Genomics

Publications

Year of publication 2015

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 Learn more
Summary

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 Learn more
Summary

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 Learn more
Summary

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 Learn more
Summary

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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Year of 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 Learn more
Summary

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 Learn more
Summary

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 Learn more
Summary

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 Learn more
Summary

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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Fabrice André, Thomas Bachelot, Frederic Commo, Mario Campone, Monica Arnedos, Véronique Dieras, Magali Lacroix-Triki, Ludovic Lacroix, Pascale Cohen, David Gentien, Jose Adélaide, Florence Dalenc, Anthony Goncalves, Christelle Levy, Jean-Marc Ferrero, Jacques Bonneterre, Claudia Lefeuvre, Marta Jimenez, Thomas Filleron, Hervé Bonnefoi (2014 Feb 11)

Comparative genomic hybridisation array and DNA sequencing to direct treatment of metastatic breast cancer: a multicentre, prospective trial (SAFIR01/UNICANCER).

The Lancet. Oncology : 267-74 : DOI : 10.1016/S1470-2045(13)70611-9 Learn more
Summary

Breast cancer is characterised by genomic alterations. We did a multicentre molecular screening study to identify abnormalities in individual patients with the aim of providing targeted therapy matched to individuals’ genomic alterations.

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D Gentien, O Kosmider, F Nguyen-Khac, B Albaud, A Rapinat, A G Dumont, F Damm, T Popova, R Marais, M Fontenay, S Roman-Roman, O A Bernard, M-H Stern (2014 Jan 17)

A common alternative splicing signature is associated with SF3B1 mutations in malignancies from different cell lineages.

Leukemia : 1355-7 : DOI : 10.1038/leu.2014.28 Learn more
Summary

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Year of publication 2013

F Valet, P de Cremoux, F Spyratos, N Servant, M E Dujaric, D Gentien, J Lehmann-Che, V Scott, B Sigal-Zafrani, M C Mathieu, P Bertheau, J M Guinebretière, J Y Pierga, S Delaloge, S Giacchetti, E Brain, O Tembo, M Marty, B Asselain (2013 Oct 8)

Challenging single- and multi-probesets gene expression signatures of pathological complete response to neoadjuvant chemotherapy in breast cancer: experience of the REMAGUS 02 phase II trial.

Breast (Edinburgh, Scotland) : 1052-9 : DOI : 10.1016/j.breast.2013.08.015 Learn more
Summary

This study was designed to identify predictive signatures of pathological complete response (pCR) in breast cancer treated by taxane-based regimen, using clinicopathological variables and transcriptomic data (Affymetrix Hgu133 Plus 2.0 devices). The REMAGUS 02 trial (n = 153,training set) and the publicly available M.D. Anderson data set (n = 133, validation set) were used. A re-sampling method was applied. All predictive models were defined using logistic regression and their classification performances were tested through Area Under the Curve (AUC) estimation. A stable set of 42 probesets (31 genes) differentiate pCR or no pCR samples. Single-or 2-probesets signatures, mainly related to ER pathway, were equally predictive of pCR with AUC greater then 0.80. Models including probesets associated with ESR1, MAPT, CA12 or PIGH presented good classification performances. When clinical variables were entered into the model, only CA12 and PIGH, remained informative (p = 0.05 and p = 0.005) showing that a combination of a few genes provided robust and reliable prediction of pCR.

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Manuel Jorge Rodrigues, David Gentien, Marc-Henri Stern, Laurence Desjardins, Jérôme Couturier (2013 Jul 27)

Genomic amplification is not a frequent event in uveal melanomas.

The American journal of pathology : 638 : DOI : 10.1016/j.ajpath.2013.04.032 Learn more
Summary

This Correspondence relates to the article by Lake et al that reported copy number and genotyping analysis on formalin-fixed, paraffin-embedded samples using genome-wide SNP arrays version 6.0.

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Cristovão Moreira Sousa, John Russel McGuire, Morgane Sonia Thion, David Gentien, Pierre de la Grange, Sophie Tezenas du Montcel, Anne Vincent-Salomon, Alexandra Durr, Sandrine Humbert (2013 Jan 10)

The Huntington disease protein accelerates breast tumour development and metastasis through ErbB2/HER2 signalling.

EMBO molecular medicine : 309-25 : DOI : 10.1002/emmm.201201546 Learn more
Summary

In Huntington disease (HD), polyglutamine expansion in the huntingtin protein causes specific neuronal death. The consequences of the presence of mutant huntingtin in other tissues are less well understood. Here we propose that mutant huntingtin influences breast cancer progression. Indeed, we show that mammary tumours appear earlier in mouse breast cancer models expressing mutant huntingtin as compared to control mice expressing wild-type huntingtin. Tumours bearing mutant huntingtin have a modified gene expression pattern that reflects enhanced aggressiveness with the overexpression of genes favouring invasion and metastasis. In agreement, mutant huntingtin accelerates epithelial to mesenchymal transition and enhances cell motility and invasion. Also, lung metastasis is higher in HD conditions than in control mice. Finally, we report that in HD, the dynamin dependent endocytosis of the ErbB2/HER2 receptor tyrosine kinase is reduced. This leads to its accumulation and to subsequent increases in cell motility and proliferation. Our study may thus have important implications for both cancer and HD.

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Year of publication 2011

P Cottu, E Marangoni, F Assayag, P de Cremoux, A Vincent-Salomon, Ch Guyader, L de Plater, C Elbaz, N Karboul, J J Fontaine, S Chateau-Joubert, P Boudou-Rouquette, S Alran, V Dangles-Marie, D Gentien, M-F Poupon, D Decaudin (2011 Oct 18)

Modeling of response to endocrine therapy in a panel of human luminal breast cancer xenografts.

Breast cancer research and treatment : 595-606 : DOI : 10.1007/s10549-011-1815-5 Learn more
Summary

Resistance to endocrine therapy is a major complication of luminal breast cancer and studies of the biological features of hormonal resistance are limited by the lack of adequate preclinical models. The aim of this study is to establish and characterize a panel of primary human luminal breast carcinoma xenografts, and to evaluate their response to endocrine therapies. Four hundred and twenty-three tumor fragments obtained directly from patients have been grafted in the interscapular fatpad of Swiss nude mice. After stable engraftment with estradiol supplementation, xenografted tumors have been validated by conventional pathology and immunohistochemistry examination, and additional molecular studies. In vivo tumor growth and response to different endocrine treatments were evaluated. We have engrafted 423 tumors including 314 ER+ tumors, and 8 new luminal breast cancer xenografts have been obtained (2.5%). Tumor take was much lower for luminal tumors than for non-luminal tumors (2.5 vs. 24.7%, P < 0.0001), and was associated with two independent criteria, i.e., ER status (P < 0.0001) and a high grade tumor (P = 0.05). Histological and immunohistochemical analyses performed on patient's tumors and xenografts showed striking similarities in the tumor morphology as well as in the expression level of ER, PR, and HER2. Response to hormone therapy, evaluated in 6 luminal models, showed different sensitivities, thus exhibiting heterogeneity similar to what is observed in the clinic. We have established a panel of primary human luminal breast cancer xenografts, recapitulating the biological and clinical behaviors of patient tumors, and therefore suitable for further preclinical experiments.

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Debbie Montjean, Pierre De La Grange, David Gentien, Audrey Rapinat, Stéphanie Belloc, Paul Cohen-Bacrie, Yves Menezo, Moncef Benkhalifa (2011 Oct 13)

Sperm transcriptome profiling in oligozoospermia.

Journal of assisted reproduction and genetics : 3-10 : DOI : 10.1007/s10815-011-9644-3 Learn more
Summary

Investigate in what extent sperm transcriptome of infertile men is different from that of fertile individuals.

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