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Research & Development


Partnerships play an important role in our activities and we value establishing and maintaining strong relationships with our contacts within the scientific, academic and business communities. We are engaged in several joint research projects at national and international levels, some of them publicly funded.


Below are listed some of the current projects in which we are involved.

Single Cell Analysis

  • PELICAN: Single-cell transcriptome analysis in pleural fluids


    Single-cell transcriptome analysis for the diagnostic, prognostic and theranostic evaluation of patients with malignant cancer: pleural effusion fluids used as a new liquid biopsy


    The pleura is a frequent metastatic site during the evolution of cancers, which can lead to a symptomatic (pain, dyspnea) accumulation of pleural fluid that contains tumor and immune cells. To improve patients’ comfort this fluid is removed via chest draining, and the recovered liquid is typically considered as biological waste and in many cases discarded. PELICAN is built to investigate cells present in the pleural fluid and evaluate their potential in terms of diagnosis, prognosis and theragnosis, making this fluid a new liquid biopsy for cancer.
    The project is based on Cellenion's unique CellenONE™ single cell isolation technology and expertise in immuno-oncology, genomics and next generation sequencing of the Léon Bérard Center (CLB, Lyon, FRANCE). These two entities have clustered around this project to bring the power of these technologies to the patient as quickly as possible. The objective is to demonstrate that cells contained in the pleural fluid of cancer patients could be exploited for diagnosis and prognosis by direct characterization of their transcriptome and used for development of cellular models derived from patients to better understand and anticipate mechanisms of resistance to systemic treatments

    Duration: 2 years 10/2018 – 09/2020

    Budget : 1M euro, Grant : 300k€

    Program type: Proof Of Concept, Cancéropôle Lyon Auvergne Rhône-Alpes
    Involved partners:



    Thank you for the support:

  • SCAnIO: Cost-Effective Platform for Single-Cell Analysis in Immuno-Oncology


    Cost-Effective Platform for Single-Cell Analysis in Immuno-Oncology


    Research in oncology is experiencing a revolution related to the rise of immuno-oncology treatments. Development of those treatments requires a detailed knowledge of the targeted tissues (tumor and immune system) with a special focus on their intrinsic heterogeneity. Access to this information is now possible with the emergence of technologies allowing transcriptome analysis of the multitude of unique cells constituting a tissue. However, implementation and use of those technologies are limited and expensive, reducing R&D throughput. The complexity of data interpretation also represents a barrier to their routine use.
    The companies AltraBio and Cellenion, as well as the Léon Bérard Center, have decided to come together to develop specific technologies and create a high-throughput platform for sorting and analyzing multi-parametric single cells in immuno-oncology. The aim of this project will be to set up a methodological and optimized chain ranging from tissue dissociation to data analysis, through optimized isolation and fluorescence sorting of cells at a reduced price. The result of the project will be the establishment of a service platform dedicated to R & D issues in the field of immuno-oncology.

    Duration: 2 years 12/2018 – 11/2020

    Budget : 1,4M euro, Grant : 750k€

    Program type: R&D Booster, La région Auvergne Rhône-Alpes

    Involved partners:


    Thank you for the support:

  • Post-Metagenomics and -Metatranscriptomics Microbiota Analyses

     Post-Metagenomics and -Metatranscriptomics Microbiota Analyses using cellenONE® Technology

    Microorganisms are found in diverse ecosystems and organisms. They are part of essential processes within plants and animals and therefore a key in ecological patterns and diseases understanding. With our lack of knowledge on microbes, many hypotheses are rising as new guidelines for microbiota studies. A recent theory of evolution, the Black Queen Hypothesis (BQH), suggests that organisms could adapt to their environment by loss of trait or function, and not only by complexification. These theories and hypotheses are difficult to demonstrate in natural environments, since the respective attribution of functional traits to the different populations and individuals remains technically limited by the meta-genomic and meta-transcriptomic approaches currently used.

    This thesis project aims to explore the influence of BQH on the assembly of the microbiota by developing isolation and sequencing techniques for single cells, going beyond the limits of meta-omics.

    The single cell approach will give access to the organizational level of the individual, population and community and the expression of microbiota genomes.

    This PhD project is carried out between Cellenion, ECOBIO, UMR academic partner and the OSUR Environmental and Human Genomics platform.

    The CellenONE device recently acquired within the GEH platform is used to isolate bacterial cells from environmental samples (plant microbiota, soil). The cellenONE device allows to get high quality results as its features are optimum for microbes manipulation. The beforehand visualisation and automated imaging, gentle cell manipulation, pico-liter scale volumes, and relative high-throughput will altogether help decreasing the sample contamination and cost, increase the viability of the cells and the isolation accuracy. Bacterial cell-wide genome and transcriptome amplification tools will be used, and a pipeline for high throughput analysis of bacterial genomes and transcriptomes will be developed.

    Duration: January 2020 - January 2023

    Program Type: Bourse CIFRE

    Involved Partners:


    Thanks for the support:



  • iLite: Innovation for Liver Tissue Engineering


    Innovation for Liver Tissue Engineering


    Main objectives of this project are to build an external bioartificial liver, a liver-on-chip as well as a bioengineered liver. In the present project, bioconstruction of the liver is performed by the assembly of building blocks –liver organoids, vascular networks and biliary networks- built separately and then integrated into a scaffold. Vascular and biliary networks are produced by a mix of technologies comprising organotypic culture, micropatterning and stereolithography. Liver organoids are produced by bioprinting as sheets or spheroids, involving hepatocytes, endothelial cells and cholangiocytes, or as liver buds obtained from stem cells. A special interest is given on producing a functional biliary network which has been a missing element in all previous attempts to produce bioartificial liver.
    By the end of the 5-year project, the consortium aim to provide a prototype of an external bioartificial liver to be used for phase I and II clinical studies as well as a prototype liver-on-chip device ready for use by pharmaceutical companies producing new drugs. These goals will be reached by an interdisciplinary approach bringing together researcher from several Universities, Research Institute and small companies who master innovative technologies of bio-construction.

    Duration: 5 years 10/2016 – 09/2021

    Budget : 28M€, Grant : 9M€

    Program type: Recherche Hospitalo-Universitaire en santé (RHU) funded by the French National Research Agency (ANR)

    Involved partners:



    Thank you for the support: