A Fast, Easy, and Customizable Eight-Color Flow Cytometric Method for Analysis of the Cellular Content of Bronchoalveolar Lavage Fluid in the Mouse.

The cell composition of bronchoalveolar lavage fluid (BAL) is an important indicator of airway inflammation. It is commonly determined by cytocentrifuging leukocytes on slides, then staining, identifying, and counting them as eosinophils, neutrophils, macrophages, or lymphocytes according to morphological criteria under light microscopy, where it is not always easy to distinguish macrophages from lymphocytes. We describe here a one-step, easy-to-use, and easy-to-customize 8-color flow cytometric method for performing differential cell count and comparing it to morphological counts on stained cytospins. This method identifies BAL cells by a simultaneous one-step immunolabeling procedure using antibodies to identify T cells, B cells, neutrophils, eosinophils, and macrophages. Morphological analysis of flow-sorted cell subsets is used to validate this protocol. An important advantage of this basic flow cytometry protocol is the ability to customize it by the addition of antibodies to study receptor expression at leukocyte cell surfaces and identify subclasses of inflammatory cells as needed. © 2017 by John Wiley & Sons, Inc.

Contribution of serotonin to cardiac remodeling associated with hypertensive diastolic ventricular dysfunction in rats.

OBJECTIVE: Left-ventricular hypertrophy and interstitial fibrosis are the main pathophysiological factors of heart failure with preserved ejection fraction. Blockade of the serotonin 5-HT2B receptor (5-HT2BR) has been shown to reduce cardiac hypertrophy, oxidative stress, and extracellular cell matrix activation. In this study, we evaluated the effects of the 5-HT2BR blockade, on hemodynamic and cardiac remodeling, in spontaneously hypertensive rats (SHRs) that display a diastolic dysfunction with preserved ejection fraction. METHOD: Thirty-seven-week-old SHRs were randomized in four groups receiving either saline, the selective 5-HT2BR antagonist RS-127445 (1 mg/kg per day), a calcium channel blocker nicardipine (6 mg/kg per day), or RS-127445 + nicardipine. During the 14 weeks of treatment period, cardiac function and blood pressure were monitored by echocardiography and tail-cuff. Finally, electrocardiograms and invasive hemodynamics were obtained before blood collection. Heart was analyzed for morphology and mRNA expression. A complementary study evaluated the cardiac and vascular effects of serotonin on wild-type and mice knockout for the 5-HT2BR (Htr2B) and/or the 5-HT2AR (Htr2A). RESULTS: Despite the left ventricular 5-HT2BR overexpression, 5-HT2BR blockade by RS-127445 did not affect left ventricular hypertrophy and fibrosis in SHRs. This antagonist did not improve diastolic dysfunction, neither alone nor in combination with nicardipine, although it induced plasma brain natriuretic peptide decrease. Moreover, RS-127445 amplified subendocardial fibrosis and favored left ventricular dilatation. Finally, a subendocardial left ventricular fibrosis was induced by chronic serotonin in wild-type mice, which was increased in Htr2B animals, but prevented in Htr2A and Htr2A/2B mice, and could be explained by a contribution of the endothelial 5-HT2BRs to coronary vasodilatation. CONCLUSION: This work is the first to identify a cardioprotective function of the 5-HT2BR in an integrated model of diastolic dysfunction with preserved ejection fraction.

Analysis of mammalian gene function through broad-based phenotypic screens across a consortium of mouse clinics.

The function of the majority of genes in the mouse and human genomes remains unknown. The mouse embryonic stem cell knockout resource provides a basis for the characterization of relationships between genes and phenotypes. The EUMODIC consortium developed and validated robust methodologies for the broad-based phenotyping of knockouts through a pipeline comprising 20 disease-oriented platforms. We developed new statistical methods for pipeline design and data analysis aimed at detecting reproducible phenotypes with high power. We acquired phenotype data from 449 mutant alleles, representing 320 unique genes, of which half had no previous functional annotation. We captured data from over 27,000 mice, finding that 83% of the mutant lines are phenodeviant, with 65% demonstrating pleiotropy. Surprisingly, we found significant differences in phenotype annotation according to zygosity. New phenotypes were uncovered for many genes with previously unknown function, providing a powerful basis for hypothesis generation and further investigation in diverse systems.

Old spontaneously hypertensive rats gather together typical features of human chronic left-ventricular dysfunction with preserved ejection fraction.

OBJECTIVE: Heart failure with preserved left-ventricular ejection fraction (HF-PEF) is an entity leading to pulmonary congestion because of impaired diastolic filling. This syndrome usually strikes those who have experienced a long history of hypertension or metabolic risk factors. Pathophysiological mechanisms are not fully understood, and standard therapy is not established. Relevant preclinical models are still lacking. The aim of this work was to evaluate aging spontaneously hypertensive rats (SHRs) as a model of HF-PEF. METHODS: Serial echocardiographic and blood pressure (BP) measurements were performed in 28, 36, 43, 47 and 51-week-old SHRs and their normotensive controls (Wistar-Kyoto rats). In 52-53-week-old animals, final investigations included ECG, invasive left-ventricular (LV) and aortic catheterization, brain natriuretic peptide (BNP) plasma concentrations, ventricular reverse transcription-qPCR evaluations (ß-myosin heavy chain, atrial natriuretic peptide, BNP, sarco/endoplasmic reticulum calcium ATPase 2a and collagens 1a, 3a and 2a) and cardiac histology. RESULTS: SHRs develop a progressive alteration of the early diastole, some of the echocardiographic parameters being not sensitive to BP reduction by the calcium blocker, nicardipine. The systolic function evaluated by echocardiography and invasive catheterization was preserved. When the observation period was over, an increase in collagen synthesis and deposits were identified in subendocardial layers. This attested a probable myocardial ischemia that was confirmed by ECG changes of the ST segment. BNP increased in the blood and at the mRNA level in the myocardium. CONCLUSION: When aging, SHRs progressively develop HF-PEF showed by impaired LV relaxation and hypertrophy, BNP increase but preserved contractility and fibrosis. This model seems pertinent for further pharmacological preclinical studies in the field.

On the encoding of proteins for disordered regions prediction.

Disordered regions, i.e., regions of proteins that do not adopt a stable three-dimensional structure, have been shown to play various and critical roles in many biological processes. Predicting and understanding their formation is therefore a key sub-problem of protein structure and function inference. A wide range of machine learning approaches have been developed to automatically predict disordered regions of proteins. One key factor of the success of these methods is the way in which protein information is encoded into features. Recently, we have proposed a systematic methodology to study the relevance of various feature encodings in the context of disulfide connectivity pattern prediction. In the present paper, we adapt this methodology to the problem of predicting disordered regions and assess it on proteins from the 10th CASP competition, as well as on a very large subset of proteins extracted from PDB. Our results, obtained with ensembles of extremely randomized trees, highlight a novel feature function encoding the proximity of residues according to their accessibility to the solvent, which is playing the second most important role in the prediction of disordered regions, just after evolutionary information. Furthermore, even though our approach treats each residue independently, our results are very competitive in terms of accuracy with respect to the state-of-the-art. A web-application is available at http://m24.giga.ulg.ac.be:81/x3Disorder.

On the relevance of sophisticated structural annotations for disulfide connectivity pattern prediction.

Disulfide bridges strongly constrain the native structure of many proteins and predicting their formation is therefore a key sub-problem of protein structure and function inference. Most recently proposed approaches for this prediction problem adopt the following pipeline: first they enrich the primary sequence with structural annotations, second they apply a binary classifier to each candidate pair of cysteines to predict disulfide bonding probabilities and finally, they use a maximum weight graph matching algorithm to derive the predicted disulfide connectivity pattern of a protein. In this paper, we adopt this three step pipeline and propose an extensive study of the relevance of various structural annotations and feature encodings. In particular, we consider five kinds of structural annotations, among which three are novel in the context of disulfide bridge prediction. So as to be usable by machine learning algorithms, these annotations must be encoded into features. For this purpose, we propose four different feature encodings based on local windows and on different kinds of histograms. The combination of structural annotations with these possible encodings leads to a large number of possible feature functions. In order to identify a minimal subset of relevant feature functions among those, we propose an efficient and interpretable feature function selection scheme, designed so as to avoid any form of overfitting. We apply this scheme on top of three supervised learning algorithms: k-nearest neighbors, support vector machines and extremely randomized trees. Our results indicate that the use of only the PSSM (position-specific scoring matrix) together with the CSP (cysteine separation profile) are sufficient to construct a high performance disulfide pattern predictor and that extremely randomized trees reach a disulfide pattern prediction accuracy of [Formula: see text] on the benchmark dataset SPX[Formula: see text], which corresponds to [Formula: see text] improvement over the state of the art. A web-application is available at http://m24.giga.ulg.ac.be:81/x3CysBridges.

The peroxisome proliferator-activated receptor α agonist fenofibrate decreases airway reactivity to methacholine and increases endothelial nitric oxide synthase phosphorylation in mouse lung.

In the present study, we have investigated the effect of the peroxisome proliferator-activated receptor α (PPARα) agonist fenofibrate on airway reactivity and the role of the endothelial nitric oxide synthase (eNOS)/NO pathway in this effect. Airway reactivity to methacholine was assessed in C57BL/6 mice treated or not with fenofibrate by whole-body plethysmography. In some experiments, animals were administered with the NOS inhibitor L-NAME, one hour before airway reactivity measurement. Expression and phosphorylation of eNOS were evaluated in lung homogenates from fenofibrate and control animals using Western blotting. Fenofibrate dose and time dependently decreased airway reactivity to methacholine in mice. A statistically significant (P < 0.05) reduction was observed after a treatment of 10 days with a dose of 3 or 15 mg/day fenofibrate. Mice treated with fenofibrate and administered with l-NAME exhibited similar reactivity to methacholine than vehicle-treated mice administered with the NOS inhibitor, suggesting that NO mediates fenofibrate-induced decrease in airway reactivity. eNOS levels remained unchanged in the lung from mice treated with fenofibrate, but phosphorylation of the enzyme at Ser-1177 was increased by 118% (P < 0.05). Taken together, our data demonstrate that fenofibrate downregulates airway reactivity to methacholine in the mouse and suggest that this effect could involve an increase in NO generation through an enhanced eNOS phosphorylation.

Regulation of peroxisome proliferator-activated receptor-alpha expression during lung inflammation.

Peroxisome proliferator-activated receptor-alpha (PPARalpha) is implicated in the control of airway inflammation. However, little is known so far about PPARalpha expression and regulation in the lung. Our aim was to assess PPARalpha expression in the lung from normal mice, as well as to investigate its regulation during airway inflammation or in response to anti-inflammatory agents. The PPARalpha activator, fenofibrate, the glucocorticoid, dexamethasone or vehicle was administered to normal mice, to mice exposed to tumor necrosis factor-alpha (TNF-alpha) or lipopolysaccharide (LPS) or to ovalbumin (OVA)-sensitized and challenged animals. PPARalpha expression was assessed by quantifying PPARalpha mRNA levels using real-time quantitative PCR after reverse-transcription of total lung RNA. Airway inflammation was evaluated by determining total and differential cell counts, as well as TNF-alpha production in bronchoalveolar lavage fluids. PPARalpha mRNA was found at significant levels in the lung from normal mice. This expression was increased by 65% (p<0.05) and 55% (p<0.05) in animals treated with fenofibrate and dexamethasone, respectively. In mice exposed to TNF-alpha or LPS, as well as in animals sensitized and challenged with OVA, that exhibited airway inflammation, PPARalpha mRNA was decreased by 60% (p<0.05), 43% (p<0.05) and 50% (p<0.05), respectively. In mice exposed to LPS, down-regulation of PPARalpha was maximal at 4h, whereas TNF-alpha production and cell infiltration peaked at 2 and 24h, respectively. In the lung of mice exposed to LPS or OVA and treated with fenofibrate or dexamethasone, PPARalpha down-regulation was suppressed, while airway inflammation was abolished. Our data showed that PPARalpha is constitutively expressed in mouse lung and down-regulated in response to TNF-alpha or upon acute or allergic airway inflammation. Fenofibrate and dexamethasone upregulated PPARalpha in normal lung and suppressed PPARalpha down-regulation associated with airway inflammation. Taken together, our data show that PPARalpha expression is inversely regulated with lung inflammation.

Suppression of allergen-induced airway inflammation and immune response by the peroxisome proliferator-activated receptor-alpha agonist fenofibrate.

In the present study, we have assessed the effect of the peroxisome proliferator-activated receptor-alpha (PPARalpha) agonist fenofibrate on allergen-induced airway inflammation and immune response. C57BL/6 or PPARalpha knock-out (PPARalpha(-/-)) mice were sensitized with ovalbumin and challenged with ovalbumin alone or with ovalbumin+lipopolysaccharides. Fenofibrate was administered to allergen-exposed animals during challenge only or from the day prior to sensitization to the end of challenge. Inflammation and immune response were assessed by determining cell counts and cytokine levels in bronchoalveolar lavage fluids, expression of the transcription factors Gata-3 and T-bet in lung tissue and ovalbumin-specific IgE and IgG2a in serum. Treatment with fenofibrate (0.15-15 mg/day) during allergen challenge dose-dependently reduced airway inflammatory cell infiltrate induced by ovalbumin in C57BL/6 mice. Reduction reached 74.3% (P<0.001) in animals treated with 15 mg/day of the PPARalpha agonist, whereas this treatment failed to suppress cell infiltrate induced by allergen in PPARalpha(-/-) mice. In addition, when administered from the day prior to sensitization to the end of challenge, fenofibrate (15 mg/day) triggered switching of the immune response to allergen towards a Th1 profile, as evidenced by an increase in IgG2a levels, a reduction in IL(interleukin)-4 and IL-5 together with an increase in interferon-gamma, and a decrease in Gata-3/T-bet expression ratio. Upon challenge with ovalbumin+lipopolysaccharides, sensitized mice developed a severe inflammatory response characterized by infiltration of eosinophils, neutrophils, lymphocytes and macrophages and by increased release of IL-4, IL-5, tumor necrosis factor-alpha, macrophage-inflammatory protein-2 and monocyte chemoattractant protein-1. Administration of fenofibrate during allergen challenge dramatically reduced all responses. In conclusion, our data clearly demonstrate that fenofibrate exhibits an anti-inflammatory activity in allergic asthma, including in severe conditions, and that the PPARalpha agonist is also capable of switching the immune response to allergen towards a Th1 profile when given from the day prior to sensitization.

Regulation of inflammation by PPARs: a future approach to treat lung inflammatory diseases?

Lung inflammatory diseases, such as acute lung injury (ALI), asthma, chronic obstructive pulmonary disease (COPD) and lung fibrosis, represent a major health problem worldwide. Although glucocorticoids are the most potent anti-inflammatory drug in asthma, they exhibit major side effects and have poor activity in lung inflammatory disorders such as ALI or COPD. Therefore, there is growing need for the development of alternative or new therapies to treat inflammation in the lung. Peroxisome proliferator-activated receptors (PPARs), including the three isotypes PPARalpha, PPARbeta (or PPARdelta) and PPARgamma, are transcription factors belonging to the nuclear hormone receptor superfamily. PPARs, and in particular PPARalpha and PPARgamma, are well known for their critical role in the regulation of energy homeostasis by controlling expression of a variety of genes involved in lipid and carbohydrate metabolism. Synthetic ligands of the two receptor isotypes, the fibrates and the thiazolidinediones, are clinically used to treat dyslipidaemia and type 2 diabetes, respectively. Recently however, PPARalpha and PPARgamma have been shown to exert a potent anti-inflammatory activity, mainly through their ability to downregulate pro-inflammatory gene expression and inflammatory cell functions. The present article reviews the current knowledge of the role of PPARalpha and PPARgamma in controlling inflammation, and presents different findings suggesting that PPARalpha and PPARgamma activators may be helpful in the treatment of lung inflammatory diseases.

Exposure to endotoxins during sensitization prevents further endotoxin-induced exacerbation of airway inflammation in a mouse model of allergic asthma.

BACKGROUND: We have shown previously that lipopolysaccharides (LPS) inhibited airway inflammation in allergen-sensitized and challenged mice when administered during sensitization, while exacerbating the inflammation when given upon challenge. We have here investigated the effect of LPS administered during both sensitization and challenge on airway inflammation, as well as on the profile of the T-helper (Th) response to allergen. METHODS: Mice were sensitized and challenged with ovalbumin (OVA), in the presence or absence of effective doses of LPS, namely 1 mug during sensitization and 1 ng during challenge. Inflammation was assessed by measuring cell counts and cytokine levels in bronchoalveolar lavage fluid (BALF). The profile of the Th response was determined by quantifying OVA-specific IgE and IgG2a in serum and Th1/Th2 cytokines in the culture medium of splenocytes and in BALF. RESULTS: Allergen-induced airway eosinophilia was increased in mice exposed to LPS during challenge only when compared with controls, whereas it was similarly reduced in animals exposed during sensitization only and during both sensitization and challenge. Mice exposed to LPS during sensitization only or during both sensitization and challenge also displayed a decrease in IgE and an increase in IgG2a, suggesting a switch in the immune response toward the Th1 profile. This was confirmed by quantification of Th1/Th2 cytokines in culture medium of splenocytes and in BALF. CONCLUSIONS: Our data demonstrate that exposure to endotoxins during sensitization prevents allergen-induced airway inflammation, as well as its exacerbation triggered by further exposure to endotoxins during challenge, while switching the immune response to allergen from a Th2 to a Th1 profile.

PPARalpha downregulates airway inflammation induced by lipopolysaccharide in the mouse.

BACKGROUND: Inflammation is a hallmark of acute lung injury and chronic airway diseases. In chronic airway diseases, it is associated with profound tissue remodeling. Peroxisome proliferator-activated receptor-alpha (PPARalpha) is a ligand-activated transcription factor, that belongs to the nuclear receptor family. Agonists for PPARalpha have been recently shown to reduce lipopolysaccharide (LPS)- and cytokine-induced secretion of matrix metalloproteinase-9 (MMP-9) in human monocytes and rat mesangial cells, suggesting that PPARalpha may play a beneficial role in inflammation and tissue remodeling. METHODS: We have investigated the role of PPARalpha in a mouse model of LPS-induced airway inflammation characterized by neutrophil and macrophage infiltration, by production of the chemoattractants, tumor necrosis factor-alpha (TNF-alpha), keratinocyte derived-chemokine (KC), macrophage inflammatory protein-2 (MIP-2) and monocyte chemoattractant protein-1 (MCP-1), and by increased MMP-2 and MMP-9 activity in bronchoalveolar lavage fluid (BALF). The role of PPARalpha in this model was studied using both PPARalpha-deficient mice and mice treated with the PPARalpha activator, fenofibrate. RESULTS: Upon intranasal exposure to LPS, PPARalpha-/- mice exhibited greater neutrophil and macrophage number in BALF, as well as increased levels of TNF-alpha, KC, MIP-2 and MCP-1, when compared to PPARalpha+/+ mice. PPARalpha-/- mice also displayed enhanced MMP-9 activity. Conversely, fenofibrate (0.15 to 15 mg/day) dose-dependently reduced the increase in neutrophil and macrophage number induced by LPS in wild-type mice. In animals treated with 15 mg/day fenofibrate, this effect was associated with a reduction in TNF-alpha, KC, MIP-2 and MCP-1 levels, as well as in MMP-2 and MMP-9 activity. PPARalpha-/- mice treated with 15 mg/day fenofibrate failed to exhibit decreased airway inflammatory cell infiltrate, demonstrating that PPARalpha mediates the anti-inflammatory effect of fenofibrate. CONCLUSION: Using both genetic and pharmacological approaches, our data clearly show that PPARalpha downregulates cell infiltration, chemoattractant production and enhanced MMP activity triggered by LPS in mouse lung. This suggests that PPARalpha activation may have a beneficial effect in acute or chronic inflammatory airway disorders involving neutrophils and macrophages.