High-quality analyses
AltraBio harnesses its renowned expertise in bioinformatics, biostatistics, and biology to offer services in the analysis and interpretation of various omics data types (genomics, epigenomics, transcriptomics, proteomics, etc.).
Our team collaborates closely with clients and partners for each project to ensure their goals are met.
Expertise in biostatistics and bioinformatics
Before conducting differential analyses, we implement various methods to assess the data quality and its consistency with the experimental design. We specifically address outliers and effects unrelated to the design to correct them in agreement with of our client/partner. This ensures the relevance of the analysis performed.
Experimental designs may involve multiple factors such as donor, cell type, treatment, dose, and timepoints, allowing for analysis from various perspectives. To address the biological question(s) of the study, AltraBio identifies the most appropriate statistical model (paired design, batch effect correction, estimation of hidden factors, outlier weighting, etc.).
AltraBio has the expertise to integrate various types of data (multi-omics, cytometry, medical data, etc.). We employ supervised and unsupervised machine learning for various applications including biomarker identification, classification, predictive models for diagnostics or treatment response. Our clients benefit from our strong proficiency in utilizing state-of-the-art machine learning algorithms to extract maximum value from their data.
Expertise in biology
Biological processes and pathways are identified through the implementation of various complementary methods of functional category enrichment. These automated 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 to extract meaning. In the interpretation phase, we consider the biological question(s) that initiated the study and evaluate the results while integrating biological knowledge available in scientific literature and databases. Our goal is to understand the biological mechanisms at play and formulate new hypotheses for validation. Examples of synthetic diagrams produced by AltraBio can be found in figures S8A and S9A of this article).
Reporting
All the work conducted is summarized in a comprehensive report provided to our client/partner and explained during a video conference. This exchange allows us to clarify the chosen methodological approaches and their results, ensuring that our client/partner has the best understanding of their data.
The results of statistical analysis are also accessible through the WikiBioPath web interface, providing our clients/partners with a set of visualisation and analysis tools to continue exploring their data. They can easily visualize volcano plots, generate new heat maps, perform PCA, and conduct enrichment analyses on gene selections.
Our publications in Omics Data Analysis
2023
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}
}
Meier, Johannes P; Möbus, Selina; Heigl, Florian; Asbach-Nitzsche, Alexandra; Niller, Hans Helmut; Plentz, Annelie; Avsar, Korkut; Heiß-Neumann, Marion; Schaaf, Bernhard; Cassens, Uwe; Seese, Bernd; Teschner, Daniel; Handzhiev, Sabin; Graf, Uwe; Lübbert, Christoph; Steinmaurer, Monika; Kontogianni, Konstantina; Berg, Christoph; Maieron, Andreas; Blaas, Stefan H; Wagner, Ralf; Deml, Ludwig; Barabas, Sascha
Performance of T-Track TB, a Novel Dual Marker RT-qPCR-Based Whole-Blood Test for Improved Detection of Active Tuberculosis Journal Article
In: Diagnostics (Basel), vol. 13, no. 4, 2023, ISSN: 2075-4418.
@article{pmid36832246,
title = {Performance of T-Track TB, a Novel Dual Marker RT-qPCR-Based Whole-Blood Test for Improved Detection of Active Tuberculosis},
author = {Johannes P Meier and Selina Möbus and Florian Heigl and Alexandra Asbach-Nitzsche and Hans Helmut Niller and Annelie Plentz and Korkut Avsar and Marion Heiß-Neumann and Bernhard Schaaf and Uwe Cassens and Bernd Seese and Daniel Teschner and Sabin Handzhiev and Uwe Graf and Christoph Lübbert and Monika Steinmaurer and Konstantina Kontogianni and Christoph Berg and Andreas Maieron and Stefan H Blaas and Ralf Wagner and Ludwig Deml and Sascha Barabas},
doi = {10.3390/diagnostics13040758},
issn = {2075-4418},
year = {2023},
date = {2023-02-01},
urldate = {2023-02-01},
journal = {Diagnostics (Basel)},
volume = {13},
number = {4},
abstract = {Tuberculosis (TB) is one of the leading causes of death by an infectious disease. It remains a major health burden worldwide, in part due to misdiagnosis. Therefore, improved diagnostic tests allowing the faster and more reliable diagnosis of patients with active TB are urgently needed. This prospective study examined the performance of the new molecular whole-blood test T-Track TB, which relies on the combined evaluation of and mRNA levels, and compared it to that of the QuantiFERON-TB Gold Plus (QFT-Plus) enzyme-linked immunosorbent assay (ELISA). Diagnostic accuracy and agreement analyses were conducted on the whole blood of 181 active TB patients and 163 non-TB controls. T-Track TB presented sensitivity of 94.9% and specificity of 93.8% for the detection of active TB vs. non-TB controls. In comparison, the QFT-Plus ELISA showed sensitivity of 84.3%. The sensitivity of T-Track TB was significantly higher ( < 0.001) than that of QFT-Plus. The overall agreement of T-Track TB with QFT-Plus to diagnose active TB was 87.9%. Out of 21 samples with discordant results, 19 were correctly classified by T-Track TB while misclassified by QFT-Plus (T-Track TB-positive/QFT-Plus-negative), and two samples were misclassified by T-Track TB while correctly classified by QFT-Plus (T-Track TB-negative/QFT-Plus-positive). Our results demonstrate the excellent performance of the T-Track TB molecular assay and its suitability to accurately detect TB infection and discriminate active TB patients from non-infected controls.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Coutier, Julien; Auvré, Frédéric; Lemaître, Gilles; Lataillade, Jean-Jacques; Deleuze, Jean-François; Roméo, Paul-Henri; Martin, Michèle T; Fortunel, Nicolas O
MXD4/MAD4 Regulates Human Keratinocyte Precursor Fate Journal Article
In: J Invest Dermatol, vol. 143, no. 1, pp. 105–114.e12, 2023, ISSN: 1523-1747.
@article{pmid36007550,
title = {MXD4/MAD4 Regulates Human Keratinocyte Precursor Fate},
author = {Julien Coutier and Frédéric Auvré and Gilles Lemaître and Jean-Jacques Lataillade and Jean-François Deleuze and Paul-Henri Roméo and Michèle T Martin and Nicolas O Fortunel},
doi = {10.1016/j.jid.2022.07.020},
issn = {1523-1747},
year = {2023},
date = {2023-01-01},
urldate = {2023-01-01},
journal = {J Invest Dermatol},
volume = {143},
number = {1},
pages = {105--114.e12},
abstract = {Deciphering the pathways that regulate human epidermal precursor cell fate is necessary for future developments in skin repair and graft bioengineering. Among them, characterization of pathways regulating the keratinocyte (KC) precursor immaturity versus differentiation balance is required for improving the efficiency of KC precursor ex vivo expansion. In this study, we show that the transcription factor MXD4/MAD4 is expressed at a higher level in quiescent KC stem/progenitor cells located in the basal layer of human epidermis than in cycling progenitors. In holoclone KCs, stable short hairpin-RNA‒mediated decreased expression of MXD4/MAD4 increases MYC expression, whose modulation increases the proliferation of KC precursors and maintenance of their clonogenic potential and preserves the functionality of these precursors in three-dimensional epidermis organoid generation. Altogether, these results characterize MXD4/MAD4 as a major piece of the stemness puzzle in the human epidermis KC lineage and pinpoint an original avenue for ex vivo expansion of human KC precursors.},
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pubstate = {published},
tppubtype = {article}
}