Involved group members: Miikka Vikkula, Nisha Limaye, Mustapha Amyere, Pascal Brouillard, Hélène Antoine-Poirel
(Collaboration with Catherine Godfraind)
Elucidating molecular processes associated to tumor’s development, or genetic anomalies related to their diagnosis or prognosis, is an on-going process needed for their understanding and characterization. It is also a required step for further improvement of patient’s treatment. Such analyses were undergone with various tumor types:
- Oligodendrogliomas, a brain tumor mostly affecting adults.
We related the now classical 1p/19q co-deletion to a histological glioma aspect, but also linked additional genetic anomalies to pathological features associated to ologodendroglioma’s WHO grades (NAN 2003e:29;462-71).
- Ependymomas, a brain tumor occurring at all ages.
By studying methylation status of the 9p21 tumor suppressor genes (NAN 2003e:29;574-83) as well as other genetic anomalies (Molecular cancer 2007e:6;47) including gene expression profiles (Cancer 2009e:115;3955-68), one’s demonstrated ependymomas to bear specific genetic alterations according to tumor locations and patient ages. Being distinct genetic tumors with similar histology could account for the lack of prognostic value of the actual WHO grading system as one’s uses similar features for all of them (Childs Nerv Syst 2009e:25;1185-93 ; J Negat Results Biomed. 2011 May 31;10:7). Amplification of 1p was demonstrated as a biomarker of prognosis, but only in children and in the posterior fossa (Acta Neuropathol. 2012 Aug;124(2):247-57).
- Ocular melanomas, the most frequent intra-ocular malignant tumor in adults.
Part of ocular melanomas, similarly to cutaneous ones, bears an immune infiltration. At the contrary to cutaneous lesions, it is of bad prognosis significance, meanwhile related to IFN-gamma pathway (D. Narashihama et al, in preparation). The prognostic value of the latter was demonstrated to be less effective then an association of four distinct genetic anomalies amongst which, the well recognized, monosomy 3 (D. Narashihama et al, in preparation).
- Godfraind C, Rousseau E, Ruchoux MM, Scaravilli F, Vikkula M. Tumour necrosis and microvascular proliferation are associated with 9p deletion and CDKN2A alterations in 1p/19q-deleted oligodendrogliomas. Neuropathol. Appl. Neurobiol. 2003; 29(5):462-71.
- Rousseau E, Ruchoux MM, Scaravilli F, Chapon F, Vinchon M, De Smet C, Godfraind C, Vikkula M. CDKN2A, CDKN2B and p14ARF are frequently and differentially methylated in ependymal tumours. Neuropathol. Appl. Neurobiol. 2003; 29(6):574-83.
- Rousseau E, Palm T, Scaravilli F, Ruchoux MM, Figarella-Branger D, Salmon I, Ellison D, Lacroix C, Chapon F, Mikol J, Vikkula M, Godfraind C. Trisomy 19 ependymoma, a newly recognized genetico-histological association, including clear cell ependymoma. Mol. Cancer 2007; 6:47.
- Palm T, Figarella-Branger D, Chapon F, Lacroix C, Gray F, Scaravilli F, Ellison DW, Salmon I, Vikkula M, Godfraind C. Expression profiling of ependymomas unravels localization and tumor grade-specific tumorigenesis. Cancer 2009; 115(17):3955-68.
- Godfraind C. Classification and controversies in pathology of ependymomas. Childs Nerv. Syst. 2009; 25(10):1185-93.
- Ellison DW, Kocak M, Figarella-Branger D, Felice G, Catherine G, Pietsch T, Frappaz D, Massimino M, Grill J, Boyett JM, Grundy RG. Histopathological grading of pediatric ependymoma: reproducibility and clinical relevance in European trial cohorts. J. Negat. Results Biomed. 2011; 10:7.
- Godfraind C, Kaczmarska JM, Kocak M, Dalton J, Wright KD, Sanford RA, Boop FA, Gajjar A, Merchant TE, Ellison DW. Distinct disease-risk groups in pediatric supratentorial and posterior fossa ependymomas. Acta Neuropathol. 2012; 124(2):247-57.
(Collaboration with Alexandre Persu)
Pheochromocytomas and paragangliomas (PPGL) are neuroendocrine tumours arising from the adrenal medulla, and the extra-adrenal sympathetic and parasympathetic paraganglia, respectively. Pheochromocytomas and sympathetic paragangliomas are characterized by increased secretion of catecholamines and paroxystic hypertension. By contrast, parasympathetic paragangliomas are located in the head and neck region, and are usually non-secreting but can extend to vessels and nerves. One of the current project aims to look at the nature and frequency of mutations in the known predisposing genes in pheochromocytoma, paraganglioma, and to detect possible genotype-phenotype correlations. A multicentric collaboration including more than 20 hospitals from Belgium has therefore been established. Clinical information and DNA from >200 patients with pheochromocytoma and paraganglioma have been obtained. We are now focusing on second hit events, especially on somatic mutations, which would explain the development of the tumour, but also phenotype variability. Up to now, we have DNA from about 100 paraffin embedded or frozen tumours that we are sequencing for the 17 known genes with the Ion Torrent technology.
We are also studying the malignancy of PGL, in collaboration with Winand Dinjens’s laboratory in Erasmus Medical Center, Rotterdam. Using mRNA expression array, qRT-PCR, and immunohistochemistry, we identified a protein that is overexpressed in malignant PPGL, and could then be used as a predictive marker. It is the first time that such a potential marker was found. We are now performing functional assays to investigate the role of this protein in the malignant progression if the tumours.
- Persu A, Hamoir M, Grégoire V, Garin P, Duvivier E, Reychler H, Chantrain G, Mortier G, Mourad M, Maiter D, Vikkula M. High prevalence of SDHB mutations in head and neck paraganglioma in Belgium. J. Hypertens. 2008; 26(7):1395-401.
- Persu A, Amyere M, Gutierrez-Roelens I, Rustin P, Sempoux C, Lecouvet FE, Van Beers BE, Horsmans Y, De Plaen JF, MarcHamoir, Vikkula M. Rare presentation of familial paraganglioma without evidence of mutation in the SDH, RET and VHL genes: towards further genetic heterogeneity. J. Hypertens. 2009; 27(1):76-82
- Yao L, Schiavi F, Cascon A, Qin Y, Inglada-Pérez L, King EE, Toledo RA, Ercolino T, Rapizzi E, Ricketts CJ, Mori L, Giacchè M, Mendola A, Taschin E, Boaretto F, Loli P, Lacobone M, Rossi GP, Biondi B, Lima-Junior JV, Kater CE, Bex M, Vikkula M, Grossman AB, Gruber SB, Barontini M, Persu A, Castellano M, Toledo SP, Maher ER, Mannelli M, Opocher G, Robledo M, Dahia PL. Spectrum and prevalence of FP/TMEM127 gene mutations in pheochromocytomas and paragangliomas. JAMA 2010; 304(23):2611-2619.
- Evenepoel L, Papathomas TG, Krol N, Korpershoek E, de Krijger RR, Persu A, Dinjens WN. Toward an improved definition of the genetic and tumor spectrum associated with SDH germ-line mutations. Genet. Med. 2014; doi: 10.1038/gim.2014.162.
- Papathomas TG, Oudijk L, Persu A, Gill AJ, van Nederveen F, Tischler AS, Tissier F, Volante M, Matias-Guiu X, Smid M, Favier J, Rapizzi E, Libe R, Currás-Freixes M, Aydin S, Huynh T, Lichtenauer U, van Berkel A, Canu L, Domingues R, Clifton-Bligh RJ, Bialas M, Vikkula M, Baretton G, Papotti M, Nesi G, Badoual C, Pacak K, Eisenhofer G, Timmers HJ, Beuschlein F, Bertherat J, Mannelli M, Robledo M, Gimenez-Roqueplo AP, Dinjens WN, Korpershoek E, de Krijger RR. SDHB/SDHA immunohistochemistry in pheochromocytomas and paragangliomas: a multicenter interobserver variation analysis using virtual microscopy: a Multinational Study of the European Network for the Study of Adrenal Tumors (ENS@T). Mod. Pathol. 2015; doi: 10.1038/modpathol.2015.41.
Hematological Malignancies and Tumors of Soft Tissue and Bone
(Nisha Limaye, Hélène Antoine-Poirel)
The explosion in the identification of genetic biomarkers of hematological malignancies and tumors of soft tissue and bone over the past 20 years has had significant impact on diagnosis, prognosis and treatment, as well as our understanding of the genetic and epigenetic processes that lead to tumorigenesis. Our aim is to characterize genomic alterations in both types of malignancy because their oncogenic mechanisms exhibit significant similarities. Towards this end, we use a variety of techniques including conventional and molecular cytogenetics or FISH, molecular biology, and microarrays to identify partner genes in reciprocal translocations and study their functional consequences. We characterized new partner genes of known multipartner genes MLL/11q23, ABL/9q34, PDGFR/5q33, and USP6/17p13, as well as unknown partner genes. We demonstrated that the functional consequences may be more complex than transcriptional dysregulation by promoter-swap of fusion genes.
In an international therapeutic trial of children with mature B-cell lymphomas, we showed the adverse prognostic impact of chromosomal alterations of 13q and 7q, detected by cytogenetics. Using genome-wide SNP array technology, we found that most 13q alterations lead to an amplification of the microRNA 17-92 cluster, known to interact with the MYC oncogene, a finding confirmed with mature miRNA expression profiling. In addition, we detected numerous cryptic genomic alterations including partial uniparental disomies. Their prognostic value is currently under study in collaborations within different therapeutic trials across Europe.
(Mustapha Amyere, Collaboration with François Duhoux)
According to the Belgian Cancer Registry, one out of nine women in Belgium will develop breast cancer in her lifetime. It remains the first cause of death from cancer among women. A family history of breast cancer is one of the most important risk factors for the development of the disease. Indeed, individual risk increases proportionally with the number of affected relatives. Around 10% of all breast cancers are associated with a strong inherited component (hereditary breast cancers). An estimated additional 15-20% of patients affected with breast cancer will have a positive family history of breast neoplasia (one or more first- and/or second-degree relatives). Therefore, taking these numbers together, a risk linked to a positive familial history is present in approximately 20-25% of all breast cancer cases.
BRCA1 and BRCA2, two tumor suppressor genes involved in DNA repair, are the most commonly mutated genes, accounting for at least 30% of all hereditary breast cancers. In the general population, one of out 500 is carrying a germline mutation in one of these high penetrance genes, which increases their risk of presenting a breast cancer 10 to 20-fold. A carrier of a constitutional BRCA1 abnormality has a lifetime risk of breast cancer around 70%. For BRCA2, the lifetime risk is around 50%.
Next generation sequencing is an efficient method to find genetic alterations explaining monogenic diseases but also diseases with high degree of genetic heterogeneity. We are using whole exome sequencing to identify new genes for BRCA1/2-negative breast cancer.