Génomique

Publications

Année de publication : 2018

Camille Tlemsani, Eric Pasmant, Pascaline Boudou-Rouquette, Audrey Bellesoeur, Julien Even, Frédérique Larousserie, Cécile Reyes, David Gentien, Jérôme Alexandre, Michel Vidaud, Philippe Anract, Karen Leroy, François Goldwasser (2018 Jul 26)

BRCA2 Loss-of-Function and High Sensitivity to Cisplatin-Based Chemotherapy in a Patient With a Pleomorphic Soft Tissue Sarcoma: Effect of Genomic Medicine.

The American journal of the medical sciences : DOI : S0002-9629(18)30174-5 En savoir plus
Résumé

We report the case of a patient with a BRCA2 germline mutation who developed a localized pleomorphic soft tissue sarcoma of the leg with poor prognostic features. BRCA2 germline mutations were not previously reported to be associated with pleomorphic sarcoma. BRCA2 loss-of-heterozygosity was found in the tumor, resulting in a complete BRCA2 loss-of-function. BRCA2 deficiency is associated with sensitivity to cisplatin-based chemotherapy in breast and ovarian cancer patients. We used a cisplatin-based chemotherapy. A rapid major partial response was obtained, which allowed a curative and conservative surgical resection of the sarcoma followed by adjuvant irradiation. This case illustrates that sarcoma patients may present unexpected but targetable genetic abnormalities and that BRCA2 loss-of-function may be targetable in sarcoma as it is associated with enhanced sensitivity to cisplatin. Our observation emphasizes the input of genomic medicine in clinical practice, its importance for treatment decisions, and the overlap between constitutional and somatic genetics.

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Sandrine Tury, Franck Assayag, Florian Bonin, Sophie Chateau-Joubert, Jean-Luc Servely, Sophie Vacher, Véronique Becette, Martial Caly, Audrey Rapinat, David Gentien, Pierre de la Grange, Anne Schnitzler, François Lallemand, Elisabetta Marangoni, Ivan Bièche, Céline Callens (2018 Jun 8)

The iron chelator deferasirox synergizes with chemotherapy to treat triple negative breast cancers.

The Journal of pathology : DOI : 10.1002/path.5104 En savoir plus
Résumé

To ensure their high proliferation rate, tumor cells display an iron metabolic disorder with increased iron needs, making them more susceptible to iron deprivation. This vulnerability could be a therapeutic target. In breast cancers, the development of new therapeutic approaches is urgently needed for patients with triple negative tumors which frequently relapse after chemotherapy and suffer from a lack of targeted therapies. In this work, we demonstrated that deferasirox (DFX) synergizes with standard chemotherapeutic agents such as with doxorubicin, cisplatin and carboplatin to inhibit cell proliferation and induce apoptosis and autophagy in triple-negative breast cancer (TNBC) cell lines. Moreover, the combination of DFX with doxorubicin and cyclophosphamide delayed recurrences in breast cancer patient-derived xenografts without increasing the side-effects of chemotherapies alone or altering global iron storage of mice. Antitumor synergy of DFX and doxorubicin seems to involve down-regulation of the PI3K and NF-κB pathways. Iron deprivation in combination with chemotherapy could thus help to improve the effectiveness of chemotherapy in TNBC patients without increasing toxicities. This article is protected by copyright. All rights reserved.

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Sylvie Maubant, Tania Tahtouh, Amélie Brisson, Virginie Maire, Fariba Némati, Bruno Tesson, Mengliang Ye, Guillem Rigaill, Maïté Noizet, Aurélie Dumont, David Gentien, Bérengère Marty-Prouvost, Leanne de Koning, Sardar Faisal Mahmood, Didier Decaudin, Francisco Cruzalegui, Gordon C Tucker, Sergio Roman-Roman, Thierry Dubois (2018 Jun 2)

LRP5 regulates the expression of STK40, a new potential target in triple-negative breast cancers.

Oncotarget : 22586-22604 : DOI : 10.18632/oncotarget.25187 En savoir plus
Résumé

Triple-negative breast cancers (TNBCs) account for a large proportion of breast cancer deaths, due to the high rate of recurrence from residual, resistant tumor cells. New treatments are needed, to bypass chemoresistance and improve survival. The WNT pathway, which is activated in TNBCs, has been identified as an attractive pathway for treatment targeting. We analyzed expression of the WNT coreceptors LRP5 and LRP6 in human breast cancer samples. As previously described, LRP6 was overexpressed in TNBCs. However, we also showed, for the first time, that LRP5 was overexpressed in TNBCs too. The knockdown of LRP5 or LRP6 decreased tumorigenesis and , identifying both receptors as potential treatment targets in TNBC. The apoptotic effect of LRP5 knockdown was more robust than that of LRP6 depletion. We analyzed and compared the transcriptomes of cells depleted of LRP5 or LRP6, to identify genes specifically deregulated by LRP5 potentially implicated in cell death. We identified serine/threonine kinase 40 (STK40) as one of two genes specifically downregulated soon after LRP5 depletion. STK40 was found to be overexpressed in TNBCs, relative to other breast cancer subtypes, and in various other tumor types. STK40 depletion decreased cell viability and colony formation, and induced the apoptosis of TNBC cells. In addition, STK40 knockdown impaired growth in an anchorage-independent manner and slowed tumor growth . These findings identify the largely uncharacterized putative protein kinase STK40 as a novel candidate treatment target for TNBC.

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Sarah Huet, Bruno Tesson, Jean-Philippe Jais, Andrew L Feldman, Laura Magnano, Emilie Thomas, Alexandra Traverse-Glehen, Benoit Albaud, Marjorie Carrère, Luc Xerri, Stephen M Ansell, Lucile Baseggio, Cécile Reyes, Karin Tarte, Sandrine Boyault, Corinne Haioun, Brian K Link, Pierre Feugier, Armando Lopez-Guillermo, Hervé Tilly, Pauline Brice, Sandrine Hayette, Fabrice Jardin, Fritz Offner, Pierre Sujobert, David Gentien, Alain Viari, Elias Campo, James R Cerhan, Gilles Salles (2018 Feb 25)

A gene-expression profiling score for prediction of outcome in patients with follicular lymphoma: a retrospective training and validation analysis in three international cohorts.

The Lancet. Oncology : DOI : S1470-2045(18)30102-5 En savoir plus
Résumé

Patients with follicular lymphoma have heterogeneous outcomes. Predictor models to distinguish, at diagnosis, between patients at high and low risk of progression are needed. The objective of this study was to use gene-expression profiling data to build and validate a predictive model of outcome for patients treated in the rituximab era.

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Elisabetta Marangoni, Cécile Laurent, Florence Coussy, Rania El-Botty, Sophie Château-Joubert, Jean-Luc Servely, Ludmilla de Plater, Franck Assayag, Ahmed Dahmani, Elodie Montaudon, Fariba Nemati, Justine Fleury, Sophie Vacher, David Gentien, Audrey Rapinat, Pierre Foidart, Nor Eddine Sounni, Agnès Noel, Anne Vincent-Salomon, Marick Lae, Didier Decaudin, Sergio Roman-Roman, Ivan Bièche, Martine Piccart, Fabien Reyal (2018 Feb 22)

Capecitabine Efficacy Is Correlated with TYMP and RB1 Expression in PDX Established from Triple-Negative Breast Cancers.

Clinical cancer research : an official journal of the American Association for Cancer Research : 2605-2615 : DOI : 10.1158/1078-0432.CCR-17-3490 En savoir plus
Résumé

Triple-negative breast cancer (TNBC) patients with residual disease after neoadjuvant chemotherapy have a poor outcome. We developed patient-derived xenografts (PDX) from residual tumors to identify efficient chemotherapies and predictive biomarkers in a context of resistance to anthracyclines- and taxanes-based treatments. PDX were established from residual tumors of primary breast cancer patients treated in neoadjuvant setting. TNBC PDX were treated by anthracyclines, taxanes, platins, and capecitabine. Predictive biomarkers were identified by transcriptomic and immunohistologic analysis. Downregulation of was performed by siRNA in a cell line established from a PDX. Residual TNBC PDX were characterized by a high tumor take, a short latency, and a poor prognosis of the corresponding patients. With the exception of BRCA1/2-mutated models, residual PDX were resistant to anthracyclines, taxanes, and platins. Capecitabine, the oral prodrug of 5-FU, was highly efficient in 60% of PDX, with two models showing complete responses. Prior treatment of a responder PDX with 5-FU increased expression of thymidylate synthase and decreased efficacy of capecitabine. Transcriptomic and IHC analyses of 32 TNBC PDX, including both residual tumors and treatment-naïve derived tumors, identified RB1 and TYMP proteins as predictive biomarkers for capecitabine response. Finally, knockdown in a cell line established from a capecitabine-responder PDX decreased sensitivity to 5-FU treatment. We identified capecitabine as efficient chemotherapy in TNBC PDX models established from residual disease and resistant to anthracyclines, taxanes, and platins. RB1 positivity and high expression of TYMP were significantly associated with capecitabine response. .

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Année de publication : 2017

Barbara Piasecka, Darragh Duffy, Alejandra Urrutia, Hélène Quach, Etienne Patin, Céline Posseme, Jacob Bergstedt, Bruno Charbit, Vincent Rouilly, Cameron R MacPherson, Milena Hasan, Benoit Albaud, David Gentien, Jacques Fellay, Matthew L Albert, Lluis Quintana-Murci, (2017 Dec 29)

Distinctive roles of age, sex, and genetics in shaping transcriptional variation of human immune responses to microbial challenges.

Proceedings of the National Academy of Sciences of the United States of America : E488-E497 : DOI : 10.1073/pnas.1714765115 En savoir plus
Résumé

The contribution of host genetic and nongenetic factors to immunological differences in humans remains largely undefined. Here, we generated bacterial-, fungal-, and viral-induced immune transcriptional profiles in an age- and sex-balanced cohort of 1,000 healthy individuals and searched for the determinants of immune response variation. We found that age and sex affected the transcriptional response of most immune-related genes, with age effects being more stimulus-specific relative to sex effects, which were largely shared across conditions. Although specific cell populations mediated the effects of age and sex on gene expression, including CD8T cells for age and CD4T cells and monocytes for sex, we detected a direct effect of these intrinsic factors for the majority of immune genes. The mapping of expression quantitative trait loci (eQTLs) revealed that genetic factors had a stronger effect on immune gene regulation than age and sex, yet they affected a smaller number of genes. Importantly, we identified numerous genetic variants that manifested their regulatory effects exclusively on immune stimulation, including a-specific master regulator at thelocus. These response eQTLs were enriched in disease-associated variants, particularly for autoimmune and inflammatory disorders, indicating that differences in disease risk may result from regulatory variants exerting their effects only in the presence of immune stress. Together, this study quantifies the respective effects of age, sex, genetics, and cellular heterogeneity on the interindividual variability of immune responses and constitutes a valuable resource for further exploration in the context of different infection risks or disease outcomes.

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Jean-Philippe Jais, Thierry Jo Molina, Philippe Ruminy, David Gentien, Cecile Reyes, David W Scott, Lisa M Rimsza, Georges Wright, Randy D Gascoyne, Louis M Staudt, Corinne Haioun, Herve Tilly, Philippe Gaulard, Gilles A Salles, Fabrice Jardin, Karen Leroy (2017 Jul 7)

Reliable subtype classification of diffuse large B-Cell lymphoma samples from GELA LNH2003 trials using the Lymph2Cx gene expression assay.

Haematologica : DOI : haematol.2017.166827 En savoir plus
Résumé

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Wilfrid Richer, Julien Masliah-Planchon, Nathalie Clement, Irene Jimenez, Laetitia Maillot, David Gentien, Benoît Albaud, Walid Chemlali, Christine Galant, Frederique Larousserie, Pascaline Boudou-Rouquette, Amaury Leruste, Celine Chauvin, Zhi Yan Han, Jean-Michel Coindre, Pascale Varlet, Paul Freneaux, Dominique Ranchère-Vince, Olivier Delattre, Franck Bourdeaut (2017 Apr 22)

Embryonic signature distinguishes pediatric and adult rhabdoid tumors from other SMARCB1-deficient cancers.

Oncotarget : 34245-34257 : DOI : 10.18632/oncotarget.15939 En savoir plus
Résumé

Extra-cranial rhabdoid tumors (RT) are highly aggressive malignancies of infancy, characterized by undifferentiated histological features and loss of SMARCB1 expression. The diagnosis is all the more challenging that other poorly differentiated cancers lose SMARCB1 expression, such as epithelioid sarcomas (ES), renal medullary carcinomas (RMC) or undifferentiated chordomas (UC). Moreover, late cases occurring in adults are now increasingly reported, raising the question of differential diagnoses and emphasizing nosological issues. To address this issue, we have analyzed the expression profiles of a training set of 32 SMARCB1-deficient tumors (SDT), with ascertained diagnosis of RT (n = 16, all < 5 years of age), ES (n = 8, all > 10 years of age), UC (n = 3) and RMC (n = 5). As compared with other SDT, RT are characterized by an embryonic signature, and up-regulation of key-actors of de novo DNA methylation processes. Using this signature, we then analysed the expression profiling of 37 SDT to infer the appropriate diagnosis. Thirteen adult onset tumors showed strong similarity with pediatric RT, in spite of older age; by exome sequencing, these tumors also showed genomic features indistinguishable from pediatric RT. In contrary, 8 tumors were reclassified within carcinoma, ES or UC categories, while the remaining could not be related to any of those entities. Our results demonstrate that embryonic signature is shared by all RT, whatever the age at diagnosis; they also illustrate that many adult-onset SDT of ambiguous histological diagnosis are clearly different from RT. Finally, our study paves the way for the routine use of expression-based signatures to give accurate diagnosis of SDT.

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Sébastien Schaller, Dorothée Buttigieg, Alysson Alory, Arnaud Jacquier, Marc Barad, Mark Merchant, David Gentien, Pierre de la Grange, Georg Haase (2017 Mar 9)

Novel combinatorial screening identifies neurotrophic factors for selective classes of motor neurons.

Proceedings of the National Academy of Sciences of the United States of America : E2486-E2493 : DOI : 10.1073/pnas.1615372114 En savoir plus
Résumé

Numerous neurotrophic factors promote the survival of developing motor neurons but their combinatorial actions remain poorly understood; to address this, we here screened 66 combinations of 12 neurotrophic factors on pure, highly viable, and standardized embryonic mouse motor neurons isolated by a unique FACS technique. We demonstrate potent, strictly additive, survival effects of hepatocyte growth factor (HGF), ciliary neurotrophic factor (CNTF), and Artemin through specific activation of their receptor complexes in distinct subsets of lumbar motor neurons: HGF supports hindlimb motor neurons through c-Met; CNTF supports subsets of axial motor neurons through CNTFRα; and Artemin acts as the first survival factor for parasympathetic preganglionic motor neurons through GFRα3/Syndecan-3 activation. These data show that neurotrophic factors can selectively promote the survival of distinct classes of embryonic motor neurons. Similar studies on postnatal motor neurons may provide a conceptual framework for the combined therapeutic use of neurotrophic factors in degenerative motor neuron diseases such as amyotrophic lateral sclerosis, spinal muscular atrophy, and spinobulbar muscular atrophy.

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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 En savoir plus
Résumé

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 En savoir plus
Résumé

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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Année de 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 En savoir plus
Résumé

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 En savoir plus
Résumé

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 En savoir plus
Résumé

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 En savoir plus
Résumé

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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