@article{paudel_kumar_rogers_saini_patial_kulkarni_2024, title={The NLRP3 Inflammasome Is Dispensable in Methicillin-Resistant <i>Staphylococcus aureus</i> Urinary Tract Infection}, volume={13}, ISSN={["2076-0817"]}, DOI={10.3390/pathogens13020106}, abstractNote={The NLRP3 inflammasome is a cytoplasmic complex that senses molecular patterns from pathogens or damaged cells to trigger an innate immune defense response marked by the production of proinflammatory cytokines IL-1β and IL-18 and an inflammatory death called pyroptosis. The NLRP3 inflammasome is activated in the urinary tract by a variety of infectious and non-infectious insults. In this study, we investigated the role of the NLRP3 inflammasome by comparing the pathophysiology of methicillin-resistant Staphylococcus aureus (MRSA) ascending UTI in wild-type (WT) and Nlrp3−/− mice. The difference in the bacterial burden detected in the urinary tracts of MRSA-infected WT and Nlrp3−/− was not statistically significant at 6, 24, and 72 h post-infection (hpi). The levels of pro-inflammatory cytokines and chemokines as well as the numbers of granulocytes recruited to bladder and kidney tissues at 24 hpi were also similar between Nlrp3−/− and WT mice. The histopathological analysis of MRSA-infected bladder and kidney sections from Nlrp3−/− and WT mice showed similar inflammation. Overall, these results suggest that MRSA-induced urinary NLRP3 activity does not play a role in the pathophysiology of the ascending UTI.}, number={2}, journal={PATHOGENS}, author={Paudel, Santosh and Kumar, Rahul and Rogers, Kenneth A. and Saini, Yogesh and Patial, Sonika and Kulkarni, Ritwij}, year={2024}, month={Feb} }
 @article{sundar_duraisamy_choudhary_saini_silveyra_2023, title={Acute and Repeated Ozone Exposures Differentially Affect Circadian Clock Gene Expression in Mice.}, volume={5}, url={http://europepmc.org/abstract/med/37204107}, DOI={10.1002/adbi.202300045}, abstractNote={Abstract}, journal={Advanced biology}, author={Sundar, IK and Duraisamy, SK and Choudhary, I and Saini, Y and Silveyra, P}, year={2023}, month={May} }
 @article{mao_patial_saini_2023, title={Airway epithelial cell-specific deletion of HMGB1 exaggerates inflammatory responses in mice with muco-obstructive airway disease.}, url={http://europepmc.org/abstract/med/36741411}, DOI={10.3389/fimmu.2022.944772}, abstractNote={High mobility group box 1 (HMGB1), a ubiquitous chromatin-binding protein required for gene transcription regulation, is released into the extracellular microenvironment by various structural and immune cells, where it is known to act as an alarmin. Here, we investigated the role of airway epithelium-specific HMGB1 in the pathogenesis of muco-obstructive lung disease in Scnn1b-transgenic (Tg+) mouse, a model of human cystic fibrosis (CF)-like lung disease. We hypothesized that airway epithelium-derived HMGB1 modulates muco-inflammatory lung responses in the Tg+ mice. The airway epithelium-specific HMGB1-deficient mice were generated and the effects of HMGB1 deletion on immune cell recruitment, airway epithelial cell composition, mucous cell metaplasia, and bacterial clearance were determined. The airway epithelium-specific deletion of HMGB1 in wild-type (WT) mice did not result in any morphological alterations in the airway epithelium. The deficiency of HMGB1 in airway epithelial cells in the Tg+ mice, however, resulted in significantly increased infiltration of macrophages, neutrophils, and eosinophils which was associated with significantly higher levels of inflammatory mediators, including G-CSF, KC, MIP-2, MCP-1, MIP-1α, MIP-1β, IP-10, and TNF-α in the airspaces. Furthermore, as compared to the HMGB1-sufficient Tg+ mice, the airway epithelial cell-specific HMGB1-deficient Tg+ mice exhibited poor resolution of spontaneous bacterial infection. The HMGB1 deficiency in the airway epithelial cells of Tg+ mice did not alter airway epithelial cell-specific responses including epithelial cell proliferation, mucous cell metaplasia, and mucus obstruction. Collectively, our findings provide novel insights into the role of airway epithelial cell-derived HMGB1 in the pathogenesis of CF-like lung disease in Tg+ mice.}, journal={Frontiers in immunology}, author={Mao, Y and Patial, S and Saini, Y}, year={2023}, month={Jan} }
 @article{das_puthusseri_gopu_krishnan_bhagavath_bolla_saini_criner_marchetti_tang_et al._2023, title={Caveolin-1-derived peptide attenuates cigarette smoke-induced airway and alveolar epithelial injury.}, url={https://doi.org/10.1152/ajplung.00178.2022}, DOI={10.1152/ajplung.00178.2022}, abstractNote={ Chronic cigarette smoke (CS) exposure remains a major risk factor for the pathogenesis of COPD, a debilitating disease with no effective treatment. Increased caveolin-1 mediated induction of p53 and downstream plasminogen activator inhibitor-1 (PAI-1) expression contributes to CS-induced airway mucus hypersecretion and alveolar wall damage. This is reversed by caveolin-1 scaffolding domain peptide (CSP7) in preclinical models, suggesting the therapeutic potential of CSP7 for treating CS-induced lung injury (CS-LI) and COPD. }, journal={American journal of physiology. Lung cellular and molecular physiology}, author={Das, DN and Puthusseri, B and Gopu, V and Krishnan, V and Bhagavath, AK and Bolla, S and Saini, Y and Criner, GJ and Marchetti, N and Tang, H and et al.}, year={2023}, month={Aug} }
 @article{kubra_akhter_saini_kousoulas_barabutis_2022, title={Activating transcription factor 6 protects against endothelial barrier dysfunction.}, volume={11}, url={http://europepmc.org/abstract/med/35933031}, DOI={10.1016/j.cellsig.2022.110432}, abstractNote={Endothelial hyperpermeability is associated with sepsis and acute respiratory distress syndrome (ARDS). The identification of molecular pathways involved in barrier dysfunction; may reveal promising therapeutic targets to combat ARDS. Unfolded protein response (UPR) is a highly conserved molecular pathway, which ameliorates endoplasmic reticulum stress. The present work focuses on the effects of ATF6, which is a UPR sensor, in lipopolysaccharides (LPS)-induced endothelial hyperpermeability. The in vitro effects of AA147 and Ceapin-A7 in LPS-induced endothelial barrier dysfunction were investigated in bovine pulmonary artery endothelial cells (BPAEC). Small interfering (si) RNA was utilized to “silence” ATF6, and electric cell-substrate impedance sensing (ECIS) measured transendothelial resistance. Fluorescein isothiocyanate (FITC)-dextran assay was utilized to assess paracellular permeability. Protein expression levels were evaluated with Western blotting, and cell viability with MTT assay. We demonstrated that AA147 prevents LPS-induced barrier disruption by counteracting Cofilin and myosin light chain 2 (MLC2) activation, as well as VE-Cadherin phosphorylation. Moreover, this ATF6 inducer opposed LPS-triggered decrease in transendothelial resistance (TEER), as well as LPS-induced paracellular hyperpermeability. On the other hand, ATF6 suppression due to Ceapin-A7 or small interfering RNA exerted the opposite effects, and potentiated LPS-induced endothelial barrier disruption. Moderate concentrations of both ATF6 modulators did not affect cell viability. ATF6 activation protects against endothelial barrier function, suggesting that this UPR sensor may serve as a therapeutic target for sepsis and ARDS.}, journal={Cellular signalling}, author={Kubra, KT and Akhter and Saini, Y and Kousoulas, KG and Barabutis, N}, year={2022}, month={Aug} }
 @article{vo_saini_2022, title={Case report: <i>Mafb</i> promoter activity may define the alveolar macrophage dichotomy.}, url={http://europepmc.org/abstract/med/36578483}, DOI={10.3389/fimmu.2022.1050494}, abstractNote={Cre-LoxP system has been widely used to induce recombination of floxed genes of interest. Currently available macrophage promoter-specific Cre recombinase mice strains have various limitations that warrants the testing of additional Cre strains. V-maf musculoaponeurotic fibrosarcoma oncogene family, protein b -Cre (Mafb-Cre) mice label macrophages in most organs such as spleen, small intestine, lung, bone marrow, and peritoneal cavity. However, whether Mafb-Cre recombinase targets the gene recombination in alveolar macrophage remains untested. Here, we utilized MafbCre/WTR26mTmG/WT strain that expresses mTOM protein in all the cells of mouse body except for those that express Mafb-Cre-regulated mEGFP. We performed fluorescent microscopy and flow cytometry to analyze mTOM and mEGFP expression in alveolar macrophages from MafbCre/WTR26mTmG/WT mice. Our analyses revealed that the Mafb-Cre is active in only ~40% of the alveolar macrophages in an age-independent manner. While Mafb- (mTOM+/mEGFP-) and Mafb+ (mEGFP+) alveolar macrophages exhibit comparable expression of CD11b and CD11c surface markers, the surface expression of MHCII is elevated in the Mafb+ (mEGFP+) macrophages. The bone marrow-derived macrophages from MafbCre/WTR26mTmG/WT mice are highly amenable to Cre-LoxP recombination in vitro. The bone marrow depletion and reconstitution experiment revealed that ~98% of alveolar macrophages from MafbCre/WTR26mTmG/WT → WT chimera are amenable to the Mafb-Cre-mediated recombination. Finally, the Th2 stimulation and ozone exposure to the MafbCre/WTR26mTmG/WT mice promote the Mafb-Cre-mediated recombination in alveolar macrophages. In conclusion, while the Mafb-/Mafb+ dichotomy thwarts the use of Mafb-Cre for the induction of floxed alleles in the entire alveolar macrophage population, this strain provides a unique tool to induce gene deletion in alveolar macrophages that encounter Th2 microenvironment in the lung airspaces.}, journal={Frontiers in immunology}, author={Vo, T and Saini, Y}, year={2022}, month={Dec} }
 @article{lamichhane_patial_saini_2022, title={Higher susceptibility of males to bleomycin-induced pulmonary inflammation is associated with sex-specific transcriptomic differences in myeloid cells.}, volume={11}, url={http://europepmc.org/abstract/med/36087614}, DOI={10.1016/j.taap.2022.116228}, abstractNote={Idiopathic pulmonary fibrosis, a condition with likely genetic and environmental etiology, is relatively more prevalent with poor prognosis in human males. However, the underlying mechanisms for these gender-associated differences in the severity of fibrosis remain unknown. Here, we tested the hypothesis that the transcriptomic repertoire of myeloid cells determines the higher susceptibility of male mice to bleomycin (BLM)-induced lung fibrosis. Adult mice were oropharyngeally challenged with saline or BLM. Lung injury, inflammation, and fibrosis outcomes were assessed, and airspace myeloid-cells were subjected to RNA-sequencing. As compared with the female mice, the male mice manifested significantly increased lung injury, inflammation, proinflammatory cytokines (IL-6, IL-1β, IL-7, and IP-10), and fibrosis in response to BLM challenge. Interestingly, several pro-inflammatory and extracellular matrix-associated genes were significantly up-regulated in male myeloid-cells compared to female myeloid-cells in the saline-control group. Similarly, BLM challenge resulted in greater pro-inflammatory and pro-fibrotic transcriptomic changes in male compared to female myeloid cells. On the other hand, anti-inflammatory and regulatory cytokine, Il10 and Ifng respectively, were uniquely upregulated in BLM-challenged female but not in male myeloid cells when compared to their respective saline-control groups. Further, cross-sex bone marrow transplantation experiments revealed that male hematopoietic progenitor cells (HPCs) increased the granulocytic infiltration in female mice while female HPCs decreased the granulocytic infiltration in male mice post-BLM challenge. These findings suggest that there are inherent transcriptomic differences between the male and female lung myeloid cells and that the pro-inflammatory nature of male myeloid cells is sufficient to increase the susceptibility of female mice to BLM-induced inflammation.}, journal={Toxicology and applied pharmacology}, author={Lamichhane, R and Patial, S and Saini, Y}, year={2022}, month={Sep} }
 @article{lewis_patial_saini_2022, title={In Vitro Screening Method for Characterization of Macrophage Activation Responses.}, volume={8}, url={http://europepmc.org/abstract/med/36136814}, DOI={10.3390/mps5050068}, abstractNote={Macrophage activation refers to the enhanced functionality of macrophages in response to endogenous or exogenous stimuli. Due to the existence of limitless stimuli and a multitude of receptors on macrophage surfaces, the nature of activation (or acquired functioning) can be specific to the encountering stimulus. This article describes a macrophage-activation screening platform in a 96-well format. The methodology involves the generation of bone marrow-derived macrophages, their activation into two extreme activation states, and screening of activated macrophages for expression of bonafide protein biomarkers. A high-throughput and stringent assay to determine macrophage activation markers developed in this article can be adapted for biomarker determination in pathological conditions and toxicant/drug safety screening.}, journal={Methods and protocols}, author={Lewis, BW and Patial, S and Saini, Y}, year={2022}, month={Aug} }
 @article{kumar_mao_patial_saini_2022, title={Induction of whole-body gene deletion <i>via</i> R26-regulated tamoxifen-inducible Cre recombinase activity.}, url={http://europepmc.org/abstract/med/36569322}, DOI={10.3389/fphar.2022.1018798}, abstractNote={Germline deletion of certain genes causes embryonic lethality, therefore, understanding the effect of deletion of such genes on mammalian pathophysiology remains challenging. Tamoxifen (TAM)-inducible Cre recombinase is widely used for tissue-specific and temporal induction of gene deletion in mice. However, the tamoxifen treatment regimen for the generation of whole-body deletion of a gene is not yet fully standardized for the majority of organs/tissues. Accordingly, we employed GtROSA26 (R26) promoter-regulated Cre and a reporter gene expression strategy. GtROSA26 (R26) is an ubiquitous promoter and mice carrying the R26Cre−ERT2 transgene express Cre-ERT2 in all the cells. Similarly, mice carrying the R26mTOM-mEGFP transgene express mTOM (membrane-targeted tdTomato), in the absence of Cre or mEGFP (membrane-targeted enhanced green fluorescent protein), in the presence of Cre, in all the cells. The progeny carrying one allele of both transgenes were subjected to different TAM regimens, i.e., IP injections (4 injections; 1.35 mg/injection), diet (400 mg TAM-citrate/kg food), or diet (400 mg TAM-citrate/kg food) combined with either TAM-oral gavage (4 gavages; 1.35 mg/gavage) or TAM IP injections (4 injections; 1.35 mg/injection) for 2-weeks beginning at postnatal day (PND) 21 and the extent of Cre recombination in different tissues was determined at PND35. Tamoxifen administration resulted in a transient loss of body weight in all the treatment regimens with a relatively slower rate of weight gain in the TAM-diet plus TAM-oral gavage group compared to other groups. While the efficiency of Cre recombination, as determined by the expression of mEGFP protein, was variable among tissues, major tissues such as the liver, heart, lungs, spleen, and thymus—showed almost complete recombination. No recombination was evident in any of the tissues examined from the control mice. In general, the efficiency of Cre recombination was better with a combined regimen of TAM-diet with either TAM-injections or TAM-oral gavage compared to TAM-diet alone or TAM-injections alone. Our results demonstrate that a combination of TAM-diet with either TAM-injections or TAM-oral gavage can be employed for the efficient deletion of a gene in the whole body. Our findings will provide technical expertise to the researchers employing TAM-inducible Cre for the deletion of floxed genes in varied tissues.}, journal={Frontiers in pharmacology}, author={Kumar, R and Mao, Y and Patial, S and Saini, Y}, year={2022}, month={Dec} }
 @article{paudel_rogers_kumar_saini_patial_kulkarni_2022, title={NLRP3 inflammasome is dispensable in methicillin resistant<i>Staphylococcus aureus</i>urinary tract infection}, url={http://europepmc.org/abstract/PPR/PPR570823}, DOI={10.1101/2022.11.11.516235}, abstractNote={Abstract}, author={Paudel, S and Rogers, KA and Kumar, R and Saini, Y and Patial, S and Kulkarni, R}, year={2022}, month={Nov} }
 @article{vo_paudel_choudhary_patial_saini_2022, title={Ozone exposure upregulates the expression of host susceptibility protein TMPRSS2 to SARS-CoV-2.}, volume={1}, url={http://europepmc.org/abstract/med/35079032}, DOI={10.1038/s41598-022-04906-8}, abstractNote={Abstract}, journal={Scientific reports}, author={Vo, T and Paudel, K and Choudhary, I and Patial, S and Saini, Y}, year={2022}, month={Jan} }
 @article{chen_patial_saini_2022, title={Silencing of RNA binding protein, ZFP36L1, promotes epithelial-mesenchymal transition in liver cancer cells by regulating transcription factor ZEB2.}, volume={9}, url={http://europepmc.org/abstract/med/36100056}, DOI={10.1016/j.cellsig.2022.110462}, abstractNote={RNA binding proteins (RBPs) of the zinc finger protein 36 family including zinc finger protein 36 like 1 (ZFP36L1) are implicated in cancer, however, the underlying molecular mechanisms have remained unclear. These proteins function by regulating post-transcriptional gene expression upon binding to the AU-rich elements (ARE's) within the 3’untranslated regions (3’UTRs) of specific mRNAs and increasing their mRNA turnover. Here, we tested the role of ZFP36L1 in hepatocellular carcinoma (HCC) cell lines. ZFP36L1 was under-expressed among the three RBPs in a majority of the HCC cell lines. Silencing of ZFP36L1 in two of the seven HCC cell lines resulted in epithelial-mesenchymal transition (EMT) like morphological changes, which were characterized by the transition of epithelial morphology to elongated mesenchymal morphology and increased migration and invasion potential. Conversely, overexpression of ZFP36L1 abolished these changes. RNA-seq analysis of ZFP36L1-depleted HCC cells revealed a significant upregulation of an EMT-inducing transcription factor, ZEB2 (zinc-finger E-box-binding homeobox 2), and enrichment of pathways associated with mesenchymal cell development and differentiation. ZEB2 mRNA contains AREs within its 3’UTR and its stability was increased following ZFP36L1 knockdown. Conversely, ZEB2 was significantly downregulated following ZFP36L1 overexpression and ZEB2 3’UTR was regulated by ZFP36L1 in luciferase reporter assays. These data identify ZEB2 mRNA as a ZFP36L1 target in HCC cells and demonstrate that ZFP36L1 regulates EMT possibly through direct regulation of ZEB2 mRNA. In summary, our results demonstrate that ZFP36L1 suppresses EMT inliver cancer cells by down-regulating the expression of EMT-inducing transcription factor, ZEB2. These data suggest an important role of ZFP36L1 in the development, progression, and metastasis of hepatocellular cancer.}, journal={Cellular signalling}, author={Chen, J and Patial, S and Saini, Y}, year={2022}, month={Sep} }
 @article{patial_lewis_vo_choudhary_paudel_mao_singamsetty_brombacher_saini_2021, title={Myeloid-IL4Rα is an indispensable link in IL-33-ILCs-IL-13-IL4Rα axis of eosinophil recruitment in murine lungs.}, volume={7}, url={http://europepmc.org/abstract/med/34326406}, DOI={10.1038/s41598-021-94843-9}, abstractNote={Abstract}, journal={Scientific reports}, author={Patial, S and Lewis, BW and Vo, T and Choudhary, I and Paudel, K and Mao, Y and Singamsetty, D and Brombacher, F and Saini, Y}, year={2021}, month={Jul} }
 @article{choudhary_vo_paudel_yadav_mao_patial_saini_2021, title={Postnatal Ozone Exposure Disrupts Alveolar Development, Exaggerates Mucoinflammatory Responses, and Suppresses Bacterial Clearance in Developing <i>Scnn1b</i>-Tg<sup>+</sup> Mice Lungs.}, volume={8}, url={http://europepmc.org/abstract/med/34330754}, DOI={10.4049/jimmunol.2001286}, abstractNote={Abstract}, journal={Journal of immunology (Baltimore, Md. : 1950)}, author={Choudhary, I and Vo, T and Paudel, K and Yadav, R and Mao, Y and Patial, S and Saini, Y}, year={2021}, month={Jul} }
 @article{choudhary_vo_paudel_wen_gupta_kesimer_patial_saini_2021, title={Vesicular and extravesicular protein analyses from the airspaces of ozone-exposed mice revealed signatures associated with mucoinflammatory lung disease.}, volume={12}, url={http://europepmc.org/abstract/med/34853335}, DOI={10.1038/s41598-021-02256-5}, abstractNote={Abstract}, journal={Scientific reports}, author={Choudhary, I and Vo, T and Paudel, K and Wen, X and Gupta, R and Kesimer, M and Patial, S and Saini, Y}, year={2021}, month={Dec} }
 @article{bathula_chen_kumar_blackshear_saini_patial_2021, title={ZFP36L1 Regulates Fgf21 mRNA Turnover and Modulates Alcoholic Hepatic Steatosis and Inflammation in Mice.}, volume={2}, url={http://europepmc.org/abstract/med/34774847}, DOI={10.1016/j.ajpath.2021.10.017}, abstractNote={Zinc finger protein 36 like 1 (ZFP36L1) enhances the turnover of mRNAs containing AU-rich elements (AREs) in their 3'-untranslated regions (3'UTR). The physiological and pathological functions of ZFP36L1 in liver, however, remain largely unknown. Liver-specific ZFP36L1-deficient (Zfp36l1flox/flox/Cre+; L1LKO) mice were generated to investigate the role of ZFP36L1 in liver physiology and pathology. Under normal conditions, the L1LKO mice and their littermate controls (Zfp36l1flox/flox/Cre-; L1FLX) appeared normal. When fed a Lieber-DeCarli liquid diet containing alcohol, L1LKO mice were significantly protected from developing alcohol-induced hepatic steatosis, injury, and inflammation compared with L1FLX mice. Most importantly, fibroblast growth factor 21 (Fgf21) mRNA was significantly increased in the livers of alcohol diet-fed L1LKO mice compared with the alcohol diet-fed L1FLX group. The Fgf21 mRNA contains three AREs in its 3'UTR, and Fgf21 3'UTR was directly regulated by ZFP36L1 in luciferase reporter assays. Steady-state levels of Fgf21 mRNA were significantly decreased by wild-type ZFP36L1, but not by a non-binding zinc finger ZFP36L1 mutant. Finally, wild-type ZFP36L1, but not the ZFP36L1 mutant, bound to the Fgf21 3'UTR ARE RNA probe. These results demonstrate that ZFP36L1 inactivation protects against alcohol-induced hepatic steatosis and liver injury and inflammation, possibly by stabilizing Fgf21 mRNA. These findings suggest that the modulation of ZFP36L1 may be beneficial in the prevention or treatment of human alcoholic liver disease.}, journal={The American journal of pathology}, author={Bathula, CS and Chen, J and Kumar, R and Blackshear, PJ and Saini, Y and Patial, S}, year={2021}, month={Nov} }
 @article{bathula_chen_blackshear_saini_patial_2021, title={ZFP36L1 regulates <i>Fgf21</i> mRNA turnover and modulates alcoholic hepatic steatosis and inflammation in mice}, url={http://europepmc.org/abstract/PPR/PPR338718}, DOI={10.1101/2021.05.11.443631}, abstractNote={ABSTRACT}, author={Bathula, CS and Chen, J and Blackshear, PJ and Saini, Y and Patial, S}, year={2021}, month={May} }
 @article{lewis_vo_choudhary_kidder_bathula_ehre_wakamatsu_patial_patial_saini_2020, title={Ablation of IL-33 Suppresses <i>Th2</i> Responses but Is Accompanied by Sustained Mucus Obstruction in the <i>Scnn1b</i> Transgenic Mouse Model.}, volume={3}, url={http://europepmc.org/abstract/med/32060135}, DOI={10.4049/jimmunol.1900234}, abstractNote={Abstract}, journal={Journal of immunology (Baltimore, Md. : 1950)}, author={Lewis, BW and Vo, T and Choudhary, I and Kidder, A and Bathula, C and Ehre, C and Wakamatsu, N and Patial, S and Patial, S and Saini, Y}, year={2020}, month={Feb} }
 @article{choudhary_vo_paudel_patial_saini_2020, title={Compartment-specific transcriptomics of ozone-exposed murine lungs reveals sex- and cell type-associated perturbations relevant to mucoinflammatory lung diseases.}, volume={1}, url={http://europepmc.org/abstract/med/33026818}, DOI={10.1152/ajplung.00381.2020}, abstractNote={ Ozone is known to cause lung injury, and resident cells of the respiratory tract (i.e., epithelial cells and macrophages) respond to inhaled ozone in a variety of ways that affect their survival, morphology, and functioning. However, a complete understanding of the sex-associated and the cell type-specific gene expression changes in response to ozone exposure is still limited. Through transcriptome profiling, we aimed to analyze gene expression alterations and associated enrichment of biological pathways in three distinct cell type-enriched compartments of ozone-exposed murine lungs. We subchronically exposed adult male and female mice to 0.8 ppm ozone or filtered air. RNA-Seq was performed on airway epithelium-enriched airways, parenchyma, and purified airspace macrophages. Differential gene expression and biological pathway analyses were performed and supported by cellular and immunohistochemical analyses. While a majority of differentially expressed genes (DEGs) in ozone-exposed versus air-exposed groups were common between both sexes, sex-specific DEGs were also identified in all of the three tissue compartments. As compared with ozone-exposed males, ozone-exposed females had significant alterations in gene expression in three compartments. Pathways relevant to cell division and DNA repair were enriched in the ozone-exposed airways, indicating ozone-induced airway injury and repair, which was further supported by immunohistochemical analyses. In addition to cell division and DNA repair pathways, inflammatory pathways were also enriched within the parenchyma, supporting contribution by both epithelial and immune cells. Further, immune response and cytokine-cytokine receptor interactions were enriched in macrophages, indicating ozone-induced macrophage activation. Finally, our analyses also revealed the overall upregulation of mucoinflammation- and mucous cell metaplasia-associated pathways following ozone exposure. }, journal={American journal of physiology. Lung cellular and molecular physiology}, author={Choudhary, I and Vo, T and Paudel, K and Patial, S and Saini, Y}, year={2020}, month={Oct} }
 @article{patial_saini_2020, title={Lung macrophages: current understanding of their roles in Ozone-induced lung diseases.}, volume={4}, url={http://europepmc.org/abstract/med/32458707}, DOI={10.1080/10408444.2020.1762537}, abstractNote={Abstract Through the National Ambient Air Quality Standards (NAAQS), the Clean Air Act of the United States outlines acceptable levels of six different air pollutants considered harmful to humans and the environment. Included in this list is ozone (O3), a highly reactive oxidant gas, respiratory health hazard, and common environmental air pollutant at ground level. The respiratory health effects due to O3 exposure are often associated with molecular and cellular perturbations in the respiratory tract. Periodic review of NAAQS requires comprehensive scientific evaluation of the public health effects of these pollutants, which is formulated through integrated science assessment (ISA) of the most policy-relevant scientific literature. This review focuses on the protective and pathogenic effects of macrophages in the O3-exposed respiratory tract, with emphasis on mouse model-based toxicological studies. Critical findings from 39 studies containing the words O3, macrophage, mice, and lung within the full text were assessed. While some of these studies highlight the presence of disease-relevant pathogenic macrophages in the airspaces, others emphasize a protective role for macrophages in O3-induced lung diseases. Moreover, a comprehensive list of currently known macrophage-specific roles in O3-induced lung diseases is included in this review and the significant knowledge gaps that still exist in the field are outlined. In conclusion, there is a vital need in this field for additional policy-relevant scientific information, including mechanistic studies to further define the role of macrophages in response to O3.}, journal={Critical reviews in toxicology}, author={Patial, S and Saini, Y}, year={2020}, month={Apr} }
 @article{vo_paudel_choudhary_patial_saini_2020, title={Ozone exposure upregulates the expression of host susceptibility protein TMPRSS2 to SARS-CoV-2}, url={http://europepmc.org/abstract/PPR/PPR237017}, DOI={10.1101/2020.11.10.377408}, abstractNote={Abstract}, author={Vo, T and Paudel, K and Choudhary, I and Patial, S and Saini, Y}, year={2020}, month={Nov} }
 @article{lewis_choudhary_paudel_mao_sharma_wang_deshane_boucher_patial_saini_2020, title={The Innate Lymphoid System Is a Critical Player in the Manifestation of Mucoinflammatory Airway Disease in Mice.}, volume={9}, url={http://europepmc.org/abstract/med/32817334}, DOI={10.4049/jimmunol.2000530}, abstractNote={Abstract}, journal={Journal of immunology (Baltimore, Md. : 1950)}, author={Lewis, BW and Choudhary, I and Paudel, K and Mao, Y and Sharma, R and Wang, Y and Deshane, JS and Boucher, RC and Patial, S and Saini, Y}, year={2020}, month={Aug} }
 @article{saini_chen_patial_2020, title={The Tristetraprolin Family of RNA-Binding Proteins in Cancer: Progress and Future Prospects. }, volume={6}, url={http://europepmc.org/abstract/med/32545247}, DOI={10.3390/cancers12061539}, abstractNote={Post-transcriptional regulation of gene expression plays a key role in cellular proliferation, differentiation, migration, and apoptosis. Increasing evidence suggests dysregulated post-transcriptional gene expression as an important mechanism in the pathogenesis of cancer. The tristetraprolin family of RNA-binding proteins (RBPs), which include Zinc Finger Protein 36 (ZFP36; commonly referred to as tristetraprolin (TTP)), Zinc Finger Protein 36 like 1 (ZFP36L1), and Zinc Finger Protein 36 like 2 (ZFP36L2), play key roles in the post-transcriptional regulation of gene expression. Mechanistically, these proteins function by binding to the AU-rich elements within the 3′-untranslated regions of their target mRNAs and, in turn, increasing mRNA turnover. The TTP family RBPs are emerging as key regulators of multiple biological processes relevant to cancer and are aberrantly expressed in numerous human cancers. The TTP family RBPs have tumor-suppressive properties and are also associated with cancer prognosis, metastasis, and resistance to chemotherapy. Herein, we summarize the various hallmark molecular traits of cancers that are reported to be regulated by the TTP family RBPs. We emphasize the role of the TTP family RBPs in the regulation of trait-associated mRNA targets in relevant cancer types/cell lines. Finally, we highlight the potential of the TTP family RBPs as prognostic indicators and discuss the possibility of targeting these TTP family RBPs for therapeutic benefits.}, journal={Cancers}, author={Saini, Y and Chen, J and Patial, S}, year={2020}, month={Jun} }
 @article{choudhary_vo_bathula_lamichhane_lewis_looper_jeyaseelan_blackshear_saini_patial_2020, title={Tristetraprolin Overexpression in Non-hematopoietic Cells Protects Against Acute Lung Injury in Mice.}, url={http://europepmc.org/abstract/med/32983182}, DOI={10.3389/fimmu.2020.02164}, abstractNote={Tristetraprolin (TTP) is a mRNA binding protein that binds to adenylate-uridylate-rich elements within the 3′ untranslated regions of certain transcripts, such as tumor necrosis factor (Tnf) mRNA, and increases their rate of decay. Modulation of TTP expression is implicated in inflammation; however, its role in acute lung inflammation remains unknown. Accordingly, we tested the role of TTP in lipopolysaccharide (LPS)-induced acute lung injury (ALI) in mice. LPS-challenged TTP-knockout (TTPKO) mice, as well as myeloid cell-specific TTP-deficient (TTPmyeKO) mice, exhibited significant increases in lung injury, although these responses were more robust in the TTPKO. Mice with systemic overexpression of TTP (TTPΔARE) were protected from ALI, as indicated by significantly reduced neutrophilic infiltration, reduced levels of neutrophil chemoattractants, and histological parameters of ALI. Interestingly, while irradiated wild-type (WT) mice reconstituted with TTPKO hematopoietic progenitor cells (HPCs) showed exaggerated ALI, their reconstitution with the TTPΔARE HPCs mitigated ALI. The reconstitution of irradiated TTPΔARE mice with HPCs from either WT or TTPΔARE donors conferred significant protection against ALI. In contrast, irradiated TTPΔARE mice reconstituted with TTPKO HPCs had exaggerated ALI, but the response was milder as compared to WT recipients that received TTPKO HPCs. Finally, the reconstitution of irradiated TTPKO recipient mice with TTPΔARE HPCs did not confer any protection to the TTPKO mice. These data together suggest that non-HPCs-specific overexpression of TTP within the lungs protects against ALI via downregulation of neutrophil chemoattractants and reduction in neutrophilic infiltration.}, journal={Frontiers in immunology}, author={Choudhary, I and Vo, T and Bathula, CS and Lamichhane, R and Lewis, BW and Looper, J and Jeyaseelan, S and Blackshear, PJ and Saini, Y and Patial, S}, year={2020}, month={Sep} }
 @article{choudhary_vo_paudel_gupta_kesimer_patial_saini_2020, title={Vesicular and Extravesicular Protein Signatures From the Airspaces of Ozone-Exposed Mice Reflect Muco-Inflammatory Disturbances.}, url={http://europepmc.org/abstract/PPR/PPR258963}, DOI={10.21203/rs.3.rs-132766/v1}, abstractNote={Abstract}, author={Choudhary, I and Vo, T and Paudel, K and Gupta, R and Kesimer, M and Patial, S and Saini, Y}, year={2020}, month={Dec} }
 @article{lewis_patial_saini_2019, title={Immunopathology of Airway Surface Liquid Dehydration Disease.}, url={http://europepmc.org/abstract/med/31396541}, DOI={10.1155/2019/2180409}, abstractNote={The primary purpose of pulmonary ventilation is to supply oxygen (O2) for sustained aerobic respiration in multicellular organisms. However, a plethora of abiotic insults and airborne pathogens present in the environment are occasionally introduced into the airspaces during inhalation, which could be detrimental to the structural integrity and functioning of the respiratory system. Multiple layers of host defense act in concert to eliminate unwanted constituents from the airspaces. In particular, the mucociliary escalator provides an effective mechanism for the continuous removal of inhaled insults including pathogens. Defects in the functioning of the mucociliary escalator compromise the mucociliary clearance (MCC) of inhaled pathogens, which favors microbial lung infection. Defective MCC is often associated with airway mucoobstruction, increased occurrence of respiratory infections, and progressive decrease in lung function in mucoobstructive lung diseases including cystic fibrosis (CF). In this disease, a mutation in thecystic fibrosis transmembrane conductance regulator(CFTR) gene results in dehydration of the airway surface liquid (ASL) layer. Several mice models ofCftrmutation have been developed; however, none of these models recapitulate human CF-like mucoobstructive lung disease. As an alternative, theScnn1btransgenic (Scnn1b-Tg+) mouse model overexpressing a transgene encodingsodium channel nonvoltage-gated 1,beta subunit(Scnn1b) in airway club cells is available. TheScnn1b-Tg+ mouse model exhibits airway surface liquid (ASL) dehydration, impaired MCC, increased mucus production, and early spontaneous pulmonary bacterial infections. High morbidity and mortality among mucoobstructive disease patients, high economic and health burden, and lack of scientific understanding of the progression of mucoobstruction warrants in-depth investigation of the cause of mucoobstruction in mucoobstructive disease models. In this review, we will summarize published literature on theScnn1b-Tg+ mouse and analyze various unanswered questions on the initiation and progression of mucobstruction and bacterial infections.}, journal={Journal of immunology research}, author={Lewis, BW and Patial, S and Saini, Y}, year={2019}, month={Jul} }
 @article{saini_lewis_yu_dang_livraghi-butrico_del_o'neal_boucher_2018, title={Effect of LysM+ macrophage depletion on lung pathology in mice with chronic bronchitis.}, volume={4}, url={http://europepmc.org/abstract/med/29667749}, DOI={10.14814/phy2.13677}, abstractNote={Macrophages (MΦ) are key sentinels of respiratory exposure to inhaled environmental stimuli. In normal “healthy” tissues, MΦ are believed to be a dormant cell type that, upon exposure to stress‐causing stimuli, may get activated to exhibit pro‐ or anti‐inflammatory roles. To test whether stress present in chronic bronchitic (CB) airways triggers MΦ to manifest protective or detrimental responses, the DTA+ (LysM‐regulated Diphtheria Toxin A expressing) strain with partial MΦ‐deficiency was crossed with the Scnn1b‐Tg mouse model of CB and the progenies were studied at 4–5 weeks of age. Compared with DTA− littermates, the DTA+ mice had ~50% reduction in bronchoalveolar lavage (BAL) MΦ, and the recovered MΦ were immature, phenotypically distinct, and functionally defective. DTA+/Scnn1b‐Tg mice exhibited a similar depletion of LysM+ MΦ offset by a significant increase in LysM‐ MΦ in the BAL. In DTA+/Scnn1b‐Tg mice, lung disease was more severe than in DTA−/Scnn1b‐Tg littermates, as indicated by an increased incidence of mucus plugging, mucous cells, airway inflammation, higher levels of cytokines/chemokines (KC, TNF‐α, MIP‐2, M‐CSF, IL‐5, and IL‐17), and worsened alveolar airspace enlargement. DTA+/Scnn1b‐Tg mice exhibited increased occurrence of lymphoid nodules, which was concomitant with elevated levels of immunoglobulins in BAL. Collectively, these data indicate that numerical deficiency of MΦ in stressed airspaces is responded via compensatory increase in the recruitment of immature MΦ and altered non‐MΦ effector cell‐centered responses, for example, mucus production and adaptive immune defense. Overall, these data identify dynamic roles of MΦ in moderating, rather than exacerbating, the severity of lung disease in a model of CB.}, journal={Physiological reports}, author={Saini, Y and Lewis, BW and Yu, D and Dang, H and Livraghi-Butrico, A and Del, Piero F and O'Neal, WK and Boucher, RC}, year={2018}, month={Apr} }
 @article{lewis_sultana_sharma_noël_langohr_patial_penn_saini_2017, title={Early Postnatal Secondhand Smoke Exposure Disrupts Bacterial Clearance and Abolishes Immune Responses in Muco-Obstructive Lung Disease.}, volume={8}, url={http://europepmc.org/abstract/med/28667160}, DOI={10.4049/jimmunol.1700144}, abstractNote={Abstract}, journal={Journal of immunology (Baltimore, Md. : 1950)}, author={Lewis, BW and Sultana, R and Sharma, R and Noël, A and Langohr, I and Patial, S and Penn, AL and Saini, Y}, year={2017}, month={Jun} }
 @article{yu_saini_chen_ghio_dang_burns_wang_davis_randell_esther_et al._2017, title={Loss of β Epithelial Sodium Channel Function in Meibomian Glands Produces Pseudohypoaldosteronism 1-Like Ocular Disease in Mice.}, volume={1}, url={http://europepmc.org/abstract/med/29107074}, DOI={10.1016/j.ajpath.2017.09.016}, abstractNote={Human subjects with pseudohypoaldosteronism-1 because of loss-of-function mutations in epithelial sodium channel (ENaC) subunits exhibit meibomian gland (MG) dysfunction. A conditional βENaC MG knockout (KO) mouse model was generated to elucidate the pathogenesis of absent ENaC function in the MG and associated ocular surface disease. βENaC MG KO mice exhibited a striking age-dependent, female-predominant MG dysfunction phenotype, with white toothpaste-like secretions observed obstructing MG orifices at 7 weeks of age. There were compensatory increases in tear production but higher tear sodium and indexes of mucin concentration in βENaC MG KO mice. Histologically, MG acinar atrophy was observed with ductal enlargement and ductal epithelial hyperstratification. Inflammatory cell infiltration was observed in both MG and conjunctiva of βENaC MG KO mice. In older βENaC MG KO mice (5 to 11 months), significant ocular surface pathologies were noted, including corneal opacification, ulceration, neovascularization, and ectasia. Inflammation in MG and conjunctiva was confirmed by increased cytokine gene and protein expression and positive Ly-6B.2 immunostaining. Cell proliferation assays revealed lower proliferation rates of MG cells derived from βENaC MG KO than control mice, suggesting that βENaC plays a role in cell renewal of mouse MG. Loss of βENaC function resulted in MG disease and severe ocular surface damage that phenocopied aspects of human pseudohypoaldosteronism-1 MG disease and was sex dependent.}, journal={The American journal of pathology}, author={Yu, D and Saini, Y and Chen, G and Ghio, AJ and Dang, H and Burns, KA and Wang, Y and Davis, RM and Randell, SH and Esther, CR and et al.}, year={2017}, month={Oct} }
 @article{saini_wilkinson_terrell_burns_livraghi-butrico_doerschuk_o'neal_boucher_2016, title={Neonatal Pulmonary Macrophage Depletion Coupled to Defective Mucus Clearance Increases Susceptibility to Pneumonia and Alters Pulmonary Immune Responses.}, volume={2}, url={http://europepmc.org/abstract/med/26121027}, DOI={10.1165/rcmb.2014-0111oc}, abstractNote={Resident immune cells (e.g., macrophages [MΦs]) and airway mucus clearance both contribute to a healthy lung environment. To investigate interactions between pulmonary MΦ function and defective mucus clearance, a genetic model of lysozyme M (LysM) promoter-mediated MΦ depletion was generated, characterized, and crossed with the sodium channel β subunit transgenic (Scnn1b-Tg) mouse model of defective mucus clearance. Diphtheria toxin A-mediated depletion of LysM(+) pulmonary MΦs in wild-type mice with normal mucus clearance resulted in lethal pneumonia in 24% of neonates. The pneumonias were dominated by Pasteurella pneumotropica and accompanied by emaciation, neutrophilic inflammation, and elevated Th1 cytokines. The incidence of emaciation and pneumonia reached 51% when LysM(+) MΦ depletion was superimposed on the airway mucus clearance defect of Scnn1b-Tg mice. In LysM(+) MΦ-depleted Scnn1b-Tg mice, pneumonias were associated with a broader spectrum of bacterial species and a significant reduction in airway mucus plugging. Bacterial burden (CFUs) was comparable between Scnn1b-Tg and nonpneumonic LysM(+) MΦ-depleted Scnn1b-Tg mice. However, the nonpneumonic LysM(+) MΦ-depleted Scnn1b-Tg mice exhibited increased airway inflammation, the presence of neutrophilic infiltration, and increased levels of inflammatory cytokines in bronchoalveolar lavage fluid compared with Scnn1b-Tg mice. Collectively, these data identify key MΦ-mucus clearance interactions with respect to both infectious and inflammatory components of muco-obstructive lung disease.}, journal={American journal of respiratory cell and molecular biology}, author={Saini, Y and Wilkinson, KJ and Terrell, KA and Burns, KA and Livraghi-Butrico, A and Doerschuk, CM and O'Neal, WK and Boucher, RC}, year={2016}, month={Feb} }
 @article{nair_ebenezer_saini_francis_2015, title={Angiotensin II-induced hypertensive renal inflammation is mediated through HMGB1-TLR4 signaling in rat tubulo-epithelial cells.}, volume={7}, url={http://europepmc.org/abstract/med/26033363}, DOI={10.1016/j.yexcr.2015.05.011}, abstractNote={Angiotensin II is a vaso-constrictive peptide that regulates blood pressure homeostasis. Even though the inflammatory effects of AngII in renal pathophysiology have been studied, there still exists a paucity of data with regard to the mechanism of action of AngII-mediated kidney injury. The objective of this study was to elucidate the mechanistic role of HMGB1-TLR4 signaling in AngII-induced inflammation in the kidney.Rat tubular epithelial cells (NRK52E) were treated with AngII over a preset time-course. In another set of experiments, HMGB1 was neutralized and TLR4 was knocked down using small interfering RNA targeting TLR4. Cell extracts were subjected to RT-PCR, immunoblotting, flow cytometry, and ELISA.AngII-induced inflammation in NRK52E cells increased gene and protein expression of TLR4, HMGB1 and key proinflammatory cytokines (TNFα and IL1β). Pretreatment with Losartan (an AT1 receptor blocker) attenuated the AngII-induced expression of TLR4 and inflammatory cytokines. TLR4 silencing was used to elucidate the specific role played by TLR4 in AngII-induced inflammation. TLR4siRNA treatment in these cells significantly decreased the AngII-induced inflammatory effect. Consistent observations were made when the Ang II treated cells were pretreated with anti-HMGB1. Downstream activation of NFκB and rate of generation of ROS was also decreased on gene silencing of TLR4 and exposure to anti-HMGB1.These results indicate a key role for HMGB1-TLR4 signaling in AngII-mediated inflammation in the renal epithelial cells. Our data also reveal that AngII-induced effects could be alleviated by HMGB1-TLR4 inhibition, suggesting this pathway as a potential therapeutic target for hypertensive renal dysfunctions.}, journal={Experimental cell research}, author={Nair, AR and Ebenezer, PJ and Saini, Y and Francis, J}, year={2015}, month={May} }
 @article{hwang_lynn_vengellur_saini_grier_ferguson-miller_lapres_2015, title={Hypoxia Inducible Factors Modulate Mitochondrial Oxygen Consumption and Transcriptional Regulation of Nuclear-Encoded Electron Transport Chain Genes.}, volume={6}, url={http://europepmc.org/abstract/med/26030260}, DOI={10.1021/bi5012892}, abstractNote={Hypoxia inducible factor-1 (HIF1) is a stress-responsive nuclear transcription factor that is activated with a decrease in oxygen availability. HIF1 regulates the expression of genes involved in a cell's adaptation to hypoxic stress, including those with mitochondrial specific function. To gain a more comprehensive understanding of the role of HIF1 in mitochondrial homeostasis, we studied the link between hypoxia, HIF1 transactivation, and electron transport chain (ETC) function. We established immortalized mouse embryonic fibroblasts (MEFs) for HIF1α wild-type (WT) and null cells and tested whether HIF1α regulates mitochondrial respiration by modulating gene expressions of nuclear-encoded ETC components. High-throughput quantitative real-time polymerase chain reaction was performed to screen nuclear-encoded mitochondrial genes related to the ETC to identify those whose regulation was HIF1α-dependent. Our data suggest that HIF1α regulates transcription of cytochrome c oxidase (CcO) heart/muscle isoform 7a1 (Cox7a1) under hypoxia, where it is induced 1.5-2.5-fold, whereas Cox4i2 hypoxic induction was HIF1α-independent. We propose that adaptation to hypoxic stress of CcO as the main cellular oxygen consumer is mediated by induction of hypoxia-sensitive tissue-specific isoforms. We suggest that HIF1 plays a central role in maintaining homeostasis in cellular respiration during hypoxic stress via regulation of CcO activity.}, journal={Biochemistry}, author={Hwang, HJ and Lynn, SG and Vengellur, A and Saini, Y and Grier, EA and Ferguson-Miller, SM and LaPres, JJ}, year={2015}, month={Jun} }
 @article{saini_proper_dornbos_greenwood_kopec_lynn_grier_burgoon_zacharewski_thomas_et al._2015, title={Loss of Hif-2α Rescues the Hif-1α Deletion Phenotype of Neonatal Respiratory Distress In Mice.}, url={http://europepmc.org/abstract/med/26422241}, DOI={10.1371/journal.pone.0139270}, abstractNote={Hypoxia is a state of decreased oxygen reaching the tissues of the body. During prenatal development, the fetus experiences localized occurrences of hypoxia that are essential for proper organogenesis and survival. The response to decreased oxygen availability is primarily regulated by hypoxia-inducible factors (HIFs), a family of transcription factors that modulate the expression of key genes involved in glycolysis, angiogenesis, and erythropoiesis. HIF-1α and HIF-2α, two key isoforms, are important in embryonic development, and likely are involved in lung morphogenesis. We have recently shown that the inducible loss of Hif-1α in lung epithelium starting at E4.5 leads to death within an hour of parturition, with symptoms similar to neonatal respiratory distress syndrome (RDS). In addition to Hif-1α, Hif-2α is also expressed in the developing lung, although the overlapping roles of Hif-1α and Hif-2α in this context are not fully understood. To further investigate the independent role of Hif-2α in lung epithelium and its ability to alter Hif-1α-mediated lung maturation, we generated two additional lung-specific inducible Hif-α knockout models (Hif-2α and Hif-1α+Hif-2α). The intrauterine loss of Hif-2α in the lungs does not lead to decreased viability or observable phenotypic changes in the lung. More interestingly, survivability observed after the loss of both Hif-1α and Hif-2α suggests that the loss of Hif-2α is capable of rescuing the neonatal RDS phenotype seen in Hif-1α-deficient pups. Microarray analyses of lung tissue from these three genotypes identified several factors, such as Scd1, Retlnγ, and Il-1r2, which are differentially regulated by the two HIF-α isoforms. Moreover, network analysis suggests that modulation of hormone-mediated, NF-κB, C/EBPα, and c-MYC signaling are central to HIF-mediated changes in lung development.}, journal={PloS one}, author={Saini, Y and Proper, SP and Dornbos, P and Greenwood, KK and Kopec, AK and Lynn, SG and Grier, E and Burgoon, LD and Zacharewski, TR and Thomas, RS and et al.}, year={2015}, month={Sep} }
 @article{saini_dang_livraghi-butrico_kelly_jones_o'neal_boucher_2014, title={Gene expression in whole lung and pulmonary macrophages reflects the dynamic pathology associated with airway surface dehydration.}, volume={9}, url={http://europepmc.org/abstract/med/25204199}, DOI={10.1186/1471-2164-15-726}, abstractNote={Defects in airway mucosal defense, including decreased mucus clearance, contribute to the pathogenesis of human chronic obstructive pulmonary diseases. Scnn1b-Tg mice, which exhibit chronic airway surface dehydration from birth, can be used as a model to study the pathogenesis of muco-obstructive lung disease across developmental stages. To identify molecular signatures associated with obstructive lung disease in this model, gene expression analyses were performed on whole lung and purified lung macrophages collected from Scnn1b-Tg and wild-type (WT) littermates at four pathologically relevant time points. Macrophage gene expression at 6 weeks was evaluated in mice from a germ-free environment to understand the contribution of microbes to disease development.Development- and disease-specific shifts in gene expression related to Scnn1b over-expression were revealed in longitudinal analyses. While the total number of transgene-related differentially expressed genes producing robust signals was relatively small in whole lung (n = 84), Gene Set Enrichment Analysis (GSEA) revealed significantly perturbed biological pathways and interactions between normal lung development and disease initiation/progression. Purified lung macrophages from Scnn1b-Tg mice exhibited numerous robust and dynamic gene expression changes. The expression levels of Classically-activated (M1) macrophage signatures were significantly altered at post-natal day (PND) 3 when Scnn1b-Tg mice lung exhibit spontaneous bacterial infections, while alternatively-activated (M2) macrophage signatures were more prominent by PND 42, producing a mixed M1-M2 activation profile. While differentially-regulated, inflammation-related genes were consistently identified in both tissues in Scnn1b-Tg mice, there was little overlap between tissues or across time, highlighting time- and tissue-specific responses. Macrophages purified from adult germ-free Scnn1b-Tg mice exhibited signatures remarkably similar to non-germ-free counterparts, indicating that the late-phase macrophage activation profile was not microbe-dependent.Whole lung and pulmonary macrophages respond independently and dynamically to local stresses associated with airway mucus stasis. Disease-specific responses interact with normal developmental processes, influencing the final state of disease in this model. The robust signatures observed in Scnn1b-Tg lung macrophages highlight their critical role in disease pathogenesis. These studies emphasize the importance of region-, cell-type-, and time-dependent analyses to fully dissect the natural history of disease and the consequences of disease on normal lung development.}, journal={BMC genomics}, author={Saini, Y and Dang, H and Livraghi-Butrico, A and Kelly, EJ and Jones, LC and O'Neal, WK and Boucher, RC}, year={2014}, month={Sep} }
 @article{proper_saini_greenwood_bramble_downing_lapres_2013, title={Loss of hypoxia-inducible factor 2 alpha in the lung alveolar epithelium of mice leads to enhanced eosinophilic inflammation in cobalt-induced lung injury.}, volume={2}, url={http://europepmc.org/abstract/med/24218148}, DOI={10.1093/toxsci/kft253}, abstractNote={Hard metal lung disease (HMLD) is an occupational lung disease specific to inhalation of cobalt-containing particles whose mechanism is largely unknown. Cobalt is a known hypoxia mimic and stabilizer of the alpha subunits of hypoxia-inducible factors (HIFs). Previous work revealed that though HIF1α contrib utes to cobalt toxicity in vitro, loss of HIF1α in the alveolar epithelial cells does not provide in vivo protection from cobalt-induced lung inflammation. HIF1α and HIF2α show unique tissue expression profiles, and HIF2α is known to be the predominant HIF mRNA isoform in the adult lung. Thus, if HIF2α activation by cobalt contributes to pathophysiology of HMLD, we hypothesized that loss of HIF2α in lung epithelium would provide protection from cobalt-induced inflammation. Mice with HIF2α-deficiency in Club and alveolar type II epithelial cells (ATIIs) (HIF2α(Δ/Δ)) were exposed to cobalt (60 µg/day) or saline using a subacute occupational exposure model. Bronchoalveolar lavage cellularity, cytokines, qRT-PCR, and histopathology were analyzed. Results show that loss of HIF2α leads to enhanced eosinophilic inflammation and increased goblet cell metaplasia. Additionally, control mice demonstrated a mild recovery from cobalt-induced lung injury compared with HIF2α(Δ/Δ) mice, suggesting a role for epithelial HIF2α in repair mechanisms. The expression of important cytokines, such as interleukin (IL)-5 and IL-10, displayed significant differences following cobalt exposure when HIF2α(Δ/Δ) and control mice were compared. In summary, our data suggest that although loss of HIF2α does not afford protection from cobalt-induced lung inflammation, epithelial HIF2α signaling does play an important role in modulating the inflammatory and repair response in the lung.}, journal={Toxicological sciences : an official journal of the Society of Toxicology}, author={Proper, SP and Saini, Y and Greenwood, KK and Bramble, LA and Downing, NJ and Lapres, JJ}, year={2013}, month={Nov} }
 @article{patial_shahi_saini_lee_packiriswamy_appledorn_lapres_amalfitano_parameswaran_2011, title={G-protein coupled receptor kinase 5 mediates lipopolysaccharide-induced NFκB activation in primary macrophages and modulates inflammation in vivo in mice.}, volume={5}, url={http://europepmc.org/abstract/med/20945396}, DOI={10.1002/jcp.22460}, abstractNote={Abstract}, journal={Journal of cellular physiology}, author={Patial, S and Shahi, S and Saini, Y and Lee, T and Packiriswamy, N and Appledorn, DM and Lapres, JJ and Amalfitano, A and Parameswaran, N}, year={2011}, month={May} }
 @article{patial_saini_parvataneni_appledorn_dorn_lapres_amalfitano_senagore_parameswaran_2011, title={Myeloid-specific GPCR kinase-2 negatively regulates NF-κB1p105-ERK pathway and limits endotoxemic shock in mice.}, volume={3}, url={http://europepmc.org/abstract/med/20717897}, DOI={10.1002/jcp.22384}, abstractNote={Abstract}, journal={Journal of cellular physiology}, author={Patial, S and Saini, Y and Parvataneni, S and Appledorn, DM and Dorn, GW and Lapres, JJ and Amalfitano, A and Senagore, P and Parameswaran, N}, year={2011}, month={Mar} }
 @article{greenwood_proper_saini_bramble_jackson-humbles_wagner_lapres_2011, title={Neonatal epithelial hypoxia inducible factor-1α expression regulates the response of the lung to experimental asthma.}, volume={3}, url={http://europepmc.org/abstract/med/22180657}, DOI={10.1152/ajplung.00193.2011}, abstractNote={ Allergic airway disease is characterized by a T helper type 2 cell-mediated airway inflammation and airway hyperresponsiveness. Little is known about the role of hypoxia-mediated signaling in the progression of the disease. To address this knowledge gap, a mouse model was created in which doxycycline exposure induces the functional deletion of hypoxia inducible factor-1α from alveolar type II and Clara cells of the lung. When hypoxia inducible factor-1α deletion was induced during the early postnatal development period of the lung, the mice displayed an enhanced response to the ovalbumin model of allergic airway disease. These hypoxia inducible factor-1α-deficient mice exhibit increased cellular infiltrates, eosinophilia in the lavage fluid and parenchyma, and T helper type 2 cytokines, as compared with ovalbumin-treated control mice. Moreover, these hypoxia inducible factor-1α-deficient mice display increased airway resistance when compared with their control counterparts. Interestingly, if the loss of hypoxia inducible factor-1α was induced in early adulthood, the exacerbated phenotype was not observed. Taken together, these results suggest that epithelial hypoxia inducible factor-1α plays an important role in establishing the innate immunity of the lung and epithelial-specific deficiency in the transcription factor, during early postnatal development, increases the severity of inflammation and functional airway resistance, following ovalbumin challenge. Finally, these results might explain some of the chronic respiratory pathology observed in premature infants, especially those that receive supplemental oxygen. This early hyperoxic exposure, from normal ambient and supplemental oxygen, would presumably inhibit normal hypoxia inducible factor-1α signaling, mimicking the functional deletion described. }, journal={American journal of physiology. Lung cellular and molecular physiology}, author={Greenwood, KK and Proper, SP and Saini, Y and Bramble, LA and Jackson-Humbles, DN and Wagner, JG and LaPres, JJ}, year={2011}, month={Dec} }
 @article{sparkenbaugh_saini_greenwood_lapres_luyendyk_copple_maddox_ganey_roth_2011, title={The role of hypoxia-inducible factor-1α in acetaminophen hepatotoxicity.}, volume={8}, url={http://europepmc.org/abstract/med/21576378}, DOI={10.1124/jpet.111.180521}, abstractNote={Hypoxia-inducible factor-1α (HIF-1α) is a critical transcription factor that controls oxygen homeostasis in response to hypoxia, inflammation, and oxidative stress. HIF has been implicated in the pathogenesis of liver injury in which these events play a role, including acetaminophen (APAP) overdose, which is the leading cause of acute liver failure in the United States. APAP overdose has been reported to activate HIF-1α in mouse livers and isolated hepatocytes downstream of oxidative stress. HIF-1α signaling controls many factors that contribute to APAP hepatotoxicity, including mitochondrial cell death, inflammation, and hemostasis. Therefore, we tested the hypothesis that HIF-1α contributes to APAP hepatotoxicity. Conditional HIF-1α deletion was generated in mice using an inducible Cre-lox system. Control (HIF-1α-sufficient) mice developed severe liver injury 6 and 24 h after APAP overdose (400 mg/kg). HIF-1α-deficient mice were protected from APAP hepatotoxicity at 6 h, but developed severe liver injury by 24 h, suggesting that HIF-1α is involved in the early stage of APAP toxicity. In further studies, HIF-1α-deficient mice had attenuated thrombin generation and reduced plasminogen activator inhibitor-1 production compared with control mice, indicating that HIF-1α signaling contributes to hemostasis in APAP hepatotoxicity. Finally, HIF-1α-deficient animals had decreased hepatic neutrophil accumulation and plasma concentrations of interleukin-6, keratinocyte chemoattractant, and regulated upon activation normal T cell expressed and secreted compared with control mice, suggesting an altered inflammatory response. HIF-1α contributes to hemostasis, sterile inflammation, and early hepatocellular necrosis during the pathogenesis of APAP toxicity.}, journal={The Journal of pharmacology and experimental therapeutics}, author={Sparkenbaugh, EM and Saini, Y and Greenwood, KK and LaPres, JJ and Luyendyk, JP and Copple, BL and Maddox, JF and Ganey, PE and Roth, RA}, year={2011}, month={May} }
 @article{saini_greenwood_merrill_kim_patial_parameswaran_lapres_2010, title={Acute cobalt-induced lung injury and the role of hypoxia-inducible factor 1alpha in modulating inflammation.}, volume={8}, url={http://europepmc.org/abstract/med/20511350}, DOI={10.1093/toxsci/kfq155}, abstractNote={Air pollution is a critical factor in the development and exacerbation of pulmonary diseases. Ozone, automobile exhaust, cigarette smoke, and metallic dust are among the potentially harmful pollution components that are linked to disease progression. Transition metals, such as cobalt, have been identified at significant levels in air pollution. Cobalt exerts numerous biological effects, including mimicking hypoxia. Similar to hypoxia, cobalt exposure results in the stabilization of hypoxia-inducible factors (HIFs), a family of proteins that regulate the cellular response to oxygen deficit. HIFs also play an important role in innate immunity and inflammatory processes. To characterize the role of HIF1alpha, the most ubiquitously expressed HIF, in the early events during cobalt-induced lung inflammation, an inducible lung-specific HIF1alpha deletion model was employed. Control mice showed classical signs of metal-induced injury following cobalt exposure, including neutrophilic infiltration and induction of Th1 cytokines. In contrast, HIF1alpha-deficient mice exhibited pronounced eosinophil counts in bronchoalveolar lavage fluid and lung tissue complemented with Th2 cytokine induction. The timing of these results suggests that the loss of epithelial-derived HIF1alpha alters the lung's innate immune response and biases the tissue toward a Th2-mediated inflammation.}, journal={Toxicological sciences : an official journal of the Society of Toxicology}, author={Saini, Y and Greenwood, KK and Merrill, C and Kim, KY and Patial, S and Parameswaran, N and LaPres, JJ}, year={2010}, month={May} }
 @article{saini_kim_lewandowski_bramble_lapres_2009, title={Role of hypoxia-inducible factor 1{alpha} in modulating cobalt-induced lung inflammation.}, volume={2}, url={http://europepmc.org/abstract/med/19915160}, DOI={10.1152/ajplung.00252.2009}, abstractNote={Hypoxia plays an important role in development, cellular homeostasis, and pathological conditions, such as cancer and stroke. There is also growing evidence that hypoxia is an important modulator of the inflammatory process. Hypoxia-inducible factors (HIFs) are a family of proteins that regulate the cellular response to oxygen deficit, and loss of HIFs impairs inflammatory cell function. There is little known, however, about the role of epithelial-derived HIF signaling in modulating inflammation. Cobalt is capable of eliciting an allergic response and promoting HIF signaling. To characterize the inflammatory function of epithelial-derived HIF in response to inhaled cobalt, a conditional lung-specific HIF1α, the most ubiquitously expressed HIF, deletion mouse, was created. Control mice showed classic signs of metal-induced injury following cobalt exposure, including fibrosis and neutrophil infiltration. In contrast, HIF1α-deficient mice displayed a Th2 response that resembled asthma, including increased eosinophilic infiltration, mucus cell metaplasia, and chitinase-like protein expression. The results suggest that epithelial-derived HIF signaling has a critical role in establishing a tissue's inflammatory response, and compromised HIF1α signaling biases the tissue towards a Th2-mediated reaction.}, journal={American journal of physiology. Lung cellular and molecular physiology}, author={Saini, Y and Kim, KY and Lewandowski, R and Bramble, LA and Lapres, JJ}, year={2009}, month={Nov} }
 @article{saini_lapres_2008, title={HIF1alpha is essential for normal intrauterine differentiation of alveolar epithelium and surfactant production in the newborn lung of mice.}, volume={11}, url={http://europepmc.org/abstract/med/18801745}, DOI={10.1074/jbc.m805927200}, abstractNote={Neonatal respiratory distress syndrome (RDS) is mainly the result of perturbation in surfactant production and is a common complication seen in premature infants. Normal fetal lung development and alveolar cell differentiation is regulated by a network of transcription factors. Functional loss of any of these factors will alter the developmental program and impact surfactant production and normal gas exchange. During development, the fetus is exposed to varying oxygen concentrations and must be able to quickly adapt to these changes in order to survive. Hypoxia-inducible factor 1α (HIF1α) is the primary transcription factor that is responsible for regulating the cellular response to changes in oxygen tension and is essential for normal development. Its role in lung maturation is not well defined and to address this knowledge gap, a lung-specific HIF1α knock-out model has been developed. Loss of HIF1α early in lung development leads to pups that die within hours of parturition, exhibiting symptoms similar to RDS. Lungs from these pups display impaired alveolar epithelial differentiation and an almost complete loss of surfactant protein expression. Ultrastructural analysis of lungs from HIF1α deletion pups had high levels of glycogen, aberrant septal development, and decreased expression of several factors necessary for proper lung development, including HIF2α, β-catenin, and vascular endothelial growth factor. These results suggest that HIF1α is essential for proper lung maturation and alteration in its normal signaling during premature delivery might explain the pathophysiology of neonatal RDS.}, journal={The Journal of biological chemistry}, author={Saini, Y and LaPres, JJ}, year={2008}, month={Sep} }
 @article{patial_chaturvedi_rai_saini_chandra_saini_gupta_2007, title={Virus neutralizing antibody response in mice and dogs with a bicistronic DNA vaccine encoding rabies virus glycoprotein and canine parvovirus VP2.}, volume={5}, url={http://europepmc.org/abstract/med/17391817}, DOI={10.1016/j.vaccine.2007.02.051}, abstractNote={A bicistronic DNA vaccine against rabies and parvovirus infection of dogs was developed by subcloning rabies glycoprotein and canine parvovirus (CPV) VP2 genes into a bicistronic vector. After characterizing the expression of both the proteins in vitro, the bicistronic DNA vaccine was injected in mice and induced immune response was compared with monocistronic DNA vaccines. There was no significant difference in ELISA and virus neutralizing (VN) antibody responses against rabies and CPV in mice immunized with either bicistronic or monocistronic DNA vaccine. Further, there was significantly similar protection in mice immunized with either bicistronic or monocistronic rabies DNA vaccine on rabies virus challenge. Similarly, dogs immunized with monocistronic and bicistronic DNA vaccines developed comparable VN antibodies against rabies and CPV. This study indicated that bicistronic DNA vaccine can be used in dogs to induce virus neutralizing immune responses against both rabies and CPV.}, journal={Vaccine}, author={Patial, S and Chaturvedi, VK and Rai, A and Saini, M and Chandra, R and Saini, Y and Gupta, PK}, year={2007}, month={Mar} }