@article{steingruber_cyclins_2019,

title = {Cyclins B1, T1, and H differ in their molecular mode of interaction with cytomegalovirus protein kinase pUL97},

author = {Mirjam Steingruber and Lena Keller and Eileen Socher and Sabrina Ferre and Anne-Marie Hesse and Yohann Couté and Friedrich Hahn and Nicole Büscher and Bodo Plachter and Heinrich Sticht and Manfred Marschall},

doi = {10.1074/jbc.RA118.007049},

issn = {1083-351X},

year  = {2019},

date = {2019-01-01},

journal = {The Journal of Biological Chemistry},

volume = {294},

number = {15},

pages = {6188--6203},

abstract = {Human cytomegalovirus (HCMV) is a common $beta$-herpesvirus causing life-long latent infections. HCMV replication interferes with cell cycle regulation in host cells because the HCMV-encoded cyclin-dependent kinase (CDK) ortholog pUL97 extensively phosphorylates the checkpoint regulator retinoblastoma protein. pUL97 also interacts with cyclins B1, T1, and H, and recent findings have strongly suggested that these interactions influence pUL97 substrate recognition. Interestingly, here we detected profound mechanistic differences among these pUL97-cyclin interactions. Our study revealed the following. (i) pUL97 interacts with cyclins B1 and H in a manner dependent on pUL97 activity and HCMV-specific cyclin modulation, respectively. (ii) The phosphorylated state of both proteins is an important determinant of the pUL97-cyclin B1 interaction. (iii) Activated phospho-Thr-315 cyclin H is up-regulated during HCMV replication. (iv) Thr-315 phosphorylation is independent of intracellular pUL97 or CDK7 activity. (v) pUL97-mediated in vitro phosphorylation is detectable for cyclin B1 but not H. (vi) Mutual transphosphorylation between pUL97 and CDK7 is not detectable, and an MS-based phosphosite analysis indicated that pUL97 might unexpectedly not be phosphorylated in its T-loop. (vii) The binary complexes pUL97-cyclin H and CDK7-cyclin H as well as the ternary complex pUL97-cyclin-H-CDK7 are detectable in an assembly-based CoIP approach. (viii) pUL97 self-interaction can be bridged by the transcriptional cyclins T1 or H but not by the classical cell cycle-regulating B1 cyclin. Combined, our findings unravel a number of cyclin type-specific differences in pUL97 interactions and suggest a multifaceted regulatory impact of cyclins on HCMV replication.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{siebert_francisella_2019,

title = {Francisella tularensis: FupA mutation contributes to fluoroquinolone resistance by increasing vesicle secretion and biofilm formation},

author = {Claire Siebert and Helena Lindgren and Sabrina Ferré and Corinne Villers and Sandrine Boisset and Julien Perard and Anders Sjöstedt and Max Maurin and Céline Brochier-Armanet and Yohann Couté and Patricia Renesto},

doi = {10.1080/22221751.2019.1615848},

issn = {2222-1751},

year  = {2019},

date = {2019-01-01},

journal = {Emerging Microbes & Infections},

volume = {8},

number = {1},

pages = {808--822},

abstract = {Francisella tularensis is the causative agent in tularemia for which the high prevalence of treatment failure and relapse is a major concern. Directed-evolution experiments revealed that acquisition of fluoroquinolone (FQ) resistance was linked to factors in addition to mutations in DNA gyrase. Here, using F. tularensis live vaccine strain (LVS) as a model, we demonstrated that FupA/B (Fer-Utilization Protein) expression is linked to FQ susceptibility, and that the virulent strain F. tularensis subsp. tularensis SCHU S4 deleted for the homologous FupA protein exhibited even higher FQ resistance. In addition to an increased FQ minimal inhibitory concentration, LVS$Delta$fupA/B displayed tolerance toward bactericidal compounds including ciprofloxacin and gentamicin. Interestingly, the FupA/B deletion was found to promote increased secretion of outer membrane vesicles (OMVs). Mass spectrometry-based quantitative proteomic characterization of vesicles from LVS and LVS∆fupA/B identified 801 proteins, including a subset of 23 proteins exhibiting differential abundance between both strains which may therefore contribute to the reduced antibiotic susceptibility of the FupA/B-deleted strain. We also demonstrated that OMVs are key structural elements of LVS$Delta$fupA/B biofilms providing protection against FQ. These results provide a new basis for understanding and tackling antibiotic resistance and/or persistence of Francisella and other pathogenic members of the Thiotrichales class.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{lupette_architecture_2019,

title = {The architecture of lipid droplets in the diatom Phaeodactylum tricornutum},

author = {Josselin Lupette and Antoine Jaussaud and Khawla Seddiki and Christian Morabito and Sabine Brugière and Hubert Schaller and Marcel Kuntz and Jean-Luc Putaux and Pierre-Henri Jouneau and Fabrice Rébeillé and Denis Falconet and Yohann Couté and Juliette Jouhet and Marianne Tardif and Juliette Salvaing and Eric Maréchal},

url = {http://www.sciencedirect.com/science/article/pii/S2211926418309160},

doi = {10.1016/j.algal.2019.101415},

issn = {2211-9264},

year  = {2019},

date = {2019-01-01},

journal = {Algal Research},

volume = {38},

pages = {101415},

abstract = {Diatoms are a major phylum of phytoplankton biodiversity and a resource considered for biotechnological developments, as feedstock for biofuels and applications ranging from food, human health or green chemistry. They contain a secondary plastid limited by four membranes, the outermost one being connected with the endoplasmic reticulum (ER). Upon nitrogen stress, diatoms reallocate carbon to triacylglycerol storage inside lipid droplets (LDs). The comprehensive glycerolipid and sterol composition and the architecture of diatom LDs are unknown. In Phaeodactylum tricornutum, LDs are in contact with plastid, mitochondria and uncharacterized endomembranes. We purified LDs from nitrogen-starved P. tricornutum cells to high purity level (99 mol% triacylglycerol of total glycerolipids). We used the Stramenopile Lipid Droplet Protein (StLDP) as a previously validated marker for the identity of P. tricornutum LD. Amphipathic lipids surrounding LDs consist of a betaine lipid, diacylglycerylhydroxymethyltrimethyl‑$beta$‑alanine (0.4 mol%); sulfoquinovosyldiacylglycerol (0.35 mol%); phosphatidylcholine (0.15 mol%) and one sterol, brassicasterol. By contrast with whole cell extracts, the betaine lipid from LDs only contains eicosapentaenoic acid paired with palmitoleic or palmitolenic acids. This polar lipid composition suggests a budding of LDs from the cytosolic leaflet of the plastid outermost membrane. LD pigments reveal a specific accumulation of $beta$‑carotene. The LD proteome obtained from three independent biological replicates, based on stringent filtering of extracted data, and following subtraction of proteins downregulated by nitrogen starvation, highlights a core proteome of 86 proteins, including StLDP. LD-associated proteins suggest connections with vesicular trafficking (coatomer, clathrin), cytoskeleton, plastid and mitochondria. Unsuspected LD-associated function includes protein synthesis (ribosomes), folding (chaperones), posttranslational modifications and quality control (ubiquitination and ERAD pathway), possibly preparing translation of specific mRNAs. The detection of histone proteins, as previously demonstrated in drosophila embryo LDs, also suggests the storage of nucleosome components, preparing cell division and chromatin packaging, when cells are not stressed anymore.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{bouchnak_unraveling_2019,

title = {Unraveling Hidden Components of the Chloroplast Envelope Proteome: Opportunities and Limits of Better MS Sensitivity},

author = {Imen Bouchnak and Sabine Brugière and Lucas Moyet and Sophie Le Gall and Daniel Salvi and Marcel Kuntz and Marianne Tardif and Norbert Rolland},

doi = {10.1074/mcp.RA118.000988},

issn = {1535-9484},

year  = {2019},

date = {2019-01-01},

journal = {Molecular & cellular proteomics: MCP},

volume = {18},

number = {7},

pages = {1285--1306},

abstract = {The chloroplast is a major plant cell organelle that fulfills essential metabolic and biosynthetic functions. Located at the interface between the chloroplast and other cell compartments, the chloroplast envelope system is a strategic barrier controlling the exchange of ions, metabolites and proteins, thus regulating essential metabolic functions (synthesis of hormones precursors, amino acids, pigments, sugars, vitamins, lipids, nucleotides etc.) of the plant cell. However, unraveling the contents of the chloroplast envelope proteome remains a difficult challenge; many proteins constituting this functional double membrane system remain to be identified. Indeed, the envelope contains only 1% of the chloroplast proteins (i.e. 0.4% of the whole cell proteome). In other words, most envelope proteins are so rare at the cell, chloroplast, or even envelope level, that they remained undetectable using targeted MS studies. Cross-contamination of chloroplast subcompartments by each other and by other cell compartments during cell fractionation, impedes accurate localization of many envelope proteins. The aim of the present study was to take advantage of technologically improved MS sensitivity to better define the proteome of the chloroplast envelope (differentiate genuine envelope proteins from contaminants). This MS-based analysis relied on an enrichment factor that was calculated for each protein identified in purified envelope fractions as compared with the value obtained for the same protein in crude cell extracts. Using this approach, a total of 1269 proteins were detected in purified envelope fractions, of which, 462 could be assigned an envelope localization by combining MS-based spectral count analyses with manual annotation using data from the literature and prediction tools. Many of such proteins being previously unknown envelope components, these data constitute a new resource of significant value to the broader plant science community aiming to define principles and molecular mechanisms controlling fundamental aspects of plastid biogenesis and functions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{moulin_towards_2019,

title = {Towards a molecular understanding of the water purification properties of Moringa seed proteins},

author = {M Moulin and E Mossou and L Signor and S Kieffer-Jaquinod and H M Kwaambwa and F Nermark and P Gutfreund and E P Mitchell and M Haertlein and V T Forsyth and A R Rennie},

doi = {10.1016/j.jcis.2019.06.071},

issn = {1095-7103},

year  = {2019},

date = {2019-01-01},

journal = {Journal of Colloid and Interface Science},

volume = {554},

pages = {296--304},

abstract = {Seed extracts from Moringa oleifera are of wide interest for use in water purification where they can play an important role in flocculation; they also have potential as anti-microbial agents. Previous work has focused on the crude protein extract. Here we describe the detailed biophysical characterization of individual proteins from these seeds. The results provide new insights relating to the active compounds involved. One fraction, designated Mo-CBP3, has been characterized at a molecular level using a range of biochemical and biophysical techniques including liquid chromatography, X-ray diffraction, mass spectrometry, and neutron reflection. The interfacial behavior is of particular interest in considering water purification applications and interactions with both charged (e.g. silica) and uncharged (alumina) surfaces were studied. The reflection studies show that, in marked contrast to the crude extract, only a single layer of the purified Mo-CBP3 binds to a silica interface and that there is no binding to an alumina interface. These observations are consistent with the crystallographic structure of Mo-CBP3-4, which is one of the main isoforms of the Mo-CBP3 fraction. The results are put in context of previous studies of the properties of the crude extract. This work shows possible routes to development of separation processes that would be based on the specific properties of individual proteins.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{hajj_chehade_soluble_2019,

title = {A Soluble Metabolon Synthesizes the Isoprenoid Lipid Ubiquinone},

author = {Mahmoud Hajj Chehade and Ludovic Pelosi and Cameron David Fyfe and Laurent Loiseau and Bérengère Rascalou and Sabine Brugière and Katayoun Kazemzadeh and Chau-Duy-Tam Vo and Lidia Ciccone and Laurent Aussel and Yohann Couté and Marc Fontecave and Frédéric Barras and Murielle Lombard and Fabien Pierrel},

doi = {10.1016/j.chembiol.2018.12.001},

issn = {2451-9448},

year  = {2019},

date = {2019-01-01},

journal = {Cell Chemical Biology},

volume = {26},

number = {4},

pages = {482----492.e7},

abstract = {Ubiquinone (UQ) is a polyprenylated lipid that is conserved from bacteria to humans and is crucial to cellular respiration. How the cell orchestrates the efficient synthesis of UQ, which involves the modification of extremely hydrophobic substrates by multiple sequential enzymes, remains an unresolved issue. Here, we demonstrate that seven Ubi proteins form the Ubi complex, a stable metabolon that catalyzes the last six reactions of the UQ biosynthetic pathway in Escherichia coli. The SCP2 domain of UbiJ forms an extended hydrophobic cavity that binds UQ intermediates inside the 1-MDa Ubi complex. We purify the Ubi complex from cytoplasmic extracts and demonstrate that UQ biosynthesis occurs in this fraction, challenging the current thinking of a membrane-associated biosynthetic process. Collectively, our results document a rare case of stable metabolon and highlight how the supramolecular organization of soluble enzymes allows the modification of hydrophobic substrates in a hydrophilic environment.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{sentausa_insertion_2019,

title = {Insertion sequences drive the emergence of a highly adapted human pathogen},

author = {Erwin Sentausa and Pauline Basso and Alice Berry and Annie Adrait and Gwendoline Bellement and Yohann Couté and Stephen Lory and Sylvie Elsen and Ina Attrée},

doi = {10.1099/mgen.0.000265},

issn = {2057-5858},

year  = {2019},

date = {2019-01-01},

journal = {Microbial Genomics},

abstract = {Pseudomonas aeruginosa is a highly adaptive opportunistic pathogen that can have serious health consequences in patients with lung disorders. Taxonomic outliers of P. aeruginosa of environmental origin have recently emerged as infectious for humans. Here, we present the first genome-wide analysis of an isolate that caused fatal haemorrhagic pneumonia. In two clones, CLJ1 and CLJ3, sequentially recovered from a patient with chronic pulmonary disease, insertion of a mobile genetic element into the P. aeruginosa chromosome affected major virulence-associated phenotypes and led to increased resistance to the antibiotics used to combat the infection. Comparative genome, proteome and transcriptome analyses revealed that this ISL3-family insertion sequence disrupted the genes for flagellar components, type IV pili, O-specific antigens, translesion polymerase and enzymes producing hydrogen cyanide. Seven-fold more insertions were detected in the later isolate, CLJ3, than in CLJ1, some of which modified strain susceptibility to antibiotics by disrupting the genes for the outer-membrane porin OprD and the regulator of $beta$-lactamase expression AmpD. In the Galleria mellonella larvae model, the two strains displayed different levels of virulence, with CLJ1 being highly pathogenic. This study revealed insertion sequences to be major players in enhancing the pathogenic potential of a P. aeruginosa taxonomic outlier by modulating both its virulence and its resistance to antimicrobials, and explains how this bacterium adapts from the environment to a human host.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{braun_toxoplasma_2019,

title = {The Toxoplasma effector TEEGR promotes parasite persistence by modulating NF-$kappa$B signalling via EZH2},

author = {Laurence Braun and Marie-Pierre Brenier-Pinchart and Pierre-Mehdi Hammoudi and Dominique Cannella and Sylvie Kieffer-Jaquinod and Julien Vollaire and Véronique Josserand and Bastien Touquet and Yohann Couté and Isabelle Tardieux and Alexandre Bougdour and Mohamed-Ali Hakimi},

doi = {10.1038/s41564-019-0431-8},

issn = {2058-5276},

year  = {2019},

date = {2019-01-01},

journal = {Nature Microbiology},

volume = {4},

number = {7},

pages = {1208--1220},

abstract = {The protozoan parasite Toxoplasma gondii has co-evolved with its homeothermic hosts (humans included) strategies that drive its quasi-asymptomatic persistence in hosts, hence optimizing the chance of transmission to new hosts. Persistence, which starts with a small subset of parasites that escape host immune killing and colonize the so-called immune privileged tissues where they differentiate into a low replicating stage, is driven by the interleukin 12 (IL-12)-interferon-$gamma$ (IFN-$gamma$) axis. Recent characterization of a family of Toxoplasma effectors that are delivered into the host cell, in which they rewire the host cell gene expression, has allowed the identification of regulators of the IL-12-IFN-$gamma$ axis, including repressors. We now report on the dense granule-resident effector, called TEEGR (Toxoplasma E2F4-associated EZH2-inducing gene regulator) that counteracts the nuclear factor-$kappa$B (NF-$kappa$B) signalling pathway. Once exported into the host cell, TEEGR ends up in the nucleus where it not only complexes with the E2F3 and E2F4 host transcription factors to induce gene expression, but also promotes shaping of a non-permissive chromatin through its capacity to switch on EZH2. Remarkably, EZH2 fosters the epigenetic silencing of a subset of NF-$kappa$B-regulated cytokines, thereby strongly contributing to the host immune equilibrium that influences the host immune response and promotes parasite persistence in mice.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{darrieutort-laffite_rotator_2019,

title = {Rotator Cuff Tenocytes Differentiate into Hypertrophic Chondrocyte-Like Cells to Produce Calcium Deposits in an Alkaline Phosphatase-Dependent Manner},

author = {Christelle Darrieutort-Laffite and Paul Arnolfo and Thomas Garraud and Annie Adrait and Yohann Couté and Guy Louarn and Valérie Trichet and Pierre Layrolle and Benoit Le Goff and Frédéric Blanchard},

doi = {10.3390/jcm8101544},

issn = {2077-0383},

year  = {2019},

date = {2019-01-01},

journal = {Journal of Clinical Medicine},

volume = {8},

number = {10},

abstract = {Calcific tendonitis is a frequent cause of chronic shoulder pain. Its cause is currently poorly known. The objectives of this study were to better characterize the cells and mechanisms involved in depositing apatite crystals in human tendons. Histologic sections of cadaveric calcified tendons were analyzed, and human calcific deposits from patients undergoing lavage of their calcification were obtained to perform infrared spectroscopy and mass spectrometry-based proteomic characterizations. In vitro, the mineralization ability of human rotator cuff cells from osteoarthritis donors was assessed by alizarin red or Von Kossa staining. Calcifications were amorphous areas surrounded by a fibrocartilaginous metaplasia containing hypertrophic chondrocyte-like cells that expressed tissue non-specific alkaline phosphatase (TNAP) and ectonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1), which are two key enzymes of the mineralization process. Calcific deposits were composed of apatite crystals associated with proteins involved in bone and cartilage development and endochondral bone growth. In vitro, tenocyte-like cells extracted from the rotator cuff were able to mineralize in osteogenic cultures, and expressed TNAP, type X COLLAGEN, and MMP13, which are hypertrophic chondrocytes markers. The use of a TNAP inhibitor significantly prevented mineral deposits. We provide evidence that tenocytes have a propensity to differentiate into hypertrophic chondrocyte-like cells to produce TNAP-dependent calcium deposits. We believe that these results may pave the way to identifying regulating factors that might represent valuable targets in calcific tendonitis.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{bhalla_interactome_2019,

title = {Interactome of the yeast RNA polymerase III transcription machinery constitutes several chromatin modifiers and regulators of the genes transcribed by RNA polymerase II},

author = {Pratibha Bhalla and Dipti Vinayak Vernekar and Benoit Gilquin and Yohann Couté and Purnima Bhargava},

doi = {10.1016/j.gene.2018.12.037},

issn = {1879-0038},

year  = {2019},

date = {2019-01-01},

journal = {Gene},

volume = {702},

pages = {205--214},

abstract = {Eukaryotic transcription is a highly regulated fundamental life process. A large number of regulatory proteins and complexes, many of them with sequence-specific DNA-binding activity are known to influence transcription by RNA polymerase (pol) II with a fine precision. In comparison, only a few regulatory proteins are known for pol III, which transcribes genes encoding small, stable, non-translated RNAs. The pol III transcription is precisely regulated under various stress conditions. We used pol III transcription complex (TC) components TFIIIC (Tfc6), pol III (Rpc128) and TFIIIB (Brf1) as baits and mass spectrometry to identify their potential interactors in vivo. A large interactome constituting chromatin modifiers, regulators and factors of transcription by pol I and pol II supports the possibility of a crosstalk between the three transcription machineries. The association of proteins and complexes involved in various basic life processes like ribogenesis, RNA processing, protein folding and degradation, DNA damage response, replication and transcription underscores the possibility of the pol III TC serving as a signaling hub for communication between the transcription and other cellular physiological activities under normal growth conditions. We also found an equally large number of proteins and complexes interacting with the TC under nutrient starvation condition, of which at least 25% were non-identical under the two conditions. The data reveal the possibility of a large number of signaling cues for pol III transcription against adverse conditions, necessary for an efficient co-ordination of various cellular functions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{jeudy_exploration_2019,

title = {Exploration of the propagation of transpovirons within Mimiviridae reveals a unique example of commensalism in the viral world},

author = {Sandra Jeudy and Lionel Bertaux and Jean-Marie Alempic and Audrey Lartigue and Matthieu Legendre and Lucid Belmudes and Sébastien Santini and Nadège Philippe and Laure Beucher and Emanuele G Biondi and Sissel Juul and Daniel J Turner and Yohann Couté and Jean-Michel Claverie and Chantal Abergel},

doi = {10.1038/s41396-019-0565-y},

issn = {1751-7370},

year  = {2019},

date = {2019-01-01},

journal = {The ISME journal},

abstract = {Acanthamoeba-infecting Mimiviridae are giant viruses with dsDNA genome up to 1.5 Mb. They build viral factories in the host cytoplasm in which the nuclear-like virus-encoded functions take place. They are themselves the target of infections by 20-kb-dsDNA virophages, replicating in the giant virus factories and can also be found associated with 7-kb-DNA episomes, dubbed transpovirons. Here we isolated a virophage (Zamilon vitis) and two transpovirons respectively associated to B- and C-clade mimiviruses. We found that the virophage could transfer each transpoviron provided the host viruses were devoid of a resident transpoviron (permissive effect). If not, only the resident transpoviron originally isolated from the corresponding virus was replicated and propagated within the virophage progeny (dominance effect). Although B- and C-clade viruses devoid of transpoviron could replicate each transpoviron, they did it with a lower efficiency across clades, suggesting an ongoing process of adaptive co-evolution. We analysed the proteomes of host viruses and virophage particles in search of proteins involved in this adaptation process. This study also highlights a unique example of intricate commensalism in the viral world, where the transpoviron uses the virophage to propagate and where the Zamilon virophage and the transpoviron depend on the giant virus to replicate, without affecting its infectious cycle.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{dellaglio_identification_2019,

title = {Identification of the Arabidopsis calmodulin-dependent NAD+ kinase that sustains the elicitor-induced oxidative burst},

author = {Elisa Dell'Aglio and Cecile Giustini and Alexandra Kraut and Yohann Couté and Alex Costa and Guillaume Decros and Yves Gibon and Christian Mazars and Michel Matringe and Giovanni Finazzi and Gilles Curien},

doi = {10.1104/pp.19.00912},

issn = {1532-2548},

year  = {2019},

date = {2019-01-01},

journal = {Plant Physiology},

abstract = {NADP(H) is an essential cofactor of multiple metabolic processes in all living organisms, and in plants, NADP(H) is required as the substrate of Ca2+-dependent NADPH oxidases, which catalyze a reactive oxygen species burst in response to various stimuli. While NADP+ production in plants has long been known to involve a calmodulin (CaM)/Ca2+- dependent NAD+ kinase, the nature of the enzyme catalyzing this activity has remained enigmatic, as has its role in plant physiology. Here, we used proteomic, biochemical, molecular and in vivo analyses to identify an Arabidopsis (Arabidopsis thaliana) protein that catalyzes NADP+ production exclusively in the presence of CaM/Ca2+. This enzyme, which we named NAD kinase-CaM dependent (NADKc), has a CaM-binding peptide located in its N-terminal region and displays peculiar biochemical properties as well as different domain organization compared to known plant NAD+ kinases. In response to a pathogen elicitor, activity of NADKc, which is associated with the mitochondrial periphery, contributes to an increase in the cellular NADP+ concentration and to the amplification of the elicitor-induced oxidative burst. Based on a phylogenetic analysis and enzymatic assays, we propose the CaM/Ca2+-dependent NAD+ kinase activity found in photosynthetic organisms is carried out by NADKc-related proteins. Thus, NADKc represents the missing link between Ca2+ signalling, metabolism and the oxidative burst.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{chapelle_dissecting_2019,

title = {Dissecting the Shared and Context-Dependent Pathways Mediated by the p140Cap Adaptor Protein in Cancer and in Neurons},

author = {Jennifer Chapelle and Oksana Sorokina and Colin McLean and Vincenzo Salemme and Annalisa Alfieri and Costanza Angelini and Alessandro Morellato and Annie Adrait and Elisabetta Menna and Michela Matteoli and Yohann Couté and Ugo Ala and Emilia Turco and Paola Defilippi and Douglas J Armstrong},

url = {https://www.frontiersin.org/article/10.3389/fcell.2019.00222/full},

doi = {10.3389/fcell.2019.00222},

issn = {2296-634X},

year  = {2019},

date = {2019-01-01},

journal = {Frontiers in Cell and Developmental Biology},

volume = {7},

pages = {222},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{sonego_usp1_2019,

title = {USP1 links platinum resistance to cancer cell dissemination by regulating Snail stability},

author = {Maura Sonego and Ilenia Pellarin and Alice Costa and Gian Luca Rampioni Vinciguerra and Michela Coan and Alexandra Kraut and Sara D'Andrea and Alessandra Dall'Acqua and Dan Cacsire Castillo-Tong and Daniela Califano and Simona Losito and Riccardo Spizzo and Yohann Couté and Andrea Vecchione and Barbara Belletti and Monica Schiappacassi and Gustavo Baldassarre},

doi = {10.1126/sciadv.aav3235},

issn = {2375-2548},

year  = {2019},

date = {2019-01-01},

journal = {Science Advances},

volume = {5},

number = {5},

pages = {eaav3235},

abstract = {Resistance to platinum-based chemotherapy is a common event in patients with cancer, generally associated with tumor dissemination and metastasis. Whether platinum treatment per se activates molecular pathways linked to tumor spreading is not known. Here, we report that the ubiquitin-specific protease 1 (USP1) mediates ovarian cancer cell resistance to platinum, by regulating the stability of Snail, which, in turn, promotes tumor dissemination. At the molecular level, we observed that upon platinum treatment, USP1 is phosphorylated by ATM and ATR and binds to Snail. Then, USP1 de-ubiquitinates and stabilizes Snail expression, conferring resistance to platinum, increased stem cell-like features, and metastatic ability. Consistently, knockout or pharmacological inhibition of USP1 increased platinum sensitivity and decreased metastatic dissemination in a Snail-dependent manner. Our findings identify Snail as a USP1 target and open the way to a novel strategy to overcome platinum resistance and more successfully treat patients with ovarian cancer.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{louwagie_ultrasensitive_2019,

title = {Ultrasensitive Quantification of Recombinant Proteins Using AAA-MS},

author = {Mathilde Louwagie and Sylvie Kieffer-Jaquinod and Virginie Brun},

doi = {10.1007/978-1-4939-9639-1_1},

issn = {1940-6029},

year  = {2019},

date = {2019-01-01},

journal = {Methods in Molecular Biology (Clifton, N.J.)},

volume = {2030},

pages = {1--10},

abstract = {Recombinant proteins are essential components of therapeutic, biotechnological, food, and household products. In some cases, recombinant proteins must be purified and their quantity and/or concentration precisely determined. In this chapter, we describe a protocol for the quantification of purified recombinant proteins. The protocol is based on a microwave-assisted acidic hydrolysis of the target protein followed by high-resolution mass spectrometry (HRMS) analysis of the hydrolytic products. Absolute quantification is obtained by adding controlled amounts of labeled amino acids that serve as standards.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{chiumento_ruminococcin_2019,

title = {Ruminococcin C, a promising antibiotic produced by a human gut symbiont},

author = {Steve Chiumento and Clarisse Roblin and Sylvie Kieffer-Jaquinod and Sybille Tachon and Chloé Leprètre and Christian Basset and Dwi Aditiyarini and Hamza Olleik and Cendrine Nicoletti and Olivier Bornet and Olga Iranzo and Marc Maresca and Renaud Hardré and Michel Fons and Thierry Giardina and Estelle Devillard and Françoise Guerlesquin and Yohann Couté and Mohamed Atta and Josette Perrier and Mickael Lafond and Victor Duarte},

doi = {10.1126/sciadv.aaw9969},

issn = {2375-2548},

year  = {2019},

date = {2019-01-01},

journal = {Science Advances},

volume = {5},

number = {9},

pages = {eaaw9969},

abstract = {A major public health challenge today is the resurgence of microbial infections caused by multidrug-resistant strains. Consequently, novel antimicrobial molecules are actively sought for development. In this context, the human gut microbiome is an under-explored potential trove of valuable natural molecules, such as the ribosomally-synthesized and post-translationally modified peptides (RiPPs). The biological activity of the sactipeptide subclass of RiPPs remains under-characterized. Here, we characterize an antimicrobial sactipeptide, Ruminococcin C1, purified from the caecal contents of rats mono-associated with Ruminococcus gnavus E1, a human symbiont. Its heterologous expression and post-translational maturation involving a specific sactisynthase establish a thioether network, which creates a double-hairpin folding. This original structure confers activity against pathogenic Clostridia and multidrug-resistant strains but no toxicity towards eukaryotic cells. Therefore, the Ruminococcin C1 should be considered as a valuable candidate for drug development and its producer strain R. gnavus E1 as a relevant probiotic for gut health enhancement.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nguyen_designing_2019,

title = {Designing an In Silico Strategy to Select Tissue-Leakage Biomarkers Using the Galaxy Framework},

author = {Lien Nguyen and Virginie Brun and Florence Combes and Valentin Loux and Yves Vandenbrouck},

doi = {10.1007/978-1-4939-9164-8_18},

issn = {1940-6029},

year  = {2019},

date = {2019-01-01},

journal = {Methods in Molecular Biology (Clifton, N.J.)},

volume = {1959},

pages = {275--289},

abstract = {Knowledge-based approaches using large-scale biological ("omics") data are a powerful way to identify mechanistic biomarkers, provided that scientists have access to computational solutions even when they have little programming experience or bioinformatics support. To achieve this goal, we designed a set of tools under the Galaxy framework to allow biologists to define their own strategy for reproducible biomarker selection. These tools rely on retrieving experimental data from public databases, and applying successive filters derived from information relating to disease pathophysiology. A step-by-step protocol linking these tools was implemented to select tissue-leakage biomarker candidates of myocardial infarction. A list of 24 candidates suitable for experimental assessment by MS-based proteomics is proposed. These tools have been made publicly available at http://www.proteore.org , allowing researchers to reuse them in their quest for biomarker discovery.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{beurton_physical_2019,

title = {Physical and functional interaction between SET1/COMPASS complex component CFP-1 and a Sin3S HDAC complex in C. elegans},

author = {Flore Beurton and Przemyslaw Stempor and Matthieu Caron and Alex Appert and Yan Dong and Ron A -J Chen and David Cluet and Yohann Couté and Marion Herbette and Ni Huang and Hélène Polveche and Martin Spichty and Cécile Bedet and Julie Ahringer and Francesca Palladino},

doi = {10.1093/nar/gkz880},

issn = {1362-4962},

year  = {2019},

date = {2019-01-01},

journal = {Nucleic Acids Research},

abstract = {The CFP1 CXXC zinc finger protein targets the SET1/COMPASS complex to non-methylated CpG rich promoters to implement tri-methylation of histone H3 Lys4 (H3K4me3). Although H3K4me3 is widely associated with gene expression, the effects of CFP1 loss vary, suggesting additional chromatin factors contribute to context dependent effects. Using a proteomics approach, we identified CFP1 associated proteins and an unexpected direct link between Caenorhabditis elegans CFP-1 and an Rpd3/Sin3 small (SIN3S) histone deacetylase complex. Supporting a functional connection, we find that mutants of COMPASS and SIN3 complex components genetically interact and have similar phenotypic defects including misregulation of common genes. CFP-1 directly binds SIN-3 through a region including the conserved PAH1 domain and recruits SIN-3 and the HDA-1/HDAC subunit to H3K4me3 enriched promoters. Our results reveal a novel role for CFP-1 in mediating interaction between SET1/COMPASS and a Sin3S HDAC complex at promoters.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{borges_distinguishing_2019,

title = {Distinguishing between Spectral Clustering and Cluster Analysis of Mass Spectra},

author = {Hélène Borges and Romain Guibert and Olga Permiakova and Thomas Burger},

doi = {10.1021/acs.jproteome.8b00516},

issn = {1535-3907},

year  = {2019},

date = {2019-01-01},

journal = {Journal of Proteome Research},

volume = {18},

number = {1},

pages = {571--573},

abstract = {The term "spectral clustering" is sometimes used to refer to the clustering of mass spectrometry data. However, it also classically refers to a family of popular clustering algorithms. To avoid confusion, a more specific term could advantageously be coined.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{wieczorek_protein-level_2019,

title = {Protein-Level Statistical Analysis of Quantitative Label-Free Proteomics Data with ProStaR},

author = {Samuel Wieczorek and Florence Combes and Hélène Borges and Thomas Burger},

doi = {10.1007/978-1-4939-9164-8_15},

issn = {1940-6029},

year  = {2019},

date = {2019-01-01},

journal = {Methods in Molecular Biology (Clifton, N.J.)},

volume = {1959},

pages = {225--246},

abstract = {ProStaR is a software tool dedicated to differential analysis in label-free quantitative proteomics. Practically, once biological samples have been analyzed by bottom-up mass spectrometry-based proteomics, the raw mass spectrometer outputs are processed by bioinformatics tools, so as to identify peptides and quantify them, by means of precursor ion chromatogram integration. Then, it is classical to use these peptide-level pieces of information to derive the identity and quantity of the sample proteins before proceeding with refined statistical processing at protein-level, so as to bring out proteins which abundance is significantly different between different groups of samples. To achieve this statistical step, it is possible to rely on ProStaR, which allows the user to (1) load correctly formatted data, (2) clean them by means of various filters, (3) normalize the sample batches, (4) impute the missing values, (5) perform null hypothesis significance testing, (6) check the well-calibration of the resulting p-values, (7) select a subset of differentially abundant proteins according to some false discovery rate, and (8) contextualize these selected proteins into the Gene Ontology. This chapter provides a detailed protocol on how to perform these eight processing steps with ProStaR.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pinaud_molecular_2019,

title = {Molecular characterisation of immunological memory following homologous or heterologous challenges in the schistosomiasis vector snail, Biomphalaria glabrata},

author = {Silvain Pinaud and Anaïs Portet and Jean-François Allienne and Lucid Belmudes and Cécile Saint-Beat and Nathalie Arancibia and Richard Galinier and Louis Du Pasquier and David Duval and Benjamin Gourbal},

doi = {10.1016/j.dci.2018.12.001},

issn = {1879-0089},

year  = {2019},

date = {2019-01-01},

journal = {Developmental and Comparative Immunology},

volume = {92},

pages = {238--252},

abstract = {Invertebrate immune response may be primed by a current infection in a sustained manner, leading to the failure of a secondary infection with the same pathogen. The present study focuses on the Schistosomiasis vector snail Biomphalaria glabrata, in which a specific genotype-dependent immunological memory was demonstrated as a shift from a cellular to a humoral immune response. Herein, we investigate the complex molecular bases associated with this genotype-dependant immunological memory response. We demonstrate that Biomphalaria regulates a polymorphic set of immune recognition molecules and immune effector repertoires to respond to different strains of Schistosoma parasites. These results suggest a combinatorial usage of pathogen recognition receptors (PRRs) that distinguish different strains of parasites during the acquisition of immunological memory. Immunizations also show that snails become resistant after exposure to parasite extracts. Hemolymph transfer and a label-free proteomic analysis proved that circulating hemolymph compounds can be produced and released to more efficiently kill the newly encountered parasite of the same genetic lineage.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{deutsch_human_2019,

title = {Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0},

author = {Eric W Deutsch and Lydie Lane and Christopher M Overall and Nuno Bandeira and Mark S Baker and Charles Pineau and Robert L Moritz and Fernando Corrales and Sandra Orchard and Jennifer E Van Eyk and Young-Ki Paik and Susan T Weintraub and Yves Vandenbrouck and Gilbert S Omenn},

doi = {10.1021/acs.jproteome.9b00542},

issn = {1535-3907},

year  = {2019},

date = {2019-01-01},

journal = {Journal of Proteome Research},

abstract = {The Human Proteome Organization's (HUPO) Human Proteome Project (HPP) developed Mass Spectrometry (MS) Data Interpretation Guidelines that have been applied since 2016. These guidelines have helped ensure that the emerging draft of the complete human proteome is highly accurate and with low numbers of false-positive protein identifications. Here, we describe an update to these guidelines based on consensus-reaching discussions with the wider HPP community over the past year. The revised 3.0 guidelines address several major and minor identified gaps. We have added guidelines for emerging data independent acquisition (DIA) MS workflows and for use of the new Universal Spectrum Identifier (USI) system being developed by the HUPO Proteomics Standards Initiative (PSI). In addition, we discuss updates to the standard HPP pipeline for collecting MS evidence for all proteins in the HPP, including refinements to minimum evidence. We present a new plan for incorporating MassIVE-KB into the HPP pipeline for the next (HPP 2020) cycle in order to obtain more comprehensive coverage of public MS data sets. The main checklist has been reorganized under headings and subitems, and related guidelines have been grouped. In sum, Version 2.1 of the HPP MS Data Interpretation Guidelines has served well, and this timely update to version 3.0 will aid the HPP as it approaches its goal of collecting and curating MS evidence of translation and expression for all predicted ∼20 000 human proteins encoded by the human genome.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{626b,

title = {Dissociating effect of salivary gland extract from Ixodes ricinus on human fibroblasts: Potential impact on Borrelia transmission},

author = {A Boeuf and G Schnell and Q Bernard and A Kern and B Westermann and L Ehret-Sabatier and A Grillon and F Schramm and B Jaulhac and N Boulanger},

doi = {10.1016/j.ttbdis.2018.12.005},

year  = {2018},

date = {2018-12-23},

journal = {Ticks Tick Borne Dis.},

volume = {10},

number = {2},

pages = {433–441},

note = {2012/29},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{625b,

title = {Analysis of femurs from mice embarked on board BION-M1 biosatellite reveals a decrease in immune cell development, including B cells, after 1 wk of recovery on Earth},

author = {G Tascher and M Gerbaix and P Maes and B Chazarin and S Ghislin and E Antropova and G Vassilieva and N Ouzren-Zarhloul and G Gauquelin-Koch and L Vico and JP. Frippiat and F Bertile},

doi = {10.1096/fj.201801463R},

year  = {2018},

date = {2018-12-06},

journal = {FASEB J.},

volume = {33},

number = {3},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{jonckheere_short-_2018,

title = {Short- and long-term efficacy of electroconvulsive stimulation in animal models of depression: The essential role of neuronal survival},

author = {Julie Jonckheere and Jean-Christophe Deloulme and Gaëlle Dall'Igna and Nicolas Chauliac and Albane Pelluet and Anne-Sophie Nguon and Celia Lentini and Jacques Brocard and Eric Denarier and Sabine Brugière and Yohann Couté and Christophe Heinrich and Christophe Porcher and Jérôme Holtzmann and Annie Andrieux and Marie-Françoise Suaud-Chagny and Sylvie Gory-Fauré},

doi = {10.1016/j.brs.2018.08.001},

issn = {1876-4754},

year  = {2018},

date = {2018-12-01},

journal = {Brain Stimulation},

volume = {11},

number = {6},

pages = {1336--1347},

abstract = {BACKGROUND: Severe and medication-resistant psychiatric diseases, such as major depressive disorder, bipolar disorder or schizophrenia, can be effectively and rapidly treated by electroconvulsive therapy (ECT). Despite extensive long-standing clinical use, the neurobiological mechanisms underlying the curative action of ECT remain incompletely understood. 

OBJECTIVE: Unravel biological basis of electroconvulsive stimulation (ECS) efficacy, the animal equivalent of ECT. 

METHODS: Using MAP6 KO mouse, a genetic model that constitutively exhibits features relevant to some aspects of depression; we analyzed the behavioral and biological consequences of ECS treatment alone (10 stimulations over a 2-week period) and associated with a continuation protocol (2 stimulations per week for 5 weeks). 

RESULTS: ECS treatment had a beneficial effect on constitutive behavioral defects. We showed that behavioral improvement is associated with a strong increase in the survival and integration of neurons born before ECS treatment. Retroviral infection revealed the larger number of integrated neurons to exhibit increased dendritic complexity and spine density, as well as remodeled synapses. Furthermore, our results show that ECS triggers a cortical increase in synaptogenesis. A sustained newborn neuron survival rate, induced by ECS treatment, is associated with the behavioral improvement, but relapse occurred 40 days after completing the ECS treatment. However, a 5-week continuation protocol following the initial ECS treatment led to persistent improvement of behavior correlated with sustained rate survival of newborn neurons. 

CONCLUSION: Altogether, these results reveal that increased synaptic connectivity and extended neuronal survival are key to the short and long-term efficacy of ECS.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{albaret_externalized_2018,

title = {Externalized Keratin 8: A Target at the Interface of Microenvironment and Intracellular Signaling in Colorectal Cancer Cells},

author = {Marie Alexandra Albaret and Claudine Vermot-Desroches and Arnaud Paré and Jean-Xavier Roca-Martinez and Lucie Malet and Jad Esseily and Laetitia Gerossier and Johan Brière and Nathalie Pion and Virginie Marcel and Frédéric Catez and Geneviève De Souza and Boris Vuillermoz and Franck Doerflinger and Emilie Lavocat and Olivier Subiger and Carine Rousset and Corinne Bresson and Elodie Mandon and Anass Jawhari and Pierre Falson and Mélissa Jasmin and Yohann Couté and Hichem-Claude Mertani and Pierre Saintigny and Jean-Jacques Diaz},

doi = {10.3390/cancers10110452},

issn = {2072-6694},

year  = {2018},

date = {2018-11-01},

journal = {Cancers},

volume = {10},

number = {11},

abstract = {Accumulating evidence supports the remarkable presence at the membrane surface of cancer cells of proteins, which are normally expressed in the intracellular compartment. Although these proteins, referred to as externalized proteins, represent a highly promising source of accessible and druggable targets for cancer therapy, the mechanisms via which they impact cancer biology remain largely unexplored. The aim of this study was to expose an externalized form of cytokeratin 8 (eK8) as a key player of colorectal tumorigenesis and characterize its mode of action. To achieve this, we generated a unique antagonist monoclonal antibody (D-A10 MAb) targeting an eight-amino-acid-long domain of eK8, which enabled us to ascertain the pro-tumoral activity of eK8 in both KRAS-mutant and wild-type colorectal cancers (CRC). We showed that this pro-tumoral activity involves a bidirectional eK8-dependent control of caspase-mediated apoptosis in vivo and of the plasminogen-induced invasion process in cellulo. Furthermore, we demonstrated that eK8 is anchored at the plasma membrane supporting this dual function. We, therefore, identified eK8 as an innovative therapeutic target in CRC and provided a unique MAb targeting eK8 that displays anti-neoplastic activities that could be useful to treat CRC, including those harboring KRAS mutations.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{hahn_novel_2018,

title = {Novel cytomegalovirus-inhibitory compounds of the class pyrrolopyridines show a complex pattern of target binding that suggests an unusual mechanism of antiviral activity},

author = {Friedrich Hahn and Corina Hutterer and Christophe Henry and Stuart T Hamilton and Hanife Strojan and Alexandra Kraut and Ulrike Schulte and Martin Schütz and Stephan Kohrt and Christina Wangen and José Pfizer and Yohann Couté and William D Rawlinson and Stefan Strobl and Manfred Marschall},

doi = {10.1016/j.antiviral.2018.09.012},

issn = {1872-9096},

year  = {2018},

date = {2018-11-01},

journal = {Antiviral Research},

volume = {159},

pages = {84--94},

abstract = {Human cytomegalovirus (HCMV) is a major human pathogen with seropositivity rates in the adult population ranging between 40% and 95%. HCMV infection is associated with severe pathology, such as life-threatening courses of infection in immunocompromised individuals and neonates. Current standard therapy with valganciclovir has the disadvantage of adverse side effects and viral drug resistance. A novel anti-HCMV drug, letermovir, has been approved recently, so that improved therapy options are available. Nevertheless, even more so far unexploited classes of compounds and molecular modes of action will be required for a next generation of antiherpesviral treatment strategies. In this study, we focused on the analysis of the antiviral potency of a novel class of compounds, i.e. pyrrolopyridine analogs, and identified both hit compounds and their target protein candidates. In essence, we provide novel evidence as follows: (i) screening hit SC88941 is highly active in inhibiting HCMV replication in primary human fibroblasts with an EC50 value of 0.20 ± 0.01 μM in the absence of cytotoxicity, (ii) inhibition occurs at the early-late stage of viral protein production and shows reinforcing effects upon LMV cotreatment, (iii) among the viruses analyzed, antiviral activity was most pronounced against β-herpesviruses (HCMV, HHV-6A) and intermediate against adenovirus (HAdV-2), (iv) induction of SC88941 resistance was not detectable, thus differed from the induction of ganciclovir resistance, (v) a linker-coupled model compound was used for mass spectrometry-based target identification, thus yielding several drug-binding target proteins and (vi) a first confocal imaging approach used for addressing intracellular effects of SC88941 indicated qualitative and quantitative alteration of viral protein expression and localization. Thus, our findings suggest a multifaceted pattern of compound-target binding in connection with an unusual mode of action, opening up further opportunities of antiviral drug development.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{borges_distinguishing_2018,

title = {Distinguishing between Spectral Clustering and Cluster Analysis of Mass Spectra},

author = {Hélène Borges and Romain Guibert and Olga Permiakova and Thomas Burger},

doi = {10.1021/acs.jproteome.8b00516},

issn = {1535-3907},

year  = {2018},

date = {2018-11-01},

journal = {Journal of Proteome Research},

abstract = {The term "spectral clustering" is sometimes used to refer to the clustering of mass spectrometry data. However, it also classically refers to a family of popular clustering algorithms. To avoid confusion, a more specific term could advantageously be coined.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{dominguez-medina_neutral_2018,

title = {Neutral mass spectrometry of virus capsids above 100 megadaltons with nanomechanical resonators},

author = {Sergio Dominguez-Medina and Shawn Fostner and Martial Defoort and Marc Sansa and Ann-Kathrin Stark and Mohammad Abdul Halim and Emeline Vernhes and Marc Gely and Guillaume Jourdan and Thomas Alava and Pascale Boulanger and Christophe Masselon and Sébastien Hentz},

doi = {10.1126/science.aat6457},

issn = {1095-9203},

year  = {2018},

date = {2018-11-01},

journal = {Science (New York, N.Y.)},

volume = {362},

number = {6417},

pages = {918--922},

abstract = {Measurement of the mass of particles in the mega- to gigadalton range is challenging with conventional mass spectrometry. Although this mass range appears optimal for nanomechanical resonators, nanomechanical mass spectrometers often suffer from prohibitive sample loss, extended analysis time, or inadequate resolution. We report on a system architecture combining nebulization of the analytes from solution, their efficient transfer and focusing without relying on electromagnetic fields, and the mass measurements of individual particles using nanomechanical resonator arrays. This system determined the mass distribution of textasciitilde30-megadalton polystyrene nanoparticles with high detection efficiency and effectively performed molecular mass measurements of empty or DNA-filled bacteriophage T5 capsids with masses up to 105 megadaltons using less than 1 picomole of sample and with an instrument resolution above 100.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{do_trim9_2018,

title = {TRIM9 and TRIM67 Are New Targets in Paraneoplastic Cerebellar Degeneration},

author = {Le Duy Do and Stéphanie L Gupton and Kunikazu Tanji and Joubert Bastien and Sabine Brugière and Yohann Couté and Isabelle Quadrio and Véronique Rogemond and Nicole Fabien and Virginie Desestret and Jérôme Honnorat},

doi = {10.1007/s12311-018-0987-5},

issn = {1473-4230},

year  = {2018},

date = {2018-10-01},

journal = {Cerebellum (London, England)},

abstract = {To describe autoantibodies (Abs) against tripartite motif-containing (TRIM) protein 9 and 67 in two patients with paraneoplastic cerebellar degeneration (PCD) associated with lung adenocarcinoma. Abs were characterized using immunohistochemistry, Western blotting, cultures of murine cortical, and hippocampal neurons, immunoprecipitation, mass spectrometry, knockout mice for Trim9 and 67, and cell-based assay. Control samples included sera from 63 patients with small cell lung cancer without any paraneoplastic neurological syndrome, 36 patients with lung adenocarcinoma and PNS, CSF from 100 patients with autoimmune encephalitis, and CSF from 165 patients with neurodegenerative diseases. We found Abs targeting TRIM9 and TRIM67 at high concentration in the serum and the cerebrospinal fluid (CSF) of a 78-year-old woman and a 65-year-old man. Both developed subacute severe cerebellar ataxia. Brain magnetic resonance imaging found no abnormality and no cerebellar atrophy. Both had CSF inflammation with mild pleiocytosis and a few oligoclonal bands. We identified a pulmonary adenocarcinoma, confirming the paraneoplastic neurological syndrome in both patients. They received immunomodulatory and cancer treatments without improvement of cerebellar ataxia, even though both were in remission of their cancer (for more than 10 years in one patient). Anti-TRIM9 and anti-TRIM67 Abs were specific to these two patients. All control serum and CSF samples tested were negative for anti-TRIM9 and 67. Anti-TRIM9 and anti-TRIM67 Abs appeared to be specific biomarkers of PCD and should be added to the panel of antigens tested when this is suspected.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{volz_trihelix_2018,

title = {The Trihelix transcription factor GT2-like 1 (GTL1) promotes salicylic acid metabolism, and regulates bacterial-triggered immunity},

author = {Ronny Völz and Soon-Kap Kim and Jianing Mi and Kiruthiga G Mariappan and Xiujie Guo and Jean Bigeard and Santiago Alejandro and Delphine Pflieger and Naganand Rayapuram and Salim Al-Babili and Heribert Hirt},

doi = {10.1371/journal.pgen.1007708},

issn = {1553-7404},

year  = {2018},

date = {2018-10-01},

journal = {PLoS genetics},

volume = {14},

number = {10},

pages = {e1007708},

abstract = {The Trihelix Transcription factor GT2-like 1 (GTL1) was previously shown to be a key regulator of ploidy-dependent trichome growth and drought tolerance. Here, we report that GTL1 plays an important role in coordinating plant immunity. We show that gtl1 mutants are compromised in the regulation of basal immunity, microbial pattern-triggered immunity (PTI) and effector-triggered RIN4-mediated immunity. Transcriptome analysis revealed that GTL1 positively regulates defense genes and inhibits factors that mediate growth and development. By performing hormonal measurements and chromatin-immunoprecipitation studies, we found GTL1 to coordinate genes involved in salicylic acid metabolism, transport and response. Interaction studies and comparative transcriptomics to known data sets revealed that GTL1 is part of the MPK4 pathway and regulates oppositely the expression of differentially expressed genes in mpk4 plants. We introduced the gtl1 mutation in the mpk4 mutant and thereby partially suppressed its dwarfism and the high resistance against a bacterial invader. Our data show that GTL1 is part of the MPK4 pathway and acts as a positive regulator of bacterial-triggered immunity and SA homeostasis.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gervais2018,

title = {Small molecule-based targeting of TTD-A dimerization to control TFIIH transcriptional activity represents a potential strategy for anticancer therapy},

author = {Virginie Gervais and Isabelle Muller Pierre-Olivier Mari and Amandine Mourcet and Kumar Tekwani Movellan and Pascal Ramos and Julien Marcoux and Valérie Guillet and Sumaira Javaid and Odile Burlet-Schiltz and Georges Czaplicki and Alain Milon and Giuseppina Giglia-Mari},

doi = {10.1074/jbc.RA118.003444},

year  = {2018},

date = {2018-09-28},

journal = {J Biol Chem.},

volume = {293},

number = {39},

pages = {14974-14988},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{shiota_nut_2018,

title = {Nut Directs p300-Dependent, Genome-Wide Ħ4 Hyperacetylation in Male Germ Cells},

author = {Hitoshi Shiota and Sophie Barral and Thierry Buchou and Minjia Tan and Yohann Couté and Guillaume Charbonnier and Nicolas Reynoird and Fayçal Boussouar and Matthieu Gérard and Mingrui Zhu and Lisa Bargier and Denis Puthier and Florent Chuffart and Ekaterina Bourova-Flin and Sarah Picaud and Panagis Filippakopoulos and Afsaneh Goudarzi and Ziad Ibrahim and Daniel Panne and Sophie Rousseaux and Yingming Zhao and Saadi Khochbin},

doi = {10.1016/j.celrep.2018.08.069},

issn = {2211-1247},

year  = {2018},

date = {2018-09-01},

journal = {Cell Reports},

volume = {24},

number = {13},

pages = {3477--3487.e6},

abstract = {Nuclear protein in testis (Nut) is a universal oncogenic driver in the highly aggressive NUT midline carcinoma, whose physiological function in male germ cells has been unclear. Here we show that expression of Nut is normally restricted to post-meiotic spermatogenic cells, where its presence triggers p300-dependent genome-wide histone H4 hyperacetylation, which is essential for the completion of histone-to-protamine exchange. Accordingly, the inactivation of Nut induces male sterility with spermatogenesis arrest at the histone-removal stage. Nut uses p300 and/or CBP to enhance acetylation of H4 at both K5 and K8, providing binding sites for the first bromodomain of Brdt, the testis-specific member of the BET family, which subsequently mediates genome-wide histone removal. Altogether, our data reveal the detailed molecular basis of the global histone hyperacetylation wave, which occurs before the final compaction of the male genome.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nguyen_identification_2018,

title = {Identification of cartilage oligomeric matrix protein as biomarker predicting abatacept response in rheumatoid arthritis patients with insufficient response to a first anti-TNFα treatment},

author = {Minh Vu Chuong Nguyen and Annie Adrait and Athan Baillet and Candice Trocmé and Jacques-Eric Gottenberg and Philippe Gaudin},

doi = {10.1016/j.jbspin.2018.09.005},

issn = {1778-7254},

year  = {2018},

date = {2018-09-01},

journal = {Joint, Bone, Spine: Revue Du Rhumatisme},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{mato_liver_2018,

title = {Liver cancer-associated changes to the proteome: what deserves clinical focus?},

author = {José M Mato and Félix Elortza and Shelly C Lu and Virginie Brun and Alberto Paradela and Fernando J Corrales},

doi = {10.1080/14789450.2018.1521277},

issn = {1744-8387},

year  = {2018},

date = {2018-09-01},

journal = {Expert Review of Proteomics},

volume = {15},

number = {9},

pages = {749--756},

abstract = {INTRODUCTION: Hepatocellular carcinoma (HCC) is recognized as the fifth most common neoplasm and currently represents the second leading form of cancer-related death worldwide. Despite great progress has been done in the understanding of its pathogenesis, HCC represents a heavy societal and economic burden as most patients are still diagnosed at advanced stages and the 5-year survival rate remain below 20%. Early detection and revolutionary therapies that rely on the discovery of new molecular biomarkers and therapeutic targets are therefore urgently needed to develop precision medicine strategies for a more efficient management of patients. Areas covered: This review intends to comprehensively analyse the proteomics-based research conducted in the last few years to address some of the principal still open riddles in HCC biology, based on the identification of molecular drivers of tumor progression and metastasis. Expert commentary: The technical advances in mass spectrometry experienced in the last decade have significantly improved the analytical capacity of proteome wide studies. Large-scale protein and protein variant (post-translational modifications) identification and quantification have allowed detailed dissections of molecular mechanisms underlying HCC progression and are already paving the way for the identification of clinically relevant proteins and the development of their use on patient care.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Locard-Paulet2018,

title = {VisioProt-MS: interactive 2D maps from intact protein mass spectrometry},

author = {Marie Locard-Paulet and Julien Parra and Renaud Albigot and Emmanuelle Mouton-Barbosa and Laurent Bardi and Odile Burlet-Schiltz and Julien Marcoux},

doi = {10.1093/bioinformatics/bty680},

year  = {2018},

date = {2018-08-06},

journal = {Bioinformatics},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Vinel2018,

title = {The exerkine apelin reverses age-associated sarcopenia},

author = {Claire Vinel and Laura Lukjanenko and Aurélie Batut and Simon Deleruyelle and Jean-Philippe Pradère and Sophie Le Gonidec and Alizée Dortignac and Nancy Geoffre and Ophélie Pereira and Sonia Karaz and Umji Lee and Mylène Camus and Karima Chaoui and Etienne Mouisel and Anne Bigot and Vincent Mouly and Mathieu Vigneau and Allan F. Pagano and Angèle Chopard and Fabien Pillard and Sophie Guyonnet and Matteo Cesari and Odile Burlet-Schiltz and Marco Pahor and Jérôme N. Feige and Bruno Vellas and Philippe Valet and Cédric Dray},

doi = {10.1038/s41591-018-0131-6},

year  = {2018},

date = {2018-07-30},

journal = {Nat Med.},

volume = {24},

number = {9},

pages = {1360-71},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Jonik-Nowak2018,

title = {PIP30/FAM192A is a novel regulator of the nuclear proteasome activator PA28γ},

author = {Beata Jonik-Nowak and Thoma Menneteau and Didier Fesquet and Véronique Baldin and Catherine Bonne-Andrea and Francisca Méchali and Bertrand Fabre and Prisca Boisguerin and Sylvain Rossi and Corinne Henriquet and Martine Pugnière and Manuelle Ducoux-Petit and Odile Burlet-Schiltz and Angus I. Lamond and Philippe Fort and Séverine Boulon and Mari-Pierre Bousquet and Olivier Coux},

doi = {10.1073/pnas.1722299115},

year  = {2018},

date = {2018-07-10},

journal = {Proc Natl Acad Sci U S A.},

volume = {115},

number = {28},

pages = {E6477-E6486},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gaud2018,

title = {The costimulatory molecule CD226 signals through VAV1 to amplify TCR signals and promote IL-17 production by CD4+ T cells},

author = {Guillaume Gaud and Romain Roncagalli and Karima Chaoui and Isabelle Bernard and Julien Familiades Colacios and Sahar Kassem and Bernard Monsarrat and Odile Burlet-Schiltz and Anne Gonzalez Peredo and Bernard Malissen and Abdelhadi Saoudi},

doi = {10.1126/scisignal.aar3083},

year  = {2018},

date = {2018-07-10},

volume = {11},

number = {538},

pages = {eaar3083},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Behrens2018,

title = {Homodimer Architecture of QTRT2, the Noncatalytic Subunit of the Eukaryotic tRNA-Guanine Transglycosylase},

author = {Christina Behrens and Inna Biela and Stéphanie Petiot-Bécard Botzanowski and Sarah Cianférani and Christoph P. Sager and Gerhard Klebe and Andreas Heine and Klaus Reuter},

doi = {10.1021/acs.biochem.8b00294},

year  = {2018},

date = {2018-06-04},

journal = {Biochemistry},

volume = {57},

number = {26},

pages = {3953–3965},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{frohlich_synthesis_2018,

title = {Synthesis of Artemisinin-Derived Dimers, Trimers and Dendrimers: Investigation of Their Antimalarial and Antiviral Activities Including Putative Mechanisms of Action},

author = {Tony Fröhlich and Friedrich Hahn and Lucid Belmudes and Maria Leidenberger and Oliver Friedrich and Barbara Kappes and Yohann Couté and Manfred Marschall and Svetlana B Tsogoeva},

doi = {10.1002/chem.201800729},

issn = {1521-3765},

year  = {2018},

date = {2018-06-01},

journal = {Chemistry (Weinheim an Der Bergstrasse, Germany)},

volume = {24},

number = {32},

pages = {8103--8113},

abstract = {Generation of dimers, trimers and dendrimers of bioactive compounds is an approach that has recently been developed for the discovery of new potent drug candidates. Herein, we present the synthesis of new artemisinin-derived dimers and dendrimers and investigate their action against malaria parasite Plasmodium falciparum 3D7 strain and human cytomegalovirus (HCMV). Dimer 7 was the most active compound (EC50 1.4 nm) in terms of antimalarial efficacy and was even more effective than the standard drugs dihydroartemisinin (EC50 2.4 nm), artesunic acid (EC50 8.9 nm) and chloroquine (EC50 9.8 nm). Trimer 4 stood out as the most active agent against HCMV in vitro replication and exerted an EC50 value of 0.026 μm, representing an even higher activity than the two reference drugs ganciclovir (EC50 2.60 μm) and artesunic acid (EC50 5.41 μm). In addition, artemisinin-derived dimer 13 and trimer 15 were for the first time both immobilized on TOYOPEARL AF-Amino-650M beads and used for mass spectrometry-based target identification experiments using total lysates of HCMV-infected primary human fibroblasts. Two major groups of novel target candidates, namely cytoskeletal and mitochondrial proteins were obtained. Two putatively compound-binding viral proteins, namely major capsid protein (MCP) and envelope glycoprotein pUL132, which are both essential for HCMV replication, were identified.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{jacob_pepa_2018,

title = {PEPA test: fast and powerful differential analysis from relative quantitative proteomics data using shared peptides},

author = {Laurent Jacob and Florence Combes and Thomas Burger},

doi = {10.1093/biostatistics/kxy021},

issn = {1468-4357},

year  = {2018},

date = {2018-06-01},

journal = {Biostatistics (Oxford, England)},

abstract = {We propose a new hypothesis test for the differential abundance of proteins in mass-spectrometry based relative quantification. An important feature of this type of high-throughput analyses is that it involves an enzymatic digestion of the sample proteins into peptides prior to identification and quantification. Due to numerous homology sequences, different proteins can lead to peptides with identical amino acid chains, so that their parent protein is ambiguous. These so-called shared peptides make the protein-level statistical analysis a challenge and are often not accounted for. In this article, we use a linear model describing peptide-protein relationships to build a likelihood ratio test of differential abundance for proteins. We show that the likelihood ratio statistic can be computed in linear time with the number of peptides. We also provide the asymptotic null distribution of a regularized version of our statistic. Experiments on both real and simulated datasets show that our procedures outperforms state-of-the-art methods. The procedures are available via the pepa.test function of the DAPAR Bioconductor R package.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Denadai-Souza2018,

title = {Functional Proteomic Profiling of Secreted Serine Proteases in Health and Inflammatory Bowel Disease},

author = {Alexandre Denadai-Souza and Chrystelle Bonnart and Núria Solà Tapias and Marlène Marcellin and Brendan Gilmore Alric and Delphine Bonnet and Odile Burlet-Schiltz and Morley D. Hollenberg and Nathalie Vergnolle and Céline Deraison},

doi = {10.1038/s41598-018-26282-y},

year  = {2018},

date = {2018-05-18},

journal = {Sci Rep},

volume = {8},

number = {1},

pages = {7834},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lefebvre2018,

title = {HadD, a novel fatty acid synthase type II protein, is essential for alpha- and epoxy-mycolic acid biosynthesis and mycobacterial fitness},

author = {Cyril Lefebvre and Richard Boulon and Manuelle Ducoux and Sabine Gavalda and Françoise Laval and Stevie Jamet and Nathalie Eynard and Anne Lemassu and Kaymeuang Cam and Marie-Pierre Bousquet and Fabienne Bardou and Odile Burlet-Schiltz and Mamadou Daffé and Annaïck Quémard},

doi = {10.1038/s41598-018-24380-5},

year  = {2018},

date = {2018-04-16},

journal = {Sci Rep},

volume = {8},

number = {1},

pages = {6034},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Cayrol2018,

title = {Environmental allergens induce allergic inflammation through proteolytic maturation of IL-33},

author = {Corinne Cayrol and Anaïs Duval and Pauline Schmitt and Stéphane Roga and Mylène Camusand Alexandre Stella and Odile Burlet-Schiltz and Anne Gonzalez Peredo and Jean-Philippe Girard},

doi = {10.1038/s41590-018-0067-5},

year  = {2018},

date = {2018-03-21},

journal = {Nat Immunol},

volume = {19},

number = {4},

pages = {375-385},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Garcia2018,

title = {Data-Independent Acquisition Coupled to Visible Laser-Induced Dissociation at 473 nm (DIA-LID) for Peptide-Centric Specific Analysis of Cysteine-Containing Peptide Subset},

author = {Lény Garcia and Marion Girod and Magali Rompais and Philippe Dugourd and Christine Carapito and Jérôme Lemoine},

doi = {10.1021/acs.analchem.7b04821},

year  = {2018},

date = {2018-03-20},

journal = {Anal Chem.},

volume = {90},

number = {6},

pages = {3928-3935},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1311,

title = {Arginine-selective bioconjugation with 4-azidophenyl glyoxal: application to the single and dual functionalisation of native antibodies},

author = {I Dovgan and S Erb and S Hessmann and S Ursuegui and C Michel and C Muller and G Chaubet and S Cianférani and A Wagner},

doi = {10.1039/c7ob02844j},

year  = {2018},

date = {2018-02-21},

journal = {Org Biomol Chem.},

volume = {16},

number = {8},

pages = {1305-1311},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1312,

title = {The Circulating Protease Persephone Is an Immune Sensor for Microbial Proteolytic Activities Upstream of the Drosophila Toll Pathway},

author = {N Issa and N Guillaumot and E Lauret and N Matt and C Schaeffer-Reiss and A Van Dorsselaer and J M Reichhart and F Veillard},

doi = {10.1016/j.molcel.2018.01.029},

year  = {2018},

date = {2018-02-15},

journal = {Mol Cell},

volume = {69},

number = {4},

pages = {539-550 e6},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1307,

title = {An online four-dimensional HICxSEC-IMxMS methodology for proof-of-concept characterization of antibody drug conjugates},

author = {A Ehkirch and V D'Atri and F Rouvière and O Hernandez-Alba and A Goyon and O Colas and M Sarrut and A Beck and D Guillarme and S Heinisch and S Cianférani},

doi = {10.1021/acs.analchem.7b02110},

year  = {2018},

date = {2018-02-06},

journal = {Anal Chem.},

volume = {90},

number = {3},

pages = {1578-1586},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{lacombe_proteomic_2018,

title = {Proteomic characterization of human exhaled breath condensate},

author = {Maud Lacombe and Caroline Marie-Desvergne and Florence Combes and Alexandra Kraut and Christophe Bruley and Yves Vandenbrouck and Véronique Chamel Mossuz and Yohann Couté and Virginie Brun},

doi = {10.1088/1752-7163/aa9e71},

issn = {1752-7163},

year  = {2018},

date = {2018-02-01},

journal = {Journal of Breath Research},

volume = {12},

number = {2},

pages = {021001},

abstract = {To improve biomedical knowledge and to support biomarker discovery studies, it is essential to establish comprehensive proteome maps for human tissues and biofluids, and to make them publicly accessible. In this study, we performed an in-depth proteomics characterization of exhaled breath condensate (EBC), a sample obtained non-invasively by condensation of exhaled air that contains submicron droplets of airway lining fluid. Two pooled samples of EBC, each obtained from 10 healthy donors, were processed using a straightforward protocol based on sample lyophilization, in-gel digestion and liquid chromatography tandem-mass spectrometry analysis. Two 'technical' control samples were processed in parallel to the pooled samples to correct for exogenous protein contamination. A total of 229 unique proteins were identified in EBC among which 153 proteins were detected in both EBC pooled samples. A detailed bioinformatics analysis of these 153 proteins showed that most of the proteins identified corresponded to proteins secreted in the respiratory tract (lung, bronchi). Eight proteins were salivary proteins. Our dataset is described and has been made accessible through the ProteomeXchange database (dataset identifier: PXD007591) and is expected to be useful for future MS-based biomarker studies using EBC as the diagnostic specimen.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}