Diagnosis and monitoring:

The cancer biology unit is the site of the regional (Poitou-Charentes) platform for the molecular genetics of cancer; it has been awarded the labels of the French health care directorate general (DGOS) and the French national cancer institute (Inca). Clear evidence of the current importance of personalized medicine led l‘Institut national du cancer to the realization, in 2006, that existing platforms needed to establish as a priority the development, in all regional cancerology centers, of an “identity card” for different tumors. Large-scale objectives, they have been formulated as follows:

Mesure 21: As a general rule, to guarantee equal access to treatments and innovations.

Action 21.2: More specifically, to develop platforms for the molecular genetics of cancer with access to molecular tests.

Labelled in 2006, our platform covers a population base, according to the 2017 census, of  1,807,865 inhabitants.

Personalized medicine is the possibility, for a given patient, to obtain his or her molecular profile: search for the mutations, translocations, fusion transcripts of his or her tumor, the objectives being identification of the anomaly/ies responsible for the activation of a signaling pathway essential to survival of the tumor and subsequent proposal, with regard to the anomaly, of targeted therapy. The therapeutic choice will consequently be based on identification of the anomaly or bio-marker.

The laboratory consists in two medical units (MU):

Medical molecular oncology unit  (Pr L. Karayan-Tapon).

Medical molecular oncology and hematology unit (Dr J.-C. Chomel).

Activity in 2019 8.7M  B/BHN a year.

Laboratory technical environment

The service has a complete molecular biology equipment (extraction of nucleic acids robot, PCR and PCR in real time machines, pyrosequencing device, capillary sequencers, CGH array, Access array, IlluminaMiSeq, et NextSeq, digital PCR…). It also has data analysis and interpretation softwares (GeneMapper, Chromas, Pyromark, Mutation Surveyor, Alamut …) to run molecular tests that allow molecular treatment for cancer patients.

The following technologies have been developed in the laboratory:

• Extraction of nucleic acids (genomic DNA and total RNA) from different biological samples (blood, bone marrow,  ganglions, tumor, pleural liquids), paraffin sections and frozen tissue.
• Control and dosing of nucleic acids.
• Reverse transcription.
• Characterization of mutations by high throughput sequencing.
• Search for known point mutations by allele-specific PCR RFLP, PCR , allele-specific PCR in real time.
• Search for mutations by DGGE.
• Characterization of mutations by pyrosequencing
• Characterization of mutations by direct double-stranded sequencing.
• Mutant allele assay by quantitative PCR in the presence of a standard range of plasmids.
• Fusion transcript assay by quantitative RT-PCR in presence of a standard range of plasmids (evaluation of residual disease).
• FISH on paraffin-embedded tissue for cytogenetics of solid tumors.
• Digital PCR to search for circulating tumoral DNA
• CGH array

Molecular tests run in the cancer biology laboratory

Solid tumors :

• RAS, BRAF or INCa panel mutations detection in colorectal cancers
• EGFr or INCa panel mutations detection in lung cancers
• c-KIT and PDGFr or INCa panel mutations detection in digestive system cancers
• Detection of 1p19q codeletion, IDH1 and IDH2 mutations, and MGMT methylation in gliomas.
• BRAF detection in thyroid tumors
• BRAF and c-KIT mutations detection in melanomas
• FIXL2 mutations detection in ovarian tumors
• ALK, ROS1 rearrangement detection in lung cancers
• HER2 amplification detection in breast and stomach cancers
• BRCA1 and BRCA2 mutations detection in ovarian cancers
• molecular signature research in breast cancers (“Endoprédict”)
• RNAseq (NTRK1,2,3) rearrangement research

Oncology and hematology :

• molecular rearrangement detection during diagnosis in acute myeloid and lymphoid leukemia, MPD neoplasias and non-Hodgkin’s malignant lymphoma.
• molecular monitoring for acute leukemia and MPD syndroms after treatment by conventional therapy, targeted therapy or hematopoietic stem cells allograft.
• tyrosine kinase inhibitors resistance study in BCR-ABL positive leukemia.
• mutations NGS highlight in acute myeloid leukemia
• NGS preliminary analysis of chronic lymphoid leukemia before targeted treatment.

Pedagogical project

One of the major present-day priorities in cancerology is improved knowledge of applied cancer biology. Indeed, organization of personalized medicine in cancerology necessitates not only “true” general knowledge of the routes of carcinogeneis, but also specific knowledge of the cancer biology of a given organ with the highlighting of driver genes and the functional disruptions arising from the ensuing oncogene addiction. Treatment of cancer patients is multidisciplinary, and the  cancer biology teaching necessitates a multidisciplinary approach.

It is important, given today’s evolution in cancer biology, to train professionals with competence in the biology of cancer, specifically as regards biological validation of health-oriented somatic gene examinations.  Validation analyses are presently carried out on resection specimens for solid tumors, and also in blood, bone marrow and lymph nodes for malignant hemopathies. In the coming years these diagnostic, prognostic and theranostic tests will evolve and will probably involve biological liquids: circulating DNA/RNA, circulating cancer cells…

Professional tasks require molecular cancer diagnosis skill. Interns must learn :

• cancerogenesis fundamentals and mecanisms
• organs and tissues particularities in bio-cancerology (tumors integrated biology)
• molecular biology theoretical fundamentals (nuclear and proteinic acids) and analysis technics and tools theoretical fundamentals in molecular biology.

On this basis, the laboratory is a formation privileged place for specialized biology interns (molecular medecine, tumors somatic genetics, solid tumors cytogenetic), but also for medical oncology and molecular pathology.

Participation in the activities of cooperating groups:  Cancéropôle GO, INCa, ANOCEF

Supervising university unit:  Cancerology –Radiotherapy 4702

Towards targeted cancer treatment
CHU Magazine n°63 – December 2011