frontometaphyseal Dysplasia (FMD) and cardiospondylocarpofacial syndrome (CSCFS), respectively, rare multisystem syndromes, where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1,471 CHD patients with extracardiac anomalies (syndromic CHD, sCHD), 2,405 patients with nonsyndromic CHD (nsCHD) and 45,082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD, but not in nsCHD. Detailed characterization of tak1-/-and tab2-/- zebrafish mutants revealed cardiac defects (dilated atrium, trabeculation defects, tachycardia and reduced contractility) as well as extracardiac developmental anomalies. RNA sequencing of tak1-/- mutant hearts showed downregulation of genes encoding core cardiac transcription factors, sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA-C is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules, including ligands of the TGFB/BMP superfamily. Consistent with these findings, CRISPR/Cas9-mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro, while FMD-causing mutations in TAK1 reduced its ciliary localization. In conclusion, our data establishes a central role for TAK1 and its upstream regulators in cardiac development and syndromic CHD, coordinated via the primary cilium.

developmental biology↗

bioRxiv2024

TL1A/DR3 signaling regulates the generation of pathogenic Th9 cells in experimental inflammatory bowel disease

ObjectiveDeath receptor 3 (DR3) and its ligand tumor necrosis factor like ligand 1A (TL1A), are involved in the regulation of the balance between effector and regulatory T cells in IBD. New evidence suggests a role of IL-9-secreting Th9 cells in the pathogenesis of ulcerative colitis (UC), although the molecular pathways through which IL-9 and Th9 cells may mediate intestinal inflammation in Crohns disease (CD) are still unclear. DesignWe investigated the role of DR3 signaling in the differentiation of Th9 cells in mouse models of CD-like ileitis and colitis, including SAMP1/YitFc (SAMP) mice. ResultsPolarized-Th9 cells with functional DR3 from SAMP WT (Th9WT) harbor a pro-inflammatory signature compared to DR3-deficient Th9 cells that were obtained from DR3-/-xSAMP mice (Th9KO). Conversely, ablation of DR3 signaling generated anti-inflammatory responses, as reflected by higher numbers of IL-10 producing cells in DR3-/-xSAMP mice. Additionally, RNA-seq and phosphoproteomic analyses showed that inflammatory pathways are significantly more activated in Th9WT than in Th9KO cells. Finally, in the T-cell adoptive transfer model, Th9KO cells were less colitogenic than Th9WT, while IL-9 blockade diminished the severity of intestinal inflammation, indicating a crucial role of functional DR3 receptor in Th9 cells pathogenicity. ConclusionWe describe herein that a functional DR3 receptor is required for the pathogenicity of Th9 cells, thus, constituting a novel mechanism by which TL1A/DR3 signaling mediates experimental CD-like ileitis. The TL1A/DR3/Th9 pro-inflammatory pathway may offer a novel therapeutic target for patients with CD. What is already known on this topic - TL1A/DR3 system plays a pivotal role in the pathogenesis of Crohns disease like ileitis. - Th9 cells are a novel subset of T lymphocytes mainly producing the pro-inflammatory cytokine IL-9 which contributes to intestinal inflammation. - Those finding provided us with a strong rationale to investigate IL-9-producing cells in our SAMP1/YitFc mouse model of CD-like ileitis. What this study adds - DR3 receptor is involved in the regulation and progression of intestinal inflammation by promoting Th9 cell differentiation and pathogenicity. - Using RNA-seq and phosphoproteomic comparative analyses we were able to characterize Th9 cells with and without functional DR3 receptor showing that presence of DR3 confers a pro-inflammatory signature to Th9 cells. - We describe a novel role of DR3 in Th9 cells development that appears to regulate their pro-inflammatory phenotype in models of CD-like ileitis and colitis. How this study might affect research, practice or policy - TLA1/DR3 axis and Th9 cells may be useful as therapeutic targets in CD.

immunology↗