Publications, 2019

Blum, Y., Meiller, C., Quetel, L., Elarouci, N., Ayadi, M., Tashtanbaeva, D., Armenoult, L., Montagne, F., Tranchant, R., Renier, A., et al. (2019). Dissecting heterogeneity in malignant pleural mesothelioma through histo-molecular gradients for clinical applications. Nat Commun 10, 1333.

Branzoli, F., Pontoizeau, C., Tchara, L., Di Stefano, A.L., Kamoun, A., Deelchand, D.K., Valabrègue, R., Lehéricy, S., Sanson, M., Ottolenghi, C., et al. (2019). Cystathionine as a marker for 1p/19q codeleted gliomas by in vivo magnetic resonance spectroscopy. Neuro-Oncology.

Cantini, L., Kairov, U., de Reyniès, A., Barillot, E., Radvanyi, F., and Zinovyev, A. (2019). Assessing reproducibility of matrix factorization methods in independent transcriptomes. Bioinformatics.

Job, S., Draskovic, I., Burnichon, N., Buffet, A., Cros, J., Lépine, C., Venisse, A., Robidel, E., Verkarre, V., Meatchi, T., et al. (2019). Telomerase Activation and ATRX Mutations Are Independent Risk Factors for Metastatic Pheochromocytoma and Paraganglioma. Clin. Cancer Res. 25, 760–770.

Nicolle, R., Raffenne, J., Paradis, V., Couvelard, A., de Reynies, A., Blum, Y., and Cros, J. (2019). Prognostic Biomarkers in Pancreatic Cancer: Avoiding Errata When Using the TCGA Dataset. Cancers (Basel) 11.

Rochel, N., Krucker, C., Coutos-Thévenot, L., Osz, J., Zhang, R., Guyon, E., Zita, W., Vanthong, S., Hernandez, O.A., Bourguet, M., et al. (2019). Recurrent activating mutations of PPARγ associated with luminal bladder tumors. Nat Commun 10, 253.

Tonon, L., Fromont, G., Boyault, S., Thomas, E., Ferrari, A., Sertier, A.-S., Kielbassa, J., Le Texier, V., Kamoun, A., Elarouci, N., et al. (2019). Mutational Profile of Aggressive, Localised Prostate Cancer from African Caribbean Men Versus European Ancestry Men. Eur. Urol. 75, 11–15.

Weinstein, A.M., Giraldo, N.A., Petitprez, F., Julie, C., Lacroix, L., Peschaud, F., Emile, J.-F., Marisa, L., Fridman, W.H., Storkus, W.J., et al. (2019). Association of IL-36γ with tertiary lymphoid structures and inflammatory immune infiltrates in human colorectal cancer. Cancer Immunol. Immunother. 68, 109–120.

Publications, 2018

Balbinot, C., Armant, O., Elarouci, N., Marisa, L., Martin, E., De Clara, E., Onea, A., Deschamps, J., Beck, F., Freund, J.-N., et al. (2018). The Cdx2 homeobox gene suppresses intestinal tumorigenesis through non-cell-autonomous mechanisms. J. Exp. Med. 215, 911–926.

Beuselinck, B., Verbiest, A., Couchy, G., Job, S., de Reynies, A., Meiller, C., Albersen, M., Verkarre, V., Lerut, E., Méjean, A., et al. (2018). Pro-angiogenic gene expression is associated with better outcome on sunitinib in metastatic clear-cell renal cell carcinoma. Acta Oncol 57, 498–508.

Bokhari, A., Jonchere, V., Lagrange, A., Bertrand, R., Svrcek, M., Marisa, L., Buhard, O., Greene, M., Demidova, A., Jia, J., et al. (2018). Targeting nonsense-mediated mRNA decay in colorectal cancers with microsatellite instability. Oncogenesis 7, 70.

George, J., Walter, V., Peifer, M., Alexandrov, L.B., Seidel, D., Leenders, F., Maas, L., Müller, C., Dahmen, I., Delhomme, T.M., et al. (2018). Integrative genomic profiling of large-cell neuroendocrine carcinomas reveals distinct subtypes of high-grade neuroendocrine lung tumors. Nat Commun 9, 1048.

Javelaud, D., De Reyniès, A., and Mauviel, A. (2018). How Bad Is the Hedgehog? GLI-Dependent, Hedgehog-Independent Cancers on the Importance of Biomarkers for Proper Patients Selection. J. Investig. Dermatol. Symp. Proc. 19, S87–S88.

Jonchere, V., Marisa, L., Greene, M., Virouleau, A., Buhard, O., Bertrand, R., Svrcek, M., Cervera, P., Goloudina, A., Guillerm, E., et al. (2018). Identification of Positively and Negatively Selected Driver Gene Mutations Associated With Colorectal Cancer With Microsatellite Instability. Cell Mol Gastroenterol Hepatol 6, 277–300.

Kamoun, A., Cancel-Tassin, G., Fromont, G., Elarouci, N., Armenoult, L., Ayadi, M., Irani, J., Leroy, X., Villers, A., Fournier, G., et al. (2018). Comprehensive molecular classification of localized prostate adenocarcinoma reveals a tumour subtype predictive of non-aggressive disease. Ann. Oncol. 29, 1814–1821.

Lenglet, M., Robriquet, F., Schwarz, K., Camps, C., Couturier, A., Hoogewijs, D., Buffet, A., Knight, S.J.L., Gad, S., Couvé, S., et al. (2018). Identification of a new VHL exon and complex splicing alterations in familial erythrocytosis or von Hippel-Lindau disease. Blood 132, 469–483.

Lomberk, G., Blum, Y., Nicolle, R., Nair, A., Gaonkar, K.S., Marisa, L., Mathison, A., Sun, Z., Yan, H., Elarouci, N., et al. (2018). Distinct epigenetic landscapes underlie the pathobiology of pancreatic cancer subtypes. Nat Commun 9, 1978.

Marisa, L., Svrcek, M., Collura, A., Becht, E., Cervera, P., Wanherdrick, K., Buhard, O., Goloudina, A., Jonchère, V., Selves, J., et al. (2018). The Balance Between Cytotoxic T-cell Lymphocytes and Immune Checkpoint Expression in the Prognosis of Colon Tumors. J. Natl. Cancer Inst. 110.

Petitprez, F., Vano, Y.A., Becht, E., Giraldo, N.A., de Reyniès, A., Sautès-Fridman, C., and Fridman, W.H. (2018a). Transcriptomic analysis of the tumor microenvironment to guide prognosis and immunotherapies. Cancer Immunol. Immunother. 67, 981–988.

Petitprez, F., Sun, C.-M., Lacroix, L., Sautès-Fridman, C., de Reyniès, A., and Fridman, W.H. (2018b). Quantitative Analyses of the Tumor Microenvironment Composition and Orientation in the Era of Precision Medicine. Front Oncol 8, 390.

Puleo, F., Nicolle, R., Blum, Y., Cros, J., Marisa, L., Demetter, P., Quertinmont, E., Svrcek, M., Elarouci, N., Iovanna, J., et al. (2018). Stratification of Pancreatic Ductal Adenocarcinomas Based on Tumor and Microenvironment Features. Gastroenterology.

Rosenberg, S., Ducray, F., Alentorn, A., Dehais, C., Elarouci, N., Kamoun, A., Marie, Y., Tanguy, M.-L., De Reynies, A., Mokhtari, K., et al. (2018). Machine Learning for Better Prognostic Stratification and Driver Gene Identification Using Somatic Copy Number Variations in Anaplastic Oligodendroglioma. Oncologist.

Uchuya-Castillo, J., Aznar, N., Frau, C., Martinez, P., Le Nevé, C., Marisa, L., Penalva, L.O.F., Laurent-Puig, P., Puisieux, A., Scoazec, J.-Y., et al. (2018). Increased expression of the thyroid hormone nuclear receptor TRα1 characterizes intestinal tumors with high Wnt activity. Oncotarget 9, 30979–30996.

Verbiest, A., Lambrechts, D., Van Brussel, T., Couchy, G., Wozniak, A., Méjean, A., Lerut, E., Oudard, S., Verkarre, V., Job, S., et al. (2018a). Polymorphisms in the Von Hippel-Lindau Gene Are Associated With Overall Survival in Metastatic Clear-Cell Renal-Cell Carcinoma Patients Treated With VEGFR Tyrosine Kinase Inhibitors. Clin Genitourin Cancer.

Verbiest, A., Couchy, G., Job, S., Caruana, L., Lerut, E., Oyen, R., de Reyniès, A., Tosco, L., Joniau, S., Van Poppel, H., et al. (2018b). Molecular Subtypes of Clear-cell Renal Cell Carcinoma are Prognostic for Outcome After Complete Metastasectomy. Eur. Urol.

Verbiest, A., Couchy, G., Job, S., Zucman-Rossi, J., Caruana, L., Lerut, E., Oyen, R., de Reyniès, A., Laguerre, B., Rioux-Leclercq, N., et al. (2018c). Molecular Subtypes of Clear Cell Renal Cell Carcinoma Are Associated With Outcome During Pazopanib Therapy in the Metastatic Setting. Clin Genitourin Cancer 16, e605–e612.

Publications, 2017

Bian, B., Bigonnet, M., Gayet, O., Loncle, C., Maignan, A., Gilabert, M., Moutardier, V., Garcia, S., Turrini, O., Delpero, J.-R., et al. (2017). Gene expression profiling of patient-derived pancreatic cancer xenografts predicts sensitivity to the BET bromodomain inhibitor JQ1: implications for individualized medicine efforts. EMBO Mol Med 9, 482–497.

Bubien, V., Bonnet, F., Dupiot-Chiron, J., Barouk-Simonet, E., Jones, N., de Reynies, A., MacGrogan, G., Sevenet, N., Letouzé, E., and Longy, M. (2017). Combined tumor genomic profiling and exome sequencing in a breast cancer family implicates ATM in tumorigenesis: A proof of principle study. Genes Chromosomes Cancer 56, 788–799.

Jalaguier, S., Teyssier, C., Nait Achour, T., Lucas, A., Bonnet, S., Rodriguez, C., Elarouci, N., Lapierre, M., and Cavaillès, V. (2017). Complex regulation of LCoR signaling in breast cancer cells. Oncogene 36, 4790–4801.

Nguyen, A., Moussallieh, F.M., Mackay, A., Cicek, A.E., Coca, A., Pierre Chenard, M., Weingertner, N., Lhermitte, B., Letouzé, E., Guérin, E., et al. (2017). Characterization of the transcriptional and metabolic responses of pediatric high grade gliomas to mTOR-HIF-1a axis inhibition. Oncotarget.

Nicolle, R., Blum, Y., Marisa, L., Loncle, C., Gayet, O., Moutardier, V., Turrini, O., Giovannini, M., Bian, B., Bigonnet, M., et al. (2017). Pancreatic Adenocarcinoma Therapeutic Targets Revealed by Tumor-Stroma Cross-Talk Analyses in Patient-Derived Xenografts. Cell Rep 21, 2458–2470.

Pandey, S., Mourcin, F., Marchand, T., Nayar, S., Guirriec, M., Pangault, C., Monvoisin, C., Amé-Thomas, P., Guilloton, F., Dulong, J., et al. (2017). IL-4/CXCL12 loop is a key regulator of lymphoid stroma function in follicular lymphoma. Blood 129, 2507–2518.

Patitucci, C., Couchy, G., Bagattin, A., Cañeque, T., de Reyniès, A., Scoazec, J.-Y., Rodriguez, R., Pontoglio, M., Zucman-Rossi, J., Pende, M., et al. (2017). Hepatocyte nuclear factor 1α suppresses steatosis-associated liver cancer by inhibiting PPARγ transcription. J. Clin. Invest. 127, 1873–1888.

Pilati, C., Taieb, J., Balogoun, R., Marisa, L., de Reyniès, A., and Laurent-Puig, P. (2017). CDX2 prognostic value in stage II/III resected colon cancer is related to CMS classification. Ann. Oncol. 28, 1032–1035.

Romain, B., Benbrika-Nehmar, R., Marisa, L., Legrain, M., Lobstein, V., Oravecz, A., Poidevin, L., Bour, C., Freund, J.-N., Duluc, I., et al. (2017). Histone hypoacetylation contributes to CXCL12 downregulation in colon cancer: impact on tumor growth and cell migration. Oncotarget 8, 38351–38366.

Tranchant, R., Quetel, L., Tallet, A., Meiller, C., Renier, A., de Koning, L., de Reynies, A., Le Pimpec-Barthes, F., Zucman-Rossi, J., Jaurand, M.-C., et al. (2017). Co-occurring Mutations of Tumor Suppressor Genes, LATS2 and NF2, in Malignant Pleural Mesothelioma. Clin. Cancer Res. 23, 3191–3202.

Publications, 2016

Becht, E., Giraldo, N.A., Lacroix, L., Buttard, B., Elarouci, N., Petitprez, F., Selves, J., Laurent-Puig, P., Sautès-Fridman, C., Fridman, W.H., et al. (2016a). Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression. Genome Biol. 17, 218.

Becht, E., Giraldo, N.A., Germain, C., de Reyniès, A., Laurent-Puig, P., Zucman-Rossi, J., Dieu-Nosjean, M.-C., Sautès-Fridman, C., and Fridman, W.H. (2016b). Immune Contexture, Immunoscore, and Malignant Cell Molecular Subgroups for Prognostic and Theranostic Classifications of Cancers. Adv. Immunol. 130, 95–190.

Becht, E., de Reyniès, A., Giraldo, N.A., Pilati, C., Buttard, B., Lacroix, L., Sèlves, J., Sautès-Fridman, C., Laurent-Puig, P., and Fridman, W.-H. (2016c). Immune and stromal classification of colorectal cancer is associated with molecular subtypes and relevant for precision immunotherapy. Clin. Cancer Res.

Buhard, O., Lagrange, A., Guilloux, A., Colas, C., Chouchène, M., Wanherdrick, K., Coulet, F., Guillerm, E., Dorard, C., Marisa, L., et al. (2016). HSP110 T17 simplifies and improves the microsatellite instability testing in patients with colorectal cancer. J. Med. Genet.

Callari, M., Cappelletti, V., Aiuto, F. D’, Musella, V., Lembo, A., Petel, F., Karn, T., Iwamoto, T., Provero, P., Daidone, M.G., et al. (2016). Subtype-Specific Metagene-Based Prediction of Outcome after Neoadjuvant and Adjuvant Treatment in Breast Cancer. Clin. Cancer Res. 22, 337–345.

Kamoun, A., Idbaih, A., Dehais, C., Elarouci, N., Carpentier, C., Letouzé, E., Colin, C., Mokhtari, K., Jouvet, A., Uro-Coste, E., et al. (2016). Integrated multi-omics analysis of oligodendroglial tumours identifies three subgroups of 1p/19q co-deleted gliomas. Nat Commun 7, 11263.

Thuault, S., Comunale, F., Hasna, J., Fortier, M., Planchon, D., Elarouci, N., De Reynies, A., Bodin, S., Blangy, A., and Gauthier-Rouvière, C. (2016). The RhoE/ROCK/ARHGAP25 signaling pathway controls cell invasion by inhibition of Rac activity. Mol. Biol. Cell 27, 2653–2661.

Publications, 2015

Amé-Thomas, P., Hoeller, S., Artchounin, C., Misiak, J., Braza, M.S., Jean, R., Le Priol, J., Monvoisin, C., Martin, N., Gaulard, P., et al. (2015). CD10 delineates a subset of human IL-4 producing follicular helper T cells involved in the survival of follicular lymphoma B cells. Blood 125, 2381–2385.

Amin, R., Mourcin, F., Uhel, F., Pangault, C., Ruminy, P., Dupré, L., Guirriec, M., Marchand, T., Fest, T., Lamy, T., et al. (2015). DC-SIGN-expressing macrophages trigger activation of mannosylated IgM B-cell receptor in follicular lymphoma. Blood 126, 1911–1920.

Becht, E., Giraldo, N.A., Beuselinck, B., Job, S., Marisa, L., Vano, Y., Oudard, S., Zucman-Rossi, J., Laurent-Puig, P., Sautès-Fridman, C., et al. (2015a). Prognostic and theranostic impact of molecular subtypes and immune classifications in renal cell cancer (RCC) and colorectal cancer (CRC). Oncoimmunology 4, e1049804.

Becht, E., de Reyniès, A., and Fridman, W.H. (2015b). Integrating tumor microenvironment with cancer molecular classifications. Genome Med 7, 115.

Bertoin, F., Letouzé, E., Grignani, P., Patey, M., Rossignol, S., Libé, R., Pasqual, C., Lardière-Deguelte, S., Hoeffel-Fornes, C., Gaillard, D., et al. (2015). Genome-wide paternal uniparental disomy as a cause of beckwith-wiedemann syndrome associated with recurrent virilizing adrenocortical tumors. Horm. Metab. Res. 47, 497–503.

Le Bescont, A., Vitte, A.-L., Debernardi, A., Curtet, S., Buchou, T., Vayr, J., de Reyniès, A., Ito, A., Guardiola, P., Brambilla, C., et al. (2015). Receptor-Independent Ectopic Activity of Prolactin Predicts Aggressive Lung Tumors and Indicates HDACi-Based Therapeutic Strategies. Antioxid. Redox Signal. 23, 1–14.

Beuselinck, B., Job, S., Becht, E., Karadimou, A., Verkarre, V., Couchy, G., Giraldo, N., Rioux-Leclercq, N., Molinié, V., Sibony, M., et al. (2015a). Molecular subtypes of clear cell renal cell carcinoma are associated with sunitinib response in the metastatic setting. Clin. Cancer Res. 21, 1329–1339.

Beuselinck, B., Jean-Baptiste, J., Couchy, G., Job, S., De Reynies, A., Wolter, P., Théodore, C., Gravis, G., Rousseau, B., Albiges, L., et al. (2015b). RANK/OPG ratio of expression in primary clear-cell renal cell carcinoma is associated with bone metastasis and prognosis in patients treated with anti-VEGFR-TKIs. Br. J. Cancer 113, 1313–1322.

Castro-Vega, L.J., Letouzé, E., Burnichon, N., Buffet, A., Disderot, P.-H., Khalifa, E., Loriot, C., Elarouci, N., Morin, A., Menara, M., et al. (2015). Multi-omics analysis defines core genomic alterations in pheochromocytomas and paragangliomas. Nat Commun 6, 6044.

De Cubas, A.A., Korpershoek, E., Inglada-Pérez, L., Letouzé, E., Currás-Freixes, M., Fernández, A.F., Comino-Méndez, I., Schiavi, F., Mancikova, V., Eisenhofer, G., et al. (2015). DNA Methylation Profiling in Pheochromocytoma and Paraganglioma Reveals Diagnostic and Prognostic Markers. Clin. Cancer Res. 21, 3020–3030.

Guinney, J., Dienstmann, R., Wang, X., de Reyniès, A., Schlicker, A., Soneson, C., Marisa, L., Roepman, P., Nyamundanda, G., Angelino, P., et al. (2015). The consensus molecular subtypes of colorectal cancer. Nat. Med. 21, 1350–1356.

Hanns, E., Job, S., Coliat, P., Wasylyk, C., Ramolu, L., Pencreach, E., Suarez-Carmona, M., Herfs, M., Ledrappier, S., Macabre, C., et al. (2015). Human Papillomavirus-related tumours of the oropharynx display a lower tumour hypoxia signature. Oral Oncol. 51, 848–856.

Labreche, K., Simeonova, I., Kamoun, A., Gleize, V., Chubb, D., Letouzé, E., Riazalhosseini, Y., Dobbins, S.E., Elarouci, N., Ducray, F., et al. (2015). TCF12 is mutated in anaplastic oligodendroglioma. Nat Commun 6, 7207.

Lebret, T., Neuzillet, Y., Houede, N., Rebouissou, S., Bernard-Pierrot, I., Reynies, A.D., Benhamou, S., Allory, Y., and Radvanyi, F. (2015). Identification of targeted therapy for an aggressive subgroup of muscle-invasive bladder cancers. Molecular & Cellular Oncology.

Lefèvre, L., Omeiri, H., Drougat, L., Hantel, C., Giraud, M., Val, P., Rodriguez, S., Perlemoine, K., Blugeon, C., Beuschlein, F., et al. (2015). Combined transcriptome studies identify AFF3 as a mediator of the oncogenic effects of β-catenin in adrenocortical carcinoma. Oncogenesis 4, e161.

Manceau, G., Marisa, L., Boige, V., Duval, A., Gaub, M.-P., Milano, G., Selves, J., Olschwang, S., Jooste, V., le Legrain, M., et al. (2015). PIK3CA mutations predict recurrence in localized microsatellite stable colon cancer. Cancer Med 4, 371–382.

Villanueva, A., Portela, A., Sayols, S., Battiston, C., Hoshida, Y., Méndez-González, J., Imbeaud, S., Letouzé, E., Hernandez-Gea, V., Cornella, H., et al. (2015). DNA methylation-based prognosis and epidrivers in hepatocellular carcinoma. Hepatology 61, 1945–1956.

Publications, 2014

Ablain, J., Rice, K., Soilihi, H., de Reynies, A., Minucci, S., and de Thé, H. (2014). Activation of a promyelocytic leukemia–tumor protein 53 axis underlies acute promyelocytic leukemia cure. Nature Medicine 20, 167–174.

Assie, G., Letouze, E., Fassnacht, M., Jouinot, A., Luscap, W., Barreau, O., Omeiri, H., Rodriguez, S., Perlemoine, K., Rene-Corail, F., et al. (2014). Integrated genomic characterization of adrenocortical carcinoma. Nat Genet 46, 607–612.

Bénit, P., Letouzé, E., Rak, M., Aubry, L., Burnichon, N., Favier, J., Gimenez-Roqueplo, A.-P., and Rustin, P. (2014). Unsuspected task for an old team: Succinate, fumarate and other Krebs cycle acids in metabolic remodeling. Biochimica et Biophysica Acta (BBA) – Bioenergetics 1837, 1330–1337.

Biton, A., Bernard-Pierrot, I., Lou, Y., Krucker, C., Chapeaublanc, E., Rubio-Pérez, C., López-Bigas, N., Kamoun, A., Neuzillet, Y., Gestraud, P., et al. (2014). Independent component analysis uncovers the landscape of the bladder tumor transcriptome and reveals insights into luminal and basal subtypes. Cell Rep. 9, 1235–1245.

Brambilla, C., Laffaire, J., Lantuejoul, S., Moro-Sibilot, D., Mignotte, H., Arbib, F., Toffart, A.-C., Petel, F., Hainaut, P., Rousseaux, S., et al. (2014). Lung squamous cell carcinomas with basaloid histology represent a specific molecular entity. Clin. Cancer Res. 20, 5777–5786.

Collura, A., Lagrange, A., Svrcek, M., Marisa, L., Buhard, O., Guilloux, A., Wanherdrick, K., Dorard, C., Taieb, A., Saget, A., et al. (2014). Patients With Colorectal Tumors With Microsatellite Instability and Large Deletions in HSP110 T17 Have Improved Response to 5-Fluorouracil–Based Chemotherapy. Gastroenterology 146, 401–411.e1.

Doyen, J., Letouzé, E., Marisa, L., de Reyniès, A., Milano, G., Etienne-Grimaldi, M.-C., Olschwang, S., Gaedcke, J., Ghadimi, M., and Gérard, J.-P. (2014). High-resolution analysis of DNA copy number alterations in rectal cancer: correlation with metastasis, survival, and mRNA expression. Strahlenther Onkol 190, 1028–1036.

Figarella-Branger, D., Mokhtari, K., Dehais, C., Jouvet, A., Uro-Coste, E., Colin, C., Carpentier, C., Forest, F., Maurage, C.-A., Vignaud, J.-M., et al. (2014). Mitotic index, microvascular proliferation, and necrosis define 3 groups of 1p/19q codeleted anaplastic oligodendrogliomas associated with different genomic alterations. Neuro-Oncology 16, 1244–1254.

Guillaud-Bataille, M., Ragazzon, B., de Reyniès, A., Chevalier, C., Francillard, I., Barreau, O., Steunou, V., Guillemot, J., Tissier, F., Rizk-Rabin, M., et al. (2014). IGF2 promotes growth of adrenocortical carcinoma cells, but its overexpression does not modify phenotypic and molecular features of adrenocortical carcinoma. PLoS ONE 9, e103744.

Hadoux, J., Favier, J., Scoazec, J.-Y., Leboulleux, S., Al Ghuzlan, A., Caramella, C., Déandreis, D., Borget, I., Loriot, C., Chougnet, C., et al. (2014). SDHB mutations are associated with response to temozolomide in patients with metastatic pheochromocytoma or paraganglioma. Int. J. Cancer 135, 2711–2720.

Kirzin, S., Marisa, L., Guimbaud, R., De Reynies, A., Legrain, M., Laurent-Puig, P., Cordelier, P., Pradère, B., Bonnet, D., Meggetto, F., et al. (2014). Sporadic early-onset colorectal cancer is a specific sub-type of cancer: a morphological, molecular and genetics study. PLoS ONE 9, e103159.

Malouf, G.G., Job, S., Paradis, V., Fabre, M., Brugières, L., Saintigny, P., Vescovo, L., Belghiti, J., Branchereau, S., Faivre, S., et al. (2014). Transcriptional profiling of pure fibrolamellar hepatocellular carcinoma reveals an endocrine signature. Hepatology 59, 2228–2237.

Morin, A., Letouzé, E., Gimenez-Roqueplo, A.-P., and Favier, J. (2014). Oncometabolites-driven tumorigenesis: From genetics to targeted therapy. Int. J. Cancer 135, 2237–2248.

Pilati, C., Letouzé, E., Nault, J.-C., Imbeaud, S., Boulai, A., Calderaro, J., Poussin, K., Franconi, A., Couchy, G., Morcrette, G., et al. (2014). Genomic Profiling of Hepatocellular Adenomas Reveals Recurrent FRK-Activating Mutations and the Mechanisms of Malignant Transformation. Cancer Cell 25, 428–441.

Rebouissou, S., Bernard-Pierrot, I., de Reyniès, A., Lepage, M.-L., Krucker, C., Chapeaublanc, E., Hérault, A., Kamoun, A., Caillault, A., Letouzé, E., et al. (2014). EGFR as a potential therapeutic target for a subset of muscle-invasive bladder cancers presenting a basal-like phenotype. Sci Transl Med 6, 244ra91.

Reyes-Botero, G., Dehais, C., Idbaih, A., Martin-Duverneuil, N., Lahutte, M., Carpentier, C., Letouzé, E., Chinot, O., Loiseau, H., Honnorat, J., et al. (2014). Contrast enhancement in 1p/19q-codeleted anaplastic oligodendrogliomas is associated with 9p loss, genomic instability, and angiogenic gene expression. Neuro-Oncology 16, 662–670.

De Reynies, A., Jaurand, M.-C., Renier, A., Couchy, G., Hysi, I., Elarouci, N., Galateau-Salle, F., Copin, M.-C., Hofman, P., Cazes, A., et al. (2014). Molecular Classification of Malignant Pleural Mesothelioma: Identification of a Poor Prognosis Subgroup Linked to the Epithelial-to-Mesenchymal Transition. Clinical Cancer Research 20, 1323–1334.

Vitaliano-Prunier, A., Halftermeyer, J., Ablain, J., de Reynies, A., Peres, L., Le Bras, M., Metzger, D., and de Thé, H. (2014). Clearance of PML/RARA-bound promoters suffice to initiate APL differentiation. Blood 124, 3772–3780.

Publications, 2013

Auguste T, Travert M, Tarte K, Amé-Thomas P, Artchounin C, Martin-Garcia N, de Reyniès A, de Leval L, Gaulard P, Delfau-Larue MH (2013). ROQUIN/RC3H1 alterations are not found in angioimmunoblastic T-cell lymphoma. PLoS One. 8(6), e64536.

Barreau, O., Assié, G., Wilmot-Roussel, H., Ragazzon, B., Baudry, C., Perlemoine, K., René-Corail, F., Bertagna, X., Dousset, B., Hamzaoui, N., et al. (2013). Identification of a CpG island methylator phenotype in adrenocortical carcinomas. J. Clin. Endocrinol. Metab. 98, E174–184.

Bertucci, F., Finetti, P., Roche, H., Le Doussal, J.M., Marisa, L., Martin, A.L., Lacroix-Triki, M., Blanc-Fournier, C., Jacquemier, J., Peyro-Saint-Paul, H., et al. (2013). Comparison of the prognostic value of genomic grade index, Ki67 expression and mitotic activity index in early node-positive breast cancer patients. Ann. Oncol. 24, 625–632.

Bisig B, de Reyniès A, Bonnet C, Sujobert P, Rickman DS, Marafioti T, Delsol G, Lamant L, Gaulard P, de Leval L (2013). CD30-positive peripheral T-cell lymphomas share molecular and phenotypic features. Haematologica. 98(8), 1250-8.

Collura, A., Marisa, L., Trojan, D., Buhard, O., Lagrange, A., Saget, A., Bombled, M., Méchighel, P., Ayadi, M., Muleris, M., et al. (2013). Extensive characterization of sphere models established from colorectal cancer cell lines. Cell. Mol. Life Sci. 70, 729–742.

El Behi M, Krumeich S, Lodillinsky C, Kamoun A, Tibaldi L, Sugano G, de Reyniès A, Chapeaublanc E, Laplanche A, Lebret T, Allory Y, Radvanyi F, Lantz O, Eiján AM, Bernard-Pierrot I, Théry C (2013). An essential role for decorin in bladder cancer invasiveness. EMBO Mol Med. 5(12), 1835-51.

Jung, A., Job, S., Ledrappier, S., Macabre, C., Abecassis, J., de Reyniès, A., Wasylyk, B. (2013). A poor prognosis subtype of HNSCC is consistently observed across methylome, transcriptome and miRNome analysis. Clin. Cancer Res. 19, 4174-84.

Jung, A.C., Guihard, S., Krugell, S., Ledrappier, S., Brochot, A., Dalstein, V., Job, S., de Reyniès, A., Noël, G., Wasylyk, B., et al. (2013). CD8-alpha T-cell infiltration in human papillomavirus-related oropharyngeal carcinoma correlates with improved patient prognosis. Int. J. Cancer 132, E26–36.

Letouzé, E., Martinelli, C., Loriot, C., Burnichon, N., Abermil, N., Ottolenghi, C., Janin, M., Menara, M., Nguyen, A.T., Benit, P., et al. (2013). SDH Mutations Establish a Hypermethylator Phenotype in Paraganglioma. Cancer Cell 23, 739–752.

Manceau, G., Letouzé, E., Guichard, C., Didelot, A., Cazes, A., Corté, H., Fabre, E., Pallier, K., Imbeaud, S., Le Pimpec-Barthes, F., et al. (2013). Recurrent inactivating mutations of ARID2 in non-small cell lung carcinoma. Int. J. Cancer 132, 2217–2221.

Marisa, L., de Reyniès, A., Duval, A., Selves, J., Gaub, M.P., Vescovo, L., Etienne-Grimaldi, M.-C., Schiappa, R., Guenot, D., Ayadi, M., et al. (2013). Gene Expression Classification of Colon Cancer into Molecular Subtypes: Characterization, Validation, and Prognostic Value. PLoS Medicine 10, e1001453.

Mikaelian, I., Malek, M., Gadet, R., Viallet, J., Garcia, A., Girard-Gagnepain, A., Hesling, C., Gillet, G., Gonzalo, P., Rimokh, R., et al. (2013). Genetic and pharmacologic inhibition of mTORC1 promotes EMT by a TGF-β-independent mechanism. Cancer Res. 73, 6621–6631.

Nault JC, de Reyniès A, Villanueva A, Calderaro J, Rebouissou S, Couchy G, Decaens T, Franco D, Imbeaud S, Rousseau F, Azoulay D, Saric J, Blanc JF, Balabaud C, Bioulac-Sage P, Laurent A, Laurent-Puig P, Llovet JM, Zucman-Rossi J. (2013). A Hepatocellular Carcinoma 5-Gene Score Associated with Survival of Patients Following Liver Resection. Gastroenterology. 145(1), 176-87.

Rousseaux S, Debernardi A, Baptiste B, Vitte A-L, Vesin A, Nagy-Mignotte H, Moro-Sibilot D, Brichon P-Y, Lantuejoul S, Hainaut P, Laffaire J, de Reyniès A , Beer D. G., Timsit J-F, Brambilla C, Brambilla E, Khochbin S. (2013). Ectopic activation of germline and placenta genes identifies aggressive metastasis-prone lung cancers. Science Translational Medicine, 5(186):186ra66.

Thuault, S., Hayashi, S., Lagirand-Cantaloube, J., Plutoni, C., Comunale, F., Delattre, O., Relaix, F., and Gauthier-Rouvière, C. (2013). P-cadherin is a direct PAX3-FOXO1A target involved in alveolar rhabdomyosarcoma aggressiveness. Oncogene 32, 1876–1887.

Wilmot Roussel H, Vezzosi D, Rizk-Rabin M, Barreau O, Ragazzon B, René-Corail F, de Reyniès A, Bertherat J, Assié G (2013). Identification of gene expression profiles associated with cortisol secretion in adrenocortical adenomas. J Clin Endocrinol Metab. 98, 1109-21.

Publications, 2012

Banneau, G., Ayadi, M., Armenoult, L., and Carvalho, E. (2012). Homogenization of cartilage tumors to extract total RNA to microarray and sequencing analysis using Precellys bead-beating technology. Biotechniques 52, 196–197.

Barreau, O., de Reyniès, A., Wilmot-Roussel, H., Guillaud-Bataille, M., Auzan, C., René-Corail, F., Tissier, F., Dousset, B., Bertagna, X., Bertherat, J., et al. (2012). Clinical and pathophysiological implications of chromosomal alterations in adrenocortical tumors: an integrated genomic approach. J. Clin. Endocrinol. Metab. 97, E301–311.

Bonnet, F., Guedj, M., Jones, N., Sfar, S., Brouste, V., Elarouci, N., Banneau, G., Orsetti, B., Primois, C., Lara, C.T. de Reyniès, A. et al. (2012). An array CGH based genomic instability index (G2I) is predictive of clinical outcome in breast cancer and reveals a subset of tumors without lymph node involvement but with poor prognosis. BMC Medical Genomics 5, 54.

Burnichon, N., Buffet, A., Parfait, B., Letouzé, E., Laurendeau, I., Loriot, C., Pasmant, E., Abermil, N., Valeyrie-Allanore, L., Bertherat, J., et al. (2012). Somatic NF1 inactivation is a frequent event in sporadic pheochromocytoma. Hum. Mol. Genet. 21, 5397–5405.

Filhol, O., Ciais, D., Lajaunie, C., Charbonnier, P., Foveau, N., Vert, J.-P., and Vandenbrouck, Y. (2012). DSIR: Assessing the Design of Highly Potent siRNA by Testing a Set of Cancer-Relevant Target Genes. PLoS ONE 7, e48057.

Fouret, R., Laffaire, J., Hofman, P., Beau-Faller, M., Mazieres, J., Validire, P., Girard, P., Camilleri-Bröet, S., Vaylet, F., Leroy-Ladurie, F., et al. (2012). A comparative and integrative approach identifies ATPase family, AAA domain containing 2 as a likely driver of cell proliferation in lung adenocarcinoma. Clin. Cancer Res. 18, 5606–5616.

Gérard JP, Baulieux J, Doyen J, Gal J, Letouze E, Olschwang S, Chapet O, Romestaing P. (2012) Towards a « Lyon molecular signature » to individualize the treatment of rectal cancer. Prognostic analysis of a prospective cohort of 94 rectal cancers T1-2-3 Nx MO to be the basis of a molecular signature. Cancer Radiother.16(8), 688-96.

Guedj, M., Marisa, L., de Reyniès, A., Orsetti, B., Schiappa, R., Bibeau, F., MacGrogan, G., Lerebours, F., Finetti, P., Longy, M., et al. (2012). A refined molecular taxonomy of breast cancer. Oncogene 31, 1196–1206.

Guichard, C., Amaddeo, G., Imbeaud, S., Ladeiro, Y., Pelletier, L., Maad, I.B., Calderaro, J., Bioulac-Sage, P., Letexier, M., Degos, F., et al. (2012). Integrated analysis of somatic mutations and focal copy-number changes identifies key genes and pathways in hepatocellular carcinoma. Nat. Genet. 44, 694–698.

Idbaih A, Ducray F, Dehais C, Courdy C, Carpentier C, de Bernard S, Uro-Coste E, Mokhtari K, Jouvet A, Honnorat J, Chinot O, Ramirez C, Beauchesne P, Benouaich-Amiel A, et al. (2012). SNP array analysis reveals novel genomic abnormalities including copy neutral loss of heterozygosity in anaplastic oligodendrogliomas. PLoS One. 7(10), e45950.

Letouzé, E., Rosati, R., Komechen, H., Doghman, M., Marisa, L., Flück, C., de Krijger, R.R., van Noesel, M.M., Mas, J.-C., Pianovski, M.A.D., et al. (2012a). SNP array profiling of childhood adrenocortical tumors reveals distinct pathways of tumorigenesis and highlights candidate driver genes. J. Clin. Endocrinol. Metab. 97, E1284–1293.

Letouzé, E., Sow, A., Petel, F., Rosati, R., Figueiredo, B.C., Burnichon, N., Gimenez-Roqueplo, A.-P., Lalli, E., and de Reyniès, A. (2012b). Identity by Descent Mapping of Founder Mutations in Cancer Using High-Resolution Tumor SNP Data. PLoS ONE 7, e35897.

Loriot, C., Burnichon, N., Gadessaud, N., Vescovo, L., Amar, L., Libé, R., Bertherat, J., Plouin, P.-F., Jeunemaitre, X., Gimenez-Roqueplo, A.-P., et al. (2012). Epithelial to mesenchymal transition is activated in metastatic pheochromocytomas and paragangliomas caused by SDHB gene mutations. J. Clin. Endocrinol. Metab. 97, E954–962.

Missiaglia, E., Williamson, D., Chisholm, J., Wirapati, P., Pierron, G., Petel, F., Concordet, J.-P., Thway, K., Oberlin, O., Pritchard-Jones, K., et al. (2012). PAX3/FOXO1 fusion gene status is the key prognostic molecular marker in rhabdomyosarcoma and significantly improves current risk stratification. J. Clin. Oncol. 30, 1670–1677.

Rebouissou, S., Hérault, A., Letouzé, E., Neuzillet, Y., Laplanche, A., Ofualuka, K., Maillé, P., Leroy, K., Riou, A., Lepage, M.-L., et al. (2012). CDKN2A homozygous deletion is associated with muscle invasion in FGFR3-mutated urothelial bladder carcinoma. J. Pathol. 227, 315–324.

Rouault, A., Banneau, G., Macgrogan, G., Jones, N., Elarouci, N., Barouk-Simonet, E., Venat, L., Coupier, I., Letouzé, E., de Reyniès, A., et al. (2012). Deletion of chromosomes 13q and 14q is a common feature of tumors with BRCA2 mutations. PLoS ONE 7, e52079.

Travert, M., Huang, Y., de Leval, L., Martin-Garcia, N., Delfau-Larue, M.-H., Berger, F., Bosq, J., Brière, J., Soulier, J., Macintyre, E., et al. (2012). Molecular features of hepatosplenic T-cell lymphoma unravels potential novel therapeutic targets. Blood 119, 5795–5806.

Publications, 2011

Burnichon, N., Lepoutre-Lussey, C., Laffaire, J., Gadessaud, N., Molinié, V., Hernigou, A., Plouin, P.-F., Jeunemaitre, X., Favier, J., and Gimenez-Roqueplo, A.-P. (2011a). A novel TMEM127 mutation in a patient with familial bilateral pheochromocytoma. Eur. J. Endocrinol. 164, 141–145.

Burnichon, N., Vescovo, L., Amar, L., Libé, R., de Reyniès, A., Venisse, A., Jouanno, E., Laurendeau, I., Parfait, B., Bertherat, J., et al. (2011b). Integrative genomic analysis reveals somatic mutations in pheochromocytoma and paraganglioma. Hum. Mol. Genet. 20, 3974–3985.

Dorard, C., de Thonel, A., Collura, A., Marisa, L., Svrcek, M., Lagrange, A., Jego, G., Wanherdrick, K., Joly, A.L., Buhard, O., et al. (2011). Expression of a mutant HSP110 sensitizes colorectal cancer cells to chemotherapy and improves disease prognosis. Nat. Med. 17, 1283–1289.

Jean, D., Thomas, E., Manié, E., Renier, A., de Reyniès, A., Lecomte, C., Andujar, P., Fleury-Feith, J., Galateau-Sallé, F., Giovannini, M., et al. (2011). Syntenic relationships between genomic profiles of fiber-induced murine and human malignant mesothelioma. Am. J. Pathol. 178, 881–894.

Laffaire, J., Everhard, S., Idbaih, A., Crinière, E., Marie, Y., de Reyniès, A., Schiappa, R., Mokhtari, K., Hoang-Xuan, K., Sanson, M., et al. (2011). Methylation profiling identifies 2 groups of gliomas according to their tumorigenesis. Neuro-oncology 13, 84–98.

Ragazzon, B., Assié, G., and Bertherat, J. (2011). Transcriptome analysis of adrenocortical cancers: from molecular classification to the identification of new treatments. Endocr. Relat. Cancer 18, R15–27.

Publications, 2010

Ayoub, C., Wasylyk, C., Li, Y., Thomas, E., Marisa, L., Robé, A., Roux, M., Abecassis, J., de Reyniès, A., and Wasylyk, B. (2010). ANO1 amplification and expression in HNSCC with a high propensity for future distant metastasis and its functions in HNSCC cell lines. Br. J. Cancer 103, 715–726.

Banneau, G., Guedj, M., MacGrogan, G., de Mascarel, I., Velasco, V., Schiappa, R., Bonadona, V., David, A., Dugast, C., Gilbert-Dussardier, B., et al. (2010). Molecular apocrine differentiation is a common feature of breast cancer in patients with germline PTEN mutations. Breast Cancer Res. 12, R63.

Bryant, C.M., Albertus, D.L., Kim, S., Chen, G., Brambilla, C., Guedj, M., Arima, C., Travis, W.D., Yatabe, Y., Takahashi, T., et al. (2010). Clinically relevant characterization of lung adenocarcinoma subtypes based on cellular pathways: an international validation study. PLoS ONE 5, e11712.

Burnichon, N., Brière, J.-J., Libé, R., Vescovo, L., Rivière, J., Tissier, F., Jouanno, E., Jeunemaitre, X., Bénit, P., Tzagoloff, A., et al. (2010). SDHA is a tumor suppressor gene causing paraganglioma. Hum. Mol. Genet. 19, 3011–3020.

Cairo, S., Wang, Y., de Reyniès, A., Duroure, K., Dahan, J., Redon, M.-J., Fabre, M., McClelland, M., Wang, X.W., Croce, C.M., et al. (2010). Stem cell-like micro-RNA signature driven by Myc in aggressive liver cancer. Proc. Natl. Acad. Sci. U.S.A. 107, 20471–20476.

Chibon, F., Lagarde, P., Salas, S., Pérot, G., Brouste, V., Tirode, F., Lucchesi, C., de Reyniès, A., Kauffmann, A., Bui, B., et al. (2010). Validated prediction of clinical outcome in sarcomas and multiple types of cancer on the basis of a gene expression signature related to genome complexity. Nat. Med. 16, 781–787.

Cizkova M, Cizeron-Clairac G, Vacher S, Susini A, Andrieu C, Lidereau R, Bièche I (2010). Gene expression profiling reveals new aspects of PIK3CA mutation in ERalpha-positive breast cancer: major implication of the Wnt signaling pathway. PLoS One. 5(12), e15647.

Ducray, F., de Reyniès, A., Chinot, O., Idbaih, A., Figarella-Branger, D., Colin, C., Karayan-Tapon, L., Chneiweiss, H., Wager, M., Vallette, F., et al. (2010). An ANOCEF genomic and transcriptomic microarray study of the response to radiotherapy or to alkylating first-line chemotherapy in glioblastoma patients. Mol. Cancer 9, 234.

Huang, Y., de Reyniès, A., de Leval, L., Ghazi, B., Martin-Garcia, N., Travert, M., Bosq, J., Brière, J., Petit, B., Thomas, E., et al. (2010). Gene expression profiling identifies emerging oncogenic pathways operating in extranodal NK/T-cell lymphoma, nasal type. Blood 115, 1226–1237.

Jardin, F., Jais, J.-P., Molina, T.-J., Parmentier, F., Picquenot, J.-M., Ruminy, P., Tilly, H., Bastard, C., Salles, G.-A., Feugier, P., et al. (2010). Diffuse large B-cell lymphomas with CDKN2A deletion have a distinct gene expression signature and a poor prognosis under R-CHOP treatment: a GELA study. Blood 116, 1092–1104.

Jeanmougin, M., de Reyniès, A., Marisa, L., Paccard, C., Nuel, G., and Guedj, M. (2010). Should We Abandon the t-Test in the Analysis of Gene Expression Microarray Data: A Comparison of Variance Modeling Strategies. PLoS ONE 5, e12336.

Job B, Bernheim A, Beau-Faller M, Camilleri-Broët S, Girard P, Hofman P, Mazières J, Toujani S, Lacroix L, Laffaire J, Dessen P, Fouret P; LG Investigators. Genomic aberrations in lung adenocarcinoma in never smokers. PLoS One. 2010 Dec 6;5(12):e15145.

Jung, A.C., Briolat, J., Millon, R., de Reyniès, A., Rickman, D., Thomas, E., Abecassis, J., Clavel, C., and Wasylyk, B. (2010). Biological and clinical relevance of transcriptionally active human papillomavirus (HPV) infection in oropharynx squamous cell carcinoma. Int. J. Cancer 126, 1882–1894.

Perkins, G., Lièvre, A., Ramacci, C., Méatchi, T., de Reyniès, A., Emile, J.-F., Boige, V., Tomasic, G., Bachet, J.-B., Bibeau, F., et al. (2010). Additional value of EGFR downstream signaling phosphoprotein expression to KRAS status for response to anti-EGFR antibodies in colorectal cancer. Int. J. Cancer 127, 1321–1331.

Ragazzon, B., Libé, R., Gaujoux, S., Assié, G., Fratticci, A., Launay, P., Clauser, E., Bertagna, X., Tissier, F., de Reyniès, A., et al. (2010). Transcriptome analysis reveals that p53 and {beta}-catenin alterations occur in a group of aggressive adrenocortical cancers. Cancer Res. 70, 8276–8281.

Salas, S., Chibon, F., Noguchi, T., Terrier, P., Ranchere-Vince, D., Lagarde, P., Benard, J., Forget, S., Blanchard, C., Dômont, J., et al. (2010). Molecular characterization by array comparative genomic hybridization and DNA sequencing of 194 desmoid tumors. Genes Chromosomes Cancer 49, 560–568.

Williamson, D., Missiaglia, E., de Reyniès, A., Pierron, G., Thuille, B., Palenzuela, G., Thway, K., Orbach, D., Laé, M., Fréneaux, P., et al. (2010). Fusion gene-negative alveolar rhabdomyosarcoma is clinically and molecularly indistinguishable from embryonal rhabdomyosarcoma. J. Clin. Oncol. 28, 2151–2158.

Publications, 2009

Corbin, M., de Reyniès, A., Rickman, D.S., Berrebi, D., Boccon-Gibod, L., Cohen-Gogo, S., Fabre, M., Jaubert, F., Faussillon, M., Yilmaz, F., et al. (2009). WNT/beta-catenin pathway activation in Wilms tumors: a unifying mechanism with multiple entries? Genes Chromosomes Cancer 48, 816–827.

Favier, J., Brière, J.-J., Burnichon, N., Rivière, J., Vescovo, L., Benit, P., Giscos-Douriez, I., de Reyniès, A., Bertherat, J., Badoual, C., et al. (2009). The Warburg Effect Is Genetically Determined in Inherited Pheochromocytomas. PLoS ONE 4, e7094.

Pérot, G., Derré, J., Coindre, J.-M., Tirode, F., Lucchesi, C., Mariani, O., Gibault, L., Guillou, L., Terrier, P., and Aurias, A. (2009). Strong smooth muscle differentiation is dependent on myocardin gene amplification in most human retroperitoneal leiomyosarcomas. Cancer Res. 69, 2269–2278.

Rebouissou, S., Amessou, M., Couchy, G., Poussin, K., Imbeaud, S., Pilati, C., Izard, T., Balabaud, C., Bioulac-Sage, P., and Zucman-Rossi, J. (2009). Frequent in-frame somatic deletions activate gp130 in inflammatory hepatocellular tumours. Nature 457, 200–204.

de Reyniès, A., Assié, G., Rickman, D.S., Tissier, F., Groussin, L., René-Corail, F., Dousset, B., Bertagna, X., Clauser, E., and Bertherat, J. (2009). Gene expression profiling reveals a new classification of adrenocortical tumors and identifies molecular predictors of malignancy and survival. J. Clin. Oncol. 27, 1108–1115.

Zagani, R., Hamzaoui, N., Cacheux, W., de Reyniès, A., Terris, B., Chaussade, S., Romagnolo, B., Perret, C., and Lamarque, D. (2009). Cyclooxygenase-2 inhibitors down-regulate osteopontin and Nr4A2-new therapeutic targets for colorectal cancers. Gastroenterology 137, 1358–1366.e1–3.

Publications, 2008

Cairo, S., Armengol, C., de Reyniès, A., Wei, Y., Thomas, E., Renard, C.-A., Goga, A., Balakrishnan, A., Semeraro, M., Gresh, L., et al. (2008). Hepatic stem-like phenotype and interplay of Wnt/beta-catenin and Myc signaling in aggressive childhood liver cancer. Cancer Cell 14, 471–484.

Decaens, T., Godard, C., de Reyniès, A., Rickman, D.S., Tronche, F., Couty, J.-P., Perret, C., and Colnot, S. (2008). Stabilization of beta-catenin affects mouse embryonic liver growth and hepatoblast fate. Hepatology 47, 247–258.

Ducray, F., Idbaih, A., de Reyniès, A., Bièche, I., Thillet, J., Mokhtari, K., Lair, S., Marie, Y., Paris, S., Vidaud, M., et al. (2008). Anaplastic oligodendrogliomas with 1p19q codeletion have a proneural gene expression profile. Mol. Cancer 7, 41.

Hacein-Bey-Abina, S., Garrigue, A., Wang, G.P., Soulier, J., Lim, A., Morillon, E., Clappier, E., Caccavelli, L., Delabesse, E., Beldjord, K., et al. (2008). Insertional oncogenesis in 4 patients after retrovirus-mediated gene therapy of SCID-X1. J. Clin. Invest. 118, 3132–3142.

Idbaih, A., Marie, Y., Lucchesi, C., Pierron, G., Manié, E., Raynal, V., Mosseri, V., Hoang-Xuan, K., Kujas, M., Brito, I., et al. (2008). BAC array CGH distinguishes mutually exclusive alterations that define clinicogenetic subtypes of gliomas. Int. J. Cancer 122, 1778–1786.

Idbaih, A., Paris, S., Boisselier, B., Marie, Y., Sanson, M., Thillet, J., Hoang-Xuan, K., and Delattre, J.-Y. (2008b). Mutational analysis of Rac2 in gliomas. J. Neurooncol. 87, 365–366.

Jais, J.-P., Haioun, C., Molina, T.J., Rickman, D.S., de Reyniès, A., Berger, F., Gisselbrecht, C., Brière, J., Reyes, F., Gaulard, P., et al. (2008). The expression of 16 genes related to the cell of origin and immune response predicts survival in elderly patients with diffuse large B-cell lymphoma treated with CHOP and rituximab. Leukemia 22, 1917–1924.

Janoueix-Lerosey, I., Lequin, D., Brugières, L., Ribeiro, A., de Pontual, L., Combaret, V., Raynal, V., Puisieux, A., Schleiermacher, G., Pierron, G., et al. (2008). Somatic and germline activating mutations of the ALK kinase receptor in neuroblastoma. Nature 455, 967–970.

Ladeiro, Y., Couchy, G., Balabaud, C., Bioulac-Sage, P., Pelletier, L., Rebouissou, S., and Zucman-Rossi, J. (2008). MicroRNA profiling in hepatocellular tumors is associated with clinical features and oncogene/tumor suppressor gene mutations. Hepatology 47, 1955–1963.

de Reyniès, A., Boige, V., Milano, G., Faivre, J., and Laurent-Puig, P. (2008). KRAS mutation signature in colorectal tumors significantly overlaps with the cetuximab response signature. J. Clin. Oncol. 26, 2228–2230; author reply 2230–2231.

Rickman, D.S., Millon, R., de Reyniès, A., Thomas, E., Wasylyk, C., Muller, D., Abecassis, J., and Wasylyk, B. (2008). Prediction of future metastasis and molecular characterization of head and neck squamous-cell carcinoma based on transcriptome and genome analysis by microarrays. Oncogene 27, 6607–6622.

Publications, 2007

Bertheau, P., Turpin, E., Rickman, D.S., Espié, M., de Reyniès, A., Feugeas, J.-P., Plassa, L.-F., Soliman, H., Varna, M., de Roquancourt, A., et al. (2007). Exquisite sensitivity of TP53 mutant and basal breast cancers to a dose-dense epirubicin-cyclophosphamide regimen. PLoS Med. 4, e90.

Boyault, S., Rickman, D.S., de Reyniès, A., Balabaud, C., Rebouissou, S., Jeannot, E., Hérault, A., Saric, J., Belghiti, J., Franco, D., et al. (2007). Transcriptome classification of HCC is related to gene alterations and to new therapeutic targets. Hepatology 45, 42–52.

Clappier, E., Cuccuini, W., Kalota, A., Crinquette, A., Cayuela, J.-M., Dik, W.A., Langerak, A.W., Montpellier, B., Nadel, B., Walrafen, P., et al. (2007). The C-MYB locus is involved in chromosomal translocation and genomic duplications in human T-cell acute leukemia (T-ALL), the translocation defining a new T-ALL subtype in very young children. Blood 110, 1251–1261.

Condomines, M., Hose, D., Raynaud, P., Hundemer, M., De Vos, J., Baudard, M., Moehler, T., Pantesco, V., Moos, M., Schved, J.-F., et al. (2007). Cancer/testis genes in multiple myeloma: expression patterns and prognosis value determined by microarray analysis. J. Immunol. 178, 3307–3315.

Fasseu, M., Aplan, P.D., Chopin, M., Boissel, N., Bories, J.-C., Soulier, J., von Boehmer, H., Sigaux, F., and Regnault, A. (2007). p16INK4A tumor suppressor gene expression and CD3epsilon deficiency but not pre-TCR deficiency inhibit TAL1-linked T-lineage leukemogenesis. Blood 110, 2610–2619.

Idbaih, A., Boisselier, B., Sanson, M., Crinière, E., Liva, S., Marie, Y., Carpentier, C., Paris, S., Laigle-Donadey, F., Mokhtari, K., et al. (2007). Tumor genomic profiling and TP53 germline mutation analysis of first-degree relative familial gliomas. Cancer Genet. Cytogenet. 176, 121–126.

Lamant, L., de Reyniès, A., Duplantier, M.-M., Rickman, D.S., Sabourdy, F., Giuriato, S., Brugières, L., Gaulard, P., Espinos, E., and Delsol, G. (2007). Gene-expression profiling of systemic anaplastic large-cell lymphoma reveals differences based on ALK status and two distinct morphologic ALK+ subtypes. Blood 109, 2156–2164.

de Leval, L., Rickman, D.S., Thielen, C., de Reyniès, A. de, Huang, Y.-L., Delsol, G., Lamant, L., Leroy, K., Brière, J., Molina, T., et al. (2007). The gene expression profile of nodal peripheral T-cell lymphoma demonstrates a molecular link between angioimmunoblastic T-cell lymphoma (AITL) and follicular helper T (TFH) cells. Blood 109, 4952–4963.

Mahtouk, K., Hose, D., Raynaud, P., Hundemer, M., Jourdan, M., Jourdan, E., Pantesco, V., Baudard, M., De Vos, J., Larroque, M., et al. (2007). Heparanase influences expression and shedding of syndecan-1, and its expression by the bone marrow environment is a bad prognostic factor in multiple myeloma. Blood 109, 4914–4923.

Mariani, O., Brennetot, C., Coindre, J.-M., Gruel, N., Ganem, C., Delattre, O., Stern, M.-H., and Aurias, A. (2007). JUN oncogene amplification and overexpression block adipocytic differentiation in highly aggressive sarcomas. Cancer Cell 11, 361–374.

Renard, C.-A., Labalette, C., Armengol, C., Cougot, D., Wei, Y., Cairo, S., Pineau, P., Neuveut, C., de Reyniès, A., Dejean, A., et al. (2007). Tbx3 is a downstream target of the Wnt/beta-catenin pathway and a critical mediator of beta-catenin survival functions in liver cancer. Cancer Res. 67, 901–910.

Rocques, N., Abou Zeid, N., Sii-Felice, K., Lecoin, L., Felder-Schmittbuhl, M.-P., Eychène, A., and Pouponnot, C. (2007). GSK-3-mediated phosphorylation enhances Maf-transforming activity. Mol. Cell 28, 584–597.

dos Santos, N.R., Rickman, D.S., de Reyniès, A., Cormier, F., Williame, M., Blanchard, C., Stern, M.-H., and Ghysdael, J. (2007). Pre-TCR expression cooperates with TEL-JAK2 to transform immature thymocytes and induce T-cell leukemia. Blood 109, 3972–3981.

Tirode, F., Laud-Duval, K., Prieur, A., Delorme, B., Charbord, P., and Delattre, O. (2007). Mesenchymal stem cell features of Ewing tumors. Cancer Cell 11, 421–429.

Vincent-Salomon, A., Ganem-Elbaz, C., Manié, E., Raynal, V., Sastre-Garau, X., Stoppa-Lyonnet, D., Stern, M.-H., and Heard, E. (2007). X inactive-specific transcript RNA coating and genetic instability of the X chromosome in BRCA1 breast tumors. Cancer Res. 67, 5134–5140.

Publications, 2006

Benhamouche, S., Decaens, T., Godard, C., Chambrey, R., Rickman, D.S., Moinard, C., Vasseur-Cognet, M., Kuo, C.J., Kahn, A., Perret, C., et al. (2006). Apc tumor suppressor gene is the “zonation-keeper” of mouse liver. Dev. Cell 10, 759–770.

Clappier, E., Cuccuini, W., Cayuela, J.M., Vecchione, D., Baruchel, A., Dombret, H., Sigaux, F., and Soulier, J. (2006). Cyclin D2 dysregulation by chromosomal translocations to TCR loci in T-cell acute lymphoblastic leukemias. Leukemia 20, 82–86.

Duplantier, M.M., Lamant, L., Sabourdy, F., de Reyniès, A., Delsol, G., and Espinos, E. (2006). Serpin A1 is overexpressed in ALK+ anaplastic large cell lymphoma and its expression correlates with extranodal dissemination. Leukemia 20, 1848–1854.

Moreaux, J., Hose, D., Reme, T., Jourdan, E., Hundemer, M., Legouffe, E., Moine, P., Bourin, P., Moos, M., Corre, J., et al. (2006). CD200 is a new prognostic factor in multiple myeloma. Blood 108, 4194–4197.

Palomero, T., Lim, W.K., Odom, D.T., Sulis, M.L., Real, P.J., Margolin, A., Barnes, K.C., O’Neil, J., Neuberg, D., Weng, A.P., et al. (2006). NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth. Proc. Natl. Acad. Sci. U.S.A. 103, 18261–18266.

de Reyniès, A., Geromin, D., Cayuela, J.-M., Petel, F., Dessen, P., Sigaux, F., and Rickman, D.S. (2006). Comparison of the latest commercial short and long oligonucleotide microarray technologies. BMC Genomics 7, 51.

Vert, J.-P., Foveau, N., Lajaunie, C., and Vandenbrouck, Y. (2006). An accurate and interpretable model for siRNA efficacy prediction. BMC Bioinformatics 7, 520.

Publications, 2005

de Fraipont, F., El Atifi, M., Cherradi, N., Le Moigne, G., Defaye, G., Houlgatte, R., Bertherat, J., Bertagna, X., Plouin, P.-F., Baudin, E., et al. (2005). Gene expression profiling of human adrenocortical tumors using complementary deoxyribonucleic Acid microarrays identifies several candidate genes as markers of malignancy. J. Clin. Endocrinol. Metab. 90, 1819–1829.

Janoueix-Lerosey, I., Hupé, P., Maciorowski, Z., La Rosa, P., Schleiermacher, G., Pierron, G., Liva, S., Barillot, E., and Delattre, O. (2005). Preferential occurrence of chromosome breakpoints within early replicating regions in neuroblastoma. Cell Cycle 4, 1842–1846.

Schaack, B., Reboud, J., Combe, S., Fouqué, B., Berger, F., Boccard, S., Filhol-Cochet, O., and Chatelain, F. (2005). A “DropChip” cell array for DNA and siRNA transfection combined with drug screening. NanoBiotechnology 1, 183-189.

Soulier, J., Clappier, E., Cayuela, J.-M., Regnault, A., García-Peydró, M., Dombret, H., Baruchel, A., Toribio, M.-L., and Sigaux, F. (2005). HOXA genes are included in genetic and biologic networks defining human acute T-cell leukemia (T-ALL). Blood 106, 274–286.

Publications, 2004

Chibon, F., Mariani, O., Derré, J., Mairal, A., Coindre, J.-M., Guillou, L., Sastre, X., Pédeutour, F., and Aurias, A. (2004). ASK1 (MAP3K5) as a potential therapeutic target in malignant fibrous histiocytomas with 12q14-q15 and 6q23 amplifications. Genes Chromosomes Cancer 40, 32–37.

Orsetti, B., Nugoli, M., Cervera, N., Lasorsa, L., Chuchana, P., Ursule, L., Nguyen, C., Redon, R., du Manoir, S., Rodriguez, C., et al. (2004). Genomic and expression profiling of chromosome 17 in breast cancer reveals complex patterns of alterations and novel candidate genes. Cancer Res. 64, 6453–6460.

Publications, 2002

Redon, R., Hussenet, T., Bour, G., Caulee, K., Jost, B., Muller, D., Abecassis, J., and du Manoir, S. (2002). Amplicon mapping and transcriptional analysis pinpoint cyclin L as a candidate oncogene in head and neck cancer. Cancer Res. 62, 6211–6217.