The oncogenomics platform
This platform allows the detection of alterations of the genome and/or of its expression in tumours for diagnosis purposes as well as for research purposes.
This allows a refined characterization of the tumour and the development of targeted therapies, which show reduced secondary effects and are less harmful to healthy tissues than standard therapies.
Genomic analyses are required for the development of personalized medicine: identifying the treatment which is most adapted to each patient and to each type and each sub-type of tumour.
The oncogenomics platform establishes genomic, gene expression and DNA methylation profiles of various cancers on human pan-genome 244k array CGH (Agilent Technologies, since 2006), U133 Plus 2.0 (Affymetrix), and promotor array (Agilent Technologies), respectively. Mutations are identified by Sanger DNA sequencing.
These facilities have benefited from strong support from local authorities through the Canceropôle PACA programs, French institutions for cancer research and for clinical research in collaborations with the AP-HM, and have allowed the analysis of large clinical series.
Management & contact: Dr Max Chaffanet, François Bertucci & Daniel Birnbaum
Date of creation: 2000
Staff (CRCM and others): 5 MDs, 5 technicians, 1 engineer, 1 bioinformatician students (Master, PhD)
Proteomics and Mass Spectrometry
Proteomics technologies allow the simultaneous (structural and functional) analysis of large sets of protein samples both for medical (diagnosis, prognosis,…) and research purposes.
Since its creation in 2002, the CRCM Proteomics facility has set-up new technologies to study proteomes and to answer the increasing demand in this field. Today, the CRCM Proteomics facility belongs to Marseille Proteomics MaP (Marseille Protéomique). MaP is a four-site proteomics facility, which besides mass spectrometry offers a wide panel of complementary techniques for protein identification and characterization, biomolecule quantification, biomarker discovery, binding studies and bioinformatics services. MaP is labelled IBiSA since its creation in 2008 and offers partnership, collaborative and fee-for-service opportunities for basic and clinical research but also for industry. This structuration led to strengthen expertise in the diverse proteomics field and technologies needed to accompany local, national or international scientific projects.
At CRCM, MaP has specifically set up quantitative based mass spectrometry methods (iTRAQ, label-free, SILAC) for the discovery of biomarkers in clinical proteomics as well as for more fundamental research. Long-time expertise in “Interactomic projects” using affinity purification and mass spectrometry (AP-MS), which led to the discovery of numerous new protein complexes, remained a specificity of our site. We also decipher protein complexes using yeast two hybrid approaches (Y2H).
Others Proteomics approaches as two-dimensional electrophoresis using Differential in-Gel Electrophoresis (2DE-DiGE), chemoproteomics are some technologies that we also propose.
Management & contact: Pr Jean-Paul Borg, Anthony Gonçalvès, Stéphane Audebert, Luc Camoin and Nelson Dusetti
Date of creation: 2002
Staff (CRCM and others): 9.2 FTE ; 1 scientific coordinator, 4 project managers, 4 engineers, 1 technician, 1 Bioinformatics specialist, 1 PhD student and Master students
The CRCM Integrative Bioinformatics platform Cibi
The CRCM Integrative Bioinformatics platform Cibi develops its own tools and maintains an expertise on existing bioinformatics data analysis packages, which is required for the analysis of complex and large data sets. It offers a wide range of expertise ranging from high throughput biological data management, to multi-technology data integration, public repositories data mining (Gene Expression Omnibus, ArrayExpress) and genomics and proteomics data analysis. Its expertise in bioinformatics covers DNA array analysis, ChIP-Chip, Comprehensive Genomics Hybridization (CGH), SNPs, gene interaction networks (human interactome) and proteomics.
Specifically, it offers transcriptome-interactome integration and meta-analysis in the transcriptome (integrated analysis of multiple datasets), using a pipeline developed locally called ITI (Integration-Transcriptome Interactome), available either for unsupervised (version 1.0) or supervised analysis (version 2.0).
For data management, the platform has developed the database Djeen, (Database for Joomla!’s extensible engine). Djeen allows for multi technological data management (CGH-SNPs-DNA microarray, Chip-Chip arrays and Flow Cytometry data) and is specifically designed for clinical/experimental annotation in a high throughput manner.
Cibi offers collaborative and fee-for-service opportunities to help laboratories set up their own Djeen database, and design integrated and cross technological analysis.
Management & contact: Dr Ghislain Bidaut
Date of creation: 2008
Staff (CRCM and others): 2 Engineers
Datacentre IT and Scientific Computing of CRCM (DISC) Platform
The evolution of research through research method "in silico" and not just "in vivo" (test on animals ) or "in vitro" (test performed in the test tube ) , require high-performance infrastructure for computing and storage.
Based on computer simulation or modeling, in silico methods are new methods for testing chemicals. The results of existing tests are used to model to predict and evaluate the properties of chemical substances on the human body and the environment. In this way , it is possible to predict and assess the nature of a particular chemical substance used in a particular context , and without the need for animal testing or living cells .
Benefits of the use of " in silico " methods are potentially huge, because they can reduce animal testing , reduce research costs and delays and production , to test a large number of chemicals , of increase the quality and quantity of information
DISC is the computing and operating centre for scientific data of the CRCM.
Thought primarily as a tool for research, this platform provides a computing environment with strong means and support necessary for the development of new tools and new applications and methods for the development of computing-based scientific projects.
It is also an exchange area, which brings together an established community as well as new players around the computing and exploitation of scientific data at CRCM. DISC is a vital gateway across users and national and international networks related to computing.
The platform services are directed specifically to all engineers and researcher from the CRCM and IPC teams and platform, as well as their collaborators, at the national and international level, but also to industrial partners for their needs in the field of scientific computing.
The networks of partners of the DISC platform are: MobyleNet (Bioinformatics and chemoinformatics tools), ReNaBi (Bioinformatics Computing Grid), ENMR (European Grid computing for computational tools related to NMR, Molecular Modelling, Molecular Docking, …).
In addition to user support, DISC proposes the following services:
- A high-performance computing infrastructure, allowing running and testing applications and codes in conditions of highly parallelized computation.
- An offer of virtualization to quickly deploy specifics computing or development environment.
- Space for the storage and preservation of scientific data.
- Visualization tools for advanced remote displays from personal computers without high performance graphics card.
Management & contact: Bernard Chetrit
Date of creation: 2012
Staff (CRCM and others): 2 engineers
The molecular pathology platform
This joint IPC/AP-HM platform is first dedicated to pathology, that is the morphological and molecular analysis of patient tissue sections both for medical and for research purposes. Accordingly it performs conventional stains on formalin-fixed paraffin embedded samples and immunohistochemistry (IHC).
In addition semi-thin and ultrathin sections can be prepared for electron microscopy, as well as histoenzymology on frozen material. The platform also performs proteome analysis on tissue microarrays (TMA).
More than 5,000 samples with clinical data available are stored in TMA and can be provided for research purposes. Automated computer-assisted quantification of immunoprecipitates is used to allow standardized and objective analysis of IHC results. After image cropping of the slides, automated densitometric measurements of immunoprecipitates in each TMA scores individually. The resulting quantitative data are appropriate for statistical analysis.
In addition molecular studies are routinely performed in order to assess the occurrence of recurrent genetic alterations recorded in solid tumours and leukemia that help to classify them and predict prognostic and therapeutic responses.
Management & contact: Pr Luc Xerri at IPC
Date of creation: 2006
Location: IPC and AP-HM
Staff (CRCM and others): 10 MDs, 20 technicians, 1 quality controller