Genomics

Publications

Year of publication 2017

S Lemaître, A Lecler, C Lévy-Gabriel, C Reyes, L Desjardins, D Gentien, M Zmuda, P V Jacomet, L Lumbroso-Le Rouic, R Dendale, A Vincent-Salomon, G Pierron, O Galatoire, N Cassoux (2017 Jan 28)

Evisceration and ocular tumors: What are the consequences?

Journal francais d'ophtalmologie : 93-101 : DOI : S0181-5512(16)30343-6 Learn more
Summary

Evisceration can be performed for blind, painful eyes. This surgery can promote the dissemination of tumor cells within the orbit if an ocular tumor has been missed preoperatively.

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Roman Rouzier, Aurelie Roulot, Arthur H Jeiranian, Namratha Ram, Jean Marc Guinebretiere, Anne Vincent Salomon, David Gentien (2017 Jan 11)

Denaturing fixatives are compatible with the NanoString nCounter(®) platform and the Prosigna(®) assay.

New biotechnology : 37-41 : DOI : S1871-6784(16)32312-3 Learn more
Summary

The objective of this study was to establish that the denaturing fixative, formalin and acetic acid (AFA), is equivalent to neutral-buffered formalin (NBF) on the nCounter system using the Prosigna assay. Twenty-five previously resected tumors from breast cancer patients were apportioned and fixed with either NBF or AFA prior to embedding in paraffin. Differentially fixed and paraffin embedded tissue pairs were sectioned and pathological review was performed according to the Prosigna assay protocol. RNA was isolated using the Prosigna assay kit and analyzed using the NanoString nCounter Dx Analysis system. 47 of the 50 blocks (94%) passed RNA quality control (QC) criteria and were collectively designated as the analysis set. We found that RNA yield and purity (A260/A280) were not significantly different between the fixatives within the analysis set. In the analysis of ROR score, the tissue pairs had a Pearson Correlation Coefficient of 0.91, similar to the correlation observed between paired tissue blocks using a single fixative in previous studies. Subtype concordance between differentially fixed tissue pairs was high (K=0.80). No significant bias or variability in risk of recurrence (ROR) score attributable to fixative was detected in this study. Further analysis revealed that sample pairs with larger differences in ROR score were limited to nearly-depleted tissue blocks containing large amounts of normal tissue due to proximity of the tumor margin. The results of this study demonstrate that the fixative, AFA, does not contribute significantly to bias and variability of assay results.

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Year of publication 2016

Franck Assayag, André Nicolas, Sophie Vacher, Catherine Dehainault, Ivan Bieche, Didier Meseure, Isabelle Aerts, Nathalie Cassoux, Claude Houdayer, François Doz, Didier Decaudin (2016 Sep 23)

Combination of Carboplatin and Bevacizumab Is an Efficient Therapeutic Approach in Retinoblastoma Patient-Derived Xenografts.

Investigative ophthalmology & visual science : 4916-4926 : DOI : 10.1167/iovs.15-18725 Learn more
Summary

Retinoblastoma (Rb) is a rare childhood cancer of the retina with a survival rate of 95% in children living in high-income countries, after appropriate therapies such as chemotherapy, local ophthalmologic treatment, and radiotherapy. However, due to inactivation of the RB1 gene, all bilateral and almost 15% of unilateral retinoblastoma patients have a higher risk of s econdary cancers, especially sarcomas. Hence, new nonmutagen treatments are warranted. Therefore, we investigated the efficacy of therapy using anti-VEGF antibody bevacizumab, either alone or with carboplatin, in well-characterized Rb patient-derived xenografts (PDXs).

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Alejandra Urrutia, Darragh Duffy, Vincent Rouilly, Céline Posseme, Raouf Djebali, Gabriel Illanes, Valentina Libri, Benoit Albaud, David Gentien, Barbara Piasecka, Milena Hasan, Magnus Fontes, Lluis Quintana-Murci, Matthew L Albert, (2016 Aug 30)

Standardized Whole-Blood Transcriptional Profiling Enables the Deconvolution of Complex Induced Immune Responses.

Cell reports : 2777-91 : DOI : 10.1016/j.celrep.2016.08.011 Learn more
Summary

Systems approaches for the study of immune signaling pathways have been traditionally based on purified cells or cultured lines. However, in vivo responses involve the coordinated action of multiple cell types, which interact to establish an inflammatory microenvironment. We employed standardized whole-blood stimulation systems to test the hypothesis that responses to Toll-like receptor ligands or whole microbes can be defined by the transcriptional signatures of key cytokines. We found 44 genes, identified using Support Vector Machine learning, that captured the diversity of complex innate immune responses with improved segregation between distinct stimuli. Furthermore, we used donor variability to identify shared inter-cellular pathways and trace cytokine loops involved in gene expression. This provides strategies for dimension reduction of large datasets and deconvolution of innate immune responses applicable for characterizing immunomodulatory molecules. Moreover, we provide an interactive R-Shiny application with healthy donor reference values for induced inflammatory genes.

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Mathieu Chicard, Sandrine Boyault, Leo Colmet Daage, Wilfrid Richer, David Gentien, Gaelle Pierron, Eve Lapouble, Angela Bellini, Nathalie Clement, Isabelle Iacono, Stéphanie Bréjon, Marjorie Carrere, Cécile Reyes, Toby Hocking, Virginie Bernard, Michel Peuchmaur, Nadège Corradini, Cécile Faure-Conter, Carole Coze, Dominique Plantaz, Anne Sophie Defachelles, Estelle Thebaud, Marion Gambart, Frédéric Millot, Dominique Valteau-Couanet, Jean Michon, Alain Puisieux, Olivier Delattre, Valérie Combaret, Gudrun Schleiermacher (2016 Jul 22)

Genomic copy number profiling using circulating free tumor DNA highlights heterogeneity in neuroblastoma.

Clinical cancer research : an official journal of the American Association for Cancer Research : DOI : clincanres.0500.2016 Learn more
Summary

The tumor genomic copy number profile is of prognostic significance in neuroblastoma (NB) patients. We have studied the genomic copy number profile of cell free DNA (cfDNA) and compared this to primary tumor aCGH at diagnosis.

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David Vallerand, Gérald Massonnet, Fatima Kébir, David Gentien, Zofia Maciorowski, Pierre De la Grange, Brigitte Sigal-Zafrani, Marion Richardson, Sandrine Humbert, Aurélie Thuleau, Franck Assayag, Ludmilla de Plater, André Nicolas, Suzy Scholl, Elisabetta Marangoni, Stefan Weigand, Sergio Roman-Roman, Ariel Savina, Didier Decaudin (2016 Jul 9)

Characterization of Breast Cancer Preclinical Models Reveals a Specific Pattern of Macrophage Polarization.

PloS one : e0157670 : DOI : 10.1371/journal.pone.0157670 Learn more
Summary

Drug discovery efforts have focused on the tumor microenvironment in recent years. However, few studies have characterized the stroma component in patient-derived xenografts (PDXs) and genetically engineered mouse models (GEMs). In this study, we characterized the stroma in various models of breast cancer tumors in mice. We performed transcriptomic and flow cytometry analyses on murine populations for a series of 25 PDXs and the two most commonly used GEMs (MMTV-PyMT and MMTV-erBb2). We sorted macrophages from five models. We then profiled gene expression in these cells, which were also subjected to flow cytometry for phenotypic characterization. Hematopoietic cell composition, mostly macrophages and granulocytes, differed between tumors. Macrophages had a specific polarization phenotype related to their M1/M2 classification and associated with the expression of genes involved in the recruitment, invasion and metastasis processes. The heterogeneity of the stroma component of the models studied suggests that tumor cells modify their microenvironment to satisfy their needs. Our observations suggest that such models are of relevance for preclinical studies.

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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 Learn more
Summary

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 Learn more
Summary

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 Learn more
Summary

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 Learn more
Summary

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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Year of 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 Learn more
Summary

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 Learn more
Summary

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 Learn more
Summary

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 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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