Clinical Research Group 2 « Genetics of solid tumors »
Pr Florence PEDEUTOUR, PU-PH, Team Leader
The Laboratory of Solid Tumor Genetics was created in 2004 in the context of launch of the first the National Plan Against Cancer. The goal of this creation was to develop a translational activity in the field of genetics of solid tumors.
We are involved both in a clinical activity (affiliation: Nice University Hospital (CHU de Nice) and in a research program (affiliation: IRCAN). Our two main research interests are focused on genetics of soft tissue tumors and renal cell carcinomas, respectively. In addition, we closely interact with the French National Cancer Institute (INCa), the Cancéropôle Provence-Alpes-Côte d’Azur and the French Sarcoma Group (GSF-GETO). We also have a teaching and tutorial activity in oncology and genetics at the Faculty of Medicine of Nice as well as in national courses.
CLINICAL ACTIVITY IN SOMATIC CANCER GENETICS
The 28 French regional platforms were created in 2006 on the behalf of INCa in order to provide molecular tests for diagnosis and for predictive response to personalized targeted drugs (http://www.e-cancer.fr/soins/plates-formes-hospitalieres-de-genetique-moleculaire). Our clinical laboratory belongs to the Platform of Molecular Genetics of Cancers of the eastern part of Provence-Alpes-Côte d’Azur (PACA-est) region (six laboratories including ours; regional coordinator: F. Pedeutour).
Cytogenetic and molecular diagnosis
We provide a comprehensive test panel for diagnosis and evaluation of solid tumors, such as pediatric tumors, tumors of soft tissues and bones, brain tumors, skin tumors or renal tumors. We perform cytogenetic and molecular analyses as complementary tools of histopathological diagnosis, in collaboration with pathologists, surgeons and oncologists. We receive each year more than a thousand fresh, frozen or fixed-paraffin-embedded samples for chromosomal or molecular analyses. Depending on the indication and nature of the biological samples, we do cytogenetic analysis including preparation of karyotypes, metaphase and interphase based fluorescence in situ hybridization (FISH), comparative genomic hybridization based array (CGH array) as well as molecular analysis including mutation detection by RT-PCR, pyrosequencing, real time PCR or Sanger sequencing. The detection of somatic chromosomal alterations such as genomic amplification, translocations, fusion genes, deletions or DNA sequence anomalies such as nucleotide mutations is a powerful ancillary tool for diagnosis of solid tumors and therapeutic management. It helps the distinction between benign and malignant tumors and the recognition of a variety of malignant tumor types or subtypes. In particular, we are expert in the field of molecular diagnoses in sarcomas. Chromosomal analyses are also helpful for evaluation of prognosis (a typical example is the detection of MYCN amplification in neuroblastomas or genomic profiles in choroid melanomas).
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Predictive molecular tests
A part of our clinical activity consists in detection of DNA mutations that are predictive of response or non-response to targeted therapies, such as tyrosine kinase inhibitors or monoclonal antibodies. The main current indications are mutations of KRAS, BRAF, EGFR, ALK, HER2, KIT and PDGFRA in colon cancers, lung cancers, melanomas and stromal gastro-intestinal tumors (GIST).
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CLINICAL RESEARCH PROJECTS
Our research projects are closely related to our clinical activity. We aim: -1) to identify novel chromosomal and genetic anomalies in order to improve classification and diagnosis of solid tumors and -2) to explore the functional consequences of these novel anomalies.
Our current research projects are mainly dedicated to :
Molecular rearrangements and dysregulation of HMGA2 in adipose tissue tumors
Adipose tissue tumors are the most frequent human tumors. They are mainly represented by lipomas that are very common benign lesions. The malignant adipose tumors include three main subtypes, well-differentiated and dedifferentiated liposarcomas, myxoid and round cell liposarcomas and pleomorphic liposarcomas. The current challenges for improving the surgical and therapeutic management of adipose tumors are identification of novel diagnostic and prognostic markers as well as of therapeutic targets.
Strikingly, it can be noted the high frequency of rearrangements of chromosome 12 long arm (12q). Indeed, chromosomal anomalies in lipomas mainly involve structural balanced and non-balanced alterations of chromosome 12 long arm in the region of HMGA2 (12q14.3) whereas amplification of the 12q14-15 region including MDM2 is the hallmark of well-differentiated/dedifferentiated liposarcomas and rearrangements of DDIT3 (12q13.3) are characteristic of myxoid liposarcomas. We have shown that HMGA2 is rearranged not only in lipomas but is also recurrently amplified in well-differentiated/dedifferentiated liposarcomas (Italiano et al., 2008 and 2009). We also recently reported the first observation of overexpression of HMGA2 in a unique case of lipomatosis (Saada et al., 2012). We therefore hypothesize that HMGA2 is a key gene in adipose lesions and tumors. We have shown that HMGA2 overexpression in lipomas is not always associated to chromosome 12q anomalies and is not significantly correlated to inhibition of let7 miRNA expression (Bianchini et al., 2011). Our aim is to understand the complex mechanisms of dysregulation of HMGA2 and how these alterations contribute to adipose tissue pathogenesis.
Genomic characterization of renal cell carcinomas
Renal cell carcinomas (RCC) account for approximately 10 500 novel cases/year in France and are responsible of the death of 4000 patients/year. The last World Health Organization (WHO) classification describes ten types of RCC, the most frequent of which are clear cell RCC followed by papillary RCC and chromophobe RCC. A precise and reliable histopathological typing of RCC is crucial since survival and response to treatment is variable from one type to another. Notably, since 2006 treatment of clear cell RCC has dramatically benefited from the use of targeted antiangiogenic molecules. However diagnosis of RCC is often difficult and approximately 15% of cases remain “unclassified”. Though some correlations between histology and genetics have been well established (for instance, deletion of VHL gene at 3p25 in clear cell RCC, trisomy 7 and 17 in papillary RCC or hypodiploidy in chromophobe RCC), programs of exploration of genomic and molecular profiles of RCC are necessary to improve our knowledge of these tumors. To note, a particular subtype, RCC with Xp11 translocation and rearrangement of TFE3 has been individualized thanks to chromosomal studies.
Since 2005 we have established a collaboration with the departments of Urology (PR Amiel) and the central laboratory of pathology (Pr Michiels) of Nice university hospital. We have karyotyped all RCC operated in the urology department (50/year). We have extended the chromosomal analyses by combining additional immunohistochemistry, FISH and array-CGH analysies. We have focused our research on two types of morphologically challenging RCC: RCC with Xp11 translocation and type 2-papillary RCC. Our aim is to use genomic tools to provide a better characterization of unclassified and rare subtypes of RCC.
" Identification of novel genetic markers in renal tumors "
Diagnosis and treatment of renal cancer : a major issue
The management of renal cell carcinoma (RCC) is a major health issue. Both the incidence of metastatic disease at the time of initial diagnosis and the rate of mortality are high. The diagnosis of RCC is based on morphological, immunohistochemical and genetic features. The classification of the World Health Organization (WHO) lists ten types of renal cell tumors. Clear cell RCC (ccRCC) and papillary RCC (pRCC) are the most frequent types. Genetic analysis of RCC is of great diagnostic use and helps for understanding the pathogenesis of these tumors. The therapeutic management of patients has been improved by genetic data in ccRCC. Indeed, it is well established that the VHL gene is inactivated in ccRCC. This inactivation results in tumor angiogenesis through the HIF/VEGF pathway and is the basis of the development of anti-angiogenic therapies to treat metastatic disease. We believe that the genetic characterization of pRCC might result in assessment of personalized treatments. pRCC classically show a gain of chromosomes 7 and 17 and loss of the Y chromosome (Figure 1). Moreover, approximately 10% of sporadic pRCC present mutations in the MET gene (Figure 2).
Figure 1 :Characteristic quantitative genomic profile of a papillary renal cell carcinoma showing a gain of chromosome 7 and 17 and a loss of chromosome Y (▼), additional anomalies are also present (▼).
Figure 2 :Reverse-direction sequencing of the exon 16 of the MET gene. A point mutation c.3334C>T ; p.His1112Tyr (*)is observed. Mutations within exons 14 to 19 of MET are observed in approximately 13% of papillary renal cellcarcinoma of type 1.
Since 2005, in collaboration with the Department of Urology (Pr Amiel) and the Central Laboratory of Pathology (Pr Michiels), renal tumors operated at the University Hospital of Nice have been systematically studied by molecular cytogenetic methods. We also established a collaboration with the Department of Pathology of Princess Grace Hospital in Monaco (Dr Dupré). Our approach combines comparative genomic hybridization on microarray (array-CGH), fluorescence in situ hybridization (FISH), conventional karyotyping and targeted sequencing. In collaboration with the genomic platform of IRCAN (team leader G. Cristofari), we also integrate targeted high-throughput sequencing.
Our aim is to identify new genetic markers of renal tumors, useful for diagnosis and treatment. We are particularly interested in "unclassified" tumors such as tumor combining several types of RCC (1,2,3,4) or challenging diagnosis tumors such as pRCC type 2. We hypothesize that the entity pRCC of type 2 is actually a heterogeneous group of tumors. Some pRCC type 2 derive from pRCC type 1 while some may correspond to distinct origin. In addition, some rare benign renal tumors can be difficult to diagnose correctly and would benefit from a better genetic characterization. This is the case of metanephric adenomas (4). We are also interested in studying genetic factors of predisposition to RCC (5).
References and publications
(1) Haudebourg J, Hoch B, Fabas T, Burel-Vandenbos F, Carpentier X, Amiel J, Cardot-Leccia N, Michiels JF, Pedeutour F. A novel case of t(X;1)(p11.2;p34) in a renal cell carcinoma with TFE3 rearrangement and favorable outcome in a 57-year-old patient. Cancer Genet Cytogenet. 2010;200(2):75‑78.
(2) Haudebourg J, Hoch B, Fabas T, Cardot-Leccia N, Burel-Vandenbos F, Vieillefond A, Amiel J, Michiels JF, Pedeutour F. Strength of molecular cytogenetic analyses for adjusting the diagnosis of renal cell carcinomas with both clear cells and papillary features: a study of three cases. Virchows Arch. 2010;457(3):397‑404.
(3) Calderaro J, Moroch J, Pierron G, Pedeutour F, Maillé P, Soyeux P, de la Taille A, Couturier J, Vieillefond A, Rousselet MC, Delattre O, Allory Y. SMARCB1/INI1 inactivation in renal medullary carcinoma, Histopathology, 2012, 61:428-35.
(4) Dadone B, Ambrosetti D, Carpentier X, Duranton-Tanneur V, Burel-Vandenbos F, Amiel J, Pedeutour F. A renal metanephric adenoma showing both a 2p16-24 deletion and a BRAF V600E mutation: a synergistic role for a tumor suppressor gene on chromosome 2p and BRAF activation? Cancer Genet. Sous presse
(5) Doyen J, Carpentier X, Haudebourg J, Hoch B, Karmous-Benailly H, Ambrosetti D, Fabas T, Amiel J, Lambert JC, Pedeutour F. Renal cell carcinoma and a constitutional t(11;22)(q23;q11.2): case report and review of the potential link between the constitutional t(11;22) and cancer. Cancer Genet. 2012;205(11):603‑607.
Research Team IRCAN :
Hospital Team (Hospital Center of Nice) :
DELLE MONACHE Véronique, ASH
DURANTON-TANNEUR Valérie, Ingénieur Biologiste
Tel : +33 (0)4 93 37 70 12