High-quality analyses
AltraBio deploys its recognized expertise in bioinformatics, biostatistic and biology to provide services in the analysis and interpretation of all types of omics data (genomics, epigenomics, transcriptomics, proteomics…).
For each project, AltraBio’s team works in interaction with its clients/partners in order to reach their goals.
Expertise in biostatistics and bioinformatics
Prior to performing differential analyses, various methods are implemented to assess the quality of the data and their agreement with the experimental design. We specifically control for outliers and for effects unrelated to the design in order to correct them with the agreement of our client/partner. Thus the relevance of the performed analysis is guaranteed.
Experimental designs may consist of multiple factors (donor, cell type, treatment, dose, timepoints…) and thus can be analyzed from multiple angles. To answer the biological question(s) of the study, AltraBio determines the most suitable statistical model (paired design, batch effect correction, hidden factor estimation, weighting of outliers…).
AltraBio possesses the know-how to integrate different types of data (multi-omics, cytometry, medical data…). Supervised and unsupervised machine learning can be implemented for various applications: biomarker identification, classification, predictive models for diagnostic or response to treatment. Thus our clients benefit from our strong expertise in using up-to-date machine learning algorithms to extract the maximum value from their data.
Expertise in biology
Biological processes and pathways are identified thanks to the implementation of various and complementary methods of functional categories enrichment. These automatic results are then reviewed to assess their relevance with the biological context of the study.
Beyond providing lists of molecules and biological pathways, AltraBio’s role is also to extract meaning. To this end, the interpretation phase takes into account the biological question(s) at the origin of the study and assesses the results while integrating the biological knowledge available in the scientific literature and databases. The goal is to understand the biological mechanisms at play and to formulate new hypotheses to be validated (examples of synthetic diagrams produced by AltraBio in figures S8A and S9A of this article).
Reporting
All of the work carried out is summarized in a complete report transferred to our client/partner and explained during a video conference. This exchange makes it possible to explain the chosen methodological approaches and their results as well as to ensure that our client/partner has the best understanding of their data.
Statistical analysis results are also available in the WikiBioPath web interface which provides our clients/partners a set of visualisation and analysis tools which enables them to continue the exploration of their data. They can easily visualise their volcano plots and generate new heat maps, PCA and enrichment analyses on gene selections.
Our publications in Omics Data Analysis
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 Journal Article
In: Aging (Albany NY), vol. 15, no. 22, pp. 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 Journal Article
In: Cell Rep, vol. 42, no. 7, pp. 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 Journal Article
In: 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}
}