Publications by authors named "Romain Ladouce"

10 Publications

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Proteomic response of β-lactamases-producing Enterobacter cloacae complex strain to cefotaxime-induced stress.

Pathog Dis 2016 07 8;74(5). Epub 2016 May 8.

Mediterranean Institute for Life Sciences, Meštovićevo šetalište 45, 21000 Split, Croatia.

Bacteria of the Enterobacter cloacae complex are among the ten most common pathogens causing nosocomial infections in the USA. Consequently, increased resistance to β-lactam antibiotics, particularly expanded-spectrum cephalosporins like cefotaxime (CTX), poses a serious threat. Differential In-Gel Electrophoresis (DIGE), followed by LC-MS/MS analysis and bioinformatics tools, was employed to investigate the survival mechanisms of a multidrug-resistant E. hormaechei subsp. steigerwaltii 51 carrying several β-lactamase-encoding genes, including the 'pandemic' blaCTX-M-15 After exposing the strain with sub-minimal inhibitory concentration (MIC) of CTX, a total of 1072 spots from the whole-cell proteome were detected, out of which 35 were differentially expressed (P ≤ 0.05, fold change ≥1.5). Almost 50% of these proteins were involved in cell metabolism and energy production, and then cell wall organization/virulence, stress response and transport. This is the first study investigating the whole-cell proteomic response related to the survival of β-lactamases-producing strain, belonging to the E. cloacae complex when exposed to β-lactam antibiotic. Our data support the theory of a multifactorial synergistic effect of diverse proteomic changes occurring in bacterial cells during antibiotic exposure, depicting the complexity of β-lactam resistance and giving us an insight in the key pathways mediating the antibiotic resistance in this emerging opportunistic pathogen.
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http://dx.doi.org/10.1093/femspd/ftw045DOI Listing
July 2016

Oxi-DIGE: A novel proteomic approach for detecting and quantifying carbonylated proteins.

Free Radic Biol Med 2014 Oct 10;75 Suppl 1:S23. Epub 2014 Dec 10.

Sorbonne Universités, UPMC Univ Paris 06 (CNRS UMR 8256, INSERM U1164), Biological adaptation and aging - IBPS, France.

Proteins are involved in key cellular functions and our health and wellness depends on their quality. Accumulation of oxidatively damaged proteins is a hallmark of deleterious processes such increased oxidative stress, chronic inflammation, ageing and age-related diseases. Thus, quantifying and identifying oxidized proteins is a biomarker of choice for monitoring biological ageing and/or the efficiency of anti-oxidant, ant-inflammatory and anti-ageing therapies. However, the absence of reliable tools for analyses has inhibited its establishment as the gold standard for measuring the efficacy of anti-ageing and age related diseases interventions. Herein, we present a novel proteomics technology, named Oxi-DIGE?, which provides a significant improvement in terms of specificity, reproducibility and statistical support for proteomic analysis of carbonylated proteins. In Oxi-DIGE, protein carbonyls are labelled with fluorescent hydrazide probes that bind specifically to carbonyl groups in proteins. Experimental groups (e.g. control and experimental samples) are labelled with different flurophore-binded hydrazides that fluoresce light at different wavelengths, producing different colour fluorescence. Thus samples from different experimental groups are co-resolved on a single 2D gel. Increased accuracy is provided due to: (i) reduced false positives by using an exogenous synthetic fluorescent tag; (ii) multiplexing, that is the possibility to run multiple samples on the same gel, (iii) the use of an internal standard on each gel which eliminates inter-gel variations and provides an increased statistical confidence. In addition, the resolution of the carbonyl groups is improved, forming distinct spots that can be identified by mass spectrometry. ?Patent Application (M. Baraibar, R. Ladouce., B. Friguet, A method for detecting and/or quantifying carbonylated proteins (WO/2012/175519) filed by UPMC and referring to the technology described in this abstract.
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http://dx.doi.org/10.1016/j.freeradbiomed.2014.10.739DOI Listing
October 2014

CD4(+) T cell surface alpha enolase is lower in older adults.

Mech Ageing Dev 2015 Dec 1;152:56-62. Epub 2015 Oct 1.

Life and Health Sciences, Aston Research Centre for Healthy Ageing, Aston University, Birmingham B4 7ET, UK. Electronic address:

To identify novel cell ageing markers in order to gain insight into ageing mechanisms, we adopted membrane enrichment and comparison of the CD4(+) T cell membrane proteome (purified by cell surface labelling using Sulfo-NHS-SS-Biotin reagent) between healthy young (n=9, 20-25 years) and older (n=10; 50-70 years) male adults. Following two-dimensional gel electrophoresis (2DE) to separate pooled membrane proteins in triplicates, the identity of protein spots with age-dependent differences (p<0.05 and >1.4 fold difference) was determined using liquid chromatography-mass spectrometry (LC-MS/MS). Seventeen protein spot density differences (ten increased and seven decreased in the older adult group) were observed between young and older adults. From spot intensity analysis, CD4(+) T cell surface α-enolase was decreased in expression by 1.5 fold in the older age group; this was verified by flow cytometry (n=22) and qPCR with significantly lower expression of cellular α-enolase mRNA and protein compared to young adult CD4(+) T cells (p<0.05). In an independent age-matched case-control study, lower CD4(+) T cell surface α-enolase expression was observed in age-matched patients with cardiovascular disease (p<0.05). An immune-modulatory role has been proposed for surface α-enolase and our findings of decreased expression suggest that deficits in surface α-enolase merit investigation in the context of immune dysfunction during ageing and vascular disease.
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http://dx.doi.org/10.1016/j.mad.2015.09.005DOI Listing
December 2015

In subfertile couple, abdominal fat loss in men is associated with improvement of sperm quality and pregnancy: a case-series.

PLoS One 2014 10;9(2):e86300. Epub 2014 Feb 10.

Service d'Histologie-Embryologie-Cytogénétique-CECOS, Hôpital Jean Verdier (AP-HP), Bondy, France ; Unité de Recherche en Epidémiologie Nutritionnelle, INSERM U557, INRA, CNAM, Université Paris 13, CRNH IdF, Bobigny, France.

Background: The impact of overweight among men of reproductive-age may affect fertility. Abdominal fat, more than body mass index, is an indicator of higher metabolic risk, which seems to be involved in decreasing sperm quality. This study aims to assess the relationship between abdominal fat and sperm DNA fragmentation and the effect of abdominal fat loss, among 6 men in subfertile couples.

Methods: Sperm DNA fragmentation, abdominal fat and metabolic and hormonal profiles were measured in the 6 men before and after dietary advices. Seminal oxidative stress and antioxidant markers were determined.

Results: After several months of a lifestyle program, all 6 men lost abdominal fat (patient 1: loss of 3 points of abdominal fat, patient 2: loss of 3 points, patient 3: loss of 2 points, patient 4: loss of 1 point, patient 5: loss of 4 points and patient 6: loss of 13 points). At the same time, their rate of sperm DNA fragmentation decreased: 9.5% vs 31%, 24% vs 43%, 18% vs 47%, 26.3% vs 66%, 25.4% vs 35% and 1.7% vs 25%. Also, an improvement in both metabolic (significant decrease in triglycerides and total cholesterol; p = 0.0139) and hormonal (significant increase in testosterone/oestradiol ratio; p = 0.0139) blood profiles was observed after following the lifestyle program. In seminal plasma, the amount of SOD2 has significantly increased (p = 0.0139) while in parallel carbonylated proteins have decreased. Furthermore, all spouses got pregnant. All pregnancies were brought to term.

Conclusion: This study shows specifically that sperm DNA fragmentation among men in subfertile couples could be affected by abdominal fat, but improvement of lifestyle factor may correct this alteration. The effect of specific abdominal fat loss on sperm quality needs further investigation. The reduction of oxidative stress may be a contributing factor.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0086300PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3919721PMC
October 2014

Proteome modulation in H9c2 cardiac cells by microRNAs miR-378 and miR-378.

Mol Cell Proteomics 2014 Jan 25;13(1):18-29. Epub 2013 Sep 25.

Team 1: Genetic and physiopathology of muscular tissues.

MicroRNAs are a novel class of powerful endogenous regulators of gene expression. MiR-378 and miR-378* are localized in the first intron of the Ppargc1b gene that codes the transcriptional co-activator PGC-1β. The latter regulates energy expenditure as well as mitochondrial biogenesis. The miR-378:miR-378* hairpin is highly expressed in cardiac cells. To better assess their role in cardiomyocytes, we identified miR-378 and miR-378* targets via a proteomic screen. We established H9c2 cellular models of overexpression of miR-378 and miR-378* and identified a total of 86 down-regulated proteins in the presence of either one of these miRs. Functional annotation clustering showed that miR-378 and miR-378* regulate related pathways in cardiomyocytes, including energy metabolism, notably glycolysis, cytoskeleton, notably actin filaments and muscle contraction. Using bioinformatics algorithms we found that 20 proteins were predicted as direct targets of the miRs. We validated eight of these targets by quantitative RT-PCR and luciferase reporter assay. We found that miR-378 targets lactate dehydrogenase A and impacts on cell proliferation and survival whereas miR-378* targets cytoskeleton proteins actin and vimentin. Proteins involved in endoplasmic reticulum stress response such as chaperone and/or calcium buffering proteins GRP78, PPIA (cyclophilin A), calumenin, and GMMPA involved in glycosylation are repressed by these miRs. Our results show that the miR-378/378* hairpin establishes a connection among energy metabolism, cytoskeleton remodeling, and endoplasmic reticulum function through post-transcriptional regulation of key proteins involved in theses pathways.
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http://dx.doi.org/10.1074/mcp.M113.030569DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3879613PMC
January 2014

Proteome alteration in oxidative stress-sensitive methionine sulfoxide reductase-silenced HEK293 cells.

Free Radic Biol Med 2013 Dec 27;65:1023-1036. Epub 2013 Aug 27.

Laboratoire de Biologie Cellulaire du Vieillissement, UR4, IFR83, Université Pierre et Marie Curie-Paris 6, 75005 Paris, France. Electronic address:

Methionine sulfoxide reductases (Msr's) are key enzymes proficient in catalyzing the reduction of oxidized methionines. This reductive trait is essential to maintaining cellular redox homeostasis from bacteria to mammals and is also regarded as a potential mechanism to regulate protein activities and signaling pathways, considering the inactivating effects that can be induced by methionine oxidation. In this study, we have generated stable human embryonic kidney HEK293 clones with an altered Msr system by silencing the expression of the main Msr elements-MsrA, MsrB1, or MsrB2. The isolated clones--the single mutants MsrA, MsrB1, and MsrB2 and double mutant MsrA/B1-show a reduced Msr activity and an exacerbated sensitivity toward oxidative stress. A two-dimensional difference in-gel electrophoresis analysis was performed on the Msr-silenced cells grown under basal conditions or submitted to oxidative stress. This proteomic analysis revealed that the disruption of the Msr system mainly affects proteins with redox, cytoskeletal or protein synthesis, and maintenance roles. Interestingly, most of the proteins found altered in the Msr mutants were also identified as potential Msr substrates and have been associated with redox or aging processes in previous studies. This study, through an extensive analysis of Msr-inhibited mutants, offers valuable input on the cellular network of a crucial maintenance system such as methionine sulfoxide reductases.
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http://dx.doi.org/10.1016/j.freeradbiomed.2013.08.008DOI Listing
December 2013

Differential expression and glycative damage affect specific mitochondrial proteins with aging in rat liver.

Biochim Biophys Acta 2013 Dec 30;1832(12):2057-67. Epub 2013 Jul 30.

Université Paris Diderot-Paris 7, Sorbonne Paris Cité, UFR SDV, 75205 Paris Cedex 13, France; Laboratoire de Biologie Cellulaire du Vieillissement, UR4-UPMC, IFR 83, Université Pierre et Marie Curie-Paris 6, 75252 Paris Cedex 05, France. Electronic address:

Aging is accompanied by the gradual deterioration of cell functions. Particularly, mitochondrial dysfunction, associated with an accumulation of damaged proteins, is of key importance due to the central role of these organelles in cellular metabolism. However, the detailed molecular mechanisms involved in such impairment have not been completely elucidated. In the present study, proteomic analyses looking at both changes at the expression level as well as to glycative modifications of the mitochondrial proteome were performed. Two-dimensional difference gel electrophoresis analysis revealed 16 differentially expressed proteins with aging. Thirteen exhibited a decreased expression and are crucial enzymes related to OXPHOS chain complex I/V components, TCA cycle or fatty acid β-oxidation reaction. On the other hand, 2 enzymes involved in fatty acid β-oxidation cycle were increased in aged mitochondria. Immunodetection and further identification of glycated proteins disclosed a set of advanced glycation end product-modified proteins, including 6 enzymes involved in the fatty acid β-oxidation process, and 2 enzymes of the TCA/urea cycles. A crucial antioxidant enzyme, catalase, was among the most strongly glycated proteins. In addition, several AGE-damaged enzymes (aldehyde dehydrogenase 2, medium chain acyl-CoA dehydrogenase and 3-ketoacyl-CoA dehydrogenase) exhibited a decreased activity with age. Taken together, these data suggest that liver mitochondria in old rats suffer from a decline in their capacity for energy production, due to (i) decreased expression of OXPHOS complex I/V components and (ii) glycative damage to key fatty acid β-oxidation and TCA/urea cycle enzymes.
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http://dx.doi.org/10.1016/j.bbadis.2013.07.015DOI Listing
December 2013

Proteomic quantification and identification of carbonylated proteins upon oxidative stress and during cellular aging.

J Proteomics 2013 Oct 18;92:63-70. Epub 2013 May 18.

Laboratoire de Biologie Cellulaire du Vieillissement, UR4-IFR83, Université Pierre et Marie Curie-Paris 6, 4 place Jussieu, 75252 Paris Cedex 05, France.

Unlabelled: Increased protein carbonyl content is a hallmark of cellular and organismal aging. Protein damage leading to the formation of carbonyl groups derives from direct oxidation of several amino acid side chains but can also derive through protein adducts formation with lipid peroxidation products and dicarbonyl glycating compounds. All these modifications have been implicated during oxidative stress, aging and age-related diseases. However, in most cases, the proteins targeted by these deleterious modifications as well as their consequences have not yet been clearly identified. Indeed, this is essential to determine whether and how these modified proteins are impacting on cellular function, on the development of the senescent phenotype and the pathogenesis of age-related diseases. In this context, protein modifications occurring during aging and upon oxidative stress as well as main proteomic methods for detecting, quantifying and identifying oxidized proteins are described. Relevant proteomics studies aimed at monitoring the extent of protein carbonylation and identifying the targeted proteins in the context of aging and oxidative stress are also presented. Proteomics approaches, i.e. fluorescent based 2D-gel electrophoresis and mass spectrometry methods, represent powerful tools for monitoring at the proteome level the extent of protein oxidative and related modifications and for identifying the targeted proteins.

Biological Significance: Accumulation of damaged macromolecules, including oxidatively damaged (carbonylated) proteins, is a hallmark of cellular and organismal aging. Since protein carbonyls are the most commonly used markers of protein oxidation, different methods have been developed for the detection and quantification of carbonylated proteins. The identification of these protein targets is of valuable interest in order to understand the mechanisms by which damaged proteins accumulate and potentially affect cellular functions during oxidative stress, cellular senescence and/or aging in vivo. The specificity of hydrazide derivatives to carbonyl groups and the presence of a wide range of functional groups coupled to the hydrazide, allowed the design of novel strategies for the detection and quantification of carbonylated proteins. Of note is the importance of fluorescent probes for monitoring carbonylated proteins. Proteomics approaches, i.e. fluorescent based 2D-gel electrophoresis and mass spectrometry methods, represent powerful tools for monitoring at the proteome level the extent of protein oxidative and related modifications and for identifying the targeted proteins. This article is part of a Special Issue entitled: Posttranslational Protein modifications in biology and Medicine.
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http://dx.doi.org/10.1016/j.jprot.2013.05.008DOI Listing
October 2013

Oxidative stress-induced proteome alterations target different cellular pathways in human myoblasts.

Free Radic Biol Med 2011 Oct 5;51(8):1522-32. Epub 2011 Jul 5.

Laboratoire de Biologie Cellulaire du Vieillissement, UR4, Université Pierre et Marie Curie-Paris 6, 75252 Paris Cedex 05, France.

Although increased oxidative stress has been associated with the impairment of proliferation and function of adult human muscle stem cells, proteins either involved in the stress response or damaged by oxidation have not been identified. A parallel proteomics approach was performed for analyzing the protein expression profile as well as proteins preferentially oxidized upon hydrogen peroxide-induced oxidative stress. Fifteen proteins involved in the oxidative stress response were identified. Among them, protein spots identified as peroxiredoxins 1 and 6, glyceraldehyde-3-phosphate dehydrogenase, and α-enolase were shifted to a more acidic isoelectric point upon oxidative stress, indicating posttranslational modifications. Oxidized proteins were evidenced by immunodetection of derivatized carbonyl groups followed by identification by mass spectrometry. The carbonylated proteins identified are mainly cytosolic and involved in carbohydrate metabolism, cellular assembly, cellular homeostasis, and protein synthesis and degradation. Pathway analysis revealed skeletal and muscular disorders, cell death, and cancer-related as the main molecular networks altered. Interestingly, these pathways were focused on two distinct proteins: p53 for altered protein expression and huntingtin for increased protein carbonylation. This study emphasizes the importance of performing analysis addressing different aspects of the cellular proteome to have a more accurate view of their changes upon stress.
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http://dx.doi.org/10.1016/j.freeradbiomed.2011.06.032DOI Listing
October 2011

Muscle creatine kinase deficiency triggers both actin depolymerization and desmin disorganization by advanced glycation end products in dilated cardiomyopathy.

J Biol Chem 2011 Oct 17;286(40):35007-19. Epub 2011 Jul 17.

Department of Aging, UPMC University Paris 6, 75005 Paris, France.

Alterations in the balance of cytoskeleton as well as energetic proteins are involved in the cardiac remodeling occurring in dilated cardiomyopathy (DCM). We used two-dimensional DIGE proteomics as a discovery approach to identify key molecular changes taking place in a temporally controlled model of DCM triggered by cardiomyocyte-specific serum response factor (SRF) knock-out in mice. We identified muscle creatine kinase (MCK) as the primary down-regulated protein followed by α-actin and α-tropomyosin down-regulation leading to a decrease of polymerized F-actin. The early response to these defects was an increase in the amount of desmin intermediate filaments and phosphorylation of the αB-crystallin chaperone. We found that αB-crystallin and desmin progressively lose their striated pattern and accumulate at the intercalated disk and the sarcolemma, respectively. We further show that desmin is a preferential target of advanced glycation end products (AGE) in mouse and human DCM. Inhibition of CK in cultured cardiomyocytes is sufficient to recapitulate both the actin depolymerization defect and the modification of desmin by AGE. Treatment with either cytochalasin D or glyoxal, a cellular AGE, indicated that both actin depolymerization and AGE contribute to desmin disorganization. Heat shock-induced phosphorylation of αB-crystallin provides a transient protection of desmin against glyoxal in a p38 MAPK-dependent manner. Our results show that the strong down-regulation of MCK activity contributes to F-actin instability and induces post-translational modification of αB-crystallin and desmin. Our results suggest that AGE may play an important role in DCM because they alter the organization of desmin filaments that normally support stress response and mitochondrial functions in cardiomyocytes.
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http://dx.doi.org/10.1074/jbc.M111.252395DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3186397PMC
October 2011