Effects of Hypocalcemic Vitamin D Analogs in the Expression of DNA Damage Induced in Minilungs from hESCs: Implications for Lung Fibrosis

Magro-Lopez, Esmeralda; Chamorro-Herrero, Irene; Zambrano, Alberto

doi:10.3390/ijms23094921

Cited by 3 publications

(1 citation statement)

References 50 publications

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“…At the same time, using the SigCom LINCS resource ( 45 ), maxacalcitol, a derivative of vitamin D used to treat skin disorders ( 95 ) is identified as the only drug that up-regulates many of the genes in the subnetwork. This observation is in concordance with prior literature where vitamin D analogs have been shown to cause DNA damage and cellular senescence in epithelial type II cells ( 96 ).…”

Section: Resultssupporting

confidence: 93%

Enrichr-KG: bridging enrichment analysis across multiple libraries

Evangelista

Xie

Marino

et al. 2023

Nucleic Acids Research

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Gene and protein set enrichment analysis is a critical step in the analysis of data collected from omics experiments. Enrichr is a popular gene set enrichment analysis web-server search engine that contains hundreds of thousands of annotated gene sets. While Enrichr has been useful in providing enrichment analysis with many gene set libraries from different categories, integrating enrichment results across libraries and domains of knowledge can further hypothesis generation. To this end, Enrichr-KG is a knowledge graph database and a web-server application that combines selected gene set libraries from Enrichr for integrative enrichment analysis and visualization. The enrichment results are presented as subgraphs made of nodes and links that connect genes to their enriched terms. In addition, users of Enrichr-KG can add gene-gene links, as well as predicted genes to the subgraphs. This graphical representation of cross-library results with enriched and predicted genes can illuminate hidden associations between genes and annotated enriched terms from across datasets and resources. Enrichr-KG currently serves 26 gene set libraries from different categories that include transcription, pathways, ontologies, diseases/drugs, and cell types. To demonstrate the utility of Enrichr-KG we provide several case studies. Enrichr-KG is freely available at: https://maayanlab.cloud/enrichr-kg.

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Section: Resultssupporting

confidence: 93%

Enrichr-KG: bridging enrichment analysis across multiple libraries

Evangelista

Xie

Marino

et al. 2023

Nucleic Acids Research

View full text Add to dashboard Cite

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Modeling of Respiratory Diseases Evolving with Fibrosis from Organoids Derived from Human Pluripotent Stem Cells

Chamorro-Herrero

Zambrano

2023

IJMS

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Respiratory disease is one of the leading causes of morbidity and mortality worldwide. There is no cure for most diseases, which are treated symptomatically. Hence, new strategies are required to deepen the understanding of the disease and development of therapeutic strategies. The advent of stem cell and organoid technology has enabled the development of human pluripotent stem cell lines and adequate differentiation protocols for developing both airways and lung organoids in different formats. These novel human-pluripotent-stem-cell-derived organoids have enabled relatively accurate disease modeling. Idiopathic pulmonary fibrosis is a fatal and debilitating disease that exhibits prototypical fibrotic features that may be, to some extent, extrapolated to other conditions. Thus, respiratory diseases such as cystic fibrosis, chronic obstructive pulmonary disease, or the one caused by SARS-CoV-2 may reflect some fibrotic aspects reminiscent of those present in idiopathic pulmonary fibrosis. Modeling of fibrosis of the airways and the lung is a real challenge due to the large number of epithelial cells involved and interaction with other cell types of mesenchymal origin. This review will focus on the status of respiratory disease modeling from human-pluripotent-stem-cell-derived organoids, which are being used to model several representative respiratory diseases, such as idiopathic pulmonary fibrosis, cystic fibrosis, chronic obstructive pulmonary disease, and COVID-19.

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Cellular and Molecular Genetic Mechanisms of Lung Fibrosis Development and the Role of Vitamin D: A Review

Enzel,

Kriventsov,

Sataieva

et al. 2024

IJMS

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Idiopathic pulmonary fibrosis remains a relevant problem of the healthcare system with an unfavorable prognosis for patients due to progressive fibrous remodeling of the pulmonary parenchyma. Starting with the damage of the epithelial lining of alveoli, pulmonary fibrosis is implemented through a cascade of complex mechanisms, the crucial of which is the TGF-β/SMAD-mediated pathway, involving various cell populations. Considering that a number of the available drugs (pirfenidone and nintedanib) have only limited effectiveness in slowing the progression of fibrosis, the search and justification of new approaches aimed at regulating the immune response, cellular aging processes, programmed cell death, and transdifferentiation of cell populations remains relevant. This literature review presents the key modern concepts concerning molecular genetics and cellular mechanisms of lung fibrosis development, based mainly on in vitro and in vivo studies in experimental models of bleomycin-induced pulmonary fibrosis, as well as the latest data on metabolic features, potential targets, and effects of vitamin D and its metabolites.

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Effects of Hypocalcemic Vitamin D Analogs in the Expression of DNA Damage Induced in Minilungs from hESCs: Implications for Lung Fibrosis

Cited by 3 publications

References 50 publications

Enrichr-KG: bridging enrichment analysis across multiple libraries

Enrichr-KG: bridging enrichment analysis across multiple libraries

Modeling of Respiratory Diseases Evolving with Fibrosis from Organoids Derived from Human Pluripotent Stem Cells

Cellular and Molecular Genetic Mechanisms of Lung Fibrosis Development and the Role of Vitamin D: A Review

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