Biology subjects

Prakash, Y. S.

Publications and source records attributed to Prakash, Y. S..

9 recordsLinked to original sources

bioRxiv2026

Mechanosensitive Piezo Channels Contribute to Airway Changes in Chronic Obstructive Pulmonary Disease

As an intrinsically mechanosensitive organ, the lung experiences a range of mechanical forces. Chronic obstructive pulmonary disease (COPD) involves abnormal macroscopic cellular and extracellular matrix (ECM) changes that impact mechanical properties of the lung. Mechanosensitive Piezo1/2 channels are expressed in the lung including on airway smooth muscle cells (ASM) that mediate cellular responses to stretch and ECM biomechanics. The expression and roles of Piezos in COPD lung ASM are not known. We hypothesized that Piezo expression and activation are altered in COPD lung ASM influencing ECM regulation. Distribution of Piezo proteins in ASM and epithelium of small airways of COPD stage II and IV vs. non-COPD controls was assessed using immunohistochemistry and ImageJ (n=10-17/group). Isolated ASM cells from control (n=6) vs. COPD stage II and IV patients (n=3 each stage) were exposed to stretch or the Piezo1 agonist Yoda1 followed by measurement of ECM gene and protein expression. Less Piezo2 staining was observed in COPD IV patients compared to controls, with lesser area and intensity of staining in the epithelial layer, and lower intensity of staining in ASM and small airways as a whole. Fura-2-based imaging of ASM Ca2+ showed lower influx after Yoda1 exposure in COPD II compared to control and COPD IV. Gene expression of Piezo1 increased upon stretching in controls but not in COPD ASM, while Piezo2 protein expression decreased with stretching in all groups. Yoda1 treatment resulted in decreased collagen1, fibulin1 and periostin gene and collagen 1 and periostin protein expression in ASM. Overall, these results support a role for Piezo activation in abnormal ECM-ASM cell crosstalk in COPD.

physiology↗

bioRxiv2025

3-Mercaptopyruvate Sulfurtransferase (MPST) Regulates Mitochondrial Metabolism and Epithelial Differentiation in Neonatal Patient-derived Airway Cells

Early-life airway epithelial development relies on tightly coordinated mitochondrial metabolic programs, yet the pathways that govern normal epithelial maturation during this vulnerable developmental window remain poorly defined. Hyperoxia disrupts airway epithelial maturation, contributing to lung injury and airway remodeling in infants with bronchopulmonary dysplasia (BPD), underscoring the need to identify mitochondrial pathways that regulate early epithelial differentiation. 3-Mercaptopyruvate sulfurtransferase (MPST), a mitochondrial sulfur metabolism enzyme, supports mitochondrial metabolic and bioenergetic function, but its role in human airway epithelial development is unknown. In this study, we used neonatal patient-derived tracheal airway epithelial cells (nTAECs) in a three-dimensional air-liquid interface (ALI) model to show that hyperoxia reduces MPST protein abundance. To determine how MPST loss alters early epithelial differentiation and metabolic homeostasis we used RNAi to knock down MPST during ALI differentiation. MPST loss in nTAECs induced early (ALI day 3) transcriptomic shifts involving mitochondrial metabolic pathways, epithelial differentiation programs, and stress-response signature corresponding with decreased ciliated cell numbers during mid-differentiation phase (ALI day 7). Metabolic flux analysis revealed significantly reduced mitochondrial respiration without compensatory increase in glycolysis, indicative of disrupted metabolic flexibility. Together, these data show that MPST is essential for maintaining mitochondrial metabolic integrity necessary for normal airway epithelial development. Loss of MPST creates a developmental vulnerability that may contribute to hyperoxia-induced airway injury in neonates. Targeting MPST-dependent pathways could represent a new strategy to preserve airway health in infants at risk for BPD airway remodeling. NEW & NOTEWORTHYThis study identifies MPST as a previously unrecognized regulator of neonatal airway epithelial development. In our neonatal patient-derived three-dimensional organotypic model, hyperoxia reduces MPST, and MPST loss alters mitochondrial metabolism and epithelial differentiation programs. These findings indicate that MPST deficiency contributes to mitochondrial dysfunction under hyperoxic conditions and highlight MPST-linked pathways as potential therapeutic targets to mitigate early-life airway injury and remodeling relevant to infants with bronchopulmonary dysplasia.

developmental biology↗

bioRxiv2025

Loss of miRNA-153 promotes endothelial-to-mesenchymal transition and compromises lung vascular integrity

Endothelial-to-mesenchymal transition (EndMT) is a biological process through which lung vascular endothelial cells (ECs) transdifferentiate into mesenchymal-like cells. EndMT has recently been implicated in the development and progression of pulmonary vascular remodeling in pulmonary hypertension (PH); however, its underlying regulatory mechanisms remain incompletely understood. MicroRNAs (miRNAs) are key post-transcriptional regulators of EC gene expression and cellular responses to various stimuli. Notably, microRNA-153 (miR-153) has been shown to directly target SNAI1 to modulate epithelial-to-mesenchymal transition (EMT), a process closely related to EndMT and extensively studied in cancer. Whether miR-153 also participates in EndMT regulation, however, remains unknown. In this study, we demonstrate that 72-hour hypoxic exposure induces SNAI1-mediated EndMT in human lung vascular ECs. Hypoxia also increased cell proliferation and disrupted intercellular junctions, leading to enhanced endothelial permeability. Reduced miR-153 expression was observed in both hypoxia- and TGF-{beta}1-induced EndMT, as well as in ECs isolated from PH patients exhibiting an EndMT phenotype. Similar to hypoxia, TGF-{beta}1 promoted EC permeability. Loss of miR-153 enhanced SNAI1-mediated EndMT, endothelial survival, and permeability under normoxic conditions, whereas miR-153 overexpression attenuated EndMT induced by hypoxia or TGF-{beta}1. However, miR-153 restoration did not completely recover endothelial barrier integrity disrupted by these stimuli. In conclusion, miR-153 serves as a critical regulator of EndMT, maintaining endothelial identity and barrier function. Therapeutic delivery of miR-153 may therefore represent a novel strategy to inhibit EndMT and attenuate pulmonary vascular remodeling in PH.

physiology↗

bioRxiv2025

Quantitative Proteomics Links Mitochondrial Dysfunction to Metabolic Changes and Epithelial Differentiation Defects in Hyperoxia-Exposed Neonatal Airway Cells

Premature infants often require supplemental oxygen therapy, however, exposure to supraphysiological oxygen (hyperoxia) can disrupt normal lung development and contribute to bronchopulmonary dysplasia (BPD). Mitochondrial dysfunction is increasingly recognized as a contributor to hyperoxia-induced BPD. However, the effects of hyperoxia on mitochondrial function and mucociliary differentiation in the developing upper airway epithelium remain poorly understood. This study tested the hypothesis that hyperoxia impairs neonatal airway mucociliary differentiation by disrupting mitochondrial bioenergetic function. Neonatal tracheal airway epithelial cells (nTAECs) from term infants (n=5) were cultured in a 3D air-liquid interface (ALI) model and exposed to 60% O2 during the mid-phase of differentiation (ALI day 7-14). Cellular phenotype was assessed using immunofluorescence staining and gene expression analyses. Mitochondrial function was evaluated through Seahorse metabolic flux analysis, and global protein changes were characterized by quantitative proteomics. Hyperoxia exposure significantly impaired terminal epithelial differentiation, characterized by reductions in ciliated and goblet cells. Seahorse assay revealed a decrease in baseline oxygen consumption and mitochondrial ATP production, accompanied by a compensatory increase in glycolytic ATP production. Quantitative proteomics identified disruption of mitochondrial Complex I as a central feature of the hyperoxic response. Downstream proteomic pathway analyses further confirmed the metabolic shift from mitochondrial to glycolytic ATP production and demonstrated altered epithelial differentiation pathways, including NOTCH and TGF-{beta} signaling. These findings reveal that moderate hyperoxia impairs mitochondrial bioenergetics and alters metabolic programming, leading to disrupted mucociliary differentiation. Future in vivo studies should evaluate mitochondrial oxidative fitness as a therapeutic target in neonatal lung disease. NEW & NOTEWORTHYWe report that moderate hyperoxia during a critical window of mucociliary differentiation disrupts terminal maturation in neonatal airway epithelial cells cultured in a 3D model. Hyperoxia induced mitochondrial bioenergetic dysfunction and metabolic reprogramming, with proteomic analysis identifying Complex I disruption as a key driver of impaired differentiation. Overall, these findings reveal a previously underrecognized link between mitochondrial bioenergetics and airway epithelial development, positioning metabolic dysfunction as an early trigger of hyperoxia-induced neonatal airway injury.

developmental biology↗

bioRxiv2024

Store-operated Ca2+ entry is involved in endothelium-to-mesenchymal transition in lung vascular endothelial cells

Endothelial-to-mesenchymal transition (EndMT) is a biological process that converts endothelial cells to mesenchymal cells with increased proliferative and migrative abilities. EndMT has been implicated in the development of pulmonary vascular remodeling in pulmonary arterial hypertension (PAH), a fatal and progressive lung vascular disease. Transforming growth factor {beta}1 (TGF-{beta}1), an inflammatory cytokine, is known to induce EndMT in many types of endothelial cells including lung vascular endothelial cells (LVEC). An increase in cytosolic free Ca2+ concentration ([Ca2+]cyt) is a major stimulus for cellular proliferation and phenotypic transition, but it is unknown whether Ca2+ signaling is involved in EndMT. In this study we tested the hypothesis that TGF-{beta}1-induced EndMT in human LVEC is Ca2+-dependent. Treatment of LVEC with TGF-{beta}1 for 5-7 days resulted in increase in SNAI1/2 expression, induction of EndMT, upregulation of STIM/Orai1 and enhancement of store-operated Ca2+ entry (SOCE). Removal (or chelation) of extracellular or intracellular Ca2+ with EGTA or BAPTA-AM respectively abolished EndMT in response to TGF-{beta}1. Moreover, EGTA diminished TGF-{beta}1-induced increase in SNAI in a dose-dependent manner. Knockdown of either STIM1 or Orai1 was sufficient to prevent TGF-{beta}-mediated increase in SNAI1/2 and EndMT, but did not rescue the continuous adherent junctions. Blockade of Orai1 channels by AnCoA4 inhibited TGF-{beta}-mediated EndMT and restored PECAM1-positive continuous adherent junctions. In conclusion, intracellular Ca2+ signaling plays a critical role in TGF-{beta}-associated EndMT through enhanced SOCE and STIM1-Orai1 interaction. Thus, targeting Ca2+ signaling pathways regulating EndMT may be a novel therapeutic approach to treat PAH and other forms of pre-capillary pulmonary hypertension. New & NoteworthyEndMT has been reported to contribute to the pathogenesis of PH. In this study we aimed to determine the role of Ca2+ signaling in the development of EndMT in human lung vascular endothelial cells. Our data suggest that TGF-{beta}1 requires store-operated Ca2+ entry through STIM1/Orai channels to induce SNAI-mediated EndMT. For the first time we demonstrated that TGF-{beta}1-induced EndMT is Ca2+-dependent event while inhibition of STIM1/Orai interaction attenuated EndMT in response to TGF-{beta}1.

cell biology↗

bioRxiv2024

Fibroblast-derived osteoglycin promotes epithelial cell repair

There is an urgent need for innovative pharmacological treatments targeting defective epithelial repair in chronic diseases, such as chronic obstructive pulmonary disease. The mesenchymal niche is a critical regulator in epithelial stem cell activation during repair. We hypothesized that secreted factors in this interaction are potent drug targets. Utilizing a cutting-edge proteomics-guided drug discovery strategy, we explored the lung fibroblast secretome to uncover impactful drug targets. Our lung organoid assays identified several regenerative ligands, with the secreted matrix protein osteoglycin (OGN) surprisingly showing the most profound effects. Transcriptomic analyses revealed that OGN enhances alveolar progenitor cell differentiation, boosts reactive oxygen species detoxification, reduces cellular senescence, and strengthens fibroblast-epithelial crosstalk. Critically, OGN expression was diminished in COPD patients and smoke-exposed mice. An active fragment of OGN, encompassing leucine-rich repeat regions 4-7, demonstrated regenerative potential akin to full-length OGN. This fragment significantly ameliorated elastase-induced lung injury precision-cut lung slices and improved lung function in vivo. These findings highlight lung fibroblast-derived OGN as a pivotal secreted protein for alveolar epithelial growth, positioning its active fragment as a promising therapeutic for epithelial repair in individuals with accelerated lung tissue damage.

pharmacology and toxicology↗

bioRxiv2022

Age-associated Differences in the Human Lung Extracellular Matrix

IntroductionExtracellular matrix (ECM) remodelling has been associated with chronic lung diseases. However, information about specific age-associated differences in lung ECM is currently limited. In this study we aimed to identify and localize age-associated ECM differences in human lung using comprehensive transcriptomic, proteomic and immunohistochemical analyses. MethodsOur previously identified age-associated gene expression signature of the lung was re-analysed limiting it to an aging signature based on 270 control patients (37-80 years) and focused on the Matrisome core geneset using geneset enrichment analysis. To validate the age-associated transcriptomic differences on protein level, we compared the age-associated ECM genes (F <0.05) with a profile of age-associated proteins identified from a lung tissue proteomics dataset from 9 control patients (49-76 years) (FDR<0.05). Extensive immunohistochemical analysis was used to localize the age-associated ECM differences in lung tissues from control patients (9-82 years). ResultsComparative analysis of transcriptomic and proteomic data identified 7 ECM proteins with higher expression with age at both gene and protein level: COL1A1, COL6A1, COL6A2, COL14A1, FBLN2, LTBP4 and LUM. With immunohistochemistry we demonstrated higher protein expression with age for COL6A2 in whole tissue, parenchyma, airway wall and blood vessel, for COL14A1 in bronchial epithelium and blood vessel, and for FBLN2 and COL1A1 in lung parenchyma. ConclusionOur study revealed that higher age is associated with lung ECM remodelling, with specific differences occurring in defined regions within the lung. These differences may affect lung structure and physiology with aging and as such may increase susceptibility for developing chronic lung diseases. Key messagesO_ST_ABSWhat is already known on this topicC_ST_ABSsummarise the state of scientific knowledge on this subject before you did your study and why this study needed to be done. In animal models, it has been demonstrated that aging alters the composition of the lung ECM, with more deposition of collagen and degradation of elastin. Similar ECM differences have been observed in age-associated chronic lung diseases, including COPD; moreover, we observed in lung tissue that several ECM genes associate differently with age in COPD patients compared to non-COPD controls(1). Detailed knowledge on age-associated changes in specific ECM proteins as well as regional differences within the lung is lacking. What this study addssummarise what we now know as a result of this study that we did not know before. We identified 7 age-associated ECM proteins i.e. COL1A1, COL6A1, COL6A2 COL14A1, FBLN2, LTBP4 and LUM with higher transcript and protein levels in human lung tissue with age. Extensive immunohistochemical analysis revealed significant age-associated differences for 3 of these ECM proteins in specific compartments of the lung, with the most notable differences in the blood vessels and parenchyma. How this study might affect research, practice, or policysummarise the implications of this study. The identification of age-associated differences in specific human lung ECM proteins lays a new foundation for the investigation of ECM differences in age-associated chronic lung diseases. Additionally, examining the function of these age-associated ECM proteins and their cellular interactions in lung injury and repair responses may provide novel insight in mechanisms underlying chronic lung diseases.

molecular biology↗

bioRxiv2020

Docosahexaenoic acid (DHA), a nutritional supplement, modulates steroid insensitivity in asthma

Asthmatics with poor steroid responsiveness are now found to use health services at higher frequency and contribute to socio-economic burden disproportionately. We have previously shown that a ω-6 fatty acid metabolite leads to a severe and steroid insensitive asthma-like condition in mice. Here, we investigated the role of retinoid-x-receptor gamma (RXRγ) and Docosahexaenoic acid (DHA), a ω3 fatty acid rexinoid ligand of RXR, on the features of steroid insensitivity in asthmatic condition. RXRγ was found to be reduced in the lungs of human asthmatics and mice with steroid insensitive allergic airway inflammation. RXRγ knockdown in naïve mice led to spontaneous asthma like features whereas RXRγ knockdown in allergic mice led to steroid insensitive asthma features. We observed while RXRγ binds to the glucocorticoid receptor (GR) gene and regulates its transcription, DHA increases the GRα expression in human bronchial epithelial cells and reverses the steroid insensitive features in mice with allergic airway inflammation. Docosahexaenoic acid (DHA), a ligand of RXR, was reduced in the sera of steroid-insensitive asthmatics. We conclude that DHA may prove to be a promising steroid sensitizing agent for the treatment of steroid insensitive asthmatics.Summary The molecular regulation of glucocorticoid receptor by retinoid-x-receptor gamma (RXRgama) has an implication in steroid insensitive asthma as we found that Docosahexaenoic acid (DHA), a nutritional supplement and natural ligand of RXRgamma, improves steroid sensitivity in steroid insensitive mice model of asthma and DHA levels are found to be low in steroid insensitive asthmatic patients.Competing Interest StatementThe authors have declared no competing interest.Abbreviations usedAAIAllergic airway inflammationAHRAirway hyper-responsivenessATRAAll-trans retinoic acidAUArbitrary unitsBALBronchoalveolar lavageBEAS-2BHuman bronchial epithelial cellsCECockroach allergen extractChIPChromatin Immunoprecipitation9CRA9-cis retinoic acidDEXDexamethasoneDHADocosahexaenoic acidDMSODimethyl sulfoxideELISAEnzyme-linked immunosorbent assayGAPDHGlyceraldehyde 3-phosphate dehydrogenaseGLucGaussia luciferaseGRαGlucocorticoid receptor alphaGREGlucocorticoid receptor elementH & EHaematoxylin and eosinIFNγInterferon gammaIgEImmunoglobulinE ILInterleukinKCKeratinocyte chemoattractant15-LOX15-lipoxygenaseMCF-7Human breast adenocarcinoma cell lineMCP1-αMonocyte chemoattractant protein1-αNF-κBNuclear Factor kappa-light-chain-enhancer of activated B cellsO.EOverexpressionOVAOvalbuminp38-MAPKp38 mitogen-activated protein kinasePBSPhosphate buffered salineRARRetinoic acid receptorPDTCPyrrolidinedithiocarbamateRXRERexinoid receptor elementRXRγRetinoid-x-receptor gamma13-S-HODE13-hydroxyoctadecadienoic acidSEMStandard error meansiRNASmall interfering RNASTAT-6Signal transducer and activator of transcription 6ThT helperVEHVehicleView Full Text

immunology↗

bioRxiv2018

Thymic Stromal Lymphopoietin Promotes Proliferation and Contractility of Human Pulmonary Artery Smooth Muscle

Hypoxia is a well-recognized risk factor in several pulmonary vascular diseases including pulmonary hypertension (PH). Furthermore, hypoxia-associated inflammatory changes enhance the structural and functional changes in the pulmonary artery (PA) of PH patients. Understanding the mechanisms that link hypoxia and inflammation, particularly early in disease, is key to development of novel therapeutic avenues for PH. Thymic stromal lymphopoietin (TSLP) is an \"early\" inflammatory mediator thought to be critical in diseases such as asthma, chronic obstructive pulmonary disease and atopic dermatitis. TSLP has canonical effects on the immune system, but can also have non-canonical effects on resident lung cells, e.g. airway smooth muscle. Currently, the expression and role of TSLP in the PA is unknown. We hypothesized that locally-produced TSLP potentiates the effects of hypoxia in PA remodeling and contractility relevant to PH. Experiments in human PA endothelial cells (PAECs) and smooth muscle cells (PASMCs) found PAECs to be a larger source of TSLP which targets PASMCs to enhance intracellular Ca2+ responses to vasoconstrictor agonist as well as cell proliferation, acting via a number of signaling cascades including Stat3 and PI3/Akt. Hypoxia, acting via HIF1, enhanced PAEC production of TSLP, and promoted TSLP effects on PASMCs. Interestingly, TSLP per se enhance HIF1a. Overall, these novel data highlight a role for TSLP in hypoxia effects on the PA, and thus relevance for inflammation in PH.

physiology↗