Publications - ProFI Proteomics

Azevedo-Favory, J; Gaspin, C; Ayadi, L; Montacie, C; Marchand, V; Jobet, E; Rompais, M; Carapito, C; Motorin, Y; Saez-Vasquez, J

Mapping rRNA 2'-O-methylations and identification of C/D snoRNAs in Arabidopsis thaliana plants Article de journal

RNA Biol, p. 1-18, 2021, ISSN: 1555-8584 (Electronic) 1547-6286 (Linking), (Azevedo-Favory, J Gaspin, C Ayadi, L Montacie, C Marchand, V Jobet, E Rompais, M Carapito, C Motorin, Y Saez-Vasquez, J eng 2021/02/19 06:00 RNA Biol. 2021 Feb 17:1-18. doi: 10.1080/15476286.2020.1869892.).

Résumé | Liens

Beinsteiner, B; Markov, G V; Erb, S; Chebaro, Y; McEwen, A G; Cianferani, S; Laudet, V; Moras, D; Billas, I M L

A structural signature motif enlightens the origin and diversification of nuclear receptors Article de journal

PLoS Genet, 17 (4), p. e1009492, 2021, ISSN: 1553-7404 (Electronic) 1553-7390 (Linking), (Beinsteiner, Brice Markov, Gabriel V Erb, Stephane Chebaro, Yassmine McEwen, Alastair G Cianferani, Sarah Laudet, Vincent Moras, Dino Billas, Isabelle M L eng 2021/04/22 06:00 PLoS Genet. 2021 Apr 21;17(4):e1009492. doi: 10.1371/journal.pgen.1009492. eCollection 2021 Apr.).

Résumé | Liens

@article{684,
title = {A structural signature motif enlightens the origin and diversification of nuclear receptors},
author = {B Beinsteiner and G V Markov and S Erb and Y Chebaro and A G McEwen and S Cianferani and V Laudet and D Moras and I M L Billas},
url = {https://www.ncbi.nlm.nih.gov/pubmed/33882063},
doi = {10.1371/journal.pgen.1009492},
issn = {1553-7404 (Electronic)
1553-7390 (Linking)},
year = {2021},
date = {2021-01-01},
journal = {PLoS Genet},
volume = {17},
number = {4},
pages = {e1009492},
abstract = {Nuclear receptors are ligand-activated transcription factors that modulate gene regulatory networks from embryonic development to adult physiology and thus represent major targets for clinical interventions in many diseases. Most nuclear receptors function either as homodimers or as heterodimers. The dimerization is crucial for gene regulation by nuclear receptors, by extending the repertoire of binding sites in the promoters or the enhancers of target genes via combinatorial interactions. Here, we focused our attention on an unusual structural variation of the alpha-helix, called pi-turn that is present in helix H7 of the ligand-binding domain of RXR and HNF4. By tracing back the complex evolutionary history of the pi-turn, we demonstrate that it was present ancestrally and then independently lost in several nuclear receptor lineages. Importantly, the evolutionary history of the pi-turn motif is parallel to the evolutionary diversification of the nuclear receptor dimerization ability from ancestral homodimers to derived heterodimers. We then carried out structural and biophysical analyses, in particular through point mutation studies of key RXR signature residues and showed that this motif plays a critical role in the network of interactions stabilizing homodimers. We further showed that the pi-turn was instrumental in allowing a flexible heterodimeric interface of RXR in order to accommodate multiple interfaces with numerous partners and critical for the emergence of high affinity receptors. Altogether, our work allows to identify a functional role for the pi-turn in oligomerization of nuclear receptors and reveals how this motif is linked to the emergence of a critical biological function. We conclude that the pi-turn can be viewed as a structural exaptation that has contributed to enlarging the functional repertoire of nuclear receptors.},
note = {Beinsteiner, Brice
Markov, Gabriel V
Erb, Stephane
Chebaro, Yassmine
McEwen, Alastair G
Cianferani, Sarah
Laudet, Vincent
Moras, Dino
Billas, Isabelle M L
eng
2021/04/22 06:00
PLoS Genet. 2021 Apr 21;17(4):e1009492. doi: 10.1371/journal.pgen.1009492. eCollection 2021 Apr.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Fermer

Bertile, F; Habold, C; Maho, Le Y; Giroud, S

Body Protein Sparing in Hibernators: A Source for Biomedical Innovation Article de journal

Front Physiol, 12 , p. 634953, 2021, ISSN: 1664-042X (Print) 1664-042X (Linking), (2011/34).

Résumé | Liens

@article{709,
title = {Body Protein Sparing in Hibernators: A Source for Biomedical Innovation},
author = {F Bertile and C Habold and Y Le Maho and S Giroud},
url = {https://www.ncbi.nlm.nih.gov/pubmed/33679446},
doi = {10.3389/fphys.2021.634953},
issn = {1664-042X (Print)
1664-042X (Linking)},
year = {2021},
date = {2021-01-01},
journal = {Front Physiol},
volume = {12},
pages = {634953},
abstract = {Proteins are not only the major structural components of living cells but also ensure essential physiological functions within the organism. Any change in protein abundance and/or structure is at risk for the proper body functioning and/or survival of organisms. Death following starvation is attributed to a loss of about half of total body proteins, and body protein loss induced by muscle disuse is responsible for major metabolic disorders in immobilized patients, and sedentary or elderly people. Basic knowledge of the molecular and cellular mechanisms that control proteostasis is continuously growing. Yet, finding and developing efficient treatments to limit body/muscle protein loss in humans remain a medical challenge, physical exercise and nutritional programs managing to only partially compensate for it. This is notably a major challenge for the treatment of obesity, where therapies should promote fat loss while preserving body proteins. In this context, hibernating species preserve their lean body mass, including muscles, despite total physical inactivity and low energy consumption during torpor, a state of drastic reduction in metabolic rate associated with a more or less pronounced hypothermia. The present review introduces metabolic, physiological, and behavioral adaptations, e.g., energetics, body temperature, and nutrition, of the torpor or hibernation phenotype from small to large mammals. Hibernating strategies could be linked to allometry aspects, the need for periodic rewarming from torpor, and/or the ability of animals to fast for more or less time, thus determining the capacity of individuals to save proteins. Both fat- and food-storing hibernators rely mostly on their body fat reserves during the torpid state, while minimizing body protein utilization. A number of them may also replenish lost proteins during arousals by consuming food. The review takes stock of the physiological, molecular, and cellular mechanisms that promote body protein and muscle sparing during the inactive state of hibernation. Finally, the review outlines how the detailed understanding of these mechanisms at play in various hibernators is expected to provide innovative solutions to fight human muscle atrophy, to better help the management of obese patients, or to improve the ex vivo preservation of organs.},
note = {2011/34},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Fermer

Proteins are not only the major structural components of living cells but also ensure essential physiological functions within the organism. Any change in protein abundance and/or structure is at risk for the proper body functioning and/or survival of organisms. Death following starvation is attributed to a loss of about half of total body proteins, and body protein loss induced by muscle disuse is responsible for major metabolic disorders in immobilized patients, and sedentary or elderly people. Basic knowledge of the molecular and cellular mechanisms that control proteostasis is continuously growing. Yet, finding and developing efficient treatments to limit body/muscle protein loss in humans remain a medical challenge, physical exercise and nutritional programs managing to only partially compensate for it. This is notably a major challenge for the treatment of obesity, where therapies should promote fat loss while preserving body proteins. In this context, hibernating species preserve their lean body mass, including muscles, despite total physical inactivity and low energy consumption during torpor, a state of drastic reduction in metabolic rate associated with a more or less pronounced hypothermia. The present review introduces metabolic, physiological, and behavioral adaptations, e.g., energetics, body temperature, and nutrition, of the torpor or hibernation phenotype from small to large mammals. Hibernating strategies could be linked to allometry aspects, the need for periodic rewarming from torpor, and/or the ability of animals to fast for more or less time, thus determining the capacity of individuals to save proteins. Both fat- and food-storing hibernators rely mostly on their body fat reserves during the torpid state, while minimizing body protein utilization. A number of them may also replenish lost proteins during arousals by consuming food. The review takes stock of the physiological, molecular, and cellular mechanisms that promote body protein and muscle sparing during the inactive state of hibernation. Finally, the review outlines how the detailed understanding of these mechanisms at play in various hibernators is expected to provide innovative solutions to fight human muscle atrophy, to better help the management of obese patients, or to improve the ex vivo preservation of organs.

Fermer

Bertile, F; Plumel, M; Maes, P; Hirschler, A; Challet, E

Daytime Restricted Feeding Affects Day-Night Variations in Mouse Cerebellar Proteome Article de journal

Front Mol Neurosci, 14 , p. 613161, 2021, ISSN: 1662-5099 (Print) 1662-5099 (Linking), (2012/26).

Résumé | Liens

@article{708,
title = {Daytime Restricted Feeding Affects Day-Night Variations in Mouse Cerebellar Proteome},
author = {F Bertile and M Plumel and P Maes and A Hirschler and E Challet},
url = {https://www.ncbi.nlm.nih.gov/pubmed/33912010},
doi = {10.3389/fnmol.2021.613161},
issn = {1662-5099 (Print)
1662-5099 (Linking)},
year = {2021},
date = {2021-01-01},
journal = {Front Mol Neurosci},
volume = {14},
pages = {613161},
abstract = {The cerebellum harbors a circadian clock that can be shifted by scheduled mealtime and participates in behavioral anticipation of food access. Large-scale two-dimensional difference gel electrophoresis (2D-DIGE) combined with mass spectrometry was used to identify day-night variations in the cerebellar proteome of mice fed either during daytime or nighttime. Experimental conditions led to modified expression of 89 cerebellar proteins contained in 63 protein spots. Five and 33 spots were changed respectively by time-of-day or feeding conditions. Strikingly, several proteins of the heat-shock protein family (i.e., Hsp90aa1, 90ab1, 90b1, and Hspa2, 4, 5, 8, 9) were down-regulated in the cerebellum of daytime food-restricted mice. This was also the case for brain fatty acid protein (Fabp7) and enzymes involved in oxidative phosphorylation (Ndufs1) or folate metabolism (Aldh1l1). In contrast, aldolase C (Aldoc or zebrin II) and pyruvate carboxylase (Pc), two enzymes involved in carbohydrate metabolism, and vesicle-fusing ATPase (Nsf) were up-regulated during daytime restricted feeding, possibly reflecting increased neuronal activity. Significant feeding x time-of-day interactions were found for changes in the intensity of 20 spots. Guanine nucleotide-binding protein G(o) subunit alpha (Gnao1) was more expressed in the cerebellum before food access. Neuronal calcium-sensor proteins [i.e., parvalbumin (Pvalb) and visinin-like protein 1 (Vsnl1)] were inversely regulated in daytime food-restricted mice, compared to control mice fed at night. Furthermore, expression of three enzymes modulating the circadian clockwork, namely heterogeneous nuclear ribonucleoprotein K (Hnrnpk), serine/threonine-protein phosphatases 1 (Ppp1cc and Ppp1cb subunits) and 5 (Ppp5), was differentially altered by daytime restricted feeding. Besides cerebellar proteins affected only by feeding conditions or daily cues, specific changes in in protein abundance before food access may be related to behavioral anticipation of food access and/or feeding-induced shift of the cerebellar clockwork.},
note = {2012/26},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Fermer

The cerebellum harbors a circadian clock that can be shifted by scheduled mealtime and participates in behavioral anticipation of food access. Large-scale two-dimensional difference gel electrophoresis (2D-DIGE) combined with mass spectrometry was used to identify day-night variations in the cerebellar proteome of mice fed either during daytime or nighttime. Experimental conditions led to modified expression of 89 cerebellar proteins contained in 63 protein spots. Five and 33 spots were changed respectively by time-of-day or feeding conditions. Strikingly, several proteins of the heat-shock protein family (i.e., Hsp90aa1, 90ab1, 90b1, and Hspa2, 4, 5, 8, 9) were down-regulated in the cerebellum of daytime food-restricted mice. This was also the case for brain fatty acid protein (Fabp7) and enzymes involved in oxidative phosphorylation (Ndufs1) or folate metabolism (Aldh1l1). In contrast, aldolase C (Aldoc or zebrin II) and pyruvate carboxylase (Pc), two enzymes involved in carbohydrate metabolism, and vesicle-fusing ATPase (Nsf) were up-regulated during daytime restricted feeding, possibly reflecting increased neuronal activity. Significant feeding x time-of-day interactions were found for changes in the intensity of 20 spots. Guanine nucleotide-binding protein G(o) subunit alpha (Gnao1) was more expressed in the cerebellum before food access. Neuronal calcium-sensor proteins [i.e., parvalbumin (Pvalb) and visinin-like protein 1 (Vsnl1)] were inversely regulated in daytime food-restricted mice, compared to control mice fed at night. Furthermore, expression of three enzymes modulating the circadian clockwork, namely heterogeneous nuclear ribonucleoprotein K (Hnrnpk), serine/threonine-protein phosphatases 1 (Ppp1cc and Ppp1cb subunits) and 5 (Ppp5), was differentially altered by daytime restricted feeding. Besides cerebellar proteins affected only by feeding conditions or daily cues, specific changes in in protein abundance before food access may be related to behavioral anticipation of food access and/or feeding-induced shift of the cerebellar clockwork.

Fermer

Bons, J; Husson, G; Chion, M; Bonnet, M; Maumy-Bertrand, M; Delalande, F; Cianferani, S; Bertrand, F; Picard, B; Carapito, C

Combining label-free and label-based accurate quantifications with SWATH-MS: Comparison with SRM and PRM for the evaluation of bovine muscle type effects Article de journal

Proteomics, 21 (10), p. e2000214, 2021, ISSN: 1615-9861 (Electronic) 1615-9853 (Linking), (Bons, Joanna Husson, Gauthier Chion, Marie Bonnet, Muriel Maumy-Bertrand, Myriam Delalande, Francois Cianferani, Sarah Bertrand, Frederic Picard, Brigitte Carapito, Christine eng Germany 2021/03/19 06:00 Proteomics. 2021 May;21(10):e2000214. doi: 10.1002/pmic.202000214. Epub 2021 Mar 30.).

Résumé | Liens

@article{695,
title = {Combining label-free and label-based accurate quantifications with SWATH-MS: Comparison with SRM and PRM for the evaluation of bovine muscle type effects},
author = {J Bons and G Husson and M Chion and M Bonnet and M Maumy-Bertrand and F Delalande and S Cianferani and F Bertrand and B Picard and C Carapito},
url = {https://www.ncbi.nlm.nih.gov/pubmed/33733615},
doi = {10.1002/pmic.202000214},
issn = {1615-9861 (Electronic)
1615-9853 (Linking)},
year = {2021},
date = {2021-01-01},
journal = {Proteomics},
volume = {21},
number = {10},
pages = {e2000214},
abstract = {Mass spectrometry has proven to be a valuable tool for the accurate quantification of proteins. In this study, the performances of three targeted approaches, namely selected reaction monitoring (SRM), parallel reaction monitoring (PRM) and sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH-MS), to accurately quantify ten potential biomarkers of beef meat tenderness or marbling in a cohort of 64 muscle samples were evaluated. So as to get the most benefit out of the complete MS2 maps that are acquired in SWATH-MS, an original label-free quantification method to estimate protein amounts using an I-spline regression model was developed. Overall, SWATH-MS outperformed SRM in terms of sensitivity and dynamic range, while PRM still performed the best, and all three strategies showed similar quantification accuracies and precisions for the absolute quantification of targets of interest. This targeted picture was extended by 585 additional proteins for which amounts were estimated using the label-free approach on SWATH-MS; thus, offering a more global profiling of muscle proteomes and further insights into muscle type effect on candidate biomarkers of beef meat qualities as well as muscle metabolism.},
note = {Bons, Joanna
Husson, Gauthier
Chion, Marie
Bonnet, Muriel
Maumy-Bertrand, Myriam
Delalande, Francois
Cianferani, Sarah
Bertrand, Frederic
Picard, Brigitte
Carapito, Christine
eng
Germany
2021/03/19 06:00
Proteomics. 2021 May;21(10):e2000214. doi: 10.1002/pmic.202000214. Epub 2021 Mar 30.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Fermer

Bragantini, B; Charron, C; Bourguet, M; Paul, A; Tiotiu, D; Rothe, B; Marty, H; Terral, G; Hessmann, S; Decourty, L; Chagot, M E; Strub, J M; Massenet, S; Bertrand, E; Quinternet, M; Saveanu, C; Cianferani, S; Labialle, S; Manival, X; Charpentier, B

The box C/D snoRNP assembly factor Bcd1 interacts with the histone chaperone Rtt106 and controls its transcription dependent activity Article de journal

Nat Commun, 12 (1), p. 1859, 2021, ISSN: 2041-1723 (Electronic) 2041-1723 (Linking), (2008/37).

Résumé | Liens

Dalzon, B; Devcic, J; Bons, J; Torres, A; Diemer, H; Ravanel, S; Collin-Faure, V; Cianferani, S; Carapito, C; Rabilloud, T

A proteomic view of cellular responses of macrophages to copper when added as ion or as copper-polyacrylate complex Article de journal

J Proteomics, 239 , p. 104178, 2021, ISSN: 1876-7737 (Electronic) 1874-3919 (Linking), (2014/29).

Résumé | Liens

@article{697,
title = {A proteomic view of cellular responses of macrophages to copper when added as ion or as copper-polyacrylate complex},
author = {B Dalzon and J Devcic and J Bons and A Torres and H Diemer and S Ravanel and V Collin-Faure and S Cianferani and C Carapito and T Rabilloud},
url = {https://www.ncbi.nlm.nih.gov/pubmed/33662612},
doi = {10.1016/j.jprot.2021.104178},
issn = {1876-7737 (Electronic)
1874-3919 (Linking)},
year = {2021},
date = {2021-01-01},
journal = {J Proteomics},
volume = {239},
pages = {104178},
abstract = {Copper is an essential metal for life, but is toxic at high concentrations. In mammalian cells, two copper transporters are known, CTR1 and CTR2. In order to gain insights on the possible influence of the import pathway on cellular responses to copper, two copper challenges were compared: one with copper ion, which is likely to use preferentially CTR1, and one with a copper-polyacrylate complex, which will be internalized via the endosomal pathway and is likely to use preferentially CTR2. A model system consisting in the J774A1 mouse macrophage system, with a strong endosomal/lysosomal pathway, was used. In order to gain wide insights into the cellular responses to copper, a proteomic approach was used. The proteomic results were validated by targeted experiments, and showed differential effects of the import mode on cellular physiology parameters. While the mitochondrial transmembrane potential was kept constant, a depletion in the free glutahione content was observed with copper (ion and polylacrylate complex). Both copper-polyacrylate and polyacrylate induced perturbations in the cytoskeleton and in phagocytosis. Inflammatory responses were also differently altered by copper ion and copper-polyacrylate. Copper-polyacrylate also perturbed several metabolic enzymes. Lastly, enzymes were used as a test set to assess the predictive value of proteomics. SIGNIFICANCE: Proteomic profiling provides an in depth analysis of the alterations induced on cells by copper under two different exposure modes to this metal, namely as the free ion or as a complex with polyacrylate. The cellular responses were substantially different between the two exposure modes, although some cellular effects are shared, such as the depletion in free glutathione. Targeted experiments were used to confirm the proteomic results. Some metabolic enzymes showed altered activities after exposure to the copper-polyacrylate complex. The basal inflammatory responses were different for copper ion and for the copper-polyacrylate complex, while the two forms of copper inhibited lipopolysaccharide-induced inflammatory responses.},
note = {2014/29},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Fermer

Copper is an essential metal for life, but is toxic at high concentrations. In mammalian cells, two copper transporters are known, CTR1 and CTR2. In order to gain insights on the possible influence of the import pathway on cellular responses to copper, two copper challenges were compared: one with copper ion, which is likely to use preferentially CTR1, and one with a copper-polyacrylate complex, which will be internalized via the endosomal pathway and is likely to use preferentially CTR2. A model system consisting in the J774A1 mouse macrophage system, with a strong endosomal/lysosomal pathway, was used. In order to gain wide insights into the cellular responses to copper, a proteomic approach was used. The proteomic results were validated by targeted experiments, and showed differential effects of the import mode on cellular physiology parameters. While the mitochondrial transmembrane potential was kept constant, a depletion in the free glutahione content was observed with copper (ion and polylacrylate complex). Both copper-polyacrylate and polyacrylate induced perturbations in the cytoskeleton and in phagocytosis. Inflammatory responses were also differently altered by copper ion and copper-polyacrylate. Copper-polyacrylate also perturbed several metabolic enzymes. Lastly, enzymes were used as a test set to assess the predictive value of proteomics. SIGNIFICANCE: Proteomic profiling provides an in depth analysis of the alterations induced on cells by copper under two different exposure modes to this metal, namely as the free ion or as a complex with polyacrylate. The cellular responses were substantially different between the two exposure modes, although some cellular effects are shared, such as the depletion in free glutathione. Targeted experiments were used to confirm the proteomic results. Some metabolic enzymes showed altered activities after exposure to the copper-polyacrylate complex. The basal inflammatory responses were different for copper ion and for the copper-polyacrylate complex, while the two forms of copper inhibited lipopolysaccharide-induced inflammatory responses.

Fermer

Deffieu, M S; Cesonyte, I; Delalande, F; Boncompain, G; Dorobantu, C; Song, E; Lucansky, V; Hirschler, A; Cianferani, S; Perez, F; Carapito, C; Gaudin, R

Rab7-harboring vesicles are carriers of the transferrin receptor through the biosynthetic secretory pathway Article de journal

Sci Adv, 7 (2), 2021, ISSN: 2375-2548 (Electronic) 2375-2548 (Linking), (Deffieu, Maika S Cesonyte, Ieva Delalande, Francois Boncompain, Gaelle Dorobantu, Cristina Song, Eli Lucansky, Vincent Hirschler, Aurelie Cianferani, Sarah Perez, Franck Carapito, Christine Gaudin, Raphael eng 2021/02/02 06:00 Sci Adv. 2021 Jan 8;7(2). pii: 7/2/eaba7803. doi: 10.1126/sciadv.aba7803. Print 2021 Jan.).

Résumé | Liens

Delfosse, V; Huet, T; Harrus, D; Granell, M; Bourguet, M; Gardia-Parege, C; Chiavarina, B; Grimaldi, M; Mevel, Le S; Blanc, P; Huang, D; Gruszczyk, J; Demeneix, B; Cianferani, S; Fini, J B; Balaguer, P; Bourguet, W

Mechanistic insights into the synergistic activation of the RXR-PXR heterodimer by endocrine disruptor mixtures Article de journal

Proc Natl Acad Sci U S A, 118 (1), 2021, ISSN: 1091-6490 (Electronic) 0027-8424 (Linking), (2019/06).

Résumé | Liens

@article{699,
title = {Mechanistic insights into the synergistic activation of the RXR-PXR heterodimer by endocrine disruptor mixtures},
author = {V Delfosse and T Huet and D Harrus and M Granell and M Bourguet and C Gardia-Parege and B Chiavarina and M Grimaldi and S Le Mevel and P Blanc and D Huang and J Gruszczyk and B Demeneix and S Cianferani and J B Fini and P Balaguer and W Bourguet},
url = {https://www.ncbi.nlm.nih.gov/pubmed/33361153},
doi = {10.1073/pnas.2020551118},
issn = {1091-6490 (Electronic)
0027-8424 (Linking)},
year = {2021},
date = {2021-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {118},
number = {1},
abstract = {Humans are chronically exposed to mixtures of xenobiotics referred to as endocrine-disrupting chemicals (EDCs). A vast body of literature links exposure to these chemicals with increased incidences of reproductive, metabolic, or neurological disorders. Moreover, recent data demonstrate that, when used in combination, chemicals have outcomes that cannot be predicted from their individual behavior. In its heterodimeric form with the retinoid X receptor (RXR), the pregnane X receptor (PXR) plays an essential role in controlling the mammalian xenobiotic response and mediates both beneficial and detrimental effects. Our previous work shed light on a mechanism by which a binary mixture of xenobiotics activates PXR in a synergistic fashion. Structural analysis revealed that mutual stabilization of the compounds within the ligand-binding pocket of PXR accounts for the enhancement of their binding affinity. In order to identify and characterize additional active mixtures, we combined a set of cell-based, biophysical, structural, and in vivo approaches. Our study reveals features that confirm the binding promiscuity of this receptor and its ability to accommodate bipartite ligands. We reveal previously unidentified binding mechanisms involving dynamic structural transitions and covalent coupling and report four binary mixtures eliciting graded synergistic activities. Last, we demonstrate that the robust activity obtained with two synergizing PXR ligands can be enhanced further in the presence of RXR environmental ligands. Our study reveals insights as to how low-dose EDC mixtures may alter physiology through interaction with RXR-PXR and potentially several other nuclear receptor heterodimers.},
note = {2019/06},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Fermer

Erb, S; Cianferani, S; Marcoux, J

Hands on Native Mass Spectrometry Analysis of Multi-protein Complexes Article de journal

Methods Mol Biol, 2247 , p. 173-191, 2021, ISSN: 1940-6029 (Electronic) 1064-3745 (Linking), (Erb, Stephane Cianferani, Sarah Marcoux, Julien eng Research Support, Non-U.S. Gov't 2020/12/11 06:00 Methods Mol Biol. 2021;2247:173-191. doi: 10.1007/978-1-0716-1126-5_10.).

Résumé | Liens

Ghoroghi, S; Mary, B; Larnicol, A; Asokan, N; Klein, A; Osmani, N; Busnelli, I; Delalande, F; Paul, N; Halary, S; Gros, F; Fouillen, L; Haeberle, A M; Royer, C; Spiegelhalter, C; Andre-Gregoire, G; Mittelheisser, V; Detappe, A; Murphy, K; Timpson, P; Carapito, R; Blot-Chabaud, M; Gavard, J; Carapito, C; Vitale, N; Lefebvre, O; Goetz, J G; Hyenne, V

Ral GTPases promote breast cancer metastasis by controlling biogenesis and organ targeting of exosomes Article de journal

Elife, 10 , 2021, ISSN: 2050-084X (Electronic) 2050-084X (Linking), (Ghoroghi, Shima Mary, Benjamin Larnicol, Annabel Asokan, Nandini Klein, Annick Osmani, Nael Busnelli, Ignacio Delalande, Francois Paul, Nicodeme Halary, Sebastien Gros, Frederic Fouillen, Laetitia Haeberle, Anne-Marie Royer, Cathy Spiegelhalter, Coralie Andre-Gregoire, Gwennan Mittelheisser, Vincent Detappe, Alexandre Murphy, Kendelle Timpson, Paul Carapito, Raphael Blot-Chabaud, Marcel Gavard, Julie Carapito, Christine Vitale, Nicolas Lefebvre, Olivier Goetz, Jacky G Hyenne, Vincent eng PLBIO19-291/Institut National Du Cancer ANR-10-INBS-08-03/Agence Nationale de la Recherche ANR-19-CE44-0019/Agence Nationale de la Recherche ANR-11-INBS- 0010/Agence Nationale de la Recherche Exosomics/Canceropole Grand Est Vesmatic/Plan Cancer Exosomics/Region Est England 2021/01/07 06:00 Elife. 2021 Jan 6;10. pii: 61539. doi: 10.7554/eLife.61539.).

Résumé | Liens

@article{706,
title = {Ral GTPases promote breast cancer metastasis by controlling biogenesis and organ targeting of exosomes},
author = {S Ghoroghi and B Mary and A Larnicol and N Asokan and A Klein and N Osmani and I Busnelli and F Delalande and N Paul and S Halary and F Gros and L Fouillen and A M Haeberle and C Royer and C Spiegelhalter and G Andre-Gregoire and V Mittelheisser and A Detappe and K Murphy and P Timpson and R Carapito and M Blot-Chabaud and J Gavard and C Carapito and N Vitale and O Lefebvre and J G Goetz and V Hyenne},
url = {https://www.ncbi.nlm.nih.gov/pubmed/33404012},
doi = {10.7554/eLife.61539},
issn = {2050-084X (Electronic)
2050-084X (Linking)},
year = {2021},
date = {2021-01-01},
journal = {Elife},
volume = {10},
abstract = {Cancer extracellular vesicles (EVs) shuttle at distance and fertilize pre-metastatic niches facilitating subsequent seeding by tumor cells. However, the link between EV secretion mechanisms and their capacity to form pre-metastatic niches remains obscure. Using mouse models, we show that GTPases of the Ral family control, through the phospholipase D1, multi-vesicular bodies homeostasis and tune the biogenesis and secretion of pro-metastatic EVs. Importantly, EVs from RalA or RalB depleted cells have limited organotropic capacities in vivoand are less efficient in promoting metastasis. RalA and RalB reduce the EV levels of the adhesion molecule MCAM/CD146, which favors EV-mediated metastasis by allowing EVs targeting to the lungs. Finally, RalA, RalB, and MCAM/CD146, are factors of poor prognosis in breast cancer patients. Altogether, our study identifies RalGTPases as central molecules linking the mechanisms of EVs secretion and cargo loading to their capacity to disseminate and induce pre-metastatic niches in a CD146-dependent manner.},
note = {Ghoroghi, Shima
Mary, Benjamin
Larnicol, Annabel
Asokan, Nandini
Klein, Annick
Osmani, Nael
Busnelli, Ignacio
Delalande, Francois
Paul, Nicodeme
Halary, Sebastien
Gros, Frederic
Fouillen, Laetitia
Haeberle, Anne-Marie
Royer, Cathy
Spiegelhalter, Coralie
Andre-Gregoire, Gwennan
Mittelheisser, Vincent
Detappe, Alexandre
Murphy, Kendelle
Timpson, Paul
Carapito, Raphael
Blot-Chabaud, Marcel
Gavard, Julie
Carapito, Christine
Vitale, Nicolas
Lefebvre, Olivier
Goetz, Jacky G
Hyenne, Vincent
eng
PLBIO19-291/Institut National Du Cancer
ANR-10-INBS-08-03/Agence Nationale de la Recherche
ANR-19-CE44-0019/Agence Nationale de la Recherche
ANR-11-INBS- 0010/Agence Nationale de la Recherche
Exosomics/Canceropole Grand Est
Vesmatic/Plan Cancer
Exosomics/Region Est
England
2021/01/07 06:00
Elife. 2021 Jan 6;10. pii: 61539. doi: 10.7554/eLife.61539.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Fermer

Launay, K; Amalian, J A; Laurent, E; Oswald, L; Ouahabi, Al A; Burel, A; Dufour, F; Carapito, C; Clement, J L; Lutz, J F; Charles, L; Gigmes, D

Precise Alkoxyamine Design to Enable Automated Tandem Mass Spectrometry Sequencing of Digital Poly(phosphodiester)s Article de journal

Angew Chem Int Ed Engl, 60 (2), p. 917-926, 2021, ISSN: 1521-3773 (Electronic) 1433-7851 (Linking), (Launay, Kevin Amalian, Jean-Arthur Laurent, Eline Oswald, Laurence Al Ouahabi, Abdelaziz Burel, Alexandre Dufour, Florent Carapito, Christine Clement, Jean-Louis Lutz, Jean-Francois Charles, Laurence Gigmes, Didier eng Research Support, Non-U.S. Gov't Germany 2020/09/24 06:00 Angew Chem Int Ed Engl. 2021 Jan 11;60(2):917-926. doi: 10.1002/anie.202010171. Epub 2020 Nov 10.).

Résumé | Liens

@article{692b,
title = {Precise Alkoxyamine Design to Enable Automated Tandem Mass Spectrometry Sequencing of Digital Poly(phosphodiester)s},
author = {K Launay and J A Amalian and E Laurent and L Oswald and A Al Ouahabi and A Burel and F Dufour and C Carapito and J L Clement and J F Lutz and L Charles and D Gigmes},
url = {https://www.ncbi.nlm.nih.gov/pubmed/32964618},
doi = {10.1002/anie.202010171},
issn = {1521-3773 (Electronic)
1433-7851 (Linking)},
year = {2021},
date = {2021-01-01},
journal = {Angew Chem Int Ed Engl},
volume = {60},
number = {2},
pages = {917-926},
abstract = {A major step towards reliable reading of information coded in the sequence of long poly(phosphodiester)s was previously achieved by introducing an alkoxyamine spacer between information sub-segments. However, MS/MS decoding had to be performed manually to safely identify useful fragments of low abundance compared to side-products from the amide-based alkoxyamine used. Here, alternative alkoxyamines were designed to prevent side-reactions and enable automated MS/MS sequencing. Different styryl-TEMPO spacers were prepared to increase radical delocalization and stiffness of the structure. Their dissociation behavior was investigated by EPR and best results were obtained with spacers containing in-chain benzyl ring, with no side-reaction during synthesis or sequencing. Automated decoding of these polymers was performed using the MS-DECODER software, which interprets fragmentation data recorded for each sub-segment and re-align them in their original order based on location tags.},
note = {Launay, Kevin
Amalian, Jean-Arthur
Laurent, Eline
Oswald, Laurence
Al Ouahabi, Abdelaziz
Burel, Alexandre
Dufour, Florent
Carapito, Christine
Clement, Jean-Louis
Lutz, Jean-Francois
Charles, Laurence
Gigmes, Didier
eng
Research Support, Non-U.S. Gov't
Germany
2020/09/24 06:00
Angew Chem Int Ed Engl. 2021 Jan 11;60(2):917-926. doi: 10.1002/anie.202010171. Epub 2020 Nov 10.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Fermer

Lehot, V; Kuhn, I; Nothisen, M; Erb, S; Kolodych, S; Cianferani, S; Chaubet, G; Wagner, A

Non-specific interactions of antibody-oligonucleotide conjugates with living cells Article de journal

Sci Rep, 11 (1), p. 5881, 2021, ISSN: 2045-2322 (Electronic) 2045-2322 (Linking), (Lehot, Victor Kuhn, Isabelle Nothisen, Marc Erb, Stephane Kolodych, Sergii Cianferani, Sarah Chaubet, Guilhem Wagner, Alain eng England 2021/03/17 06:00 Sci Rep. 2021 Mar 15;11(1):5881. doi: 10.1038/s41598-021-85352-w.).

Résumé | Liens

Oerum, S; Catala, M; Bourguet, M; Gilet, L; Barraud, P; Cianferani, S; Condon, C; Tisne, C

Structural studies of RNase M5 reveal two-metal-ion supported two-step dsRNA cleavage for 5S rRNA maturation Article de journal

RNA Biol, p. 1-11, 2021, ISSN: 1555-8584 (Electronic) 1547-6286 (Linking), (Oerum, Stephanie Catala, Marjorie Bourguet, Maxime Gilet, Laetitia Barraud, Pierre Cianferani, Sarah Condon, Ciaran Tisne, Carine eng 2021/02/06 06:00 RNA Biol. 2021 Feb 23:1-11. doi: 10.1080/15476286.2021.1885896.).

Résumé | Liens

Picini, F; Schneider, S; Gavat, O; Jentzsch, Vargas A; Tan, J; Maaloum, M; Strub, J M; Tokunaga, S; Lehn, J M; Moulin, E; Giuseppone, N

Supramolecular Polymerization of Triarylamine-Based Macrocycles into Electroactive Nanotubes Article de journal

J Am Chem Soc, 143 (17), p. 6498-6504, 2021, ISSN: 1520-5126 (Electronic) 0002-7863 (Linking), (Picini, Flavio Schneider, Susanne Gavat, Odile Vargas Jentzsch, Andreas Tan, Junjun Maaloum, Mounir Strub, Jean-Marc Tokunaga, Shoichi Lehn, Jean-Marie Moulin, Emilie Giuseppone, Nicolas eng 2021/04/10 06:00 J Am Chem Soc. 2021 May 5;143(17):6498-6504. doi: 10.1021/jacs.1c00623. Epub 2021 Apr 9.).

Résumé | Liens

Postic, G; Andreani, J; Marcoux, J; Reys, V; Guerois, R; Rey, J; Mouton-Barbosa, E; Vandenbrouck, Y; Cianferani, S; Burlet-Schiltz, O; Labesse, G; Tuffery, P

Proteo3Dnet: a web server for the integration of structural information with interactomics data Article de journal

Nucleic Acids Res, 2021, ISSN: 1362-4962 (Electronic) 0305-1048 (Linking), (Postic, Guillaume Andreani, Jessica Marcoux, Julien Reys, Victor Guerois, Raphael Rey, Julien Mouton-Barbosa, Emmanuelle Vandenbrouck, Yves Cianferani, Sarah Burlet-Schiltz, Odile Labesse, Gilles Tuffery, Pierre eng England 2021/05/09 06:00 Nucleic Acids Res. 2021 May 8. pii: 6272410. doi: 10.1093/nar/gkab332.).

Résumé | Liens

@article{702,
title = {Proteo3Dnet: a web server for the integration of structural information with interactomics data},
author = {G Postic and J Andreani and J Marcoux and V Reys and R Guerois and J Rey and E Mouton-Barbosa and Y Vandenbrouck and S Cianferani and O Burlet-Schiltz and G Labesse and P Tuffery},
url = {https://www.ncbi.nlm.nih.gov/pubmed/33963857},
doi = {10.1093/nar/gkab332},
issn = {1362-4962 (Electronic)
0305-1048 (Linking)},
year = {2021},
date = {2021-01-01},
journal = {Nucleic Acids Res},
abstract = {Proteo3Dnet is a web server dedicated to the analysis of mass spectrometry interactomics experiments. Given a flat list of proteins, its aim is to organize it in terms of structural interactions to provide a clearer overview of the data. This is achieved using three means: (i) the search for interologs with resolved structure available in the protein data bank, including cross-species remote homology search, (ii) the search for possibly weaker interactions mediated through Short Linear Motifs as predicted by ELM-a unique feature of Proteo3Dnet, (iii) the search for protein-protein interactions physically validated in the BioGRID database. The server then compiles this information and returns a graph of the identified interactions and details about the different searches. The graph can be interactively explored to understand the way the core complexes identified could interact. It can also suggest undetected partners to the experimentalists, or specific cases of conditionally exclusive binding. The interest of Proteo3Dnet, previously demonstrated for the difficult cases of the proteasome and pragmin complexes data is, here, illustrated in the context of yeast precursors to the small ribosomal subunits and the smaller interactome of 14-3-3zeta frequent interactors. The Proteo3Dnet web server is accessible at http://bioserv.rpbs.univ-paris-diderot.fr/services/Proteo3Dnet/.},
note = {Postic, Guillaume
Andreani, Jessica
Marcoux, Julien
Reys, Victor
Guerois, Raphael
Rey, Julien
Mouton-Barbosa, Emmanuelle
Vandenbrouck, Yves
Cianferani, Sarah
Burlet-Schiltz, Odile
Labesse, Gilles
Tuffery, Pierre
eng
England
2021/05/09 06:00
Nucleic Acids Res. 2021 May 8. pii: 6272410. doi: 10.1093/nar/gkab332.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Fermer

Optimized Sample Preparation and Data Processing of Data-Independent Acquisition Methods for the Robust Quantification of Trace-Level Host Cell Protein Impurities in Antibody Drug Products Article de journal

J Proteome Res, 20 (1), p. 923-931, 2021, ISSN: 1535-3907 (Electronic) 1535-3893 (Linking), (Pythoud, Nicolas Bons, Joanna Mijola, Geoffroy Beck, Alain Cianferani, Sarah Carapito, Christine eng Research Support, Non-U.S. Gov't 2020/10/06 06:00 J Proteome Res. 2021 Jan 1;20(1):923-931. doi: 10.1021/acs.jproteome.0c00664. Epub 2020 Oct 4.).

Résumé | Liens

@article{,
title = {Optimized Sample Preparation and Data Processing of Data-Independent Acquisition Methods for the Robust Quantification of Trace-Level Host Cell Protein Impurities in Antibody Drug Products},
url = {https://www.ncbi.nlm.nih.gov/pubmed/33016074},
doi = {10.1021/acs.jproteome.0c00664},
issn = {1535-3907 (Electronic)
1535-3893 (Linking)},
year = {2021},
date = {2021-01-01},
journal = {J Proteome Res},
volume = {20},
number = {1},
pages = {923-931},
abstract = {Host cell proteins (HCPs) are a major class of bioprocess-related impurities generated by the host organism and are generally present at low levels in purified biopharmaceutical products. The monitoring of these impurities is identified as an important critical quality attribute of monoclonal antibody (mAb) formulations not only due to the potential risk for the product stability and efficacy but also concerns linked to the immunogenicity of some of them. While overall HCP levels are usually monitored by enzyme-linked immunosorbent assay (ELISA), mass spectrometry (MS)-based approaches have been emerging as powerful and promising alternatives providing qualitative and quantitative information. However, a major challenge for liquid chromatography (LC)-MS-based methods is to deal with the wide dynamic range of drug products and the extreme sensitivity required to detect trace-level HCPs. In this study, we developed powerful and reproducible MS-based analytical workflows coupling optimized and efficient sample preparations, the library-free data-independent acquisition (DIA) method, and stringent validation criteria. The performances of several preparation protocols and DIA versus classical data-dependent acquisition (DDA) were evaluated using a series of four commercially available drug products. Depending on the selected protocols, the user has access to different information: on the one hand, a deep profiling of tens of identified HCPs and on the other hand, accurate and reproducible (coefficients of variation (CVs) < 12%) quantification of major HCPs. Overall, a final global HCP amount of a few tens of ng/mg mAb in these mAb samples was measured, while reaching a sensitivity down to the sub-ng/mg mAb level. Thus, this straightforward and robust approach can be intended as a routine quality control for any drug product analysis.},
note = {Pythoud, Nicolas
Bons, Joanna
Mijola, Geoffroy
Beck, Alain
Cianferani, Sarah
Carapito, Christine
eng
Research Support, Non-U.S. Gov't
2020/10/06 06:00
J Proteome Res. 2021 Jan 1;20(1):923-931. doi: 10.1021/acs.jproteome.0c00664. Epub 2020 Oct 4.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Fermer

Schleiss, C; Carapito, R; Fornecker, L M; Muller, L; Paul, N; Tahar, O; Pichot, A; Tavian, M; Nicolae, A; Miguet, L; Mauvieux, L; Herbrecht, R; Cianferani, S; Freund, J N; Carapito, C; Maumy-Bertrand, M; Bahram, S; Bertrand, F; Vallat, L

Temporal multiomic modeling reveals a B-cell receptor proliferative program in chronic lymphocytic leukemia Article de journal

Leukemia, 35 (5), p. 1463-1474, 2021, ISSN: 1476-5551 (Electronic) 0887-6924 (Linking), (Schleiss, Cedric Carapito, Raphael Fornecker, Luc-Matthieu Muller, Leslie Paul, Nicodeme Tahar, Ouria Pichot, Angelique Tavian, Manuela Nicolae, Alina Miguet, Laurent Mauvieux, Laurent Herbrecht, Raoul Cianferani, Sarah Freund, Jean-Noel Carapito, Christine Maumy-Bertrand, Myriam Bahram, Seiamak Bertrand, Frederic Vallat, Laurent eng ANR-11-LABX-0070_Transplantex/Agence Nationale de la Recherche (French National Research Agency) C13055MS/Institut National Du Cancer (French National Cancer Institute) England 2021/04/10 06:00 Leukemia. 2021 May;35(5):1463-1474. doi: 10.1038/s41375-021-01221-5. Epub 2021 Apr 8.).

Résumé | Liens

@article{704,
title = {Temporal multiomic modeling reveals a B-cell receptor proliferative program in chronic lymphocytic leukemia},
author = {C Schleiss and R Carapito and L M Fornecker and L Muller and N Paul and O Tahar and A Pichot and M Tavian and A Nicolae and L Miguet and L Mauvieux and R Herbrecht and S Cianferani and J N Freund and C Carapito and M Maumy-Bertrand and S Bahram and F Bertrand and L Vallat},
url = {https://www.ncbi.nlm.nih.gov/pubmed/33833385},
doi = {10.1038/s41375-021-01221-5},
issn = {1476-5551 (Electronic)
0887-6924 (Linking)},
year = {2021},
date = {2021-01-01},
journal = {Leukemia},
volume = {35},
number = {5},
pages = {1463-1474},
abstract = {B-cell receptor (BCR) signaling is crucial for the pathophysiology of most mature B-cell lymphomas/leukemias and has emerged as a therapeutic target whose effectiveness remains limited by the occurrence of mutations. Therefore, deciphering the cellular program activated downstream this pathway has become of paramount importance for the development of innovative therapies. Using an original ex vivo model of BCR-induced proliferation of chronic lymphocytic leukemia cells, we generated 108 temporal transcriptional and proteomic profiles from 1 h up to 4 days after BCR activation. This dataset revealed a structured temporal response composed of 13,065 transcripts and 4027 proteins, comprising a leukemic proliferative signature consisting of 430 genes and 374 proteins. Mathematical modeling of this complex cellular response further highlighted a transcriptional network driven by 14 early genes linked to proteins involved in cell proliferation. This group includes expected genes (EGR1/2, NF-kB) and genes involved in NF-kB signaling modulation (TANK, ROHF) and immune evasion (KMO, IL4I1) that have not yet been associated with leukemic cells proliferation. Our study unveils the BCR-activated proliferative genetic program in primary leukemic cells. This approach combining temporal measurements with modeling allows identifying new putative targets for innovative therapy of lymphoid malignancies and also cancers dependent on ligand-receptor interactions.},
note = {Schleiss, Cedric
Carapito, Raphael
Fornecker, Luc-Matthieu
Muller, Leslie
Paul, Nicodeme
Tahar, Ouria
Pichot, Angelique
Tavian, Manuela
Nicolae, Alina
Miguet, Laurent
Mauvieux, Laurent
Herbrecht, Raoul
Cianferani, Sarah
Freund, Jean-Noel
Carapito, Christine
Maumy-Bertrand, Myriam
Bahram, Seiamak
Bertrand, Frederic
Vallat, Laurent
eng
ANR-11-LABX-0070_Transplantex/Agence Nationale de la Recherche (French National Research Agency)
C13055MS/Institut National Du Cancer (French National Cancer Institute)
England
2021/04/10 06:00
Leukemia. 2021 May;35(5):1463-1474. doi: 10.1038/s41375-021-01221-5. Epub 2021 Apr 8.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Fermer

Wagner-Rousset, E; Colas, O; Chenu, S; Francois, Y N; Guillarme, D; Cianferani, S; Tsybin, Y O; Sjogren, J; Delobel, A; Beck, A

Fast Afucosylation Profiling of Glycoengineered Antibody Subunits by Middle-Up Mass Spectrometry Article de journal

Methods Mol Biol, 2271 , p. 73-83, 2021, ISSN: 1940-6029 (Electronic) 1064-3745 (Linking), (Wagner-Rousset, Elsa Colas, Olivier Chenu, Stephane Francois, Yannis-Nicolas Guillarme, Davy Cianferani, Sarah Tsybin, Yury O Sjogren, Jonathan Delobel, Arnaud Beck, Alain eng 2021/04/29 06:00 Methods Mol Biol. 2021;2271:73-83. doi: 10.1007/978-1-0716-1241-5_5.).

Résumé | Liens

Mori, Daiki; Grégoire, Claude; Voisinne, Guillaume; Celis-Gutierrez, Javier; Aussel, Rudy; Girard, Laura; è, Myl; è, Marl; Argenty, Jérémy; Burlet-Schiltz, Odile; Fiore, Frédéric; de Peredo, Anne; Malissen, Marie; Roncagalli, Romain; Malissen, Bernard

The T cell CD6 receptor operates a multitask signalosome with opposite functions in T cell activation. Article de journal

The Journal of experimental medicine, 218 (2), 2021.

Résumé | Liens

Froment, Carine; Zanolli, Clément; Hourset, Mathilde; Mouton-Barbosa, Emmanuelle; Moreira, Andreia; Burlet-Schiltz, Odile; Mollereau, Catherine

Protein sequence comparison of human and non-human primate tooth proteomes. Article de journal

Journal of proteomics, 231 , p. 104045, 2021.

Résumé | Liens

è, Hél; Blanckaert, Vincent; Veidl, Brigitte; Burlet-Schiltz, Odile; Pichereaux, Carole; Gargaros, Audrey; Marchand, Justine; î, Beno

Application of pulsed electric fields for the biocompatible extraction of proteins from the microalga Haematococcus pluvialis. Article de journal

Bioelectrochemistry (Amsterdam, Netherlands), 137 , p. 107588, 2021.

Résumé | Liens

@article{Gateau2021,
title = {Application of pulsed electric fields for the biocompatible extraction of proteins from the microalga Haematococcus pluvialis.},
author = {Hél{è}ne Gateau and Vincent Blanckaert and Brigitte Veidl and Odile Burlet-Schiltz and Carole Pichereaux and Audrey Gargaros and Justine Marchand and Beno{î}t Schoefs},
doi = {10.1016/j.bioelechem.2020.107588},
year = {2021},
date = {2021-01-01},
journal = {Bioelectrochemistry (Amsterdam, Netherlands)},
volume = {137},
pages = {107588},
address = {Netherlands},
abstract = {This study aims to employ a pulsed electric field (PEF) treatment for the biocompatible (non-destructive) extraction of proteins from living cells of the green microalga Haematococcus pluvialis. Using a field strength of 1 kV cm(-1), we achieved the extraction of 10.2 µg protein per mL of culture, which corresponded to 46% of the total amount of proteins that could be extracted by complete destructive extraction (i.e. the grinding of biomass with glass beads). We found that the extraction yield was not improved by stronger field strengths and was not dependent on the pulse frequency. A biocompatibility index (BI) was defined as the relative abundance of cells that remained alive after the PEF treatment. This index relied on measurements of several physiological parameters after a PEF treatment. It was found that at 1 kV cm(-1) that cultures recovered after 72 h. Therefore, these PEF conditions constituted a good compromise between protein extraction efficiency and culture survival. To characterize the PEF treatment further at a molecular level, mass spectrometry-based proteomics analyses of PEF-prepared extracts was used. This led to the identification of 52 electro-extracted proteins. Of these, only 16 proteins were identified when proteins were extracted with PEF at 0.5 cm(-1). They belong to core metabolism, stress response and cell movement. Unassigned proteins were also extracted. Their physiological implications and possible utilization in food as alimentary complements are discussed.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Fermer

Zhai, Yunhao; Celis-Gutierrez, Javier; Voisinne, Guillaume; Mori, Daiki; Girard, Laura; Burlet-Schiltz, Odile; de Peredo, Anne Gonzalez; Roncagalli, Romain; Malissen, Bernard

Opposing regulatory functions of the TIM3 (HAVCR2) signalosome in primary effector T cells as revealed by quantitative interactomics. Article de journal

Cellular & molecular immunology, 2020.

Liens

Eren, Elif; è, Rémi Plan; Bagayoko, Salimata; Bordignon, Pierre-Jean; Chaoui, Karima; Hessel, Audrey; Santoni, Karin; Pinilla, Miriam; Lagrange, Brice; Burlet-Schiltz, Odile; Howard, Jonathan C; Henry, Thomas; Yamamoto, Masahiro; Meunier, Etienne

Irgm2 and Gate-16 cooperatively dampen Gram-negative bacteria-induced caspase-11 response. Article de journal

EMBO reports, 21 (11), p. e50829, 2020.

Résumé | Liens

Klein, Julie; Caubet, Cécile; è, Myl; Makridakis, Manousos; Denis, Colette; Gilet, Marion; è, Guyl; Rascalou, Simon; Neau, Eric; Garrigues, Luc; du Boullay, Olivier; Mischak, Harald; Monsarrat, Bernard; Burlet-Schiltz, Odile; Vlahou, Antonia; Saulnier-Blache, Jean Sébastien; Bascands, Jean-Loup; Schanstra, Joost P

Connectivity mapping of glomerular proteins identifies dimethylaminoparthenolide as a new inhibitor of diabetic kidney disease. Article de journal

Scientific reports, 10 (1), p. 14898, 2020.

Résumé | Liens

@article{Klein2020,
title = {Connectivity mapping of glomerular proteins identifies dimethylaminoparthenolide as a new inhibitor of diabetic kidney disease.},
author = {Julie Klein and Cécile Caubet and Myl{è}ne Camus and Manousos Makridakis and Colette Denis and Marion Gilet and Guyl{è}ne Feuillet and Simon Rascalou and Eric Neau and Luc Garrigues and Olivier du Boullay and Harald Mischak and Bernard Monsarrat and Odile Burlet-Schiltz and Antonia Vlahou and Jean Sébastien Saulnier-Blache and Jean-Loup Bascands and Joost P Schanstra},
doi = {10.1038/s41598-020-71950-7},
year = {2020},
date = {2020-09-01},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {14898},
abstract = {While blocking the renin angiotensin aldosterone system (RAAS) has been the main therapeutic strategy to control diabetic kidney disease (DKD) for many years, 25-30% of diabetic patients still develop the disease. In the present work we adopted a systems biology strategy to analyze glomerular protein signatures to identify drugs with potential therapeutic properties in DKD acting through a RAAS-independent mechanism. Glomeruli were isolated from wild type and type 1 diabetic (Ins2Akita) mice treated or not with the angiotensin-converting enzyme inhibitor (ACEi) ramipril. Ramipril efficiently reduced the urinary albumin/creatine ratio (ACR) of Ins2Akita mice without modifying DKD-associated renal-injuries. Large scale quantitative proteomics was used to identify the DKD-associated glomerular proteins (DKD-GPs) that were ramipril-insensitive (RI-DKD-GPs). The raw data are publicly available via ProteomeXchange with identifier PXD018728. We then applied an in silico drug repurposing approach using a pattern-matching algorithm (Connectivity Mapping) to compare the RI-DKD-GPs's signature with a collection of thousands of transcriptional signatures of bioactive compounds. The sesquiterpene lactone parthenolide was identified as one of the top compounds predicted to reverse the RI-DKD-GPs's signature. Oral treatment of 2 months old Ins2Akita mice with dimethylaminoparthenolide (DMAPT, a water-soluble analogue of parthenolide) for two months at 10 mg/kg/d by gavage significantly reduced urinary ACR. However, in contrast to ramipril, DMAPT also significantly reduced glomerulosclerosis and tubulointerstitial fibrosis. Using a system biology approach, we identified DMAPT, as a compound with a potential add-on value to standard-of-care ACEi-treatment in DKD.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Fermer

Bouyssié, D; Hesse, A M; Mouton-Barbosa, E; Rompais, M; Macron, C; Carapito, C; de Peredo, A G; Couté, Y; Dupierris, V; Burel, A; Menetrey, J P; Kalaitzakis, A; Poisat, J; Romdhani, A; Burlet-Schiltz, O; Cianférani, S; Garin, J; Bruley, C

Proline: an efficient and user-friendly software suite for large-scale proteomics Article de journal

Bioinformatics, 36 (10), p. 3148-3155, 2020.

Liens

Pirro, M; Rombouts, Y; Stella, A; Neyrolles, O; Burlet-Schiltz, O; van Vliet, S J; de Ru, A H; Mohammed, Y; Wuhrer, M; van Veelen, P A; Hensbergen, P J

Characterization of Macrophage Galactose-type Lectin (MGL) ligands in colorectal cancer cell lines Article de journal

Biochim Biophys Acta Gen Subj, 1864 (4), p. 129513, 2020.

Liens

Locard-Paulet, Marie; Bouyssié, David; Froment, Carine; Burlet-Schiltz, Odile; Jensen, Lars J

Journal of proteome research, 19 (3), p. 1338–1345, 2020.

Résumé | Liens

Ibrahim, M; Ayoub, D; Wasselin, T; Dorsselaer, Van A; Maho, Le Y; Raclot, T; Bertile, F

Alterations in rat adipose tissue transcriptome and proteome in response to prolonged fasting Article de journal

Biological Chemistry, 401 (3), p. 389-405, 2020.

Liens

Bonnet, M; Soulat, J; Bons, J; Leger, S; Koning, De L; Carapito, C; Picard, B

Quantification of biomarkers for beef meat qualities using a combination of Parallel Reaction Monitoring- and antibody-based proteomics Article de journal

Food Chem, 317 , p. 126376., 2020.

Liens

Locard-Paulet, M; Bouyssié, D; Froment, C; Burlet-Schiltz, O; Jensen, L J

J. Proteome Res., 19 (3), p. 1338–1345, 2020.

Liens

Imbert, C; Montfort, A; Fraisse, M; Marcheteau, E; Gilhodes, J; Martin, E; Bertrand, F; Marcellin, M; Burlet-Schiltz, O; Peredo, A G; Garcia, V; Carpentier, S; Tartare-Deckert, S; Brousset, P; Rochaix, P; Puisset, F; Filleron, T; Meyer, N; Lamant, L; Levade, T; Ségui, B; Andrieu-Abadie, N; Colacios, C

Resistance of melanoma to immune checkpoint inhibitors is overcome by targeting the sphingosine kinase-1 Article de journal

Nat Commun, 11 (1), p. 437, 2020.

Liens

Froment, C; Hourset, M; S?enz-Oyh?r?guy, N; Mouton-Barbosa, E; Willmann, C; Zanolli, C; Esclassan, R; Donat, R; Th?ves, C; Burlet-Schiltz, O; Mollereau, C

Analysis of 5000 year-old human teeth using optimized large-scale and targeted proteomics approaches for detection of sex-specific peptides Article de journal

J Proteomics, 211 , p. 103548, 2020.

Liens

Clement, E; Lazar, I; Attané, C; Carrié, L; Dauvillier, S; Ducoux-Petit, M; Estève, D; Menneteau, T; Moutahir, M; Gonidec, Le S; Dalle, S; Valet, P; Burlet-Schiltz, O; Muller, C; Nieto, L

Adipocyte extracellular vesicles carry enzymes and fatty acids that stimulate mitochondrial metabolism and remodeling in tumor cells Article de journal

EMBO J., 39 (3), p. e102525, 2020.

Liens

Santin, Yohan; Fazal, Loubina; Sainte-Marie, Yannis; Sicard, Pierre; Maggiorani, Damien; Tortosa, Florence; Yücel, Yasemin Yücel; Teyssedre, Lise; Rouquette, Jacques; Marcellin, Marlene; Vindis, Cécile; Shih, Jean C; Lairez, Olivier; Burlet-Schiltz, Odile; Parini, Angelo; Lezoualc'h, Frank; Mialet-Perez, Jeanne

Mitochondrial 4-HNE derived from MAO-A promotes mitoCa(2+) overload in chronic postischemic cardiac remodeling. Article de journal

Cell death and differentiation, 27 (6), p. 1907–1923, 2020.

Résumé | Liens

@article{Santin2020,
title = {Mitochondrial 4-HNE derived from MAO-A promotes mitoCa(2+) overload in chronic postischemic cardiac remodeling.},
author = {Yohan Santin and Loubina Fazal and Yannis Sainte-Marie and Pierre Sicard and Damien Maggiorani and Florence Tortosa and Yasemin Yücel Yücel and Lise Teyssedre and Jacques Rouquette and Marlene Marcellin and Cécile Vindis and Jean C Shih and Olivier Lairez and Odile Burlet-Schiltz and Angelo Parini and Frank Lezoualc'h and Jeanne Mialet-Perez},
doi = {10.1038/s41418-019-0470-y},
year = {2020},
date = {2020-01-01},
journal = {Cell death and differentiation},
volume = {27},
number = {6},
pages = {1907--1923},
abstract = {Chronic remodeling postmyocardial infarction consists in various maladaptive changes including interstitial fibrosis, cardiomyocyte death and mitochondrial dysfunction that lead to heart failure (HF). Reactive aldehydes such as 4-hydroxynonenal (4-HNE) are critical mediators of mitochondrial dysfunction but the sources of mitochondrial 4-HNE in cardiac diseases together with its mechanisms of action remain poorly understood. Here, we evaluated whether the mitochondrial enzyme monoamine oxidase-A (MAO-A), which generates H(2)O(2) as a by-product of catecholamine metabolism, is a source of deleterious 4-HNE in HF. We found that MAO-A activation increased mitochondrial ROS and promoted local 4-HNE production inside the mitochondria through cardiolipin peroxidation in primary cardiomyocytes. Deleterious effects of MAO-A/4-HNE on cardiac dysfunction were prevented by activation of mitochondrial aldehyde dehydrogenase 2 (ALDH2), the main enzyme for 4-HNE metabolism. Mechanistically, MAO-A-derived 4-HNE bound to newly identified targets VDAC and MCU to promote ER-mitochondria contact sites and MCU higher-order complex formation. The resulting mitochondrial Ca(2+) accumulation participated in mitochondrial respiratory dysfunction and loss of membrane potential, as shown with the protective effects of the MCU inhibitor, RU360. Most interestingly, these findings were recapitulated in a chronic model of ischemic remodeling where pharmacological or genetic inhibition of MAO-A protected the mice from 4-HNE accumulation, MCU oligomer formation and Ca(2+) overload, thus mitigating ventricular dysfunction. To our knowledge, these are the first evidences linking MAO-A activation to mitoCa(2+) mishandling through local 4-HNE production, contributing to energetic failure and postischemic remodeling.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Fermer

Froment, Carine; Hourset, Mathilde; Sáenz-Oyhéréguy, Nancy; Mouton-Barbosa, Emmanuelle; Willmann, Claire; Zanolli, Clément; Esclassan, Rémi; Donat, Richard; è, Catherine Th; Burlet-Schiltz, Odile; Mollereau, Catherine

Analysis of 5000 year-old human teeth using optimized large-scale and targeted proteomics approaches for detection of sex-specific peptides. Article de journal

Journal of proteomics, 211 , p. 103548, 2020.

Résumé | Liens

Del Corpo, Daniele ; Fullone, Maria R; Miele, Rossella; ë, Micka; Pontiggia, Daniela; Grisel, Sacha; Kieffer‐Jaquinod, Sylvie; Giardina, Thierry; Bellincampi, Daniela; Lionetti, Vincenzo

AtPME17 is a functional $backslash$textitArabidopsis thaliana pectin methylesterase regulated by its PRO region that triggers PME activity in the resistance to $backslash$textitBotrytis cinerea Article de journal

Molecular Plant Pathology, p. mpp.13002, 2020, ISSN: 1464-6722, 1364-3703.

Liens

Farhat, Dayana C; Swale, Christopher; Dard, Céline; Cannella, Dominique; Ortet, Philippe; Barakat, Mohamed; Sindikubwabo, Fabien; Belmudes, Lucid; De Bock, Pieter-Jan ; Couté, Yohann; Bougdour, Alexandre; Hakimi, Mohamed-Ali

A MORC-driven transcriptional switch controls Toxoplasma developmental trajectories and sexual commitment Article de journal

Nature Microbiology, 2020, ISSN: 2058-5276.

Liens

Di Giovanni, D; Lepetit, D; Guinet, B; Bennetot, B; Boulesteix, M; Couté, Y; Bouchez, O; Ravallec, M; Varaldi, J

A behavior-manipulating virus relative as a source of adaptive genes for Drosophila parasitoids Article de journal

Molecular Biology and Evolution, 2020, ISSN: 1537-1719.

Résumé | Liens

Adhikari, Subash; Nice, Edouard C; Deutsch, Eric W; Lane, Lydie; Omenn, Gilbert S; Pennington, Stephen R; Paik, Young-Ki; Overall, Christopher M; Corrales, Fernando J; Cristea, Ileana M; Van Eyk, Jennifer E; Uhlén, Mathias; Lindskog, Cecilia; Chan, Daniel W; Bairoch, Amos; Waddington, James C; Justice, Joshua L; LaBaer, Joshua; Rodriguez, Henry; He, Fuchu; Kostrzewa, Markus; Ping, Peipei; Gundry, Rebekah L; Stewart, Peter; Srivastava, Sanjeeva; Srivastava, Sudhir; Nogueira, Fabio C S; Domont, Gilberto B; Vandenbrouck, Yves; Lam, Maggie P Y; Wennersten, Sara; Vizcaino, Juan Antonio; Wilkins, Marc; Schwenk, Jochen M; Lundberg, Emma; Bandeira, Nuno; Marko-Varga, Gyorgy; Weintraub, Susan T; Pineau, Charles; Kusebauch, Ulrike; Moritz, Robert L; Ahn, Seong Beom; Palmblad, Magnus; Snyder, Michael P; Aebersold, Ruedi; Baker, Mark S

A high-stringency blueprint of the human proteome Article de journal

Nature Communications, 11 (1), p. 5301, 2020, ISSN: 2041-1723.

Résumé | Liens

@article{adhikari_high-stringency_2020,
title = {A high-stringency blueprint of the human proteome},
author = {Subash Adhikari and Edouard C Nice and Eric W Deutsch and Lydie Lane and Gilbert S Omenn and Stephen R Pennington and Young-Ki Paik and Christopher M Overall and Fernando J Corrales and Ileana M Cristea and Jennifer E {Van Eyk} and Mathias Uhlén and Cecilia Lindskog and Daniel W Chan and Amos Bairoch and James C Waddington and Joshua L Justice and Joshua LaBaer and Henry Rodriguez and Fuchu He and Markus Kostrzewa and Peipei Ping and Rebekah L Gundry and Peter Stewart and Sanjeeva Srivastava and Sudhir Srivastava and Fabio C S Nogueira and Gilberto B Domont and Yves Vandenbrouck and Maggie P Y Lam and Sara Wennersten and Juan Antonio Vizcaino and Marc Wilkins and Jochen M Schwenk and Emma Lundberg and Nuno Bandeira and Gyorgy Marko-Varga and Susan T Weintraub and Charles Pineau and Ulrike Kusebauch and Robert L Moritz and Seong Beom Ahn and Magnus Palmblad and Michael P Snyder and Ruedi Aebersold and Mark S Baker},
doi = {10.1038/s41467-020-19045-9},
issn = {2041-1723},
year = {2020},
date = {2020-01-01},
journal = {Nature Communications},
volume = {11},
number = {1},
pages = {5301},
abstract = {The Human Proteome Organization (HUPO) launched the Human Proteome Project (HPP) in 2010, creating an international framework for global collaboration, data sharing, quality assurance and enhancing accurate annotation of the genome-encoded proteome. During the subsequent decade, the HPP established collaborations, developed guidelines and metrics, and undertook reanalysis of previously deposited community data, continuously increasing the coverage of the human proteome. On the occasion of the HPP's tenth anniversary, we here report a 90.4% complete high-stringency human proteome blueprint. This knowledge is essential for discerning molecular processes in health and disease, as we demonstrate by highlighting potential roles the human proteome plays in our understanding, diagnosis and treatment of cancers, cardiovascular and infectious diseases.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Fermer

Monestier, Marie; ï, Ana; Lamboux, Aline; Cuillel, Martine; Pignot-Paintrand, Isabelle; Cassio, Doris; Charbonnier, Peggy; Um, Khémary; Harel, Amélie; Bohic, Sylvain; Gateau, Christelle; Balter, Vincent; Brun, Virginie; Delangle, Pascale; Mintz, Elisabeth

A liver-targeting Cu( textlessspan style= Article de journal

Metallomics, p. 10.1039.D0MT00069H, 2020, ISSN: 1756-5901, 1756-591X.

Résumé | Liens

Van Gool, Alain ; Corrales, Fernado; ć, Mirjana {Č}olovi; ć, Danijela Krsti; Oliver-Martos, Begona; Martínez-Cáceres, Eva; Jakasa, Ivone; Gajski, Goran; Brun, Virginie; Kyriacou, Kyriacos; Burzynska-Pedziwiatr, Izabela; Wozniak, Lucyna Alicja; Nierkens, Stephan; Pascual García, César ; Katrlik, Jaroslav; Bojic-Trbojevic, Zanka; Vacek, Jan; Llorente, Alicia; Antohe, Felicia; Suica, Viorel; Suarez, Guillaume; T'Kindt, Ruben; Martin, Petra; Penque, Deborah; Martins, Ines Lanca; Bodoki, Ede; Iacob, Bogdan-Cezar; Aydindogan, Eda; Timur, Suna; Allinson, John; Sutton, Christopher; Luider, Theo; Wittfooth, Saara; Sammar, Marei

Analytical techniques for multiplex analysis of protein biomarkers Article de journal

Expert Review of Proteomics, p. 1–17, 2020, ISSN: 1744-8387.

Résumé | Liens

@article{van_gool_analytical_2020,
title = {Analytical techniques for multiplex analysis of protein biomarkers},
author = {Alain {Van Gool} and Fernado Corrales and Mirjana {Č}olovi{ć} and Danijela Krsti{ć} and Begona Oliver-Martos and Eva Martínez-Cáceres and Ivone Jakasa and Goran Gajski and Virginie Brun and Kyriacos Kyriacou and Izabela Burzynska-Pedziwiatr and Lucyna Alicja Wozniak and Stephan Nierkens and César {Pascual García} and Jaroslav Katrlik and Zanka Bojic-Trbojevic and Jan Vacek and Alicia Llorente and Felicia Antohe and Viorel Suica and Guillaume Suarez and Ruben T'Kindt and Petra Martin and Deborah Penque and Ines Lanca Martins and Ede Bodoki and Bogdan-Cezar Iacob and Eda Aydindogan and Suna Timur and John Allinson and Christopher Sutton and Theo Luider and Saara Wittfooth and Marei Sammar},
doi = {10.1080/14789450.2020.1763174},
issn = {1744-8387},
year = {2020},
date = {2020-01-01},
journal = {Expert Review of Proteomics},
pages = {1--17},
abstract = {INTRODUCTION: The importance of biomarkers for pharmaceutical drug development and clinical diagnostics is more significant than ever in the current shift toward personalized medicine. Biomarkers have taken a central position either as companion markers to support drug development and patient selection, or as indicators aiming to detect the earliest perturbations indicative of disease, minimizing therapeutic intervention or even enabling disease reversal. Protein biomarkers are of particular interest given their central role in biochemical pathways. Hence, capabilities to analyze multiple protein biomarkers in one assay are highly interesting for biomedical research.
AREAS COVERED: We here review multiple methods that are suitable for robust, high throughput, standardized, and affordable analysis of protein biomarkers in a multiplex format. We describe innovative developments in immunoassays, the vanguard of methods in clinical laboratories, and mass spectrometry, increasingly implemented for protein biomarker analysis. Moreover, emerging techniques are discussed with potentially improved protein capture, separation, and detection that will further boost multiplex analyses.
EXPERT COMMENTARY: The development of clinically applied multiplex protein biomarker assays is essential as multi-protein signatures provide more comprehensive information about biological systems than single biomarkers, leading to improved insights in mechanisms of disease, diagnostics, and the effect of personalized medicine.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Fermer

Couté, Yohann; Bruley, Christophe; Burger, Thomas

Beyond target-decoy competition: stable validation of peptide and protein identifications in mass spectrometry-based discovery proteomics Article de journal

Analytical Chemistry, 2020, ISSN: 1520-6882.

Résumé | Liens

Lacombe, Maud; Jaquinod, Michel; Belmudes, Lucid; Couté, Yohann; Ramus, Claire; Combes, Florence; Burger, Thomas; Mintz, Elisabeth; Barthelon, Justine; Leroy, Vincent; Poujois, Aurélia; Lachaux, Alain; Woimant, France; Brun, Virginie

Comprehensive and comparative exploration of the $backslash$textitAtp7b $^backslashtextrm−/−$ mouse plasma proteome Article de journal

Metallomics, p. 10.1039.C9MT00225A, 2020, ISSN: 1756-5901, 1756-591X.

Résumé | Liens

@article{lacombe_comprehensive_2020,
title = {Comprehensive and comparative exploration of the $backslash$textitAtp7b $^backslashtextrm−/−$ mouse plasma proteome},
author = {Maud Lacombe and Michel Jaquinod and Lucid Belmudes and Yohann Couté and Claire Ramus and Florence Combes and Thomas Burger and Elisabeth Mintz and Justine Barthelon and Vincent Leroy and Aurélia Poujois and Alain Lachaux and France Woimant and Virginie Brun},
url = {http://xlink.rsc.org/?DOI=C9MT00225A},
doi = {10.1039/C9MT00225A},
issn = {1756-5901, 1756-591X},
year = {2020},
date = {2020-01-01},
journal = {Metallomics},
pages = {10.1039.C9MT00225A},
abstract = {Wilson's disease (WD) is a rare genetic disease caused by mutations in the
ATP7B
gene. In this study, we used MS-based proteomics to explore the plasma proteome of the
Atp7b
−/−
mouse, a genetic and phenotypic model for WD.

,

Wilson's disease (WD), a rare genetic disease caused by mutations in the
ATP7B
gene, is associated with altered expression and/or function of the copper-transporting ATP7B protein, leading to massive toxic accumulation of copper in the liver and brain. The
Atp7b
−/−
mouse, a genetic and phenotypic model of WD, was developed to provide new insights into the pathogenic mechanisms of WD. Many plasma proteins are secreted by the liver, and impairment of liver function can trigger changes to the plasma proteome. High standard proteomics workflows can identify such changes. Here, we explored the plasma proteome of the
Atp7b
−/−
mouse using a mass spectrometry (MS)-based proteomics workflow combining unbiased discovery analysis followed by targeted quantification. Among the 367 unique plasma proteins identified, 7 proteins were confirmed as differentially abundant between
Atp7b
−/−
mice and wild-type littermates, and were directly linked to WD pathophysiology (regeneration of liver parenchyma, plasma iron depletion,
etc.
). We then adapted our targeted proteomics assay to quantify human orthologues of these proteins in plasma from copper-chelator-treated WD patients. The plasma proteome changes observed in the
Atp7b
−/−
mouse were not confirmed in these samples, except for alpha-1 antichymotrypsin, levels of which were decreased in WD patients compared to healthy individuals. Plasma ceruloplasmin was investigated in both the
Atp7b
−/−
mouse model and human patients; it was significantly decreased in the human form of WD only. In conclusion, MS-based proteomics is a method of choice to identify proteome changes in murine models of disrupted metal homeostasis, and allows their validation in human cohorts.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Fermer

Wilson's disease (WD) is a rare genetic disease caused by mutations in the
ATP7B
gene. In this study, we used MS-based proteomics to explore the plasma proteome of the
Atp7b
−/−
mouse, a genetic and phenotypic model for WD.

,

Wilson's disease (WD), a rare genetic disease caused by mutations in the
ATP7B
gene, is associated with altered expression and/or function of the copper-transporting ATP7B protein, leading to massive toxic accumulation of copper in the liver and brain. The
Atp7b
−/−
mouse, a genetic and phenotypic model of WD, was developed to provide new insights into the pathogenic mechanisms of WD. Many plasma proteins are secreted by the liver, and impairment of liver function can trigger changes to the plasma proteome. High standard proteomics workflows can identify such changes. Here, we explored the plasma proteome of the
Atp7b
−/−
mouse using a mass spectrometry (MS)-based proteomics workflow combining unbiased discovery analysis followed by targeted quantification. Among the 367 unique plasma proteins identified, 7 proteins were confirmed as differentially abundant between
Atp7b
−/−
mice and wild-type littermates, and were directly linked to WD pathophysiology (regeneration of liver parenchyma, plasma iron depletion,
etc.
). We then adapted our targeted proteomics assay to quantify human orthologues of these proteins in plasma from copper-chelator-treated WD patients. The plasma proteome changes observed in the
Atp7b
−/−
mouse were not confirmed in these samples, except for alpha-1 antichymotrypsin, levels of which were decreased in WD patients compared to healthy individuals. Plasma ceruloplasmin was investigated in both the
Atp7b
−/−
mouse model and human patients; it was significantly decreased in the human form of WD only. In conclusion, MS-based proteomics is a method of choice to identify proteome changes in murine models of disrupted metal homeostasis, and allows their validation in human cohorts.

Fermer

Jeudy, Sandra; Bertaux, Lionel; Alempic, Jean-Marie; Lartigue, Audrey; Legendre, Matthieu; Belmudes, Lucid; Santini, Sébastien; è, Nad; Beucher, Laure; Biondi, Emanuele G; Juul, Sissel; Turner, Daniel J; Couté, Yohann; Claverie, Jean-Michel; Abergel, Chantal

Exploration of the propagation of transpovirons within Mimiviridae reveals a unique example of commensalism in the viral world Article de journal

The ISME journal, 14 (3), p. 727–739, 2020, ISSN: 1751-7370.

Résumé | Liens

@article{jeudy_exploration_2020,
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 Nad{è}ge 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 = {2020},
date = {2020-01-01},
journal = {The ISME journal},
volume = {14},
number = {3},
pages = {727--739},
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}
}

Fermer

Nguyen, Minh Vu Chuong; ï, Ana; Adrait, Annie; Defendi, Federica; Couté, Yohann; Baillet, Athan; Guigue, Lisa; Gottenberg, Jacques-Eric; Dumestre-Pérard, Chantal; Brun, Virginie; Gaudin, Philippe

Fetuin-A and thyroxin binding globulin predict rituximab response in rheumatoid arthritis patients with insufficient response to anti-TNF$alpha$ Article de journal

Clinical Rheumatology, 2020, ISSN: 1434-9949.

Résumé | Liens

@article{nguyen_fetuin-and_2020,
title = {Fetuin-A and thyroxin binding globulin predict rituximab response in rheumatoid arthritis patients with insufficient response to anti-TNF$alpha$},
author = {Minh Vu Chuong Nguyen and Ana{ï}s Courtier and Annie Adrait and Federica Defendi and Yohann Couté and Athan Baillet and Lisa Guigue and Jacques-Eric Gottenberg and Chantal Dumestre-Pérard and Virginie Brun and Philippe Gaudin},
doi = {10.1007/s10067-020-05030-6},
issn = {1434-9949},
year = {2020},
date = {2020-01-01},
journal = {Clinical Rheumatology},
abstract = {OBJECTIVES: Rheumatoid arthritis (RA) is a debilitating disease, but patient management and treatment have been revolutionized since the advent of bDMARDs. However, about one third of RA patients do not respond to specific bDMARD treatment without clear identified reasons. Different bDMARDs must be tried until the right drug is found. Here, we sought to identify a predictive protein signature to stratify patient responsiveness to rituximab (RTX) among patients with an insufficient response to a first anti-TNF$alpha$ treatment.
METHODS: Serum samples were collected at baseline before RTX initiation. A proteomics study comparing responders and nonresponders was conducted to identify and select potential predictive biomarkers whose concentration was measured by quantitative assays. Logistic regression was performed to determine the best biomarker combination to predict good or nonresponse to RTX (EULAR criteria after 6 months' treatment).
RESULTS: Eleven biomarkers potentially discriminating between responders and nonresponders were selected following discovery proteomics. Quantitative immunoassays and univariate statistical analysis showed that fetuin-A and thyroxine binding globulin (TBG) presented a good capacity to discriminate between patient groups. A logistic regression analysis revealed that the combination of fetuin-A plus TBG could accurately predict a patient's responsiveness to RTX with an AUC of 0.86, sensitivity of 80%, and a specificity of 79%.
CONCLUSION: In RA patients for whom a first anti-TNF$alpha$ treatment has failed, the serum abundance of fetuin-A and TBG before initiating RTX treatment is an indicator for their response status at 6 months. ClinicalTrials.gov identifier: NCT01000441.Key Points• Proteomic analysis revealed 11 putative predictive biomarkers to discriminate rituximab responder vs. nonresponder RA patients.• Fetuin-A and TBG are significantly differentially expressed at baseline in rituximab responder vs. nonresponder RA patients.• Algorithm combining fetuin-A and TBG accurately predicts response to rituximab in RA patients with insufficient response to TNFi.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Fermer

OBJECTIVES: Rheumatoid arthritis (RA) is a debilitating disease, but patient management and treatment have been revolutionized since the advent of bDMARDs. However, about one third of RA patients do not respond to specific bDMARD treatment without clear identified reasons. Different bDMARDs must be tried until the right drug is found. Here, we sought to identify a predictive protein signature to stratify patient responsiveness to rituximab (RTX) among patients with an insufficient response to a first anti-TNF$alpha$ treatment.
METHODS: Serum samples were collected at baseline before RTX initiation. A proteomics study comparing responders and nonresponders was conducted to identify and select potential predictive biomarkers whose concentration was measured by quantitative assays. Logistic regression was performed to determine the best biomarker combination to predict good or nonresponse to RTX (EULAR criteria after 6 months' treatment).
RESULTS: Eleven biomarkers potentially discriminating between responders and nonresponders were selected following discovery proteomics. Quantitative immunoassays and univariate statistical analysis showed that fetuin-A and thyroxine binding globulin (TBG) presented a good capacity to discriminate between patient groups. A logistic regression analysis revealed that the combination of fetuin-A plus TBG could accurately predict a patient's responsiveness to RTX with an AUC of 0.86, sensitivity of 80%, and a specificity of 79%.
CONCLUSION: In RA patients for whom a first anti-TNF$alpha$ treatment has failed, the serum abundance of fetuin-A and TBG before initiating RTX treatment is an indicator for their response status at 6 months. ClinicalTrials.gov identifier: NCT01000441.Key Points• Proteomic analysis revealed 11 putative predictive biomarkers to discriminate rituximab responder vs. nonresponder RA patients.• Fetuin-A and TBG are significantly differentially expressed at baseline in rituximab responder vs. nonresponder RA patients.• Algorithm combining fetuin-A and TBG accurately predicts response to rituximab in RA patients with insufficient response to TNFi.

Fermer

è, Hél; ï, Hélo; Vegna, Serena; Lahlali, Thomas; Pons, Caroline; Michelet, Maud; Couté, Yohann; Belmudes, Lucid; Chadeuf, Gilliane; Kim, Yujin; Di Bernardo, Ariel ; Jalaguier, Pascal; ï, Fran{ç}ois-Lo; Fusil, Floriane; Rivoire, Michel; Arnold, Lee D; Lopatin, Uri; Combet, Christophe; Zoulim, Fabien; Grierson, David; Chabot, Benoit; Lucifora, Julie; Durantel, David; Salvetti, Anna

Hepatitis B virus Core protein nuclear interactome identifies SRSF10 as a host RNA-binding protein restricting HBV RNA production Article de journal

PLoS pathogens, 16 (11), p. e1008593, 2020, ISSN: 1553-7374.

Résumé | Liens

@article{chabrolles_hepatitis_2020,
title = {Hepatitis B virus Core protein nuclear interactome identifies SRSF10 as a host RNA-binding protein restricting HBV RNA production},
author = {Hél{è}ne Chabrolles and Hélo{ï}se Auclair and Serena Vegna and Thomas Lahlali and Caroline Pons and Maud Michelet and Yohann Couté and Lucid Belmudes and Gilliane Chadeuf and Yujin Kim and Ariel {Di Bernardo} and Pascal Jalaguier and Fran{ç}ois-Lo{ï}c Cosset and Floriane Fusil and Michel Rivoire and Lee D Arnold and Uri Lopatin and Christophe Combet and Fabien Zoulim and David Grierson and Benoit Chabot and Julie Lucifora and David Durantel and Anna Salvetti},
doi = {10.1371/journal.ppat.1008593},
issn = {1553-7374},
year = {2020},
date = {2020-01-01},
journal = {PLoS pathogens},
volume = {16},
number = {11},
pages = {e1008593},
abstract = {Despite the existence of a preventive vaccine, chronic infection with Hepatitis B virus (HBV) affects more than 250 million people and represents a major global cause of hepatocellular carcinoma (HCC) worldwide. Current clinical treatments, in most of cases, do not eliminate viral genome that persists as a DNA episome in the nucleus of hepatocytes and constitutes a stable template for the continuous expression of viral genes. Several studies suggest that, among viral factors, the HBV core protein (HBc), well-known for its structural role in the cytoplasm, could have critical regulatory functions in the nucleus of infected hepatocytes. To elucidate these functions, we performed a proteomic analysis of HBc-interacting host-factors in the nucleus of differentiated HepaRG, a surrogate model of human hepatocytes. The HBc interactome was found to consist primarily of RNA-binding proteins (RBPs), which are involved in various aspects of mRNA metabolism. Among them, we focused our studies on SRSF10, a RBP that was previously shown to regulate alternative splicing (AS) in a phosphorylation-dependent manner and to control stress and DNA damage responses, as well as viral replication. Functional studies combining SRSF10 knockdown and a pharmacological inhibitor of SRSF10 phosphorylation (1C8) showed that SRSF10 behaves as a restriction factor that regulates HBV RNAs levels and that its dephosphorylated form is likely responsible for the anti-viral effect. Surprisingly, neither SRSF10 knock-down nor 1C8 treatment modified the splicing of HBV RNAs but rather modulated the level of nascent HBV RNA. Altogether, our work suggests that in the nucleus of infected cells HBc interacts with multiple RBPs that regulate viral RNA metabolism. Our identification of SRSF10 as a new anti-HBV restriction factor offers new perspectives for the development of new host-targeted antiviral strategies.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Fermer

van Lis, Robert; è, Sabine Brugi; Baffert, Carole; Couté, Yohann; Nitschke, Wolfgang; Atteia, Ariane

Hybrid cluster proteins in a photosynthetic microalga Article de journal

The FEBS journal, 287 (4), p. 721–735, 2020, ISSN: 1742-4658.

Résumé | Liens

Adrait, Annie; Dumonceau, Jean-Marc; Delhaye, Myriam; Annessi-Ramseyer, Isabelle; Frossard, Jean-Louis; Coute, Yohann; Farina, Annarita

Liquid Biopsy of Bile based on Targeted Mass Spectrometry for the Diagnosis of Malignant Biliary Strictures Article de journal

Clinical and Translational Science, 2020, ISSN: 1752-8062.

Résumé | Liens

Couté, Yohann; Kraut, Alexandra; Zimmermann, Christine; Büscher, Nicole; Hesse, Anne-Marie; Bruley, Christophe; De Andrea, Marco ; Wangen, Christina; Hahn, Friedrich; Marschall, Manfred; Plachter, Bodo

Mass Spectrometry-Based Characterization of the Virion Proteome, Phosphoproteome, and Associated Kinase Activity of Human Cytomegalovirus Article de journal

Microorganisms, 8 (6), p. 820, 2020, ISSN: 2076-2607.

Résumé | Liens

Crespo, Marion; Damont, Annelaure; Blanco, Melina; Lastrucci, Emmanuelle; Kennani, Sara El; ô, C; Khattabi, Laila El; Terrier, Samuel; Louwagie, Mathilde; Kieffer-Jaquinod, Sylvie; Hesse, Anne-Marie; Bruley, Christophe; Chantalat, Sophie; ô, Jér; ç, Fran; Battail, Christophe; Cocquet, Julie; Pflieger, Delphine

Multi-omic analysis of gametogenesis reveals a novel signature at the promoters and distal enhancers of active genes Article de journal

Nucleic Acids Research, 48 (8), p. 4115–4138, 2020, ISSN: 0305-1048, 1362-4962.

Résumé | Liens

@article{crespo_multi-omic_2020,
title = {Multi-omic analysis of gametogenesis reveals a novel signature at the promoters and distal enhancers of active genes},
author = {Marion Crespo and Annelaure Damont and Melina Blanco and Emmanuelle Lastrucci and Sara El Kennani and C{ô}me Ialy-Radio and Laila El Khattabi and Samuel Terrier and Mathilde Louwagie and Sylvie Kieffer-Jaquinod and Anne-Marie Hesse and Christophe Bruley and Sophie Chantalat and Jér{ô}me Govin and Fran{ç}ois Fenaille and Christophe Battail and Julie Cocquet and Delphine Pflieger},
url = {https://academic.oup.com/nar/article/48/8/4115/5809165},
doi = {10.1093/nar/gkaa163},
issn = {0305-1048, 1362-4962},
year = {2020},
date = {2020-01-01},
journal = {Nucleic Acids Research},
volume = {48},
number = {8},
pages = {4115--4138},
abstract = {Abstract
Epigenetic regulation of gene expression is tightly controlled by the dynamic modification of histones by chemical groups, the diversity of which has largely expanded over the past decade with the discovery of lysine acylations, catalyzed from acyl-coenzymes A. We investigated the dynamics of lysine acetylation and crotonylation on histones H3 and H4 during mouse spermatogenesis. Lysine crotonylation appeared to be of significant abundance compared to acetylation, particularly on Lys27 of histone H3 (H3K27cr) that accumulates in sperm in a cleaved form of H3. We identified the genomic localization of H3K27cr and studied its effects on transcription compared to the classical active mark H3K27ac at promoters and distal enhancers. The presence of both marks was strongly associated with highest gene expression. Assessment of their co-localization with transcription regulators (SLY, SOX30) and chromatin-binding proteins (BRD4, BRDT, BORIS and CTCF) indicated systematic highest binding when both active marks were present and different selective binding when present alone at chromatin. H3K27cr and H3K27ac finally mark the building of some sperm super-enhancers. This integrated analysis of omics data provides an unprecedented level of understanding of gene expression regulation by H3K27cr in comparison to H3K27ac, and reveals both synergistic and specific actions of each histone modification.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Fermer

Kloehn, Joachim; Oppenheim, Rebecca D; Siddiqui, Ghizal; De Bock, Pieter-Jan ; Kumar Dogga, Sunil ; Coute, Yohann; Hakimi, Mohamed-Ali; Creek, Darren J; Soldati-Favre, Dominique

Multi-omics analysis delineates the distinct functions of sub-cellular acetyl-CoA pools in Toxoplasma gondii Article de journal

BMC Biology, 18 (1), p. 67, 2020, ISSN: 1741-7007.

Liens

Sansa, Marc; Defoort, Martial; Brenac, Ariel; Hermouet, Maxime; Banniard, Louise; Fafin, Alexandre; Gely, Marc; Masselon, Christophe; Favero, Ivan; Jourdan, Guillaume; Hentz, Sébastien

Optomechanical mass spectrometry Article de journal

Nature Communications, 11 (1), p. 3781, 2020, ISSN: 2041-1723.

Résumé | Liens

Postic, Guillaume; Marcoux, Julien; Reys, Victor; Andreani, Jessica; Vandenbrouck, Yves; Bousquet, Marie-Pierre; Mouton-Barbosa, Emmanuelle; Cianférani, Sarah; Burlet-Schiltz, Odile; Guerois, Raphael; Labesse, Gilles; Tufféry, Pierre

Probing Protein Interaction Networks by Combining MS-Based Proteomics and Structural Data Integration. Article de journal

Journal of proteome research, 19 (7), p. 2807–2820, 2020.

Résumé

Dia, Maya; Gomez, Ludovic; Thibault, Helene; Tessier, Nolwenn; Leon, Christelle; Chouabe, Christophe; Ducreux, Sylvie; Gallo-Bona, Noelle; Tubbs, Emily; Bendridi, Nadia; Chanon, Stephanie; Leray, Aymeric; Belmudes, Lucid; Couté, Yohann; Kurdi, Mazen; Ovize, Michel; Rieusset, Jennifer; Paillard, Melanie

Reduced reticulum–mitochondria Ca2+ transfer is an early and reversible trigger of mitochondrial dysfunctions in diabetic cardiomyopathy Article de journal

Basic Research in Cardiology, 115 (6), p. 74, 2020, ISSN: 0300-8428, 1435-1803.

Résumé | Liens

@article{dia_reduced_2020,
title = {Reduced reticulum–mitochondria Ca2+ transfer is an early and reversible trigger of mitochondrial dysfunctions in diabetic cardiomyopathy},
author = {Maya Dia and Ludovic Gomez and Helene Thibault and Nolwenn Tessier and Christelle Leon and Christophe Chouabe and Sylvie Ducreux and Noelle Gallo-Bona and Emily Tubbs and Nadia Bendridi and Stephanie Chanon and Aymeric Leray and Lucid Belmudes and Yohann Couté and Mazen Kurdi and Michel Ovize and Jennifer Rieusset and Melanie Paillard},
url = {http://link.springer.com/10.1007/s00395-020-00835-7},
doi = {10.1007/s00395-020-00835-7},
issn = {0300-8428, 1435-1803},
year = {2020},
date = {2020-01-01},
journal = {Basic Research in Cardiology},
volume = {115},
number = {6},
pages = {74},
abstract = {Abstract

Type 2 diabetic cardiomyopathy features Ca
2+
signaling abnormalities, notably an altered mitochondrial Ca
2+
handling. We here aimed to study if it might be due to a dysregulation of either the whole Ca
2+
homeostasis, the reticulum–mitochondrial Ca
2+
coupling, and/or the mitochondrial Ca
2+
entry through the uniporter. Following a 16-week high-fat high-sucrose diet (HFHSD), mice developed cardiac insulin resistance, fibrosis, hypertrophy, lipid accumulation, and diastolic dysfunction when compared to standard diet. Ultrastructural and proteomic analyses of cardiac reticulum–mitochondria interface revealed tighter interactions not compatible with Ca
2+
transport in HFHSD cardiomyocytes. Intramyocardial adenoviral injections of Ca
2+
sensors were performed to measure Ca
2+
fluxes in freshly isolated adult cardiomyocytes and to analyze the direct effects of in vivo type 2 diabetes on cardiomyocyte function. HFHSD resulted in a decreased IP3R–VDAC interaction and a reduced IP3-stimulated Ca
2+
transfer to mitochondria, with no changes in reticular Ca
2+
level, cytosolic Ca
2+
transients, and mitochondrial Ca
2+
uniporter function. Disruption of organelle Ca
2+
exchange was associated with decreased mitochondrial bioenergetics and reduced cell contraction, which was rescued by an adenovirus-mediated expression of a reticulum-mitochondria linker. An 8-week diet reversal was able to restore cardiac insulin signaling, Ca
2+
transfer, and cardiac function in HFHSD mice. Therefore, our study demonstrates that the reticulum–mitochondria Ca
2+
miscoupling may play an early and reversible role in the development of diabetic cardiomyopathy by disrupting primarily the mitochondrial bioenergetics. A diet reversal, by counteracting the MAM-induced mitochondrial Ca
2+
dysfunction, might contribute to restore normal cardiac function and prevent the exacerbation of diabetic cardiomyopathy.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Fermer

Began, Jakub; Cordier, Baptiste; Březinová, Jana; Delisle, Jordan; Hexnerová, Rozálie; Srb, Pavel; Rampírová, Petra; ž, Milan Ko; Baudet, Mathieu; Couté, Yohann; Galinier, Anne; Veverka, Václav; Doan, Thierry; Strisovsky, Kvido

Rhomboid intramembrane protease YqgP licenses bacterial membrane protein quality control as adaptor of FtsH textlessspan style= Article de journal

The EMBO Journal, 2020, ISSN: 0261-4189, 1460-2075.

Liens

Lezzerini, Marco; Penzo, Marianna; ç, Marie-Fran; Marques Dos Santos Vieira, Carolina ; Saby, Manon; Elfrink, Hyung L; Diets, Illja J; Hesse, Anne-Marie; Couté, Yohann; Gastou, Marc; Nin-Velez, Alexandra; Nikkels, Peter G J; Olson, Alexandra N; Zonneveld-Huijssoon, Evelien; Jongmans, Marjolijn C J; Zhang, GuangJun; van Weeghel, Michel; Houtkooper, Riekelt H; Wlodarski, Marcin W; Kuiper, Roland P; Bierings, Marc B; van der Werff Ten Bosch, Jutte ; Leblanc, Thierry; Montanaro, Lorenzo; Dinman, Jonathan D; Da Costa, Lydie ; Gleizes, Pierre-Emmanuel; MacInnes, Alyson W

Ribosomal protein gene RPL9 variants can differentially impair ribosome function and cellular metabolism Article de journal

Nucleic Acids Research, 48 (2), p. 770–787, 2020, ISSN: 1362-4962.

Résumé | Liens

@article{lezzerini_ribosomal_2020,
title = {Ribosomal protein gene RPL9 variants can differentially impair ribosome function and cellular metabolism},
author = {Marco Lezzerini and Marianna Penzo and Marie-Fran{ç}oise O'Donohue and Carolina {Marques Dos Santos Vieira} and Manon Saby and Hyung L Elfrink and Illja J Diets and Anne-Marie Hesse and Yohann Couté and Marc Gastou and Alexandra Nin-Velez and Peter G J Nikkels and Alexandra N Olson and Evelien Zonneveld-Huijssoon and Marjolijn C J Jongmans and GuangJun Zhang and Michel van Weeghel and Riekelt H Houtkooper and Marcin W Wlodarski and Roland P Kuiper and Marc B Bierings and Jutte {van der Werff Ten Bosch} and Thierry Leblanc and Lorenzo Montanaro and Jonathan D Dinman and Lydie {Da Costa} and Pierre-Emmanuel Gleizes and Alyson W MacInnes},
doi = {10.1093/nar/gkz1042},
issn = {1362-4962},
year = {2020},
date = {2020-01-01},
journal = {Nucleic Acids Research},
volume = {48},
number = {2},
pages = {770--787},
abstract = {Variants in ribosomal protein (RP) genes drive Diamond-Blackfan anemia (DBA), a bone marrow failure syndrome that can also predispose individuals to cancer. Inherited and sporadic RP gene variants are also linked to a variety of phenotypes, including malignancy, in individuals with no anemia. Here we report an individual diagnosed with DBA carrying a variant in the 5'UTR of RPL9 (uL6). Additionally, we report two individuals from a family with multiple cancer incidences carrying a RPL9 missense variant. Analysis of cells from these individuals reveals that despite the variants both driving pre-rRNA processing defects and 80S monosome reduction, the downstream effects are remarkably different. Cells carrying the 5'UTR variant stabilize TP53 and impair the growth and differentiation of erythroid cells. In contrast, ribosomes incorporating the missense variant erroneously read through UAG and UGA stop codons of mRNAs. Metabolic profiles of cells carrying the 5'UTR variant reveal an increased metabolism of amino acids and a switch from glycolysis to gluconeogenesis while those of cells carrying the missense variant reveal a depletion of nucleotide pools. These findings indicate that variants in the same RP gene can drive similar ribosome biogenesis defects yet still have markedly different downstream consequences and clinical impacts.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Fermer

Crespo, Marion; Luense, Lacey J; Arlotto, Marie; Jialei, Hu; Dorsey, Jean; Garcia-Oliver, Encar; Shah, Parisha P; Pflieger, Delphine; Berger, Shelley L; ô, Jér

Systematic genetic and proteomic screens during gametogenesis identify H2BK34 methylation as an evolutionary conserved meiotic mark Article de journal

Epigenetics & Chromatin, 13 (35), p. 1–23, 2020.

Liens

Hahn, Friedrich; Niesar, Aischa; Wangen, Christina; Wild, Markus; Grau, Benedikt; Herrmann, Lars; Capci, Aysun; Adrait, Annie; Couté, Yohann; Tsogoeva, Svetlana B; Marschall, Manfred

Target verification of artesunate-related antiviral drugs: assessing the role of mitochondrial and regulatory proteins by click chemistry and fluorescence labeling Article de journal

Antiviral Research, p. 104861, 2020, ISSN: 01663542.

Liens

Vandenbrouck, Yves; Pineau, Charles; Lane, Lydie

The Functionally Unannotated Proteome of Human Male Tissues: A Shared Resource to Uncover New Protein Functions Associated with Reproductive Biology Article de journal

Journal of Proteome Research, 2020, ISSN: 1535-3907.

Résumé | Liens

@article{vandenbrouck_functionally_2020,
title = {The Functionally Unannotated Proteome of Human Male Tissues: A Shared Resource to Uncover New Protein Functions Associated with Reproductive Biology},
author = {Yves Vandenbrouck and Charles Pineau and Lydie Lane},
doi = {10.1021/acs.jproteome.0c00516},
issn = {1535-3907},
year = {2020},
date = {2020-01-01},
journal = {Journal of Proteome Research},
abstract = {In the context of the Human Proteome Project, we built an inventory of 412 functionally unannotated human proteins for which experimental evidence at the protein level exists (uPE1) and which are highly expressed in tissues involved in human male reproduction. We implemented a strategy combining literature mining, bioinformatics tools to collate annotation and experimental information from specific molecular public resources, and efficient visualization tools to put these unknown proteins into their biological context (protein complexes, tissue and subcellular location, expression pattern). The gathered knowledge allowed pinpointing five uPE1 for which a function has recently been proposed and which should be updated in protein knowledge bases. Furthermore, this bioinformatics strategy allowed to build new functional hypotheses for five other uPE1s in link with phenotypic traits that are specific to male reproductive function such as ciliogenesis/flagellum formation in germ cells (CCDC112 and TEX9), chromatin remodeling (C3orf62) and spermatozoon maturation (CCDC183). We also discussed the enigmatic case of MAGEB proteins, a poorly documented cancer/testis antigen subtype. Tools used and computational outputs produced during this study are freely accessible via ProteoRE (http://www.proteore.org), a Galaxy-based instance, for reuse purposes. We propose these five uPE1s should be investigated in priority by expert laboratories and hope that this inventory and shared resources will stimulate the interest of the community of reproductive biology.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Fermer

Ngo, Tuan-Dung; Perdu, Caroline; Jneid, Bakhos; Ragno, Michel; Novion Ducassou, Julia ; Kraut, Alexandra; Couté, Yohann; Stopford, Charles; Attree, Ina; Rietsch, Arne; Faudry, Eric

The PopN gate-keeper complex acts on the ATPase PscN to regulate the T3SS secretion switch from early to middle substrates in Pseudomonas aeruginosa Article de journal

Journal of Molecular Biology, 2020, ISSN: 0022-2836.

Résumé | Liens

Lamboux, Aline; Couchonnal-Bedoya, Eduardo; Guillaud, Olivier; Laurencin, Chloé; ç, Laurence Lion-Fran; Belmalih, Abdelouahed; Mintz, Elisabeth; Brun, Virginie; Bost, Muriel; Lachaux, Alain; Balter, Vincent

The blood copper isotopic composition is a prognostic indicator of the hepatic injury in Wilson disease Article de journal

Metallomics: Integrated Biometal Science, 2020, ISSN: 1756-591X.

Résumé | Liens

@article{lamboux_blood_2020,
title = {The blood copper isotopic composition is a prognostic indicator of the hepatic injury in Wilson disease},
author = {Aline Lamboux and Eduardo Couchonnal-Bedoya and Olivier Guillaud and Chloé Laurencin and Laurence Lion-Fran{ç}ois and Abdelouahed Belmalih and Elisabeth Mintz and Virginie Brun and Muriel Bost and Alain Lachaux and Vincent Balter},
doi = {10.1039/d0mt00167h},
issn = {1756-591X},
year = {2020},
date = {2020-01-01},
journal = {Metallomics: Integrated Biometal Science},
abstract = {Wilson disease (WD) is an autosomal recessive disorder of copper (Cu) metabolism. The gene responsible for WD, ATP7B, is involved in the cellular transport of Cu, and mutations in the ATP7B gene induce accumulation of Cu in the liver and ultimately in the brain. In a pilot study, the natural variations of copper stable isotope ratios (65Cu/63Cu) in the serum of WD patients have been shown to differ from that of healthy controls. In the present study, we challenged these first results by measuring the 65Cu/63Cu ratios in the blood of treated (n = 25), naïve patients (n = 11) and age matched healthy controls (n = 75). The results show that naïve patients and healthy controls exhibit undistinguishable 65Cu/63Cu ratios, implying that the Cu isotopic ratio cannot serve as a reliable diagnostic biomarker. The type of treatment (d-penicillamine vs. triethylenetetramine) does not affect the 65Cu/63Cu ratios in WD patients, which remain constant regardless of the type and duration of the treatment. In addition, the 65Cu/63Cu ratios do not vary in naïve patients after the onset of the treatment. However, the 65Cu/63Cu ratios decrease with the degree of liver fibrosis and the gradient of the phenotypic presentation, i.e. presymptomatic, hepatic and neurologic. To get insights into the mechanisms at work, we study the effects of the progress of the WD on the organism by measuring the Cu concentrations and the 65Cu/63Cu ratios in the liver, feces and plasma of 12 and 45 week old Atp7b-/- mice. The evolution of the 65Cu/63Cu ratios is marked by a decrease in all tissues. The results show that 63Cu accumulates in the liver preferentially to 65Cu due to the preferential cellular entry of 63Cu and the impairment of the 63Cu exit by ceruloplasmin. The hepatic accumulation of monovalent 63Cu+ is likely to fuel the production of free radicals, which is potentially an explanation of the pathogenicity of WD. Altogether, the results suggest that the blood 65Cu/63Cu ratio recapitulates WD progression and is a potential prognostic biomarker of WD.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Fermer

Wilson disease (WD) is an autosomal recessive disorder of copper (Cu) metabolism. The gene responsible for WD, ATP7B, is involved in the cellular transport of Cu, and mutations in the ATP7B gene induce accumulation of Cu in the liver and ultimately in the brain. In a pilot study, the natural variations of copper stable isotope ratios (65Cu/63Cu) in the serum of WD patients have been shown to differ from that of healthy controls. In the present study, we challenged these first results by measuring the 65Cu/63Cu ratios in the blood of treated (n = 25), naïve patients (n = 11) and age matched healthy controls (n = 75). The results show that naïve patients and healthy controls exhibit undistinguishable 65Cu/63Cu ratios, implying that the Cu isotopic ratio cannot serve as a reliable diagnostic biomarker. The type of treatment (d-penicillamine vs. triethylenetetramine) does not affect the 65Cu/63Cu ratios in WD patients, which remain constant regardless of the type and duration of the treatment. In addition, the 65Cu/63Cu ratios do not vary in naïve patients after the onset of the treatment. However, the 65Cu/63Cu ratios decrease with the degree of liver fibrosis and the gradient of the phenotypic presentation, i.e. presymptomatic, hepatic and neurologic. To get insights into the mechanisms at work, we study the effects of the progress of the WD on the organism by measuring the Cu concentrations and the 65Cu/63Cu ratios in the liver, feces and plasma of 12 and 45 week old Atp7b-/- mice. The evolution of the 65Cu/63Cu ratios is marked by a decrease in all tissues. The results show that 63Cu accumulates in the liver preferentially to 65Cu due to the preferential cellular entry of 63Cu and the impairment of the 63Cu exit by ceruloplasmin. The hepatic accumulation of monovalent 63Cu+ is likely to fuel the production of free radicals, which is potentially an explanation of the pathogenicity of WD. Altogether, the results suggest that the blood 65Cu/63Cu ratio recapitulates WD progression and is a potential prognostic biomarker of WD.

Fermer

Roblin, Clarisse; Chiumento, Steve; Bornet, Olivier; Nouailler, Matthieu; Müller, Christina S; Jeannot, Katy; Basset, Christian; Kieffer-Jaquinod, Sylvie; Couté, Yohann; Torelli, Stéphane; Le Pape, Laurent ; Schünemann, Volker; Olleik, Hamza; De La Villeon, Bruno ; Sockeel, Philippe; Di Pasquale, Eric ; Nicoletti, Cendrine; Vidal, Nicolas; Poljak, Leonora; Iranzo, Olga; Giardina, Thierry; Fons, Michel; Devillard, Estelle; Polard, Patrice; Maresca, Marc; Perrier, Josette; Atta, Mohamed; ç, Fran; Lafond, Mickael; Duarte, Victor

The unusual structure of Ruminococcin C1 antimicrobial peptide confers clinical properties Article de journal

Proceedings of the National Academy of Sciences of the United States of America, 2020, ISSN: 1091-6490.

Résumé | Liens

@article{roblin_unusual_2020,
title = {The unusual structure of Ruminococcin C1 antimicrobial peptide confers clinical properties},
author = {Clarisse Roblin and Steve Chiumento and Olivier Bornet and Matthieu Nouailler and Christina S Müller and Katy Jeannot and Christian Basset and Sylvie Kieffer-Jaquinod and Yohann Couté and Stéphane Torelli and Laurent {Le Pape} and Volker Schünemann and Hamza Olleik and Bruno {De La Villeon} and Philippe Sockeel and Eric {Di Pasquale} and Cendrine Nicoletti and Nicolas Vidal and Leonora Poljak and Olga Iranzo and Thierry Giardina and Michel Fons and Estelle Devillard and Patrice Polard and Marc Maresca and Josette Perrier and Mohamed Atta and Fran{ç}oise Guerlesquin and Mickael Lafond and Victor Duarte},
doi = {10.1073/pnas.2004045117},
issn = {1091-6490},
year = {2020},
date = {2020-01-01},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
abstract = {The emergence of superbugs developing resistance to antibiotics and the resurgence of microbial infections have led scientists to start an antimicrobial arms race. In this context, we have previously identified an active RiPP, the Ruminococcin C1, naturally produced by Ruminococcus gnavus E1, a symbiont of the healthy human intestinal microbiota. This RiPP, subclassified as a sactipeptide, requires the host digestive system to become active against pathogenic Clostridia and multidrug-resistant strains. Here we report its unique compact structure on the basis of four intramolecular thioether bridges with reversed stereochemistry introduced posttranslationally by a specific radical-SAM sactisynthase. This structure confers to the Ruminococcin C1 important clinical properties including stability to digestive conditions and physicochemical treatments, a higher affinity for bacteria than simulated intestinal epithelium, a valuable activity at therapeutic doses on a range of clinical pathogens, mediated by energy resources disruption, and finally safety for human gut tissues.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Fermer

Sokolovska, Nataliya; Permiakova, Olga; Forslund, Sofia K; Zucker, Jean-Daniel

Using Unlabeled Data to Discover Bivariate Causality with Deep Restricted Boltzmann Machines Article de journal

IEEE/ACM transactions on computational biology and bioinformatics, 17 (1), p. 358–364, 2020, ISSN: 1557-9964.

Résumé | Liens

@article{sokolovska_using_2020,
title = {Using Unlabeled Data to Discover Bivariate Causality with Deep Restricted Boltzmann Machines},
author = {Nataliya Sokolovska and Olga Permiakova and Sofia K Forslund and Jean-Daniel Zucker},
doi = {10.1109/TCBB.2018.2879504},
issn = {1557-9964},
year = {2020},
date = {2020-01-01},
journal = {IEEE/ACM transactions on computational biology and bioinformatics},
volume = {17},
number = {1},
pages = {358--364},
abstract = {An important question in microbiology is whether treatment causes changes in gut flora, and whether it also affects metabolism. The reconstruction of causal relations purely from non-temporal observational data is challenging. We address the problem of causal inference in a bivariate case, where the joint distribution of two variables is observed. We consider, in particular, data on discrete domains. The state-of-the-art causal inference methods for continuous data suffer from high computational complexity. Some modern approaches are not suitable for categorical data, and others need to estimate and fix multiple hyper-parameters. In this contribution, we introduce a novel method of causal inference which is based on the widely used assumption that if X causes Y, then P(X) and P(Y$backslash$textbarX) are independent. We propose to explore a semi-supervised approach where P(Y$backslash$textbarX) and P(X) are estimated from labeled and unlabeled data respectively, whereas the marginal probability is estimated potentially from much more (cheap unlabeled) data than the conditional distribution. We validate the proposed method on the standard cause-effect pairs. We illustrate by experiments on several benchmarks of biological network reconstruction that the proposed approach is very competitive in terms of computational time and accuracy compared to the state-of-the-art methods. Finally, we apply the proposed method to an original medical task where we study whether drugs confound human metagenome.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Fermer

Allison, T M; Barran, P E; Benesch, J L P; Cianferani, S; Degiacomi, M T; Gabelica, V; Grandori, R; Marklund, E G; Menneteau, T; Migas, L G; Politis, A; Sharon, M; Sobott, F; Thalassinos, K

Software requirements for the analysis and interpretation of native ion mobility mass spectrometry data Article de journal

Anal Chem, 2020, ISSN: 1520-6882 (Electronic) 0003-2700 (Linking), (review, pas de projet LSMBO).

Liens

Allison, T M; Barran, P E; Cianferani, S; Degiacomi, M T; Gabelica, V; Grandori, R; Marklund, E G; Menneteau, T; Migas, L G; Politis, A; Sharon, M; Sobott, F; Thalassinos, K; Benesch, J L P

Computational strategies and challenges for using native ion mobility mass spectrometry in biophysics and structural biology Article de journal

Anal Chem, 2020, ISSN: 1520-6882 (Electronic) 0003-2700 (Linking), (review pas de projet LSMBO).

Liens

Botzanowski, T; Hernandez-Alba, O; Malissard, M; Wagner-Rousset, E; Desligniere, E; Colas, O; Haeuw, J F; Beck, A; Cianferani, S

Middle Level IM-MS and CIU Experiments for Improved Therapeutic Immunoglobulin Subclass Fingerprinting Article de journal

Anal Chem, 92 (13), p. 8827-8835, 2020, ISSN: 1520-6882 (Electronic) 0003-2700 (Linking).

Liens

Castro, C N; Rosenzwajg, M; Carapito, R; Shahrooei, M; Konantz, M; Khan, A; Miao, Z; Gross, M; Tranchant, T; Radosavljevic, M; Paul, N; Stemmelen, T; Pitoiset, F; Hirschler, A; Nespola, B; Molitor, A; Rolli, V; Pichot, A; Faletti, L E; Rinaldi, B; Friant, S; Mednikov, M; Karauzum, H; Aman, M J; Carapito, C; Lengerke, C; Ziaee, V; Eyaid, W; Ehl, S; Alroqi, F; Parvaneh, N; Bahram, S

NCKAP1L defects lead to a novel syndrome combining immunodeficiency, lymphoproliferation, and hyperinflammation Article de journal

J Exp Med, 217 (12), 2020, ISSN: 1540-9538 (Electronic) 0022-1007 (Linking), (????).

Liens

Chabrol, E; Stojko, J; Nicolas, A; Botzanowski, T; Fould, B; Antoine, M; Cianferani, S; Ferry, G; Boutin, J A

VHH characterization.Recombinant VHHs: Production, characterization and affinity Article de journal

Anal Biochem, 589 , p. 113491, 2020, ISSN: 1096-0309 (Electronic) 0003-2697 (Linking).

Liens

Charles, L; Mondal, T; Greff, V; Razzini, M; Monnier, V; Burel, A; Carapito, C; Lutz, J F

Optimal conditions for tandem mass spectrometric sequencing of information-containing nitrogen-substituted polyurethanes Article de journal

Rapid Commun Mass Spectrom, 34 (14), p. e8815, 2020, ISSN: 1097-0231 (Electronic) 0951-4198 (Linking), (????).

Liens

Ciudad, S; Puig, E; Botzanowski, T; Meigooni, M; Arango, A S; Do, J; Mayzel, M; Bayoumi, M; Chaignepain, S; Maglia, G; Cianferani, S; Orekhov, V; Tajkhorshid, E; Bardiaux, B; Carulla, N

Abeta(1-42) tetramer and octamer structures reveal edge conductivity pores as a mechanism for membrane damage Article de journal

Nat Commun, 11 (1), p. 3014, 2020, ISSN: 2041-1723 (Electronic) 2041-1723 (Linking), (2018/12).

Liens

Dovgan, I; Ehkirch, A; Lehot, V; Kuhn, I; Koniev, O; Kolodych, S; Hentz, A; Ripoll, M; Ursuegui, S; Nothisen, M; Cianferani, S; Wagner, A

On the use of DNA as a linker in antibody-drug conjugates: synthesis, stability and in vitro potency Article de journal

Sci Rep, 10 (1), p. 7691, 2020, ISSN: 2045-2322 (Electronic) 2045-2322 (Linking), (2019-05).

Liens

Duivelshof, B L; Desligniere, E; Hernandez-Alba, O; Ehkirch, A; Toftevall, H; Sjogren, J; Cianferani, S; Beck, A; Guillarme, D; D'Atri, V

Glycan-Mediated Technology for Obtaining Homogeneous Site-Specific Conjugated Antibody-Drug Conjugates: Synthesis and Analytical Characterization by Using Complementary Middle-up LC/HRMS Analysis Article de journal

Anal Chem, 92 (12), p. 8170-8177, 2020, ISSN: 1520-6882 (Electronic) 0003-2700 (Linking), (pas de manips au LSMBO).

Liens

Farras, M; Miret, J; Camps, M; Roman, R; Martinez, O; Pujol, X; Erb, S; Ehkirch, A; Cianferani, S; Casablancas, A; Cairo, J J

Homogeneous antibody-drug conjugates: DAR 2 anti-HER2 obtained by conjugation on isolated light chain followed by mAb assembly Article de journal

MAbs, 12 (1), p. 1702262, 2020, ISSN: 1942-0870 (Electronic) 1942-0862 (Linking), (2018/06).

Liens

Hernandez-Alba, O; Ehkirch, A; Beck, A; Cianferani, S

Analysis of ADCs by Native Mass Spectrometry Article de journal

Methods Mol Biol, 2078 , p. 197-211, 2020, ISSN: 1940-6029 (Electronic) 1064-3745 (Linking), (review).

Liens

Humbert, N; Kovalenko, L; Saladini, F; Giannini, A; Pires, M; Botzanowski, T; Cherenok, S; Boudier, C; Sharma, K K; Real, E; Zaporozhets, O A; Cianferani, S; Seguin-Devaux, C; Poggialini, F; Botta, M; Zazzi, M; Kalchenko, V I; Mori, M; Mely, Y

(Thia)calixarenephosphonic Acids as Potent Inhibitors of the Nucleic Acid Chaperone Activity of the HIV-1 Nucleocapsid Protein with a New Binding Mode and Multitarget Antiviral Activity Article de journal

ACS Infect Dis, 6 (4), p. 687-702, 2020, ISSN: 2373-8227 (Electronic) 2373-8227 (Linking).

Résumé | Liens

@article{658,
title = {(Thia)calixarenephosphonic Acids as Potent Inhibitors of the Nucleic Acid Chaperone Activity of the HIV-1 Nucleocapsid Protein with a New Binding Mode and Multitarget Antiviral Activity},
author = {N Humbert and L Kovalenko and F Saladini and A Giannini and M Pires and T Botzanowski and S Cherenok and C Boudier and K K Sharma and E Real and O A Zaporozhets and S Cianferani and C Seguin-Devaux and F Poggialini and M Botta and M Zazzi and V I Kalchenko and M Mori and Y Mely},
url = {https://www.ncbi.nlm.nih.gov/pubmed/32045204},
doi = {10.1021/acsinfecdis.9b00290},
issn = {2373-8227 (Electronic) 2373-8227 (Linking)},
year = {2020},
date = {2020-01-01},
journal = {ACS Infect Dis},
volume = {6},
number = {4},
pages = {687-702},
abstract = {The nucleocapsid protein (NC) is a highly conserved protein that plays key roles in HIV-1 replication through its nucleic acid chaperone properties mediated by its two zinc fingers and basic residues. NC is a promising target for antiviral therapy, particularly to control viral strains resistant to currently available drugs. Since calixarenes with antiviral properties have been described, we explored the ability of calixarene hydroxymethylphosphonic or sulfonic acids to inhibit NC chaperone properties and exhibit antiviral activity. By using fluorescence-based assays, we selected four calixarenes inhibiting NC chaperone activity with submicromolar IC50 values. These compounds were further shown by mass spectrometry, isothermal titration calorimetry, and fluorescence anisotropy to bind NC with no zinc ejection and to compete with nucleic acids for the binding to NC. Molecular dynamic simulations further indicated that these compounds interact via their phosphonate or sulfonate groups with the basic surface of NC but not with the hydrophobic plateau at the top of the folded fingers. Cellular studies showed that the most soluble compound CIP201 inhibited the infectivity of wild-type and drug-resistant HIV-1 strains at low micromolar concentrations, primarily targeting the early steps of HIV-1 replication. Moreover, CIP201 was also found to inhibit the flipping and polymerization activity of reverse transcriptase. Calixarenes thus form a class of noncovalent NC inhibitors, endowed with a new binding mode and multitarget antiviral activity.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Fermer

Kenny, H C; Tascher, G; Ziemianin, A; Rudwill, F; Zahariev, A; Chery, I; Gauquelin-Koch, G; Barielle, M P; Heer, M; Blanc, S; O'Gorman, D J; Bertile, F

Effectiveness of Resistive Vibration Exercise and Whey Protein Supplementation Plus Alkaline Salt on the Skeletal Muscle Proteome Following 21 Days of Bed Rest in Healthy Males Article de journal

J Proteome Res, 19 (8), p. 3438-3451, 2020, ISSN: 1535-3907 (Electronic) 1535-3893 (Linking), (2011/34).

Liens

Laurens, C; Parmar, A; Murphy, E; Carper, D; Lair, B; Maes, P; Vion, J; Boulet, N; Fontaine, C; Marquès, M; Larrouy, D; Harant, I; Thalamas, C; Montastier, E; Caspar-Baugil, S; Bourlier, V; Tavernier, G; Grolleau, J L; Bouloumié, A; Langin, D; Viguerie, N; Bertile, F; Blanc, S; Glisezinski, De I; O’Gorman, D; Moro, C

Growth and differentiation factor 15 is secreted by skeletal muscle during exercise and promotes lipolysis in humans Article de journal

JCI Insight, 5 (6), p. E131870, 2020, (2016/26).

Lefeuvre, B; Cantero, P; Ehret-Sabatier, L; Lenormand, C; Barthel, C; Po, C; Parveen, N; Grillon, A; Jaulhac, B; Boulanger, N

Effects of topical corticosteroids and lidocaine on Borrelia burgdorferi sensu lato in mouse skin: potential impact to human clinical trials Article de journal

Sci Rep, 10 (1), p. 10552, 2020, ISSN: 2045-2322 (Electronic) 2045-2322 (Linking), (2012/30).

Liens

Luu, B E; Lefai, E; Giroud, S; Swenson, J E; Chazarin, B; Gauquelin-Koch, G; Arnemo, J M; Evans, A L; Bertile, F; Storey, K B

MicroRNAs facilitate skeletal muscle maintenance and metabolic suppression in hibernating brown bears Article de journal

J Cell Physiol, 235 (4), p. 3984-3993, 2020, ISSN: 1097-4652 (Electronic) 0021-9541 (Linking), (2011/34).

Liens

Perraud, Q; Cantero, P; Roche, B; Gasser, V; Normant, V P; Kuhn, L; Hammann, P; Mislin, G L A; Ehret-Sabatier, L; Schalk, I J

Phenotypic Adaption of Pseudomonas aeruginosa by Hacking Siderophores Produced by Other Microorganisms Article de journal

Mol Cell Proteomics, 19 (4), p. 589-607, 2020, ISSN: 1535-9484 (Electronic) 1535-9476 (Linking), (2015/28).

Liens

Postic, G; Marcoux, J; Reys, V; Andreani, J; Vandenbrouck, Y; Bousquet, M P; Mouton-Barbosa, E; Cianferani, S; Burlet-Schiltz, O; Guerois, R; Labesse, G; Tuffery, P

Probing Protein Interaction Networks by Combining MS-Based Proteomics and Structural Data Integration Article de journal

J Proteome Res, 19 (7), p. 2807-2820, 2020, ISSN: 1535-3907 (Electronic) 1535-3893 (Linking), (pas de projet, pas de manips au labo).

Liens

Sabou, M; Doderer-Lang, C; Leyer, C; Konjic, A; Kubina, S; Lennon, S; Rohr, O; Viville, S; Cianferani, S; Candolfi, E; Pfaff, A W; Brunet, J

Toxoplasma gondii ROP16 kinase silences the cyclin B1 gene promoter by hijacking host cell UHRF1-dependent epigenetic pathways Article de journal

Cell Mol Life Sci, 77 (11), p. 2141-2156, 2020, ISSN: 1420-9071 (Electronic) 1420-682X (Linking).

Liens

Sornay, C; Hessmann, S; Erb, S; Dovgan, I; Ehkirch, A; Botzanowski, T; Cianferani, S; Wagner, A; Chaubet, G

Investigating Ugi / Passerini multicomponent reactions for the Site-Selective Conjugation of Native Trastuzumab Article de journal

Chemistry, 2020, ISSN: 1521-3765 (Electronic) 0947-6539 (Linking), (2018/30).

Liens

Spenle, C; Loustau, T; Murdamoothoo, D; Erne, W; la Divonne, Beghelli-de Forest S; Veber, R; Petti, L; Bourdely, P; Morgelin, M; Brauchle, E M; Cremel, G; Randrianarisoa, V; Camara, A; Rekima, S; Schaub, S; Nouhen, K; Imhof, T; Hansen, U; Paul, N; Carapito, R; Pythoud, N; Hirschler, A; Carapito, C; Dumortier, H; Mueller, C G; Koch, M; Schenke-Layland, K; Kon, S; Sudaka, A; Anjuere, F; Obberghen-Schilling, Van E; Orend, G

Tenascin-C Orchestrates an Immune-Suppressive Tumor Microenvironment in Oral Squamous Cell Carcinoma Article de journal

Cancer Immunol Res, 2020, ISSN: 2326-6074 (Electronic) 2326-6066 (Linking), (????).

Liens

Tessier, R; Nandi, R K; Dwyer, B G; Abegg, D; Sornay, C; Ceballos, J; Erb, S; Cianferani, S; Wagner, A; Chaubet, G; Adibekian, A; Waser, J

Ethynylation of Cysteine Residues: From Peptides to Proteins in Vitro and in Living Cells Article de journal

Angew Chem Int Ed Engl, 59 (27), p. 10961-10970, 2020, ISSN: 1521-3773 (Electronic) 1433-7851 (Linking).

Liens

Thompson, D; Cognat, V; Goodfellow, M; Koechler, S; Heintz, D; Carapito, C; Dorsselaer, Van A; Mahmoud, H; Sangal, V; Ismail, W

Phylogenomic Classification and Biosynthetic Potential of the Fossil Fuel-Biodesulfurizing Rhodococcus Strain IGTS8 Article de journal

Front Microbiol, 11 , p. 1417, 2020, ISSN: 1664-302X (Print) 1664-302X (Linking), (???).

Liens

Wagner, E; Colas, O; Chenu, S; Goyon, A; Murisier, A; Cianferani, S; Francois, Y; Fekete, S; Guillarme, D; D'Atri, V; Beck, A

Determination of size variants by CE-SDS for approved therapeutic antibodies: Key implications of subclasses and light chain specificities Article de journal

J Pharm Biomed Anal, 184 , p. 113166, 2020, ISSN: 1873-264X (Electronic) 0731-7085 (Linking), (pas de manip MS).

Liens

Wagner-Rousset, E; Colas, O; Francois, Y N; Heinisch, S; Guillarme, D; Cianferani, S; Beck, A

Drug Loading and Distribution of ADCs After Reduction or IdeS Digestion and Reduction Article de journal

Methods Mol Biol, 2078 , p. 187-195, 2020, ISSN: 1940-6029 (Electronic) 1064-3745 (Linking), (pas de manip MS LSMBO).

Liens

Bonnet, M; Soulat, J; Bons, J; Leger, S; Koning, De L; Carapito, C; Picard, B

Quantification of biomarkers for beef meat qualities using a combination of Parallel Reaction Monitoring- and antibody-based proteomics Article de journal

Food Chem, 317 , p. 126376, 2020, ISSN: 1873-7072 (Electronic) 0308-8146 (Linking), (???).

Résumé | Liens

Ibrahim, M; Ayoub, D; Wasselin, T; Dorsselaer, Van A; Maho, Le Y; Raclot, T; Bertile, F

Alterations in rat adipose tissue transcriptome and proteome in response to prolonged fasting. Article de journal

Biological Chemistry, 401 (3), p. 389-405, 2020, (2009/41).

Belorusova, A Y; Bourguet, M; Hessmann, S; Chalhoub, S; Kieffer, B; Cianferani, S; Rochel, N

Molecular determinants of MED1 interaction with the DNA bound VDR-RXR heterodimer Article de journal

Nucleic Acids Res, 48 (19), p. 11199-11213, 2020, ISSN: 1362-4962 (Electronic) 0305-1048 (Linking), (Belorusova, Anna Y Bourguet, Maxime Hessmann, Steve Chalhoub, Sandra Kieffer, Bruno Cianferani, Sarah Rochel, Natacha eng Research Support, Non-U.S. Gov't England 2020/09/30 06:00 Nucleic Acids Res. 2020 Nov 4;48(19):11199-11213. doi: 10.1093/nar/gkaa775.).

Résumé | Liens

@article{691,
title = {Molecular determinants of MED1 interaction with the DNA bound VDR-RXR heterodimer},
author = {A Y Belorusova and M Bourguet and S Hessmann and S Chalhoub and B Kieffer and S Cianferani and N Rochel},
url = {https://www.ncbi.nlm.nih.gov/pubmed/32990725},
doi = {10.1093/nar/gkaa775},
issn = {1362-4962 (Electronic) 0305-1048 (Linking)},
year = {2020},
date = {2020-01-01},
journal = {Nucleic Acids Res},
volume = {48},
number = {19},
pages = {11199-11213},
abstract = {The MED1 subunit of the Mediator complex is an essential coactivator of nuclear receptor-mediated transcriptional activation. While structural requirements for ligand-dependent binding of classical coactivator motifs of MED1 to numerous nuclear receptor ligand-binding domains have been fully elucidated, the recognition of the full-length or truncated coactivator by full nuclear receptor complexes remain unknown. Here we present structural details of the interaction between a large part of MED1 comprising its structured N-terminal and the flexible receptor-interacting domains and the mutual heterodimer of the vitamin D receptor (VDR) and the retinoid X receptor (RXR) bound to their cognate DNA response element. Using a combination of structural and biophysical methods we show that the ligand-dependent interaction between VDR and the second coactivator motif of MED1 is crucial for complex formation and we identify additional, previously unseen, interaction details. In particular, we identified RXR regions involved in the interaction with the structured N-terminal domain of MED1, as well as VDR regions outside the classical coactivator binding cleft affected by coactivator recruitment. These findings highlight important roles of each receptor within the heterodimer in selective recognition of MED1 and contribute to our understanding of the nuclear receptor-coregulator complexes.},
note = {Belorusova, Anna Y
Bourguet, Maxime
Hessmann, Steve
Chalhoub, Sandra
Kieffer, Bruno
Cianferani, Sarah
Rochel, Natacha
eng
Research Support, Non-U.S. Gov't
England
2020/09/30 06:00
Nucleic Acids Res. 2020 Nov 4;48(19):11199-11213. doi: 10.1093/nar/gkaa775.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Fermer

Bernard, Q; Grillon, A; Lenormand, C; Ehret-Sabatier, L; Boulanger, N

Skin Interface, a Key Player for Borrelia Multiplication and Persistence in Lyme Borreliosis Article de journal

Trends Parasitol, 36 (3), p. 304-314, 2020, ISSN: 1471-5007 (Electronic) 1471-4922 (Linking), (2012/30).

Résumé | Liens

Boyer, C; Cussonneau, L; Brun, C; Deval, C; de Barros, Pais J P; Chanon, S; Bernoud-Hubac, N; Daira, P; Evans, A L; Arnemo, J M; Swenson, J E; Gauquelin-Koch, G; Simon, C; Blanc, S; Combaret, L; Bertile, F; Lefai, E

Specific shifts in the endocannabinoid system in hibernating brown bears Article de journal

Front Zool, 17 (1), p. 35, 2020, ISSN: 1742-9994 (Print) 1742-9994 (Linking), (2011/34).

Résumé | Liens

@article{680,
title = {Specific shifts in the endocannabinoid system in hibernating brown bears},
author = {C Boyer and L Cussonneau and C Brun and C Deval and J P Pais de Barros and S Chanon and N Bernoud-Hubac and P Daira and A L Evans and J M Arnemo and J E Swenson and G Gauquelin-Koch and C Simon and S Blanc and L Combaret and F Bertile and E Lefai},
url = {https://www.ncbi.nlm.nih.gov/pubmed/33292302},
doi = {10.1186/s12983-020-00380-y},
issn = {1742-9994 (Print) 1742-9994 (Linking)},
year = {2020},
date = {2020-01-01},
journal = {Front Zool},
volume = {17},
number = {1},
pages = {35},
abstract = {In small hibernators, global downregulation of the endocannabinoid system (ECS), which is involved in modulating neuronal signaling, feeding behavior, energy metabolism, and circannual rhythms, has been reported to possibly drive physiological adaptation to the hibernating state. In hibernating brown bears (Ursus arctos), we hypothesized that beyond an overall suppression of the ECS, seasonal shift in endocannabinoids compounds could be linked to bear's peculiar features that include hibernation without arousal episodes and capacity to react to external disturbance. We explored circulating lipids in serum and the ECS in plasma and metabolically active tissues in free-ranging subadult Scandinavian brown bears when both active and hibernating. In winter bear serum, in addition to a 2-fold increase in total fatty acid concentration, we found significant changes in relative proportions of circulating fatty acids, such as a 2-fold increase in docosahexaenoic acid C22:6 n-3 and a decrease in arachidonic acid C20:4 n-6. In adipose and muscle tissues of hibernating bears, we found significant lower concentrations of 2-arachidonoylglycerol (2-AG), a major ligand of cannabinoid receptors 1 (CB1) and 2 (CB2). Lower mRNA level for genes encoding CB1 and CB2 were also found in winter muscle and adipose tissue, respectively. The observed reduction in ECS tone may promote fatty acid mobilization from body fat stores, and favor carbohydrate metabolism in skeletal muscle of hibernating bears. Additionally, high circulating level of the endocannabinoid-like compound N-oleoylethanolamide (OEA) in winter could favor lipolysis and fatty acid oxidation in peripheral tissues. We also speculated on a role of OEA in the conservation of an anorexigenic signal and in the maintenance of torpor during hibernation, while sustaining the capacity of bears to sense stimuli from the environment.},
note = {2011/34},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Fermer

Dalzon, B; Aude-Garcia, C; Diemer, H; Bons, J; Marie-Desvergne, C; Perard, J; Dubosson, M; Collin-Faure, V; Carapito, C; Sanglier-Cianferani, S; Carriere, M; Rabilloud, T

The longer the worse: a combined proteomic and targeted study of the long-termversusshort-term effects of silver nanoparticles on macrophages Article de journal

Environmental Science-Nano, 7 (7), p. 2032-2046, 2020, ISSN: 2051-8153, (2014/29).

Résumé | Liens

@article{694,
title = {The longer the worse: a combined proteomic and targeted study of the long-termversusshort-term effects of silver nanoparticles on macrophages},
author = {B Dalzon and C Aude-Garcia and H Diemer and J Bons and C Marie-Desvergne and J Perard and M Dubosson and V Collin-Faure and C Carapito and S Sanglier-Cianferani and M Carriere and T Rabilloud},
url = {<Go to ISI>://WOS:000549099000010},
doi = {10.1039/c9en01329f},
issn = {2051-8153},
year = {2020},
date = {2020-01-01},
journal = {Environmental Science-Nano},
volume = {7},
number = {7},
pages = {2032-2046},
abstract = {Despite considerable research effort devoted to the study of the effects of silver nanoparticles on mammalian cells in recent years, data on the potential long term effects of this nanomaterial remain scarce, and centered on epithelial cells. The aim of this study was to explore the effects of silver nanoparticles on macrophages. To this end, RAW 264.7 murine macrophages were exposed to either 1 mu g ml(-1)silver nanoparticles for 20 days,i.e.a chronic exposure scheme, or to 20 mu g ml(-1)silver nanoparticles for 24 hours,i.e.an acute exposure scheme. A proteomic study was then conducted to study and compare the cellular responses to both exposure schemes. They proved to be essentially different, and stronger for the chronic exposure scheme. Targeted validation studies showed effects of chronic exposure to silver nanoparticles on detoxifying enzymes such as flavin reductase, which was increased, and on central metabolism enzymes such as triose phosphate isomerase, the activity of which decreased under chronic exposure to silver nanoparticles. Chronic exposure to silver nanoparticles also induced a decrease of reduced glutathione content, a decreased phagocytic activity and reduced macrophage responses to lipopolysaccharide, as exemplified by nitric oxide and interleukin 6 production. Overall, chronic exposure to silver nanoparticles induced stronger effects than acute exposure on macrophages in the metabolic (glutathione level, mitochondrial potential) and functional (phagocytosis, cytokine production) parameters tested.},
note = {2014/29},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Fermer

Desligniere, E; Ehkirch, A; Botzanowski, T; Beck, A; Hernandez-Alba, O; Cianferani, S

Toward Automation of Collision-Induced Unfolding Experiments through Online Size Exclusion Chromatography Coupled to Native Mass Spectrometry Article de journal

Anal Chem, 92 (19), p. 12900-12908, 2020, ISSN: 1520-6882 (Electronic) 0003-2700 (Linking), (Desligniere, Evolene Ehkirch, Anthony Botzanowski, Thomas Beck, Alain Hernandez-Alba, Oscar Cianferani, Sarah eng Research Support, Non-U.S. Gov't 2020/09/05 06:00 Anal Chem. 2020 Oct 6;92(19):12900-12908. doi: 10.1021/acs.analchem.0c01426. Epub 2020 Sep 18.).

Résumé | Liens

@article{690,
title = {Toward Automation of Collision-Induced Unfolding Experiments through Online Size Exclusion Chromatography Coupled to Native Mass Spectrometry},
author = {E Desligniere and A Ehkirch and T Botzanowski and A Beck and O Hernandez-Alba and S Cianferani},
url = {https://www.ncbi.nlm.nih.gov/pubmed/32886492},
doi = {10.1021/acs.analchem.0c01426},
issn = {1520-6882 (Electronic) 0003-2700 (Linking)},
year = {2020},
date = {2020-01-01},
journal = {Anal Chem},
volume = {92},
number = {19},
pages = {12900-12908},
abstract = {Ion mobility (IM)-based collision-induced unfolding (CIU) has gained increasing attention to probe gas-phase unfolding of proteins and their noncovalent complexes, notably for biotherapeutics. CIU detects subtle conformational changes of proteins and emerges as an attractive alternative to circumvent poor IM resolution. However, CIU still lacks in automation for buffer exchange and data acquisition, precluding its wide adoption. We present here an automated workflow for CIU experiments, from sample preparation to data interpretation using online size exclusion chromatography coupled to native IM mass spectrometry (SEC-CIU). Online automated SEC-CIU experiments offer several benefits over nanoESI-CIU, among which are (i) improved and fast desalting compared to manual buffer exchange used for classical CIU experiments; (ii) drastic reduction of the overall data collection time process; and (iii) maintaining the number of unfolding transitions. We then evaluate the potential of SEC-CIU to distinguish monoclonal antibody (mAb) subclasses, illustrating the efficiency of our method for rapid mAb subclass identification at both intact and middle levels. Finally, we demonstrate that CIU data acquisition time can be further reduced either by setting up a scheduled CIU method relying on diagnostic trap collision voltages or by implementing mAb-multiplexed SEC-CIU analyses to maximize information content in a single experiment. Altogether, our results confirm the suitability of SEC-CIU to automate CIU experiments, particularly for the fast characterization of next-generation mAb-based products.},
note = {Desligniere, Evolene
Ehkirch, Anthony
Botzanowski, Thomas
Beck, Alain
Hernandez-Alba, Oscar
Cianferani, Sarah
eng
Research Support, Non-U.S. Gov't
2020/09/05 06:00
Anal Chem. 2020 Oct 6;92(19):12900-12908. doi: 10.1021/acs.analchem.0c01426. Epub 2020 Sep 18.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Fermer

Ibrahim, M; Wasselin, T; Challet, E; Dorsselaer, Van A; Maho, Le Y; Raclot, T; Bertile, F

Transcriptional Changes Involved in Atrophying Muscles during Prolonged Fasting in Rats Article de journal

Int J Mol Sci, 21 (17), 2020, ISSN: 1422-0067 (Electronic) 1422-0067 (Linking), (Ibrahim, Marianne Wasselin, Thierry Challet, Etienne Van Dorsselaer, Alain Le Maho, Yvon Raclot, Thierry Bertile, Fabrice eng ANR-05-BLAN-0069/Agence Nationale de la Recherche ANR-10-INSB-08-03/Proteomics French Infrastructure (ProFI) Switzerland 2020/08/23 06:00 Int J Mol Sci. 2020 Aug 20;21(17). pii: ijms21175984. doi: 10.3390/ijms21175984.).

Résumé | Liens

@article{681b,
title = {Transcriptional Changes Involved in Atrophying Muscles during Prolonged Fasting in Rats},
author = {M Ibrahim and T Wasselin and E Challet and A Van Dorsselaer and Y Le Maho and T Raclot and F Bertile},
url = {https://www.ncbi.nlm.nih.gov/pubmed/32825252},
doi = {10.3390/ijms21175984},
issn = {1422-0067 (Electronic) 1422-0067 (Linking)},
year = {2020},
date = {2020-01-01},
journal = {Int J Mol Sci},
volume = {21},
number = {17},
abstract = {Food deprivation resulting in muscle atrophy may be detrimental to health. To better understand how muscle mass is regulated during such a nutritional challenge, the current study deciphered muscle responses during phase 2 (P2, protein sparing) and phase 3 (P3, protein mobilization) of prolonged fasting in rats. This was done using transcriptomics analysis and a series of biochemistry measurements. The main findings highlight changes for plasma catabolic and anabolic stimuli, as well as for muscle transcriptome, energy metabolism, and oxidative stress. Changes were generally consistent with the intense use of lipids as fuels during P2. They also reflected increased muscle protein degradation and repressed synthesis, in a more marked manner during P3 than P2 compared to the fed state. Nevertheless, several unexpected changes appeared to be in favor of muscle protein synthesis during fasting, notably at the level of the phosphatidylinositol-3-kinase (PI3K)/protein kinase B (AKT)/mammalian target of rapamycin (mTOR) signaling pathway, transcription and translation processes, and the response to oxidative stress. Such mechanisms might promote protein sparing during P2 and prepare the restoration of the protein compartment during P3 in anticipation of food intake for optimizing the effects of an upcoming refeeding, thereby promoting body maintenance and survival. Future studies should examine relevance of such targets for improving nitrogen balance during catabolic diseases.},
note = {Ibrahim, Marianne
Wasselin, Thierry
Challet, Etienne
Van Dorsselaer, Alain
Le Maho, Yvon
Raclot, Thierry
Bertile, Fabrice
eng
ANR-05-BLAN-0069/Agence Nationale de la Recherche
ANR-10-INSB-08-03/Proteomics French Infrastructure (ProFI)
Switzerland
2020/08/23 06:00
Int J Mol Sci. 2020 Aug 20;21(17). pii: ijms21175984. doi: 10.3390/ijms21175984.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Fermer

Lacoux, C; Wacheul, L; Saraf, K; Pythoud, N; Huvelle, E; Figaro, S; Graille, M; Carapito, C; Lafontaine, D L J; Heurgue-Hamard, V

The catalytic activity of the translation termination factor methyltransferase Mtq2-Trm112 complex is required for large ribosomal subunit biogenesis Article de journal

Nucleic Acids Res, 48 (21), p. 12310-12325, 2020, ISSN: 1362-4962 (Electronic) 0305-1048 (Linking), (Lacoux, Caroline Wacheul, Ludivine Saraf, Kritika Pythoud, Nicolas Huvelle, Emmeline Figaro, Sabine Graille, Marc Carapito, Christine Lafontaine, Denis L J Heurgue-Hamard, Valerie eng Research Support, Non-U.S. Gov't England 2020/11/10 06:00 Nucleic Acids Res. 2020 Dec 2;48(21):12310-12325. doi: 10.1093/nar/gkaa972.).

Résumé | Liens

@article{693,
title = {The catalytic activity of the translation termination factor methyltransferase Mtq2-Trm112 complex is required for large ribosomal subunit biogenesis},
author = {C Lacoux and L Wacheul and K Saraf and N Pythoud and E Huvelle and S Figaro and M Graille and C Carapito and D L J Lafontaine and V Heurgue-Hamard},
url = {https://www.ncbi.nlm.nih.gov/pubmed/33166396},
doi = {10.1093/nar/gkaa972},
issn = {1362-4962 (Electronic) 0305-1048 (Linking)},
year = {2020},
date = {2020-01-01},
journal = {Nucleic Acids Res},
volume = {48},
number = {21},
pages = {12310-12325},
abstract = {The Mtq2-Trm112 methyltransferase modifies the eukaryotic translation termination factor eRF1 on the glutamine side chain of a universally conserved GGQ motif that is essential for release of newly synthesized peptides. Although this modification is found in the three domains of life, its exact role in eukaryotes remains unknown. As the deletion of MTQ2 leads to severe growth impairment in yeast, we have investigated its role further and tested its putative involvement in ribosome biogenesis. We found that Mtq2 is associated with nuclear 60S subunit precursors, and we demonstrate that its catalytic activity is required for nucleolar release of pre-60S and for efficient production of mature 5.8S and 25S rRNAs. Thus, we identify Mtq2 as a novel ribosome assembly factor important for large ribosomal subunit formation. We propose that Mtq2-Trm112 might modify eRF1 in the nucleus as part of a quality control mechanism aimed at proof-reading the peptidyl transferase center, where it will subsequently bind during translation termination.},
note = {Lacoux, Caroline
Wacheul, Ludivine
Saraf, Kritika
Pythoud, Nicolas
Huvelle, Emmeline
Figaro, Sabine
Graille, Marc
Carapito, Christine
Lafontaine, Denis L J
Heurgue-Hamard, Valerie
eng
Research Support, Non-U.S. Gov't
England
2020/11/10 06:00
Nucleic Acids Res. 2020 Dec 2;48(21):12310-12325. doi: 10.1093/nar/gkaa972.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Fermer

Launay, K; Amalian, J A; Laurent, E; Oswald, L; Ouahabi, Al A; Burel, A; Dufour, F; Carapito, C; Clement, J L; Lutz, J F; Charles, L; Gigmes, D

Precise Alkoxyamine Design to Enable Automated Tandem Mass Spectrometry Sequencing of Digital Poly(phosphodiester)s Article de journal

Angew Chem Int Ed Engl, 2020, ISSN: 1521-3773 (Electronic) 1433-7851 (Linking), (Launay, Kevin Amalian, Jean-Arthur Laurent, Eline Oswald, Laurence Al Ouahabi, Abdelaziz Burel, Alexandre Dufour, Florent Carapito, Christine Clement, Jean-Louis Lutz, Jean-Francois Charles, Laurence Gigmes, Didier eng ANR-16-CE29-0004-01/Agence Nationale de la Recherche ANR-16-CE29-0004-02/Agence Nationale de la Recherche Germany 2020/09/24 06:00 Angew Chem Int Ed Engl. 2020 Sep 22. doi: 10.1002/anie.202010171.).

Résumé | Liens

@article{692,
title = {Precise Alkoxyamine Design to Enable Automated Tandem Mass Spectrometry Sequencing of Digital Poly(phosphodiester)s},
author = {K Launay and J A Amalian and E Laurent and L Oswald and A Al Ouahabi and A Burel and F Dufour and C Carapito and J L Clement and J F Lutz and L Charles and D Gigmes},
url = {https://www.ncbi.nlm.nih.gov/pubmed/32964618},
doi = {10.1002/anie.202010171},
issn = {1521-3773 (Electronic) 1433-7851 (Linking)},
year = {2020},
date = {2020-01-01},
journal = {Angew Chem Int Ed Engl},
abstract = {A major step towards reliable reading of information coded in the sequence of long poly(phosphodiester)s was previously achieved by introducing an alkoxyamine spacer between information sub-segments. However, MS/MS decoding had to be performed manually to safely identify useful fragments of low abundance compared to side-products from the amide-based alkoxyamine used. Here, alternative alkoxyamines were designed to prevent side-reactions and enable automated MS/MS sequencing. Different styryl-TEMPO spacers were prepared to increase radical delocalization and stiffness of the structure. Their dissociation behavior was investigated by EPR and best results were obtained with spacers containing in-chain benzyl ring, with no side-reaction during synthesis or sequencing. Automated decoding of these polymers was performed using the MS-DECODER software, which interprets fragmentation data recorded for each sub-segment and re-align them in their original order based on location tags.},
note = {Launay, Kevin
Amalian, Jean-Arthur
Laurent, Eline
Oswald, Laurence
Al Ouahabi, Abdelaziz
Burel, Alexandre
Dufour, Florent
Carapito, Christine
Clement, Jean-Louis
Lutz, Jean-Francois
Charles, Laurence
Gigmes, Didier
eng
ANR-16-CE29-0004-01/Agence Nationale de la Recherche
ANR-16-CE29-0004-02/Agence Nationale de la Recherche
Germany
2020/09/24 06:00
Angew Chem Int Ed Engl. 2020 Sep 22. doi: 10.1002/anie.202010171.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Fermer

Nguyen, A; Nguyen, D; Nguyen, Phong T X; Sebastiani, M; Dorr, S; Hernandez-Alba, O; Debaene, F; Cianferani, S; Heine, A; Klebe, G; Reuter, K

The Importance of Charge in Perturbing the Aromatic Glue Stabilizing the Protein-Protein Interface of Homodimeric tRNA-Guanine Transglycosylase Article de journal

ACS Chem Biol, 15 (11), p. 3021-3029, 2020, ISSN: 1554-8937 (Electronic) 1554-8929 (Linking), (Nguyen, Andreas Nguyen, Dzung Phong Nguyen, Tran Xuan Sebastiani, Maurice Dorr, Stefanie Hernandez-Alba, Oscar Debaene, Francois Cianferani, Sarah Heine, Andreas Klebe, Gerhard Reuter, Klaus eng Research Support, Non-U.S. Gov't 2020/11/10 06:00 ACS Chem Biol. 2020 Nov 20;15(11):3021-3029. doi: 10.1021/acschembio.0c00700. Epub 2020 Nov 9.).

Résumé | Liens

@article{689b,
title = {The Importance of Charge in Perturbing the Aromatic Glue Stabilizing the Protein-Protein Interface of Homodimeric tRNA-Guanine Transglycosylase},
author = {A Nguyen and D Nguyen and T X Phong Nguyen and M Sebastiani and S Dorr and O Hernandez-Alba and F Debaene and S Cianferani and A Heine and G Klebe and K Reuter},
url = {https://www.ncbi.nlm.nih.gov/pubmed/33166460},
doi = {10.1021/acschembio.0c00700},
issn = {1554-8937 (Electronic) 1554-8929 (Linking)},
year = {2020},
date = {2020-01-01},
journal = {ACS Chem Biol},
volume = {15},
number = {11},
pages = {3021-3029},
abstract = {Bacterial tRNA-guanine transglycosylase (Tgt) is involved in the biosynthesis of the modified tRNA nucleoside queuosine present in the anticodon wobble position of tRNAs specific for aspartate, asparagine, histidine, and tyrosine. Inactivation of the tgt gene leads to decreased pathogenicity of Shigella bacteria. Therefore, Tgt constitutes a putative target for Shigellosis drug therapy. Since it is only active as homodimer, interference with dimer-interface formation may, in addition to active-site inhibition, provide further means to disable this protein. A cluster of four aromatic residues seems important to stabilize the homodimer. We mutated residues of this aromatic cluster and analyzed each mutated variant with respect to the dimer and thermal stability or enzyme activity by applying native mass spectrometry, a thermal shift assay, enzyme kinetics, and X-ray crystallography. Our structural studies indicate a strong influence of pH on the homodimer stability. Apparently, protonation of a histidine within the aromatic cluster supports the collapse of an essential structural motif within the dimer interface at slightly acidic pH.},
note = {Nguyen, Andreas
Nguyen, Dzung
Phong Nguyen, Tran Xuan
Sebastiani, Maurice
Dorr, Stefanie
Hernandez-Alba, Oscar
Debaene, Francois
Cianferani, Sarah
Heine, Andreas
Klebe, Gerhard
Reuter, Klaus
eng
Research Support, Non-U.S. Gov't
2020/11/10 06:00
ACS Chem Biol. 2020 Nov 20;15(11):3021-3029. doi: 10.1021/acschembio.0c00700. Epub 2020 Nov 9.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Fermer

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