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Modeling fibrotic alveolar transitional cells with pluripotent stem cell-derived alveolar organoids.Life Science Alliance Aug 2023Repeated injury of the lung epithelium is proposed to be the main driver of idiopathic pulmonary fibrosis (IPF). However, available therapies do not specifically target...
Repeated injury of the lung epithelium is proposed to be the main driver of idiopathic pulmonary fibrosis (IPF). However, available therapies do not specifically target the epithelium and human models of fibrotic epithelial damage with suitability for drug discovery are lacking. We developed a model of the aberrant epithelial reprogramming observed in IPF using alveolar organoids derived from human-induced pluripotent stem cells stimulated with a cocktail of pro-fibrotic and inflammatory cytokines. Deconvolution of RNA-seq data of alveolar organoids indicated that the fibrosis cocktail rapidly increased the proportion of transitional cell types including the aberrant basaloid phenotype recently identified in the lungs of IPF patients. We found that epithelial reprogramming and extracellular matrix (ECM) production persisted after removal of the fibrosis cocktail. We evaluated the effect of the two clinically approved compounds for IPF, nintedanib and pirfenidone, and found that they reduced the expression of ECM and pro-fibrotic mediators but did not completely reverse epithelial reprogramming. Thus, our system recapitulates key aspects of IPF and is a promising system for drug discovery.
Topics: Humans; Alveolar Epithelial Cells; Lung; Idiopathic Pulmonary Fibrosis; Fibrosis; Pluripotent Stem Cells; Organoids
PubMed: 37230801
DOI: 10.26508/lsa.202201853 -
Respiratory Research Nov 2023Idiopathic pulmonary fibrosis (IPF) is a heterogeneous disease that is pathologically characterized by areas of normal-appearing lung parenchyma, active fibrosis...
BACKGROUND
Idiopathic pulmonary fibrosis (IPF) is a heterogeneous disease that is pathologically characterized by areas of normal-appearing lung parenchyma, active fibrosis (transition zones including fibroblastic foci) and dense fibrosis. Defining transcriptional differences between these pathologically heterogeneous regions of the IPF lung is critical to understanding the distribution and extent of fibrotic lung disease and identifying potential therapeutic targets. Application of a spatial transcriptomics platform would provide more detailed spatial resolution of transcriptional signals compared to previous single cell or bulk RNA-Seq studies.
METHODS
We performed spatial transcriptomics using GeoMx Nanostring Digital Spatial Profiling on formalin-fixed paraffin-embedded (FFPE) tissue from 32 IPF and 12 control subjects and identified 231 regions of interest (ROIs). We compared normal-appearing lung parenchyma and airways between IPF and controls with histologically normal lung tissue, as well as histologically distinct regions within IPF (normal-appearing lung parenchyma, transition zones containing fibroblastic foci, areas of dense fibrosis, and honeycomb epithelium metaplasia).
RESULTS
We identified 254 differentially expressed genes (DEGs) between IPF and controls in histologically normal-appearing regions of lung parenchyma; pathway analysis identified disease processes such as EIF2 signaling (important for cap-dependent mRNA translation), epithelial adherens junction signaling, HIF1α signaling, and integrin signaling. Within IPF, we identified 173 DEGs between transition and normal-appearing lung parenchyma and 198 DEGs between dense fibrosis and normal lung parenchyma; pathways dysregulated in both transition and dense fibrotic areas include EIF2 signaling pathway activation (upstream of endoplasmic reticulum (ER) stress proteins ATF4 and CHOP) and wound healing signaling pathway deactivation. Through cell deconvolution of transcriptome data and immunofluorescence staining, we confirmed loss of alveolar parenchymal signals (AGER, SFTPB, SFTPC), gain of secretory cell markers (SCGB3A2, MUC5B) as well as dysregulation of the upstream regulator ATF4, in histologically normal-appearing tissue in IPF.
CONCLUSIONS
Our findings demonstrate that histologically normal-appearing regions from the IPF lung are transcriptionally distinct when compared to similar lung tissue from controls with histologically normal lung tissue, and that transition zones and areas of dense fibrosis within the IPF lung demonstrate activation of ER stress and deactivation of wound healing pathways.
Topics: Humans; Eukaryotic Initiation Factor-2; Idiopathic Pulmonary Fibrosis; Lung; Transcriptome; Fibrosis
PubMed: 37978501
DOI: 10.1186/s12931-023-02572-6 -
Oncogene Nov 2023Epithelial tissue homeostasis is closely associated with the self-renewal and differentiation behaviors of epithelial stem cells (ESCs). p63, a well-known marker of... (Review)
Review
Epithelial tissue homeostasis is closely associated with the self-renewal and differentiation behaviors of epithelial stem cells (ESCs). p63, a well-known marker of ESCs, is an indispensable factor for their biological activities during epithelial development. The diversity of p63 isoforms expressed in distinct tissues allows this transcription factor to have a wide array of effects. p63 coordinates the transcription of genes involved in cell survival, stem cell self-renewal, migration, differentiation, and epithelial-to-mesenchymal transition. Through the regulation of these biological processes, p63 contributes to, not only normal epithelial development, but also epithelium-derived cancer pathogenesis. In this review, we provide an overview of the role of p63 in epithelial stemness regulation, including self-renewal, differentiation, proliferation, and senescence. We describe the differential expression of TAp63 and ΔNp63 isoforms and their distinct functional activities in normal epithelial tissues and in epithelium-derived tumors. Furthermore, we summarize the signaling cascades modulating the TAp63 and ΔNp63 isoforms as well as their downstream pathways in stemness regulation.
Topics: Humans; Tumor Suppressor Proteins; Transcription Factors; Epithelium; Neoplasms; Protein Isoforms; Phosphoproteins
PubMed: 37848625
DOI: 10.1038/s41388-023-02859-4 -
Biochemical Pharmacology Jul 2023With the continuous progress of atherosclerosis research, the significant pathological change of it--vascular calcification (VC), gains increasing attention. In recent... (Review)
Review
With the continuous progress of atherosclerosis research, the significant pathological change of it--vascular calcification (VC), gains increasing attention. In recent years, numerous studies have demonstrated that it is an independent predictor of death risk of cardiovascular disease, and it has a strong correlation with poor clinical prognosis. As the world's population continues to age, the occurrence of VC is expected to reach its highest point in the near future. Therefore, it is essential to investigate ways to prevent or even reverse this process for clinical purposes. Endothelial-to-mesenchymal transition (EndMT) describes the progressive differentiation of endothelial cells into mesenchymal stem cells (MSCs) under various stimuli and acquisition of pluripotent cell characteristics. More and more studies show that EndMT plays a vital role in various cardiovascular diseases, including atherosclerosis, vascular calcification and heart valvular disease. EndMT is also involved in the formation and progression of VC. This review vividly describes the history, characteristics of EndMT and how it affects the endothelial cell process, then focuses on the relationship between vascular endothelium, EndMT, amino acid metabolism, and vascular calcification. Finally, it overviews the signal pathway of EndMT and drugs targeting EndMT, hoping to provide new ideas and a theoretical basis for studying potential therapeutic targets of VC.
Topics: Humans; Endothelial Cells; Vascular Calcification; Cardiovascular Diseases; Endothelium, Vascular; Atherosclerosis
PubMed: 37589048
DOI: 10.1016/j.bcp.2023.115579 -
Clinics in Laboratory Medicine Jun 2024Urothelial carcinoma is characterized by the presence of a wide spectrum of histopathologic features and molecular alterations that contribute to its morphologic and... (Review)
Review
Urothelial carcinoma is characterized by the presence of a wide spectrum of histopathologic features and molecular alterations that contribute to its morphologic and genomic heterogeneity. It typically harbors high rates of somatic mutations with considerable genomic and transcriptional complexity and heterogeneity that is reflective of its varied histomorphologic and clinical features. This review provides an update on the recent advances in the molecular characterization and novel molecular taxonomy of urothelial carcinoma and variant histologies.
Topics: Humans; Carcinoma, Transitional Cell; Mutation; Urinary Bladder Neoplasms; Urologic Neoplasms; Urothelium
PubMed: 38821640
DOI: 10.1016/j.cll.2023.08.010 -
Life Science Alliance Mar 2024Chronic obstructive pulmonary disease (COPD), a devastating and irreversible lung disease, causes structural and functional defects in the bronchial epithelium, the...
Chronic obstructive pulmonary disease (COPD), a devastating and irreversible lung disease, causes structural and functional defects in the bronchial epithelium, the (ir)reversibility of which remains unexplored in vitro. This study aimed to investigate the persistence of COPD-related epithelial defects in long-term airway epithelial cultures derived from non-smokers, smokers, and COPD patients. Barrier function, polarity, cell commitment, epithelial-to-mesenchymal transition, and inflammation were evaluated and compared with native epithelium characteristics. The role of inflammation was explored using cytokines. We show that barrier dysfunction, compromised polarity, and lineage abnormalities observed in smokers and COPD persisted for up to 10 wk. Goblet cell hyperplasia was associated with recent cigarette smoke exposure. Conversely, increased IL-8/CXCL-8 release and abnormal epithelial-to-mesenchymal transition diminished over time. These ex vivo observations matched surgical samples' abnormalities. Cytokine treatment induced COPD-like changes in control cultures and reactivated epithelial-to-mesenchymal transition in COPD cells. In conclusion, these findings suggest that the airway epithelium of smokers and COPD patients retains a multidimensional memory of its original state and previous cigarette smoke-induced injuries, maintaining these abnormalities for extended periods.
Topics: Humans; Smokers; Epithelial Cells; Cells, Cultured; Pulmonary Disease, Chronic Obstructive; Epithelium; Cytokines; Inflammation
PubMed: 38158219
DOI: 10.26508/lsa.202302341 -
Gut Microbes Dec 2023Intestinal microbes impact the health of the intestine and organs distal to the gut. is a human intestinal microbe that promotes normal gut transit, the...
Intestinal microbes impact the health of the intestine and organs distal to the gut. is a human intestinal microbe that promotes normal gut transit, the anti-inflammatory immune system, wound healing, normal social behavior in mice, and prevents bone reabsorption. Oxytocin impacts these functions and oxytocin signaling is required for -mediated wound healing and social behavior; however, the events in the gut leading to oxytocin stimulation and beneficial effects are unknown. Here we report evolutionarily conserved oxytocin production in the intestinal epithelium through analysis of single-cell RNA-Seq datasets and imaging of human and mouse intestinal tissues. Moreover, human intestinal organoids produce oxytocin, demonstrating that the intestinal epithelium is sufficient to produce oxytocin. We find that facilitates oxytocin secretion from human intestinal tissue and human intestinal organoids. Finally, we demonstrate that stimulation of oxytocin secretion by is dependent on the gut hormone secretin, which is produced in enteroendocrine cells, while oxytocin itself is produced in enterocytes. Altogether, this work demonstrates that oxytocin is produced and secreted from enterocytes in the intestinal epithelium in response to secretin stimulated by . This work thereby identifies oxytocin as an intestinal hormone and provides mechanistic insight into avenues by which gut microbes promote host health.
Topics: Humans; Animals; Mice; Secretin; Oxytocin; Gastrointestinal Microbiome; Gastrointestinal Hormones; Intestinal Mucosa; Limosilactobacillus reuteri
PubMed: 37698879
DOI: 10.1080/19490976.2023.2256043 -
Science Advances Jul 2023During intestinal organogenesis, equipotent epithelial progenitors mature into phenotypically distinct stem cells that are responsible for lifelong maintenance of the...
During intestinal organogenesis, equipotent epithelial progenitors mature into phenotypically distinct stem cells that are responsible for lifelong maintenance of the tissue. While the morphological changes associated with the transition are well characterized, the molecular mechanisms underpinning the maturation process are not fully understood. Here, we leverage intestinal organoid cultures to profile transcriptional, chromatin accessibility, DNA methylation, and three-dimensional (3D) chromatin conformation landscapes in fetal and adult epithelial cells. We observed prominent differences in gene expression and enhancer activity, which are accompanied by local changes in 3D organization, DNA accessibility, and methylation between the two cellular states. Using integrative analyses, we identified sustained Yes-Associated Protein (YAP) transcriptional activity as a major gatekeeper of the immature fetal state. We found the YAP-associated transcriptional network to be regulated at various levels of chromatin organization and likely to be coordinated by changes in extracellular matrix composition. Together, our work highlights the value of unbiased profiling of regulatory landscapes for the identification of key mechanisms underlying tissue maturation.
Topics: Adult; Humans; Epigenomics; Intestinal Mucosa; Intestines; Epithelium; Chromatin
PubMed: 37436997
DOI: 10.1126/sciadv.adf9460 -
Progress in Retinal and Eye Research Jul 2023Corneal and conjunctival epithelia arise from a common ancestral ectoderm cell, then diverge into distinct lineages. The former develops into a multilayered stratified... (Review)
Review
Corneal and conjunctival epithelia arise from a common ancestral ectoderm cell, then diverge into distinct lineages. The former develops into a multilayered stratified squamous epithelium, the latter into an expansive mucous membrane that stretches the eyelid margin to the cornea's outskirts. The limbus, which intersects these epithelia, is purported to harbor corneal stem cells. Intrinsic programs that prevent these neighbouring epithelia from mixing and changing identity have not been elucidated, however microenvironmental cues that emanate following tissue damage and ensuing disease, dictate cell fate choices including those that influence form and function. Plasticity of ocular surface epithelia is gauged by their ability to undergo epithelial-mesenchymal transition, transdifferentiation, dedifferentiation and metaplastic transformation. Elucidating the molecular mechanism by which these rare and unusual phenomena arise, and persuading cells to either revert to their original state or remain newly committed, could be exploited into game-changing therapeutics for patients with corneal blindness and other diseases.
Topics: Humans; Epithelium; Cornea; Cell Differentiation; Epithelium, Corneal; Conjunctiva
PubMed: 36418216
DOI: 10.1016/j.preteyeres.2022.101148 -
JCI Insight Nov 2023Retinitis pigmentosa (RP) is the most common inherited retinal disease (IRD) and is characterized by photoreceptor degeneration and progressive vision loss. We report 4...
Retinitis pigmentosa (RP) is the most common inherited retinal disease (IRD) and is characterized by photoreceptor degeneration and progressive vision loss. We report 4 patients presenting with RP from 3 unrelated families with variants in TBC1D32, which to date has never been associated with an IRD. To validate TBC1D32 as a putative RP causative gene, we combined Xenopus in vivo approaches and human induced pluripotent stem cell-derived (iPSC-derived) retinal models. Our data showed that TBC1D32 was expressed during retinal development and that it played an important role in retinal pigment epithelium (RPE) differentiation. Furthermore, we identified a role for TBC1D32 in ciliogenesis of the RPE. We demonstrated elongated ciliary defects that resulted in disrupted apical tight junctions, loss of functionality (delayed retinoid cycling and altered secretion balance), and the onset of an epithelial-mesenchymal transition-like phenotype. Last, our results suggested photoreceptor differentiation defects, including connecting cilium anomalies, that resulted in impaired trafficking to the outer segment in cones and rods in TBC1D32 iPSC-derived retinal organoids. Overall, our data highlight a critical role for TBC1D32 in the retina and demonstrate that TBC1D32 mutations lead to RP. We thus identify TBC1D32 as an IRD-causative gene.
Topics: Humans; Induced Pluripotent Stem Cells; Retina; Retinitis Pigmentosa; Retinal Degeneration; Retinal Pigment Epithelium; Adaptor Proteins, Signal Transducing
PubMed: 37768732
DOI: 10.1172/jci.insight.169426