Génomique

Publications

Année de publication : 2016

Zachary A Gurard-Levin, Laurence O W Wilson, Vera Pancaldi, Sophie Postel-Vinay, Fabricio G Sousa, Cécile Reyes, Elisabetta Marangoni, David Gentien, Alfonso Valencia, Yves Pommier, Paul Cottu, Genevieve Almouzni (2016 May 20)

Chromatin regulators as a guide for cancer treatment choice.

Molecular cancer therapeutics : DOI : molcanther.1008.2015 En savoir plus
Résumé

The limited capacity to predict a patient’s response to distinct chemotherapeutic agents is a major hurdle in cancer management. The efficiency of a large fraction of current cancer therapeutics (radio- and chemotherapies) is influenced by chromatin structure. Reciprocally, alterations in chromatin organization may impact resistance mechanisms. Here, we explore how the mis-expression of chromatin regulators-factors involved in the establishment and maintenance of functional chromatin domains-can inform about the extent of docetaxel response. We exploit gene Affymetrix and NanoString gene expression data for a set of chromatin regulators generated from breast cancer patient-derived xenograft (PDX) models and patient samples treated with docetaxel. Random Forest classification reveals specific panels of chromatin regulators, including key components of the SWI/SNF chromatin remodeler, which readily distinguish docetaxel high-responders and poor-responders. Further exploration of SWI/SNF components in the comprehensive NCI-60 dataset reveals that the expression inversely correlates with docetaxel sensitivity. Finally, we show that loss of the SWI/SNF subunit BRG1 (SMARCA4) in a model cell line leads to enhanced docetaxel sensitivity. Altogether, our findings identify chromatin regulators as biomarkers for drug response as well as therapeutic targets to sensitize patients towards docetaxel and combat drug resistance.

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Nabil Amirouchene-Angelozzi, Estelle Frisch-Dit-Leitz, Guillaume Carita, Ahmed Dahmani, Chloé Raymondie, Géraldine Liot, David Gentien, Fariba Némati, Didier Decaudin, Sergio Roman-Roman, Marie Schoumacher (2016 Mar 19)

The mTOR inhibitor Everolimus synergizes with the PI3K inhibitor GDC0941 to enhance anti-tumor efficacy in uveal melanoma.

Oncotarget : DOI : 10.18632/oncotarget.8054 En savoir plus
Résumé

Uveal Melanoma (UM) is the most frequent malignant ocular tumor in adults. While the primary tumor is efficiently treated by surgery and/or radiotherapy, about one third of UM patients develop metastases, for which no effective treatment is currently available. The PKC, MAPK and PI3K/AKT/mTOR signaling cascades have been shown to be associated with tumor growth. However, none of the compounds against those pathways results in tumor regression when used as single agents. To identify more effective therapeutic strategies for UM patients, we performed a combination screen using seven targeted agents inhibiting PKC, MEK, AKT, PI3K and mTOR in a panel of ten UM cell lines, representative of the UM disease. We identified a strong synergy between the mTOR inhibitor Everolimus and the PI3K inhibitor GDC0941. This combination resulted in an increase in apoptosis in several UM cell lines compared to monotherapies and enhanced the anti-tumor effect of each single agent in two patient-derived xenografts. Furthermore, we showed that the synergism between the two drugs was associated with the relief by GDC0491 of a reactivation of AKT induced by Everolimus. Altogether, our results highlight a novel and effective combination strategy, which could be beneficial for UM patients.

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Henriette Poaty, David Gentien, Cecile Reyes and Jacques Silou (2016 Feb 25)

Macroscopic Analysis of Fetus Having Arhinencephaly, Synophthalmia and Holoprosencephaly

Human Genetics & Embryology : DOI : dx.doi.org/10.4172/2161-0436.1000135 En savoir plus
Résumé

We report here a macroscopic analysis of one fetus conserved in Bouin then in formol having an arhinencephaly, synophthalmia associated with holoprosencephaly. We aimed to relate the various etiologies of observed anomalies in conjunction with the literature review. To perform the study, a fetopathologic examination including autopsy and radiologic analysis were done. Assay of FISH and OncoScan were made. Fetopathologic examination showed severe craniofacial malformations associated with extracranial defects including persistent troncus arteriosus communis, abnormal lung lobulation, extremities deformities and single umbilical artery. FISH and OncoSan had given unsuccessful results, because nucleic acids were highly degraded. The macroscopic examination of the fetus having arhinencephaly and synophthalmia highlights asymptomatology association with holoprosencephaly sequence and visceral defects.

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D Mouttet, M Laé, M Caly, D Gentien, S Carpentier, H Peyro-Saint-Paul, A Vincent-Salomon, R Rouzier, B Sigal-Zafrani, X Sastre-Garau, F Reyal (2016 Feb 2)

Estrogen-Receptor, Progesterone-Receptor and HER2 Status Determination in Invasive Breast Cancer. Concordance between Immuno-Histochemistry and MapQuant™ Microarray Based Assay.

PloS one : e0146474 : DOI : 10.1371/journal.pone.0146474 En savoir plus
Résumé

Hormone receptor status and HER2 status are of critical interest in determining the prognosis of breast cancer patients. Their status is routinely assessed by immunohistochemistry (IHC). However, it is subject to intra-laboratory and inter-laboratory variability. The aim of our study was to compare the estrogen receptor, progesterone receptor and HER2 status as determined by the MapQuant™ test to the routine immuno-histochemical tests in early stage invasive breast cancer in a large comprehensive cancer center.

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Année de publication : 2015

Laure Piqueret-Stephan, Charles Marcaillou, Cécile Reyes, Aurélie Honoré, Mélanie Letexier, David Gentien, Nathalie Droin, Ludovic Lacroix, Jean-Yves Scoazec, Philippe Vielh (2015 Oct 28)

Massively parallel DNA sequencing from routinely processed cytological smears.

Cancer cytopathology : 241-53 : DOI : 10.1002/cncy.21639 En savoir plus
Résumé

Data generated by next-generation sequencing technologies have a pivotal role in precision medicine. These high-throughput techniques are preferentially performed on fresh tissue, but there is an increasing need for protocols adapted to materials derived from formalin-fixed, paraffin-embedded tissue and cytology specimens.

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Julien Calderaro, Julien Masliah-Planchon, Wilfrid Richer, Laetitia Maillot, Pascale Maille, Ludovic Mansuy, Claire Bastien, Alexandre de la Taille, Hélène Boussion, Cécile Charpy, Anne Jourdain, Claire Bléchet, Gaelle Pierron, David Gentien, Laurence Choudat, Christophe Tournigand, Olivier Delattre, Yves Allory, Franck Bourdeaut (2015 Oct 5)

Balanced Translocations Disrupting SMARCB1 Are Hallmark Recurrent Genetic Alterations in Renal Medullary Carcinomas.

European urology : DOI : S0302-2838(15)00935-5 En savoir plus
Résumé

Renal medullary carcinoma (RMC) is a rare and highly aggressive neoplasm that most often occurs in the setting of sickle cell trait or sickle cell disease (SCD). Most patients present with metastatic disease resistant to conventional chemotherapy, and therefore there is an urgent need for molecular insight to propose new therapies.

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Christophe Le Tourneau, Jean-Pierre Delord, Anthony Gonçalves, Céline Gavoille, Coraline Dubot, Nicolas Isambert, Mario Campone, Olivier Trédan, Marie-Ange Massiani, Cécile Mauborgne, Sebastien Armanet, Nicolas Servant, Ivan Bièche, Virginie Bernard, David Gentien, Pascal Jezequel, Valéry Attignon, Sandrine Boyault, Anne Vincent-Salomon, Vincent Servois, Marie-Paule Sablin, Maud Kamal, Xavier Paoletti, (2015 Jun 22)

Molecularly targeted therapy based on tumour molecular profiling versus conventional therapy for advanced cancer (SHIVA): a multicentre, open-label, proof-of-concept, randomised, controlled phase 2 trial.

The Lancet. Oncology : 1324-34 : DOI : 10.1016/S1470-2045(15)00188-6 En savoir plus
Résumé

Molecularly targeted agents have been reported to have anti-tumour activity for patients whose tumours harbour the matching molecular alteration. These results have led to increased off-label use of molecularly targeted agents on the basis of identified molecular alterations. We assessed the efficacy of several molecularly targeted agents marketed in France, which were chosen on the basis of tumour molecular profiling but used outside their indications, in patients with advanced cancer for whom standard-of-care therapy had failed.

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Céline Baldeyron, Amélie Brisson, Bruno Tesson, Fariba Némati, Stéphane Koundrioukoff, Elie Saliba, Leanne De Koning, Elise Martel, Mengliang Ye, Guillem Rigaill, Didier Meseure, André Nicolas, David Gentien, Didier Decaudin, Michelle Debatisse, Stéphane Depil, Francisco Cruzalegui, Alain Pierré, Sergio Roman-Roman, Gordon C Tucker, Thierry Dubois (2015 May 26)

TIPIN depletion leads to apoptosis in breast cancer cells.

Molecular oncology : 1580-98 : DOI : 10.1016/j.molonc.2015.04.010 En savoir plus
Résumé

Triple-negative breast cancer (TNBC) is the breast cancer subgroup with the most aggressive clinical behavior. Alternatives to conventional chemotherapy are required to improve the survival of TNBC patients. Gene-expression analyses for different breast cancer subtypes revealed significant overexpression of the Timeless-interacting protein (TIPIN), which is involved in the stability of DNA replication forks, in the highly proliferative associated TNBC samples. Immunohistochemistry analysis showed higher expression of TIPIN in the most proliferative and aggressive breast cancer subtypes including TNBC, and no TIPIN expression in healthy breast tissues. The depletion of TIPIN by RNA interference impairs the proliferation of both human breast cancer and non-tumorigenic cell lines. However, this effect may be specifically associated with apoptosis in breast cancer cells. TIPIN silencing results in higher levels of single-stranded DNA (ssDNA), indicative of replicative stress (RS), in TNBC compared to non-tumorigenic cells. Upon TIPIN depletion, the speed of DNA replication fork was significantly decreased in all BC cells. However, TIPIN-depleted TNBC cells are unable to fire additional replication origins in response to RS and therefore undergo apoptosis. TIPIN knockdown in TNBC cells decreases tumorigenicity in vitro and delays tumor growth in vivo. Our findings suggest that TIPIN is important for the maintenance of DNA replication and represents a potential treatment target for the worst prognosis associated breast cancers, such as TNBC.

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Sylvie Maubant, Bruno Tesson, Virginie Maire, Mengliang Ye, Guillem Rigaill, David Gentien, Francisco Cruzalegui, Gordon C Tucker, Sergio Roman-Roman, Thierry Dubois (2015 Apr 8)

Transcriptome analysis of Wnt3a-treated triple-negative breast cancer cells.

PloS one : e0122333 : DOI : 10.1371/journal.pone.0122333 En savoir plus
Résumé

The canonical Wnt/β-catenin pathway is activated in triple-negative breast cancer (TNBC). The activation of this pathway leads to the expression of specific target genes depending on the cell/tissue context. Here, we analyzed the transcriptome of two different TNBC cell lines to define a comprehensive list of Wnt target genes. The treatment of cells with Wnt3a for 6h up-regulated the expression (fold change > 1.3) of 59 genes in MDA-MB-468 cells and 241 genes in HCC38 cells. Thirty genes were common to both cell lines. Beta-catenin may also be a transcriptional repressor and we found that 18 and 166 genes were down-regulated in response to Wnt3a treatment for 6h in MDA-MB-468 and HCC38 cells, respectively, of which six were common to both cell lines. Only half of the activated and the repressed transcripts have been previously described as Wnt target genes. Therefore, our study reveals 137 novel genes that may be positively regulated by Wnt3a and 104 novel genes that may be negatively regulated by Wnt3a. These genes are involved in the Wnt pathway itself, and also in TGFβ, p53 and Hedgehog pathways. Thorough characterization of these novel potential Wnt target genes may reveal new regulators of the canonical Wnt pathway. The comparison of our list of Wnt target genes with those published in other cellular contexts confirms the notion that Wnt target genes are tissue-, cell line- and treatment-specific. Genes up-regulated in Wnt3a-stimulated cell lines were more strongly expressed in TNBC than in luminal A breast cancer samples. These genes were also overexpressed, but to a much lesser extent, in HER2+ and luminal B tumors. We identified 72 Wnt target genes higher expressed in TNBCs (17 with a fold change >1.3) which may reflect the chronic activation of the canonical Wnt pathway that occurs in TNBC tumors.

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Ronan Chaligné, Tatiana Popova, Marco-Antonio Mendoza-Parra, Mohamed-Ashick M Saleem, David Gentien, Kristen Ban, Tristan Piolot, Olivier Leroy, Odette Mariani, Hinrich Gronemeyer, Anne Vincent-Salomon, Marc-Henri Stern, Edith Heard (2015 Feb 6)

The inactive X chromosome is epigenetically unstable and transcriptionally labile in breast cancer.

Genome research : 488-503 : DOI : 10.1101/gr.185926.114 En savoir plus
Résumé

Disappearance of the Barr body is considered a hallmark of cancer, although whether this corresponds to genetic loss or to epigenetic instability and transcriptional reactivation is unclear. Here we show that breast tumors and cell lines frequently display major epigenetic instability of the inactive X chromosome, with highly abnormal 3D nuclear organization and global perturbations of heterochromatin, including gain of euchromatic marks and aberrant distributions of repressive marks such as H3K27me3 and promoter DNA methylation. Genome-wide profiling of chromatin and transcription reveal modified epigenomic landscapes in cancer cells and a significant degree of aberrant gene activity from the inactive X chromosome, including several genes involved in cancer promotion. We demonstrate that many of these genes are aberrantly reactivated in primary breast tumors, and we further demonstrate that epigenetic instability of the inactive X can lead to perturbed dosage of X-linked factors. Taken together, our study provides the first integrated analysis of the inactive X chromosome in the context of breast cancer and establishes that epigenetic erosion of the inactive X can lead to the disappearance of the Barr body in breast cancer cells. This work offers new insights and opens up the possibility of exploiting the inactive X chromosome as an epigenetic biomarker at the molecular and cytological levels in cancer.

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Oumou Goundiam, Pierre Gestraud, Tatiana Popova, Thibault De la Motte Rouge, Virginie Fourchotte, David Gentien, Philippe Hupé, Véronique Becette, Claude Houdayer, Sergio Roman-Roman, Marc-Henri Stern, Xavier Sastre-Garau (2015 Jan 9)

Histo-genomic stratification reveals the frequent amplification/overexpression of CCNE1 and BRD4 genes in non-BRCAness high grade ovarian carcinoma.

International journal of cancer : 1890-900 : DOI : 10.1002/ijc.29568 En savoir plus
Résumé

The treatment of epithelial ovarian cancer (EOC) is narrowly focused despite the heterogeneity of this disease in which outcomes remain poor. To stratify EOC patients for targeted therapy, we developed an approach integrating expression and genomic analyses including the BRCAness status. Gene expression and genomic profiling were used to identify genes recurrently (>5%) amplified and overexpressed in 105 EOC. The LST (Large-scale State Transition) genomic signature of BRCAness was applied to define molecular subgroups of EOC. Amplified/overexpressed genes clustered mainly in 3q, 8q, 19p and 19q. These changes were generally found mutually exclusive. In the 85 patients for which the genomic signature could be determined, genomic BRCAness was found in 52 cases (61.1%) and non-BRCAness in 33 (38.8%). A striking mutual exclusivity was observed between BRCAness and amplification/overexpression data. Whereas 3q and 8q alterations were preferentially observed in BRCAness EOC, most alterations on chromosome 19 were in non-BRCAness cases. CCNE1 (19q12) and BRD4 (19p13.1) amplification/overexpression was found in 19/33 (57.5%) of non-BRCAness cases. Such disequilibrium was also found in the TCGA EOC data set used for validation. Potential target genes are frequently amplified/overexpressed in non-BRCAness EOC. We report that BRD4, already identified as a target in several tumor models, is a new potential target in high grade non-BRCAness ovarian carcinoma.

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Année de publication : 2014

Valentina Boeva, Tatiana Popova, Maxime Lienard, Sebastien Toffoli, Maud Kamal, Christophe Le Tourneau, David Gentien, Nicolas Servant, Pierre Gestraud, Thomas Rio Frio, Philippe Hupé, Emmanuel Barillot, Jean-François Laes (2014 Jul 14)

Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data.

Bioinformatics (Oxford, England) : 3443-50 : DOI : 10.1093/bioinformatics/btu436 En savoir plus
Résumé

Because of its low cost, amplicon sequencing, also known as ultra-deep targeted sequencing, is now becoming widely used in oncology for detection of actionable mutations, i.e. mutations influencing cell sensitivity to targeted therapies. Amplicon sequencing is based on the polymerase chain reaction amplification of the regions of interest, a process that considerably distorts the information on copy numbers initially present in the tumor DNA. Therefore, additional experiments such as single nucleotide polymorphism (SNP) or comparative genomic hybridization (CGH) arrays often complement amplicon sequencing in clinics to identify copy number status of genes whose amplification or deletion has direct consequences on the efficacy of a particular cancer treatment. So far, there has been no proven method to extract the information on gene copy number aberrations based solely on amplicon sequencing.

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Nabil Amirouchene-Angelozzi, Fariba Nemati, David Gentien, André Nicolas, Amaury Dumont, Guillaume Carita, Jacques Camonis, Laurence Desjardins, Nathalie Cassoux, Sophie Piperno-Neumann, Pascale Mariani, Xavier Sastre, Didier Decaudin, Sergio Roman-Roman (2014 Jul 5)

Establishment of novel cell lines recapitulating the genetic landscape of uveal melanoma and preclinical validation of mTOR as a therapeutic target.

Molecular oncology : 1508-20 : DOI : 10.1016/j.molonc.2014.06.004 En savoir plus
Résumé

Uveal melanoma (UM) is the most common primary tumor of the eye in adults. There is no standard adjuvant treatment to prevent metastasis and no effective therapy in the metastatic setting. We have established a unique panel of 7 UM cell lines from either patient’s tumors or patient-derived tumor xenografts (PDXs). This panel recapitulates the molecular landscape of the disease in terms of genetic alterations and mutations. All the cell lines display GNAQ or GNA11 activating mutations, and importantly four of them display BAP1 (BRCA1 associated protein-1) deficiency, a hallmark of aggressive disease. The mTOR pathway was shown to be activated in most of the cell lines independent of AKT signaling. mTOR inhibitor Everolimus reduced the viability of UM cell lines and significantly delayed tumor growth in 4 PDXs. Our data suggest that mTOR inhibition with Everolimus, possibly in combination with other agents, may be considered as a therapeutic option for the management of uveal melanoma.

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Paul Cottu, Ivan Bièche, Franck Assayag, Rania El Botty, Sophie Chateau-Joubert, Aurélie Thuleau, Thomas Bagarre, Benoit Albaud, Audrey Rapinat, David Gentien, Pierre de la Grange, Vonick Sibut, Sophie Vacher, Rana Hatem, Jean-Luc Servely, Jean-Jacques Fontaine, Didier Decaudin, Jean-Yves Pierga, Sergio Roman-Roman, Elisabetta Marangoni (2014 Jun 21)

Acquired resistance to endocrine treatments is associated with tumor-specific molecular changes in patient-derived luminal breast cancer xenografts.

Clinical cancer research : an official journal of the American Association for Cancer Research : 4314-25 : DOI : 10.1158/1078-0432.CCR-13-3230 En savoir plus
Résumé

Patients with luminal breast cancer (LBC) often become endocrine resistant over time. We investigated the molecular changes associated with acquired hormonoresistances in patient-derived xenografts of LBC.

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C Le Tourneau, X Paoletti, N Servant, I Bièche, D Gentien, T Rio Frio, A Vincent-Salomon, V Servois, J Romejon, O Mariani, V Bernard, P Huppe, G Pierron, F Mulot, C Callens, J Wong, C Mauborgne, E Rouleau, C Reyes, E Henry, Q Leroy, P Gestraud, P La Rosa, L Escalup, E Mitry, O Trédan, J-P Delord, M Campone, A Goncalves, N Isambert, C Gavoille, M Kamal (2014 Apr 26)

Randomised proof-of-concept phase II trial comparing targeted therapy based on tumour molecular profiling vs conventional therapy in patients with refractory cancer: results of the feasibility part of the SHIVA trial.

British journal of cancer : 17-24 : DOI : 10.1038/bjc.2014.211 En savoir plus
Résumé

The SHIVA trial is a multicentric randomised proof-of-concept phase II trial comparing molecularly targeted therapy based on tumour molecular profiling vs conventional therapy in patients with any type of refractory cancer. RESULTS of the feasibility study on the first 100 enrolled patients are presented.

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