Proteogenomics and ecotoxicoproteomics

We have pioneered the field of proteogenomics, the alliance of omics to gain deeper insights into non-model organisms. 

Gouveia et al., 2019 https://doi.org/10.1016/j.jprot.2018.12.001

This expertise was successfully applied to numerous aquatic animals employed in ecotoxicology studies. Specific biomarkers can be highlighted for example in amphipods exposed to pollutants and systematically measured by mass spectrometry to qualify the quality of our environment.

ecotox
Gouveia et al., 2019 https://doi.org/10.1016/j.jprot.2018.12.001

This novel proteomic application we have developed and exemplified is now routinely used for environmental diagnostics in numerous laboratories. We are now extending the use of proteomics for diagnostics of soil health and for improving agriculture yields.

  • Almunia C, Gouveia D, Armengaud J (2022) Sample preparation for proteogenomics of aquatic invertebrates. Methods in Molecular Biology, in press.

  • Pujic P, Alloisio N, Miotello G, Armengaud J, Abrouk D, Fournier F, Normand P (2022) The proteogenome of symbiotic Frankia alni in Alnus glutinosa nodules. Microorganisms 10(3):651. doi: 10.3390/microorganisms10030651.

  • Armengaud J (2022) Protecting our environment, a motivating outdoor game for proteomics! Proteomics 22(10):e2200055. doi: 10.1002/pmic.202200055.

  • Dumas T, Courant F, Almunia C, Boccard J, Rosain D, Duporté G, Armengaud J, Fenet H, Gomez E (2021) An integrated metabolomics and proteogenomics approach reveals molecular alterations following carbamazepine exposure in the male mussel Mytilus galloprovincialis. Chemosphere 286:131793. doi.org/10.1016/j.chemosphere.2021.131793.

  • Cosio C, Degli Esposti D, Almunia C, Gaillet V, Sartelet H, Armengaud J, Chaumot A, Geffard O, Geffard A (2021) Subcellular distribution of dietary methyl-mercury in Gammarus fossarum and its impact on the amphipod proteome. Environmental Science & Technology 55(15):10514-10523. doi: 10.1021/acs.est.1c02385

  • Koenig N, Almunia C, Bonnal-Conduzorgues A, Armengaud J, Chaumot A, Geffard O, Esposti DD (2021) Co-expression network analysis identifies novel molecular pathways associated with cadmium and pyriproxyfen testicular toxicity in Gammarus fossarum. Aquat Toxicol. 235:105816. doi: 10.1016/j.aquatox.2021.105816.

  • Rosner A, Armengaud J, Ballarin L, Barnay-Verdier S, Cima F, Varela Coelho A, Domart-Coulon I, Drobne D, Genevière AM, Jemec Kokalj A,  Kotlarska E, Lyons DM, Mass T, Paz G, Pazdro K, Perić L, Ramšak A, Rakers S, Rinkevich B, Spagnuolo A, Sugni  M, Cambier S (2021) Stem cells of aquatic invertebrates as an advanced tool for assessing ecotoxicological impacts. SciTotal Environ 771:144565. doi: 10.1016/j.scitotenv.2020.144565.

  • Leprêtre M, Faury N, Segarra A, Claverol S, Degremont L, Palos Ladeiro M, Armengaud J, Renault T, Morga B (2021) Comparative proteomics of ostreid herpesvirus 1 and Pacific oyster interactions with two families exhibiting contrasted susceptibility to viral infection. Frontiers in Immunology 11:621994. doi:10.3389/fimmu.2020.621994

  • Leprêtre M, Palos-Ladeiro M, Faugere J, Almunia C, Lemoine J, Armengaud J, Geffard A, Salvador A (2020) From shotgun to targeted proteomics: rapid Scout-MRM assay development for monitoring potential immunomarkers in Dreissena polymorpha. Anal Bioanal Chem. 412:7333-7347. doi: 10.1007/s00216-020-02868-2.

  • Faugere J, Gouveia D, Ayciriex S, Chaumot A, Almunia C, François A, Armengaud J, Lemoine J, Geffard O, Degli-Esposti D, Salvador A (2020) High-multiplexed monitoring of protein biomarkers in the sentinel Gammarus fossarum by targeted scout-MRM assay, a new vision for ecotoxicoproteomics. J Proteomics. 226:103901. doi: 10.1016/j.jprot.2020.103901.

  • Leprêtre M, Almunia C, Armengaud J, Le Guernic A, Salvador A, Geffard A, Palos-Ladeiro M (2020) Identification of immune-related proteins of Dreissena polymorpha hemocytes and plasma involved in host-microbe interactions by differential proteomics. Sci Rep. 10(1):6226. doi: 10.1038/s41598-020-63321-z.

  • Cogne Y, Gouveia D, Chaumot A, Degli-Esposti D, Geffard O, Pible O, Almunia C, Armengaud J (2020) Proteogenomics-guided Evaluation of RNA-seq Assembly and Protein Database Construction for Emergent Model Organisms. Proteomics. e1900261. doi: 10.1002/pmic.201900261.