Des analyses de qualité
AltraBio met en oeuvre son expertise reconnue en bioinformatique et biostatistique pour l’analyse et la valorisation de tout type de données OMIQUES (génomique, transcriptomique, protéomique, épigénomique…).
Pour chaque projet, l’équipe d’AltraBio est en interaction avec ses clients/partenaires pour s’adapter à leurs attentes.
Expertise en biostatistique et bio informatique
Les plans expérimentaux comportent, dans certains cas, de multiples facteurs (donneur, type cellulaire, type de traitement, temps, dose…) et peuvent être analysés sous de multiples angles. Pour répondre aux questions biologiques de l’étude, AltraBio définit les modèles d’analyse statistique les mieux adaptés (modèle appariés, corrections effets batch, estimation d’effet caché, pondération des outliers…).
Expertise en biologie
Au delà de la génération de listes de molécules et catégories fonctionnelles, le rôle d’AltraBio est aussi d’en extraire le sens. C’est pourquoi la phase d’interprétation prend en compte la/les questions biologiques à l’origine de l’étude, évalue l’ensemble des résultats en y intégrant la connaissance biologique disponible dans la littérature scientifique et les bases de données publiques. L’objectif est de comprendre les mécanismes biologiques mis en jeu et de formuler de nouvelles hypothèses à valider (exemples de schémas synthétiques délivrés par AltraBio, figures S8A et S9A de cet article).
Rendus
L’ensemble du travail réalisé est synthétisé dans un rapport complet remis et commenté à nos clients/partenaires sous forme d’une présentation orale. Cet échange permet d’expliquer les approches méthodologiques choisies et leurs résultats et de s’assurer que nos clients/partenaires ont la meilleure compréhension de leur données.
Les résultats de l’étude statistique sont également accessibles par l’interface web WikiBioPath qui met à disposition de nos partenaires/clients un ensemble d’outils de visualisation et d’analyses pour leur permettre de continuer à explorer leurs données. Ils peuvent ainsi facilement visualiser leurs volcano plots et générer de nouvelles heat maps, ACP et analyses d’enrichissement sur des ensembles de gènes définis par des critères d’intérêt.
Nos publications en analyses omiques
2023
Nedachi, Taku; Bonod, Christelle; Rorteau, Julie; Chinoune, Wafae; Ishiuchi, Yuri; Hughes, Sandrine; Gillet, Benjamin; Bechetoille, Nicolas; Sigaudo-Roussel, Dominique; Lamartine, Jérôme
Chronological aging impacts abundance, function and microRNA content of extracellular vesicles produced by human epidermal keratinocytes Article de journal
Dans: Aging (Albany NY), vol. 15, no. 22, p. 12702–12722, 2023, ISSN: 1945-4589.
@article{pmid38015712,
title = {Chronological aging impacts abundance, function and microRNA content of extracellular vesicles produced by human epidermal keratinocytes},
author = {Taku Nedachi and Christelle Bonod and Julie Rorteau and Wafae Chinoune and Yuri Ishiuchi and Sandrine Hughes and Benjamin Gillet and Nicolas Bechetoille and Dominique Sigaudo-Roussel and Jérôme Lamartine},
doi = {10.18632/aging.205245},
issn = {1945-4589},
year = {2023},
date = {2023-11-01},
urldate = {2023-11-01},
journal = {Aging (Albany NY)},
volume = {15},
number = {22},
pages = {12702--12722},
abstract = {The disturbance of intercellular communication is one of the hallmarks of aging. The goal of this study is to clarify the impact of chronological aging on extracellular vesicles (EVs), a key mode of communication in mammalian tissues. We focused on epidermal keratinocytes, the main cells of the outer protective layer of the skin which is strongly impaired in the skin of elderly. EVs were purified from conditioned medium of primary keratinocytes isolated from infant or aged adult skin. A significant increase of the relative number of EVs released from aged keratinocytes was observed whereas their size distribution was not modified. By small RNA sequencing, we described a specific microRNA (miRNA) signature of aged EVs with an increase abundance of miR-30a, a key regulator of barrier function in human epidermis. EVs from aged keratinocytes were found to be able to reduce the proliferation of young keratinocytes, to impact their organogenesis properties in a reconstructed epidermis model and to slow down the early steps of skin wound healing in mice, three features observed in aged epidermis. This work reveals that intercellular communication mediated by EVs is modulated during aging process in keratinocytes and might be involved in the functional defects observed in aged skin.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Roux, Natacha; Miura, Saori; Dussenne, Mélanie; Tara, Yuki; Lee, Shu-Hua; de Bernard, Simon; Reynaud, Mathieu; Salis, Pauline; Barua, Agneesh; Boulahtouf, Abdelhay; Balaguer, Patrick; Gauthier, Karine; Lecchini, David; Gibert, Yann; Besseau, Laurence; Laudet, Vincent
The multi-level regulation of clownfish metamorphosis by thyroid hormones Article de journal
Dans: Cell Rep, vol. 42, no. 7, p. 112661, 2023, ISSN: 2211-1247.
@article{pmid37347665,
title = {The multi-level regulation of clownfish metamorphosis by thyroid hormones},
author = {Natacha Roux and Saori Miura and Mélanie Dussenne and Yuki Tara and Shu-Hua Lee and Simon de Bernard and Mathieu Reynaud and Pauline Salis and Agneesh Barua and Abdelhay Boulahtouf and Patrick Balaguer and Karine Gauthier and David Lecchini and Yann Gibert and Laurence Besseau and Vincent Laudet},
doi = {10.1016/j.celrep.2023.112661},
issn = {2211-1247},
year = {2023},
date = {2023-06-01},
urldate = {2023-06-01},
journal = {Cell Rep},
volume = {42},
number = {7},
pages = {112661},
abstract = {Most marine organisms have a biphasic life cycle during which pelagic larvae transform into radically different juveniles. In vertebrates, the role of thyroid hormones (THs) in triggering this transition is well known, but how the morphological and physiological changes are integrated in a coherent way with the ecological transition remains poorly explored. To gain insight into this question, we performed an integrated analysis of metamorphosis of a marine teleost, the false clownfish (Amphiprion ocellaris). We show how THs coordinate a change in color vision as well as a major metabolic shift in energy production, highlighting how it orchestrates this transformation. By manipulating the activity of liver X regulator (LXR), a major regulator of metabolism, we also identify a tight link between metabolic changes and metamorphosis progression. Strikingly, we observed that these regulations are at play in the wild, explaining how hormones coordinate energy needs with available resources during the life cycle.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Sanlaville, Amélien; Voissière, Aurélien; Poujol, Dominique; Hubert, Margaux; André, Suzanne; Perret, Clémence; Foy, Jean-Philippe; Goutagny, Nadège; Malfroy, Marine; Durand, Isabelle; Châlons-Cottavoz, Marie; Valladeau-Guilemond, Jenny; Saintigny, Pierre; Puisieux, Alain; Caux, Christophe; Michallet, Marie-Cécile; Puisieux, Isabelle; Bendriss-Vermare, Nathalie
CD4 T cells and neutrophils contribute to epithelial-mesenchymal transition in breast cancer Article de journal
Dans: bioRxiv, 2023.
@article{Sanlaville2023.02.15.528594,
title = {CD4 T cells and neutrophils contribute to epithelial-mesenchymal transition in breast cancer},
author = {Amélien Sanlaville and Aurélien Voissière and Dominique Poujol and Margaux Hubert and Suzanne André and Clémence Perret and Jean-Philippe Foy and Nadège Goutagny and Marine Malfroy and Isabelle Durand and Marie Châlons-Cottavoz and Jenny Valladeau-Guilemond and Pierre Saintigny and Alain Puisieux and Christophe Caux and Marie-Cécile Michallet and Isabelle Puisieux and Nathalie Bendriss-Vermare},
url = {https://www.biorxiv.org/content/early/2023/02/15/2023.02.15.528594},
doi = {10.1101/2023.02.15.528594},
year = {2023},
date = {2023-02-15},
urldate = {2023-01-01},
journal = {bioRxiv},
publisher = {Cold Spring Harbor Laboratory},
abstract = {Epithelial-mesenchymal transition (EMT) is a central oncogenic mechanism, contributing both to transformation and metastatic dissemination. Inflammation and innate immune cells are known to favor EMT induction, but the role of adaptive immunity still remains unclear. Using an original murine mammary tumor model in immune cell subpopulation depletion experiments, we demonstrated that tumor cells maintain their epithelial phenotype in mice deficient for adaptive immune response, but undergo EMT in the presence of T-cells. This phenotypic conversion involves the major contribution of CD4 T cells, but not CD8 T cells nor B cells, undoubtedly demonstrating the pro-EMT role of CD4 T cells specifically among adaptive immune cells. Moreover, combined intra-tumor immune infiltrate and transcriptomic analyses of murine mammary tumors with various EMT phenotype revealed an inverse correlation between mesenchymal tumor cell and intratumoral neutrophil proportions, due to the reduced ability of mesenchymal cells to recruit neutrophils. Last, selective in vivo depletion of neutrophils and transcriptomic analysis of human breast tumor cohorts demonstrated the pro-EMT role of neutrophils and suggest a cooperation with CD4 T cells in EMT promotion. Collectively, our data highlight a novel mechanism of EMT regulation by both innate and adaptive immune compartments.Competing Interest StatementThe authors have declared no competing interest.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}