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1.
Ophthalmologica ; 234(3): 151-9, 2015.
Article in English | MEDLINE | ID: mdl-26337381

ABSTRACT

PURPOSE: Age-related macular degeneration (AMD) is the main cause of visual loss in the elderly population. With the use of anti-vascular endothelial growth factor, the visual outcomes of exudative AMD patients have been improved. This study was aimed at assessing the quality of life (QoL) of exudative AMD patients treated with ranibizumab and at determining its drivers in a real-life setting. METHODS: We performed a national, cross-sectional, observational survey based on questionnaires sent to members of French associations relative to AMD between December 2012 and March 2013. Patients suffering from exudative AMD with at least one intravitreal injection of ranibizumab within the last 6 months were included. Demographics, AMD characteristics, visual acuity (VA) and past and ongoing treatments were collected. The 25-item National Eye Institute Visual Function Questionnaire (NEI-VFQ-25) was self-administered. A multivariate model was used to identify QoL drivers. RESULTS: 416 questionnaires fulfilled the complete criteria for both QoL and cost analyses. The mean age of exudative AMD patients was 78.0 years and bilateral involvement was reported in 60.4%. The overall mean QoL score was 53.4. Mental health, driving and role difficulties were the most widely affected domains. After bivariate analyses, long-term illness status, worse VA and higher number of unpaid aids were associated with worse QoL, with odds ratios of 2.4, 5.2 and 11.6, respectively. The mean cost per year and per patient was 1,741 EUR. The main components of costs were aids and services and the purchase of visual equipment. CONCLUSIONS: The main predictors of QoL in exudative AMD patients treated with ranibizumab are VA outcomes, home healthcare and social services provided to the patients.


Subject(s)
Quality of Life/psychology , Wet Macular Degeneration/psychology , Aged , Aged, 80 and over , Angiogenesis Inhibitors/economics , Angiogenesis Inhibitors/therapeutic use , Cost of Illness , Cross-Sectional Studies , Exudates and Transudates , Female , Humans , Intravitreal Injections , Male , Middle Aged , Ranibizumab/economics , Ranibizumab/therapeutic use , Sickness Impact Profile , Surveys and Questionnaires , Vascular Endothelial Growth Factor A/antagonists & inhibitors , Visual Acuity/physiology , Wet Macular Degeneration/drug therapy , Wet Macular Degeneration/physiopathology
2.
Nucleic Acids Res ; 40(19): 9691-704, 2012 Oct.
Article in English | MEDLINE | ID: mdl-22855560

ABSTRACT

Many tools are available to analyse genomes but are often challenging to use in a cell type-specific context. We have developed a method similar to the isolation of nuclei tagged in a specific cell type (INTACT) technique [Deal,R.B. and Henikoff,S. (2010) A simple method for gene expression and chromatin profiling of individual cell types within a tissue. Dev. Cell, 18, 1030-1040; Steiner,F.A., Talbert,P.B., Kasinathan,S., Deal,R.B. and Henikoff,S. (2012) Cell-type-specific nuclei purification from whole animals for genome-wide expression and chromatin profiling. Genome Res., doi:10.1101/gr.131748.111], first developed in plants, for use in Drosophila neurons. We profile gene expression and histone modifications in Kenyon cells and octopaminergic neurons in the adult brain. In addition to recovering known gene expression differences, we also observe significant cell type-specific chromatin modifications. In particular, a small subset of differentially expressed genes exhibits a striking anti-correlation between repressive and activating histone modifications. These genes are enriched for transcription factors, recovering those known to regulate mushroom body identity and predicting analogous regulators of octopaminergic neurons. Our results suggest that applying INTACT to specific neuronal populations can illuminate the transcriptional regulatory networks that underlie neuronal cell identity.


Subject(s)
Drosophila/genetics , Genomics/methods , Neurons/metabolism , Animals , Cell Fractionation/methods , Cell Nucleus/genetics , Chromatin/metabolism , Drosophila/metabolism , Gene Expression Profiling , Gene Silencing , Histones/metabolism , Luminescent Proteins/genetics , Transcription Factors/genetics
3.
Bioanalysis ; 16(7): 77-119, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38389403

ABSTRACT

The 17th Workshop on Recent Issues in Bioanalysis (17th WRIB) took place in Orlando, FL, USA on June 19-23, 2023. Over 1000 professionals representing pharma/biotech companies, CROs, and multiple regulatory agencies convened to actively discuss the most current topics of interest in bioanalysis. The 17th WRIB included 3 Main Workshops and 7 Specialized Workshops that together spanned 1 week to allow an exhaustive and thorough coverage of all major issues in bioanalysis of biomarkers, immunogenicity, gene therapy, cell therapy and vaccines. Moreover, in-depth workshops on "EU IVDR 2017/746 Implementation and impact for the Global Biomarker Community: How to Comply with these NEW Regulations" and on "US FDA/OSIS Remote Regulatory Assessments (RRAs)" were the special features of the 17th edition. As in previous years, WRIB continued to gather a wide diversity of international, industry opinion leaders and regulatory authority experts working on both small and large molecules as well as gene, cell therapies and vaccines to facilitate sharing and discussions focused on improving quality, increasing regulatory compliance, and achieving scientific excellence on bioanalytical issues. This 2023 White Paper encompasses recommendations emerging from the extensive discussions held during the workshop and is aimed to provide the bioanalytical community with key information and practical solutions on topics and issues addressed, in an effort to enable advances in scientific excellence, improved quality and better regulatory compliance. Due to its length, the 2023 edition of this comprehensive White Paper has been divided into three parts for editorial reasons. This publication (Part 3) covers the recommendations on Gene Therapy, Cell therapy, Vaccines and Biotherapeutics Immunogenicity. Part 1A (Mass Spectrometry Assays and Regulated Bioanalysis/BMV), P1B (Regulatory Inputs) and Part 2 (Biomarkers, IVD/CDx, LBA and Cell-Based Assays) are published in volume 16 of Bioanalysis, issues 8 and 9 (2024), respectively.


Subject(s)
Biological Assay , Technology , Biological Assay/methods , Biomarkers/analysis , Cell- and Tissue-Based Therapy , Immunotherapy, Active
4.
Arthritis Rheum ; 63(6): 1527-33, 2011 Jun.
Article in English | MEDLINE | ID: mdl-21360520

ABSTRACT

OBJECTIVE: There is increasing evidence of a role for Toll-like receptors (TLRs) in inflammatory arthritis. The extra domain A (ED-A)-containing isoform of fibronectin is generated under pathologic conditions such as rheumatoid arthritis, and ED-A has been identified as an endogenous TLR-4 ligand. Leukotriene B4 (LTB4) and polymorphonuclear neutrophils (PMNs) play a critical role in murine models of inflammatory arthritis. The aim of this study was therefore to investigate the putative effects of ED-A on leukotriene biosynthesis and PMN migration through TLR signaling. METHODS: The effect of recombinant human ED-A (rhED-A) on leukotriene biosynthesis was evaluated in isolated human blood PMNs and monocytes by high-performance liquid chromatography. The capacity of rhED-A to stimulate PMN migration was evaluated using a transendothelial/matrix migration assay in vitro and the mouse air-pouch model in vivo. RESULTS: Recombinant human ED-A efficiently primed the biosynthesis of LTB4 in PMN and monocyte suspensions. This priming effect was dependent on TLR-4 activation, since the TLR-4-signaling inhibitor CLI-095 completely blocked the effect of rhED-A but not that of other TLR ligands (R-848, Pam2 CSK4) or cytokines. Moreover, rhED-A stimulated transendothelial migration of PMNs in vitro, which was inhibited by 50-60% with the LTB4 receptor 1 (BLT1) antagonist CP105,696 or the cytosolic phospholipase A2 α inhibitor pyrrophenone. In vivo, rhED-A induced a significant PMN recruitment into the air pouch of C3H/HeOuJ mice (expressing functional TLR-4), but not in C3H/HeJ mice (expressing nonsignaling TLR-4). CONCLUSION: These results demonstrate the ability of rhED-A to promote LTB4 biosynthesis and PMN migration through TLR-4 activation, thus providing new insights on TLR-dependent mechanisms of regulation of LTB4 biosynthesis and PMN infiltration in inflammatory joint diseases.


Subject(s)
Fibronectins/pharmacology , Leukotriene B4/biosynthesis , Leukotrienes/biosynthesis , Neutrophils/metabolism , Toll-Like Receptor 4/metabolism , Animals , Anti-Inflammatory Agents/pharmacology , Benzopyrans/pharmacology , Carboxylic Acids/pharmacology , Cytokines/pharmacology , Female , Fibronectins/chemistry , Humans , Imidazoles/pharmacology , Leukotriene B4/antagonists & inhibitors , Lipopeptides/pharmacology , Mice , Mice, Inbred C3H , Mice, Inbred C57BL , Monocytes/metabolism , Protein Isoforms/metabolism , Pyrrolidines/pharmacology , Recombinant Proteins/metabolism , Sulfonamides/pharmacology , Transendothelial and Transepithelial Migration/drug effects
5.
FASEB J ; 24(2): 637-47, 2010 Feb.
Article in English | MEDLINE | ID: mdl-19843712

ABSTRACT

Activation of toll-like receptors (TLRs) and polymorphonuclear leukocyte (PMN) accumulation at infection sites are critical events of host defense. The involvement of leukotriene (LT) B(4) and platelet-activating factor (PAF) in TLR ligand-induced activation of inflammatory cell functions is essentially unknown. Using an in vitro model of human PMN migration through human endothelial cell monolayers, we demonstrate that prototypic ligands of TLR1/2, 2/6, 3, 4, 5, and 7/8 promote PMN migration, an effect markedly inhibited by 3 LTB(4) receptor antagonists (70-80% inhibition at 100 nM compared to vehicle-treated cells), 3 PAF receptor antagonists (20-50% inhibition at 10 nM), 3 LT biosynthesis inhibitors (75-85% inhibition at 100 nM), and 1 cytosolic phospholipase A(2)alpha (cPLA(2)alpha) inhibitor (90% inhibition at 1 microM). Accordingly, selected TLR ligands caused Ser-505-phosphorylation of cPLA(2)alpha and measurable LTB(4) and PAF biosynthesis in the transmigration assay. As negative controls, interleukin-8- and formyl-methionyl-leucyl-phenylalanine-elicited migration in vitro was not inhibited either by an LTB(4) receptor antagonist or by the cPLA(2)alpha inhibitor. Finally, LTB(4) and PAF receptor antagonists inhibited (up to approximately 65% at optimal doses) TLR ligand-induced PMN infiltration in the mouse air-pouch model. These studies unravel the critical involvement of de novo LTB(4) and PAF biosynthesis in PMN migration elicited by TLR ligands.


Subject(s)
Cell Movement/drug effects , Leukotriene B4/physiology , Neutrophils/physiology , Platelet Activating Factor/physiology , Toll-Like Receptors/physiology , Animals , Azepines/pharmacology , Dihydropyridines/pharmacology , Female , Flagellin/pharmacology , Humans , Imidazoles/pharmacology , Ligands , Mice , Mice, Inbred C57BL , Poly I-C/pharmacology , Propionates/pharmacology , Quinolines/pharmacology , Thienopyridines , Toll-Like Receptors/agonists , Toll-Like Receptors/immunology , Triazoles/pharmacology
6.
G3 (Bethesda) ; 10(1): 143-150, 2020 01 07.
Article in English | MEDLINE | ID: mdl-31676507

ABSTRACT

RNA-seq has become the standard tool for collecting genome-wide expression data in diverse fields, from quantitative genetics and medical genomics to ecology and developmental biology. However, RNA-seq library preparation is still prohibitive for many laboratories. Recently, the field of single-cell transcriptomics has reduced costs and increased throughput by adopting early barcoding and pooling of individual samples -producing a single final library containing all samples. In contrast, RNA-seq protocols where each sample is processed individually are significantly more expensive and lower throughput than single-cell approaches. Yet, many projects depend on individual library generation to preserve important samples or for follow-up re-sequencing experiments. Improving on currently available RNA-seq methods we have developed TM3'seq, a 3'-enriched library preparation protocol that uses Tn5 transposase and preserves sample identity at each step. TM3'seq is designed for high-throughput processing of individual samples (96 samples in 6h, with only 3h hands-on time) at a fraction of the cost of commercial kits ($1.5 per sample). The protocol was tested in a range of human and Drosophila melanogaster RNA samples, recovering transcriptomes of the same quality and reliability than the commercial NEBNext kit. We expect that the cost- and time-efficient features of TM3'seq make large-scale RNA-seq experiments more permissive for the entire scientific community.


Subject(s)
RNA-Seq/methods , 3' Untranslated Regions , Animals , Costs and Cost Analysis , Drosophila melanogaster , Female , Humans , RNA, Messenger/chemistry , RNA, Messenger/genetics , RNA-Seq/economics , RNA-Seq/standards , Reproducibility of Results
7.
Elife ; 92020 01 15.
Article in English | MEDLINE | ID: mdl-31939737

ABSTRACT

The anatomy of many neural circuits is being characterized with increasing resolution, but their molecular properties remain mostly unknown. Here, we characterize gene expression patterns in distinct neural cell types of the Drosophila visual system using genetic lines to access individual cell types, the TAPIN-seq method to measure their transcriptomes, and a probabilistic method to interpret these measurements. We used these tools to build a resource of high-resolution transcriptomes for 100 driver lines covering 67 cell types, available at http://www.opticlobe.com. Combining these transcriptomes with recently reported connectomes helps characterize how information is transmitted and processed across a range of scales, from individual synapses to circuit pathways. We describe examples that include identifying neurotransmitters, including cases of apparent co-release, generating functional hypotheses based on receptor expression, as well as identifying strong commonalities between different cell types.


In the brain, large numbers of different types of neurons connect with each other to form complex networks. In recent years, researchers have made great progress in mapping all the connections between these cells, creating 'wiring diagrams' known as connectomes. However, charting the connections between neurons does not give all the answers as to how the brain works; for example, it does not necessarily reveal the nature of the information two connected cells exchange. Assessing which genes are switched on in different neurons can give insight into neuronal properties that are not obvious from physical connections alone. To fill that knowledge gap, Davis, Nern et al. aimed to measure the genes expressed in a well-characterized network of neurons in the fruit fly visual system. First, 100 fly strains were established, each carrying a single type of neuron colored with a fluorescent marker. Then, a biochemical approach was developed to extract the part of the cell that contains the genetic code from the neurons with the marker. Finally, a statistical tool was used to assess which genes were on in each type of neurons. This led to the creation of a database that shows whether 15,000 genes in each neuron type across 100 fly strains were switched on. Combining this information with previous knowledge about the flies' visual system revealed new information: for example, it helped to understand which chemicals the neurons use to communicate, and whether certain cells activate or inhibit each other. The work by Davis, Nern et al. demonstrates how genetic approaches can complement other methods, and it offers a new tool for other scientists to use in their work. With more advanced genetic methods, it may one day become possible to better grasp how complex brains in other organisms are organized, and how they are disrupted in disease.


Subject(s)
Connectome , Genome , Neurons/physiology , Animals , Drosophila/genetics , Drosophila/physiology , Gene Expression , Probability , Transcriptome , Visual Pathways/metabolism
8.
Elife ; 82019 04 12.
Article in English | MEDLINE | ID: mdl-30977723

ABSTRACT

Understanding the principles governing neuronal diversity is a fundamental goal for neuroscience. Here, we provide an anatomical and transcriptomic database of nearly 200 genetically identified cell populations. By separately analyzing the robustness and pattern of expression differences across these cell populations, we identify two gene classes contributing distinctly to neuronal diversity. Short homeobox transcription factors distinguish neuronal populations combinatorially, and exhibit extremely low transcriptional noise, enabling highly robust expression differences. Long neuronal effector genes, such as channels and cell adhesion molecules, contribute disproportionately to neuronal diversity, based on their patterns rather than robustness of expression differences. By linking transcriptional identity to genetic strains and anatomical atlases, we provide an extensive resource for further investigation of mouse neuronal cell types.


Subject(s)
Brain/anatomy & histology , Brain/cytology , Gene Expression Profiling , Neurons/physiology , Animals , Mice
9.
Biochim Biophys Acta ; 1771(9): 1235-45, 2007 Sep.
Article in English | MEDLINE | ID: mdl-17643350

ABSTRACT

In the present study, we characterized the generation of prostaglandin (PG)E2 in human neutrophils. We found that the Ca2+-dependent type IV cytosolic phospholipase A2 (cPLA2) was pivotally involved in the COX-2-mediated generation of PGE2 in response to a calcium ionophore, as determined by the use of selected PLA2 inhibitors. PGE2 biosynthesis elicited by bacterial-derived peptides or by phagocytic stimuli acting on cell surface receptors also showed to be dependent on cPLA2 activity. We then assessed metabolism of unesterified arachidonic acid (AA), and observed that PGE2 production becomes favored over that of LTB4 with higher AA concentrations. Withdrawal of calcium prevented the generation of PGE2 in response to a calcium ionophore but did not affect the up-regulation of COX-2 or its capacity to convert AA, thus limiting its implication at the level of cPLA2 activation. Of the main eicosanoids produced by neutrophils, only LTB4 was able to up-regulate COX-2 expression. Finally, the only PGE synthase isoform found in neutrophils is microsomal PGE synthase-1; it co-localized with COX-2 and its expression appeared mainly constitutive. These results highlight key differences in regulatory processes of the 5-LO and COX pathways, and enhance our knowledge at several levels in the PGE2 biosynthesis in neutrophils.


Subject(s)
Cyclooxygenase 2/metabolism , Dinoprostone/biosynthesis , Neutrophils/metabolism , Signal Transduction/physiology , Arachidonate 5-Lipoxygenase/metabolism , Arachidonic Acid/chemistry , Arachidonic Acid/metabolism , Calcimycin/metabolism , Calcium/metabolism , Enzyme Activation , Group IV Phospholipases A2/antagonists & inhibitors , Group IV Phospholipases A2/metabolism , Humans , Ionophores/metabolism , Isoenzymes/metabolism , Leukotriene B4/metabolism , Microsomes/enzymology , Monocytes/metabolism , Thromboxane A2/metabolism
10.
FASEB J ; 21(7): 1575-85, 2007 May.
Article in English | MEDLINE | ID: mdl-17264163

ABSTRACT

Toll-like receptors (TLR) recognize pathogen-associated molecular patterns and play important roles in the innate immune system. While single-stranded viral RNA is the natural ligand of TLR7/TLR8, the imidazoquinoline resiquimod (R-848) is recognized as a potent synthetic agonist of TLR7/TLR8. We investigated the effects of TLR7/8 activation on lipid mediator production in polymorphonuclear leukocytes exposed to R-848. Although R-848 had minimal effects by itself, it strongly enhanced leukotriene B4 formation on subsequent stimulation by fMLP, platelet-activating factor, and the ionophore A23187. R-848 acted via TLR8 but not TLR7 as shown by the lack of effect of the TLR7-specific ligand imiquimod. Priming with R-848 also resulted in enhanced arachidonic acid release and platelet-activating factor formation following fMLP stimulation, as well as enhanced prostaglandin E2 synthesis following the addition of arachidonic acid. Western blot analysis demonstrated that R-848 induced the phosphorylation of the cytosolic phospholipase A2alpha, promoted 5-lipoxygenase translocation and potently stimulated the expression of the type 2 cyclooxygenase. Bafilomycin A1, an inhibitor of endosomal acidification, efficiently inhibited all R-848-induced effects. These studies demonstrate that TLR8 signaling strongly promotes inflammatory lipid mediator biosynthesis and provide novel insights on innate immune response to viral infections.


Subject(s)
Dinoprostone/biosynthesis , Imidazoles/pharmacology , Leukotriene B4/biosynthesis , Neutrophils/drug effects , Platelet Activating Factor/biosynthesis , Toll-Like Receptor 7/drug effects , Toll-Like Receptor 8/drug effects , Humans , Imidazoles/metabolism , Inflammation Mediators/metabolism , Neutrophils/immunology , Neutrophils/metabolism , RNA Viruses/immunology , Signal Transduction , Toll-Like Receptor 7/metabolism , Toll-Like Receptor 8/metabolism
11.
J Leukoc Biol ; 79(5): 1043-51, 2006 May.
Article in English | MEDLINE | ID: mdl-16501051

ABSTRACT

Leukotrienes (LT) and platelet-activating factor (PAF) are important lipid mediators of inflammation. We and others reported previously that autacoids such as adenosine, histamine, prostaglandin E2, and beta-adrenergic agents inhibit LT biosynthesis in activated human polymorphonuclear leukocytes (PMN). In this study, we demonstrate that CGS-21680 (a selective agonist of the adenosine A2A receptor) and histamine also potently inhibit PAF biosynthesis in agonist [formyl Met-Leu-Phe (fMLP)]- and thapsigargin-activated human PMN. The observed inhibitions of PAF biosynthesis were reversed effectively by exogenous 1-O-alkyl-lyso-sn-glyceryl-3-phosphocholine (lyso-PAF), suggesting that these effects of CGS-21680 and histamine implicate the blockade of cytosolic phospholipase A2alpha (cPLA2alpha) activity and lyso-PAF release and that the acetyl-coenzyme A/lyso-PAF acetyl transferase is not inhibited by the autacoids. Accordingly, the cPLA2alpha inhibitor pyrrophenone completely blocked PAF formation, and lyso-PAF similarly prevented this effect of pyrrophenone. The inhibitory effects of CGS-21680 and histamine on PAF biosynthesis were prevented by the protein kinase A inhibitor H-89, supporting roles for the Gs -coupled receptors A2A and H2, respectively, and cyclic adenosine monophosphate in the inhibitory mechanism. The fMLP-induced phosphorylations of p38 and extracellular signal-regulated kinase 1/2 were not altered significantly by the CGS-21680, indicating that inhibition of these kinases is not involved in the inhibitory effect of the adenosine A2A receptor ligand on LT and PAF biosynthesis. These data further emphasize the multiple and potent inhibitory effects of adenosine and histamine on leukocyte functions, in particular, on the biosynthesis of two classes of important lipid mediators and their putative regulatory roles in immune processes in health and diseases.


Subject(s)
Adenosine/metabolism , Histamine/metabolism , Neutrophils/metabolism , Phospholipases A/metabolism , Platelet Activating Factor/analogs & derivatives , Platelet Activating Factor/antagonists & inhibitors , Adenosine/analogs & derivatives , Adenosine/pharmacology , Adenosine A2 Receptor Agonists , Antihypertensive Agents/pharmacology , Cells, Cultured , Enzyme Inhibitors/pharmacology , Group IV Phospholipases A2 , Histamine/pharmacology , Humans , Leukotrienes/biosynthesis , MAP Kinase Signaling System/drug effects , MAP Kinase Signaling System/physiology , Membrane Lipids/metabolism , Neutrophils/drug effects , Neutrophils/immunology , Phenethylamines/pharmacology , Phospholipases A/antagonists & inhibitors , Phospholipases A/immunology , Phospholipids/metabolism , Phosphorylation/drug effects , Platelet Activating Factor/biosynthesis , Platelet Activating Factor/metabolism , Pyrrolidines/pharmacology , Receptor, Adenosine A2A/metabolism , Receptors, Formyl Peptide/drug effects , Receptors, Formyl Peptide/metabolism , Receptors, Histamine H2/drug effects , Receptors, Histamine H2/metabolism
12.
Biochem J ; 393(Pt 1): 211-8, 2006 Jan 01.
Article in English | MEDLINE | ID: mdl-16144515

ABSTRACT

FLAP (5-lipoxygenase-activating protein) is a nuclear transmembrane protein involved in the biosynthesis of LTs (leukotrienes) and other 5-LO (5-lipoxygenase) products. However, little is known about its mechanism of action. In the present study, using cross-linkers, we demonstrate that FLAP is present as a monomer and a homodimer in human PMN (polymorphonuclear cells). The functional relevance of the FLAP dimer in LT biosynthesis was assessed in different experimental settings. First, the 5-LO substrate AA (arachidonic acid) concomitantly disrupted the FLAP dimer (at > or =10 microM) and inhibited LT biosynthesis. Secondly, using Sf9 cells expressing active and inactive FLAP mutants and 5-LO, we observed that the FLAP mutants capable of supporting 5-LO product biosynthesis also form the FLAP dimer, whereas inactive FLAP mutants do not. Finally, we showed that FLAP inhibitors such as MK-0591 which block LT biosynthesis in human PMN, disrupt the FLAP dimer in PMN membranes with a similar IC50. The present study demonstrates that LT biosynthesis in intact cells not only requires the presence of FLAP but its further organization into a FLAP homodimer.


Subject(s)
Carrier Proteins/chemistry , Carrier Proteins/metabolism , Leukotrienes/biosynthesis , Membrane Proteins/chemistry , Membrane Proteins/metabolism , Neutrophils/metabolism , 5-Lipoxygenase-Activating Proteins , Animals , Arachidonic Acid/metabolism , Carrier Proteins/antagonists & inhibitors , Cell Line , Dimerization , Humans , Membrane Proteins/antagonists & inhibitors
13.
G3 (Bethesda) ; 7(4): 1339-1347, 2017 04 03.
Article in English | MEDLINE | ID: mdl-28280212

ABSTRACT

Species of the Drosophila melanogaster species subgroup, including the species D. simulans, D. mauritiana, D. yakuba, and D. santomea, have long served as model systems for studying evolution. However, studies in these species have been limited by a paucity of genetic and transgenic reagents. Here, we describe a collection of transgenic and genetic strains generated to facilitate genetic studies within and between these species. We have generated many strains of each species containing mapped piggyBac transposons including an enhanced yellow fluorescent protein (EYFP) gene expressed in the eyes and a ϕC31 attP site-specific integration site. We have tested a subset of these lines for integration efficiency and reporter gene expression levels. We have also generated a smaller collection of other lines expressing other genetically encoded fluorescent molecules in the eyes and a number of other transgenic reagents that will be useful for functional studies in these species. In addition, we have mapped the insertion locations of 58 transposable elements in D. virilis that will be useful for genetic mapping studies.


Subject(s)
Drosophila/genetics , Alleles , Animals , Animals, Genetically Modified , DNA Transposable Elements/genetics , Drosophila simulans/genetics , Eye/metabolism , Gene Expression Regulation , Genomics , Green Fluorescent Proteins/metabolism , Mutagenesis, Insertional/genetics , Species Specificity , Transgenes
14.
Elife ; 5: e11613, 2016 Mar 07.
Article in English | MEDLINE | ID: mdl-26949250

ABSTRACT

Rod and cone photoreceptors are highly similar in many respects but they have important functional and molecular differences. Here, we investigate genome-wide patterns of DNA methylation and chromatin accessibility in mouse rods and cones and correlate differences in these features with gene expression, histone marks, transcription factor binding, and DNA sequence motifs. Loss of NR2E3 in rods shifts their epigenomes to a more cone-like state. The data further reveal wide differences in DNA methylation between retinal photoreceptors and brain neurons. Surprisingly, we also find a substantial fraction of DNA hypo-methylated regions in adult rods that are not in active chromatin. Many of these regions exhibit hallmarks of regulatory regions that were active earlier in neuronal development, suggesting that these regions could remain undermethylated due to the highly compact chromatin in mature rods. This work defines the epigenomic landscapes of rods and cones, revealing features relevant to photoreceptor development and function.


Subject(s)
Epigenesis, Genetic , Retinal Cone Photoreceptor Cells/physiology , Retinal Rod Photoreceptor Cells/physiology , Animals , DNA/metabolism , Gene Expression Profiling , Histones/metabolism , Methylation , Mice , Transcription Factors/metabolism
15.
Neuron ; 86(6): 1369-84, 2015 Jun 17.
Article in English | MEDLINE | ID: mdl-26087164

ABSTRACT

Neuronal diversity is essential for mammalian brain function but poses a challenge to molecular profiling. To address the need for tools that facilitate cell-type-specific epigenomic studies, we developed the first affinity purification approach to isolate nuclei from genetically defined cell types in a mammal. We combine this technique with next-generation sequencing to show that three subtypes of neocortical neurons have highly distinctive epigenomic landscapes. Over 200,000 regions differ in chromatin accessibility and DNA methylation signatures characteristic of gene regulatory regions. By footprinting and motif analyses, these regions are predicted to bind distinct cohorts of neuron subtype-specific transcription factors. Neuronal epigenomes reflect both past and present gene expression, with DNA hyper-methylation at developmentally critical genes appearing as a novel epigenomic signature in mature neurons. Taken together, our findings link the functional and transcriptional complexity of neurons to their underlying epigenomic diversity.


Subject(s)
Gene Expression Regulation, Developmental , Neocortex/cytology , Neurons/classification , Neurons/metabolism , Animals , Cell Nucleolus/metabolism , Chromatin Immunoprecipitation , DNA Methylation/physiology , Epigenomics/methods , Gene Expression Profiling , Green Fluorescent Proteins/genetics , Mice , Mice, Transgenic , Microtubule-Associated Proteins/genetics , Microtubule-Associated Proteins/metabolism , Nerve Tissue Proteins/genetics , Nerve Tissue Proteins/metabolism , Proto-Oncogene Proteins c-myc/genetics , Proto-Oncogene Proteins c-myc/metabolism
16.
Br J Pharmacol ; 141(4): 552-61, 2004 Feb.
Article in English | MEDLINE | ID: mdl-14744809

ABSTRACT

1. Histamine is generally regarded as a pro-inflammatory mediator in diseases such as allergy and asthma. A growing number of studies, however, suggest that this autacoid is also involved in the downregulation of human polymorphonuclear leukocyte (PMN) functions and inflammatory responses through activation of the Gs-coupled histamine H(2) receptor. 2. We report here that histamine inhibits thapsigargin- and ligand (PAF and fMLP)-induced leukotriene (LT) biosynthesis in human PMN in a dose-dependent manner. 3. The suppressive effect of histamine on LT biosynthesis was abrogated by the histamine H(2) receptor antagonists cimetidine, ranitidine, and tiotidine. In contrast, the histamine H(1), H(3), and H(4) receptor antagonists used in this study were ineffective in counteracting the inhibitory effect of histamine on the biosynthesis of LT in activated human PMN. 4. The inhibition of LT biosynthesis by histamine was characterized by decreased arachidonic acid release and 5-lipoxygenase translocation to the nuclear membrane. 5. Incubation of PMN with the cAMP-dependent protein kinase (PKA) inhibitor N-[2-(p-bromocinnamylamino)ethyl]-5-isoquinoline-sulfonamide prevented the inhibitory effect of histamine on LT biosynthesis, suggesting an important role for PKA in this effect of histamine on LT biosynthesis in PMN. 6. These data provide the first evidences that, similarly to adenosine and prostaglandin E(2), histamine is a potent suppressor of LT biosynthesis, and support the concept that histamine may play a dual role in the regulation of inflammation.


Subject(s)
Cyclic AMP/physiology , Histamine/pharmacology , Leukotrienes/biosynthesis , Neutrophils/metabolism , Receptors, Histamine H2/metabolism , Sulfonamides , Arachidonate 5-Lipoxygenase/metabolism , Arachidonic Acid/metabolism , Calcium/metabolism , Cyclic AMP-Dependent Protein Kinases/antagonists & inhibitors , Cyclic AMP-Dependent Protein Kinases/metabolism , Depression, Chemical , Dose-Response Relationship, Drug , Enzyme Inhibitors/pharmacology , Histamine Agonists/pharmacology , Histamine Antagonists/pharmacology , Humans , In Vitro Techniques , Isoquinolines/pharmacology , Leukotriene B4/biosynthesis , Neutrophils/drug effects , Nuclear Envelope/drug effects , Nuclear Envelope/enzymology , Phospholipases A/metabolism , Stimulation, Chemical , Translocation, Genetic/genetics
17.
J Biol Chem ; 281(1): 129-36, 2006 Jan 06.
Article in English | MEDLINE | ID: mdl-16275640

ABSTRACT

Elevation of the intracellular cAMP concentration in agonist-activated human neutrophils (PMN) leads to the concomitant inhibitions of arachidonic acid (AA) release, 5-lipoxygenase (5-LO) translocation, and leukotriene (LT) biosynthesis. We report herein that exogenous AA completely prevents cAMP-dependent inhibition of 5-LO translocation and LT biosynthesis in agonist-activated PMN. Moreover, the group IVA phospholipase A2 inhibitor pyrrophenone and the MEK inhibitor U-0126 inhibited AA release and 5-LO translocation in activated PMN, and these effects were also prevented by exogenous AA, demonstrating a functional link between AA release and 5-LO translocation. Polyunsaturated fatty acids of the C18 and C20 series containing at least three double bonds located from carbon 9 (or closer to the carboxyl group) were equally effective as AA in restoring 5-LO translocation in pyrrophenone-treated agonist-activated PMN. Importantly, experiments with the 5-LO-activating protein inhibitor MK-0591 and the intracellular Ca2+ chelator BAPTA-AM demonstrated that the AA-regulated 5-LO translocation is FLAP- and Ca2+-dependent. Finally, the redox and competitive 5-LO inhibitors L-685,015, L-739,010, and L-702,539 (but not cyclooxygenase inhibitors) efficiently substituted for AA to reverse the pyrrophenone inhibition of 5-LO translocation, indicating that the site of regulation of 5-LO translocation by AA is at or in the vicinity of the catalytic site. This report demonstrates that AA regulates the translocation of 5-LO in human PMN and unravels a novel mechanism of the cAMP-mediated inhibition of LT biosynthesis.


Subject(s)
Arachidonate 5-Lipoxygenase/metabolism , Arachidonic Acid/pharmacology , Neutrophils/drug effects , Neutrophils/metabolism , Nuclear Envelope/enzymology , Biological Transport/drug effects , Biological Transport/physiology , Calcium/metabolism , Chelating Agents/pharmacology , Cyclic AMP/metabolism , Egtazic Acid/analogs & derivatives , Egtazic Acid/pharmacology , Humans , Leukotrienes/biosynthesis , Lipoxygenase Inhibitors
18.
J Cell Sci ; 118(Pt 7): 1437-47, 2005 Apr 01.
Article in English | MEDLINE | ID: mdl-15769843

ABSTRACT

Neutrophils, which are often the first to migrate at inflamed sites, can generate leukotriene B(4) from the 5-lipoxygenase pathway and prostaglandin E(2) through the inducible cyclooxygenase-2 pathway. Adenosine, an endogenous autacoid with several anti-inflammatory properties, blocks the synthesis of leukotriene B(4) while it potentiates the cyclooxygenase-2 pathway in fMLP-treated neutrophils, following activation of the A(2A) receptor. Using the murine air pouch model of inflammation, we observed that inflammatory leukocytes from mice lacking the A(2A) receptor have less cyclooxygenase-2 induction than wild-type animals. In human leukocytes, A(2A) receptor activation specifically elicited potentiation of cyclooxygenase-2 in neutrophils, but not in monocytes. Signal transduction studies indicated that the cAMP, ERK1/2, PI-3K and p38K intracellular pathways are implicated both in the direct upregulation of cyclooxygenase-2 and in its potentiation. Together, these results indicate that neutrophils are particularly important mediators of adenosine's effects. Given the uncontrolled inflammatory phenotype observed in knockout mice and in view of the potent inhibitory actions of prostaglandin E(2) on inflammatory cells, an increased cyclooxygenase-2 expression resulting from A(2A) receptor activation, observed particularly in neutrophils, may take part in an early modulatory mechanism promoting anti-inflammatory activities of adenosine.


Subject(s)
Adenosine/pharmacology , Anti-Inflammatory Agents, Non-Steroidal/pharmacology , Cyclooxygenase Inhibitors/pharmacology , Inflammation/enzymology , Neutrophils/enzymology , Prostaglandin-Endoperoxide Synthases/drug effects , Animals , Anti-Inflammatory Agents, Non-Steroidal/administration & dosage , Cyclooxygenase 1 , Cyclooxygenase 2 , Cyclooxygenase 2 Inhibitors , Disease Models, Animal , Humans , Inflammation/chemically induced , Inflammation/immunology , Injections, Subcutaneous , Leukocytes/drug effects , Leukocytes/enzymology , Leukocytes/immunology , Lipopolysaccharides , Membrane Proteins , Mice , Mice, Knockout , Mice, Transgenic , Neutrophils/drug effects , Prostaglandin-Endoperoxide Synthases/immunology , Receptor, Adenosine A2A/deficiency , Receptor, Adenosine A2A/drug effects , Receptor, Adenosine A2A/immunology , Signal Transduction/drug effects , Signal Transduction/genetics , Signal Transduction/immunology , Time Factors
19.
Mol Pharmacol ; 62(2): 250-6, 2002 Aug.
Article in English | MEDLINE | ID: mdl-12130675

ABSTRACT

5-Lipoxygenase (5-LO) catalyzes the transformation of arachidonic acid to leukotrienes (LT). In stimulated human PMN, activation of 5-LO involves calcium, p38 MAP kinase (p38) phosphorylation, and translocation of 5-LO from the cytosol to nuclear membranes containing the 5-LO activating protein (FLAP). In this study, cAMP-elevating agents such as isoproterenol, prostaglandin E(2), CGS-21680 (an adenosine A(2a) receptor agonist), the type IV phosphodiesterase inhibitor RO 20-1724, the adenylate cyclase activator forskolin, and the Gs-protein activator cholera toxin all inhibited LT biosynthesis and 5-LO translocation to the nucleus in cytokine-primed human PMN stimulated with platelet-activating factor and in human PMN stimulated with the endomembrane Ca(2+)-ATPase blocker thapsigargin. Furthermore, monophosphorothioate analogs of cAMP, which activate protein kinase A (PKA), also inhibited LT biosynthesis and 5-LO translocation in stimulated cells. Treatment of PMN with CGS-21680 also prevented the phosphorylation of p38 by thapsigargin. Treatment of PMN with the PKA inhibitors H-89 and KT-5720 prevented the inhibitory effect of cAMP-elevating agents on LT biosynthesis, 5-LO translocation, and p38 phosphorylation, whereas the p38 inhibitor SB 203,580 dose-dependently inhibited arachidonic acid-induced LT biosynthesis. The 5-LO translocation was also inhibitable by the FLAP antagonist MK-0591 and correlated with LT biosynthesis in all experimental conditions tested. These results indicate that cAMP-mediated PKA activation in PMN results in the concomitant inhibition of 5-LO translocation and LT biosynthesis and support a role of p38 in the signaling pathway involved. This represents the first physiological down-regulation mechanism of 5-LO translocation in human PMN.


Subject(s)
Arachidonate 5-Lipoxygenase/metabolism , Cyclic AMP/metabolism , Leukotrienes/biosynthesis , Neutrophils/enzymology , Biological Transport , Humans , Neutrophils/metabolism
20.
J Lipid Res ; 44(6): 1182-91, 2003 Jun.
Article in English | MEDLINE | ID: mdl-12639971

ABSTRACT

Arachidonic acids (AA) and linoleic acids (LAs) are metabolized, in several tissues, to hydroxylated metabolites that are important mediators of many physiological and pathophysiological processes. The conjugation of leukotriene B4 (LTB4), 5-hydroxyeicosatetraenoic acid (HETE), 12-HETE, 15-HETE, and 13-hydroxyoctadecadienoic acid (HODE) by the human UDP-glucuronosyltransferase (UGT) enzymes was investigated. All substrates tested were efficiently conjugated by human liver microsomes to polar derivatives containing the glucuronyl moiety as assessed by mass spectrometry. The screening analyses with stably expressed UGT enzymes in HK293 showed that glucuronidation of LTB4 was observed with UGT1A1, UGT1A3, UGT1A8, and UGT2B7, whereas UGT1A1, UGT1A3, UGT1A4, and UGT1A9 also conjugated most of the HETEs and 13-HODE. LA and AA metabolites also appear to be good substrates for the UGT2B subfamily members, especially for UGT2B4 and UGT2B7 that conjugate all HETE and 13-HODE. Interestingly, UGT2B10 and UGT2B11, which are considered as orphan enzymes since no conjugation activity has so far been demonstrated with these enzymes, conjugated 12-HETE, 15-HETE, and 13-HODE. In summary, our data showed that several members of UGT1A and UGT2B families are capable of converting LA and AA metabolites into glucuronide derivatives, which is considered an irreversible step to inactivation and elimination of endogenous substances from the body.


Subject(s)
Arachidonic Acids/metabolism , Glucuronides/metabolism , Glucuronosyltransferase/metabolism , Linoleic Acid/metabolism , Androsterone/metabolism , Cells, Cultured , Enzyme Stability , Glucuronides/chemistry , Glucuronosyltransferase/genetics , Humans , Kinetics , Linoleic Acid/chemistry , Mass Spectrometry , Microsomes, Liver/metabolism , Substrate Specificity , Transfection
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