Campuses

As France's leading biocluster, Genopole is an incubator for cutting-edge projects in biotechnology. Located in the city of Évry, just south of Paris, Genopole provides a unique environment for scientists and entrepreneurs seeking to advance research and innovation.

Discover >

Advantages

Genopole accompanies researchers, postdocs and start-up entrepreneurs through all the phases of their projects to ensure the best possible conditions for business development.

Discover >

Genopole’s citizens

Every day, at Genopole, researchers, entrepreneurs and students cross paths, share ideas and unite forces in a veritable melting pot for innovation.

Discover >

Highlights

Giving wings to research and empowering employment in our community are cornerstones of Genopole's mission. Catch up on recent scientific advances, the accomplishments of our biotech actors and the events that enliven the biocluster.

Discover >

Innovate with us

Discover >
Highlights

A tool to digitize organs


Sysfate at Genoscope has combined image analysis and genomics to create MULTILAYER, a tool to digitize biological tissues and organs.
SYSFATE SYSFATE

The Sysfate laboratory was created within the Genomics Metabolics unit at Genoscope through a Genopole Atige grant. The lab’s director, Marco Mendoza, and his team have developed MULTILAYER, a method for furnishing spatial digital images of activity in biological tissues. The team took inspiration from image analysis and admixed their expertise in “omics” (genomics, transcriptomics, etc.) to create the tool.

MULTILAYER thus reveals the functional structuration of an organ or tissue.

The method will be of particular interest for developing solutions in molecular diagnostics.

The function of a biological tissue or organ is determined by the activity of its constituent cells, or more precisely by the expression or non-expression of their genes.
Spatial transcriptomics* is a technique for analyzing the expression levels of a large group of genes simultaneously at the scale of a tissue or organ. From a histological section, the technique furnishes a two-dimensional image of gene expression therein, presented as points distributed evenly over the tissue. The functional map of the tissue can represent a thousand genes and several thousand positions, resulting together in millions of analyzable sequences. Such a quantity of data requires specific statistical and bioinformatics methods. To improve upon current methods, Marco Mendoza and his team at the Sysfate lab (Genoscope) have developed MULTILAYER and described its performance in an article published on 7 May 2021 in Cell Systems.

MULTILAYER analyzes a biological section and assigns to each spatial point in the tissue a measurement, called a gexel by the team for its analogousness with the pixels that make up a digital image. A gexel represents the expression of a thousand genes at a point in the tissue. Compared to conventional statistical methods, the novel nature of MULTILAYER is to be found in its analysis of gexels not as independent entities but as a continuity: adjacent gexels showing similar genetic expression profiles have weight in the analysis of any one gexel. Indeed, from a biological standpoint, contiguous cells should have a greater chance of a shared destiny and thus a shared genetic programming. The Sysfate team’s algorithm also mines known information centralized in databases, notably for gene co-expression, which can potentially indicate groups of genes associated with a given function.

MULTILAYER thus “digitizes” tissue into biologically pertinent substructures.

SysFate - Mapping a pancreas cut by Multilalayer
MULTILAYER has identified 6 functional cellular communities (6 colors) in the fabric, including strongly associated with tumor, cancer progression and ability to produce metastases.

In their article, the Sysfate researchers demonstrated MULTILAYER’s ability to identify functional zones from spatial transcriptomics data derived not only from heart tissue sections and a range of tumor tissues (below figure) but also from an entire mouse embryo, which the tool was able to stratify into regions corresponding perfectly to known anatomical structures (opposite figure).

MULTILAYER is freely available as an autonomous computer program: https://github.com/SysFate/MULTILAYER

 

An algorithm to obtain the functional cards of the organs


By uniting expertise in image analysis and in genomics, the Sysfate team was able to create a first version of an algorithm for the molecular analysis of tissues or organs that, when combined with spatial transcriptomics, may lead to functional maps of all of the organs in the human body. Such a feat would contribute to a better understanding of pathologies and the development of molecular diagnostics in the field of personalized medicine.

  • * Spatial transcriptomics

    Spatial transcriptomics produces spatial maps of gene expression within a tissue or organ. The method is built upon the fixation of groups of oligonucleotide mRNA (a product of gene expression) probes on a slide, upon which a tissue section will be placed.

    The mRNA are analyzed after separation, but a DNA barcode identifying the position of the trapped mRNA enables spatial reconstruction.

  • Reference

    Inferring biologically relevant molecular tissue substructures by agglomerative clustering of digitized spatial transcriptomes with multilayer. Cell Systems (2021)

    https://doi.org/10.1016/j.cels.2021.04.008

Article posted on 10 June 2021

Share
Highlights

Latest news


Alexis Biton and Paul Carouen - Genopole - visiting the Research Triangle Park (USA) accompanied by 3 Genopole's companies

Genopole strengthens its ties with the Research Triangle Park

From Monday March 20 to Thursday March 24, Genopole's Partnership & Business Development team visited the Research Triangle Park biopark in North Carolina to strengthen scientific and industrial collaborations.

Discover
l’équipe « Dystrophies musculaires progressives » du laboratoire Généthon

Shining light on a key mechanism of Duchenne muscular dystrophy

A Genethon team has provided new insights on a complex genetic mechanism involved in mitochondrial dysfunction in Duchenne muscular dystrophy.

Discover
A trio of genome sites associated with arterial hypertension

A trio of genome sites associated with arterial hypertension

Researchers from the CNRGH and PARCC have identified three loci associated with an increased risk of developing primary hyperaldosteronism, a leading cause of arterial hypertension.

Discover
Genoscope - CNS - Genopole's laboratory

The story of the domestic donkey told by its genome

Genoscope participated in the sequencing of the DNA of 250 donkeys in a study revealing the domestication of this species highly contributive to human activities to this day.

Discover
Galaxy-SynBioCAD: accelerating the arrival of green chemistry

Galaxy-SynBioCAD: accelerating the arrival of green chemistry

Conceived by the Genomics Metabolics Unit, Galaxy-SynBioCAD accelerates biological design and engineering for the production of next generation chemical compounds.

Discover
Equipe Sysfate de l'UMR 8030 - projet T-Fitness

T-FITNESS: Toward empowering CAR-T therapies for solid tumors

The Genopole team SysFate is participating in the international project T-FITNESS. The project, selected by the European Innovation Council, aims to resolve the difficulty of T-cell exhaustion in CAR-T therapies for solid tumors.

Discover
Ynsect & Genoscope : Vers la sélection génomique des insectes d’élevage

Toward the genomic selection of farmed insects

France is historically a land of livestock farming. Cows for meat or milk, sheep, pigs, fowl of all sorts; France rears them all. And insects! With its genomic selection project for Tenebrio molitor beetles, the Genopole company Ÿnsect and its biocluster partner, the sequencing center Genoscope, are making France a pioneer in insect farming.

Discover
Couverture de la revue Cell Genomics - Le plancton

A feat in the study of planktonic life

A Genoscope research team was part of a pioneering study in environmental genomics. The researchers were able to at least partially reconstitute the genomes of close to 700 eukaryote species.

Discover
Logos Istem & Généthon

A two-drug combination to treat limb-girdle muscular dystrophies and cystic fibrosis

The I-Stem and Genethon laboratories have identified a promising drug combination in the setting of three genetic diseases sharing similar molecular mechanisms.

Discover
IBISC - IA qui diagnostique et explique grâce à un réseau de neurones

An artificial intelligence to diagnose and explain

The IBISC laboratory has conceived an architecturally-innovative neural network able to provide not only a diagnostic prediction but also a biological explanation.

Discover
Christophe Lanneau - Research & Platforms Department Director

News from the human genome

The 1 April edition of Science announced the publication of the human genome with the previously-missing 8% now added to it. Comments from the Genopole Director of Research.

Discover
CNRGH - Consequences of phthalate exposure during pregnancy

Consequences of phthalate exposure during pregnancy

Jörg Tost and his team of the National Center of Human Genomics Research (CNRGH; CEA) were part of a large collaborative study aimed at determining the genome-wide correlation between phthalate exposure during pregnancy and methylation of placental DNA.

Discover
INtegrare / Généthon - Efficacité à long terme de la thérapie génique d’un déficit immunitaire

Long-term efficacy for an immunodeficiency gene therapy

A gene therapy conceived by Genethon has been shown to confer long-term efficacy against Wiskott-Aldrich syndrome, an immune deficiency disorder.

Discover
I-Stem, IPSEN & LMN recreate the human muscle-nerve system

A cellular model to recreate the human muscle-nerve system

Researchers from I-Stem, IPSEN and LMN have conceived a cellular muscle-nerve model to test the therapeutic potential of botulinum toxins in vitro.

Discover
Genoscope - CNS - Genopole's laboratory

Filling the gaps in the banana’s genome

Des chercheurs de Genoscope en collaboration avec une équipe du Cirad sont parvenus à reconstituer la séquence intégrale de chromosomes de bananier.

Discover
traitement des plaies diabétiques issu de peau et d’écailles de poissons

CERITD: Treating deep wounds with fish skin

CERITD and the South Île-de-France Medical Center are testing an innovative, natural fish-skin-based treatment for diabetic foot ulcers.

Discover
muscle fiber

Signs of myopathy detected before muscle formation

An I-Stem team has revealed very early embryonic molecular signs of Duchenne muscular dystrophy occurring upstream of muscle development itself

Discover
Neurons representation - Cells affected by CMT

Gene therapy for Charcot-Marie-Tooth disease makes headway

A gene therapy for Charcot-Marie-Tooth disease has been shown to be efficacious in an animal-model study cosigned by a research team created through Genopole support.

Discover
LAST - Makeup by Global Bioenergies

Global Bioenergies launches its makeup brand

Interview with Marc Delcourt, founder and CEO of Global Bioenergies, launches its makeup brand : LAST

Discover
NEB France celebrate 10 years @ Genopole

New England Biolabs France Celebrates 10 Years!

Its French affiliate arrived at Genopole in 2011 and to mark its 10th anniversary in France, the company invites you to participate in monthly activities to be held throughout 2021.

Discover
View all >
With the support from
Région île de France