The Paris Cancer Institute CARPEM institute oncogenetics program is run by a multidisciplinary team composed by geneticists, genetic counsellors, psychologists and/or psychiatrist, gastroenterologists, oncologists, endocrinologists, dermatologists, molecular geneticists and pathologists.
Major objectives are :
1) to inform patients affected by frequent or rare tumors and to propose genetic testing when appropriate;
2) to identify constitutional pathogenic variants;
3) to propose recommendations for specific management and surveillance in accordance with specialists of the main organs involved (see screening program);
4) to offer predictive genetic counselling to the relatives of patients with a hereditary predisposition.
To be easily accessible to patients of both sites, the oncogenetics program is taking place into two oncogenetics clinics located at HEGP and CCH.
This clinic, labeled by the French National Cancer Institute (INCa) from 2002, performed 2353 consultations in 2018. Taking account of the incidence of different cancers, a broad offer of genetic counselling is proposed to at-risk patients and their relatives, managed at hEGP or CCH, with a suspicion of hereditary breast and ovarian or prostatic cancers as well as for those with a suspicion to a genetic predisposition to colorectal cancers on both sites. In total four different physicians (1 geneticist: P. Laurent-Puig; 3 gastroenterologists: G. Perkins, A. Zaanan, M. Dhooge) and three genetic counsellors are involved (D. Molière A-M. Birot, S Farelly). Regarding rare cancers and/or rare tumors, a dedicated geneticist and a genetic counsellor (A-P. Gimenez Roqueplo, A-M. Birot) are available in the genetic consultation of HEGP whereas different specialists, but graduates in oncogenetics, are available at CCH in Endocrinology department (for neuroendocrine tumors, A Jouinot, G Assié, J Bertherat), in Oncology department (for sarcomas, C Tlemsani) and in Dermatology department (for melanomas and other skin tumors, JC Chanal and S Guegan). Psychiatrist (K. Lahlou-Laforet) or psychologist (I. Molley-Massol) is available on both sites.
For frequent cancers, our oncogenetics physicians are part of regional support network helping patients with hereditary predisposition to frequent cancer to improve their follow-up: the PRED-IdF network, for patients with predisposition to digestive tract cancer, and the SAR network, for patients with predisposition to breast and ovarian cancer.
We are also part of a regional committee of digestive oncogenetics, for the collegial discussion of difficult cases of suspicion of predisposition to digestive tracts cancer syndroms , gathering genetics counsellors and oncogeneticists from Ile de France (CODIF : Comité d’Oncogénétique Digestive d’Ile de France).
Genetic tests are carried out in the molecular genetic laboratories of both sites that analyzed 2062 patients at germline level in 2018. Constitutional tests are mainly based on next generation sequencing with dedicated panels developed by a unique laboratory. We have implemented at Cochin laboratory (N. Hamzaoui, E. Pasmant) the NGS analysis of consensus panels of cancer genes with clear clinical utility for hereditary colorectal cancer syndromes (APC, BMPR1A, CDH1, EPCAM, MLH1, MSH2, MSH6, MUTYH, PMS2, POLD1, POLE, PTEN, SMAD4 and STK11) and hereditary breast and ovarian cancer syndromes (BRCA1, BRCA2, PALB2, TP53, CDH1, PTEN, RAD51C, RAD51D, MLH1, MSH2, MSH6, PMS2 and EPCAM) that have been recommended by the GGC-Unicancer group. Cochin laboratory (N. Hamzaoui, E. Pasmant) has also developed specific multigene panels for hereditary pancreatic cancer and hereditary prostate cancer. Cochin and HEGP laboratories developed specific NGS panels dedicated to rare tumor predisposition syndromes including neuroendocrine tumors (N. Burnichon, A. Buffet, MO. North), renal cancers (N. Burnichon), neurofibromatosis type 1 (D. Vidaud, E. Pasmant), and neurofibromatosis type 2 and schwannomatosis (B. Parfait).
MOLECULAR TUMOR BOARD
The geneticists involved in this program participate to the CARPEM Institute multidisciplinary molecular tumor board, reassembling physicians with varying expertise, organized twice by month. Results from NGS panel tests or exome and /or RNA sequencing are discussed. The incidental germline variations are evaluated and discussed, and patients are then quickly referred to a genetics consultation. Germline results are explained to the patients by geneticists.
Three members of our board (Anne-Paule Gimenez-Roqueplo, Eric Pasmant, Pierre Laurent-Puig) are directors of different INSERM research teams, located at the PARCC, the Cochin Institute, and the Cordeliers research centers, that tackle both basic and translational science in oncology with human genetics, biomarker identification, and innovative therapeutic proof-of-concept in using cutting-edge technologies. This proximity between basic and clinical research grandly helps the prompt transfer of innovations from bench to beside and the development of translational research projects which are promptly endorsed by all the oncogenetics team.
Our clinical research programs are mainly based on collections or registries developed on site. For instance, rare adrenal tumors are the main focus of the French COMETE network funded in 1993 and currently led by AP Gimenez-Roqueplo. This network, firstly centred at HEGP and Cochin, organizes clinical and biological sample collection at national level and was the support of numerous research studies (3 PHRC, 1 PRTK). Thanks to this invaluable collection of such rare cancers considerable progresses were made. Notably, the APGR’s team demonstrated that pheochromocytoma and paraganglioma (PPGL) are the cancers the most impacted by the genetics (78% of the PPGL COMETE collection was explained by germline or somatic genetic alterations) and led a gene discovery program allowing the identification of three different PPGL susceptibility genes in patients enrolled in the COMETE collection, the last one is SLC25A11(Buffet, Cancer Res, 2018). A custom PPGL multi-gene panel for NGS assay for both germline and tumor DNA screening has been developed at HEGP and validated retrospectively and prospectively with 824 DNAs of the collection. This NGS assay was certified by the French Committee for Accreditation (standard EN ISO 15189: 2012) and used in routine practice (Benaim, J Med Genet, 2019). Recently, we demonstrated with a national retrospective multicentre clinical study that the knowledge of the germline SDHx or VHL mutation status at the time of diagnosis has a positive impact in the management and outcome of patients and definitely sustained the US and EU recommendations which stated that all patients with PPGL should benefit from a genetic counselling and a genetic test by NGS (Buffet, J Clin Endocrinol Metab, 2019). The French registry for SDHx-related PPGL (PGL.R), which is managed at HEGP, is currently the support of a clinical study dedicated to test the hypothesis that environmental factors, such as succinate dehydrogenase inhibitors widely used as pesticides, may trigger tumor development in SDHx mutation carriers. PGL.R is also the support of clinical research studies dedicated to establish screening protocols in mutation carriers (Gravel, Eur Radiol, 2016).
Another clinical research program is dedicated to neurofibromatosis type 1 and type 2 (NF1 and NF2), two complex tumor-predisposition disorders showing inter-individual variations in the timing of the clinical manifestations and the severity of features. Thanks to 3 consecutive national funding (PHRC: 2002, 2005, and 2010), a large NF1 cohort (>1,500 NF1 patients) was built in France in collaboration with Pr. Wolkenstein (Paris Est Créteil University). Based on the NF-France cohort analysis, we provided evidence that genetic modifiers, unlinked to the NF1 locus, contributed to NF1 variable expressivity. Taking advantage of the NF France cohort, we are conducting an association study at the genome wide level (E. Pasmant). For each NF1 patient, the phenotype was recorded using a standardized questionnaire (eCRF) and the NF1 genotype was determined using a dedicated NGS panel developed at the Cochin hospital (Pasmant, Eur J Hum Genet, 2015). This GWAS project is carried out in collaboration with the French National Genotyping Center (director: Jean-François Deleuze).
We developed 2 types of clinical research in frequent tumors: interventional and observational.
We participate to the conception of a trial testing the effect of chemoprevention by low-dose aspirin of new or recurrent colorectal adenomas in patients with Lynch syndrome (AAS Lynch trial) which evaluate the effect of aspirin in Lynch syndrome patients (NCT02813824). The main hypothesis to be tested is that aspirin could decrease colorectal adenoma recurrence evaluated during high quality follow-up by colonic chromo-endoscopy in Lynch syndrome patients. Two hundred eighty-eight patients out of the 850 were included and our center included 29 patients in the first year leading it to the top 3 participating centers.
We recently conducted a study (NCT02570516) comparing two techniques of colonoscopy in Lynch syndrome patients: the indigo carmin chromoendoscopy (ICC) and the narrow-band imaging (NBI), a virtual chromoendoscopy technique. These two technics were compared in a multicenter trial for detecting colonic adenomas in patients with LS. We were unable to demonstrate the noninferiority assumption of NBI compared with combined NBI and ICC. Although less time consuming, colonoscopy using the third-generation NBI cannot be recommended to replace ICC in patients with LS (Cellier et al. Am J Gastroenterol2019).
Compared to sporadic colorectal cancer, only very few studies have assessed nutritional habits of patients with Lynch Syndrome, and the influence of these nutritional factors on familial colorectal cancer: except for smoking habits and adiposity, which both seem to increase the risk of colorectal tumors in Lynch syndrome, other lifestyle factors, such as physical activity, alcohol or diet have not or only scarcely been studied. To better inform subjects with Lynch Syndrome on factors that could effectively reduce their risk of developing colorectal cancer, there is a need to closely evaluate their dietary behavior and to understand the role of lifestyle behaviors, especially dietary factors. We invite patients with LS to participate to the The NutriNet-Santé program a web-based cohort launched in 2009 in France with the objective of studying the associations between nutrition and health, as well as the determinants of dietary behaviors and nutritional status. This will allow us to determine which are the dietary behaviors adopted by lynch syndrome patients.
We included all the families and individuals identified with a Lynch syndrome in our institution into the French Observatory for the Lynch Syndrome, OFELy, a national clinical and biological base dedicated to research on Lynch syndrome.
The first integrative multi-omics analysis in PPGL has classified this tumor into 5 different molecular entities mainly driven by distinct germline and/or somatic mutations in cancer susceptibility genes. This analysis has revealed the importance of driver mutations in the molecular signature and the biomarkers newly identified have been transferred for routine diagnosis (Castro-Vega, Nat Commun 2015). These data have paved the way towards the establishment of precision medicine strategies for PPGL patients reinforced by set-up a translational research program entitled “The COMETE-network, towards an easy-to use adrenal cancer/tumor identity card” funded by the INCa. New biomarkers able to predict tumor aggressiveness, including lncRNAs (Job, Endocr Rel Cancer, 2019), miR signature (Calsina, Theranostics, 2019) and tumoral SDHB-independent risk factors for malignancy (Job, Clin Can Res, 2019), were validated. All those new biomarkers have demonstrated their prognostic value and are ready to be measured in routine practice. The next step will be to evaluate whether the analysis of tumor biomarkers can be complemented by analyses of liquid biopsies for the diagnosis, prognosis and follow-up of patients.
Main of the tumorigenic effects related to SDHx mutations are linked to the succinate accumulation which acts as an oncometabolite. A method of noninvasive detection of succinate by in vivo 1H-MRS was developed as specific biomarker of SDHx mutation in mouse model of Sdhb-deficient tumours. The sequence was then successively transferred into the radiology department of HEGP to prospectively assess its diagnostic performances of the sequence for the identification of SDH deficiency in PPGL. Sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of 1H-MRS SUCCES were respectively assessed to 87%, 100%, 100%, 90%, and 94% allowing to conclude that detection of succinate using 1H-MRS is a highly specific and sensitive hallmark of SDH-deficiency in PPGL (Lussey-Lepoutre, Eur J Nucl Med Mol Imaging, 2019)
Patients affected by neurofibromatosis type 1 have an increased risk for malignant and non-malignant tumors compared with the general population. Neurofibromas are one of the major clinical features of NF1. They are benign peripheral nerve sheath tumors which consist in a proliferation of Schwann cells showing somatic inactivation of the NF1 WT allele. The malignant transformation of neurofibromas into MPNSTs (Malignant Peripheral Nerve Sheath Tumors) is the leading cause of death in NF1 patients. In 2014, we demonstrated for the first time that PRC2 (Polycomb Repressive Complex 2) played a key role in the development of NF1-associated MPNSTs, in an international collaborative study (De Readt, Nature, 2014). PRC2 is involved in maintaining transcriptional repression. EZH1/2, the catalytic PRC2 components, function as histone methyltransferase that di- and tri-methylates lysine 27 on histone 3. Recently, we investigated whether the absence of EZH2 mutations in MPNST is due to a PRC2 noncanonical function of the enzyme or to redundancy with EZH1. Through genetic and pharmacological analyses, we showed that EZH2 has no PRC2-independent function and we provided evidence that the compensatory function of EZH1 explained the tumor-type specific mutation patterns of PRC2 in MPNSTs (Wassef, Proc Natl Acad Sci U S A, 2019). We now aim to identify vulnerabilities associated with PRC2 mutations with two approaches: chemical and genetic screen.
NF1 somatic alterations are also found in sporadic cancers. Several studies showed that NF1 somatic mutations are found with a frequency at around 5% considering all subtypes of cancers. Lung cancers belong to cancers with frequent NF1 somatic mutations according TCGA data. We confirmed that 18% of lung adenocarcinoma samples harbored NF1 somatic mutations in a cohort of 154 patients from HEGP using targeted NGS. We were also able to establish a genotype-phenotype correlation (Tlemsani Cancer Med2019). This work has been done thanks to a SIRIC CARPEM funding. Following these results, we developed cell models of NF1 mutated using the CRISPR-Cas9 system. We showed that NF1 loss-of-function triggered RAS-MAPK pathway activation. Homozygous NF1 mutated cells seemed to be more aggressive in vitrocompared to heterozygous and wild type mutated cells. In vitro pharmacological screens showed that only homozygous NF1 mutated cells are sensitive to MEK inhibitors. In order to identify synthetic lethal targets in NF1-mutant cells, we aim to carry out a genome-wide genetic screen using the CRISPR/CAS9 technology. Such screens aim at identifying sgRNAs that are lost over time, to infer genes that are essential for survival or proliferation. This will narrow-down a list of potential targets to the most promising candidates. The next steps of this project will be to establish if the model of carcinogenesis and epigenetic alterations we found in MPNST are identical in case of sporadic NF1 mutated tumors in lung cancers but also in other NF1 mutated sporadic cancers.
POLE 3’-5’ exonuclease domain contributes to DNA replication fidelity. Germline missense mutations in POLE exonuclease domain cause polymerase proofreading-associated polyposis (PPAP) syndrome. Defective polymerase proofreading contributes to human malignancy by promoting genomic instability. Highly penetrant germline heterozygous mutations in the proofreading domains of the POLE gene predispose to colorectal cancer and other malignancies. This tumour predisposition condition is now known as polymerase proofreading-associated polyposis syndrome. The germline variant alleles have been shown to reduce proofreading activity and cause a mutator phenotype in yeast. Assessing pathogenicity of POLE missense mutations is a challenge Our ability to predict the phenotypic consequences of a genetic variant in the human genome remains poor. Individual in vitro assays have shown that several cancer-associated pathogenic POLE variants have reduced exonuclease activity and fidelity. As the exonuclease function of POLE is key for replication fidelity, one commonly used assay measures whether expression of a POLE variant can induce hypermutability. Recently using yeast functional assays, we created nine POLE missense variants with directed mutagenesis and showed they were associated with a hypermutator phenotype in yeast fluctuation assays. However, experimental assessments of POLE single variants have been limited in several ways. First, they are typically performed post hoc and have not kept pace with the discovery of VUS. Second, assays expressing variants are laborious and need “one by one” assays. Recent genome editing approaches and next generation sequencing technologies provide a potential means to overcome these challenges but has yet to be applied to characterize any appreciable number of variants in POLE.
We are developing a functional genomic test in Cochin Hospital to provide a comprehensive analysis of all possible missense mutations in the POLE proofreading domain with saturation genome editing in the cognate yeast gene.
Physicians of the oncogenetic clinics are involved in the formation of students of the French oncogenetics degree (DIU d’oncogénétique). They also took part in the redaction of national recommendations and expertise for the screening and the follow up of patients with genetic predisposition to frequent and rare cancers:
Biologists of the oncogenetics laboratory are involved in the formation of students in genetics and oncogenetics. They are implicated in teaching and training at different levels :
With a view to the development of the Genomic France 2025 plan, we would like to offer patients included in this program of exhaustive characterization of the genetic alterations of their tumors a coordinated management of the incident discoveries within this framework.
We plan to develop consultations dedicated to this indication and provide educational information of the patients involved in this program.
We will continue our clinical and translational research efforts in our areas of expertise (rare and frequent tumours) in order to promote the transfer of advances in translational research to the clinic.
|Name Surname||Title/Position||Speciality||Research Unit||Resarch Team|
|Anne-Paule GIMENEZ-ROQUEPLO||Pr||Oncogenetics||PARCC UMR970||Genetics and metabolism of rare cancers|
|Eric PASMANT||Dr||Molecular oncogenetics||Institut Cochin||Genetics and epigenetics of rare tumors|
|Pierre LAURENT-PUIG||Pr||Oncogenetics||UMRS 1138 Centre de recherche des Cordeliers||Personalized medicine, pharmacogenomics, therapeutic optimization|
|Nadim HAMZAOUI||MD PhD||Molecular oncogenetics||Institut Cochin||Genomics and epigenetics of rare tumors|
|Virginie VERKARRE||MD, PhD||Pathologist||PARCC UMR970||Genetics and metabolism of rare cancers|
|Geraldine PERKINS||MD||Gastroenterologist||UMRS 1138 Centre de recherche des Cordeliers||Personalized medicine, pharmacogenomics, therapeutic optimization|
|Marion DHOOGE||MD||Gastroenterologist||Institut Cochin||Genetics and epigenetics of rare tumors|
|Camille TLEMSANI||MD, PhD||Medical oncology||Institut Cochin||Genomics and epigenetics of rare tumors|
|Nelly BURNICHON||Pr||Molecular Oncogenetics||PARCC UMR970||Genetics and metabolism of rare cancers|
|Helène BLONS||Pr||Molecular Oncogenetics||UMRS 1138 Centre de recherche des Cordeliers||Personalized medicine, pharmacogenomics, therapeutic optimization|
|Karen LEROY||Pr||Oncology (molecular biology)||UMRS 1138 Centre de recherche des Cordeliers||Inflammation, complement and cancer|
|Judith FAVIER||PhD||Research director||PARCC UMR970||Genetics and metabolism of rare cancers|
|Audrey LUPO MANSUET||MD, PhD||Pathologist||UMRS 1138 Centre de recherche des Cordeliers||Cancer, immune control and escape|
|Anne-Marie BIROT||Genetic counsellor||–||–|
|Isabelle MOLLEY MASSOL||Psychologist||–||–|
The selected following publications highlight the strength of clinical and translational research developed in the oncogenetics program:
|Sponsor Title||Phase||NCT number||Coordinator/investigator|
|Effect of Chemoprevention by Low-dose Aspirin of New or Recurrent Colorectal Adenomas in Patients With Lynch Syndrome Etude AAS-Lynch –||III||NCT02813824||Robert Benhamouzing / Geraldine Perkins|
Centre Universitaire des Saints-Pères Etage 4 – Pièce 446B 45 rue des Saints-Pères -75006 Paris
Carina Binet : Secrétaire Général du CARPEM
Tél. : 01 76 53 43 85 – email@example.com
Aurore Hattabi, PhD : Coordinatrice Scientifique du CARPEM
Tél : 01 76 53 43 85 – firstname.lastname@example.org