Biology subjects

Bacchetta, M.

Publications and source records attributed to Bacchetta, M..

5 recordsLinked to original sources

bioRxiv2025

T-cell Multiomic Analysis Identifies Subsets and Mechanisms of Interaction with Epithelial Cells in Idiopathic Pulmonary Fibrosis

Idiopathic pulmonary fibrosis (IPF) is a fatal interstitial lung disease characterized by progressive scarring and respiratory failure, with a median survival of 3-5 years. While T-cell numbers are elevated in IPF lungs, their contributions to fibrosis beyond inflammation remain poorly understood. Here, we performed multiplex imaging and single-cell RNA and protein profiling on [~]90,000 CD3 T-cells from control and fibrotic lungs, revealing eleven distinct subsets of CD4 and CD8 T-cells. Among these, we identified a rare CD56 regulatory T-cell subset that is highly activated in fibrosis and exhibits a sustained immunosuppressive phenotype. CXCR4/MIF signaling emerged as a central axis mediating T-cell-epithelial interactions, while epidermal growth factor receptor (EGFR) and TGF{beta} pathways dominated in multiple T-cell subsets. Our findings demonstrate that T-cells in IPF adopt nonclassical activation patterns, driven by epithelial interactions and the fibrotic microenvironment. These studies provide a foundation for exploring novel therapeutic strategies in IPF lungs by modulating T-cell behavior and communication networks.

immunology↗

bioRxiv2024

Enhancing Cytoplasmic Expression of Exogenous mRNA through Dynamic Mechanical Stimulation

Ionizable lipid nanoparticles (LNPs) have been pivotal in combating COVID-19, and numerous preclinical and clinical studies have highlighted their potential in nucleic acid-based therapies and vaccines. However, the effectiveness of endosomal escape for the nucleic acid cargos encapsulated in LNPs is still low, leading to suboptimal treatment outcomes and side effects. Hence, improving endosomal escape is crucial for enhancing the efficacy of nucleic acid delivery using LNPs. Here, a mechanical oscillation (frequency: 65 Hz) is utilized to prompt the LNP-mediated endosomal escape. The results reveal this mechanical oscillation can induce the combination and fusion between LNPs with opposite surface charges, enhance endosomal escape of mRNA, and increase the transfection efficiency of mRNA. Additionally, cell viability remains high at 99.3% after treatment with oscillation, which is comparable to that of untreated cells. Furthermore, there is no obvious damage to mitochondrial membrane potential and Golgi apparatus integrity. Thus, this work presents a user-friendly and safe approach to enhancing endosomal escape of mRNA and boosting gene expression. As a result, our work can be potentially utilized in both research and clinical fields to facilitate LNP-based delivery by enabling more effective release of LNP-encapsulated cargos from endosomes.

bioengineering↗

bioRxiv2023

Akt Drives TGF-beta-induced Over-secretion of DKK1 and Impairment of Cystic Fibrosis Airway Epithelium Polarity

Epithelial polarity is fundamental in maintaining barrier integrity and tissue protection. In cystic fibrosis (CF), apicobasal polarity of the airway epithelium is lost, resulting in increased apical fibronectin deposition and enhanced susceptibility to bacterial infections. Here we show that CFTR mutation in primary human airway epithelial cells (HAECs) and CFTR knockdown in a HAEC line promote the overexpression and over-secretion of TGF-{beta}1 and DKK1 when cultured at air-liquid interface (ALI). These dynamic changes result in hyperactivation of the TGF-{beta} pathway and inhibition of the Wnt pathway through degradation of {beta}-catenin leading to imbalanced proliferation and polarization. The abnormal interplay between TGF-{beta} and Wnt signaling pathways is further enhanced by aberrant Akt signaling. Pharmacological manipulation of TGF-{beta}, Wnt, and Akt pathways restored polarization of the CF epithelium. Our data shed new insights into the signaling pathways that fine-tune apicobasal polarization and also highlight new therapeutic strategies in preventing infections in CF HAECs.

cell biology↗

bioRxiv2023

Cell type-specific and disease-associated eQTL in the human lung

Common genetic variants confer substantial risk for chronic lung diseases, including pulmonary fibrosis (PF). Defining the genetic control of gene expression in a cell-type-specific and context-dependent manner is critical for understanding the mechanisms through which genetic variation influences complex traits and disease pathobiology. To this end, we performed single-cell RNA-sequencing of lung tissue from 67 PF and 49 unaffected donors. Employing a pseudo-bulk approach, we mapped expression quantitative trait loci (eQTL) across 38 cell types, observing both shared and cell type-specific regulatory effects. Further, we identified disease-interaction eQTL and demonstrated that this class of associations is more likely to be cell-type specific and linked to cellular dysregulation in PF. Finally, we connected PF risk variants to their regulatory targets in disease-relevant cell types. These results indicate that cellular context determines the impact of genetic variation on gene expression, and implicates context-specific eQTL as key regulators of lung homeostasis and disease.

genomics↗

bioRxiv2021

Single-cell transcriptomic assessment of cellular phenotype stability in human precision-cut lung slices

Precision-cut lung slices (PCLS) are increasingly utilized for ex vivo disease modeling, but a high-resolution characterization of cellular phenotype stability in PCLS has not been reported. Comparing the single-cell transcriptomic profile of human PCLS after five days of culture to freshly isolated human lung tissue, we found striking changes in endothelial cell and alveolar epithelial cell programs, reflecting both injury and pathways activated in static culture, while immune cell frequencies and programs remained largely intact and similar to the native lung. These cellular dynamics should be considered when utilizing PCLS as a model of the human lung.

cell biology↗